Patterns of evolution in MHC class II DQA and DQB exon 2 genes of Alpine mountain hares, Lepus timidus varronis, and sympatric and parapatric brown hares, L. europaeus, from Switzerland

In natural populations, hybridization is known to occur between a wide range of species. However, its evolutionary significance is less clear. Genes involved in fighting pathogens are considered excellent candidates for studying adaptive introgression, although both introgression and balancing selection can generate similar patterns of diversity and differentiation. Here, we compared DQA and DQB MHC class II and microsatellite allelic diversity of sympatric and parapatric mountain (Lepus timidus) and brown hare (L. europaeus) populations from Switzerland. We detected higher genetic diversity in brown hares compared to mountain hares at both MHC and microsatellite loci. We consider the observed patterns of microsatellite diversity both for L. europaeus and L. timidus as result of stochastic demographic processes while the pattern of MHC polymorphism of the studied hare populations can be explained by pathogen-driven selection. Rare bidirectional gene flow between both hare species seems to occur specifically for MHC alleles. However, the high number of shared alleles showing similar high frequency in both species suggests that reciprocally exchanged MHC alleles are being maintained via balancing selection. Adaptation to similar pathogen communities can also lead to parallel selection of MHC alleles. Positive selection, recombination and mutations have played different roles in shaping the patterns of MHC allelic diversity in and differentiation between both species. Results for the latter evolutionary forces do not show a better matching between the sympatric populations compared to the parapatric ones, suggesting a minor role of introgression for the observed evolutionary patterns of the studied hare species.

Revisiting the phylogeography and demography of European badgers (Meles meles) based on broad sampling, multiple markers and simulations

Although the phylogeography of European mammals has been extensively investigated since the 1990s, many studies were limited in terms of sampling distribution, the number of molecular markers used and the analytical techniques employed, frequently leading to incomplete postglacial recolonisation scenarios. The broad-scale genetic structure of the European badger (Meles meles) is of interest as it may result from historic restriction to glacial refugia and/or recent anthropogenic impact. However, previous studies were based mostly on samples from western Europe, making it difficult to draw robust conclusions about the location of refugia, patterns of postglacial expansion and recent demography. In the present study, continent-wide sampling and analyses with multiple markers provided evidence for two glacial refugia (Iberia and southeast Europe) that contributed to the genetic variation observed in badgers in Europe today. Approximate Bayesian computation provided support for a colonisation of Scandinavia from both Iberian and southeastern refugia. In the whole of Europe, we observed a decline in genetic diversity with increasing latitude, suggesting that the reduced diversity in the peripheral populations resulted from a postglacial expansion processes. Although MSVAR v.1.3 also provided evidence for recent genetic bottlenecks in some of these peripheral populations, the simulations performed to estimate the method's power to correctly infer the past demography of our empirical populations suggested that the timing and severity of bottlenecks could not be established with certainty. We urge caution against trying to relate demographic declines inferred using MSVAR with particular historic or climatological events.

Home-loving boreal hare mitochondria survived several invasions in Iberia: the relative roles of recurrent hybridisation and allele surfing

Genetic introgression from a resident species into an invading close relative can result from repeated hybridisation along the invasion front and/or allele surfing on the expansion wave. Cases where the phenomenon is massive and systematic, such as for hares (genus Lepus) in Iberia, would be best explained by recurrent hybridisation but this is difficult to prove because the donor populations are generally extinct. In the Pyrenean foothills, Lepus europaeus presumably replaced Lepus granatensis recently and the present species border is parallel to the direction of invasion, so that populations of L. granatensis in the contact zone represent proxies of existing variation before the invasion. Among three pairs of populations sampled across this border, we find less differentiation of mitochondrial DNA (mtDNA) across than along it, as predicted under recurrent hybridisation at the invasion front. Using autosomal microsatellite loci and X- and Y-linked diagnostic loci, we show that admixture across the border is quasi-absent, making it unlikely that lack of interspecific mtDNA differentiation results from ongoing gene flow. Furthermore, we find that the local species ranges are climatically contrasted, making it also unlikely that ongoing ecology-driven movement of the contact account for mtDNA introgression. The lack of mtDNA differentiation across the boundary is mostly due to sharing of mtDNA from a boreal species currently extinct in Iberia (Lepus timidus) whose mitochondria have thus remained in place since the last deglaciation despite successive invasions by two other species. Home-loving mitochondria thus witness past species distribution rather than ongoing exchanges across stabilised contact zones.

The rise and fall of the mountain hare (Lepus timidus) during Pleistocene glaciations: expansion and retreat with hybridization in the Iberian Peninsula

The climatic fluctuations during glaciations have affected differently arctic and temperate species. In the northern hemisphere, cooling periods induced the expansion of many arctic species to the south, while temperate species were forced to retract in southern refugia. Consequently, in some areas the alternation of these species set the conditions for competition and eventually hybridization. Hares in the Iberian Peninsula appear to illustrate this phenomenon. Populations of Iberian hare (Lepus granatensis), brown hare (Lepus europaeus) and broom hare (Lepus castroviejoi) in Northern Iberia harbour mitochondrial haplotypes from the mountain hare (Lepus timidus), a mainly boreal and arctic species presently absent from the peninsula. To understand the history of this past introgression we analysed sequence variation and geographical distribution of mitochondrial control region and cytochrome b haplotypes of L. timidus origin found in 378 specimens of these four species. Among 124 L. timidus from the Northern Palaearctic and the Alps we found substantial nucleotide diversity (2.3%) but little differentiation between populations. Based on the mismatch distribution of the L. timidus sequences, this could result from an expansion at a time of temperature decrease favourable to this arctic species. The nucleotide diversity of L. timidus mtDNA found in Iberian L. granatensis, L. europaeus and L. castroviejoi (183, 70 and 1 specimens, respectively) was of the same order as that in L. timidus over its range (1.9%), suggesting repeated introgression of multiple lineages. The structure of the coalescent of L. granatensis sequences indicates that hybridization with L. timidus was followed by expansion of the introgressed haplotypes, as expected during a replacement with competition, and occurred when temperatures started to rise, favouring the temperate species. Whether a similar scenario explains the introgression into Iberian L. europaeus remains unclear but it is possible that it hybridized with already introgressed L. granatensis.

Fluctuating asymmetry and genetic variability in the roe deer (Capreolus capreolus): a test of the developmental stability hypothesis in mammals using neutral molecular markers

Fluctuating asymmetry (FA), used as an indicator of developmental stability, has long been hypothesized to be negatively correlated with genetic variability as a consequence of more variable organisms being better suited to buffer developmental pathways against environmental stress. However, it is still a matter of debate if this is due to metabolic properties of enzymes encoded by certain key loci or rather to overall genomic heterozygosity. Previous analyses suggest that there might be a general difference between homeo- and poikilotherms in that only the latter tend to exhibit the negative correlation predicted by theory. In the present study, we addressed these questions by analysing roe deer (Capreolus capreolus) from five German populations with regard to FA in metric and non-metric skull and mandible traits as well as variability at eight microsatellite loci. Genetic variability was quantified by heterozygosity and mean d2 parameters, and although the latter did not show any relationship with FA, we found for the first time a statistically significant negative correlation of microsatellite heterozygosity and non-metric FA among populations. Because microsatellites are non-coding markers, this may be interpreted as evidence for the role of overall genomic heterozygosity in determining developmental stability. To test if the threshold character of non-metric traits is responsible for the metric vs non-metric difference we also carried out calculations where we treated our metric traits as threshold values. This, however, did not yield significant correlations between FA and genetic variability either.

Selection and recombination drive the evolution of MHC class II DRB diversity in ungulates

Major histocompatibility complex (MHC) antigen-presenting genes are the most variable loci in vertebrate genomes. Host-parasite co-evolution is assumed to maintain the excessive polymorphism in the MHC loci. However, the molecular mechanisms underlying the striking diversity in the MHC remain contentious. The extent to which recombination contributes to the diversity at MHC loci in natural populations is still controversial, and there have been only few comparative studies that make quantitative estimates of recombination rates. In this study, we performed a comparative analysis for 15 different ungulates species to estimate the population recombination rate, and to quantify levels of selection. As expected for all species, we observed signatures of strong positive selection, and identified individual residues experiencing selection that were congruent with those constituting the peptide-binding region of the human DRB gene. However, in addition for each species, we also observed recombination rates that were significantly different from zero on the basis of likelihood-permutation tests, and in other non-quantitative analyses. Patterns of synonymous and non-synonymous sequence diversity were consistent with differing demographic histories between species, but recent simulation studies by other authors suggest inference of selection and recombination is likely to be robust to such deviations from standard models. If high rates of recombination are common in MHC genes of other taxa, re-evaluation of many inference-based phylogenetic analyses of MHC loci, such as estimates of the divergence time of alleles and trans-specific polymorphism, may be required.

Invasion from the cold past: extensive introgression of mountain hare (Lepus timidus) mitochondrial DNA into three other hare species in northern Iberia

Mitochondrial DNA introgression from Lepus timidus into Lepus granatensis and Lepus europaeus was recently reported in Iberia, although L. timidus presumably retreated from this region at the end of the last ice age. Here we assess the extent of this ancient mtDNA introgression by RFLP analysis of 695 specimens representing the three hare species present in Iberia. The introgressed L. timidus lineage was found in 23 of the 37 populations sampled. It is almost fixed in L. europaeus across its Iberian range in the Pyrenean foothills, and in L. granatensis, which occupies the rest of the peninsula, it is predominant in the north and gradually disappears further south. We also found it in Lepus castroviejoi, a species endemic to Cantabria. Multiple hybridizations and, potentially, a selective advantage for the L. timidus lineage can explain the remarkable taxonomic and geographical range of this mitochondrial introgression.

Spatial patterns of mitochondrial and nuclear gene pools in chamois (Rupicapra r. rupicapra) from the Eastern Alps

We have assessed the variability of maternally (mtDNA) and biparentally (allozymes) inherited genes of 443 chamois (Rupicapra r. rupicapra) from 19 regional samples in the Eastern Alps, to estimate the degree and patterns of spatial gene pool differentiation, and their possible causes. Based on a total mtDNA-RFLP approach with 16 hexanucleotide-recognizing restriction endonucleases, we found marked substructuring of the maternal gene pool into four phylogeographic groups. A hierarchical AMOVA revealed that 67.09% of the variance was partitioned among these four mtDNA-phylogroups, whereas only 8.04% were because of partitioning among regional samples within the populations, and 24.86% due to partitioning among individuals within regional samples. We interpreted this spatial pattern of mtDNA variability as a result of immigration of chamois from different Pleistocene refugia surrounding the Alps after the withdrawal of glaciers, rather than from topographic barriers to gene flow, such as Alpine valleys, extended glaciers or woodlands. However, this striking geographical structuring of the maternal genome was not paralleled by allelic variation at 33 allozyme loci, which were used as nuclear DNA markers. Wright's hierarchical F-statistics revealed that only < or =0.45% of the explained allozymic diversity was because of partitioning among the four mtDNA-phylogroups. We conclude that this discordance of spatial patterns of nuclear and mtDNA gene pools results from a phylogeographic background and sex-specific dispersal, with higher levels of philopatry in females.

Ancient introgression of Lepus timidus mtDNA into L. granatensis and L. europaeus in the Iberian Peninsula

A 587 bp fragment of cytochrome b sequences from 90 individuals of 15 hare (Lepus) species and two outgroups were phylogenetically analysed and compared to an analysis derived from 474 bp sequences of the nuclear transferrin gene. Mountain hare (Lepus timidus) type mtDNA was observed in L. granatensis and L. europaeus from the Iberian Peninsula, far away from the extant distributional range of L. timidus. In addition to these two hare species, other hare species may also contain mtDNA from L. timidus. This species may have introgressed with other species of Lepus that occur within its present range, or where fossils indicate its historical presence during glacial periods. L. timidus mtDNA is common in the northern part of the L. granatensis range. Finally, we reassessed the phylogenetic relationships of the five European hare species based on both mitochondrial and nuclear DNA sequences.

Mitochondrial DNA variation in the European otter (Lutra lutra) and the use of spatial autocorrelation analysis in conservation

To add genetic information to the international conservation efforts on European otters Lutra lutra, we investigated the genetic population structure in and around a known "source" population of the otter, the Oberlausitz (OL) in eastern Germany. This was complemented by a first survey of genetic variation levels in the Central European otter population. Sequence analysis of 300bp of the mitochondrial control region in 76 specimens from the eastern German study region and 53 individuals from several other European populations revealed a low level of genetic variation, with only 5 haplotypes present and nucleotide diversities within populations ranging from 0.00% to 0.17%. Apart from eastern Germany, one haplotype was by far the most abundant one, from which other, only locally occurring types, could be derived by a single point mutation. This suggests a single Pleistocene refugium from which the analyzed European regions have been reinvaded after the glaciations. Within eastern Germany, two abundant haplotypes were found. Their occurrence differed significantly among subregions of eastern Germany. The uneven distribution of a locally restricted but abundant haplotype could be explained by isolation-by-distance and might reflect emigration from the OL source population to surrounding regions. This suggests that vital local populations can indeed serve as "sources" for the invasion of surrounding areas. Given a suitable genetic marker, we suggest a spatial autocorrelation analysis to monitor the genetic effect of such an emigration from a source population.