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Allopolyploidy of Capsella bursa-pastoris

This is my main research project which is going to result into a PhD thesis by the end of 2017.

2013 – present
Supervisor: Martin Lascoux.
Collaborators: Stephen Wright, Amandine Cornille, Karl Holm, Sylvain Glémin.

Shepherd's Purse Capsella bursa-pastoris growing in a pot

The occurrence of polyploidy in land plant evolution is a common phenomenon. Although the role of polyploidy in evolution is still debated, it is often associated with increased adaptability. Shepherd’s purse (Capsella bursa-pastoris) is a case in point of this phenomenon. It is a tetraploid selfing weed which originated very recently through hybridization between Capsella grandiflora (outcrosser) and Capsella orientalis (selfer). Unlike its parental species which have very restricted distribution range, C. bursa-pastoris occurs world-wide. Most likely such colonization success is attributed to its allotetraploid origin. I would like to understand how polyploidy and hybrid nature confer such colonization ability on C. bursa-pastoris.

To do that, I perform comparative genomic analyses using both whole-genome DNA sequencing and RNA-Seq data. The results of this project can be found among my publications.

Fishes of the Roof of the World

This is my side project which started as an ambition to get the National Geographic grant.

2013 – present
Collaborators: Glib Mazepa, Matthias Geiger, Fabian Herder.

Triplophysa stoliczkai and Triplophysa lacusnigri from Pamir

The Roof of the World is a metaphoric name of the Pamir mountains in Central Asia. This highland region uplifted relatively recently (12-15 Mya) and it continues to uprise (in last 100,000 years the elevation of the area increased in approximately 1 km). The growth of mountain ridges partitioned the original species ranges by geographic barriers and thus promoted allopatric speciation.  The Central Asian mountains belong to one of the 34 world’s biodiversity hotspots.

Surprisingly, the last extensive biological studies in this region are dated to 1930s. My colleagues and I organized the team of specialists in different organisms and ambitiously applied for National Geographic’s Global Exploration Fund. In 2013, our project “Hidden biodiversity on the Roof of the World” was funded and we went to the Pamirs. I was responsible for ichthyological part of the expedition. I collected some fish samples and currently study them. I analyze morphological characters, barcode specimens using the COI gene and explore the phylogenetic relationships using mitochondrial and nuclear genes.

Speciation with gene flow in Heliconius butterflies

This was my Master’s thesis research project.

2013 – 2014
Supervisor: James Mallet.
Collaborator: Kanchon Dasmahapatra.

Desitree of phylogentic signal along the genomes of Heliconius butteflies

Sequencing of whole genomes in non-model organisms provide new insights into the genomic architecture of speciation. There is particularly widespread interest in patterns of divergence with ongoing gene flow. Theory predicts that in the face of gene flow the differentiation between genomic regions under selection and the rest of the genome will be more pronounced than in the case of allopatric divergence. These regions of divergences are named “islands of speciation” and as speciation proceeds, these “islands” are expected to growth into “continents”.

I investigate the genomic pattern of divergence between Heliconius pardalinus and Heliconius elevatus, two long recognized tropical butterfly species, and demonstrate the results supporting the hypothesis that species difference can be maintained by very few genomic regions (~1% of the genome) with extensive gene flow after the speciation event. These results show that transformation of “islands of divergence” into “continents” might not be essential to maintain species differences.

You can read more about the results of this project in my thesis.

Gene expression in different organs of hybrid sculpins

This was my 6-months research training project during the Master’s studies

Sep 2012 – Feb 2013
Supervisors: Arne W. Nolte and Till Czypionka.

Gene expression heatmap of the candidate genes in different organs of a hybrid sculpin Cottus

Hybridization causes rapid genetic changes that may generate phenotypic novelty and facilitate abrupt speciation. A recent spread of invasive sculpins, a natural hybrid between Cottus perifretum and Cottus rhenanus, into the main stream of the Rhine River where parental species do not occur is a good model to study the onset of hybrid speciation. A previous study of whole-body gene expression profiles of these fishes revealed that hybrid individuals are distinguished by a number of transgressively up-regulated genes. I tested whether this up-regulation was associated with any particular organ/tissue using the microarray analysis. My results indicated that this up-regulation was rather caused by multiple evolutionary modifications in different organs/tissues.

For a technical aspect, I also verified the performance of a probes-specific microarray data normalization procedure by comparison of the result obtained by this approach and the traditional normalization method with RNA-seq data as a reference standard. The comparison further confirmed that the diversity of binding behaviors of probes should be taken into account during microarray experiments.

Phylogeography of some Indo-Pacific Mugilidae fishes

This was my 3-months research training project during the Master’s studies

Apr – Jun 2012
Supervisors: Jean-Dominique Durand and Philippe Borsa.
Phylogenetic tree of COI of some Indo-Pacific Mugilidae fishes

Biogeographic barriers of the Indo-Pacific region are thought to contribute to the isolation and diversification of sea basin populations. I compared phylogeographic patterns from mitochondrial COI sequences among several Mugilidae species which are widely distributed in the Indo-Pacific Ocean to find major biogeographic barriers. I identified that some species/phylogenetic lineages demonstrated phylogeographic structures which reflected either Indo-Pacific or mid-Indian barriers, whereas other species showed large-scale genetic homogeneity. I also provided evidence that the family Mugilidae comprises cryptic species and several polyphyletic or paraphyletic genera.

Diploid-polyploid complexes of spined loaches Cobitis

This was my thesis research project during my Master’s studies in Ukraine.

2008 – 2010
Supervisor: Gennadiy A. Shandikov.
Collaborators: Karel Janko and Lukas Choleva.

Spined loach Cobitis and erythrocyte sizes of different ploidy

Spined loaches of the genus Cobitis is a group of small bottom-dwelling fishes which possesses a unique ability to beget hybrid forms of different ploidy. Hybrids are usually tri- and tetraploid all-females which reproduce gynogenetically. Because of the need for sperm to activate egg development, these females live sympatrically with one or two parental species forming diploid-polyploid (unisexual-bisexual) complexes. These phenomena make spined loaches be an object of comprehensive investigations.

In my thesis, I assessed the diversity of spined loaches and the hybrid complexes on the territory of Eastern Ukraine, which covers a substantial part of Ponto-Caspian refugia and is still insufficiently studied. I used morphological, cytometric, allozyme and PCR–RFLP analyses. My results demonstrated that Eastern Ukraine is the most diverse region in the distribution range of spined loaches. It is inhabited by three species (Cobitis taenia s. l., Cobitis melanoleuca and Cobitis tanaitica) and seven different hybrid forms. I also discovered a new hybrid complex which unlike all other known complexes exists without the participation of Cobitis elangotoides genome.

If you have any interest in my current or past projects, feel free to contact me.