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The Arctic region is currently experiencing major modifications in sea ice extent and phenology due to global climate and anthropogenic changes. As Arctic marine ecosystems rely greatly on the presence of sea ice and its seasonal dynamics, these changes could have major impacts on Arctic biota. The ivory gull (Pagophila eburnea) is an endemic Arctic seabird whose populations are declining in Canada and Svalbard. Its affinity for sea ice makes it a good sentinel species of current changes in the high Arctic. We explored the influence of sea-ice-related features and anthropogenic subsidies on the foraging behaviour of ivory gulls during the breeding season. To this end, we analysed the movement of adult ivory gulls in north-east Greenland. We confirmed that ivory gulls use a dual foraging strategy, with birds faithful to their foraging areas at short distances from the colony, but used individual-specific areas during long-distance foraging trips. We highlight that ivory gulls are spatially specialised individuals within a generalist species. We demonstrated that human settlements attracted foraging birds, which shows that human presence in such a remote place may influence the seabird behaviour. Finally, by combining hidden Markov models and resource selection functions, we showed that ivory gulls selected highly concentrated sea ice for foraging during the breeding season. Our study provides key information on the use of space and foraging strategies of ivory gulls during the breeding season, and more broadly, how Arctic seabirds use ice features.

Aim Understanding the drivers of species distribution ranges and population genetic structure can help predict species' responses to global change, while mitigating threats to biodiversity through effective conservation measures. Here, we combined species habitat suitability through time with process-based models and genomic data to investigate the role of landscape features and functional connectivity in shaping the population genetic structure of Northern chamois. Location European Alps. Taxon Northern chamois (Rupicapra rupicapra). Methods Using a model that simulates dispersal and tracks the functional connectivity of populations over dynamic landscapes, we modelled the response of the chamois to climate change from the last glaciation (20,000 years ago) to the present. We reconstructed species habitat suitability and landscape connectivity over time and simulated cumulative divergence of populations as a proxy for genetic differentiation. We then compared simulated divergence with the actual population structure of 449 chamois (with >20 k SNPs) sampled across the Alps. Results We found that Alpine populations of chamois are structured into two main clades, located in the south-western and the eastern Alps. The contact zone between the two lineages is located near the Rhone valley in Switzerland. Simulations reproduced the geographic differentiation of populations observed in the genomic data, and limited dispersal ability and landscape connectivity co-determined the fit of the simulations to data. Main conclusions The contemporary genetic structure of the chamois across the Alps is explained by limited functional connectivity in combination with large rivers or valleys acting as dispersal barriers. The results of our analysis combining simulations with population genomics highlight how biological characteristics, habitat preference and landscapes shape population genetic structure over time and in responses to climate change. We conclude that spatial simulations could be used to improve our understanding of how landscape dynamics, shaped by geological or climatic forces, impact intra- and interspecific diversity., Journal of Biogeography, 49 (10), ISSN:0305-0270, ISSN:1365-2699

DATA AVAILABILITY: Genotypic data are deposited in DRYAD: https://doi.org/10.5061/dryad.j0zpc86gk and the raw reads have been deposited in the SRA (Bioproject: PRJNA81085).; International audience; Genetic data are useful for detecting sudden population declines in species that are difficult to study in the field. Yet this indirect approach has its own drawbacks, including population structure, mutation patterns, and generation overlap. The ivory gull (Pagophila eburnea), a long-lived Arctic seabird, is currently suffering from rapid alteration of its primary habitat (i.e., sea ice), and dramatic climatic events affecting reproduction and recruitment. However, ivory gulls live in remote areas, and it is difficult to assess the population trend of the species across its distribution. Here we present complementary microsatellite- and SNP-based genetic analyses to test a recent bottleneck genetic signal in ivory gulls over a large portion of their distribution. With attention to the potential effects of population structure, mutation patterns, and sample size, we found no significant signatures of population decline worldwide. At a finer scale, we found a significant bottleneck signal at one location in Canada. These results were compared with predictions from simulations showing how generation time and generation overlap can delay and reduce the bottleneck microsatellite heterozygosity excess signal. The consistency of the results obtained with independent methods strongly indicates that the species shows no genetic evidence of an overall decline in population size. However, drawing conclusions related to the species' population trends will require a better understanding of the effect of age structure in long-lived species. In addition, estimates of the effective global population size of ivory gulls were surprisingly low (similar to 1000 ind.), suggesting that the evolutionary potential of the species is not assured.

Seabirds rarely cross major terrestrial barriers during seasonal migration, possibly because they have a limited ability to build up fat stores. For the first time, we tracked two Ivory Gulls with GPS loggers during spring migration from the wintering area in Davis Strait to the breeding colony in north-east Greenland. While one bird migrated in March around the southern tip of Greenland, the other delayed migration until May and crossed the Greenland icecap north of 70°N, covering 1345 km in 29 h. Several aspects of the crossing were noteworthy: the track was remarkably direct, the bird made several stops (totalling 6 h) on the icecap, and the bird increased its flying altitude to nearly 3000 m over West Greenland and > 4000 m over East Greenland.

Delineating population boundaries in anthropogenic landscape is of critical importance for domains of biology that are concerned with the ecology, evolution and conservation of species. This remains particularly difficult for species where there is no obvious demarcation of geographical populations and dispersal patterns are poorly known. This is often the case in amphibian species that reproduce in aquatic habitats but live otherwise in terrestrial habitats. Sampling of such species usually occurs in the aquatic habitat (i.e., breeding sites) but these may represent neither genetically nor demographically distinct populations. Here, we analyzed the genetic structure of a stream-breeding species, the fire salamander (Salamandra salamandra) along a rural-to-urban land use gradient. We used genetic data and Bayesian clustering approaches, which rely on genetic information without assuming predefined populations, to delineate distinctive genetic units along this gradient, and compare genetic diversity between rural and urban areas. The different analytical approaches used partitioned our dataset in slightly different but highly congruent clusters, that included localities which were up to 19 km apart from each other. Genetic breaks occurred at unexpected places while several landscape features reported to act as barriers on gene flow for amphibians did not lead to genetic breaks. Our results emphasize the difficulty to delineate management units in open systems, especially for long-lived species, for which the timespan between the establishment of a barrier and its translation into clear genetic breaks will take longer than in short-lived species.

International audience; Studying the factors determining the sizes of home ranges, based on body mass, feeding style, and sociality level, is a long-standing goal at the intersection of ecology and evolution. Yet, how species-specific life history traits interact with different components of the landscape to shape differences in individual home ranges at within-population level has received much less attention. Here, we review the empirical literature on ungulates to map our knowledge of the relative effects of the key environmental drivers (resource availability, landscape heterogeneity, lethal and non-lethal risks) on the sizes of individual home ranges within a population and assess whether species' characteristics (body mass, diet, and social structure), account for observed variation in the responses of the sizes of individual home ranges to local environmental drivers. Estimating the sizes of home ranges and measuring environmental variables raise a number of methodological issues, which complicate the comparison of empirical studies. Still, from an ecological point of view, we showed that (1) a majority of papers (75%) supported the habitat productivity hypothesis, (2) the support for the influence of landscape heterogeneity was less pervasive across studies, (3) the response of cattle-type to variation in food availability was stronger than the response of moose-type, and (4) species-specific body mass or sociality level had no detectable effect on the level of support to the biological hypotheses. To our surprise, our systematic review revealed a dearth of studies focusing on the ecological drivers of the variation in the sizes of individual home ranges (only about 1% of articles that dealt with home ranges), especially in the later decade where more focus has been devoted to movement. We encourage researchers to continue providing such results with sufficient sample sizes and robust methodologies, as we still need to fully understand the link between environmental drivers and individual space use while accounting for life-history constraints.

International audience; Understanding the consequences of global change for animal movement is a major issue for conservation and management. In particular, habitat fragmentation generates increased densities of linear landscape features that can impede movements. While the influence of these features on animal movements has been intensively investigated, they may also play a key role at broader spatial scales (e.g. the home range scale) as resources, cover from predators/humans, corridors/barriers or landmarks. How space use respond to varying densities of linear features has been mostly overlooked in large herbivores, in contrast to studies done on predators. Focusing on large herbivores should provide additional insights to understand how animals solve the trade-off between energy acquisition and mortality risk. Here, we investigated the role of anthropogenic (roads and tracks) and natural (ridges, valley bottoms and forest edges) linear features on home range features in five large herbivores. We analysed an extensive GPS monitoring database of 710 individuals across nine populations, ranging from mountain areas mostly divided by natural features to lowlands that were highly fragmented by anthropogenic features. Nearly all of the linear features studied were found at the home range periphery, suggesting that large herbivores primarily use them as landmarks to delimit their home range. In contrast, for mountain species, ridges often occurred in the core range, probably related to their functional role in terms of resources and refuge. When the density of linear features was high, they no longer occurred predominantly at the home range periphery, but instead were found across much of the home range. We suggest that, in highly fragmented landscapes, large herbivores are constrained by the costs of memorising the spatial location of key features, and by the requirement for a minimum area to satisfy their vital needs. These patterns were mostly consistent in both males and females and across species, suggesting that linear features have a preponderant influence on how large herbivores perceive and use the landscape.

Many rodents, including most populations of arctic lemmings (genus Dicrostonyx and Lemmus), have cyclic population dynamics. Among the numerous hypotheses which have been proposed and tested to explain this typical characteristic of some terrestrial vertebrate communities, trophic interactions have often been presented as the most likely drivers of these periodic fluctuations. The possible role of parasites has, however, only seldom been assessed. In this study, we genetically measured the prevalence of two endoparasite taxa, eimerians and cestodes, in 372 faecal samples from collared lemmings, over a five year period and across three distant sites in Northeast Greenland. Prevalence of cestodes was low (2.7% over all sites and years) and this taxon was only found at one site (although in 4 out of 5 years) in adult hosts. By contrast, we found high prevalence for eimerians (77.7% over all sites and years), which occurred at all sites, in every year, for both age classes (at the Hochstetter Forland site where both adult and juvenile faeces were collected) and regardless of reproductive and social status inferred from the characteristics of the lemming nests where the samples had been collected. Prevalence of eimerians significantly varied among years (not among sites) and was higher for juvenile than for adult lemmings at the Hochstetter Forland site. However, higher prevalence of eimerians (Pt) was only associated with lower lemming density (Nt) at one of the three sites and we found no delayed density dependence between Nt and Pt+1 to support the parasite hypothesis. Our results show that there is no clear relation between lemming density and eimerian faecal prevalence in Northeast Greenland and hence no evidence that eimerians could be driving the cyclic population dynamics of collared lemmings in this region., Graphical abstract Image 1, Highlights • Prevalence of eimerians and cestodes was measured in collared lemming in Greenland. • Prevalence of cestodes was low (2.7%; one site only) compared to eimerians (78%). • Prevalence of eimerians was higher for juveniles and varied among years. • Prevalence of eimerians was negatively associated with lemming density at one site. • lack of delayed density dependence does not support the parasite hypothesis for lemming cycles.

International audience; Identifying inbreeding depression early in small and declining populations is essential for management and conservation decisions. Correlations between heterozygosity and fitness (HFCs) provide a way to identify inbreeding depression without prior knowledge of kinship among individuals. In Northern Quebec and Labrador, the size of two herds of migratory caribou (Riviere-George, RG and Riviere-aux-Feuilles, RAF) has declined by one to two orders of magnitude in the last three decades. This raises the question of a possible increase in inbreeding depression originating from, and possibly contributing to, the demographic decline in those populations. Here, we tested for the association of genomic inbreeding indices (estimated with 22,073 SNPs) with body mass and survival in 400 caribou sampled in RG and RAF herds between 1996 and 2016. We found no association of individual heterozygosity or inbreeding coefficient with body mass or annual survival. Furthermore, those genomic inbreeding indices remained stable over the period monitored. These results suggest that the rapid and intense demographic decline of the herds did not cause inbreeding depression in those populations. Although we found no evidence for HFCs, if demographic decline continues, it is possible that such inbreeding depression would be triggered.

Aim: In this study, we conduct a quantitative meta-analysis to investigate broad patterns of genetic variation throughout large geographic regions in order to elucidate concordant geographical patterns across species and identify common historical processes to better inform the ‘cryptic refugia’ vs. the traditional ‘southern refugia’ hypothesis debate. Location: Europe Time period: Late Pleistocene to present day. Major taxa studied: small mammals (Rodentia, Eulipotyphla) Methods: A meta-analysis was performed on large scale patterns of genetic diversity for 19 species from 59 papers. For each species, haplotype and nucleotide diversity were calculated using the mitochondrial D-loop and compared to the species range. Results: No consistent patterns were observed between mtDNA diversity indices (nucleotide and haplotype diversity) and any of the indicators of distribution examined (latitude and longitude (max, min, centre, range)). The patterns of genetic diversity observed in all the 19 species studied appear to be species-specific. Main conclusion: In contrast to the traditional southern refugial hypotheses, we found no evidence for a consistent south-north post-glacial expansion. Instead individual species appear to respond to climate oscillations in niche-specific ways. This individual nature of each species’ phylogeographical history indicates a complex web of postglacial recolonisation dynamics across Europe.

Next-generation sequencing technologies have opened a new era of research in genomics. Among these, restriction enzyme-based techniques such as restriction-site associated DNA sequencing (RADseq) or double-digest RAD-sequencing (ddRADseq) are now widely used in many population genomics fields. From DNA sampling to SNP calling, both wet and dry protocols have been discussed in the literature to identify key parameters for an optimal loci reconstruction.The impact of these parameters on downstream analyses and biological results drawn from RADseq or ddRADseq data has however not been fully explored yet. In this study, we tackled this issue by investigating the effects of ddRADseq laboratory (i.e. wet protocol) and bioinformatics (i.e. dry protocol) settings on loci reconstruction and inferred biological signal at two evolutionary scale using two systems: a complex of butterfly species (Coenonympha sp.) and populations of Common beech (Fagus sylvatica).Results suggest an impact of wet protocol parameters (DNA quantity, number of PCR cycles during library preparation) on the number of recovered reads and SNPs, the number of unique alleles and individual heterozygosity. We also found that bioinformatic settings (i.e. clustering and minimum coverage thresholds) impact loci reconstruction (e.g. number of loci, mean coverage) and SNP calling (e.g. number of SNPs, heterozygosity). We however do not detect an impact of parameter settings on three types of analysis performed with ddRADseq data: measure of genetic differentiation, estimation of individual admixture, and demographic inferences. In addition, our work demonstrates the high reproducibility and low rate of genotyping inconsistencies of the ddRADseq protocol.Thus, our study highlights the impact of wet parameters on ddRADseq protocol with strong consequences on experimental success and biological conclusions. Dry parameters affects loci reconstruction and descriptive statistics but not biological conclusion for the two studied systems. Overall, this study illustrates, with others, the relevance of ddRADseq for population and evolutionary genomics at the inter- or intraspecific scales.

International audience; The ongoing decline of sea ice threatens many Arctic taxa, including the ivory gull. Understanding how ice-edges and ice concentrations influence the distribution of the endangered ivory gulls is a prerequisite to the implementation of adequate conservation strategies. From 2007 to 2013, we used satellite transmitters to monitor the movements of 104 ivory gulls originating from Canada, Greenland, Svalbard-Norway and Russia. Although half of the positions were within 41 km of the ice-edge (75% within 100 km), approximately 80% were on relatively highly concentrated sea ice. Ivory gulls used more concentrated sea ice in summer, when close to their high-Arctic breeding ground, than in winter. The best model to explain the distance of the birds from the ice-edge included the ice concentration within approximately 10 km, the month and the distance to the colony. Given the strong links between ivory gull, ice-edge and ice concentration, its conservation status is unlikely to improve in the current context of sea-ice decline which, in turn, will allow anthropogenic activities to develop in regions that are particularly important for the species.

International audience; Sex identification of birds is relevant to studies of evolutionary biology and ecology and is often a central issue for the management and conservation of populations. The Ivory Gull Pagophila eburnea (Phipps, 1774) is a rare high-Arctic species whose main habitat is sea ice throughout the year. This species is currently listed Near Threatened by the IUCN, because populations have drastically declined in part of the species distribution in the recent past. Here we tested molecular sexing methods with different types of samples. Molecular sexing appeared to be very efficient with DNA extracted from muscle, blood, and buccal swabs, both for adults and young chicks. We also performed morphological analyses to characterize sexual size dimorphism in Ivory Gulls sampled in three distinct regions: Greenland, Svalbard, and Russia. Males were larger than females for all morphometric measurements, with little overlap between sexes. Discriminant analysis based on six morphometric variables correctly classified ~95 % of the individuals, even when using two variables only, i.e., gonys height and skull length. Therefore, both molecular and biometric methods are useful for sexing Ivory Gulls. Interestingly, our results indicate a male-biased sex ratio across all Ivory Gull populations studied, including two samples of offspring (67.8 % males).

International audience; Species may cope with rapid habitat changes by distribution shifts or adaptation to new conditions. A common feature of these responses is that they depend on how the process of dispersal connects populations, both demographically and genetically. We analyzed the genetic structure of a near-threatened high-Arctic seabird, the ivory gull (Pagophila eburnea) in order to infer the connectivity among gull colonies. We analyzed 343 individuals sampled from 16 localities across the circumpolar breeding range of ivory gulls, from northern Russia to the Canadian Arctic. To explore the roles of natal and breeding dispersal, we developed a population genetic model to relate dispersal behavior to the observed genetic structure of worldwide ivory gull populations. Our key finding is the striking genetic homogeneity of ivory gulls across their entire distribution range. The lack of population genetic structure found among colonies, in tandem with independent evidence of movement among colonies, suggests that ongoing effective dispersal is occurring across the Arctic Region. Our results contradict the dispersal patterns generally observed in seabirds where species movement capabilities are often not indicative of dispersal patterns. Model predictions show how natal and breeding dispersal may combine to shape the genetic homogeneity among ivory gull colonies separated by up to 2800 km. Although field data will be key to determine the role of dispersal for the demography of local colonies and refine the respective impacts of natal versus breeding dispersal, conservation planning needs to consider ivory gulls as a genetically homogeneous, Arctic-wide metapopulation effectively connected through dispersal.

The extremely high rate of karyotypic evolution that characterizes the shrews of the Sorex araneus group makes this group an exceptionally interesting model for population genetics and evolutionary studies. Here, we attempted to map 46 microsatellite markers at the chromosome arm level using flow-sorted chromosomes from three karyotypically different taxa of the Sorex araneus group (S. granarius and the chromosome races Cordon and Novosibirsk of S. araneus). The most likely localizations were provided for 35 markers, among which 25 were each unambiguously mapped to a single locus on the corresponding chromosomes in the three taxa, covering the three sexual chromosomes (XY1Y2) and nine of the 18 autosomal arms of the S. araneus group. The results provide further evidence for a high degree of conservation in genome organization in the S. araneus group despite the presence of numerous Robertsonian rearrangements. These markers can therefore be used to compare the genetic structure among taxa of the S. araneus group at the chromosome level and to study the role of chromosomal rearrangements in the genetic diversification and speciation process of this group.