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Contract number
Time span of the project

As of 30.01.2020

Number of staff members
scientific publications
General information

Name of the project: Phylogenetic analysis of complex selection in molecular evolution

Strategy for Scientific and Technological Development Priority Level: в

Goals and objectives

Research directions: Evolutionary genomics, functional genomics, transcriptomics, new generation sequencing

Project objective: Study of natural selection at the molecular level

The practical value of the study

  • We have detected record high level of genetic variability in Schizophyllum commune and characterized features of recombination in this species – it has been shown that crossing over occurs in regions with the lowest divergence, we have conducted assessment of effective size of the population and speed of accumulation of mutations (two main parameters affecting level of variability).
  • A method has been developed for detecting positive selection that acted in the past through impact of negative selection in populations of currently living organisms.
  • We have studied marine and freshwater populations of White Sea Stickleback and found regions of genome responsible for adaptation to fresh water, as well as assessed force of moving selection aimed at strengthening of «freshwater» alleles.
  • Our researchers have characterized the Genlisea aurea genomes – one of the smallest plant genomes and have shown reduction of the size of a genome occurs mainly due to reduction of sizes of intergenic regions.
  • We have completed sequencing and assembly of transcriptomes of 60 species of Baikal gammarus – a unique endemic «species node». Obtained data have served as the basis for phylogenetic analysis and allowed to determine genes that were subject to positive selection in the process of speciation.

Implemented results of research:

  • Knowledge of mechanisms of mutation processes will later serve as the basis for controlling these processes including control using currently developed genome editing technologies.
  • We have conducted R&D to study genetic basics of formation and development of one of the most widespread malignant tumors – hepatocarcinoma. By comparing expression profiles in healthy organisms and in tumors. It is possible to determine expression regulators (i.e. proteins controlling transcription levels of many other genes) participating in its development. Such regulators are a potential molecular target for anti-tumor medications.
  • 6 grants and 5 state R&D contracts have been completed.

Education and career development:

  • 1 doctoral dissertation, 5 candidate dissertations and 20 bachelor dissertations.
  • Over 50 per cent of members of the academic staff of the Laboratory are young scientists, students and postgraduates.

Organizational and structural changes:

  • The Laboratory has created one of the first devices for sequencing in Russia called «Illumina-2000».
  • The Laboratory has created and has been successfully using a computational cluster designed for bioinformatics calculations.
  • A complex biological laboratory has been developed on the basis of the White Sea Biological Station of the Moscow State University. It includes a research vessel, a confocal microscope, a capillary sequencer, devices for DNA amplification etc. The laboratory allows to provide the whole spectrum of research work on the ground of the White Sea Biological Station – from catching organisms that might be of interest to sequencing. This laboratory is widely used in the teaching process, in research work and for conducting schools and seminars.
  • The Laboratory has purchased, installed and introduced into operation equipment for research in the field evolutionary and functional genomics and adjacent domains: a highly productive sequencer HiSeq2000, a computation complex for processing genome data, a capillary sequencer, a confocal microscope and a research vessel for working at the White Sea Biological Station. This is a significant addition to the experimental base of the Moscow State University and it creates new opportunities for scientific work of its staff.

Other results:

  • Members of the academic staff of the Laboratory have participated in international conferences: the Conference of the Society for Molecular Biology and Evolution (SMBE), the International Plant & Animal Genome Conference and others.


  • East Tennessee State University (USA), Harvard University (USA), University of Pennsylvania (USA), University of California (USA), Welcome to University of Geneva (Switzerland), Institute of Physical and Chemical Research – RIKEN (Japan): joint research

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Naumenko S., Logacheva M., Popova N., Klepikova A., Penin A., Bazykin G., Etingova A., Mugue N., Kondrashov A., Yampolsky L.
Transcriptome-based Phylogeny of Endemic Lake Baikal Amphipod Species Flock: Fast Speciation Accompanied by Frequent Episodes of Positive Selection. Molecular Ecology 26(2): 536–553 (2017).
Seplyarskiy V.B., Andrianova M.S., Bazykin G.A.
APOBEC3A⁄B-induced Mutagenesis is Responsible for 20% of Heritable Mutations in the TpCpW Context. Genome Research 27(2): 175–184 (2017).
Seplyarskiy V.B., Logacheva M.D., Penin A.A., Baranova M.A., Leushkin E.V., Demidenko N.V., Klepikova A.V., Kondrashov F.A., Kondrashov A.S., James T.Y.
Crossing-over in a Hypervariable Species Preferentially Occurs in Regions of High Local Similarity. Molecular Biology and Evolution 31(11): 3016–3025 (2014).
Terekhanova N.V., Logacheva M.D., Penin A.A., Neretina T.V., Barmintseva A.E., Bazykin G.A., Kondrashov A.S., Mugue N.S.
Fast Evolution from Precast Bricks: Genomics of Young Freshwater Populations of Threespine Stickleback Gasterosteus Aculeatus. PLoS Genetics 10(10): e1004696 (2014).
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