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Mitochondrial DNA (mtDNA) lineages are recognized as important components of intra- and interspecific biodiversity, and allow to reveal colonization routes and phylogeographic structure of many taxa. Among these is the genus Cervus that is widely distributed across the Holarctic. We obtained sequences of complete mitochondrial genomes from 13 Cervus taxa and included them in global phylogenetic analyses of 71 Cervinae mitogenomes. The well-resolved phylogenetic trees confirmed Cervus to be monophyletic. Molecular dating based on several fossil calibration points revealed that ca . 2.6 Mya two main mitochondrial lineages of Cervus separated in Central Asia, the Western (including C. hanglu and C. elaphus ) and the Eastern (comprising C. albirostris , C. canadensis and C. nippon ). We also observed convergent changes in the composition of some mitochondrial genes in C. hanglu of the Western lineage and representatives of the Eastern lineage. Several subspecies of C. nippon and C. hanglu have accumulated a large portion of deleterious substitutions in their mitochondrial protein-coding genes, probably due to drift in the wake of decreasing population size. In contrast to previous studies, we found that the relic haplogroup B of C. elaphus was sister to all other red deer lineages and that the Middle-Eastern haplogroup E shared a common ancestor with the Balkan haplogroup C. Comparison of the mtDNA phylogenetic tree with a published nuclear genome tree may imply ancient introgressions of mtDNA between different Cervus species as well as from the common ancestor of South Asian deer, Rusa timorensis and R. unicolor , to the Cervus clade.

Demographic bottlenecks generally reduce genetic diversity through more intense genetic drift, but their net effect may vary along the genome due to the random nature of genetic drift and to local effects of recombination, mutation, and selection. Here, we analyzed the changes in genetic diversity following a bottleneck by comparing whole‐genome diversity patterns in populations with and without severe recent documented declines of Iberian (Lynx pardinus, n = 31) and Eurasian lynx (Lynx lynx, n = 29). As expected, overall genomic diversity correlated negatively with bottleneck intensity and/or duration. Correlations of genetic diversity with divergence, chromosome size, gene or functional site content, GC content, or recombination were observed in nonbottlenecked populations, but were weaker in bottlenecked populations. Also, functional features under intense purifying selection and the X chromosome showed an increase in the observed density of variants, even resulting in higher θW diversity than in nonbottlenecked populations. Increased diversity seems to be related to both a higher mutational input in those regions creating a large collection of low‐frequency variants, a few of which increase in frequency during the bottleneck to the point they become detectable with our limited sample, and the reduced efficacy of purifying selection, which affects not only protein structure and function but also the regulation of gene expression. The results of this study alert to the possible reduction of fitness and adaptive potential associated with the genomic erosion in regulatory elements. Further, the detection of a gain of diversity in ultra‐conserved elements can be used as a sensitive and easy‐to‐apply signature of genetic erosion in wild populations.

Due to their high mobility, large terrestrial predators are potentially capable of maintaining high connectivity, and therefore low genetic differentiation among populations. However, previous molecular studies have provided contradictory findings in relation to this. To elucidate patterns of genetic structure in large carnivores, we studied the genetic variability of the Eurasian lynx, Lynx lynx throughout north-eastern Europe using microsatellite, mitochondrial DNA control region and Y chromosome-linked markers. Using SAMOVA we found analogous patterns of genetic structure based on both mtDNA and microsatellites, which coincided with a relatively little evidence for male-biased dispersal. No polymorphism for the cytochrome b and ATP6 mtDNA genes and Y chromosome-linked markers were found. Lynx inhabiting a large area encompassing Finland, the Baltic countries and western Russia formed a single genetic unit, while some marginal populations were clearly divergent from others. The existence of a migration corridor was suggested to correspond with distribution of continuous forest cover. The lowest variability (in both markers) was found in lynx from Norway and Białowieża Primeval Forest (BPF), which coincided with a recent demographic bottleneck (Norway) or high habitat fragmentation (BPF). The Carpathian population, being monomorphic for the control region, showed relatively high microsatellite diversity, suggesting the effect of a past bottleneck (e.g. during Last Glacial Maximum) on its present genetic composition. Genetic structuring for the mtDNA control region was best explained by latitude and snow cover depth. Microsatellite structuring correlated with the lynx's main prey, especially the proportion of red deer (Cervus elaphus) in its diet. Eurasian lynx are capable of maintaining panmictic populations across eastern Europe unless they are severely limited by habitat continuity or a reduction in numbers. Different correlations of mtDNA and microsatellite population divergence patterns with climatic and ecological factors may suggest separate selective pressures acting on males and females in this solitary carnivore.

Local adaptations to the environment are an important aspect of the diversity of a species and their discovery, description and quantification has important implications for the fields of taxonomy, evolutionary and conservation biology. In this study, we scan genomes from several populations across the distributional range of the Eurasian lynx, with the objective of finding genomic windows under positive selection which may underlie local adaptations to different environments. A total of 394 genomic windows are found to be associated to local environmental conditions, and they are enriched for genes involved in metabolism, behaviour, synaptic organization and neural development. Adaptive genetic structure, reconstructed from SNPs in candidate windows, is considerably different than the neutral genetic structure of the species. A widespread adaptively homogeneous group is recovered occupying areas of harsher snow and temperature climatic conditions in the north‐western, central and eastern parts of the distribution. Adaptively divergent populations are recovered in the westernmost part of the range, especially within the Baltic population, but also predicted for different patches in the western and southern part of the range, associated with different snow and temperature regimes. Adaptive differentiation driven by climate does not correlate much with the subspecies taxonomic delimitations, suggesting that subspecific divergences are mostly driven by neutral processes of genetic drift and gene flow. Our results will aid the selection of source populations for assisted gene flow or genetic rescue programs by identifying what climatic patterns to look for as predictors of pre‐adaptation of individuals. Particularly, the Carpathian population is confirmed as the best source of individuals for the genetic rescue of the endangered, isolated and genetically eroded Balkan population. Additionally, reintroductions in central and western Europe, currently based mostly on Carpathian lynxes, could consider the Baltic population as an additional source to increase adaptive variation and likely improve adaptation to their milder climate.

Aim: Using sequences of complete mitochondrial genomes, our aims were: (1) to investigate the matrilineal phylogeographical structure, migration patterns and lineage coalescence times in a large, continuous population of brown bears (Ursus arctos); and (2) to develop a novel spatial genetic method to identify migration corridors and barriers. Location: North-western Eurasia: from eastern European Russia to the Baltic Sea. Methods: We sequenced the complete mitochondrial genomes of 95 brown bears. The phylogeographical resolution of complete genomes was compared to that derived from subsets of the genome, including the most commonly used shorter sequences. We conducted network and Bayesian phylogeographical analyses and developed a novel, spatially explicit, individual-based approach (called DResD) for identifying migration corridors and barriers. Results: Analysis of mitogenome sequences revealed five haplogroups, specific to particular geographical areas, exhibiting far greater resolving power than shorter sequences. Estimated coalescence times for the haplogroups ranged from 7.7 to 15.2 ka, suggesting that their divergence took place after the last glaciation. We found several migration trends, including a large westward migration from eastern European Russia towards Finland. We also found evidence of a potential barrier and a migration corridor in the south-west of the study area. Main conclusions: The use of complete mitochondrial genomes from a brown bear population in north-western Eurasia allowed us to identify phylogeographical structure, signatures of demographic history and spatial processes that had not previously been detected using shorter sequences. These findings have implications for studies on other species and populations, especially those exhibiting low mtDNA diversity. The relatively recent divergence estimates for haplogroups highlight the significance not only of the last glaciation but also of climatic fluctuations during the post-glacial period for the divergence of mammal populations in Europe. Our spatial genetic method represents a new tool for the analysis of genetic data in a geographical context and is applicable to any data that yield genetic distance matrices, including microsatellites, amplified fragment length polymorphisms (AFLPs) and single-nucleotide polymorphisms (SNPs).

Background Demographic bottlenecks erode genetic diversity and may increase endangered species’ extinction risk via decreased fitness and adaptive potential. The genetic status of species is generally assessed using neutral markers, whose dynamic can differ from that of functional variation due to selection. The MHC is a multigene family described as the most important genetic component of the mammalian immune system, with broad implications in ecology and evolution. The genus Lynx includes four species differing immensely in demographic history and population size, which provides a suitable model to study the genetic consequences of demographic declines: the Iberian lynx being an extremely bottlenecked species and the three remaining ones representing common and widely distributed species. We compared variation in the most variable exon of the MHCI and MHCII-DRB loci among the four species of the Lynx genus. Results The Iberian lynx was characterised by lower number of MHC alleles than its sister species (the Eurasian lynx). However, it maintained most of the functional genetic variation at MHC loci present in the remaining and genetically healthier lynx species at all nucleotide, amino acid, and supertype levels. Conclusions Species-wide functional genetic diversity can be maintained even in the face of severe population bottlenecks, which caused devastating whole genome genetic erosion. This could be the consequence of divergent alleles being retained across paralogous loci, an outcome that, in the face of frequent gene conversion, may have been favoured by balancing selection.

Deleterious mutations continuously accumulate in populations, building up a burden that can threaten their survival, particularly in small populations when inbreeding exposes recessive deleterious effects. Notwithstanding, this process also triggers genetic purging, which can reduce the deleterious burden and mitigate fitness inbreeding depression. Here, we analyzed 20 whole genomes from the endangered Iberian lynx and 28 from the widespread Eurasian lynx, sister species which constitute a good model to study the dynamics of deleterious mutation burden under contrasting demographies, manifested in the consistently smaller population size and distribution area of the Iberian lynx. We also derived analytical predictions for the evolution of the deleterious burden following a bottleneck. We found 11% fewer derived alleles for the more putatively deleterious missense category in the Iberian lynx than in the Eurasian lynx, which, in light of our theoretical predictions, should be ascribed to historical purging. No signs of purging were found in centromeres nor in the X chromosome, where selection against recessive deleterious alleles is less affected by demography. The similar deleterious burden levels for conspecific populations despite their contrasting recent demographies also point to sustained differences in historical population sizes since species divergence as the main driver of the augmented purging in the Iberian lynx. Beyond adding to the ongoing debate on the relationship between deleterious burden and population size, and on the impact of genetic factors in endangered species viability, this work contributes a whole-genome catalog of deleterious variants, which may become a valuable resource for future conservation efforts.

Aim Genome‐wide genetic data can provide key input for both taxonomy and conservation, but its use in this context remains limited. In this study, we performed the first genome‐wide assessment of genetic variation in two populations of the Eurasian lynx, the Balkan population, the most threatened, and the Caucasian population, a possible glacial refugium, with the aim to place them in the context of the species, investigate their demographic history and evaluate their genetic status. Location The Balkans and the Caucasus. Methods We obtained whole genome resequencing data from seven Balkan and 12 Caucasian lynx, and analysed them along with novel and existing data from other populations. Based on a total 105 whole genome and 114 mitogenome sequences, we reconstructed phylogenetic and historical relationships, ancient and recent demography, and patterns of genetic diversity and inbreeding. Results Both the Balkan and the Caucasian lynx appear as distinct mitochondrial lineages that diverged from the rest of the Eurasian lynx lineages ca. 92.6 kya, and from each other ca. 46.4 kya. Autosomal data suggest, however, that the Balkan lynx is closely related with the Carpathian population, and revealing alarmingly low genetic diversity and high inbreeding. In contrast, the Caucasian lynx shows a longer history of relative isolation from the rest of lynx populations and high genetic diversity, consistent with its large long‐term effective population size. Main conclusions The taxonomic status of the Balkan lynx remains unresolved due to the evidence of long‐term isolation in the mitogenome, contrasting with extensive autosomal admixture and intense recent genetic drift in the nuclear genome. Our results alert on genetic risks and call for the consideration of genetic rescue from closely related Carpathian lynxes. In contrast, substantial mitogenomic and autosomal divergence with no signs of genetic drift supports the identification of the Caucasian lynx as a separate subspecies with good genetic health.

Aim Our aim was to assess the population structure, genetic diversity and demographic history of the wolverine (Gulo gulo) throughout its entire Eurasian range. Additionally, we aimed to contextualize and put into perspective the state of the endangered Fennoscandian population by emphasizing its connectivity to other populations. Location The main study area covered most of the Eurasian wolverine range, with samples from Finland, Russia, Kazakhstan and Mongolia. Methods Using a 495 bp fragment of the mitochondrial DNA control region and a frequently used set of 14 microsatellite markers on an extensive dataset of samples, we assessed the population structure, genetic diversity, and demographic history of wolverines with a variety of population genetic analyses. Results According to both nuclear and mitochondrial genetic markers, Eurasian wolverines exhibit substructure, with the most distinct population located in Fennoscandia. The Fennoscandian population has undergone a genetic bottleneck, likely influencing its genetic diversity, which is notably the lowest in Eurasia. Genetic diversity in the rest of Eurasia gradually rises towards the central part of the range and decreases again in the east, although not as significantly as in the west. Main Conclusions This study reveals the population structure of wolverines across Eurasia and provides direction for allocating conservation efforts to sustain a diverse and connected wolverine population. While most of the Eurasian populations seem to be well‐connected and genetically diverse, the Fennoscandian wolverines may need better connectivity to the other Eurasian populations to ensure gene flow and long‐term persistence. Our study further highlights the importance of considering the population genetic structure and diversity of the entire species range when planning management strategies.

Aim: Climatic changes during the Late Pleistocene had major impacts on populations of plant and animal species. Brown bears and other large mammals are likely to have experienced analogous ecological pressures and phylogeographical processes. Here, we address several unresolved issues regarding the Late Pleistocene demography of brown bears: (1) the putative locations of refugia; (2) the direction of migrations across Eurasia and into North America; and (3) parallels with the demographic histories of other wild mammals and modern humans. Location: Eurasia and North America. Methods: We sequenced 110 complete mitochondrial genomes from Eurasian brown bears and combined these with published sequences from 138 brown bears and 33 polar bears. We used a Bayesian approach to obtain a joint estimate of the phylogeny and evolutionary divergence times. The inferred mutation rate was compared with estimates obtained using two additional methods. Results: Bayesian phylogenetic analysis identified seven clades of brown bears, with most individuals belonging to a very large Holarctic clade. Bears from the widespread clade 3a1, which has a distribution from Europe across Asia to Alaska, shared a common ancestor about 45,000 years ago. Main conclusions: We suggest that the Altai-Sayan region and Beringia were important Late Pleistocene refuge areas for brown bears and propose large-scale migration scenarios for bears in Eurasia and to North America. We also argue that brown bears and modern humans experienced a demographic standstill in Beringia before colonizing North America.