Isolation and gene flow in a speciation continuum in newts

Because reproductive isolation evolves gradually, hybridizing lineages inform us about the role of gene flow during speciation. We delimited nine evolutionary lineages, reconstructed the phylogeny and inferred gene flow in newts of the Lissotriton vulgaris species complex. Post-divergence gene flow, indicative of evolutionary non-independence, has been most extensive in Central Europe, while southern European lineages have acquired the hallmarks of independent species. Widespread mitochondrial introgression followed secondary contacts. The study reveals long-term persistence of evolutionary lineages and periodical genetic exchange between them: although some lineages may become extinct or fuse, others carry signatures of this complex history in their genomes.

Linkage map of Lissotriton newts and the genetic basis of reproductive isolation

Linkage maps facilitate the study of the genetic architecture of reproductive isolation. We constructed a map for newts of the Lissotriton vulgaris species complex: 1146 protein-coding genes on 12 linkage groups, equal to the haploid chromosome number, with a total length of 1484 cM. A complex pattern of transmission ratio distortion (TRD) was detected, consistent with environment-dependent mortality of individuals carrying L. montandoni alleles in two genomic segments; this suggests a role of TRD blocks in reproductive isolation. The linkage map will empower studies on the genomic architecture of divergence and interactions between the genomes of hybridizing newts.

Molecular Inversion Probes for targeted resequencing in non-model organisms

Few methods for medium-scale targeted resequencing are available for non-model organisms We explored the utility and demonstrated good performance of Molecular Inversion Probes (MIPs) in a non-model system possessing a very large and complex genome. MIP markers have numerous advantages: high specificity, high multiplexing level, low sample requirement, straightforward laboratory protocol, no need for genomic libraries and no ascertainment bias. MIP markers are thus a useful extension of the molecular toolkit and an effective solution for large-scale resequencing of tens or hundreds of kb in ecological and evolutionary studies.


A strategy to apply quantitative epistasis analysis on developmental traits


High-throughput epistatic analysis is well developed for single cells, but it is still undeveloped for multicellular complex developmental traits. As epistasis analysis is one of the most effective methods of mapping genetic interactions, we developed quantitative epistasis analysis method for two developmental traits (sex ratio and body length) of nematode Caenorhabditis elegans. We applied RNA interference on mutants to inactivate two genes, used an imaging system to quantitatively measure phenotypes, and developed a set of statistical methods to extract genetic interactions from phenotypic measurement. We showed that this method could accommodate various metazoan phenotypes with performances comparable to those methods in single cell growth studies. Comparing with qualitative observations, this method of quantitative epistasis enabled detection of new interactions involving subtle phenotypes. We confirmed the brc-1 interactions with the following genes in DNA damage response: C34F6.1him-3sdc-1, and set-2, validating the effectiveness of our method in detecting genetic interactions.


Divergence history of newts modelled in space and time

This study provides quantitative, model-based insight into the history of divergence and a longer-scale perspective on genetic exchange between the Carpathian and smooth newts. Despite introgression of nuclear genes, which followed period(s) of isolation, the species have maintained their distinctiveness, which suggests that gene flow has not affected genomic regions responsible for species-specific adaptations. The Carpathian newt hybridizes with two evolutionary lineages of the smooth newt, exchanging genes symmetrically with one of them but asymmetrically with the other. The results of our study highlight the importance of incorporating intraspecific genetic structure into the models investigating the history of divergence.

Constraint and adaptation in newt Toll-like receptor genes

Toll-like receptors (TLRs) are an essential component of innate immunity. We report the first comprehensive assessment of TLR gene variation for urodele amphibians. The Lissotriton newt TLR repertoire includes representatives of 13 families and is compositionally most similar to that of the anuran Xenopus. Purifying selection has predominated the evolution of newt TLRs in both long and medium timescales. However, we infer that TLR genes undergo distinct trajectories of adaptive evolution in closely related newt lineages. This highlights the potential of TLRs to capture the signatures of different assemblages of pathogenic microorganisms, and suggests differences between lineages in the relative roles of innate and acquired immunity.

The molecular basis of aerobic capacity

We took advantage of and experimental evolution technique that has gained popularity, dubbed evolve and resequence to measure the genetic changes underlying aerobic performance in bank voles. The dominating adaptive response to selection for this trait was in changed gene expression, whereas changes in protein structure were very subtle. The genes potentially underlying aerobic capacity in bank voles are associated with mobilizing sugars and fats from body reserves, stress response and mating behavior. If you are interested take a look for news articles about our discoveries and check out the original manuscript published in Molecular Biology and Evolution:

News articles:

Original manuscript:

The dissection of a Pleistocene refugium

We used mitochondrial DNA to examine the history of the smooth newt Lissotriton vulgaris in the Balkans. The spatial pattern of genetic differentiation revealed the existence of several independent Pleistocene refugia, only one of which (located at the northern fringe of the Balkans) contributed to post-glacial expansion into central and western Europe. We concluded that the Balkans act primarily as a reservoir for genetic diversity in this species in accordance with the refugia within refugia concept.  We also found that none of the currently recognized subspecies in L. vulgaris present in the Balkans are reciprocally monophyletic in their mtDNA and we attribute this introgressive hybridization among subspecies and possibly incomplete lineage sorting.

Alternative reproductive tactics and sex‐biased gene expression: the study of the bulb mite transcriptome.

We sequenced and analyzed the bulb mite Rhizoglyphus robini (Acari, Acaridae) transcriptome. The mites have highly divergent male phenotypes: sexually dimorphic, aggressive fighter males, possessing thickened legs of the third pair which are used to kill rivals, coexist with unarmored scrambler males. We analyzed genes expression and look what we find out []

Single Nucleotide Polymorphisms Reveal Genetic Structuring of the Carpathian Newt and Provide Evidence of Interspecific Gene Flow in the Nuclear Genome

We used a set of 139 transcriptome-derived SNP markers, to quantify genetic structure of a newt species and introgression of nuclear genes from a related species. Our study demonstrates that isolation in glacial refugia, limited dispersal and local interspecific gene flow have been the main factors determining the genetic structure of Carpathian newt.

Does sexual conflict contribute to the maintenance of alternative reproductive tactics?

Sex-limited expression of sexually antagonistic traits may help resolve intra-locus sexual conflict, but the extent of this resolution remains a subject of debate. We found that females of the bulb mite (a species in which aggressive fighters coexist with benign scramblers) from lines selected for fighters (high fitness males) are less fecund and live shorter than females from lines selected for scramblers (low fitness males). This finding suggests that intralocus sexual conflict may be an important mechanism contributing to the maintenance of genetic variation in the expression of alternative reproductive phenotypes.


Plesnar Bielak, A., Skrzynecka, A. M., Miler, K., & Radwan, J. (2014). Selection for alternative male reproductive tactics alters intralocus sexual conflict. Evolution.


Accuracy of pooled RNAseq

To test whether pooled RNA-Seq accurately predicts true allele frequencies, we analysed the liver transcriptomes of 10 bank voles. Each sample was sequenced both as an individually barcoded library and as a part of a pool. Our results indicate that pooled RNA-Seq exhibits accuracy comparable with pooled genome resequencing, but variation in expression level between individuals should be assessed and accounted for. In our paper we proposed also methods to identify putatively problematic transcripts.

Konczal, M., Koteja, P., Stuglik, M. T., Radwan, J. and Babik, W. (2014), Accuracy of allele frequency estimation using pooled RNA-Seq. Molecular Ecology Resources. doi: 10.1111/1755-0998.12186