Polar bears (PBs) are superbly adapted to the extreme Arctic environment and have become emblematic of the threat to biodiversity from global climate change. Their divergence from the lower-latitude brown bear provides a textbook example of rapid evolution of distinct phenotypes. However, limited mitochondrial and nuclear DNA evidence conflicts in the timing of PB origin as well as placement of the species within versus sister to the brown bear lineage. We gathered extensive genomic sequence data from contemporary polar, brown, and American black bear samples, in addition to a 130,000-to 110,000-y old PB, to examine this problem from a genome-wide perspective. Nuclear DNA markers reflect a species tree consistent with expectation, showing polar and brown bears to be sister species. However, for the enigmatic brown bears native to Alaska's Alexander Archipelago, we estimate that not only their mitochondrial genome, but also 5-10% of their nuclear genome, is most closely related to PBs, indicating ancient admixture between the two species. Explicit admixture analyses are consistent with ancient splits among PBs, brown bears and black bears that were later followed by occasional admixture. We also provide paleodemographic estimates that suggest bear evolution has tracked key climate events, and that PB in particular experienced a prolonged and dramatic decline in its effective population size during the last ca. 500,000 years. We demonstrate that brown bears and PBs have had sufficiently independent evolutionary histories over the last 4-5 million years to leave imprints in the PB nuclear genome that likely are associated with ecological adaptation to the Arctic environment.demographic history | hybridization | mammalian genomics | phylogenetics G enome-scale studies of speciation and admixture have become essential tools in evolutionary analyses of recently diverged lineages. For example, paradigm-shifting genomic research on archaic and anatomically modern humans has identified critical gene flow events during hominin history (1, 2). However, aside from several analyses of domesticated species and their wild relatives (e.g., ref.3), studies that use whole-genome sequencing to investigate admixture in wildlife populations are only now beginning to emerge.The bear family (Ursidae, Mammalia) represents an excellent, largely untapped model for investigating complex speciation and rapid evolution of distinct phenotypes. Although polar bears (PBs; Ursus maritimus) and brown bears (Ursus arctos) are considered separate species, analyses of fossil evidence and mitochondrial sequence data have indicated a recent divergence of PBs from within brown bears (surveyed in ref. 4). For example, phylogenetic analyses of complete mitochondrial genomes, including from a unique 130,000-to 110,000-y-old PB jawbone from Svalbard, Norway, confirmed a particularly close relationship between PB and a genetically isolated population of brown bears from the Admiralty, Baranof, and Chichagof islands in Alaska's Alexander Archipelago (hereaf...

It has been argued that the evolution of plant genome size is principally unidirectional and increasing owing to the varied action of whole-genome duplications (WGDs) and mobile element proliferation1. However, extreme genome size reductions have been reported in the angiosperm family tree. Here we report the sequence of the 82-megabase genome of the carnivorous bladderwort plant Utricularia gibba. Despite its tiny size, the U. gibba genome accommodates a typical number of genes for a plant, with the main difference from other plant genomes arising from a drastic reduction in non-genic DNA. Unexpectedly, we identified at least three rounds of WGD in U. gibba since common ancestry with tomato (Solanum) and grape (Vitis). The compressed architecture of the U. gibba genome indicates that a small fraction of intergenic DNA, with few or no active retrotransposons, is sufficient to regulate and integrate all the processes required for the development and reproduction of a complex organism.

The evolution of diversity in the marine ecosystem is poorly understood, given the relatively high potential for connectivity, especially for highly mobile species such as whales and dolphins. The killer whale (Orcinus orca) has a worldwide distribution, and individual social groups travel over a wide geographic range. Even so, regional populations have been shown to be genetically differentiated, including among different foraging specialists (ecotypes) in sympatry. Given the strong matrifocal social structure of this species together with strong resource specializations, understanding the process of differentiation will require an understanding of the relative importance of both genetic drift and local adaptation. Here we provide a high-resolution analysis based on nuclear single-nucleotide polymorphic markers and inference about differentiation at both neutral loci and those potentially under selection. We find that all population comparisons, within or among foraging ecotypes, show significant differentiation, including populations in parapatry and sympatry. Loci putatively under selection show a different pattern of structure compared to neutral loci and are associated with gene ontology terms reflecting physiologically relevant functions (e.g. related to digestion). The pattern of differentiation for one ecotype in the North Pacific suggests local adaptation and shows some fixed differences among sympatric ecotypes. We suggest that differential habitat use and resource specializations have promoted sufficient isolation to allow differential evolution at neutral and functional loci, but that the process is recent and dependent on both selection and drift.

Human exploitation of marine ecosystems is more recent in oceanic than near shore regions, yet our understanding of human impacts on oceanic food webs is comparatively poor. Few records of species that live beyond the continental shelves date back more than 60 y, and the sheer size of oceanic regions makes their food webs difficult to study, even in modern times. Here, we use stable carbon and nitrogen isotopes to study the foraging history of a generalist, oceanic predator, the Hawaiian petrel (Pterodroma sandwichensis), which ranges broadly in the Pacific from the equator to near the Aleutian Islands. Our isotope records from modern and ancient, radiocarbon-dated bones provide evidence of over 3,000 y of dietary stasis followed by a decline of ca. 1.8‰ in δ 15 N over the past 100 y. Fishery-induced trophic decline is the most likely explanation for this sudden shift, which occurs in genetically distinct populations with disparate foraging locations. Our isotope records also show that coincident with the apparent decline in trophic level, foraging segregation among petrel populations decreased markedly. Because variation in the diet of generalist predators can reflect changing availability of their prey, a foraging shift in wide-ranging Hawaiian petrel populations suggests a relatively rapid change in the composition of oceanic food webs in the Northeast Pacific. Understanding and mitigating widespread shifts in prey availability may be a critical step in the conservation of endangered marine predators such as the Hawaiian petrel.fishing | seabird | stable isotope H istorical baselines are a prerequisite to understanding the extent of human impact on a species or ecosystem. In coastal marine environments, retrospective studies show that habitat destruction and harvest of marine organisms have caused severe modifications, including trophic cascades and the regional loss of entire ecosystems (1, 2). It is difficult to assess the extent to which such impacts extend beyond continental shelves to the oceanic zone, because few chronological data are available for regions far out at sea, and the vast size of these ecosystems makes their food webs difficult to study, even in the present.In the oceanic Northeast Pacific, significant human presence began with the colonization of the Hawaiian Islands, less than 1,000 y ago (3, 4). For centuries afterward, anthropogenic impacts, such as harvesting of marine organisms, were concentrated near the Islands; only in the 20th century, with the advent of industrialized fishing, have a wide variety of oceanic organisms been exploited at a broad spatial scale (5, 6). Our understanding of how human actions such as fishing have affected oceanic food web structure is primarily derived from catch statistics, which show a temporal decline in the abundance of some targeted groups, such as tuna, and in the trophic level of global catch (6-8). However, catch statistics can be strongly affected by shifting technologies and markets, and reflect only the abundance of species that are harveste...