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The Earth's polar regions are low rates of inter‐ and intraspecific diversification. An extreme mammalian example is the Arctic ringed seal (Pusa hispida hispida), which is assumed to be panmictic across its circumpolar Arctic range. Yet, local Inuit communities in Greenland and Canada recognize several regional variants; a finding supported by scientific studies of body size variation. It is however unclear whether this phenotypic variation reflects plasticity, morphs or distinct ecotypes. Here, we combine genomic, biologging and survey data, to document the existence of a unique ringed seal ecotype in the Ilulissat Icefjord (locally 'Kangia'), Greenland; a UNESCO World Heritage site, which is home to the most productive marine‐terminating glacier in the Arctic. Genomic analyses reveal a divergence of Kangia ringed seals from other Arctic ringed seals about 240 kya, followed by secondary contact since the Last Glacial Maximum. Despite ongoing gene flow, multiple genomic regions appear under strong selection in Kangia ringed seals, including candidate genes associated with pelage coloration, growth and osmoregulation, potentially explaining the Kangia seal's phenotypic and behavioural uniqueness. The description of 'hidden' diversity and adaptations in yet another Arctic species merits a reassessment of the evolutionary processes that have shaped Arctic diversity and the traditional view of this region as an evolutionary freezer. Our study highlights the value of indigenous knowledge in guiding science and calls for efforts to identify distinct populations or ecotypes to understand how these might respond differently to environmental change. [ABSTRACT FROM AUTHOR]

We used mitochondrial DNA (mtDNA) gene sequences and nuclear microsatellite loci to investigate the extent and outcome of hybridization between the Black‐billed Gull Chroicocephalus bulleri and the Red‐billed Gull Chroicocephalus novaehollandiae scopulinus in New Zealand. Six of 26 sampled Black‐billed Gulls possessed mtDNA typical of Red‐billed Gulls, but allele frequencies at six polymorphic microsatellites provided little evidence of mixed ancestry expected in very recent hybrids. None of the Red‐billed Gulls sampled from different colonies possessed Black‐billed Gull mtDNA expected in the reciprocal cross, suggesting that hybridization in the two species typically occurs between female Red‐billed Gulls and Black‐billed Gull males. The lack of any hybrid signal in the nuclear loci indicates that there has been extensive backcrossing with Black‐billed Gulls, effectively diluting the Red‐billed Gull nuclear DNA contribution. Divergence of Red‐billed Gulls and Black‐billed Gulls occurred approximately 250 000 years ago, indicating that unsorted ancestral polymorphism is an unlikely alternative to hybridization. Comparing demographic models within an approximate Bayesian computation (ABC) framework, we confirm that the observed patterns cannot result from incomplete lineage sorting. Using an ABC random forest approach, we determined that the most likely model explaining the data is a recent introgression scenario, whereby unidirectional gene flow is re‐established following a period of strict isolation. The ability of Black‐billed and Red‐billed Gulls to successfully interbreed shows that despite significant differentiation (FST > 0.3), there has been insufficient time for the two species to develop complete reproductive isolation. The apparent one‐way transfer of Red‐billed Gull mtDNA into Black‐billed Gulls and extensive backcrossing argues against cytoplasmic–nuclear genome incompatibilities between the two species. We hypothesize that the specific mate recognition system cued on colours of soft parts normally functions to prevent hybridization, but that it can break down under demographic conditions where there is a shortage of available mates and a surplus of females in the Red‐billed Gull population. The high incidence of introgression in Black‐billed Gulls conflicts with field observations that interbreeding is extremely rare. [ABSTRACT FROM AUTHOR]

The three‐spined stickleback (Gasterosteus aculeatus) has repeatedly and independently adapted to freshwater habitats from standing genetic variation (SGV) following colonization from the sea. However, in the Mediterranean Sea G. aculeatus is believed to have gone extinct, and thus the spread of locally adapted alleles between different freshwater populations via the sea since then has been highly unlikely. This is expected to limit parallel evolution, that is the extent to which phylogenetically related alleles can be shared among independently colonized freshwater populations. Using whole genome and 2b‐RAD sequencing data, we compared levels of genetic differentiation and genetic parallelism of 15 Adriatic stickleback populations to 19 Pacific, Atlantic and Caspian populations, where gene flow between freshwater populations across extant marine populations is still possible. Our findings support previous studies suggesting that Adriatic populations are highly differentiated (average FST ≈ 0.45), of low genetic diversity and connectivity, and likely to stem from multiple independent colonizations during the Pleistocene. Linkage disequilibrium network analyses in combination with linear mixed models nevertheless revealed several parallel marine–freshwater differentiated genomic regions, although still not to the extent observed elsewhere in the world. We hypothesize that current levels of genetic parallelism in the Adriatic lineages are a relic of freshwater adaptation from SGV prior to the extinction of marine sticklebacks in the Mediterranean that has persisted despite substantial genetic drift experienced by the Adriatic stickleback isolates. [ABSTRACT FROM AUTHOR]

Oyster reef habitats are critical to coastal biodiversity and their decline has prompted restoration efforts in Australia. Knowledge gaps exist regarding the population structure and diversity of key species in these habitats. This may be critical information for the design of effective restoration programs. Sydney rock oysters (Saccostrea glomerata) are the dominant reef-forming bivalve in eastern Australia. Wild populations of S. glomerata have declined due to overharvesting, disease outbreaks, coastal development and reduced water quality. Here, we use genetic markers identified by genome-wide sequencing to investigate the genetic structure and diversity of wild Sydney rock oysters throughout their distribution in eastern Australia. We examine evidence for past population bottlenecks and spatial genetic structure associated with the East Australian Current. Analysis of 3, 400 neutral single-nucleotide polymorphisms (SNPs) revealed a single population, and an overlap with two other Saccostrea sp. at the northernmost boundary of the distribution. We detected signals of asymmetric gene flow consistent with the direction of the East Australian Current, and spatial structure patterns of limited genetic isolation by distance and spatial autocorrelation in the northern region (which experiences stronger effects of the East Australian Current) but not in the southern region of the distribution. We found no evidence of significant recent bottlenecks, with high effective population size throughout the species' range. This information will provide a baseline against which to assess the impact of restoration projects, and guide strategies for sourcing stock for the enhancement of wild oyster populations. Our results provide a positive outlook for the resilience and adaptive capacity of Sydney rock oysters, and highlight wild populations as valuable resources for aquaculture and restoration initiatives. [ABSTRACT FROM AUTHOR]

The role of geological events and Pleistocene climatic fluctuations as drivers of current patterns of genetic variation in extant species has been a topic of continued interest among evolutionary biologists. Nevertheless, comprehensive studies of widely distributed species are still rare, especially from Asia. Using geographically extensive sampling of many individuals and a large number of nuclear single nucleotide polymorphisms (SNPs), we studied the phylogeography and historical demography of Hyla annectans populations in southern China. Thirty‐five sampled populations were grouped into seven clearly defined genetic clusters that closely match phenotype‐based subspecies classification. These lineages diverged 2.32–5.23 million years ago (Ma), a timing that closely aligns with the rapid and drastic uplifting of the Qinghai‐Tibet Plateau and adjacent southwest China. Demographic analyses and species distribution models indicate that different populations of this species have responded differently to past climatic changes. In the Hengduan Mountains, most populations experienced a bottleneck, whereas the populations located outside of the Hengduan Mountains have gradually declined in size since the end of the last glaciation. In addition, the levels of phenotypic and genetic divergence were strongly correlated across major clades. These results highlight the combined effects of geological events and past climatic fluctuations, as well as natural selection, as drivers of contemporary patterns of genetic and phenotypic variation in a widely distributed anuran in Asia. [ABSTRACT FROM AUTHOR]