Ancient bears provide insights into Pleistocene ice age refugia in Southeast Alaska.

During the Late Pleistocene, major parts of North America were periodically covered by ice sheets. However, there are still questions about whether ice-free refugia were present in the Alexander Archipelago along the Southeast (SE) Alaska coast during the last glacial maximum (LGM). Numerous subfossils have been recovered from caves in SE Alaska, including American black (Ursus americanus) and brown (U. arctos) bears, which today are found in the Alexander Archipelago but are genetically distinct from mainland bear populations. Hence, these bear species offer an ideal system to investigate long-term occupation, potential refugial survival and lineage turnover. Here, we present genetic analyses based on 99 new complete mitochondrial genomes from ancient and modern brown and black bears spanning the last ~45,000 years. Black bears form two SE Alaskan subclades, one preglacial and another postglacial, that diverged >100,000 years ago. All postglacial ancient brown bears are closely related to modern brown bears in the archipelago, while a single preglacial brown bear is found in a distantly related clade. A hiatus in the bear subfossil record around the LGM and the deep split of their pre- and postglacial subclades fail to support a hypothesis of continuous occupancy in SE Alaska throughout the LGM for either species. Our results are consistent with an absence of refugia along the SE Alaska coast, but indicate that vegetation quickly expanded after deglaciation, allowing bears to recolonize the area after a short-lived LGM peak.

Phylogenomics reveals ancient and contemporary gene flow contributing to the evolutionary history of sea ducks (Tribe Mergini).

Insight into complex evolutionary histories continues to build through broad comparative phylogenomic and population genomic studies. In particular, there is a need to understand the extent and scale that gene flow contributes to standing genomic diversity and the role introgression has played in evolutionary processes such as hybrid speciation. Here, we investigate the evolutionary history of the Mergini tribe (sea ducks) by coupling multi-species comparisons with phylogenomic analyses of thousands of nuclear ddRAD-seq loci, including Z-sex chromosome and autosomal linked loci, and the mitogenome assayed across all extant sea duck species in North America. All sea duck species are strongly structured across all sampled marker types (pair-wise species ΦST > 0.2), with clear genetic assignments of individuals to their respective species, and phylogenetic relationships recapitulate known relationships. Despite strong species integrity, we identify at least 18 putative hybrids; with all but one being late generational backcrosses. Most interesting, we provide the first evidence that an ancestral gene flow event between long-tailed ducks (Clangula hyemalis) and true Eiders (Somateria spp.) not only moved genetic material into the former species, but likely generated a novel species - the Steller's eider (Polysticta stelleri) - via hybrid speciation. Despite generally low contemporary levels of gene flow, we conclude that hybridization has and continues to be an important process that shifts novel genetic variation between species within the tribe Mergini. Finally, we outline methods that permit researchers to contrast genomic patterns of contemporary versus ancestral gene flow when attempting to reconstruct potentially complex evolutionary histories.

Isolation and characterization of microsatellite loci in merlins (Falco columbarius) and cross-species amplification in gyrfalcons (F. rusticolus) and peregrine falcons (F. peregrinus).

Merlins, Falco columbarius, breed throughout temperate and high latitude habitats in Asia, Europe, and North America. Like peregrine falcons, F. peregrinus, merlins underwent population declines during the mid-to-late twentieth century, due to organochlorine-based contamination, and have subsequently recovered, at least in North American populations. To better understand levels of genetic diversity and population structuring in contemporary populations and to assess the impact of the twentieth century decline, we used genomic data archived in public databases and constructed genomic libraries to isolate and characterize a suite of 17 microsatellite markers for use in merlins. We also conducted cross-amplification experiments to determine the markers' utility in peregrine falcons and gyrfalcons, F. rusticolus. These markers provide a valuable addition to marker suites that can be used to determine individual identity and conduct genetic analyses on merlins and congeners.

Recurrent hybridization and recent origin obscure phylogenetic relationships within the 'white-headed' gull (Larus sp.) complex.

Species complexes that have undergone recent radiations are often characterized by extensive allele sharing due to recent ancestry and (or) introgressive hybridization. This can result in discordant evolutionary histories of genes and heterogeneous genomes, making delineating species limits difficult. Here we examine the phylogenetic relationships among a complex group of birds, the white-headed gulls (Aves: Laridae), which offer a unique window into the speciation process due to their recent evolutionary history and propensity to hybridize. Relationships were examined among 17 species (61 populations) using a multilocus approach, including mitochondrial and nuclear intron DNA sequences and microsatellite genotype information. Analyses of microsatellite and intron data resulted in some species-based groupings, although most species were not represented by a single cluster. Considerable allele and haplotype sharing among white-headed gull species was observed; no locus contained a species-specific clade. Despite this, our multilocus approach provided better resolution among some species than previous studies. Interestingly, most clades appear to correspond to geographic locality: our BEAST analysis recovered strong support for a northern European/Icelandic clade, a southern European/Russian clade, and a western North American/canus clade, with weak evidence for a high latitude clade spanning North America and northwestern Europe. This geographical structuring is concordant with behavioral observations of pervasive hybridization in areas of secondary contact. The extent of allele and haplotype sharing indicates that ecological and sexual selection are likely not strong enough to complete reproductive isolation within several species in the white-headed gull complex. This suggests that just a few genes are driving the speciation process.

Combined high rates of alternative breeding strategies unexpectedly found among populations of a solitary nesting raptor.

Social monogamy is the prevalent mating system in birds, but alternative strategies of extra-pair paternity (EPP) and conspecific brood parasitism (CBP) occur in many species. Raptors are virtually absent in discussions of broad taxonomic reviews regarding EPP and CBP likely because these strategies are mostly absent or at low frequency; CBP is unreported in solitary nesting raptors. In contrast, we found high frequencies of EPP (16%-31%) and CBP (15%-26%) nests among three populations of Cooper's Hawks (Accipiter cooperii) across the northern breeding range of this solitary nesting, socially monogamous species. EPP and CBP combined occurred in 42%-46% of all nests among populations and hence unexpectedly were nearly equivalent to proportions of genetically monogamous nests. Select covariates failed to predict presence of EPP and CBP in part because virtually all extra-pair adults were uncaught and likely were floaters. We found no support for the hypothesis that territorial females traded copulations for food to maximize energy intake for increased production. Our unique discoveries enhance knowledge of the extent and diversity of alternative breeding strategies among groups of avian and other animal species.

Where east meets west: Phylogeography of the high Arctic North American brant goose.

Genetic variation in Arctic species is often influenced by vicariance during the Pleistocene, as ice sheets fragmented the landscape and displaced populations to low- and high-latitude refugia. The formation of secondary contact or suture zones during periods of ice sheet retraction has important consequences on genetic diversity by facilitating genetic connectivity between formerly isolated populations. Brant geese (Branta bernicla) are a maritime migratory waterfowl (Anseriformes) species that almost exclusively uses coastal habitats. Within North America, brant geese are characterized by two phenotypically distinct subspecies that utilize disjunct breeding and wintering areas in the northern Pacific and Atlantic. In the Western High Arctic of Canada, brant geese consist of individuals with an intermediate phenotype that are rarely observed nesting outside this region. We examined the genetic structure of brant geese populations from each subspecies and areas consisting of intermediate phenotypes using mitochondrial DNA (mtDNA) control region sequence data and microsatellite loci. We found a strong east-west partition in both marker types consistent with refugial populations. Within subspecies, structure was also observed at mtDNA while microsatellite data suggested the presence of only two distinct genetic clusters. The Western High Arctic (WHA) appears to be a secondary contact zone for both Atlantic and Pacific lineages as mtDNA and nuclear genotypes were assigned to both subspecies, and admixed individuals were observed in this region. The mtDNA sequence data outside WHA suggests no or very restricted intermixing between Atlantic and Pacific wintering populations which is consistent with published banding and telemetry data. Our study indicates that, although brant geese in the WHA are not a genetically distinct lineage, this region may act as a reservoir of genetic diversity and may be an area of high conservation value given the potential of low reproductive output in this species.

Diversity, distribution, and methodological considerations of haemosporidian infections among Galliformes in Alaska.

Using samples spanning 10-degrees of latitude in Alaska, we provide the first comparative assessment of avian haemosporidia distribution of Arctic Alaska with subarctic host populations for four species of grouse and three species of ptarmigan (Galliformes). We found a high overall prevalence for at least one haemospordian genus (88%; N = 351/400), with spruce grouse (Canachites canadensis) showing the highest prevalence (100%; N = 54/54). Haemoproteus and Plasmodium lineages were only observed within grouse, while Leucocytozoon species were found within both grouse and ptarmigan. Further, different Leucocytozoon lineages were obtained from blood and tissue samples from the same individual, potentially due to the differential timing and duration of blood and tissue stages. Using different primer sets, we were able to identify different Leucocytozoon lineages within 55% (N = 44/80) of sequenced individuals, thereby detecting coinfections that may have otherwise gone undetected. The commonly used Haemoproteus/Plasmodium primers amplified Leucocytozoon for 90% (N = 103/115) of the products sequenced, highlighting the potential value of alternate primers to identify intra-genus coinfections and the importance of obtaining sequence information rather than relying solely on PCR amplification to assess parasite diversity. Overall, this dataset provides baseline information on parasite lineage distributions to assess the range expansion associated with climate change into Arctic regions and underscores methodological considerations for future studies.

DETECTION OF SPLENDIDOFILARIA SP. (ONCHOCERCIDAE:SPLENDIDOFILARIINAE) MICROFILARIA WITHIN ALASKAN GROUND-DWELLING BIRDS IN THE GROUSE SUBFAMILY TETRAONINAE USING TAQMAN PROBE-BASED REAL-TIME PCR.

Grouse and ptarmigan (Galliformes) harbor fairly diverse helminth faunas that can impact the host's health, including filarial nematodes in the genus Splendidofilaria. As host and parasite distributions are predicted to shift in response to recent climate change, novel parasites may be introduced into a region and impose additional stressors on bird populations. Limited information is available on the prevalence of filariasis in Alaska galliforms. To date, no molecular surveys have been completed. Past studies relied on examining blood smears or total body necropsies, which are time-consuming and may not detect filarial parasites with low prevalence in hosts. Therefore, we developed a TaqMan probe-based real-time PCR assay targeting the cytochrome c oxidase 1 gene (COI) of Splendidofilaria to decrease processing times and increase sensitivity as well as provide baseline data on the diversity of filariid infections in galliform species in Alaska. We screened a combined total of 708 galliform samples (678 unique individual birds) from different tissues (blood, muscle, and lung) for the presence of filarial DNA across the state of Alaska. Real-time PCR screening revealed an overall prevalence of filarial infection of 9.5% across species: Bonasa umbellus (0%, n = 23), Dendragapus fuliginosus (0%, n = 8), Falcipennis canadensis (26.8%, n = 198), Lagopus lagopus (2.6%, n = 274), Lagopus leucura (0%, n = 23), Lagopus muta (3%, n = 166), and Tympanuchus phasianellus (12.5%, n = 16). We observed microfilarial infections throughout most of Alaska except in Arctic regions and the Aleutian Islands where viable vectors may not be present.

A multigene phylogeny examining evolutionary and ecological relationships in the Australo-papuan wrens of the subfamily Malurinae (Aves).

Nucleotide sequences from four mitochondrial genes and three nuclear introns were used to examine phylogenetic relationships within the Australo-papuan fairy-wrens (Passeriformes: Maluridae: Malurinae). A well-resolved and well-supported phylogenetic hypothesis of all species in the subfamily was generated. The tree contained three clades corresponding to groups with similar plumages previously identified in earlier studies: the "bi-color," "blue," and "chestnut-shouldered" groups. The genus Malurus was not monophyletic -Malurusgrayi formed a clade with two New Guinean genera Sipodotus and Clytomyias. We recommend M. grayi be reclassified into the genus Chenorhamphus Oustalet 1898. One other taxonomic change is recommended based on the large genetic distance between the two subspecies of Chenorhamphus grayi - the elevation of C. g.campbelli to specific status (= C. campbelli). Although the family Maluridae appears to have had its origins in Australia, the DNA data supports a New Guinean origin for the Malurini (Sipodotus, Clytomyias, Chenorhamphus, Malurus).

Do common eiders nest in kin groups? Microgeographic genetic structure in a philopatric sea duck.

We investigated local genetic associations among female Pacific common eiders (Somateria mollissima v-nigrum) nesting in a stochastic Arctic environment within two groups of barrier islands (Simpson Lagoon and Mikkelsen Bay) in the Beaufort Sea, Alaska. Nonrandom genetic associations were observed among nesting females using regional spatial autocorrelation analyses for distance classes up to 1000 m in Simpson Lagoon. Nearest-neighbour analyses identified clusters of genetically related females with positive lr values observed for 0-13% and 0-7% of the comparisons in Simpson Lagoon and Mikkelsen Bay, respectively, across years. These results indicate that a proportion of females are nesting in close proximity to more genetically related individuals, albeit at low frequency. Such kin groupings may form through active association between relatives or through natal philopatry and breeding site fidelity. Eiders nest in close association with driftwood, which is redistributed annually by seasonal storms. Yet, genetic associations were still observed. Microgeographic structure may thus be more attributable to kin association than natal philopatry and site fidelity. However, habitat availability may also influence the level of structure observed. Regional structure was present only within Simpson Lagoon and this island group includes at least three islands with sufficient driftwood for colonies, whereas only one island at Mikkelsen Bay has these features. A long-term demographic study is needed to understand more fully the mechanisms that lead to fine-scale genetic structure observed in common eiders breeding in the Beaufort Sea.