Badania

The distributions of the six species constituting the smooth newt species complex

The ‘smooth newt’ Lissotriton vulgaris, consists of multiple morphologically distinct taxa. In a recent study, driven by genetic data, we recognized five species, L. graecusL. kosswigiL. lantziL. schmidtleri and a more restricted L. vulgaris. The Carpathian newt L. montandoni was confirmed as a closely related sister species. This collective of six species forms the Lissotriton vulgaris species complex. Here we 1) delineate the distribution ranges, 2) provide a distribution database, and 3) produce distribution maps for all species. This allows us to 4) highlight regions where more research is needed to determine the position of contact zones.

Wielstra_et_al_2018

 

Evolution of mate guarding under the risk of intrasexual aggression in a mite with alternative mating tactics

Mate-guarding (a situation in which male prevent guarding female from rivals) is known to evolve in response to environmental changes. We have used Rhizoglyphus robini, a bulb mite in which aggressive, armoured fighter males coexist with unarmoured scramblers, to examine how aggression risk shapes guarding behaviour. Exactly speaking we investigated whether mate-guarding by scramblers is affected by the presence of aggressive fighters. First, we show that indeed guarding male is under higher risk of being attacked than those non-guarding. Using both natural and artificially selected populations we show that males guarded longer when fighters were absent. Comparisons between lines selected for the high or low proportion of fighters and their source populations indicated that scrambler morphs evolved prolonged guarding. We also showed males can not actively shorten guarding in response to the presence of fighters in a social group. This indicates mate guarding may evolve in response to the presence or absence of fighters in populations, but males are not able to adjust guarding behaviour to the risk of being attacked by fighters.

https://www.sciencedirect.com/science/article/pii/S0003347218300162

 

 

Experimental evolution reveals balancing selection underlying coexistence of alternative male reproductive phenotypes

Alternative reproductive phenotypes (ARPs), is a situation in which within one taxa males differ in traits associated with competition for females. An example may be Rhizoglyphus robini with two heritable morphs: armoured fighters and more female-like, benign scramblers. Morphs can coexist within one population and very often their proportion is stable. Here we were wondering whether polymorphism in the genes underlying ARPs is maintained by balancing selection. If it true there should be a stable proportion of morphs which will be restored by selection after perturbation (artificial change of proportion). We tested this using experimental evolution in two types of environment: simple or spatially complex. We found that in both types of environment, the proportion of fighters came back to narrow range of 0.70-0.83 (similar to proportion reported by literature), although the rate of convergence was slower in the complex environment. Our results thus demonstrate balancing selection acting on polymorphism(s) underlying ARPs.

 

https://onlinelibrary.wiley.com/doi/10.1111/evo.13038

Proximate mechanisms of the differences in reproductive success of males bearing different alleles of Pgdh – a gene involved in a sexual conflict in bulb mite

Enzyme polymorphism in Pgdh is a striking example of single gene polymorphism involved in sexual conflict in bulb mite. Males homozygous for the S Pgdh allele were shown to achieve higher reproductive success than FF homozygous males, while negatively influencing fecundity of their female partners. In this study, we investigate proximate mechanisms responsible for the increased reproductive success of SS males. We found that males with S allele copulate quicker, more often and produce more sperm. We also confirm the negative effect that S-bearing males impose on the number of eggs produces by their female partners, showing a clear pattern of interlocus sexual conflict. We discuss that this effect is probably associated with increased copulation frequency hence the S allele-bearing males seems to be more efficient in forcing copulation and/or detecting females.

https://onlinelibrary.wiley.com/doi/10.1111/jeb.13250

Genetic variation in male attractiveness: It is time to see the forest for the trees

Mate choice (executed primarily, albeit not exclusively, by females) has been documented across a wide range of taxa, yet understanding its evolution has proven frustratingly difficult. One of the reasons, we argue, is that mate choice targets complex multivariate phenotypes of potential partners (usually – males), whereas most empirical and theoretical studies attempting to elucidate its evolution focus on single traits, such as the size or intensity of a particular sexual display character. We review theory and empirical data, showing how the crucial parameter of mate choice evolution models – genetic variance in attractiveness – can be estimated when attractiveness is a function of multiple traits. Using a simple analytical model, we show that such approach can produce biased estimates of selection pressures acting on mate choice. The bias increases with increasing number of traits contributing to attractiveness. The size, as well as direction of bias (i.e., whether we overestimate or underestimate the strength of selection on choice by studying single ‘attractive’ traits instead of overall attractiveness) further depends on the variance-covariance structure of these traits. We argue that in order to explain the evolution of female choice, we need to develop reliable measures of the actual target of such choice – that is, male attractiveness as perceived by females.

https://onlinelibrary.wiley.com/doi/full/10.1111/evo.12898

Larval and adult nutrition effects on reproductive traits in the red flour beetle

The study brings new insights into how variation in food availability at distinct life stages affects reproductive traits in red flour beetle males and females. We show that both juvenile and adult nutrition interact in shaping female fecundity, whereas male mating activity is influenced primarily by the former. Furthermore, using a powerful statistical approach of path analysis the study investigates the mechanisms behind these effects – specifically, whether the nutrition impact on reproductive traits is mediated by body mass. Surprisingly, we found no mass-mediated effects. This suggests that there must be other mechanisms through which nutrition influences reproduction.

 

https://zslpublications.onlinelibrary.wiley.com/doi/abs/10.1111/jzo.12440

Fitness effects of thermal stress differ between outcrossing and selfing populations in Caenorhabditis elegans

 

Because producing males is costly, the maintenance of outcrossing is an evolutionary puzzle. Theory predicts that it may be advantageous during adaptation to novel environments and should be selected for under environmental challenge. However, a given environmental change may influence fitness of males, females, and hermaphrodites or asexuals differently. Hence the relationship between reproductive system and dynamics of adaptation may not be driven solely by the level of outcrossing and recombination. Using Caenorhabditis elegans we show that thermal stress affects fitness of outcrossers much more drastically than that of selfers. This indicates that in addition to the level of genetic shuffling, reproductive modes may differ in the level of selective pressure experienced in novel environment. This has important implications for the extent to which finding of studies investigating the evolution of reproductive modes in the context of environmental changes can be generalized.

 

https://link.springer.com/article/10.1007/s11692-017-9413-z

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.

https://www.sciencedirect.com/science/article/pii/S1055790317303627

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.

http://www.g3journal.org/content/7/7/2115

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.

https://www.nature.com/articles/srep24051

and

http://www.molecularecologist.com/2016/07/molecular-inversion-probes-phylogenomics-without-the-excess/

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.

https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-017-0508-4

 

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.

http://onlinelibrary.wiley.com/doi/10.1111/mec.13724/full

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.

http://gbe.oxfordjournals.org/content/7/1/81

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:

http://mbe.oxfordjournals.org/content/32/6/1657.1.full

http://www.biotechniques.com/news/The-Genetics-of-a-Super-Vole/biotechniques-357623.html?service=print#.VW7oQdLtllg

Original manuscript:

http://mbe.oxfordjournals.org/cgi/reprint/msv038?ijkey=N7xjXeyIni1zifz&keytype=ref

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.

http://newtbase.eko.uj.edu.pl/static/pdf/Pabijan_et_al_2015.pdf

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 [http://onlinelibrary.wiley.com/doi/10.1002/ece3.965/pdf]

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.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0097431

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.

http://onlinelibrary.wiley.com/doi/10.1111/evo.12409/abstract

 

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

http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12186/abstract