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.

Adaptive introgression of the beta-globin cluster in two Andean waterfowl.

Introgression of beneficial alleles has emerged as an important avenue for genetic adaptation in both plant and animal populations. In vertebrates, adaptation to hypoxic high-altitude environments involves the coordination of multiple molecular and cellular mechanisms, including selection on the hypoxia-inducible factor (HIF) pathway and the blood-O2 transport protein hemoglobin (Hb). In two Andean duck species, a striking DNA sequence similarity reflecting identity by descent is present across the ~20 kb ß-globin cluster including both embryonic (HBE) and adult (HBB) paralogs, though it was yet untested whether this is due to independent parallel evolution or adaptive introgression. In this study, we find that identical amino acid substitutions in the ß-globin cluster that increase Hb-O2 affinity have likely resulted from historical interbreeding between high-altitude populations of two different distantly-related species. We examined the direction of introgression and discovered that the species with a deeper mtDNA divergence that colonized high altitude earlier in history (Anas flavirostris) transferred adaptive genetic variation to the species with a shallower divergence (A. georgica) that likely colonized high altitude more recently possibly following a range shift into a novel environment. As a consequence, the species that received these ß-globin variants through hybridization might have adapted to hypoxic conditions in the high-altitude environment more quickly through acquiring beneficial alleles from the standing, hybrid-origin variation, leading to faster evolution.

Convergent Evolution of Hemoglobin Function in High-Altitude Andean Waterfowl Involves Limited Parallelism at the Molecular Sequence Level.

A fundamental question in evolutionary genetics concerns the extent to which adaptive phenotypic convergence is attributable to convergent or parallel changes at the molecular sequence level. Here we report a comparative analysis of hemoglobin (Hb) function in eight phylogenetically replicated pairs of high- and low-altitude waterfowl taxa to test for convergence in the oxygenation properties of Hb, and to assess the extent to which convergence in biochemical phenotype is attributable to repeated amino acid replacements. Functional experiments on native Hb variants and protein engineering experiments based on site-directed mutagenesis revealed the phenotypic effects of specific amino acid replacements that were responsible for convergent increases in Hb-O2 affinity in multiple high-altitude taxa. In six of the eight taxon pairs, high-altitude taxa evolved derived increases in Hb-O2 affinity that were caused by a combination of unique replacements, parallel replacements (involving identical-by-state variants with independent mutational origins in different lineages), and collateral replacements (involving shared, identical-by-descent variants derived via introgressive hybridization). In genome scans of nucleotide differentiation involving high- and low-altitude populations of three separate species, function-altering amino acid polymorphisms in the globin genes emerged as highly significant outliers, providing independent evidence for adaptive divergence in Hb function. The experimental results demonstrate that convergent changes in protein function can occur through multiple historical paths, and can involve multiple possible mutations. Most cases of convergence in Hb function did not involve parallel substitutions and most parallel substitutions did not affect Hb-O2 affinity, indicating that the repeatability of phenotypic evolution does not require parallelism at the molecular level.

Becoming pure: identifying generational classes of admixed individuals within lesser and greater scaup populations.

Estimating the frequency of hybridization is important to understand its evolutionary consequences and its effects on conservation efforts. In this study, we examined the extent of hybridization in two sister species of ducks that hybridize. We used mitochondrial control region sequences and 3589 double-digest restriction-associated DNA sequences (ddRADseq) to identify admixture between wild lesser scaup (Aythya affinis) and greater scaup (A. marila). Among 111 individuals, we found one introgressed mitochondrial DNA haplotype in lesser scaup and four in greater scaup. Likewise, based on the site-frequency spectrum from autosomal DNA, gene flow was asymmetrical, with higher rates from lesser into greater scaup. However, using ddRADseq nuclear DNA, all individuals were assigned to their respective species with >0.95 posterior assignment probability. To examine the power for detecting admixture, we simulated a breeding experiment in which empirical data were used to create F1 hybrids and nine generations (F2-F10) of backcrossing. F1 hybrids and F2, F3 and most F4 backcrosses were clearly distinguishable from pure individuals, but evidence of admixed histories was effectively lost after the fourth generation. Thus, we conclude that low interspecific assignment probabilities (0.011-0.043) for two lesser and nineteen greater scaup were consistent with admixed histories beyond the F3 generation. These results indicate that the propensity of these species to hybridize in the wild is low and largely asymmetric. When applied to species-specific cases, our approach offers powerful utility for examining concerns of hybridization in conservation efforts, especially for determining the generational time until admixed histories are effectively lost through backcrossing.

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.

Mito-nuclear discord in six congeneric lineages of Holarctic ducks (genus Anas).

Many species have Holarctic distributions that extend across Europe, Asia and North America. Most genetics research on these species has examined only mitochondrial (mt) DNA, which has revealed wide variance in divergence between Old World (OW) and New World (NW) populations, ranging from shallow, unstructured genealogies to deeply divergent lineages. In this study, we sequenced 20 nuclear introns to test for concordant patterns of OW-NW differentiation between mtDNA and nuclear (nu) DNA for six lineages of Holarctic ducks (genus Anas). Genetic differentiation for both marker types varied widely among these lineages (idiosyncratic population histories), but mtDNA and nuDNA divergence within lineages was not significantly correlated. Moreover, compared with the association between mtDNA and nuDNA divergence observed among different species, OW-NW nuDNA differentiation was generally lower than mtDNA divergence, at least for lineages with deeply divergent mtDNA. Furthermore, coalescent estimates indicated significantly higher rates of gene flow for nuDNA than mtDNA for four of the six lineages. Thus, Holarctic ducks show prominent mito-nuclear discord between OW and NW populations, and we reject differences in sorting rates as the sole cause of the within-species discord. Male-mediated intercontinental gene flow is likely a leading contributor to this discord, although selection could also cause increased mtDNA divergence relative to weak nuDNA differentiation. The population genetics of these ducks contribute to growing evidence that mtDNA can be an unreliable indicator of stage of speciation and that more holistic approaches are needed for species delimitation.

High-altitude adaptation is accompanied by strong signatures of purifying selection in the mitochondrial genomes of three Andean waterfowl.

Evidence from a variety of organisms points to convergent evolution on the mitochondria associated with a physiological response to oxygen deprivation or temperature stress, including mechanisms for high-altitude adaptation. Here, we examine whether demography and/or selection explains standing mitogenome nucleotide diversity in high-altitude adapted populations of three Andean waterfowl species: yellow-billed pintail (Anas georgica), speckled teal (Anas flavirostris), and cinnamon teal (Spatula cyanoptera). We compared a total of 60 mitogenomes from each of these three duck species (n = 20 per species) across low and high altitudes and tested whether part(s) or all of the mitogenome exhibited expected signatures of purifying selection within the high-altitude populations of these species. Historical effective population sizes (Ne) were inferred to be similar between high- and low-altitude populations of each species, suggesting that selection rather than genetic drift best explains the reduced genetic variation found in mitochondrial genes of high-altitude populations compared to low-altitude populations of the same species. Specifically, we provide evidence that establishment of these three Andean waterfowl species in the high-altitude environment, coincided at least in part with a persistent pattern of negative purifying selection acting on oxidative phosphorylation (OXPHOS) function of the mitochondria. Our results further reveal that the extent of gene-specific purifying selection has been greatest in the speckled teal, the species with the longest history of high-altitude occupancy.

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.

Coached practice using ERCP mechanical simulator improves trainees' ERCP performance: a randomized controlled trial.

BACKGROUND AND STUDY AIMS: Preliminary data suggested that simulation practice using an endoscopic retrograde cholangiopancreatography (ERCP) mechanical simulator (EMS) improved trainees' skill. The aims of the current study were to confirm the impact of coached EMS practice at the beginning of ERCP training and to investigate whether subsequent uncoached EMS practice provides additional benefit. METHODS: Trainees entering ERCP training in 2008 (n = 8) and 2009 (n = 8) at two referral medical centers were randomized to receive a coached EMS practice either with (2009) or without (2008) subsequent uncoached practices or only routine training (controls). The outcome measures were successful deep biliary cannulation by the trainee and overall performance score as rated by blinded trainers, during the subsequent 3 months of clinical practice. RESULTS: Trainees undergoing single and multiple EMS practices were more likely than controls to achieve successful biliary cannulation (single: adjusted odds ratio [aOR] 2.89, 95 % confidence interval [CI] 2.21 - 3.80 [P < 0.001]; multiple: 3.09, 95 %CI 1.13 - 8.46 [P = 0.028]) and to have superior overall performance scores (aOR 3.29, 95 %CI 1.37 - 7.91 [P = 0.008] and 6.92, 95 %CI 3.77 - 12.69 [P < 0.001], respectively). The benefit of single and multiple EMS practices on overall performance score remained significant after adjustment for success or failure of deep biliary cannulation (aOR 2.98, 95 %CI 1.38 - 6.43 [P = 0.005] and 6.09, 95 %CI 2.40 - 15.45 [P < 0.001], respectively). The benefits of single vs. multiple EMS practices were not statistically different. CONCLUSIONS: Coached simulation using EMS improved novice trainees' success of biliary cannulation and overall ERCP performance. Additional uncoached practices did not appear to provide further benefit. Trainees should undergo a coached EMS practice at the beginning of ERCP training.

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.

Multilocus coalescent analysis of haemoglobin differentiation between low- and high-altitude populations of crested ducks (Lophonetta specularioides).

Hypoxia is a key factor determining survival, and haemoglobins are targets of selection in species native to high-altitude regions. We studied population genetic structure and evaluated evidence for local adaptation in the crested duck (Lophonetta specularioides). Differentiation, gene flow and time since divergence between highland and lowland populations were assessed for three haemoglobin genes (α(A) , α(D) , ß(A) ) and compared to seven reference loci (six autosomal introns and mtDNA). Four derived amino acid replacements were found in the globin genes that had elevated Φ(ST) values between the Andean highlands and Patagonian lowlands. A single ß(A) -globin polymorphism at a site known to influence O(2) affinity was fixed for different alleles in the two populations, whereas three α(A) - and α(D) -globin polymorphisms exhibited high heterozygosity in the highlands but not in the lowlands. Coalescent analyses supported restricted gene flow for haemoglobin alleles and mitochondrial DNA but nonzero gene flow for the introns. Simulating genetic data under a drift-migration model of selective neutrality, the ß(A) -globin fell outside the 95% confidence limit of simulated data, suggesting that directional selection is maintaining different variants in the contrasting elevational environments, thereby restricting migration of ß(A) -globin alleles. The α(A) - and α(D) -globins, by contrast, did not differ from the simulated values, suggesting that variants in these genes are either selectively neutral, or that the effects of selection could not be differentiated from background levels of population structure and linkage disequilibrium. This study illustrates the combined effects of selection and population history on inferring levels of population divergence for a species distributed across an altitudinal gradient in which selection for hypoxia resistance has likely played an important role.

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.

Gene flow in the face of countervailing selection: adaptation to high-altitude hypoxia in the betaA hemoglobin subunit of yellow-billed pintails in the Andes.

When populations become locally adapted to contrasting environments, alleles that have high fitness in only one environment may be quickly eliminated in populations adapted to other environments, such that gene flow is partly restricted. The stronger the selection, the more rapidly immigrant alleles of lower fitness will be eliminated from the population. However, gene flow may continue to occur at unlinked loci, and adaptive divergence can proceed in the face of countervailing gene flow if selection is strong relative to migration (s > m). We studied the population genetics of the major hemoglobin genes in yellow-billed pintails (Anas georgica) experiencing contrasting partial pressures of oxygen in the Andes of South America. High gene flow and weak population subdivision were evident at seven putatively neutral loci in different chromosomal linkage groups. In contrast, amino acid replacements (Ser-beta13, Ser-beta116, and Met-beta133) in the betaA hemoglobin subunit segregated by elevation between lowland and highland populations with significantly elevated F(ST). Migration rates for the betaA subunit alleles were approximately 17-24 times smaller than for five unlinked reference loci, the alphaA hemoglobin subunit (which lacks amino acid replacements) and the mitochondrial DNA control region. The betaA subunit alleles of yellow-billed pintails were half as likely to be transferred downslope, from the highlands to the lowlands, than in the opposite direction upslope. We hypothesize that migration between the lowlands and highlands is restricted by local adaptation, and the betaA hemoglobin subunit is a likely target of selection related to high-altitude hypoxia; however, gene flow may be sufficiently high to retard divergence at most unlinked loci. Individuals homozygous for lowland alleles may have relatively little difficulty dispersing to the highlands initially but may experience long-term fitness reduction. Individuals homozygous for highland genotypes, in contrast, would be predicted to have difficulty dispersing to the lowlands if their hemoglobin alleles confer high oxygen affinity, predicted to result in chronic erythrocytosis at low elevation. Heterozygous individuals may have a dispersal advantage if their hemoglobin has a wider range of function due to the presence of multiple protein isoforms with a mixture of different oxygen affinities.

Lousy grouse: Comparing evolutionary patterns in Alaska galliform lice to understand host evolution and host-parasite interactions.

Understanding both sides of host-parasite relationships can provide more complete insights into host and parasite biology in natural systems. For example, phylogenetic and population genetic comparisons between a group of hosts and their closely associated parasites can reveal patterns of host dispersal, interspecies interactions, and population structure that might not be evident from host data alone. These comparisons are also useful for understanding factors that drive host-parasite coevolutionary patterns (e.g., codivergence or host switching) over different periods of time. However, few studies have compared the evolutionary histories between multiple groups of parasites from the same group of hosts at a regional geographic scale. Here, we used genomic data to compare phylogenomic and population genomic patterns of Alaska ptarmigan and grouse species (Aves: Tetraoninae) and two genera of their associated feather lice: Lagopoecus and Goniodes. We used whole-genome sequencing to obtain hundreds of genes and thousands of single-nucleotide polymorphisms (SNPs) for the lice and double-digest restriction-associated DNA sequences to obtain SNPs from Alaska populations of two species of ptarmigan. We found that both genera of lice have some codivergence with their galliform hosts, but these relationships are primarily characterized by host switching and phylogenetic incongruence. Population structure was also uncorrelated between the hosts and lice. These patterns suggest that grouse, and ptarmigan in particular, share habitats and have likely had historical and ongoing dispersal within Alaska. However, the two genera of lice also have sufficient dissimilarities in the relationships with their hosts to suggest there are other factors, such as differences in louse dispersal ability, that shape the evolutionary patterns with their hosts.

Signatures of high-altitude adaptation in the major hemoglobin of five species of andean dabbling ducks.

Hypoxia is one of the most important factors affecting survival at high altitude, and the major hemoglobin protein is a likely target of selection. We compared population genetic structure in the alphaA and betaA hemoglobin subunits (HBA2 and HBB) of five paired lowland and highland populations of Andean dabbling ducks to unlinked reference loci. In the hemoglobin genes, parallel amino acid replacements were overrepresented in highland lineages, and one to five derived substitutions occurred at external solvent-accessible positions on the alpha and beta subunits, at alpha(1)beta(1) intersubunit contacts, or in close proximity to inositolpentaphosphate (IPP) binding sites. Coalescent analyses incorporating the stochasticity of drift and mutation indicated that hemoglobin alleles were less likely to be transferred between highland and lowland populations than unlinked alleles at five other loci. Amino acid replacements that were overrepresented in the highlands were rarely found within lowland populations, suggesting that alleles segregating at high frequency in the highlands may be maladaptive in the lowlands and vice versa. Most highland populations are probably nonmigratory and locally adapted to the Altiplano, but gene flow for several species may be sufficiently high to retard divergence at unlinked loci. Heterozygosity was elevated in the alphaA or betaA subunits of highland populations exhibiting high gene flow between the southern lowlands and the highlands and in highland species that disperse seasonally downslope to midelevation environments from the central Andean plateau. However, elevated heterozygosity occurred more frequently in the alphaA subunit but not simultaneously in both subunits, suggesting that selection may be more constrained by epistasis in the betaA subunit. Concordant patterns among multiple species with different evolutionary histories and depths of historical divergence and gene flow suggest that the major hemoglobin genes of these five dabbling duck species have evolved adaptively in response to high-altitude hypoxia in the Andes.

Gelatin sponge insertion into tympanostomy tubes: an in-vitro study to evaluate postoperative obstruction.

OBJECTIVE: To analyze the efficacy of gelatin sponge insertion into lumens of tympanostomy tubes to prevent obstruction in the presence of blood. STUDY DESIGN: In vitro model. METHODS: Absorbable gelatin sponge wicks were placed in the lumen of Ultrasil Collar Button ventilation tubes and Shepherd Grommet ventilation tubes. One half of each group was covered with blood, the other left untreated. Each tube was treated with ofloxacin solution three times daily for seven days. After treatment, the tubes were inspected. Reinspection was performed after brief suctioning. Numerical scores were given based on degree of obstruction. RESULTS: A statistically significant difference in degree of obstruction (P < 0.0001) was seen between all tubes with wicks alone versus those with blood added. After re-evaluation, there remained a statistically significant difference between tubes with wicks alone and tubes with wicks and blood (P < 0.0001). CONCLUSIONS: Gelatin sponge insertion does not prevent, and may in fact, enhance, obstruction of pressure equalization tube lumens in the presence of blood.

Coast to coast: High genomic connectivity in North American scoters.

Dispersal shapes demographic processes and therefore is fundamental to understanding biological, ecological, and evolutionary processes acting within populations. However, assessing population connectivity in scoters (Melanitta sp.) is challenging as these species have large spatial distributions that span remote landscapes, have varying nesting distributions (disjunct vs. continuous), exhibit unknown levels of dispersal, and vary in the timing of the formation of pair bonds (winter vs. fall/spring migration) that may influence the distribution of genetic diversity. Here, we used double-digest restriction-associated DNA sequence (ddRAD) and microsatellite genotype data to assess population structure within the three North American species of scoter (black scoter, M. americana; white-winged scoter, M. deglandi; surf scoter, M. perspicillata), and between their European congeners (common scoter, M. nigra; velvet scoter, M. fusca). We uncovered no or weak genomic structure (ddRAD Φ ST < 0.019; microsatellite F ST < 0.004) within North America but high levels of structure among European congeners (ddRAD Φ ST > 0.155, microsatellite F ST > 0.086). The pattern of limited genomic structure within North America is shared with other sea duck species and is often attributed to male-biased dispersal. Further, migratory tendencies (east vs. west) of female surf and white-winged scoters in central Canada are known to vary across years, providing additional opportunities for intracontinental dispersal and a mechanism for the maintenance of genomic connectivity across North America. In contrast, the black scoter had relatively elevated levels of divergence between Alaska and Atlantic sites and a second genetic cluster found in Alaska at ddRAD loci was concordant with its disjunct breeding distribution suggestive of a dispersal barrier (behavioral or physical). Although scoter populations appear to be connected through a dispersal network, a small percentage (<4%) of ddRAD loci had elevated divergence which may be useful in linking areas (nesting, molting, staging, and wintering) throughout the annual cycle.

Flyway structure in the circumpolar greater white-fronted goose.

Dispersal and migratory behavior are influential factors in determining how genetic diversity is distributed across the landscape. In migratory species, genetic structure can be promoted via several mechanisms including fidelity to distinct migratory routes. Particularly within North America, waterfowl management units have been delineated according to distinct longitudinal migratory flyways supported by banding data and other direct evidence. The greater white-fronted goose (Anser albifrons) is a migratory waterfowl species with a largely circumpolar distribution consisting of up to six subspecies roughly corresponding to phenotypic variation. We examined the rangewide population genetic structure of greater white-fronted geese using mtDNA control region sequence data and microsatellite loci from 23 locales across North America and Eurasia. We found significant differentiation in mtDNA between sampling locales with flyway delineation explaining a significant portion of the observed genetic variation (~12%). This is concordant with band recovery data which shows little interflyway or intercontinental movements. However, microsatellite loci revealed little genetic structure suggesting a panmictic population across most of the Arctic. As with many high-latitude species, Beringia appears to have played a role in the diversification of this species. A common Beringian origin of North America and Asian populations and a recent divergence could at least partly explain the general lack of structure at nuclear markers. Further, our results do not provide strong support for the various taxonomic proposals for this species except for supporting the distinctness of two isolated breeding populations within Cook Inlet, Alaska (A. a. elgasi) and Greenland (A. a. flavirostris), consistent with their subspecies status.

Landscape genetics identifies streams and drainage infrastructure as dispersal corridors for an endangered wetland bird.

Anthropogenic alterations to landscape structure and composition can have significant impacts on biodiversity, potentially leading to species extinctions. Population-level impacts of landscape change are mediated by animal behaviors, in particular dispersal behavior. Little is known about the dispersal habits of rails (Rallidae) due to their cryptic behavior and tendency to occupy densely vegetated habitats. The effects of landscape structure on the movement behavior of waterbirds in general are poorly studied due to their reputation for having high dispersal abilities. We used a landscape genetic approach to test hypotheses of landscape effects on dispersal behavior of the Hawaiian gallinule (Gallinula galeata sandvicensis), an endangered subspecies endemic to the Hawaiian Islands. We created a suite of alternative resistance surfaces representing biologically plausible a priori hypotheses of how gallinules might navigate the landscape matrix and ranked these surfaces by their ability to explain observed patterns in genetic distance among 12 populations on the island of O`ahu. We modeled effective distance among wetland locations on all surfaces using both cumulative least-cost-path and resistance-distance approaches and evaluated relative model performance using Mantel tests, a causal modeling approach, and the mixed-model maximum-likelihood population-effects framework. Across all genetic markers, simulation methods, and model comparison metrics, surfaces that treated linear water features like streams, ditches, and canals as corridors for gallinule movement outperformed all other models. This is the first landscape genetic study on the movement behavior of any waterbird species to our knowledge. Our results indicate that lotic water features, including drainage infrastructure previously thought to be of minimal habitat value, contribute to habitat connectivity in this listed subspecies.

Migration-Selection Balance Drives Genetic Differentiation in Genes Associated with High-Altitude Function in the Speckled Teal (Anas flavirostris) in the Andes.

Local adaptation frequently occurs across populations as a result of migration-selection balance between divergent selective pressures and gene flow associated with life in heterogeneous landscapes. Studying the effects of selection and gene flow on the adaptation process can be achieved in systems that have recently colonized extreme environments. This study utilizes an endemic South American duck species, the speckled teal (Anas flavirostris), which has both high- and low-altitude populations. High-altitude speckled teal (A. f. oxyptera) are locally adapted to the Andean environment and mostly allopatric from low-altitude birds (A. f. flavirostris); however, there is occasional gene flow across altitudinal gradients. In this study, we used next-generation sequencing to explore genetic patterns associated with high-altitude adaptation in speckled teal populations, as well as the extent to which the balance between selection and migration have affected genetic architecture. We identified a set of loci with allele frequencies strongly correlated with altitude, including those involved in the insulin-like signaling pathway, bone morphogenesis, oxidative phosphorylation, responders to hypoxia-induced DNA damage, and feedback loops to the hypoxia-inducible factor pathway. These same outlier loci were found to have depressed gene flow estimates, as well as being highly concentrated on the Z-chromosome. Our results suggest a multifactorial response to life at high altitudes through an array of interconnected pathways that are likely under positive selection and whose genetic components seem to be providing an effective genomic barrier to interbreeding, potentially functioning as an avenue for population divergence and speciation.