Genetic differentiation over a small spatial scale in the smooth newt (Lissotriton vulgaris)

Understanding the distribution of genetic variation is central for both population biology and conservation genetics. Genetic population structure can be primarily affected by the species’ dispersal ability, which is assumed to be limited in many amphibians. In this study, we estimated allelic differentiation metrics and FST indices to investigate genetic variation among natural breeding ponds of smooth newts (Lissotriton vulgaris) over a small spatial scale. Based on six microsatellite loci, we found a small, but significant allelic differentiation among clusters of natural breeding ponds (i.e. ‘local regions’), which result was in line with the calculation of corresponding hierarchical FST values. Analysis of molecular variance also indicated significant between-region variation in the study area. Pairwise estimations showed that only the furthermost regions differed from each other in both differentiation measures, but this difference was not attributable to geographic distances between ponds. Our results provide evidence that hierarchical genetic structure can be characteristic to breeding ponds of smooth newts on a small spatial scale in their natural breeding habitat, but dispersal distance may be less limited than previously thought in these philopatric caudates.

Sexual conflict over survival in Trinidadian Guppies

ABSTRACTSexual conflict over survival produces two distinct population genetic signatures. Fluctuating selection in males and females produces balancing selection. Additionally, at conception, allele frequencies are the same in males and females. However, loci with alleles that benefit the survival of one sex at some survival cost to the other should diverge over the course of a generation. We therefore expect that sexual conflict over survival would produce both signatures of allelic differentiation between the sexes and balancing selection. However, given the substantial mortality costs required to produce allelic differences between males and females, it remains unclear how many loci within the genome, if any at all, experience significant sexual conflict over survival. We assessed the genomes of 120 wild-caught guppies, which are expected to experience substantial predation- and pathogen-induced mortality. We identified a core list of 15 high confidence genes that show allelic differences between male and female adults. However, eight of these show evidence of having duplicated copies on the Y chromosome, suggesting that the male-specific region of the guppy Y chromosome may act as a hotspot for the resolution of conflict. We recovered just seven genes with significant male-female allelic differentiation without evidence of Y duplication, and these show elevated Tajima’s D, consistent with balancing selection from sexual conflict. Only one of these seven genes, Puf60b, shows substantial intersexual FST. Puf60b has roles in cognition and the immune system, suggesting substantial ongoing, unresolved sexual conflict related to predator and pathogen avoidance strategies.

Evaluating human autosomal loci for sexually antagonistic viability selection in two large biobanks

Sex and sexual differentiation are pervasive across the tree of life. Because females and males often have substantially different functional requirements, we expect selection to differ between the sexes. Recent studies in diverse species, including humans, suggest that sexually antagonistic viability selection creates allele frequency differences between the sexes at many different loci. However, theory and population-level simulations indicate that sex-specific differences in viability would need to be very large to produce and maintain reported levels of between-sex allelic differentiation. We address this contradiction between theoretical predictions and empirical observations by evaluating evidence for sexually antagonistic viability selection on autosomal loci in humans using the largest cohort to date (UK Biobank, n = 487,999) along with a second large, independent cohort (BioVU, n = 93,864). We performed association tests between genetically ascertained sex and autosomal loci. Although we found dozens of genome-wide significant associations, none replicated across cohorts. Moreover, closer inspection revealed that all associations are likely due to cross-hybridization with sex chromosome regions during genotyping. We report loci with potential for mis-hybridization found on commonly used genotyping platforms that should be carefully considered in future genetic studies of sex-specific differences. Despite being well powered to detect allele frequency differences of up to 0.8% between the sexes, we do not detect clear evidence for this signature of sexually antagonistic viability selection on autosomal variation. These findings suggest a lack of strong ongoing sexually antagonistic viability selection acting on single locus autosomal variation in humans.

Evaluating Human Autosomal Loci for Sexually Antagonistic Viability Selection in Two Large Biobanks

ABSTRACTSex and sexual differentiation are ubiquitous across the tree of life. Because females and males often have substantially different functional requirements, we expect selection to differ between the sexes. Recent studies in diverse species, including humans, suggest sexually antagonistic viability selection creates allele frequency differences between the sexes at many different loci. However, theory and population-level simulations indicate that sex-specific differences in viability would need to be very extreme in order to produce and maintain reported levels of between-sex allelic differentiation. We address this paradox between theoretical predictions and empirical observations by evaluating evidence for sexually antagonistic viability selection on autosomal loci in humans using the largest cohort to date (UK Biobank, n=438,427) along with a second large, independent cohort (BioVU, n=93,864). We performed association tests between genetically ascertained sex and genotypes. Although we found dozens of genome-wide significant associations, none replicated across samples. Moreover, closer inspection revealed that all associations are likely due to cross-hybridization with sex chromosome regions during genotyping. We report loci with potential for mis-hybridization found on commonly used genotyping platforms that should be carefully considered in future genetic studies of sex-specific differences. Despite being well-powered to detect allele frequency differences of up to 0.8% between the sexes, we do not detect evidence for this signature of sexually antagonistic viability selection on autosomal variation. These findings suggest a lack of strong ongoing sexually antagonistic viability selection acting on single locus autosomal variation in humans.

Adaptation by copy number variation increases insecticide resistance in fall armyworms

Insecticide resistance is a major main challenge in pest control, and understanding its genetic basis is a key topic in agricultural ecology. Detoxification genes are well-known genetic elements that play a key role in adaptation to xenobiotics. The adaptive evolution of detoxification genes by copy number variations has been interpreted as a cause of insecticide resistance. However, the same pattern can be generated by the adaptation to host-plant defense toxins as well. In this study, we tested in fall armyworms (Lepidoptera Spodoptera frugiperda) if adaptation by copy number variation is the cause of the increased level of insecticide resistance from two geographic populations with different levels of resistance and two strains with different host plants. Following the generation of an assembly with chromosome-sized scaffolds (N50 = 13.2Mb), we observed that these two populations show a significant allelic differentiation of copy number variations, which is not observed between strains. In particular, a locus with almost complete allelic differentiation (Fst > 0.8) includes a cluster of P450 genes, which are well-known key players in detoxification. Detoxification genes are overrepresented in the genes with copy number variations, and the observed copy number variation appears to have beneficial effects in general. From this result, we concluded that copy number variation of detoxification genes in fall armyworms plays a key role in the insecticide resistance but not in the adaptation to host-plants, suggesting that the evolution of insecticide resistance may occur independently from host-plant adaptation.

Application of 7 STR markers for parentage testing and genetic distance study of Equidae / Zastosowanie siedmiu markerów STR do weryfikacji pochodzenia i badania dystansu genetycznego u koniowatych

The genotyping efficiency and polymorphism of 7 microsatellite markers (AHT084, COR006, COR017, COR018, COR040, COR055, COR088) was evaluated in order to apply them to parentage testing among a number of warm-blooded, cold-blooded and primitive horse breeds and to illustrate genetic differences between the breeds investigated. The amplification and sequence structure of these STR markers was also verified in other Equidae like zebra, kulan, donkey and Przewalski horse. Microsatellite allelic differentiation was similar to the allele numbers reported, with an extremely wide allelic range observed at AHT084 locus. However, due to genotyping difficulties AHT084 is not a suitable marker for parentage testing. The use of the other 6 STR markers among most of the horse breeds studied allows excluding wrongly assigned parentage with a probability of 0.99. Fragment analysis and sequencing of STR alleles confirmed the presence of investigated tandem repeats in other Equidae species. Clustering of investigated horse breeds on the tree of Fst distance was consistent with their breeding history, clearly separating breeds into 3 horse types mentioned above.