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10:20
Dmitry Schigel
Global Biodiversity Information Facility: development goals and update 2018
Global Biodiversity Information Facility (GBIF) aggregates data arranged in datasets, which are shared by a global and
glowing network of publishing organizations, such as natural history museums, citizen science organizations, and other
institutions. Datasets are openly available from GBIF.org at four levels of information richness: i) metadata, or data
descriptors, ii) checklists, such as national, regional or thematic lists of species, iii) occurrence datasets, which
include location information for the records, and iv) sampling event datasets, which document occurrences together with
sampling effort information and often with quantitative parameters of collecting events and observations. The steady
growth of data content, improvements of GBIF.org and other tools translate into the increased and improved data use
in science and policy. Often overlooked or treated as a negligible technicality, data play an important role at all
stages of the scientific process from ideas, planning projects and funding to collecting, storage, publishing, sharing,
analyses, presentation, discovery, repeatability and reuse of findings. Biodiversity sciences and policy increasingly
become data intensive and dependent on availability and accuracy of the species occurrence data, accurate and unified
nomenclature and sequence references, documented sampling efforts and standardized methodologies, and links among different
data types. Linking traditional biodiversity data – location, time, names, images – to environmental, climate, interaction
and molecular data is not trivial and is one of the main subjects of discussions by the GBIF, Biodiversity Information
Standards (TDWG) and the related communities. GBIF encourages data capture and open data sharing using international
data standards. DOI based mechanism of data citation ensures credit to the data originators, and therefore recognition
of the field and database efforts and products as of first-class scholarly progress. GBIF strategic plan 2017–2021 is
built around five priorities: i) empower global network, ii) enhance biodiversity information infrastructure, iii) fill
data gaps, iv) improve data quality, and v) deliver relevant data. Implementation is carried out at three primary levels:
global, participant, and data publisher. The presentation will present status, progress and plans as of September 2018,
with the specific focus on collaborative opportunities for the individual researchers and teams, institutions, and countries.
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10:40
Alexey Seregin
Moscow Digital Herbarium: OCR-mining of the text data for the Russia"s largest biodiversity database
Moscow Digital Herbarium (https://plant.depo.msu.ru/) is the sixth largest library of imaged herbarium specimens in the
world. We are adding constantly new images of recently collected specimens, transcriptions of the labels, and manual
georeferences. As of 4 May 2018, Moscow Digital Herbarium hosts 911,543 images of 914,324 specimens, 101,415 captured
labels, and 109,375 georeferences. It is fully indexed in GBIF delivering to a wider community ca. 75% of occurrences
published by Russian institutions. A herbarium specimen with both a dry plant and a label mounted on a sheet of paper
is a convenient object for 2D imaging and further OCR-mining of text data. Since March 2018, we implemented the OCR
procedure for an automatic label capturing following best practices of New York, Paris, and Edinburgh herbaria (NY,
P, E). After some tests we decided to use open-source Tesseract software. Rough results of the OCR were cleaned by ca.
50 sophisticated quality-checks and mistake erasers. Finally, we left only "long" results with at least 100 characters
and 5 words. We combined up to four languages in the OCR procedure, although English + Russian were used as a default
combination. Labels with words characteristic for the German language were processed repeatedly in the German mode (ca.
2,000 labels of bryophytes). We used OCR transcriptions of labels for the following further activities. (1) Searching
for the collections of definite collectors to link the images with existed tables from which labels were initially produced.
(2) Searching for the collections with printed coordinates for quick georeferencing of these specimens. (3) Country-tagging
of the extra-Russian collections for further processing of labels using country filter. (4) Region-tagging of the Russian
collections for further processing of labels using regional filter. (5) Searching for the mistakes in manual attribution
of a country or a herbarium area and label capturing implemented earlier. Thereby, we do not use the text data mined
by the OCR instead thorough label capturing. We regard it as a powerful tool for pre-selection of specimens which makes
the database management more efficient. MW digitisation was supported in 2015–2018 by the grant #14-50-00029 from the
Russian Science Foundation (RNF).
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13:00
Varos Petrosyan, Marine Arakelyan, Fedor Osipov, Vladimir Bobrov, Evgeny Nazarenko, Natal"ya Dergunova, Felix Danielyan
The integrated database of geographical distribution of Darevskia rock lizard species in the Caucasus and Asia Minor
Knowledge of the geographical distribution of parthenogenetic (D.dahli, D.rostombekowi, D.armeniaca, D.unisexualis) and
their parental bisexual (D.valentini, D.portschinskii, D.raddei (D.nairensis), D. Mixta) species is important for understanding
their biology, for modeling ecological niches and identifying potential range due to accelerating anthropogenic warming
and global climate change. Thermoregulation of ectothermic lizards is mainly realized due to the heat received from
various thermal factors of the environment. This feature makes them more sensitive to climate change. The new data obtained
will allow the broadening of scientific notion of the ecology and speciation of Darevskia lizards, and will also help
to model possible ways of adaptation of organisms to extreme environmental conditions. The common descriptions of the
habitats of Darevskia rock lizards are often moved from one publication to another without verification. The purpose
of our work is: 1) to create a valid database by developing and carrying out computational experiments with geographic
information models by the example of bisexual and parthenogentic species; 2) to gain new knowledge about the ways and
mechanisms of the emergence of hybridization centers for parthenogenetic species and the role of biotic and abiotic
factors in the processes of reticular evolution of vertebrates. The main objectives of the study include the creation
of geoinformation models represented by the electronic library of vector maps based on the distribution data of parthenogenetic
and their parental species and their contact zones: 1. The model of distribution of 4 parthenogenetic and 4 parental
species of rock lizards and the location of possible contact areas in the past, present and in the future; 2. Models
of fundamental ecological niches of each species and identification of the main factors influencing the distribution
of each species; 3. The model of the evolution of contact zones of parental species and the territory of possible emergence
of new forms of rock lizards; 4. The model for predicting changes in the ranges of lizards and their contact areas in
the future; 5. The model of the definition of modern zones of possible formation of a new species as a result of stepwise
hybridization. The results obtained will allow a correct interpretation of the data of molecular genetics and cytogenetics,
and are of essential value for understanding the mechanisms of reticular evolution. An example of the data analysis
for rock lizards of the genus Darevskia species shows that standard descriptions of the range of species can include
false or ambiguous data. Creating a database of the species presence and documenting the locations is the only way to
obtain reliable information on the range of species to understand the mechanisms of the reticular evolution in past,
present and future. This study was supported by the RFBR № 18-34-00361, № 17-00-00427.
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13:15
Michael Pimenov, Michael Leonov,
Tatiana Ostroumova
Taxonomic and phytogeographical databases in systematics of the flowering plant family Umbelliferae/Apiaceae
Since the eighties of XX century several databases were compiled in the Botanical Garden of Moscow State University (MSU)
in collaboration with the MSU Faculty of Computational Mathematics and Cybernetics and the MSU Computer Centre. These
databases are connected with different aspects of critical investigations in systematics and geography of Umbeliferae,
one of the largest and complicated plant families. The main goal is to incorporate, save and retrieve large data on
scientific names, authors, synonyms, typification, characters, chromosome numbers, distribution and references related
to genera and species of the Umbelliferae, and to accompany monographs, revisions and articles preparation in different
aspects of the family systematics. Placing of the databases in Internet was out of our aims due to limited possibilities.
The following databases were created – GNOM (Generic NOMenclator: on nomenclature, synonymy, and distribution of World
Umbelliferae genera), CARUM (CARyologia UMbelliferarum: on chromosome numbers and karyotypes of World Umbelliferae species),
ASIUM (ASIatic UMbelliferae: on systematics and geography of the genera and species of Asia), and the special descriptive
single-purpose database on carpology of taxa , distributed in Eurasia and N Africa, being now in working out. The last
one was elaborated since fruit characters are of essential value in the family systematics. These taxon-oriented databases
reflect expert’s opinions of the authors. The monographs “The genera of the Umbelliferae. A nomenclator” (based on GNOM;
Pimenov & Leonov; Kew, 1993) and “The karyotaxonomic analysis on the Umbelliferae” (based on CARUM; Pimenov, Vasil’eva,
Leonov & Daushkevich; Enfield, NH, 2002) were published. All four databases are widely used in current work, with
a perspective of on-line publications. For the monograph “The Umbelliferae of Russia” (Pimenov & Ostroumova; Moscow,
2012) the multi-access key for taxa identification based on diagnostic character database was developed.
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13:30
Pavel Smirnov,
Julia Ermilina,
Andrey Lissovsky,
Anton Morkovin,
Yaroslav Redkin,
Julia Baranova,
Mikhail Kalyakin
Creation of electronic catalogue of big zoological collections by example of collection of Onithological Section of
Zoological Museum of Moscow State Lomonosov University
In 2018, employees of the Onithological Section of the Zoological Museum of Moscow State University completed the digitization
of collection represented by stuffed and flat skins, as well as mounted birds. To date, all the Section"s storage units
that have inventory IDs have been included in a integrated single electronic database. The bird collection of the Museum
is the second largest in Russia and is one of the twenty largest collections in the world. Digitization of this huge
massive of information was conducted by staff members together with temporary assistants under the supervision of scientific
staff. All the data were taken directly from the collection labels. The first 20 490 rows were added to the database
in 2000–2014 during the new collections registration fresh cataloguing of the type specimens. Targeted work on the creation
of a full database covered three years from January 2015 to December 2017. In the process of digitization, participants
faced a number of problems. Some of them were: duplication of inventory IDs; determination of the accurate coordinates
for the collection localities; the establishing of the correct surnames and initials of little-known collectors. The
search and correction of uncertainties in the database records is still continues. Nevertheless, we can report significant
results of the work even now. The species identification of several hundred birds was refined or processed de novo.
The exact number of storage units of the Section was determined precisely: at the moment of the end of May 2018 there
are 129 979 specimens including 2 193 downy chicks excluding birds of the permanent Museum exposition, and those sent
somewhere for exchange. Twenty one specimen represent extinct or probably extinct taxa. The most notable sources that
formed the Museum funds were collections of G.I. Langsdorf, M.M. Berezovsky, V.N. Bostanzhoglo, G.I. Polyakov, S.A.
Buturlin, V.A. Khakhlov, V.M. Gudkov, as well as the material collected by Museum staff during different years. The
creation of the network database with parallel access for several operators based on MySQL server became an important
frontier in the work of the Section, after which many of the usual operations were accelerated and optimized notably.
For the purpose of accessibility for specialists from around the world, the database is published on the official website
of the Museum and in biobank of the Moscow State University. Currently, a portion of the database for the collection
of bird tissue samples, which are the source for DNA extraction is being completed. In the nearest future we are planning
to digitize collections of alcohol preserved materials and clutches, as well as publication of articles involving data
from the electronic catalogue including the catalogue of type specimens. The work was carried out with the financial
support of the RNF grant № 14-50-00029 "Scientific foundations for the creation of a National Depository Bank of Live
Systems".
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13:45
Fyodor Malkov,
Alexey Shigarov,
Evgeny Cherkashin
Data lineage for Baikal microbiome study
The Baikal microbiome study is being conducted in Limnological Institute of SB RAS, the study is based on the next-generation
sequencing data analysis. As a result, the study generates a big volume of metagenomic data. The work considers issues
of the data lineage for Baikal microbiome study with the next-generation sequencing, from a moment when researchers
describe a sample of water or bottom sediments to publication of research results. We propose a service for data lineage
based on storage and execution of metagenomic processing and analysis pipelines. The service provides reliability and
reproducibility of published research data.
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14:00
Varos Petrosyan, Nikolay Zavyalov, Fedor Osipov, Lyudmila Khlyap, Nataliya Dergunova
Analysis of the competitive relationship and the possibility of a sympatric habitat of native Castor fiber and alien
Castor Canadensis on the territory of the European part of Russia
The appearance of Canadian beaver C. Canadensis (Cc) in Finland in 1937 was associated with the intentional introduction
of seven individuals of that species with the purpose of restoring the almost extinct Eurasian beaver C. fiber (Cf).
In those years, many zoologists recognized only one species. However, in 1973, karyological studies showed the species
differences between New World (Cc : chromosomal number (cn) =40) and Old World (Cf : cn=48) beavers, therefore Cc became
an alien species in Eurasia. In the 50s of the XXth century, after the introduction of Cc into the territory of Finland
(1937), Canadian beavers had penetrated into the territory of Russia and continued to expand their range. It is assumed
that there is a process of interpenetration and replacement of one species of beavers by another in the Karelian Isthmus
of Leningrad Region, as well as in Arkhangelsk Region. Analysis of the literature data shows that there is no an entire
opinion on the competitive relationship of two species in the future. The aim of the work is to analyze the competitive
relations between two beaver species, Cf and Cc, and give the forecast of the dynamics of the abundance of these species
in the European part of Russian territory. To achieve this goal, the following tasks were accomplished: 1. Modern trends
in the development of two beaver species populations in the territory of model Natural reserves and the subjects of
the European part of Russia were characterized; 2. The potential capacity of beaver habitats in the European part of
Russia was estimated; 3. The integral estimation of biological similarity / difference of two beaver species in the
same habitat conditions was given and an integrated raster-vector database including results of beaver settlements research
was created. In general, the parameters determining the similarities and differences in many aspects of the biology
of two species, Cf and Cc - fertility, family size, rate of maturity, life span and age composition of populations of
both species - were revealed. Such parameters explained the competitive advantage of Cc and possible replacement of
aboriginal Cf by foreign Cc . The two-species model analysis used has shown the validity of the G.F Gause principle
of competitive exclusion, i.e. the population of Cc in the joint use of spatial and fodder resources grows faster and
limits the population of Cf, so if the external conditions remain unchanged, the Cf population may die out in time.
Numerical experiment has shown that for different ecological conditions of Laplandsky, Darvinsky, Prioksko-Terrasny,
Central-Forest Oksky and Khopersky reserves, the commencement of replacement varies from 50 to 245 years. Data analysis
using a two-species model was implemented with the financial support of the RSF grant No. 16-14-10323 and data collection
by the programs of the Presidium of the Russian Academy of Sciences № 41 "Biodiversity of natural systems and biological
resources of Russia".
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14:15
Anna Andrianova, Oleg Yakubaylik
Geoinformational web-system for the analysis of the expansion of the Baikal crustaceans of the Yenisey River
Nowadays, it is generally recognized that the problem of biological pollution is one of the most important global environmental
problems of our time, it is also actual for the The Yenisey River. Invasions of alien species in new ecosystems lead
to significant changes in reservoirs - recipients, in particular, to a decrease in species diversity and the stability
of aquatic ecosystems. It is known that the damming of the Yenisey caused a radical change in the hydrological, hydrochemical
and hydrobiological regimes, especially in the afterbay of the Krasnoyarsk hydro-electric power station. Large-scale
rearrangements have also occurred in the communities of benthic invertebrate animals - zoobenthos, which is the main
food resource for most species of fish in Siberian rivers. At the same time the species diversity of bottom invertebrates
has decreased significantly, but their number has increased. The increase in figures has been caused, first of all,
by the distribution of endemic amphipods (crustaceans) from Lake Baikal through the Angara River upstream of the Yenisey.
The paper presents modern quantitative data on the distribution of Baikal amphipods in the Yenisey River from the head
to the delta inclusive, collected during field work in 2015 - 2016. The results of hydrobiological studies has been
designed in the form of geospatial database in the geoportal, which gives the possibility to visualize and process geodata,
and gives access to it from third-party applications based on cartographic web services. At this stage of the research,
information on the hydrography of the Yenisey River basin was updated. On the basis of the data from the geoportal,
prepared in accordance with the State Water Cadastre, geo-referencing of the hydrobiological monitoring observation
points to kilometer points along the fairway of the Yenisey River was carried out ("coordinate system of the river");
the use of such a coordinate system makes it possible to evaluate various parameters along the course of a river. Also,
a set of specialized layers of geospatial data was formed. Creation of a geospatial database with the results of expeditionary
work and the introduction of a geoinformational web system for information and analytical support of hydrobiological
monitoring greatly expands opportunities in the analysis and representation of geodata, forms the basis for interdisciplinary
research.
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14:30 Sergey Dudov, Ksenia Dudova,
Natalia Gamova
Study phytogeographical boundaries in Amur basin using species distribution modeling
Russian part of the Amur River catchment area is the immense territory with diverse bioclimatic conditions. The aim of
the study is to show main phytogeographical patterns of this area with using species distribution modeling (SDM) approach.
SDM allows to determine response between species occurrences and environmental conditions as well as provide understanding
of species distribution ranges with strong predictive capability. We selected 100 vascular plants species with diverse
geographical distribution over the study area and a variety of zonal and altitudinal patterns. For the first time to
East Siberia and the southern part of the Far East we form a dataset with 12371 georeferenced records and published
it via GBIF: (https://www.gbif.org/dataset/0c7bd9e3-ded7-4de4-99ec-d5145361ff48). The dataset includes specimens of
vascular plants deposited in seven major Russian herbaria: LE, MW, MHA, VLA, VBGI, NSK, and TK. collected in the Amur
Basin and adjacent seacoast in Russian Federation from 19th century. We georeferenced specimens manually using label
localities. Based on this data we calculate species distribution models using MaxEnt. We choosed climatic (CHELSA bioclim
and Global 1-km Cloud Cover variables) and remote sensing (MODIS land surface temperature, MODIS EVI) data as environmental
predictors. Obtained models are adequately reflect the species ranges in the Amur river basin. We carried out an integral
analysis of received models using clustering (Ward method). As a results we derived 11 clusters of species with similar
distribution within study extent and estimated their climatic ranges. The identidied groups of species indicate the
distribution of the main vegetation communities types. Consequently we provided new phytogeographical data of vascular
plants distribution in the Russian part of the Amur basin and mobilized herbarium specimens for further research.
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14:45
Marina Protopopova, Vasiliy Pavlichenko, Victor Chepinoga, A. Gnutikov
DNA barcoding of Waldsteinia Willd. (Rosaceae) species based on ITS and trnH-psbA nucleotide sequences
In our study, we estimated the Internal transcribed spacer region (ITS) and trnH-psbA intergenic chloroplast spacer as
possible markers for species identification of vascular plant genus Waldsteinia (Rosaceae). The comparative analysis
of the nucleotide sequences of East Asian Waldsteinia maximowiziiana, South Siberian W. ternata and W. tanzibeica, European
W. geoides and W. trifolia, North American W. fragarioides and W. parviflora was carried out. PCR was performed using
both GoTaq Flexi DNA Polymerase kit supplied with green buffer (Promega) and Q5 High-Fidelity 2X Master Mix (New England
BioLabs). PCR products were visualized on 1.5% agarose gel with ethidium bromide upon electrophoresis, gel-purified
using the GeneJET Gel Extraction Kit (Thermo Fisher Scientific), ligated into pTZ57R/T (Thermo Fisher Scientific) or
pMiniT 2.0 (New England BioLabs) plasmid vectors followed to cloning in TOP10 E. coli competent cells or directly sequenced.
Bacterial cloning was used for detection of low copy number variants of ITS region. Isolated plasmids and original amplicons
were sequenced by Sanger method using BigDye Terminator Cycle Sequencing kit v. 3.1 (Applied Biosystems) on the 3500
Genetic Analyzer (Applied Biosystems). From two spacers of ITS region for molecular identification of plants using BOLD
system ITS2 region is recommended, however, our data showed a high intraspecific and intrapopulation variation of this
region, together with a low number of systematic substitutions do not allow distinguishing of closely related species.
Thus, using of ITS2 region as a molecular marker for Waldsteinia spp. is very ambiguous. The detected levels of intra-
and interspecific ITS1 and trnH-psbA variability allow using these molecular markers for identification of Waldsteinia
species. The best results were observed in case of combining the ITS1 and trnH-psbA sequences together, which allowed
to identify species in 100% cases according the ‘best close match’ test. The study was supported by the Russian Science
Foundation (project No. 17-74-10074) and the Russian Foundation for Basic Research (projects No 16-34-60135_mol_a_dk
and 16-05-00783). The research was done using the equipment of The Core Facilities Center “Bioanalitika” and collections
of The Core Facilities Center “Bioresource Center” at Siberian Institute of Plant Physiology and Biochemistry SB RAS
(Irkutsk, Russia), IRKU, IRK and LE herbariums and Botanical Garden of Irkutsk State University.
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15:30
Pavel Frolov, Vladimir Shanin, Elena Zubkova,
Gulfina Frolova
CAMPUS-S – the model of ground layer vegetation in forest ecosystems and their contribution to the dynamics of carbon
and nitrogen
The role of ground layer vegetation is rarely taken into account when analyzing the carbon balance of the forest ecosystems.
A contribution of ground layer vegetation plants to carbon cycle in forest ecosystems can also be significant. Ground
layer vegetation is one of the leading factors influencing the process of renewal, germination of seeds, and further
development of seedlings both under the canopy of the stand and on felling areas. There are 4 types of impacts that
the ground layer vegetation has on forest regeneration processes: mechanical (a dense lichen cover can prevent the penetration
of seeds into the soil); physical (the creation of a microclimate); physiological (plants of ground layer vegetation
create competition for elements of nutrition, moisture); biochemical (influence mediated by the release of herbs of
phytoncides and colins by some species). These effects can be combined in different ways and, as a result, have both
a positive and negative effect on the first stages of forest renewal. Due to the lack of tools to predict the structural
and functional dynamics of populations of herbaceous and shrubby plants, we developed the model CAMPUS-S. The developed
model CAMPUS-S uses several modeling techniques: matrix modeling, L-systems technology and cellular automata modeling.
Species-specific data due to the genotype are defined as input data (using the technique of L-systems) for each ontogenetic
state, but their implementation in the course of modeling depends on external conditions (the technique of cellular
automata is applied). To implement the polyvariance of the transitions between ontogenetic states, the matrix modeling
method is used. The CAMPUS-S model consists of two main submodels: a submodel of the structure of populations of the
ground layer vegetation and a submodel for calculating the dynamics of biophilic elements (carbon and nitrogen) in plants
of the ground layer vegetation and soil. The space in the CAMPUS-S model is heterogeneous. The input module allows generating
or dynamic loading of the map of the microrelief, according to which the temperature and moisture of the organic and
mineral horizons of the soil are distributed in space during the simulation, and a map of locations that are inaccessible
to the simulated plants (imitation of large stones, tree trunks). The irradiance map under the canopy is dynamically
transferred from the EFIMOD model. The climatic data necessary for the functioning of the model (temperature and moisture
of the organic and mineral horizon of the soil) are generated by the statistical simulator of soil climate (SCLISS).
For climate parameters, a standard deviation is specified, which allows to regulate the oscillations of these parameters
at different points of the simulated territory. To implement the feedback mechanism between plants and soil, the integration
with the ROMUL-HUM model was implemented. The work was supported by the RFBR (18-34-00556) and the RSF (18-14-00362).
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15:45
Anastasia Popova, Igor Vladimirov,
Eugeneai Cherkashin
Forest resources of the Baikal region: vegetation dynamics under anthropogenic use
We review the theoretical and applications-specific issues of the modeling the temporal and spatial dynamics of forest
ecosystems, based on the principles of investigating dynamical models. The model used takes into account various factors
affecting the change in forest areas - fires, forest diseases, cutting, urban expansion, etc. Calculation of numerous
scenarios for the use of forest resources makes it possible to see the consequences of various managerial decisions.
The user can access the parameters of the main cutting volume, fires and tree planting. We present the results of a
computer modeling and predictive mapping for the regional model under anthropogenic use of the forest resource dynamics.
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16:00
Yuriy Avramenko
Analysis of diatoms using the logical method search
One of the methods of monitoring of the Baikal Lake ecosystem is the analysis of diatoms. Such analysis is performed
in LIN SB RAS. Diatoms are very demanding to conditions of the environment, so sometimes theirs number in specific periods
is considered to be one of the indicators of the ecological condition of the Baikal Lake. Nowadays the task of calculation
of diatoms numbers is performed manually by microscope operator which is very time-consuming process. In order to solve
such kind of tasks certain software tools have been developed, which allow to measure length and width of objects, scale
and view images. These tools have various filters that improve image perception. However, application of theirs tools
to solution of this problem is not possible due to certain limitations: some of software tools support only specific
microscope models, some tools do not perform diatom extraction. All of the software tools are not able to automatically
distinguish diatoms according to their types. The complexity of this task is caused by differences in diatoms shape
(square, round, linear etc.), size and texture. The method based on logic programming for image understanding is proposed
in order to solve the diatom extraction problem. This method is suitable for diatoms extraction, as it allows describing
every type of diatoms and performing the search. The diatom type description is a rule in Spatial Object Query Language
(SOQL). The diatom shape is described using the relation of the graphical primitives, such as line, circle or their
combinations. More complex shapes, for example, polygons, can be described using theirs combinations. Length and width
can be defined with the size of graphical primitives, the texture can be defined with pre-defined model. The example
of the rule for extraction of diatoms with rectangle shape: diatom(A,B,C,D) :- line(A,B), line(B,C), line(C,D), line(D,A),
dist (A,B) > 25, dist (A,B) < 40, dist (B,C) = 60, dist (B,C) = dist (A,D), angle (A,B,C) = 90, angle (B,C,D)
= 90, angle (C,D,A) = 90, texture(A,B,C,D, diatom_texture). The algorithm has following steps: 1. User sets the threshold
value of Energy function. 2. Features are being extracted from the image in the process of logical conclusion. It uses
Deep First Search method (DFS). 3. Once the desired feature combination which satisfies the rule is found, the value
of Energy function is computed and compared with the threshold. If the value is less than threshold then diatoms are
extracted, otherwise the search will continue. 4. Repeat step 3 until all possible combinations are not found. One of
the advantages of the proposed method is that it allows creating description of various, even not discovered yet, diatom
types in short period of time and perform theirs search. The method is robust to noise, blur and other collisions, however
usually method takes a lot of time to complete.
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16:15
Elena Istomina, Victor Chepinoga, Nikolay Popov
Modeling of areas of cladotype species of plants of the nemorose refugia of the Khamar-Daban ridge using the maximum
entropy method
Bioclimatic modeling allows not only mapping the areas of certain plant or animals species on the basis of environmental
characteristics, but also to investigate the influence of environmental factors on the occurrence of these species.
We simulated the potential areas of the three groups of species of higher vascular plants on the northern macroslope
of the Khamar-Daban ridge. For modeling we selected species whose distribution in Baikal Siberia is completely or predominantly
restricted by the Khamar-Daban ridge, which are nemorose cladotypes and included in the Red Lists of various rank. The
first group is the most numerous and includes species distributed only in the lower reaches of the river valleys and
along the foothills of the slopes. In the altitude relation they occur from 456 m (Lake Baikal level) to 700 m. The
species of the second group occur almost exclusively in the subalpine and alpine belts, starting from an altitude of
900 m. The species of third group are widely distributed both in the forest and subalpine belts from Baikal to 1600
m. As a parameters of the environment we use the relief characteristics calculated on the basis of the digital elevation
model SRTM, as well as the parameters computed from the three differently seasoned cloudless satellite images Landsat
8 (all with a resolution of 30 m) with the use of tasseled cap algorithm as well as NDVI. Using the MaxEnt software
models of potential range for each group of species is created. It is revealed that the main factor of the environment
influencing the occurrence of the species under study is altitude, and secondary factors are the vertical distance to
channel network and various Tasseled cap parameters. The distinction of potential areas of all three model species groups
reflects their different ecological requirements. The results of the simulation confirmed the conclusions obtained on
the basis of expert analysis of the investigated refugia and the confinement of species to certain locations, but allowed
us to delineate the areas of these refugia, which is difficult to do only on the basis of data on the locations of species.
In the future, it is planned to use the data obtained to more accurately determine the boundaries of the refugia of
nemorose plant species and to identify environmental factors that affect their formation. The work performed reveals
patterns of spatial distribution of biota, which are used to solve problems of conservation of biological diversity.
The work was carried out within the framework of the program of the V. B. Sochava Institute of Geography SB RAS № 0347-2016-004
и №0347-2016-003 with partial support of the Russian Foundation for Basic Research (projects № 16-05-00783).
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16:30
Elena Verkhozina, Aleksey Safarov
The use of mathematical methods in analysis of antibiotic resistance of microorganisms of lake Baikal
Currently one of the most important challenges humanity becomes a natural water pollution substances of anthropogenic nature. With the vast array of data obtained during the monitoring observations, using statistical methods allows you to identify the major patterns and complex approach to the solution of the problem. Studied microorganisms isolated from a variety of ecological niches of the ecosystem of the Lake Baikal on presence of the enzymes of the ER. Found that microorganisms are indicators of anthropogenic influence on the early stage of water pollution. The analysis for the presence of enzymes of restriction endonucleases (ER) was carried out. Long-term studies have established that a large variety of ERs is found in bacterial strains isolated from samples sampled in places where anthropogenic influence is observed (Listvyanka, Baikalsk). It was revealed that under the influence of human activity there are significant disturbances in the biosynthesis of ER enzymes in bacteria. Restriction enzymes, previously known only theoretically, were found in areas of anthropogenic influence. In the strains of bacteria isolated from the clean sections of the lake, all the ERs that we discovered are well known. To identify the conditions for the synthesis of restriction enzymes (ER) in the coastal part of the lake ecosystem. Baikal in a certain place of sampling during cluster analysis, 28 types of different types of ER were identified. Frequency of occurrence of enzymes ER can be divided into several types: 1) rare restriction enzymes (found only in a strain of a bacterium isolated from only one sample) include AccI, NcoI, SaII, ScaII, HpaII, Fun4HI, HgiEII, NruI, HgiCI, AvaII, MwoI, CauII; 2) a relatively small spread of ER (found in 2-4 samples), including XhoI, Bpu1I, EcoRV, BaII, XhoII, EspI, DraII, EcoRII, San96I, BamHI; 3) fairly common ER (identified in 6-13 samples), these include HaeIII, ClaI, MboI, PstI. It should be noted that the most common restriction enzyme MboI was found 14 samples, and this leaves 21\% of the total number of investigated (66 samples), all other ERs were less common (1.5\% - 15\% of all analyzed samples). When analyzing the data obtained, it was revealed that the sampling areas differ greatly in the number of detectable ERs (from 1 to 7). The larger the binary distance, the more differences in the spectrum of detectable ER. Differences in binary distance reach 1 (100\%), which means that ERs occurring at one point of selection are not found in samples taken elsewhere. There are two pairs of sampling points, where their spectra do not differ. Within each pair of these points, the ERs were of the same type, but the pairs themselves were different (binary distance 1 -100\%). Among the methods of statistical analysis (calculation of medians, graphic visualization of indicators, cluster analysis) the most informational method turned out to be a cluster analysis using UPGMA method with calculation of distances on the Euclidean distance measure. As the result of the research, has set many hidden factors described. Asked when the vast array of received data to identify causal relationships between variables, variability and use dispersion and correlation analysis methods. Use methods of statistical analysis allows you to identify the major patterns and complex approach to the solution of the problem. Thus, in the vast array of data obtained as the result of the research methods of statistical analysis to identify cause-and-effect relationships, determine the strength and direction of variability between variables and are considered one of the promising.
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16:45
Natalia Luzhkova,
Anastasia Myadzelets
Forest fires and landscape changes in protected area on the northeastern shore of lake Baikal
There are three large Federal Protected Areas the northeast shore of Lake Baikal: Barguzinsky State Nature Biosphere
Reserve, Zabaikalsky National Park and Frolikhinsky Wildlife Sanctuary. All of them are managed by the Federal State
Establishment “Zapovednoye Podlemorye” providing the strictest status of protection. However natural forest fires have
had great impact on landscapes and their components. Crown and ground forest fires of various intensity have burned
vast areas of subalpine, forest and coastal landscapes over the past three years. Current conditions of damaged landscapes
allow us to conduct assessment on the process of ecosystems recovery. Geosystem approach is applied to define of landscape
types and landscape (land cover) and map them; to assess burned area and to consider changed in vegetation on monitoring
plots. The Shumilikha valley in Barguzinsky Nature Reserve serves as the case study area. Here coniferous forest landscapes
were damaged in 2015. With the use of the satellite images and results of monitoring on plots, pace of landscape recovery
can be modeled for the site and territories of three protected area.
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17:00
Alexander Novakovskiy
The ExStatR plugin for biodiversity research based on Excel and statistical package R
Today the free program for statistical analysis R became more and more popular (Seefeld, Linder, 2007; Kabacoff 2015).
Now R is a "de facto" standard in most foreign and advanced Russian scientific schools and science fields. R is a freely
available language and environment for statistical computing and graphics which provides a wide variety of statistical
and graphical techniques (https://cran.r-project.org). The biggest difficulty in using the R program is stems from necessity
to create special scripts (small programs) that implement the necessary functionality. This prevents the wide expansion
of the program R, especially in the natural sciences. We developed the ExStatR software module (Novakovskiy, 2016) that
combines the Microsoft Excel spreadsheet and the R software environment. Using standard Excel spreadsheets as a data
source makes it easy to enter, store and modify data. The software environment R is used as a computing core. This allows
us easy add new or modify existing algorithms of data analysis, adjust the output parameters of table or graphic results.
The implemented algorithms for data analysis are universal. This allows using the ExStatR module in many fields of ecology
and biology. The module has a simple user interface and does not require special training to use it. To date, the following
algorithms of data analysis are designed in module: ordination (principal component analysis – PCA, Non-metric multidimensional
scaling – NMS), cluster analysis (UPGMA, Ward method, single-linkage and complete-linkage) and heat maps. Also it is
possible to coloring objects and add correlation vectors of environmental factors. The developed scheme of interaction
between Excel and R is modular. This allows designing new algorithms for data analysis and visualization of results
fast and easy. The program is freely distributed. The installation version and detailed instructions are available at
http://ib.komisc.ru/ExStatR. The research was partly supported by the Russian Foundation for Basic Research and Government
of Komi Republic (18-44-110015) References 1. Novakovskiy A.B. Interaction of Excel and statistical package R for analyzing
data in ecology // Vestnik Instituta biologi Komi SC UB RAS. – 2016. – #3. – P. 26–33. 2. Kabacoff, R.I. R in Action.
Data analysis and graphics with R. 2nd ed. – N.Y. : Manning, 2015. – 608 p. 3. Seefeld, K., Linder E. Statistics Using
R with Biological Examples – Durham : University of New Hampshire, 2007. – 325 p.
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17:15
Denis Sandanov, A Dugarova, E Kokorina
Distribution of endemic locoweed species around lake Baikal
Mountainous regions of Siberia are characterized by high diversity and endemism of locoweed species. Within Siberian
regions Baikal hemiboreal floristic province has a big number of endemic Oxytropis species. This phenomenon can be connected
with mountainous landscape and long-term isolation of steppe patches on territory around Lake Baikal. Many of endemic
species on this territory are recognized as rare and endangered and detailed studies of their distribution will contribute
to future conservation activities. Distribution models were generated using Maxent (Version 3.3.2k). Georeferenced plant
occurrence data were accessed from herbarium collections and results of own studies. We used 19 bioclimatic variables
with resolution of 0,5 arc-minutes (www.worldclim.org). All models were statistically tested, jackknife test were used
to reveal the importance of variables. Distribution analysis showed that the most part of endemic Oxytropis species
localities confined to the mountainous regions on the south of Baikal Siberia. Analysis showed high diversity and a
big number of localities of endemic locoweed species in Buryatia. Main part of studied species on the territory of Irkutsk
region can be found at the Eastern Sayan mountains and Tazheran steppes (near Olkhon island). Endemic locoweed species
in Zabaikalskii krai concentrated in Aga steppes, Kodar ridge, Chara depression, and Sokhondo nature reserve. The most
part of studied species characterized by narrow fragmented distribution with small quantity populations. More than half
of studied endemic locoweed species (13 from 23) are included to regional Red Data Books. Distribution of Oxytropis
glandulosa revealed to two main clusters: one in the Barguzin depression, second – around Eravna Lakes. Bioclimatic
modeling didn’t show new habitats suitable for this species. New localities can be found within current species distribution.
Important variables for this species are BIO7 and BIO9. Oxytropis bargusinensis mostly occur on the northern part of
Baikal Siberia. Potential distribution for this species under bioclimatic modeling included southern part of Buryatia
(valleys of rivers Selenga and Uda). Here also temperature variables (BIO1, BIO7, BIO9) have big importance on species
distribution. Research was carried out under the project granted by the Russian Foundation of Basic Research (№16-04-01399)
and Federal Budget (project № АААА-А17-117011810036-3)
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17:30 Andrey Montile,
Andrey Montile, Sergey Shavnin
Multivariant approximation of observational data characterizing biodiversity and individual development at the organisms
level
Revealing the types of elements considered as "semantic" units that determine biodiversity at the organisms level presupposes
the definition of invariant for each type that can be matched to specific heredity. In the process of individual growth
and development, different genotypes under the influence of environmental factors may have a similar dynamics of changes
in one subset of phenotypic characteristics and various in other. The selection of subsets of characteristics is determined
by the similarity of functional dependencies, often non-linear, connecting the characteristics in each subset. In fact,
this assumes the need for solution of one and the same problem by mutually combination of cluster and regression analysis
techniques traditionally used sequentially. It seems advisable to change the problematic setting that occurs when statistical
analysis (for example, regression analysis) of morphometric data is performed, namely, to obtain as large as possible
number of reliable non-duplicating formula dependencies linking the values of the characteristics determined as a result
of specific study, instead of confirming or disproving the assumption of connections availability between a priori formed
subsets of them. In addition, it is necessary to take into account the possibility of existence of dependencies, which
include variables that are not present in the observational data, in particular, characterizing the changes in the values
of the directly measured characteristics at certain intervals of time. Let"s consider the main features of the proposed
approach to data processing. An abstract scheme for presenting data (of observations) is cube which axes correspond
to: objects, variables (characteristics), moments or time ranges. When using standard methods of statistical data processing,
the cube is unfolded to object-attribute flat table with modifiable set of columns. Following problems are consistently
solving in automated mode: 1. Replenishing of the axis of attributes with "computable" variables that are absent in
the observations and using of changes in values of variables at certain intervals of time as additional attributes.
2. Identifying the relationships between variables included in the replenishment set and the formation of corresponding
set of linear and nonlinear formulaic dependencies. 3. Selecting groups of objects (corresponding level) based on the
similarity of functional dependencies. The report discusses two examples of methods described which are using for formation
of the sets of formulaic regression dependencies characterizing the features of Scots pine morphogenesis: in stands
with growth anomalies (significant deviations in growth processes from the norm) and in pine young growth in the temperature
of environment gradient (in the zone of associated gas flare impact).
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17:30 Lyudmila Kavelenova, Natalya Prokhorova,
Eugene Korchikov, Victor Fedoveev
Concerning the problems of regional reference plots system for ground support of remote sensing materials processing
The landscape complexes state assesment, including natural and anthropogenically transformed ecosystems, is the basis
for the organization of rational nature management and biological diversity conservation. A significant amount of space
materials already accumulated and constantly replenished can become the basis for a large-scale spatial and temporal
analysis of the ecosystems current status and dynamics. However, an indispensable condition for this, in our opinion,
is the support of remote sensing data processing by regionally verified materials of integrated ground survey at regional
reference plots. Within them must be presented the reference plot blocks of different status (natural, disturbed, converted,
regenerated). The existing methodology for the remote sensing materials processing, including the construction, training
and testing of classifiers, the use of spectral indices, needs to be developed due to the "non-universal" nature of
the vegetation and soil cover of the Earth. As the characteristics associated with species composition and vegetation
condition become more detailed, the importance of ground-based measurement increases. Thus, recognition of the species
composition of the tree layer, the practice of which is developed for forests in certain areas of South America, India,
the USA, China, can not be extrapolated to ecosystems of other species composition. On the example of the forest-steppe
- steppe Middle Povolzhye (Samara region) as an ecotone with a mosaic combination of preserved natural ecosystems, agro
ecosystems, urban complexes, spontaneously recovering ecosystems, we can demonstrate the need for a network of regional
reference plots for ground support of remote sensing data processing. An important point in its formation is to unite
the efforts of specialists in various fields. Some of the experience we have gained in recent years in the development
of steppe, forest ecosystems, former field deposits as reference plots has shown that one of the problems may be the
availability of accessible space images of the desired areas with high resolution, closely timed to the required deadlines.
In the near future, we plan to continue to collect ground information on the state of particularly valuable natural
communities typical for the Samara region and adjacent regions on new reference plots, as well as the selection and
cataloguing of satellite data reflecting diagnostic parameters and the time frame for their detection.
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17:30
Elena Patova, Irina Novakovskaya, Elena Madi
Electronic database of the collection of living microalgae strains and cyanoprokaryotes of the northeast of the European
part of Russia
Electronic database was created to maintain the collection of microalgae living cultures was started in the Institute
of Biology (IB) of Komi Scientific Centre in 2010 as a part of IB SYKO herbarium (https://ib.komisc.ru/sykoa). The collection
is egistered in GCM (Global Catalogue of Microorganisms) Acronym: SYKOA, WDCM Number: 1125. Today, the collection contains
more than 300 algologically pure strains of algae collected in the European Russian Northeast (Polar and Subpolar Urals,
Bolshezemelskaya tundra), isolated from soil and water samples. Also, there are several strains from soils of the Southern
Svalbard and other Arctic regions. Green algae and cyanoprokaryota/cyanobacteria form the main part of the collection.
Departments Eustigmatophyta and Xanthophyta are presented in the collection by five species. Collection includes monocultures
of dominant species of algae from different ecological groups (edaphophilous, cryophilous, nitrophilous, etc.), rare
species and taxa with uncertain systematic position. The main aims of the collection are to conserve biodiversity of
microalgae from Arctic and northern regions of the European Russia, and to collect new strains for their use in floristic,
systematic, evolutionary, molecular, genetic and ecological studies.
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17:30
Vladislav Murashko,
Alla Verkhozina
Database on the distribution of the invasive species Hordeum jubatum L. in Russia
The graphs show not only an increase in the number, but also an increase in the speed of skidding with the development
of the region and an increase in the anthropogenic press. On the map of the first finds of invasive plant species (Figure
3), the main ways of distribution of adventive species in the region are seen. These are federal highways P258 "Baikal"
(M-55) and P255 "Siberia" (M-53). In the environs of Irkutsk, 38% of the invasive species of the regions are concentrated
(34). For one of the transformer types Criticion jubatum (L.) Nevsky, the growth in the number of new locations since
the first treatment in 1976 is analyzed. The graph reflects the high aggressiveness of the species (Fig. 4).
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17:30 Elena Makeyeva, Elena Mikhalenko,
Svetlana Kubrak
DNA-barcoding in the study of rare plant species of Belarus
Among the main environmental challenges of our time, the ones associated with decline of species diversity and a decrease
in the areas of natural ecosystems stand out. The Republic of Belarus has made a significant effort to conserve and
sustainably use biological diversity. The mechanisms that provide for the maintenance of specially protected natural
areas and the Red Book of the Republic of Belarus are worth noting among the effective instruments enabling the preservation
of environmental objects. Beyond that, environmental activity entails an inventory, mapping of locations and cataloging
of rare and endangered species of plants and animals. A key milestone in ecological monitoring was the establishment
in 2013 of the Republican DNA Bank with its collections that constitute a depository of biological material apt for
long-time storage. The scientific activity of the Republican DNA Bank is based on the molecular-genetic identification
of species and verification of their taxonomic status which offers ample opportunities for collaboration in such a priority
direction as DNA-barcoding. DNA-barcoding is a widely used technique of genetic data digital representation convenient
for cataloging and storing of information on molecular features of living organisms’ genomes. The use of certain nucleotide
sequences (DNA barcodes) in biosystematics allows to accurately identify the species under study, compare related genomes,
and effectively manipulate large arrays of genetic data. As of now, the Republican DNA Bank employees have performed
research on 35 rare and endangered plant species (I-IV protection categories) collected in the National Parks “Narochansky”
and “Belovezhskaya Pushcha”. The biological material of rare plants was collected without removing them from their habitat.
Classical methods of botanical research along with simultaneous compilation of a database on morphological and ecological
geographical descriptions of every plant preceded the molecular-genetic analysis. Polymorphism of three marker sequences
ITS2, rbcL, psbA-trnH was used for DNA barcodes identification. All the information obtained is uploaded to the website
of the National Coordination Centre on Access to Genetic Resources and Benefit-sharing. With the involvement of the
Republican DNA Bank, a DNA Barcoding Centre, containing a barcode database of flora and fauna of the Republic of Belarus,
is being established. The Centre will consolidate research institutions and universities which have natural science
collections and environmental institutions of the Republic.
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17:30
Asiia Zagidullina, Vikor Mamontov, Robert Rempel
Wild forest reindeer habitat assessment in forest landscapes of eastern part of Barentz region
Boreal forests provide significant ecosystem services i.e. biodiversity and other non-timber resources. Habitat loss
is globally a threat to biodiversity and in managed boreal forests a loss of habitats is the most common factor affecting
species diversity. We made an attempt to implement classification of habitats and their ecological assessment regimes
of the pristine forests landscape of Barents region. The forested watershed are richly inhabited by endangered plant,
fungi and vertebrate species, many of which are red listed. They exhibits high diversity of natural ecosystems and can
be viewed as a representative example of the European middle and northern taiga with preserved gradient of different
successional stages and habitat types. The watershed forests are home to one of the last and the most southern remaining
populations of listed wild forest reindeer (Rangifer tarandus). To prepare maps for wildlife habitat assessment we mapped
vegetation cover, disturbances, sandy soils and roads. Classification of vegetation cover was carried out on the base
of remote sensing, forestry maps and big series of field data. To assign the classes for the selected Landsat 8 pixels,
we used the following data. GPS ground data series were available for different years. This information was used jointly
with high-resolution images Sentinel 2. To classify the Landsat 8 imaging the random forest algorithm (RF in NextGis)
was used on the base of training points (Belgiu Drogut 2016). The random generation was repeated 10 times. To generalize
the vegetation map LSL tool was used (Rempel et al. 2015). Modern conservation planning often uses a particular type
of habitat model called a resource selection function (RSF) or a resource selection probability function (RSPF). These
functions can estimate the probability that a particular piece of land will be selected for use by the species of interest.
Low probabilities of use associated with deciduous forests and areas with high linear feature density are consistent
with predation risk avoidance and landscapes with high amounts of deciduous cover and high density of low traffic linear
features. Reindeer selection for old growth conifer cover is also consistent with predation risk avoidance as well as
browse availability. The models can be used to estimate changes in expected patterns of use based on forecast changes
to the landscape.
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17:30
Yury Buyvolov,
Natalya Ivanova,
Maxim Shashkov
Biodiversity data mobilization in the Prioksko-Terrasnyi Biosphere Reserve
The Prioksko-Terrasnyi Biosphere Reserve (PTZ) was founded in 1945 and has been a part of UNESCO World Wide Network of
Biosphere Reserves since 1978. Biodiversity data mobilisation via global portals is important activity of the Reserve.
PTZ became a GBIF publisher in 2016 and was the first Russian Biosphere Reserve in GBIF network. Data mobilization is
carried out through IPT Installation of the Institute of Mathematical Problems of Biology (Russian GBIF IPT). About
27000 occurrences have been published by PTZ through GBIF.org (3 occurrence and 2 checklist datasets). The largest dataset
contains the results of phenological observations on the PTZ from 1948 to 2016 (24358 occurrences, doi 10.15468/2txjmp).
This data is used in the international projet Chronicle of Nature: Large Scale Analysis of Changing Eurasia Ecosystems
(ECN). The spiders ((Arachnida: Aranei)) are studied in detail among another taxonomic groups. Total of 284 spider species
belonging to 145 genera were founded in the Reserve, checklist of this group available via GBIF (doi 10.15468/819bz7).
The results of two-year field studies of spiders in nine different habitats of PTZ are presented in a separate occurrence
dataset (doi 10.15468/3cbyt7). Biological collections of PTZ are not digitized. However, generalized data of labels
for herbarium collection already available through GBIF (doi 10.15468/r8ybnq). We will plan to expand this data by images
of specimens. Published datasets are cited in 3 English-language articles in less than 2 years since the publication
of the first dataset. Some biodiversity data for PTZ also available via iNaturalist system (www.inaturalist.org). It
is a citizen science project and online social network of naturalists, citizen scientists, and biologists. The iNaturalist
platform is very important for promotion of ecological education in the Reserve.
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17:30
Nikolai Vorobyov, Eugeny Andronov, Yan Pukhalsky, Olga Sviridova, Veronika Pishchik
Fractal models for assessing the functional diversity of organized soil microbial communities
Soil microbial communities regularly self-organize to implement joint biochemical reactions and extract necessary nutrients
from plant substrates. When changing substrates the configuration of the microbial biosystem is automatically rearranged
evenly distributing the enzymatic load between the microbial components. In article proposed to use fractal models of
frequency-taxonomic specter of microbial communities to assess the functional diversity of the processes of self-organization
of microbial communities. The proposed mathematical methodology based on a fractal analysis of the location of operational-taxonomic
units (OTU) of microbial communities on a two-dimensional fractal portrait of these communities. Initially, the original
OTU spectrum converted into a reduced spectrum of OTU groups, in which each group combines individual OTUs that are
similar in frequency. On a two-dimensional fractal portrait of the microbial community, each OTU group represented by
a point with coordinates that depend on the frequency of occurrence of this group. As a fractal measure, in the analysis
triangles with vertices at the points of OTU groups are used. In this case, the smallest height of the triangle chosen
to be the scale of the fractal measure. The construction of triangles and their arrangement in order of increasing scale
of the fractal measure allows us to identify the first triangles, which are degenerate triangles. Degenerate triangles
on the portrait of the microbial community unite the OTU groups that are in the biosystem. The share of biosystemic
OTU groups in the microbial community determines the scale of the joint participation of soil microorganisms in biochemical
reactions (IFS is the index of fractal structures). The taxonomic composition of biosystemic OTE groups determines the
functional orientation of biochemical reactions in soil microbial communities. When analyzing the molecular genetic
data of soil samples, which moistened with pure water and exudates of rye and wheat, the values of IFS for these samples
were calculated out (0.48, 0.50, 0.52, respectively). On the this basis, it can be argued that plant exudates play an
important organizing role in the development of plant-microbial interactions.
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17:30
Mikhail Orlov
Climate data optimization for species distribution models using unsupervised machine learning
Species ditribution models (SDMs) attract growing interest of ecologists and related domain experts as a tool to connect
observations of species occurrence and environmental factors as well as to predict taxon"s geographical distribution.
Model realism and robustness are influenced by predictor relevancy, modelling method used, and various settings. Currently
entropy maximization approach implemented in MaxEnt Software gained the most attention, its alternative implementations
are also available. At the same time, the plethora of different machine learning techiques might also be helpful for
SDMs optimization. To address the problem we used 19 bioclimatic variables taken from Worldclim database (version 2.0)
with for Crimean peninsula the resolution of 15" as predictors. Actual localities of Apiacea representatives were obtained
from 3 russian herbarium (MW, MHA, LE) specimen tags. For 3 most presented species binary classifiers were trained.
Among them only Pimpinella tragium models were selected for the further work due to their highest performance. R open
source software was used solely to build and evaluate models based on various machine learning methods including maxent
(implemented in «maxnet» R package) in a uniform and reproducible way. As it is known that correlated predictors usage
lower model performance, in another part of the work we excluded several initial variables in order to reduce data dimensionality
and statistical «noise». Indeed, certain Worldclim variables are bound to be highly correlated (i.e. maximum temperature
of the hottest month and the hottest quarter, isothermality is a result of the division division of one variable by
another and therefore holds no additional information, etc.) Accordingly, we performed correlation analysis as well
as principal component analysis (PCA) and were able to establish most correlated and less contributing to the dataset
variance variables which were removed from the new reduced dataset. Lesser correlation of the new dataset variables
was evidenced and hierarchical clusterization for the two dataset was carried out. The latter separated certain climatic
regions sucessfully in both cases; the data reduction thus caused only minor changes. As a side note, the clusterization
here might by usefull for automated demarcation of climatic regions in general case. Next, various supervised machine
learning techiques were applied to train and evaluate binary classifiers for both datasets. The result suggests comparable
predictions with better perfomance in case of models trained using the reduced dataset. In conclusion, various machine
learning techniques used alonside with maxent as well as reducing predictor set (i.e. bioclimatic variables) by means
of unsupervised machine learning appears to be benificical for SDMs performance.
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17:30
Max Rykaczewski,
Joanna Gołębiewska,
Marta Jarosińska
Seed Bank as an essential part of the modern herbarium
Extreme weather conditions, ongoing deforestation and extensive agriculture cause the irreversible loss of biodiversity,
especially habitats for many plants, as well as facilitate the spread of invasive species, not only in the Tropical
regions, but also in our neighbourhood. Species that were quite common just fifty years ago, are now endangered to extinction.
By decades, herbaria were considered as a source of the information about biodiversity, but the dried specimens are
nothing more than the silent witnesses of aggressive economy of the modern world. It is not possible to restore wild
population from the DNA inside the preserved tissues of the herbarium specimens. Though, the relatively inexpensive
method – seed banking – allows to do it in an easy way. Seed bank does not only store seeds as an evidence of species
occurrence, but also gives an opportunity for farmers and researchers to find varieties that could grow in different
regions. And if the seeds are collected along the herbarium specimens, utility of the herbarium increases dramatically.
Seed banks and herbaria are considered as an effective and complementary methods of preserving the biodiversity for
further generations. There are about 1400 seed banks around the world, Svalbard Global Seed Vault being the most known,
functioning as a global repository and a backup for other seed banks. However, smaller seed banks are not less important
and value, but creating the herbarium related bank may be sensitive for miscarriage. Gathering of the seeds from the
wild populations and further storage conditions for them, as well as merging and unification of data inside the database,
are critical processes but strongly vulnerable for mistakes. Here we would like to discuss the problem and critical
checkpoints for newly established seed bank, on the basis of the experience of creating Seed Bank collection funded
along the Herbarium UGDA within the project “Protection of genetic resources of wild growing endangered species of vascular
plants of Gdańsk Pomerania”.
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09:00
Maxim Dubinin
Web-GIS and mobile tools for efficient data collection, NextGIS perspective
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-
09:20 Marie-Elise Lecoq,
Anne-Sophie Archambeau, Fabien Cavière,
Eric Chenin
Living Atlases Community
Since 2010, the Atlas of Living Australia (ALA) provides information on all the known species in Australia and contributes
to the Global Biodiversity Information Facility (GBIF). By lending access to this national open source platform, the
open and modular architecture of ALA enables re-use of ALA tools by other countries and regions. Over the years, thanks
to the ALA team and GBIF, the community has grown in different ways from production to training courses. Firstly, data
portals based on ALA but residing outside Australia, have been launched in several institutions such as INBio in Costa
Rica and Canadensys in Canada, and in the GBIF network via at least eight nodes presently operating national ALA-based
portals (e.g., Spain, Portugal, France, Sweden, Argentina, United Kingdom). Others will follow in the coming years (e.g.,
Colombia, Peru). Other countries, such as Benin, have also begun to develop their own installations with the aid of
partners in the Living Atlases Community. Secondly the experience gained by installing and customizing their own data
portals has allowed many advanced participants to share their expertise in subjects like internationalization, data
management, and customization, with others during workshops. Adding to these points, as an open source software, developers
contribute to the community by implementing new functionalities and improving the translation into several languages
for users of the software. Today, some modules are fully translated into Spanish, French, and Portuguese. One of the
main objectives of this presentation will be to present the community of Living Atlases by showing examples already
in production (Atlas of Living Australia, Canadensys, GBIF Benin, GBIF Spain or NBN Atlas), past & future projects
involving the community and highlighting how re-using existing software can be motivating and stimulating.
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09:40
Ingimar Erlingsson, Anders Telenius, Mikko Heikkinen
DINA. An Open Source web-based collection management system for natural history specimens and for publishing data at
GBIF
Authors: Ingimar Erlingsson, Mikko Heikkinen, Anders Telenius Department: Bioinformatics and Genetics Dept., Swedish
Museum of Natural History. Swedish natural history museums and collections house more than 33 million objects from all
over the world out of which 10-20% are digitized and published by the Global Biodiversity Information Facility (GBIF).
This huge backlog of more than 25 million objects is problematic in itself. In addition, the specimens already digitally
available were until recently locally curated and presented by a multitude of home-grown and commercial systems. To
remedy the inconsistencies in using different collections management solutions, a decision was made during 2014 to establish
a consortium aiming to address these problems by developing a single, unified Open Source web-based system for collections
management – DINA (“DIgital Information system for NAtural history data”, https://dina-project.net). This presentation
will give an overview and significant details of the structure, development and present status of the DINA web-based
collection management system. The national Swedish DINA consortium is governed by a steering group where all the major
natural history museums in Sweden are represented. The main responsibility for DINA systems development is located at
the Department of Bioinformatics and Genetics at the Swedish Natural History Museum in Stockholm. There is also an international
consortium involving several partners in Europe and North America adopting DINA modules of their choice, and more collaborating
partners are subsequently invited. Currently the core team of developers in Stockholm consists of a project manager,
four developers and two domain experts. The expected timeline for presenting the first pilot collections is due by the
end of 2018. DINA is designed as a loosely coupled set of web-based modules, based upon a compilation of comprehensive
guidelines for web service application programming interfaces (APIs) ensuring interoperability of modules. All DINA
components can be modified or even replaced by other components as long as they are DINA compliant. Furthermore, the
modularity enables the institutions to host only the components they need. These features will all be described herein,
as will the step-by-step SCRUM working process (reference groups – one collection at a time; focus on the data model;
continuous collaboration between domain experts and developers). Finally the data-publishing components enabling automatic
transfer of data to GBIF – including using TDWG standards (e.g. DwC Archive) will also briefly be touched upon.
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10:00
Igor Karyakin
Web-GIS “Faunistics” – the online database for crowdsourcing data collecting on biodiversity
Web-GIS “Faunistics” was launched on the Internet on December 12, 2012, at wildlifemonitoring.ru the developers of the
program are I.V. Karyakin, D.A. Kamenskiy, and E.A. Grachev. “Faunistics” is supported by Sibecocenter LLC and Panoptica
LLC (Novosibirsk). The source is used by governmental authorities for maintaining databases on Red Lists of Endangered
Species for Samara and Altai Regions of Russia. “Faunistisc” is implemented on the basis of server software under Linux
operating system Ubuntu 11.10, web server Apache 2.2.20, MySQL 5.7 database, PHP 5.4 interpreter and Phyton 2.7 and
is developed on the basis of the GoogleMaps API. The client part is written in jQuery and Knockout. The cartographic
basis used in the web-based GIS "Faunistics" consists of vector topographic maps from GoogleMaps, OpenStreetMap, Yandex-maps,
and ArcGIS, as well as satellite imagery coverage from GoogleMaps and Bing. “Faunistics” is a crowdsourcing system for
the data collecting from the wide range of users who have access to the Internet as well as geo-referencing photo-hostings.
Users can add, store and export data and geo-layers consist of polygonal, linear and point objects. Data export is possible
in HTML (photo-report), CSV, KML/KMZ, GPX, SHP, and MapInfo files, and in MSWord DOC-files (report). Web-interface of
“Faunistics” is written in Russian and English. From August 22, 2014 we implement the loading of protected area layers
from the web-GIS "Protected Areas of Russia" to “Faunistics”; on October 5, 2015 the import of observations from the
database "Online Diary of bird observations"; from September 1, 2016 “Faunistics” stored a data from the bioresource
collection of the N.K.Koltsov Institute of Developmental Biology RAS; and since December 15, 2016, it has been integrated
into GBIF. The most dynamically developed part of the “Faunistics” is “Raptors of the world” section – it contains 76
880 photos in 44 324 observations by 152 users. A “Nestboxing” section contains 2 113 photos in 1 603 observations by
13 users. A “Birds of Northern Eurasia” section is a section of the Novosibirsk community of birdwatchers and it contains
13 571 photos in 43 198 observations by 74 users. A section “Small cats of Eurasia” is a section maintained by the working
group on study and conservation of Pallas Cat in Eurasian Steppes, and it contains 886 photos in 570 observations by
37 users. A section “Semiaquatic mammals of Eurasia” is a section of initiative group on the conservation of Russian
desman and it represents the most completed source of information on observations of living colonies of the species
from 1949 to 2015. It contains 38 photos in 1 254 observations by 3 users. A section “Protected areas and anthropogenic
disturbances” contains 1 265 photos in 541 observations by 14 users. This section is in big practical use – it allows
users for rapid completing and printing acts for appeals to the prosecutor"s office on violations of environmental legislation.
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10:50
Fyodor Maslov,
Elena Kurchenko,
Varos Petrosyan
Peculiarities of dynamics of plant life forms of the meadow communities of the Ugra National Park at different conditions
of anthropogenic impact revealed by using multi-year monitoring data
Peculiarities of dynamics of plant life forms of the meadow communities of the Ugra National Park at different conditions
of anthropogenic impact revealed by using multi-year monitoring data Maslov F. A.1, Kurchenko E. I.1 , Petrosyan V.G.2
¹ Moscow State Pedagogical University, Moscow, Russia, fyodormaslov@yandex.ru ² A.N. Severtsov Institute of Ecology
and Evolution, Russian Academy of Sciences, Moscow, Russia, petrosyan@sevin.ru At present, there are significant changes
in the floristic composition and functioning of various phytocenosis under the influence of anthropogenic factors. In
this regard, a thorough and comprehensive study of these changes is needed, it is also necessary to make forecasts and
recommendations for the rational use of plant communities. The modern development of information technologies allows
an assessment of the changes occurring in plant communities quickly and effectively, to evaluate and simulate the development
of natural processes, in particular, in the economic use of meadow communities. The aim of the work is to reveal the
influence of various conditions of anthropogenic impact on the dynamics of the life forms of plant species in Zalidovo
meadows using the Lifeform Index (LI) and the Life Stability Index (LSI). The results on using different indices to
analyze the dynamics of the meadow community based on more than 50 years monitoring data for Zalidovo meadows (Kaluga
Region) are presented in the report. As model objects, six trial plots were selected, which were under different conditions
of anthropogenic impact in the period of 1961-2012. With the use of LSI it was shown that the greatest variety of life
forms was achieved on the plot that was used for all years of monitoring as a hayfield, on which perennial life forms
of meadow plants predominated. The smallest value of diversity was found in areas which were used mainly as pastures,
dominated by annual and biennial life forms. The comparative analysis of the LSI for all plots based on the one-way
factor analysis of variance (ANOVA) showed that there was not statistically significant difference between the studied
plots, which indicated a high level of the growing life form stability in the studied plots. The analysis of the dynamics
of the meadows life forms makes it possible to assert that haymaking and pasture regime affect the growth of the life
forms of meadow plants in different ways. Haymaking increases the participation of perennial life forms, and pasture
regime increases the participation of biennial and annual life forms. The conclusion is: the most optimal use of meadows
is the alternation of haymaking and pasture regime.
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11:05
Nina Filippova, Ilya Filippov
Development of regional biodiversity portal in Khanty-Mansi Autonomous Okrug-Yugra
Khanty-Mansi Autonomous Okrug – Yugra located in the central part of Western Siberia. Biodiversity-related studies are
relatively young there in line with intensive industrial development of the region in recent decades. The region poses
a few of biological collections within the Universities and Nature Reserves. Still, the Department of Natural Resources
of Yugra pays considerable attention to the sustainable use of natural resources. The advance of computer and Internet
technologies produces response in biodiversity science, thus biodiversity informatics discipline developing quickly
over last decades with considerable results in development of protocols, standards and global platforms for integration
of biodiversity data. The data flow from local, regional and national nodes to global platforms (like GBIF) where integrated
data are broadly available. On the local scale, the employment of biodiversity informatics methods for storage, analyses
and publication of biodiversity data greatly improves the quality of work. Organization of biodiversity portals promotes
education and opens the realm of science to citizens. Due to these reasons organization and development of biodiversity
portal in Yugra region would be an important and timely task. Previous experience of biodiversity information systems
in Yugra was only initial. The program on digitization of observations of Red Listed species was launched in 2010 under
support of the Department of Natural Resources. The information system UGRABIO developed through this project currently
includes about 3 thousand observations. Another case of digitization was shown by a biological collection of Yugra State
University with its database based on Specify product and available online through its web version. Some collections
of Nature Reserves have their catalogues in digital form. The demand of collections digitization seems well understood
as shown at regular workshops on Biological collections management held in Khanty-Mansiysk. Recently biologists curating
several biological collections in the region started a project on a regional biodiversity portal (YugraBio). The already
developed product Symbiota – a package of web tools for integration of separate collections databases will be used for
the portal development. The YugraBio project will include several stages: 1) a metadata database of biological collections
in Yugra will be developed, 2) major biological collections will be digitized, 3) algorithms and guidelines will be
developed during the digitization, 4) the overall structure of the portal will be developed, 5) the portal will be linked
to the national IPT node for export to national and international (GBIF) portals, 6) finally the workshops and seminars
for information dissemination should be organized. The collected massive of data in the portal would give new opportunities
for biodiversity research and sustainable management of nature resources in the Yugra region.
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11:20
Aleksey Vaganov,
Kristina Medvedeva, Tatiana Sinitsyna
Complex of open access databases of Altai State University for the purposes of the Altai-Sayan ecoregion
research
Ten years ago, to study the biological diversity of the Altai-Sayan Ecological Region (ASER), the process of developing
and creating a set of open access databases on the Internet was launched in the Altai State University (ASU, Barnaul).
To date, ten databases contributing the comprehensive study of the animal and plant world of ASER, have been developed.
The databases were created using the web interface MySQL5 phpMyAdmin 3 and located on the server of ASU (ssbg.asu.ru).
The mountain system of Altai and Sayan has a relatively small territorial area, but is the habitat of a large number
of biological objects. In 2002, David Olson and Eric Dinerstein singled out this territory as one of the 200 priority
ecoregions of the world for global conservation of biodiversity (Annals of the Missouri Botanical Garden 89: 199–224)
in their work "The global 200. Priority ecoregions for global conservation". Considering the data of 200 ecoregions,
they noted that 90 % of the world"s biodiversity is concentrated on 10 % of its territory. There is an information on
the most popular databases from the existing ones below. Biodiversity of the Altai-Sayan ecoregion (ASER) (bioaltai-sayan.ru).
The database contains an information on the biological diversity of the ASER within the territories of Russia, Mongolia,
China and Kazakhstan. The database reflects the current generally accepted systematic classification and is organized
as a list of biological objects (animals, plants, mushrooms) that are represented on the territory of the ASER. The
database contains the Russian and Latin names of the species, its distribution. Characteristics of the species include
distinctive morphological characters, its place in the accepted classification groups by distribution (rare, endemic,
etc.), as well as statuses in the Red Data Books of Russia, Mongolia, China, Kazakhstan and the IUCN list. For the most
species, distribution maps and photographs are given. Virtual Herbarium SSBG (ALTB). The electronic database of materials
of the herbarium funds of ASU (Herbarium ALTB) is available on the Internet at www.ssbg.asu.ru/altb_herbarium.php. The
structure of the database is presented as a catalog of species on the collections of ALTB, which is formed by drop-down
lists (collection, family, species, country, herbarium status) for convenience of searching and sorting. A separate
database record contains an image of the herbarium sheet (with an individual barcode number) and text information (label
content), which includes 16 items. Checklist of lichens of the Altai Territory. The database is designed to store, systematize
and search for information on the species composition of lichens of the Altai and its individual botanical-geographical
regions, species included in the Red Data Books, as well as bibliographic references to publications in which this information
is contained. For species included in the national or regional Red Data Book, the conservation status is indicated.
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11:35
Igor Pospelov
The experience of geo-referencing Central Siberia herbarium collections from the Moscow State University (MW) collection.
The digitization of D.P. Syreischikov Moscow State University Herbarium (MW) has begun in 2016. The author, working in
the Taymyr District of the Krasnoyarsk Region, set the goal of identifying all the collections of vascular plants from
this region. Author"s geo-referencing of collections (6300) was provided to MW to publish on portal also. During the
work it became clear that for the full identification of the collection from Taimyr it is necessary to view the entire
herbarium of region "Middle Siberia" (about 19500 samples). For the primary geo-referencing topographic maps 1 : 200000
used. Search locations of collection directly were conducted in the web mapping services (primarily Yandex. Maps). For
collections of XIX - beginning of XX c. map the Yenisei Province from the Atlas of Asian Russia (1914) was used. If
necessary, the reports of expeditions, publications of collectors and even biographical information about them were
studied. After finding the desired area (by toponym), the transition into coordinates in the GIS ArcGIS project was
carried out. The coordinates were specified according to the description of the place of collection and with the help
of a special script were transferred to the MS Excel table with one click; collectors, collection date and expert accuracy
of fixation in km were also entered there. After snapping the first 1000 examples areas of the main collectors determined,
which allowed the ArcGIS project to set bookmarks on 36 areas. Now it is possible to perform up to 500 points per day.
As shown, after such a "dip" in the collection of any example can be mapped with an accuracy of from 0.5 to 5 km. In
some cases, it would make sense to link not to the point with the radius of the error, but to a certain polygon or line
feature (section of the river, the passage of the road, the vicinity of the settlement, etc.). The operator of the geo-referencing
should be well aware of the natural conditions of the region and have experience in field work. Thus, geographically
localized areas of collecting, approximately corresponding to the concept of local flora, were determined. After the
initial fixation of specimens, the opportunity for in-depth work in geographic samples appears. These samples will be
used to clarify the bindings for satellite imagery, author descriptions of areas, as well as with the participation
of current collectors. It is possible to name the first results of this work. Only within the Taimyr nearly 100 new
locations of species have been identified, several species are new to the district. For the region it is possible to
consider revealed some never published local floras – for example vicinities of the Igarka and Snezhnogorsk cities.
The knowledge about the history of district flora study has greatly expanded. More than 100 sheets related to the wrong
region were revealed. A significant number of knowingly incorrect or missing definitions are noted, which requires direct
viewing in the Herbarium.
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13:00 Denis Davydov, Eugene Borovithcev, Roman Fedorov, Nadezhda Konstantinova,
Alexey Melekhin, Sergey Schalygin
Development perspectives of CRIS
Cryptogamic Russian Information System - CRIS (http://kpabg.ru/cris) is devoted to cataloging biodiversity information
of the cryptogamic organisms such as algae, fungi, lichens, and bryophytes. In contrast to DarwinCore principles with
its single species record as a baseline, CRIS is working with multispecies records. CRIS allows for users to enter different
types of data such as labels of herbarium specimens, literature references, media files etc. Rapid increase of records
number, diversification of types of materials, complication of the structure of the record forced us to switch from
CMS Drupal to modern Node.js. The major problem in CRIS is to fix issue related to slow geo-searches, which are overloading
server at the moment. Mass processing of data and other features will be convenient improvements of the system. The
modified version will have intergroup search; this will be accomplished by making connection between different sections
of CRIS. In contrast to the old version of the CRIS based on Drupal, new version will have universal numbering system
with “Universal herbarium specimen” (UHS) as a core. UHS from one herbarium may be easily converted into record of another
herbarium, when for example curator is sending specimens to another herbarium physically or give them for the loan.
The new version offers option to entering information about distantly related organisms for examples cyanoprokaryotes
and diatoms in single record. By the end of the testing period, new groups of organisms such as vascular plants, diatoms,
protists and fishes will be included in the new version of CRIS. Eventually, CRIS will have new abbreviation, which
is Complex Research Information System. The main result of this project will be development of modern, online IS, which
is not attached to the local computer. That system will provide quality free access to biodiversity data. The release
of the new version of the CRIS announced for December 2018. This study was conducted with the partial support of grants
from Russian Foundation for Basic Research (projects N 15-29-02662, 18-04-00171, 18-04-00643).
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13:15
Tatiana Ostroumova
Electronic databases for taxonomy and phytogeography of the flowering plant family Umbelliferae
The abstract was sent by M.G.Pimenov The abstract was sent by M.G.Pimenov The abstract was sent by M.G.Pimenov The abstract
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was sent by M.G.Pimenov
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13:30 O Ivanov,
M Kolesnikova, E Baisheva, S Dudov, V Fedosov, E Ignatova, M Kozhin, O Pisarenko,
M Ignatov
The Database of the Moss Flora of Russia
The database of the Moss Flora of Russia were desigened so to be maximally useful for the Moss Flora of Russia project,
but aimed also for further accumulation of data on bryophyte distribution and potentially also on various aspects of
their ecology and morphology. It currently includes over 138 000 herbarium labels from most Russian and some foreign
herbaria. The database is made in the Firebird DMS for FreeBSD, and is kept in at least two servers in the Lebedev Institute
of Physics and the Tsitsin Main Botanical Garden of the Russian Academy of Sciences. The common entrance to the database
is from http://arctoa.ru/Flora/basa.php. The database includes information on the species localities, habitats and other
standard label information. Data insertion/updating is processed by few authorized database managers through the form
for uploading Excel (*.xls) files. On addition to querries, the database can 1) visualize species distribution upon
yandex maps service; 2) comparison species compositions by selected regions; 3) show species diversity by grid squares
in the areas defined by coordinates. Authorized users obtain additional possibilities, including building maps for several
species of Russian moss flora. The data are continuously supplemented with aposteriori inserted geoposition data, and
over 60% of labels now include such data. More information is given in publication at http://arctoa.ru/ru/Archive-ru/26_1/Arctoa26_001_010.pdf.
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13:45 Timur Biktashev,
Elvira Baisheva,
Nikolai Fedorov
Geographic information system "Bryophyte diversity in the Republic of Bashkortostan"
Experience about results of grid mapping, relevant to bryophytes in Great Britain and other countries has showed possibilities
for solutions, that covers a wide range of questions about biology and ecology of species, as well as role of different
ecological factors in form of diversity and distribution of separated species, also objective rating their rarity and
protection needs. Based on consolidation results of inventory bryophytes an electronic atlas of «Bryophyte flora of
the Republic of Bashkortostan» is created. In this atlas location of species is showed as square polygons in layers.
It designed for displaying in different scale of the map. Application is built with using open source software like
DotNet Core, GeoServer, PostreSQL with PostGIS extension. LeafletJS library is using for displaying spatial data. DotNet
Core is used for web-based application. The main part of spatial data is stored in PostgreSQL database with PostGIS
extention. Geoserver is displaying spatial data for vector and raster data. Layer’s style is supported with Styled Layer
Description (SLD). Main page consist of « Bryophyta» и « Marchantiophyta». Each of them is navigated to list of species.There
is a page where contained link to source of species finding in the Republic of Bashkortostan, a list of synonyms, photo
and location species on map of Bashkortostan with scale 1:5000000. The page consist 4 information links: “Ecology”,
“Conservation value”, “Bibliography” and “Detailed species location on RB”. “Ecology” page consists of species’s location
description and 3 charts: “Occurrence within alliances of floristic classification of vegetation», «Occurrence in EUNIS
habitats» и «Elevetion range». “Conservation status” page consist information about on the needs to protect the species.
“Bibliography” - list of publications. When «Detailed species distribution within Republic of Bashkortostan» is selected,
two polygon layers of species are downloaded, which is compiled from polygon grids in WGS84 geographic system and base
tile map (by default Open Street Map (OSM) tile layer). Square’s size of first layer is 6’ long of latitude and 10’
long of longitude (10x11km) which equals with a lot of similar European resources. Second polygon layer contains polygons
which are divided to 100 pieces (36’’ long of latitude and 1’ long of longitude). This layer is designed for more detailed
researches, for instance, within protected areas. When the square is selected in polygon layers we can see links to
Bibliography about that species in current square, characteristics of habitat, person who collected data, the date of
collecting. Geographic information system will be developed and modernized for creating atlases of rare plant species
and plant community. It can integrate knowledge about bryophytes of the Republic of Bashkortostan in Russian and international
databases, which turned up relevance of results regional and national bryological researches.
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14:00 Valentina Verkhozina, Elena Verkhozina, Yurii Bukin
Analysis of bacteria found from ecosystem of lake Baikal
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14:15
Stepan Senator, Aleksey Klenin, Sergey Saksonov
Informational and analytical support of floristic diversity researches in the Middle Volga region – SALIX system
With the aim of integrating, storing, processing and using data on the floristic diversity of the Middle Volga region,
the Salix Information System (State Registration Certificate No. 2017660489 of September 22, 2017) has been developed
at the Institute of Ecology of the Volga Basin of the Russian Academy of Sciences. The Salix system allows adding and
viewing the information about plant taxa, using the extensive filtering and sorting options for taxonomic and environmental
criteria, recording plant detection points georeferenced to geographical coordinates, administrative and floristic areas,
view detection points using the Yandex.Map interface, managing the links on literary sources concerning the points of
plants and individual taxa detection. The system provides for the possibility of a single entry of an array of species-specific
floristic information for a particular point, while simultaneously matching the taxa available in the database, as well
as the possibility of introducing new taxa and new administrative areas. The Web application is built on the current
ASP.NET MVC 6 Web technology in the Visual Studio 2013 Express development environment; MS SQL Server Express 2016 is
used for data storage. The application is deployed on a server running Windows Server 2012 R2; IIS 8 serves as the Web
server. Data entry and editing, including spatial data, can be performed from any computer connected to the Internet.
In the system, it is possible to upload the filtered data to an Excel file for later analysis. Thus, the Salix information-analytical
system allows quick provision of data on floristic diversity within a large region, timely recording of the floristic
findings, taking into account the latest nomenclature changes, visualization of floral information, identification of
plant species peculiar to the area, localities of rare plants, and places of concentration of alien species including
invasive plants.
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14:30
Olga Pisarenko, Igor Artemov, Sergey Kazanovsky, Ekaterina Prelovskaya
Actualization of herbarium labels information
Date on Russia"s brioflora have a centralized accumulation platform - the database (DB) of the Moss Flora of Russia (http://arctoa.ru/Flora/basa.php).
The DB intensively develops; now it reached more than 130 000 records; the volume achieved mainly by combining of personal
DB of currently working Russian bryologists. In recent decades organization of own working materials in the form of
desktop DB has become a common practice in botanical investigations. However, the information of huge herbarium collections
remains inaccessible for operative and especially remote work. Mass scanning of herbarium specimens without label decoding
does not solve the problem. In the case of bryophytes scanning of herbarium labels without label decoding turns into
"information noise": Internet search engines by the query for moss species name gives not photos or drawings of the
species, but hundreds of label scans, that in unsystematized form have no scientific sense. Mass scanning of herbarium
specimens has to goes along with mass entering into a DB of herbarium labels, however it is an extremely laborious task
(and in the case of large herbariums and small or abscent assistant staff it looks to be impossible task). So, in the
Moss Flora of Russia DB (MFR-DB) there are absolutely not presented voluminous bryological herbaria collected by the
deceased scientists V.L. Bardunov (IRK), V.Ya. Cherdantseva (VLA), P.N. Krylov and E. Ya. Muldiyarov (TC), A.N.Vasiliev
(KRAS). The lack of information distorts the general picture of moss species distribution. For this reason some regions
(Irkutsk and Tomsk Provinces, Tyva, Khakassia, the south of the Krasnoyarsk Territory) are "white spots"on the maps
generated by the MFR-DB. To speed up of herbarium labels data transformation into electronic form a DB in MS Access
was made. The interface of the DB uses fields with drop-down lists to enter the main part of text data. An important
and convenient feature of the software is implementation of procedure for updating lists of locations, habitats and
collectors. They are replenished in parallel with filling of the DB and updated every time you enter a new record. As
a result, instead of the routine input of labels data (very often repeating), the user only needs to select the desired
value in the drop-down list or enters the initial letters of the text in the field and the desired value will be selected
automatically. Lists include non-repeating field values that occur in the labels of samples collected on the same day,
that makes them compact and easy to use. Initially, the software was created by I.Artemov as Vascular Flora BD of the
Tuva division of Herbarium of The Central siberian botanical garden (NS) . Its convenience prompted the remaining authors
to take up inventory of the old non-arranged bryological collections NSK and IRK, that is in process now. The work is
in the development of bio-resource collections (UNU № USU 440537), partly supported by RFFI (18-04-00822).
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14:45
Igor Antonov
Regional information and analytical system on insect biodiversity of the Baikal region
The problem of biodiversity conservation is topical for modern ecology, because the scale of the impact of anthropogenic
press on natural ecosystems is expanding at an accelerated pace. It is very important to study the spatial distribution
of species. Insects play a huge role in the terrestrial ecosystems of the Baikal region. Therefore, the information
and analytical system for assessing and monitoring of insect biodiversity in the Baikal region has been created. This
system is consisting of three blocks: a) relational databases, b) the geoinformation system, c) the software environment
R. Relational databases are designed to quickly find the necessary information and to automate the collection and structuring
of data. Besides, these databases were created to analyze the requested information and to create an information basis
for geoinformation system. In the structural and semantic respect, the databases consist of several parts: taxonomic,
ecological, geographic. The geoinformation system was created to study the spatial distribution of insects. It covers
the territory of three subjects of the Russian Federation (Irkutsk oblast, Republic of Buryatia and Zabaykalsky krai).
All cartographic information in the geoinformation system is organized in the form of vector and raster layers: base
(topological) layers, including rivers, roads, buildings, etc.; thematic layers (for example, entomological and landscape).
Raster layers (cosmic images and digitized paper maps) were used when creating base vector layers. Moreover, due to
the development of cartographic services on the Internet (access to high-resolution cosmic images, about 1 meter per
pixel), vector layers with a wide scale range were created, which makes it possible to create both small-scale and large-scale
thematic maps. This allows to study biodiversity at different levels. R is one of the most popular platforms for statistical
computing and graphics, because it is free, open-source software, with versions for Windows, Mac OS X, and Linux operating
systems. Besides, additional modules (“add-on packages”) are available for a variety of specific purposes. At the present
time, the features of spatial distribution of ants and buprestids have been explored by means of this information and
analytical system.
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15:30
Oksana Mikhailenko, Mars Nabiullin, Marat Bogdanov,
Nikolay Fedorov
On the analysis of the spatial and interannual features of phenological stages of forest vegetation by the use of vegetation
indices when the cloudless satellite images are limited
Climate change heavily impacts on growing conditions and expanding coverage of arboreal species and forest communities
(Vose et al, 2011; Xiao-Ying, Chun-Yu, Qing-Yu, 2013, and others). The analysis of the spatial and interannual features
of phenological stages of forest vegetation by the use of various vegetation indices (NDVI and others) proves effective
in forecast of such tendencies. The use of a logistic model is the most effective approach to the analysis of seasonal
changes of vegetation indices (Melaas et al, 2013). The model allows to calculate the time of the beginning of the seasonal
growing, the middle of the spring growing, the time of the transition to the summer growing and the rate of the seasonal
development for the period of spring development of tree stands by the inclinations of an ascending line of the diagram.
A considerable amount of cloudless satellite images is devoted to determine the gearshift points of the seasonal development
in the diagram. It is possible only for territories with an arid climate or, for example, if the medium-resolution images
MODIS are used. When Landsat 7, 8 and Sentinel 2 images are used for the mountainous forest areas of Southern Urals
Mountains there was lack of images suitable for analysis of the seasonal NDVI dynamics in a certain year. A reference
diagram constructions method was therefore developed to determine the NDVI dependence on the stage of seasonal vegetation
development; for this the interannual data were grouped together and then they were compare to NDVI for a certain year.
The interannual satellite images of some plots of the Bashkir State Reserve were used to test the method; regular terrestrial
phenological observations were conducted in these plots. The dates of the beginning of seasonal growing and the duration
of phenological stages differed in different years; thus, the average annual dates of the beginning of various phenological
stages and their durations were calculated. From this information, the time of beginning of the stages and their duration
were normalized for the certain years. After that, the position of the images on the time axis shifted in a proportionate
way. As a result, the interannual data with the same NDVI has moved to the same position in the axis of the phenological
development. With the example of the birch woods of the mountainous forest areas of Southern Urals Mountains it was
revealed that the reference diagrams enable analysis of deviations from the rate of the seasonal forest development
depending on weather conditions in certain years; they also enable to study the features of the seasonal development
of forests in areas differing in climatic conditions.
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15:45
Nikolay Fedorov, Tatyana Zharkikh,
Oksana Mikhailenko, Rafilja Bakirova
The use of NDVI for the analysis of the effect of drought on forage resources for grazing in the territory of the establishing
population of the Przewalski horse Equus ferus przewalskii Polj., 1881
One of the main challenges for the establishment of semi-free populations of rare hoofed animals in special protected
territories is a forecast of forage resources for grazing and their possible changes in years of extreme weather. In
2015, The Russian Government gave a territory for establishing a new protected area called ‘Pre-Urals Steppe’ to Orenburg
State Reserve. A semi-free population of the Przewalski horse Equus ferus przewalskii Polj., 1881 has been established
in this territory within the frame of the UNDP/GEF Project ‘Improving the coverage and management efficiency of protected
areas in the steppe biome of Russia’. In 2016, vegetation mapping was done and productivity of grassland in the main
types of vegetation was analysed by the method of recorded mown plots. A GIS map of vegetation was created and productivity
of grassland for grazing was calculated for 2016 which had favourable weather conditions (Fedorov et al., 2018). The
aim of the present study is to forecast changes in forage resources for grazing under drought stress. Cloudless Landsat-8
and Sentinel-2 images were used to analyse the normal 2016; cloudless Landsat-5 images were used to analyse the dry
2010. A correlation index of 0.77 between grass productivity in dry weight and NDVI was calculated at the time when
the recorded plots were mowed in 2016. A linear regression technique was used to determine the relationship between
grass productivity in dry weight and NDVI. The average NDVI at the time when the recorded plots were mowed was calculated
for the total grassland area (95% of the protected area); from this information, the forage resources for grazing were
determined by the regression equations. The difference between the data obtained by the regression technique and the
data from recorded mown plots was 11.4%. The analysis of grasslands for the same period in dry 2010 revealed that the
forage resources were almost four times lower than in 2016. Most of vegetation in level and elevated areas dried off
in the beginning of July, 2010; they did not recover till the late autumn. It may be predicted that the horses will
have difficulties to find forages in winter after a summer drought; a stock of hay must be reserved for such cases.
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16:00
Elena Istomina
Application of remote sensing methods for landscape mapping of the Mondy depression
A method of typological mapping of landscapes with the use of Landsat satellite images and the digital elevation model
SRTM, as well as the method of factorial-dynamic classification of landscapes, was developed and a large-scale landscape
map of the Mondy basin was created. At the first stage, the image was automatically classified using the neural network
classification method, resulting in a picture divided into 11 classes. The resulting classified image was smoothed to
remove the mosaic effect and translated into a vector map. For each unit obtained as a result of the classification
of the satellite image, the following parameters were calculated by means of spatial analysis in the GIS: belonging
to a particular ridge, category according to the classification of the image, height category, slopes and topographic
wetness index. By the combination of these parameters, each unit was assigned to a certain type of landscapes. In the
study area on the Tunkinsky goltsy ridge goltsovy steep slope screes with lichen cover landscapes, as well as birch
and larch-birch stages of restoration of larch forests are dominated, and on the Khamar-Daban ridge – larch moss and
dwarf birch forests, as well as meadows with the community of dwarf birch. The work was carried out within the framework
of the program of the V. B. Sochava Institute of Geography SB RAS with partial support of the Russian Foundation for
Basic Research (pro-jects No. 17-05-00588 and No. 16-05-00902).
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16:15
Maxim Shashkov, Natalya Ivanova, Vladimir Shanin, Pavel Grabarnik
Ground surveys vs. UAV photography: the comparison of two tree mapping techniques
Nowadays, due to the rapid development of light-weight unmanned aerial vehicles (UAV), a remote sensing systems of ultra-high
resolution became available to many researchers. The aim of this investigation was to compare the classical method (“from
below”) and the newest one, using aerial images-based method (“from above”). Our field works were carried out in Prioksko-Terrasny
Natural Reserve (Moscow region, Russia) on permanent sampling plot of 1 ha (100x100 m). A total of 779 trees with DBH
at least of 5 cm were measured during ground survey in 2016. Species and Kraft’s class were determined for each alive
tree and the radii of crown horizontal projection in four cardinal directions were measured. Crown projection of each
tree was represented as a union of 4 quarter-ellipses, and the total area of all projections was calculated. The aerial
photography by a quadcopter DJI Phantom 4 was conducted in 2017 on August, 2 from altitude of 58 m and on October, 12
(68 m). The orthophotomaps composed by means of DroneDeploy service (https://www.dronedeploy.com/) were used for manual
vectorization of visible crown projections in Quantum GIS 2.8 software. For comparison we used only alive trees of upper
canopy (1, 2, and 3 Kraft’s classes). Total area of tree crown projections according to ground-based tree mapping was
6833 m2 (269 trees), and according to aerial-based mapping it was 6883 m2 – about 1% higher (285 vectorized crowns –
6% more). When considering tree species separately, the most consistent results among two techniques were obtained for
birch: total crown area was underestimated by aerial method by 4%, while the number of trees was overestimated by 4%.
For spruce, the total area of crown projections estimated by aerial photography was 14% less than by ground-based measurements,
whereas the number of trees was 13% higher. According to the results of aerial photography, the crown projection area
for oak was underestimated by 31%, and the number of trees was less by 13%. The results for aspen and lime showed high
discrepancy between techniques, namely 1.5-2-fold overestimation of both crown projection area and number of trees for
aspen by aerial photography, and 3-fold underestimation of these parameters for lime. The discrepancy in results obtained
by two techniques can be explained by accounting at aerial photography of smaller (DBH < 5 cm) trees in gaps, which
during ground survey were omitted. One more reason can be due to the uncertainty of recognition of similarly looking
aspen, birch and lime on aerial photo. The underestimation of crown projection area with aerial photography could be
actually the overestimation of this parameter by ground survey resulted from too rough approximation of crown projection
shape. In addition, the parts of single trees’ crown, branched at small height above the ground, could be recognized
on orthophotomaps as individuals crowns. The work was supported by Russian Science Foundation (project No. 18-14-00362).
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16:30
Nikolay Fadeev, Tatyana Skripytsina, Vladimir Kurkov
Use of Remote Sensing data and GIS technologies for monitoring resources of medicinal plants
Preservation of the biodiversity of medicinal plants makes it possible to create a basis for the development and creation
of new medicines through scientifically based nature management. One of the topical tasks of botanical resource research
is the interpretation of plant communities, monitoring their condition and distribution. Remote sensing techniques provide
solutions for obtaining, analyzing and managing data at different scales: high-resolution satellite imagery and multi-spectral
channels can provide information covering large areas [1], while aerial photography with unmanned aerial vehicles (UAV)
allows you to collect comprehensive biometric information from key areas [2]. To carry out quality monitoring of plant
communities, the following conditions must be met: regular aerial photography with similar aerial survey parameters
to the same phase of vegetation. This will make it possible to obtain the best quality of the original photographic
material and successfully interpretation the medicinal plants. Studies carried out on the territory of the Tula region
in 2014-2017, showed the advisability of using the UAV for monitoring the reserves of wild medicinal plants [2]. The
planned accuracy of the created orthophoto, their photographic quality allowed confidently interprets the plant communities
during flowering. By stereoscopic images, specialists were able to determine biometric characteristics, such as plant
height and number of individuals per square meter, which led to a significant reduction in field work. Рlant resources
were estimated with an accuracy of not less than 10%. To perform the work, a complex of photogrammetric (PHOTOMOD "Rakurs")
and GIS (MapInfo Professional 12). The result of the joint work was a map and database of stocks of medicinal plants
for the study site. The use of multispectral aerial and space imagery, in addition to aerial photography data in the
visible range, scales the research of medicinal plants resources on significant areas, which should accelerate the work
on large areas. Nevertheless, one of the important problems remains the automation of interpretation of wild-growing
herb medicinal plants, connected with the peculiarity of the growth of these communities. The solution of the problem
is the application of complex analysis using digital terrain models. REFERENCES 1 Sozinov O.2015. Information technology
in the botanical resources: results and prospects. Rastytelnye resourcy.V51(3) Pp.449-462. 2 Fadeev N., Skrypitsyna
T., Kurkov V. 2016. Modern geoinformation technologies in investigation of resources medicinal plants.\Voprosy biologicheskoy,
medicinscoy y pharnmacevticheskoy khimii.\ 6. pp 68-73.
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16:45 Mikhail Puzachenko, Tatiana Chernen’kova, Nadezhda Belyaeva,
Olga Morozova
Assessment of typological diversity of vegetation cover on the basis of field data, RSD and DEM on the example of the
western part of the Moscow Region.
Assessment of biodiversity and its determinants is an urgent task of modern science. To assess the ecosystem (typological)
biodiversity of vegetation at the regional level, the main source of data is field research. Such data are point and
do not give an idea of the spatial variation of types of plant communities. Data on the relief and / or reflective characteristics
of vegetation obtained from satellites in different spectral ranges can serve as sources of quasi-continuous information
for the interpolation of typological vegetation units. The relief (DEM) is the basis for the redistribution of material-energy
flows of various levels. Multispectral remote sensing data (RSD) fix the reflection/absorption of solar radiation by
vegetation, which allows obtaining information about its state and functioning. There are several methods for interpolating
data based on the training sample, but most of them require significant computational resources for large sample sizes.
Stepwise discriminant analysis, under certain restrictions, allows processing large data sets and explicitly separates
classes, which is important in interpreting biodiversity factors. As an example of such an analysis is considered the
territory of the western part of the Moscow region, which has a complex structure of vegetation cover due to both natural
and anthropogenic factors. Based on 1087 geobotanical descriptions, 38 syntaxes in the rank of associative groups and
5 categories of vegetation types not included in the classification (small grass mixed grass, grassy meadow cuttings,
meadows, open waterlogged habitats and shrubby wet grass) were identified using the eco-phytocenotic approach . In addition,
3 categories of vegetation cover (fields, reservoirs and settlements) were identified on the basis of RSD. The overall
quality of discrimination of the allocated units from the projective covering of species in accordance with the descriptions
of vegetation was 84.5%. The source of information about the relief of the territory was SRTM data, for which the relief
characteristics (gradients, curvatures, illumination) of various levels of the hierarchical organization were calculated.
The quality of discrimination of plant units on the basis of DEM was 49.6%. Landsat 5 and 8, combined in mosaics for
March, August and September and spectral indices calculated on the basis of research channels were used as RSD. The
quality of discriminant analysis in this case was 49.8%. The quality of discrimination conducted in the joint analysis
of DEM and RSD was 64.6%. Thus, the joint use of information on the relief and RSD improves the allocation of allocated
classes by 15%. A cartographic model of the typological diversity of vegetation cover was developed.
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09:00
Alla Verhosina
Botany, informatics, geographers: experience of cooperation, results, prospects
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09:20
Ingimar Erlingsson, Niclas Gyllenstrand, Thomas Källman, Anders Telenius, James Macklin
Introducing a sequence database management system (SeqDB) at the Swedish Museum of Natural History and how to export
to external systems
Authors: Ingimar Erlingsson, Niclas Gyllenstrand, Thomas Källman, Anders Telenius,James Macklin Department: Bioinformatics
and Genetics Dept., Swedish Museum of Natural History. Natural history collections contain valuable resources, such
as type specimen for authoritative identification using approaches that include phenotyping, DNA barcoding, and whole
genome sequencing. The rapid development in DNA technology has increased the need for an efficient and well-integrated
infrastructure for DNA barcoding, including automated work flows for both a digital and physical DNA archive. This presentation
will give an overview and significant details of the structure, and the current status of the SeqDB system developed
by Agriculture and Agri-Food Canada (AAFC) and its customized implementation for the Centre for Genetic Identification
and the DNA-lab at the Swedish Museum of Natural History (SMNH). SeqDB tracks the complete workflow and provenance chain
from source specimen information through DNA extractions, PCR reactions to sequence and/or genotype data. Thus, having
the functionality as a Laboratory Information Management System (LIMS) to enable traceability. SeqDB implements the
Taxonomic Databases Working Group (TDWG) Darwin Core (DwC) standard for Biodiversity Occurrence Data, as well as the
Genome Standards Consortium (GSC) ‘Minimum Information about any (x) Sequences’ (MIxS) specification. Furthermore, SeqDB
tracks sampling metadata and DNA extractions from Next Generation Sequencing (NGS) of environmental samples and tracks
the physical samples stored in racks of pre-printed vials. All the information is presented using a graphical user interface
that features intuitive molecular workflows as well as a RESTful API that facilitates integration with external applications
and programmatic access of the data. SeqDB currently support exports to GenBank and BOLD (Barcode of Life Data Systems)
and will in the future also support exports in the GGBN DwC standards. Besides the already available functionality,
the SMNH instance of SeqDB has been extensively evaluated to handle large-scale genotyping, as part of the Swedish Environmental
Protection Agency monitoring programs. These data are publicly accessible and can be searched using a public-UI. The
long-term goal is to couple the SMNH SeqDB instance with external APIs such as Rovbase (a database hosting wildlife
observations in Scandinavia). SeqDB will provide significantly better opportunities for SMNH to rationally handle large
amounts of samples, thus enabling larger projects to be carried out based on DNA analyzes, not least DNA barcoding projects.
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09:40
Xuehong Xu, Keping Ma, Maofang Luo, Bo Liu, Hongfeng Wang, Jianhua Xue, Qinwen Lin, Wenjun Li, Zheping Xu, K. Ganeshaiah
Mapping Asia Plants: Initiative and Progress
Mapping Asia Plants: Initiative and Progress Keping Ma1,2, Xuehong Xu1,2, Maofang Luo1,2,Bo Liu1, Hongfeng Wang1, Jianhua
Xue1, Qinwen Lin1, Wenjun Li3, Zheping Xu4, K. N.Ganeshaiah5 1 Institute of Botany, Chinese Academy of Sciences, China
2 Biodiversity Committee, Chinese Academy of Sciences, China 3 Xinjiang Institute of Ecology and Geography, Chinese
Academy of Sciences, China 4 National Science Library, Chinese Academy of Sciences, China 5 University of Agricultural
Sciences, GKVK Bangalore, India Because of the huge population and rapid growth of economy, biodiversity including plants
are being seriously threatened in Asia. Researches on conservation and sustainable use of biodiversity are depended
on species cataloging and monitoring to a great extent. But till now, there is no biodiversity database infrastructure
in regional scale in Asia, while there are certain independent efforts of Biodiversity database construction in China
Mainland and China Taiwan, India, Japan and Korea, which has serious impacts on biodiversity research and protection
at regional scale in Asia. Thus, Mapping Asia Plants (MAP) was initiated at the meeting of ABCDNet（ABCDNet, www.abcdn.org）working
group on Nov., 2015, and was funded by Bureau of International Co-operation and Southeast Asia Biodiversity Research
Institute Chinese Academy of Sciences. MAP provides a database and standardized workflow for mapping Asia plant species,
distribution, and is available to comprehensive basic information and interdisciplinary data mining for plant diversity
conservation and research. MAP aims to collect, integrate Asia plant diversity resources and to construct a platform
of Asia plant diversity. Major achievements so far are as follows. Species checklist databases have been basically set
up in five sub-regions of Asia (Southeast Asia, South Asia, Northeast Asia, North Asia and Middle Asia) to the national
level, and the species checklist databases have been basically set up in 3 countries in West Asia. 1) for Southeast
Asia, a dataset of 425 families, 4873 genus, 69291 species has been set up; 2) for South Asia, a dataset of 325 families,
3817 genus, 32525 species has been set up; 3) for Middle Asia, a dataset of 169 families, 1404 genus, 9047 species has
been set up; 4) for Northeast Asia, a dataset of 417 families, 4345 genus, 42566 species has been set up; 5) for North
Asia, a dataset of 191 families, 1187 genus, 7700 species has been set up; 6) for West Asia, a dataset of 200 families,
2543 genus, 6000 species has been set up.
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10:00
Maxim Shashkov,
Natalya Ivanova
GBIF Activities in Russia: Towards a National Node
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10:50
Victor Chepinoga, Т Stepantsova
V.I. Smirnov Herbarium of Irkutsk State University (IRKU): current condition, inventory, and plans for digitalization
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11:05
Natalya Ivanova,
Maxim Shashkov, Yury Buyvolov
How much data do Russian biological collections contain?
Best known and largest Russian herbarium collections are stored in Komarov Botanical Institute (LE, more than 6 mln sheets)
and Moscov University (MW, more than 1 mln sheets). The largest zoological collection is located in Zoological institute
and counts more than 60 mln specimens. There are also many different another biological collections in Russia, but unified
list about them is absent and related information is scattered. There are 81 biocollections from Russia registered on
the Global Registry of Biodiversity Repositories (http://grbio.org). According to the portal Genetic and biological
(zoological and botanical) collections of the Russian Federation (http://www.sevin.ru/collections/), 145 herbarium collections
from 102 cities were present in Russia in 2004. During this work we founded information about 160 regional herbarium
collections with total storage more than 8 mln specimens (excluding MW and LE). There are also 4 Russian live algae
collection, total storage are 1258 living specimens (http://www.wfcc.info/). Available data on zoological collections
are poorer. Large collections are stored in the Zoological Museum of Moscow University (6378700 specimens), the Museum
of Institute of Plant and Animal Ecology (1150023 sp.), the Institute of Biology of Komi (118576 sp.) and the Museum
of National Scientific Center of Marine Biology (about 1 mln sp.). The majority of Russian biological collections are
not digitized. In our assessment total amount of digitized samples is about 1 mln, mostly presented by MW herbarium
(99.5%). This collection almost completely digitized and now available through GBIF.org (doi 10.15468/cpnhcc) and thematic
information system (https://plant.depo.msu.ru/). A small part of the LE and SVER herbaria are also digitized (1320 and
5031 sp. respectively). Generalized data of labels for herbarium collections of the Polar-Alpine Botanical Garden-Institute
of N.A. Avrorin KPABG, N.I. Vavilov Institute of Plant Genetic Resources (VIR) and the Prioksko-Terrasnyi Biosphere
Reserve also available via GBIF.org (total 39114 records; doi 10.15468/yxt7co, 10.15468/nctfm2, 10.15468/80tu83, 10.15468/xtcciv,
10.15468/cjzloe, 10.15468/r8ybnq). Thus, at least 82 million specimens are stored in Russian biological collections,
but available (via the Internet) data is only 1.2%. This work is partly supported by a GBIF - FinBIF data mobilization
grant for European Russia (project Russia-02).
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11:20
Nataliya Kovtonyuk, Irina Han, Evgeniya Gatilova
Virtual herbarium collections of the Central Siberian Botanical Garden as a resource for biodiversity study
The first herbarium at the Central Siberian botanical garden (CSBG SB RAS) was organized in 1946. Now there are two herbarium
collections in CSBG with own acronyms and registration in the Index Herbariorum (NSK and NS). Collection contains about
800 000 herbarium specimens of high vascular plants, mosses, lichens and fungi sampled in Siberia, Russian Far East,
Europe, Asia and America. Digitization of high vascular plants was initiated from type specimens by special scanner
Herbscan, supported by Andrew Mellon Foundation in 2014. Images and metadata of 800 type specimens are currently available
on the Virtual Herbaria web site at the Vienna University, Austria (http://herbarium.univie.ac.at/database) and in Jstor
(https://plants.jstor.org). Special attention was paid to providing on-line high resolution (600dpi) images and metadata
for all types specimens (Kovtonyuk, 2015, 2017). In 2017 a new research group “USU-Herbarium” was organized in CSBG
SB RAS for digitization and management of herbarium collections, our aim is to provide online access to CSBG SB RAS
herbarium collections as a worldwide resource for biodiversity study. We initiated digitization of NSK and NS high vascular
plants collections by two scanners ObjectScan 1600. Currently about 8 000 herbarium specimens were digitized at 600
dpi, images and metadata are stored in CSBG SB RAS Database generated by ScanWizard Botany and MiVapp Botany software
(Microtek, Taiwan). The largest number of samples scanned are from Primulaceae (4654), Boraginaceae (632), Athyriaceae
(566), Cystopteridaceae (352), Asteraceae (220), Plumbaginaceae (363) and Poaceae (143). The database is structured
in a way that a common user can access a specimen file that contains high resolution image and following key information:
specimen ID (= barcode), family name, scientific name (genus, species, author of taxon), collector name and collection
date, country or administrative region. Alternatively the request may be done by using key words of habitat characteristics,
for example, “pine forest”, “meadows”, etc. Images are available for download. In our internal database each image is
supplied by the following information: barcode, type status, genus name, species name, author name, subsp /var name,
family name, collectors name, field number of herbarium specimen, date (yyyy-mm-dd), country, admin region, latitude
degrees, latitude minutes, longitude degrees, longitude minutes, label text, determination name, annotation, Catalogue
of Life link and accepted name in CoL. We encourage our fellow colleagues to access herbarium collections online and
envision that such a tool will facilitate the progress on worldwide biodiversity studies.
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11:35
Dag Endresen
Building a national biodiversity information facility in Norway
Norway joined GBIF in 2004 as the 31st national country to sign the memorandum of understanding as voting participant.
The Norwegian membership in GBIF was ratified by the Ministry of Education and Research. The role as Head of Delegation
(HoD) with voting rights in the GBIF Governing Board was from the start delegated to the Research Council of Norway
(RCN). The role as Head of Delegation was in 2017 delegated to the Natural History Museum of the University of Oslo.
The GBIF Participant Node for Norway was established 1st of June 2005 at the Natural History Museum of the University
of Oslo (UiO-NHM) where the Node has been operative until today through a series of in total four funding periods (2005
to 2007, 2008 to 2011, 2012 to 2016, and 2017-2019). The Norwegian GBIF-node has (more or less) two dedicated full-time
staff members and operates in close collaboration and sharing of responsibilities with the Norwegian Biodiversity Information
Centre (NBIC) in Trondheim. Together with the ForBio Research School in Biosystematics (ForBio), the Norwegian GBIF-node
will collaborate on open data publication training in Russia and former Soviet countries in the Central Asia and Caucasus
region during the next years with funding from the Norwegian Centre for International Cooperation in Education (SIU).
Following the international conference on "Information Technologies in the Research of Biodiversity" in Irkutsk (11
to 14 September 2018), a training course on open data mobilization using GBIF and BOLD tools (15 to 19 September 2018)
will be organized by ForBio in collaboration with GBIF, the University of Bergen and the Norwegian University of Science
and Technology, as part of the SIU funded MEDUSA project. A similar workshop with funding from SIU was organized by
ForBio and GBIF together with the Shirshov Institute of Oceanology in Moscow from 15 to 17 May 2018 on "Digitization
of collections and publishing data from wet collections". The BioDATA project by ForBio and GBIF with funding from SIU
will organize a three-year training program (during 2018 to 2021) on open data mobilization together with partners from
Armenia, Belarus, Tajikistan, Belarus and Ukraine.
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13:00
Evgeniya Bukharova, Alexander Ananin, Tatyana Ananina
Database of Barguzinsky reserve
One of the objectives of the reserves is to maintain a long-term monitoring of natural complexes’ state. Barguzinsky
Reserve, being the oldest in Russia (organized in 1916) and located on the northeastern coast of Lake Baikal, is a standard
of unspoilt nature that reflects biota responses to global climate change. Regular observations of natural objects and
phenomena in Barguzinsky Reserve cover the period from the late 1930s. Currently there is a continuous dataset of observations
for 30-60 years. This data contains: inventory lists of flora and fauna; the results of accounting for the number of
major species of a ground beetles, mammals and birds; an assessment of the yield of berry and tree species; phenological
observations and climatic data series; observations of populations of rare plant species. The data is stored in 25 databases.
All available materials were used as a source for databases, including published data, primary observation files, manuscripts
of Nature Annals, and other unpublished reports. Digitization of data makes possible to systematize the primary observation
materials available in the reserve, to facilitate access to them, to preserve these observations from loss, and to perform
an inter-related analysis of long-term series of observations. At the moment inventory lists of higher vascular plants
and herbarium of the Barguzinsky Reserve are being prepared for publication in GBIF.
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13:15
Anne-Sophie Archambeau
GBIF (Global Biodiversity Information Facility): Example of a national node (France) and actions at Regional level (Europe)
GBIF—the Global Biodiversity Information Facility—is an international network and research infrastructure funded by the
world’s governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth. Over
976 million of biodiversity data from over 1170 institutions worldwide are now accessible through the GBIF portal (www.gbif.org).
The national GBIF nodes promote the GBIF activities at national and regional levels and help to mobilize the data. This
presentation will show an example of implementation in France. GBIF France animates, federates and brings its technical
support at national level. It was set up in 2006, with a dual mission: to represent GBIF in France, by providing French
scientific and political communities with the tools and services created by GBIF; and represent France in the GBIF.
At Regional level, we organise a European Nodes meeting, each year, to discuss potential actions that can be done jointly,
in order to raise the mobilisation and uses of the data at a larger scale. This presentation will present the current
contribution of European nodes in GBIF and exemple of common actions.
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13:30
Margarita Erbajeva
Biodiversity of Cenozoic ochotonids (Ochotonidae, Lagomorpha, Mammalia) in Holarctic
Ochotonids are originated in the Central Asia at the early Late Oligocene when Eocene climate changed towards dry and
continental that led to initial aridification. Tropical forest declined gradually and open landscapes, favourable ochotonids
habitat, began to distribute. The family Ochotonidae consists of two subfamilies – Sinolagomyinae and Ochotoninae. The
earliest ochotonids - sinolagomyins - were represented by the genera Bohlinotona and Sinolagomys, of which the first
appeared to be the most archaic form displaying some feature with leporids by having reduced M3. Bohlinotona pusilla,
known from Saint Jacques, China and the locality Shine Us, Mongolia, from the earliest stage of the Late Oligocene,
is characterized by well developed roots. Advanced form Bohlinotona sp. known from a number of sites in Mongolia of
the second part of Late Oligocene lack of roots completely and they differ much from B. pusilla morphologically. To
the end of Oligocene Bohlinotona disappeared. The genus Sinolagomys includes at least 7 species widely distributed in
China, Mongolia and Kazakhstan and to the end of Early Miocene they disappeared. Significant reorganisations in paleoenvironment
of Eurasia occurred in Oligocene-Miocene transition time. Landbridge between Asia and Africa and Asia and North America
appeared to surve as a migration road to exchange of fauna. Two ochotonid genera – Austrolagomys and Kenyialagomys are
known in Miocene fauna of Africa. At that time ochotonids migrated to North America, that evidenced by the genus Oreolagus
having diverse species. With the climate becoming more continental and arid at the beginning of Miocene open landscapes
became widespred in Eurasia. Ochotonids distinguished to Europe, they were represented by genera Heterolagus, Lagopsis,
Marcuinomys, Albertona, Paludotona having diverse taxa. In Asia ochotonids were abundant and contain a number of diverse
taxa. The characteristic Asian genera are Bellatona, Bellatonoides, Alloptox, Ochotonoma, Ochotonoides, Proochotona
a.o. The Pliocene time with mild and warm climate became the favourable time for ochotonid diversification, especially
for the genera Pliolagomys, Ochotonoides and Ochotona, known in the Europe, North America and Asia, they were represented
by more than 50 extinct species. At the end of Pliocene all ochotonid genera disappeared except of the genus Ochotona,
which continued to exist at the present time. Approximately 30 extant species are known of the world, one species in
the Europe, two in North America and 28 taxa are known in Asian fauna.
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13:45 Oleg Pugachev, Natalia Ananjeva, Sergey Sinev, Leonid Voyta, Roman Khalikov, Andrey Lobanov,
Igor Smirnov
Creation of Information retrieval system on the unique research collections of the Zoological Institute RAS
Zoological Institute of the Russian Academy of Sciences (ZIN) — one of the oldest scientific institutions in Russia with
unique scientific collections. In 2017, the Museum and the Institute celebrated their 185th anniversary. The unique
collection of the ZIN were collected by many generations of Russian and foreign zoologists throughout the territories
and waters of our planet. Collected during these expeditions materials are stored in the Institute, they remain imperishable
source of information on the structure and distribution of faunal diversity in space and time. The collections continue
to rise. ZIN has one of the largest zoological collections in the world, with more than 60 million of storage units.
In general, in the collections of the ZIN about 260 thousand species of animals, which is about a quarter of the known
world fauna, are presented. There is almost all the animal species inhabiting territory and waters of Russia, for many
of them the big series are stored. Several tens of thousands of type specimens of animal species stored in the collection
are of exceptional value. The content of the concept of «zoological collection» in our days of rapid progress of information
technologies and advances in molecular genetic studies quickly filled with new meanings. Currently, the collection is
rightfully regarded as a bank of scientific information and the primary tool for basic and applied biological research.
The information system should include taxonomical, type, collection, zoogeographical and bibliographic data. By using
of available server infrastructure of ZIN and information system of collection specimens created (ZIN Research Collections
portal, https://www.zin.ru/collections/), there was a possibility of selective publication of ZIN research collection
data via GBIF portal (http://ipt.zin.ru). The scientific use of the collections and depositories of integrated information
systems for faunistic biodiversity in the present context includes, as the most important modern goals, digitization
of collections and publication of information in the public domain on the Internet as well as the creation of a DNA
bank. Work is carried out within the limits of researches on a theme «Inventory of a biodiversity of animals and its
supply with information » (АААА-А18-118012990224-5) and partially carried out at support of grants of the Russian Foundation
for Basic Research N 15-04-02971 and N 15-29-02457.
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14:00
Joanna Gołębiewska,
Marta Jarosińska,
Max Rykaczewski
Flora Pomeranica Orientalis – a way to store floristic data of Gdańskie Pomerania
For many years scientists were trying to figure out how to unify and visualize data on plant range. It started around
1970s, with Hulten and Meusel, and went on from there, still being developed. To make it more accessible, in 2000 arose
GBIF, one of the most complex online databases. Due to special meaning for Gdańskie Pomerania, as the area where the
ranges of many plant species overlap, with a great diversity of natural habitats, interesting geological history and
the relatively poorly understood distribution of species, there was a need to create such an initiative in this region.
Pomerania is very important in terms of phytogeographical area of Europe, where the boundaries of the areas of many
taxa meet, eg with the (sub)Atlantic, continental or southern European type of range. It is also relatively well preserved
in naturalistic terms. The sea coast is rich in young glacial types of landscapes, numerous wetlands, peat bogs, lake
and river ecosystems, including the estuary of the great river - Vistula and Oder. Floristic data in this area has been
collected for over 150 years, at first by German botanists and naturalists, and after 1945 – Polish ones. Unfortunately,
they have not yet been unified, even though they were partly used in the work on the Atlas of distribution of vascular
plants in Poland. Large scale of a single cartogram unit adopted for a nationwide study (100 km2) did not require the
use of all data and is not enough for solving phytogeographic problems in the scale of the region. In 2006, the Westernpomeranian
Atlas of Distribution of Vascular Plants and Mushrooms (ZARRiG) was created, which purpose is to supplement and summarize
knowledge about floristic and mycological resources of north-western Poland, based on available historical and current
data. In 2017, Flora Pomeranica Orientalis was founded, covering the area largely coincides with the area of the Pomeranian
Voivodship, as well as with the geobotanical region defined as the Gdańsk Pomerania. Flora Pomeranica Orientalis is
a project held by the Herbarium of the University of Gdańsk – Herbarium Universitatis Gedanensis UGDA from the Department
of Plant Taxonomy and Nature Conservation, University of Gdańsk. It was established in cooperation with the creators
of the Westernpomeranian Atlas. The main goal of the project is to collect and archive floristic documentation from
the area of Gdańskie Pomerania in a database, which unifies the format for storing floristic data from different authors,
and thus is to be a tool enabling the integration of many separate botanical datasets into one system. Project aims
to improve the exchange of scientific information and the results of fieldwork between data authors. The database allows
users to collect and edit their own data, as well as to share data with other users. What is important, all data entered
and stored in the system are protected by copyright.
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14:15 Nadezhda Alexeeva,
Margarita Erbajeva,
Solonga Namsaraeva
Biodiversity of late Cenozoic small mammals of the south Eastern Siberia
The studied area, south of East Siberia, consists of two territories – Transbaikalia and Prebaikalia. The small mammal
(lagomorphs and rodents) record of the region covers the time span from the Late Oligocene to the Recent time. They
are the important components of modern and past mammalian faunas of Siberia. They belong at least to 12 families including
more than 40 genera. The earliest fossil records are scarce, they include Late Oligocene taxa. Miocene faunas are much
more diverse known from sites Aya, Tagai and Saray. The characharactic taxa belong to lagomorphs and rodents. The diversity
of early Pliocene faunas is high, they are represented by the genera Hypolagus, Stachomys, Lophocricetus, Sicista, Ochotonoides,
Prosiphneus, Microtodon, Microtoscoptes, Promimomys including numerous species. At the Late Pliocene the fauna is characterized
by disappearance of a number of archaic arvicolids and by increasing abundance and diversity of small mammals containing
diverse lagomorphs (Hypolagus, Ochotonoides, Ochotona) and murids (Orientalomys, Micromys). For the first time arvicolids
genera appeared, they are Mimomys, Villanyia, Pitymimomys. Moreover hamsters of the genera Kowalskia, Cricetinus, Cricetulus
and a peculiar genus Gromovia are known also. The characteristic feature of the Early Pleistocene small mammalian faunas
is an explosive radiation and abundance of ground squirrel Spermophilus and the first appearance of the genera Clethrionomys,
Cromeromys, Allactaga, the reduction in number and quantity of rooted voles Mimomys and Villanyia. Zokor Mesosiphneus
was replaced by more advanced species. The significant reorganizations in small mammal assemblages at that time occurred
due to the climatic changes towards cooler and drier. Gradually Pliocene taxa vanished and new genera of voles appeared.
At the Middle Pleistocene with further strengthening of arid conditions the inhabitants of dry landscapes became dominant
forms in the fauna. During the Late Pleistocene periglacial conditions were established in the region and cold open
landscapes were distributed widely.
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15:15
Alexander Sizykh,
Victor Voronin,
Alexey Shekhovtsov
Large-scale aerospace photography, soil-geobatanic profiling in the geobotanical mapping (discover aspects of the phytocoenotic
and biogeocoenotic diversity)
The study is based on using the method of large-scale mapping of the vegetation in conjunction with field aerospace photography
interpretation of a different scale by generating maps on a scale in 1 : 10 000 – 1 : 100 000. By laying transect-profiles
and using geobotanical descriptions for different years, it is possible to identify areas reflecting the whole spectrum
of the typological diversity and composition of the region’s communities. These model areas are representative throughout
the entire different spatial structure and diversity of vegetation communities, biogeocoenotic diversity and are the
objects of monitoring of the dynamics and genesis of communities that develop in different environmental conditions
and reflecting different plant communities of the region’s vegetation. The aim of this study is determining of main
peculiarities of structure and dynamical plant communities organization forming under the conditions of mutual development
different types of vegetation for concrete territory. A many-year monitoring in the model areas using aerospace photographs
from different years for the territory of the different region is instrumental in revealing the typological composition
of communities with a central set of plant species, diagnostic tools for communities of different conditions of development.
The selection of a territory where profiling is to be performed requires always natural phenomenon analysis, its concrete
characteristics or a particular structure and is always individual. The relief structure, taking into account differences
in relative heights, the situation of a territory in a mountain system, if available, as well as driangle system analysis
(river basin, lake coast, etc.) determine the profile site and length. A geobotanic profile aimed to reveal the spatial
variability of communities structure is established taking into account the peculiarities of vegetation communities
on the a territory depending on the range – topological, regional, zonal, etc. One of the methods for revealing structure,
spatial variability and interaction of phytocoenosis in different environments conditions with edaphic conditions, on
our opinion, can be combined soil-geobotanic profiling. Due to the application with material of perennial monitoring
and geobatanic survey on the base of aerospace photography, soil-geobotanic profiling favored the resolution of such
tasks as establishing of phytcoenotic diversity, the structure of communities forming in the different environmental
conditions concrete territory. Using methods combination of geobotanic survey with large-scale mapping of vegetation
on the base of field deciphering of aerospace photography together with phytocoenosis monitoring during different seasons
and years allow to get the dates about biogeocoenotic diversity as well.
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15:30
Eric Chenin, Morgan Mangeas, Antoine Guisan, Andrew Peterson
ANIS: "Accuracy of ecological Niches Improved by Satellite"
ANIS: "Accuracy of ecological Niches Improved by Satellite". In recent years, ecological niches models (ENM) and species
distributions models (SDMs) have developed tremendously for conservation purposes and for estimating the impacts of
global change. The main objective of ANIS project is to take full advantage of the new generation of remote sensing
data to refine SDM predictions by improving the quantification of suitable habitats for species in ENM, in complement
to classically used factors. The idea is also to make the best of the recent developments in deep learning technologies
which are able to integrate highly nonlinear and heterogeneous data, to take advantage of the availability of large
volumes of species occurrence data on GBIF (Global Biodiversity Information Facility) in order to initiate a new generation
of ENMs. Deep learning techniques, particularly adapted to process highly heterogeneous data in large volumes, will
be used as follows: Fro each species, a set of occurrences will be selected on GBIF and other portals, and available
data related to the occurrence locations will be used to train and test the deep neural networks (DNN). For each occurrence,
the following data will be used when available: . remotely-sensed information from satellite images around the occurrence
location, . temperature, rainfall, hygrometry, altitude, type of soil if known, etc. . georeferenced field landscape
pictures around the location, . other species living nearby, so as to take interactions between species into account
The models and distributions of species at global, regional and local scales resulting from the project will be made
available to the scientific community and stakeholders through a dedicated portal.
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15:45
Svetlana Pak, Alexander Abakumov
Model mapping of phytoplankton biomass from remote sensing data
As known phytoplankton is the lowest level of the trophic chain determining the aquatic ecosystem productivity. It is
possible to obtain the information about the surface phytoplankton distribution over a large area by the modern remote
methods. The satellite signal penetrates only into the upper layer, so these methods are limited. In fact, the plant
biomass volume located under the surface water layer may differ significantly from the remote data. To reconstruct the
integral biomass in the whole water column under a unit area, a vertical model of phytoplankton functioning based on
the concept of fitness function is used. The phytoplankton community is considered under its aspiration to occupy the
niche most favorable for life. In this case, the community growth rate coincides with the specific growth rate of phytoplankton.
The model solution reduces to solving the Cauchy problem for a system of ordinary differential equations with the remote
sensing data as initial conditions. The specific phytoplankton growth rate is a multiplicative dependence on the main
external environment parameters such as mineral nutrition, temperature, irradiation and others. The remote sensing data
of the Sea of Japan and Issyk-Kul Lake are used for the model testing. A verification method depends on the data available
to the researcher in addition to satellite information. We used literature data, a biogeographical description of the
Sea of Japan, as well as data obtained in vivo on Issyk-Kul Lake. The geographic object is represented by arrays of
the surface values of the chlorophyll concentration, temperature and irradiation in each node of a uniform grid, if
it is free from cloudiness. To solve the vertical model, the depth maps were digitized in order to determine the limiting
aquifer at each point of the object subjected to satellite processing. Biomass values in the areas covered by clouds
are obtained by automatic triangulation using support nodes in which the numerical solution data are correct. The model
solution visualization gives an idea of the spatial distribution of biomass within the entire zone where the photosynthesis
takes place.
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16:00
Marina Olonova, Dmitriy Feoktistov
Experience in the use of GIS tools in plant systematics and conservation
The ecological niche and the range are sufficient characteristic of the species. In turn, each species has its own unique
ecological niche, ecologo-climatic characteristics to be its important component. The MaxEnt algorithm allows not only
to obtain a species distribution model, but also to evaluate it, using the AUC. It is also possible to estimate the
impact of each bioclimatic variable on the model. The SDMtoolkits (Brown, 2014) on one hand, allows to spatially rarefy
the input data at several distances according to habitat, topographic or climatic heterogeneity. As far as the breath
of area, covered by analysis, depends on latitude, being larger at equator and the smallest at poles, the data of occurrence,
prepared for MaxEnt, should be biased. SDMtoolkits resolves this problem as well. On another hand, it can evaluate the
correlation between bioclimatic variables, and exclude the highly autocorrelated ones from being incorporated, and avoid
the mistakes in evaluation their contribution in the model. The impact of variables can be evaluated in three independent
ways: direct contribution (in percent), revaluation after permutation, and with jackknife test. The opportunities provided
by the climate modeling programs Bioclim and MaxEnt, as well as the SDMtoolkits and ENMTools applications, were implemented
in our study of bluegrasses (Poa L.). Using freely available climatic data and the data of occurrence, the bioclimatic
profiles of morphologically similar Poa palustris L., P. nemoralis L. and populations, combining the characters of their
both, treated as Aggr. P. intricata Wien., were revealed, using the Bioclim program, implemented in DIVA-GIS. The models
for their potential distribution in the current climate, in Pleistocene maximal glaciation, in interglacial and the
Middle Holocene were reconstructed with MaxEnt and applications. The comparison methods - niche-identity test (I-test),
and background test (B-test), implemented in the ENMTools program, make it possible to compare the obtained ecologo-climatical
niches. The I test allows to reveal a statistically significant difference between the niche models, calculated for
different taxa, and the second one allows to establish the divergence of niches at the genetic level, which makes these
methods an important tool for study the divergence, speciation and microevolution. We compared the ecologo-climatical
niches of all three species, and I-test has revealed their differences at a statistically significant level. The models
of potential species distribution, constructed on the basis of ecologo-climatical niches can be used not only for paleogeographical
reconstructions, but also are of a great practical value. They allow predicting the expansion of invasive species, the
possibility of the useful species introduction, the probable dynamics of ranges in accordance with various scenarios
of climate change in the future and reveal the possible locations of rare species.
ФГБУН Институт динамики систем и теории управления имени В.М. Матросова СО РАН
ФГБУН Сибирский институт физиологии и биохимии растений СО РАН
ФГБУН Институт географии им. В.Б. Сочавы СО РАН
Институт математических проблем биологии РАН – филиал ФГУ «ФИЦ прикладной математики им. М.В. Келдыша РАН»
Глобальной Информационной Системы по Биоразнообразию (GBIF)
