We provide an expansive analysis of polar bear (Ursus maritimus) circumpolar genetic variation during the last two decades of decline in their sea-ice habitat. We sought to evaluate whether their genetic diversity and structure have changed over this period of habitat decline, how their current genetic patterns compare with past patterns, and how genetic demography changed with ancient fluctuations in climate. Characterizing their circumpolar genetic structure using microsatellite data, we defined four clusters that largely correspond to current ecological and oceanographic factors: Eastern Polar Basin, Western Polar Basin, Canadian Archipelago and Southern Canada. We document evidence for recent (ca. last 1–3 generations) directional gene flow from Southern Canada and the Eastern Polar Basin towards the Canadian Archipelago, an area hypothesized to be a future refugium for polar bears as climate-induced habitat decline continues. Our data provide empirical evidence in support of this hypothesis. The direction of current gene flow differs from earlier patterns of gene flow in the Holocene. From analyses of mitochondrial DNA, the Canadian Archipelago cluster and the Barents Sea subpopulation within the Eastern Polar Basin cluster did not show signals of population expansion, suggesting these areas may have served also as past interglacial refugia. Mismatch analyses of mitochondrial DNA data from polar and the paraphyletic brown bear (U. arctos) uncovered offset signals in timing of population expansion between the two species, that are attributed to differential demographic responses to past climate cycling. Mitogenomic structure of polar bears was shallow and developed recently, in contrast to the multiple clades of brown bears. We found no genetic signatures of recent hybridization between the species in our large, circumpolar sample, suggesting that recently observed hybrids represent localized events. Documenting changes in subpopulation connectivity will allow polar nations to proactively adjust conservation actions to continuing decline in sea-ice habitat.

Theory predicts that parallel evolution should be common when the number of beneficial mutations is limited by selective constraints on protein structure. However, confirmation is scarce in natural populations. Here we studied the major haemoglobin genes of eight Andean duck lineages and compared them to 115 other waterfowl species, including the bar-headed goose (Anser indicus) and Abyssinian blue-winged goose (Cyanochen cyanopterus), two additional species living at high altitude. One to five amino acid replacements were significantly overrepresented or derived in each highland population, and parallel substitutions were more common than in simulated sequences evolved under a neutral model. Two substitutions evolved in parallel in the alpha A subunit of two (Ala-alpha 8) and five (Thr-alpha 77) taxa, and five identical beta A subunit substitutions were observed in two (Ser-beta 4, Glu-beta 94, Met-beta 133) or three (Ser-beta 13, Ser-beta 116) taxa. Substitutions at adjacent sites within the same functional protein region were also observed. Five such replacements were in exterior, solvent-accessible positions on the A helix and AB corner of the alpha A subunit. Five others were in close proximity to inositolpentaphosphate binding sites, and two pairs of independent replacements occurred at two different alpha(1)beta(1) intersubunit contacts. More than half of the substitutions in highland lineages resulted in the acquisition of serine or threonine (18 gains vs. 2 losses), both of which possess a hydroxyl group that can hydrogen bond to a variety of polar substrates. The patterns of parallel evolution observed in these waterfowl suggest that adaptation to high-altitude hypoxia has resulted from selection on unique but overlapping sets of one to five amino acid substitutions in each lineage.

Aim Deciphering the complex colonization history of island archipelagos is greatly facilitated by comprehensive phylogenies. In this study we investigate the phylogeny and biogeography of the insular reed-warblers (genus Acrocephalus) of the tropical Pacific Ocean, from Australia to eastern Polynesia.Location Oceania.Methods We used sequences of mitochondrial DNA (cytochrome b, ND2 and ATP8 genes) to infer the colonization patterns of reed-warblers endemic to Pacific islands and Australia. We sampled all known taxa of Acrocephalus in the Pacific except A. luscinius nijoi, for which no sample was available. Most taxa were represented by toe-pad samples from museum specimens collected in the 19th and 20th centuries. With a few exceptions, several specimens per taxon were sequenced independently in two institutions (Smithsonian Institution and Natural History Museum of Geneva).Results Our data indicate that Pacific reed-warblers do not form a monophyletic group, because A. luscinius luscinius from Guam falls outside the main Pacific radiation. The remaining Pacific taxa are divided into two clades: one clade includes all the reed-warblers from Micronesia (except Guam) and Australia, and two Polynesian taxa from the Line Islands and the southern Marquesas; the other clade includes all remaining Polynesian taxa. The taxa endemic to three archipelagos (Mariana, Marquesas and Society islands) are polyphyletic, suggesting several independent colonizations. Main conclusions Our results provide evidence for a complex pattern of colonization of the Pacific by reed-warblers. Calibration analyses suggest that reed-warbler lineages are much younger than the ages of the islands they occupy. Several remote archipelagos were colonized independently more than once. Consequently, we infer that the colonization of reed-warblers in the Pacific did not follow a regular, stepping-stone-like pattern. The phylogeny also suggests a previously undetected case of reverse colonization (from island to continent) for the Australian lineage and indicates that A. luscinius, as currently defined, is not monophyletic. We discuss the supertramp strategy of reed-warblers in the Pacific and show that, although Pacific reed-warblers meet some of the supertramp criteria in their aptitude for colonizing remote archipelagos, their life history characteristics do not fit the model.

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We compared levels of genetic diversity and isolation among peregrine falcons Falco peregrinus from two South Pacific island complexes (Fiji and Vanuatu: F. p. nesiotes), relative to other island and mainland populations. Fragment data from 12 microsatellite loci and sequence information from the control region of the mitochondrial DNA indicated levels of genetic variation in the South Pacific populations were lower than other island and mainland populations. Indeed, diversity varied from extremely low (Vanuatu) to completely absent (Fiji). We find little support for a hypothesis that populations on Fiji or Vanuatu were colonized via Australia. The complete lack of polymorphism in peregrine falcons of Fiji is remarkable, and to our knowledge has not been observed in a natural avian population. This lack of polymorphism, and the inability to test for decrease in polymorphism using museum samples, precludes testing whether the lack of genetic diversity in the population on Fiji is due to a recent bottleneck, or sustained isolation over evolutionary time. Increased fertility in eggs of Fiji peregrines upon outbreeding with males from other areas is consistent with inbreeding depression within a population typified by heterozygote deficiency.

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The major histocompatibility complex (MHC), which harbours the most polymorphic vertebrate genes, plays a critical role in the host–pathogen coevolutionary arms race. However, the extent to which MHC diversity determines disease susceptibility and long‐term persistence of populations is currently under debate, as recent studies have demonstrated that low MHC variability does not necessarily hamper population viability. However, these studies typically assayed small and decimated populations in species with restricted distribution, thereby making inferences about the evolutionary potential of these populations difficult. Here, we show that MHC impoverishment has not constrained the ecological radiation and flourishing of falcons (Aves: Falconidae) worldwide. We found two remarkably different patterns of MHC variation within the genus Falco. Whereas MHC variation in kestrels (the basal group within the genus) is very high, falcons exhibit ancestrally low intra‐ and interspecific MHC variability. This pattern is not due to the inadvertent survey of paralogous genes or pseudogenes. Further, patterns of variation in mitochondrial or other nuclear genes do not indicate a generalized low level of genome‐wide variability among falcons. Although a relative contribution of genetic drift cannot be completely ruled out, we propose the falcons went through an evolutionary transition, driven and maintained by natural selection, from primarily highly variable towards low polymorphic and slow‐evolving MHC genes with a very specific immune function. This study highlights that the importance of MHC diversity cannot be generalized among vertebrates, and hints at the evolution of compensatory immune mechanisms in falcons to cope with emerging and continuously evolving pathogens.

Aim Glacial refugia during the Pleistocene had major impacts on the levels and spatial apportionment of genetic diversity of species in northern latitude ecosystems. We characterized patterns of population subdivision, and tested hypotheses associated with locations of potential Pleistocene refugia and the relative contribution of these refugia to the post-glacial colonization of North America and Scandinavia by common eiders (Somateria mollissima). Specifically, we evaluated localities hypothesized as ice-free areas or glacial refugia for other Arctic vertebrates, including Beringia, the High Arctic Canadian Archipelago, Newfoundland Bank, Spitsbergen Bank and north-west Norway.Location Alaska, Canada, Norway and Sweden.Methods Molecular data from 12 microsatellite loci, the mitochondrial DNA (mtDNA) control region, and two nuclear introns were collected and analysed for 15 populations of common eiders (n = 716) breeding throughout North America and Scandinavia. Population genetic structure, historical population fluctuations and gene flow were inferred using F-statistics, analyses of molecular variance, and multilocus coalescent analyses. ResultsSignificant inter-population variation in allelic and haplotypic frequencies were observed (nuclear DNA F ST = 0.004-0.290; mtDNA F ST = 0.051-0.927). Whereas spatial differentiation in nuclear genes was concordant with subspecific designations, geographic proximity was more predictive of inter-population variance in mitochondrial DNA haplotype frequency. Inferences of historical population demography were consistent with restriction of common eiders to four geographic areas during the Last Glacial Maximum: Belcher Islands, Newfoundland Bank, northern Alaska and Svalbard. Three of these areas coincide with previously identified glacial refugia: Newfoundland Bank, Beringia and Spitsbergen Bank. Gene-flow and clustering analyses indicated that the Beringian refugium contributed little to common eider post-glacial colonization of North America, whereas Canadian, Scandinavian and southern Alaskan post-glacial colonization is likely to have occurred in a stepwise fashion from the same glacial refugium.Main conclusions Concordance of proposed glacial refugia used by common eiders and other Arctic species indicates that Arctic and subarctic refugia were important reservoirs of genetic diversity during the Pleistocene. Furthermore, suture zones identified at MacKenzie River, western Alaska/Aleutians and Scandinavia coincide with those identified for other Arctic vertebrates, suggesting that these regions were strong geographic barriers limiting dispersal from Pleistocene refugia.