St Hilda's College

E-mail:
  dmitry.filatov@plants.ox.ac.uk

Tel  +44 (0)1865 275051

Last Modified: February 2012

Population genetics and molecular evolution

Link to software (ProSeq) page: http://dps.plants.ox.ac.uk/sequencing/proseq.htm

My research interests are connected with experimental molecular population genetics and evolution. In particular, I am interested in evolution of sex chromosomes, mating systems, molecular adaptation and in speciation process. The experimental systems used in my laboratory range from plants to humans, with current main focus in plants. We use dioecious Silene latifolia to study sex chromosome evolution, population genetics of speciation and quantitative genetics of sexual dimorphism. We also use endemic Hawaiian plant genus Schiedea (Caryophyllaceae), that undergone recent ‘explosive’ adaptive radiation, to study molecular adaptation and population genetics of speciation. Recently we also started to study adaptation and speciation in Senecio and sex chromosome evolution in Silene smut fungus Microbotryum violaceum.

Research highlights:
· Recently we demonstrated that photosynthetic plant RbcL gene often evolves under positive selection (Kapralov & Filatov submitted). This was a very unexpected finding because this gene was regarded as very conservative housekeeping gene. As this gene is widely used by botanists for phylogenetic reconstructions, it may have wide implications for plant systematics.
· We discovered that rapid adaptive radiation in Hawaiian endemic plant genus Schiedea (Caryophyllaceae) was accompanied by strong adaptive selection at chloroplast photosynthetic enzyme Rubisco (Kapralov & Filatov 2006). Adaptive selection in this enzyme was most pronounced in Schiedea species that undergone significant habitat shifts (e.g. adaptation to semi-desert like conditions, or to wet shady rainforest), suggesting that it might have been involved in adaptations to diverse ecological conditions. This is one of the first examples of molecular adaptation during rapid adaptive radiation in plants.
· We reported unexpectedly strong population differentiation (Fst~0.9) for the Silene latifolia Y-linked genes (Ironside and Filatov 2005). This contrasted with little or no population differentiation for other parts of the genome, such as the X-linked or chloroplast genes (Muir and Filatov submitted). The finding of strong population differentiation in Silene Y-linked genes stimulated a new direction of research in several Silene laboratories to understand the causes of this phenomenon.
· Using comparative mapping analysis of Silene latifolia X chromosomes and homologous chromosomes in non-dioecious Silene vulgaris I demonstrated that recently evolved S. latifolia sex chromosomes have originated from a single pair of autosomes that stopped to recombine and diverged into the X and Y chromosomes (Filatov 2005 Genetics).
· In collaboration with Dr R. Moore (North Carolina State University, USA) and Prof. D. Charlesworth lab (University of Edinburgh, UK) we conducted physical mapping of the Y-linked genes in Silene latifolia and their homologs in non-dioecious S. vulgaris. Comparisons of these maps revealed that the order of the genes on the Y chromosome substantially differs from that on the X in S. latifolia and on the autosome in S. vulgaris, probably due to multiple inversions on the Y chromosome. These inversions could have played a role in cessation of recombination between the X- and Y-chromosomes in S. latifolia. (Bergero, Moore, Filatov and Charlesworth in preparation).
· I demonstrated that segregation analysis is probably the best method to search for new X- and Y-linked genes in plants (Filatov 2005 Meth. in Enzymol.) and using this method I isolated two new sex-linked genes from dioecious plant Silene latifolia (Filatov 2005 Mol. Biol. Evol.).
· Our work provided the first experimental support for the reduced DNA diversity on the plant Y chromosome (Filatov et al. 2000, 2001; Laporte et al 2005; Ironside and Filatov 2005). This supports theoretical predictions (e.g. Charlesworth & Charlesworth 2000) and helps to understand the evolutionary forces that shape sex chromosomes at the early stages of sex chromosome evolution.
· We demonstrated that different chromosomes in a plant genome might have significantly different mutation rates; in particular, Silene latifolia Y chromosome has significantly higher mutation rate than the X (Filatov and Charlesworth 2002).
· Contrary to common belief that mammalian Y-chromosomes are evolutionary deserts, we demonstrated that positive selection acts in at least two primate Y-linked genes, suggesting that adaptive Darwinian evolution may be common on mammalian Y-chromosomes (Gerrard and Filatov 2005).
· We demonstrated that genes in frequently recombining human pseudoautosomal region mutate faster than elsewhere in the genome, supporting the view that recombination might be mutagenic to some extent (Filatov and Gerrard 2003; Filatov 2004; Bussell et al 2006).

Young, J.N, Rickaby, R.E.M, Kapralov, M.V, Filatov, D.A. (2012) Adaptive signals in algal Rubisco reveal a history of ancient atmospheric carbon dioxide Philosophical Transactions of the Royal Society B: Biological Sciences. 367 (1588): pp 483-492.
doi:10.1098/rstb.2011.0145.

Dixon, C.J, Kapralov, M.V, Filatov, D.A. (2011) Gene flow and species cohesion following the spread of Schiedea globosa (Caryophyllaceae) across the Hawaiian Islands Journal of Evolutionary Biology. 24 (1): pp 1-11.
doi:10.1111/j.1420-9101.2010.02128.x.

Howell, E.C, Armstrong, S.J, Filatov, D.A. (2011) Dynamic gene order on the Silene latifolia Y chromosome Chromosoma. pp 1-10.
doi:10.1007/s00412-011-0311-3.

Kapralov, M.V, Kubien, D.S, Andersson, I, Filatov, D.A. (2011) Changes in Rubisco kinetics during the evolution of C4 Photosynthesis in Flaveria (Asteraceae) are associated with positive selection on genes encoding the enzyme Molecular Biology and Evolution. 28 (4): pp 1491-1503.
doi:10.1093/molbev/msq335.

Muir, G, Bergero, R, Charlesworth, D, Filatov, D.A. (2011) DOES LOCAL ADAPTATION CAUSE HIGH POPULATION DIFFERENTIATION OF SILENE LATIFOLIA Y CHROMOSOMES? Evolution..
doi:10.1111/j.1558-5646.2011.01410.x.

Votintseva, A.A, Filatov, D.A. (2011) DNA polymorphism in recombining and non-recombing mating-type-specific loci of the smut fungus Microbotryum Heredity. 106 (6): pp 936-944.
doi:10.1038/hdy.2010.140.

Gossmann, T.I, Song, B.-H, Windsor, A.J, Mitchell-Olds, T, Dixon, C.J, Kapralov, M.V, Filatov, D.A, Eyre-Walker, A. (2010) Genome wide analyses reveal little evidence for adaptive evolution in many plant species Molecular Biology and Evolution. 27 (8): pp 1822-1832.
doi:10.1093/molbev/msq079.

Piazza, P, Bailey, C.D, Cartolano, M, Krieger, J, Cao, J, Ossowski, S, Schneeberger, K, He, F, De, Meaux J, Hall, N, MacLeod, N, Filatov, D, Hay, A, Tsiantis, M. (2010) Arabidopsis thaliana leaf form evolved via loss of KNOX expression in leaves in association with a selective sweep Current Biology. 20 (24): pp 2223-2228.
doi:10.1016/j.cub.2010.11.037.

Ridout, K.E, Dixon, C.J, Filatov, D.A. (2010) Positive selection differs between protein secondary structure elements in Drosophila Genome Biology and Evolution. 2 (1): pp 166-179.
doi:10.1093/gbe/evq008.

Bernasconi, G, Antonovics, J, Biere, A, Charlesworth, D, Delph, L.F, Filatov, D, Giraud, T, Hood, M.E, Marais, G.A.B, McCauley, D, Pannell, J.R, Shykoff, J.A, Vyskot, B, Wolfe, L.M, Widmer, A. (2009) Silene as a model system in ecology and evolution Heredity. 103 (1): pp 5-14.
doi:10.1038/hdy.2009.34.

Filatov, D.A. (2009) Processing and population genetic analysis of multigenic datasets with ProSeq3 software Bioinformatics. 25 (23): pp 3189-3190.
doi:10.1093/bioinformatics/btp572.

Filatov, D.A, Howell, E.C, Groutides, C, Armstrong, S.J. (2009) Recent spread of a retrotransposon in the Silene latifolia genome, apart from the Y chromosome Genetics. 181 (2): pp 811-817.
doi:10.1534/genetics.108.099267.

Floyd, N, Oldham, N.J, Eyles, C.J, Taylor, S, Filatov, D.A, Brouard, M, Davis, B.G. (2009) Photoinduced, family-specific, site-selective cleavage of TIM-barrel proteins Journal of the American Chemical Society. 131 (35): pp 12518-12519.
doi:10.1021/ja9026105.

Howell, E.C, Armstrong, S.J, Filatov, D.A. (2009) Evolution of neo-sex chromosomes in Silene diclinis Genetics. 182 (4): pp 1109-1115.
doi:10.1534/genetics.109.103580.

Kapralov, M.V, Stift, M, Filatov, D.A. (2009) Evolution of Genome size in Hawaiian Endemic Genus Schiedea (Caryophyllaceae) Tropical Plant Biology. 2 (2): pp 77-83.
doi:10.1007/s12042-009-9029-2.

Votintseva, AA, Filatov, DA. (2009) Evolutionary strata in a small mating-type-specific region of the smut fungus Microbotryum violaceum Genetics. 182 (4): pp 1391-1396.
doi:10.1534/genetics.109.103192.

Armstrong, S.J, Filatov, D.A. (2008) A cytogenetic view of sex chromosome evolution in plants Cytogenetic and Genome Research. 120: pp 241-246.
doi:10.1159/000121073.

Filatov, D.A. (2008) A selective sweep in or near the Silence latifolia X-linked gene SlssX Genetics Research. 90 (1): pp 85-95.
doi:10.1017/S0016672307009056.

Muir, G, Filatov, D. (2007) A selective sweep in the chloroplast DNA of dioecious silene (Section Elisanthe) Genetics. 177 (2): pp 1239-1239.
doi:10.1534/genetics.107.071969.

BBSRC, NERC, Leverhulme Trust