Single hybrid population but multiple parental individuals at the origin of parthenogenetic rock lizards Darevskia sapphirina and D. bendimahiensis Schmidtler, & Eiselt Darevsky (1994) endemic to the area of Lake Van in East Turkey.

Among vertebrates, obligate parthenogenesis is only found in Squamata, where it always has a hybrid origin and a few lizard genera contain most of the known hybridogenous parthenogenetic taxa. Parthenogenesis thus seems to be pre-conditioned at the genus level, but it is not clear how often the encounter between two parental sexually reproducing species can result in the parthenogenetic offspring, nor whether the success of such hybridization event requires certain conditions or the specific time frame. To address this question, we studied the rock lizards of genus Darevskia, where a pair of parental species, D. valentini and D. raddei, as well as their parthenogenetic daughter species D. bendimahiensis and D. sapphirina, are found in close proximity NE of the Lake Van in East Anatolia. Using ddRAD-seq genotyping on 19 parental and 18 hybrid individuals, we found that (i) all parthenogenetic individuals from both D. bendimahiensis and D. sapphirina have a monophyletic origin tracing back to a single initial hybrid population, but their current genetic variation is geographically structured; (ii) unlike the most probable paternal ancestor, the genetically closest extant population of the maternal ancestor is not the geographically nearest one; and (iii) in the parthenogens, about 1% of loci carry multiple haplotypes, frequently differentiated by multiple substitutions. This pattern, in addition to biases in the relative frequency of haplotypes of maternal and paternal origin, does not appear compatible with a scenario of the entire parthenogenic clonal population having descended from a single pair of parental individuals. Instead, the data suggest that multiple parental individual ancestries still persist in the parthenogenetic gene pool. This supports the notion that although hybridization leading to parthenogenesis is generally rare at the level of species, it may be more common at the individual/population level once the right conditions are met.

Landscape genetics and the genetic legacy of Upper Paleolithic and Mesolithic hunter-gatherers in the modern Caucasus.

This study clarifies the role of refugia and landscape permeability in the formation of the current genetic structure of peoples of the Caucasus. We report novel genome-wide data for modern individuals from the Caucasus, and analyze them together with available Paleolithic and Mesolithic individuals from Eurasia and Africa in order (1) to link the current and ancient genetic structures via landscape permeability, and (2) thus to identify movement paths between the ancient refugial populations and the Caucasus. The ancient genetic ancestry is best explained by landscape permeability implying that human movement is impeded by terrain ruggedness, swamps, glaciers and desert. Major refugial source populations for the modern Caucasus are those of the Caucasus, Anatolia, the Balkans and Siberia. In Rugged areas new genetic signatures take a long time to form, but once they do so, they remain for a long time. These areas act as time capsules harboring genetic signatures of ancient source populations and making it possible to help reconstruct human history based on patterns of variation today.

Genotypic similarities among the parthenogenetic Darevskia rock lizards with different hybrid origins.

BACKGROUND: The majority of parthenogenetic vertebrates derive from hybridization between sexually reproducing species, but the exact number of hybridization events ancestral to currently extant clonal lineages is difficult to determine. Usually, we do not know whether the parental species are able to contribute their genes to the parthenogenetic vertebrate lineages after the initial hybridization. In this paper, we address the hypothesis, whether some genotypes of seven phenotypically distinct parthenogenetic rock lizards (genus Darevskia) could have resulted from back-crosses of parthenogens with their presumed parental species. We also tried to identify, as precise as possible, the ancestral populations of all seven parthenogens. RESULTS: We analysed partial mtDNA sequences and microsatellite genotypes of all seven parthenogens and their presumed ansectral species, sampled across the entire geographic range of parthenogenesis in this group. Our results confirm the previous designation of the parental species, but further specify the maternal populations that are likely ancestral to different parthenogenetic lineages. Contrary to the expectation of independent hybrid origins of the unisexual taxa, we found that genotypes at multiple loci were shared frequently between different parthenogenetic species. The highest proportions of shared genotypes were detected between (i) D. sapphirina and D. bendimahiensis and (ii) D. dahli and D. armeniaca, and less often between other parthenogens. In case (ii), genotypes at the remaining loci were notably distinct. CONCLUSIONS: We suggest that both observations (i-ii) can be explained by two parthenogenetic forms tracing their origin to a single initial hybridization event. In case (ii), however, occasional gene exchange between the unisexual and the parental bisexual species could have taken place after the onset of parthenogenetic reproduction. Indeed, backcrossed polyploid hybrids are relatively frequent in Darevskia, although no direct evidence of recent gene flow has been previously documented. Our results further suggest that parthenogens are losing heterozygosity as a result of allelic conversion, hence their fitness is expected to decline over time as genetic diversity declines. Backcrosses with the parental species could be a rescue mechanism which might prevent this decline, and therefore increase the persistance of unisexual forms.

Altitudinal Effects on Innate Immune Response of a Subterranean Rodent.

Immune defense is costly to maintain and deploy, and the optimal investment into immune defense depends on risk of infection. Altitude is a natural environmental factor that is predicted to affect parasite abundance, with lower parasite abundance predicted at higher altitudes due to stronger environmental stressors, which reduce parasite transmission. Using high and low altitude populations of the Turkish blind mole-rat (TBMR) Nannospalax xanthodon, we tested for effects of altitude on constitutive innate immune defense. Field studies were performed with 32 wild animals in 2017 and 2018 from two low- and one high-altitude localities in the Central Taurus Mountains, at respective altitudes of 1010 m, 1115 m, and 2900 m above sea level. We first compared innate standing immune defense as measured by the bacteria-killing ability of blood serum. We then measured corticosterone stress hormone levels, as stressful conditions may affect immune response. Finally, we compared prevalence and intensity of gastrointestinal parasites of field-captured TBMR. We found that the bacteria-killing ability of serum is greater in the mole-rat samples from high altitude. There was no significant difference in stress (corticosterone) levels between altitude categories. Coccidian prevalence and abundance were significantly higher in 2017 than 2018 samples, but there was no significant difference in prevalence, abundance, or intensity between altitudes, or between sexes. Small sample sizes may have reduced power to detect true differences; nevertheless, this study provides support that greater standing innate immunity in high altitude animals may reflect greater investment into constitutive defense.

The Role of Retrotransposons in Gene Family Expansions in the Human and Mouse Genomes.

Retrotransposons comprise a large portion of mammalian genomes. They contribute to structural changes and more importantly to gene regulation. The expansion and diversification of gene families have been implicated as sources of evolutionary novelties. Given the roles retrotransposons play in genomes, their contribution to the evolution of gene families warrants further exploration. In this study, we found a significant association between two major retrotransposon classes, LINEs and LTRs, and lineage-specific gene family expansions in both the human and mouse genomes. The distribution and diversity differ between LINEs and LTRs, suggesting that each has a distinct involvement in gene family expansion. LTRs are associated with open chromatin sites surrounding the gene families, supporting their involvement in gene regulation, whereas LINEs may play a structural role promoting gene duplication. Our findings also suggest that gene family expansions, especially in the mouse genome, undergo two phases. The first phase is characterized by elevated deposition of LTRs and their utilization in reshaping gene regulatory networks. The second phase is characterized by rapid gene family expansion due to continuous accumulation of LINEs and it appears that, in some instances at least, this could become a runaway process. We provide an example in which this has happened and we present a simulation supporting the possibility of the runaway process. Altogether we provide evidence of the contribution of retrotransposons to the expansion and evolution of gene families. Our findings emphasize the putative importance of these elements in diversification and adaptation in the human and mouse lineages.

Migration-selection balance at multiple Loci and selection on dominance and recombination.

A steady influx of a single deleterious multilocus genotype will impose genetic load on the resident population and leave multiple descendants carrying various numbers of the foreign alleles. Provided that the foreign types are rare at equilibrium, and all immigrant genes are eventually eliminated by selection, the population structure can be inferred explicitly from the branching process taking place within a single immigrant lineage. Unless the migration and recombination rates were high, this novel method gives a close approximation to the simulation with all possible multilocus genotypes considered. Once the load and the foreign genotypes frequencies are known, it becomes possible to estimate selection acting on the invading modifiers of (i) dominance and (ii) recombination rate on the foreign gene block. We found that the modifiers of the (i) type are able to invade faster than the type (ii) modifier, however, this result only applies in the strong selection/low migration/low recombination scenario. Varying the number of genes in the immigrant genotype can have a non-monotonic effect on the migration load and the modifier's invasion rate: although blocks carrying more genes can give rise to longer lineages, they also experience stronger selection pressure. The heaviest load is therefore imposed by the genotypes carrying moderate numbers of genes.

Invasion of gene duplication through masking for maladaptive gene flow.

Gene duplication can increase an organism's ability to mask the effect of deleterious alleles present in the population, but this is typically a small effect when the source of the genetic variation is mutation. Migration can introduce orders of magnitude more deleterious alleles per generation and may therefore be an important force acting on the structure of genomes. Using formal analytical methods, we study the invasion of haplotypes containing two copies of the resident allele, assuming that a single-locus equilibrium is already established in a continent-island model of migration. Provided that the immigrant allele can be completely masked by multiple functional gene copies, a new duplication will deterministically spread so long as duplicate haplotypes are, on average, fitter than single-copy haplotypes. When fitness depends on the number of immigrant allele copies and their masking ability then the threshold for invasion depends on the rate of immigration and the rate of recombination between the gene copies. Results from several special cases, including formation of protein dimers and Dobzhansky-Muller incompatibilities, suggest that duplications can invade in a wide range of selection regimes. We hypothesize that duplication in response to gene flow may provide an explanation for the high levels of polymorphism in gene copy number observed in natural populations.

One- and two-locus population models with differential viability between sexes: parallels between haploid parental selection and genomic imprinting.

A model of genomic imprinting with complete inactivation of the imprinted allele is shown to be formally equivalent to the haploid model of parental selection. When single-locus dynamics are considered, an internal equilibrium is possible only if selection acts in the opposite directions in males and females. I study a two-locus version of the latter model, in which maternal and paternal effects are attributed to the single alleles at two different loci. A necessary condition for the allele frequency equilibria to remain on the linkage equilibrium surface is the multiplicative interaction between maternal and paternal fitness parameters. In this case the equilibrium dynamics are independent at both loci and results from the single-locus model apply. When fitness parameters are additive, analytic treatment was not possible but numerical simulations revealed that stable polymorphism characterized by association between loci is possible only in several special cases in which maternal and paternal fitness contributions are precisely balanced. As in the single-locus case, antagonistic selection in males and females is a necessary condition for the maintenance of polymorphism. I also show that the above two-locus results of the parental selection model are very sensitive to the inclusion of weak directional selection on the individual's own genotypes.

Hybridization of Bombina bombina and B. variegata (Anura, Discoglossidae) at a sharp ecotone in western Ukraine: comparisons across transects and over time.

Bombina bombina and B. variegata are two anciently diverged toad taxa that have adapted to different breeding habitats yet hybridize freely in zones of overlap where their parapatric distributions meet. Here, we report on a joint genetic and ecological analysis of a hybrid zone in the vicinity of Stryi in western Ukraine. We used five unlinked allozyme loci, two nuclear single nucleotide polymorphisms and a mitochondrial DNA haplotype as genetic markers. Parallel allele frequency clines with a sharp central step occur across a sharp ecotone, where transitions in aquatic habitat, elevation, and terrestrial vegetation coincide. The width of the hybrid zone, estimated as the inverse of the maximum gradient in allele frequency, is 2.3 km. This is the smallest of four estimates derived from different clinal transects across Europe. We argue that the narrow cline near Stryi is mainly due to a combination of habitat distribution and habitat preference. Adult toads show a preference for either ponds (B. bombina) or puddles (B. variegata), which is known to affect the distribution of genotypes within the hybrid zones. At Stryi, it should cause a reduction of the dispersal rate across the ecotone and thus narrow the cline. A detailed comparison of all five intensively studied Bombina transects lends support to the hypothesis that habitat distribution plus habitat preference can jointly affect the structure of hybrid zones and, ultimately, the resulting barriers to gene flow between differentiated gene pools. This study also represents a resampling of an area that was last studied more than 70 years ago. Our allele-frequency clines largely coincide with those that were described then on the basis of morphological variation. However, we found asymmetrical introgression of B. variegata genes into B. bombina territory along the bank of a river.