Diet adaptation in dogs

Current postdoc project.

2018 – present

Supervisor: Erik Axelsson

Place: Uppsala University, Sweden.

Dog silhouette

A comparison of patterns of genetic variation between dogs and wolfs revealed that selection had targeted the genes responsible for starch digestion, glucose absorption, and the ability to store glucose as fat in dogs, indicating that dogs had experienced an adaptive shift from a protein to more carbohydrate-based energy metabolism. Dogs also show the wide distribution for copy number variation of the gene coding for pancreatic amylase (AMY2B), the enzyme that breaks starch into maltose in the small intestine, while in wolf this gene is mostly present in one copy. This suggests that the efficacy of starch digestion may vary among dog breeds. Thus, dogs represent a unique model to study the genetic basis of metabolic adaptations during domestication. In my research, I aim to localize mutations that are likely to underlie these metabolic adaptations by analyzing large-scale population genomic and transcriptomics data.

Allopolyploidy of Capsella bursa-pastoris

PhD thesis.

2013 – 2018

Supervisor: Martin Lascoux.

Collaborators: Stephen Wright, Sylvain Glémin, Amandine Cornille, Karl Holm, Pascal Milesi.

Place: Uppsala University, Sweden.

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 that 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 worldwide. Most likely such colonization success is attributed to its allotetraploid origin. In my thesis, I tried to understand how polyploidy and hybrid nature confer such colonization ability on C. bursa-pastoris.

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

Fishes of the Roof of the World

Side project that started as an ambition to get the National Geographic grant.

2013 – present

Collaborators: Glib Mazepa, Matthias Geiger, Fabian Herder, and others.

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

Master’s thesis project.

2013 – 2014

Supervisors: James Mallet and Kanchon Dasmahapatra.

Place: Harvard University, USA.

Desitree of phylogenetic signal along the genomes of Heliconius butterflies

Sequencing of whole genomes in non-model organisms provides 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 grow into “continents”.

I investigated the genomic pattern of divergence between Heliconius pardalinus and Heliconius elevatus, two long recognized tropical butterfly species, and demonstrated 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 the 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 Master’s thesis.

Gene expression in different organs of hybrid sculpins

6-months research training project during Master’s studies

Sep 2012 – Feb 2013

Supervisors: Arne W. Nolte and Till Czypionka.

Place: Max Planck Institute for Evolutionary Biology, Germany.

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 probe-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 Indo-Pacific Mugilidae

3-months research training during Master’s studies

Apr – Jun 2012

Supervisors: Jean-Dominique Durand and Philippe Borsa.

Place: IRD, University of Montpellier II, France.

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 that are widely distributed in the Indo-Pacific Ocean to find major biogeographic barriers. I identified that some species/phylogenetic lineages demonstrated phylogeographic structures that 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

Master’s thesis project during my studies in Ukraine.

2008 – 2010

Supervisor: Gennadiy A. Shandikov.

Collaborators: Karel Janko and Lukas Choleva.

Place: V. N. Karazin Kharkiv National University, Ukraine, and Institute of Animal Physiology and Genetics, Czech Republic.

Spined loach Cobitis and erythrocyte sizes of different ploidy

Spined loaches of the genus Cobitis is a group of small bottom-dwelling fishes that 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 that 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.