dryad_ovda

Genetic data at 15 microsatellite loci, Dall's sheep, Wrangell-St. Elias National Park and Preserve, Alaska, US

Intraspecific evolutionary relationships among peregrine falcons in western North American high latitudes

<div><p>Subspecies relationships within the peregrine falcon (<i>Falco peregrinus</i>) have been long debated because of the polytypic nature of melanin-based plumage characteristics used in subspecies designations and potential differentiation of local subpopulations due to philopatry. In North America, understanding the evolutionary relationships among subspecies may have been further complicated by the introduction of captive bred peregrines originating from non-native stock, as part of recovery efforts associated with mid 20^th century population declines resulting from organochloride pollution. Alaska hosts all three nominal subspecies of North American peregrine falcons–<i>F</i>. <i>p</i>. <i>tundrius</i>, <i>anatum</i>, and <i>pealei</i>–for which distributions in Alaska are broadly associated with nesting locales within Arctic, boreal, and south coastal maritime habitats, respectively. Unlike elsewhere, populations of peregrine falcon in Alaska were not augmented by captive-bred birds during the late 20^th century recovery efforts. Population genetic differentiation analyses of peregrine populations in Alaska, based on sequence data from the mitochondrial DNA control region and fragment data from microsatellite loci, failed to uncover genetic distinction between populations of peregrines occupying Arctic and boreal Alaskan locales. However, the maritime subspecies, <i>pealei</i>, was genetically differentiated from Arctic and boreal populations, and substructured into eastern and western populations. Levels of interpopulational gene flow between <i>anatum</i> and <i>tundrius</i> were generally higher than between <i>pealei</i> and either <i>anatum</i> or <i>tundrius</i>. Estimates based on both marker types revealed gene flow between augmented Canadian populations and unaugmented Alaskan populations. While we make no attempt at formal taxonomic revision, our data suggest that peregrine falcons occupying habitats in Alaska and the North Pacific coast of North America belong to two distinct regional groupings–a coastal grouping (<i>pealei</i>) and a boreal/Arctic grouping (currently <i>anatum</i> and <i>tundrius</i>)–each comprised of discrete populations that are variously intra-regionally connected.</p></div

Hierarchical analyses of variance for hypothesized groupings, based on data from 11 microsatellite loci (top) and mtDNA sequence data (bottom).

<p>Shown are fixation indices and percentage of the total variance explained by the hypothesized regional grouping and significance. The first grouping (Model A) tests the hypothesis that genetic variation is partitioned along currently accepted subspecies designations (e.g., <i>F</i>. <i>p</i>. <i>tundrius</i>, <i>F</i>. <i>p</i>. <i>anatum</i>, and <i>F</i>. <i>p</i>. <i>pealei</i>, with SJI placed with <i>pealei</i>). Bold values are significantly different from zero (<i>P</i> < 0.05 for mtDNA data; <i>P</i> < 0.0045 for microsatellite data).</p

Unrooted reduced median network illustrating relationships among 15 mtDNA control region haplotypes observed among 169 peregrine falcons assayed from northern North American populations.

<p><i>F</i>. <i>p</i>. <i>tundrius</i> populations are indicated in blue, <i>F</i>. <i>p</i>. <i>anatum</i> in yellow, <i>F</i>. <i>p</i>. <i>pealei</i> in red (hatched red for NPAC, SOLID red for the Aleutian Island locales), and the population on SJI in orange. The size of the circle node corresponds to the frequency of each haplotype.</p

Genetic diversity, neutrality and growth indices for 11 microsatellite loci and mitochondrial control region sequence data.

<p>Genetic diversity, neutrality and growth indices for 11 microsatellite loci and mitochondrial control region sequence data.</p

Results of full gene flow model (all parameters allowed to vary independently) illustrating polarity and rates of evolutionary dispersal calculated from mtDNA control region data.

<p>Effective number of female migrants per generation (N_fm) and 95% confidence intervals are listed for each population pair in parentheses, where the columns are the population of origin and the rows are the population destination. Comparisons in bold text indicate the dominant direction of asymmetrical gene flow between population pairs with non-overlapping 95% confidence intervals. For example, the full model estimated asymmetrical gene flow between the SJI and NPAC, with significantly more gene flow from Interior Alaska into SCCOA(N_fm = 6.3 [CI = 1.7–23.6]) than from SCCOA into Interior Alaska (N_fm = 0.2 [CI = 0.0–0.9]). Values in gray cells represent comparisons with overlapping 95% confidence intervals. For example, the full model estimated asymmetrical gene flow between the SJI and NPAC, with significantly more gene flow from Interior Alaska into SCCOA(N_fm = 6.3 [CI = 1.7–23.6]) than from SCCOA into Interior Alaska (N_fm = 0.2 [CI = 0.0–0.9]). Total immigration for each population is shown in the right-most column, and emigration in the bottom row. Total immigration and emigration rates were calculated by totaling mean gene flow values to and from each individual population. Interior Alaska = YUK, POR and TAN, pooled; Aleutians = ANDR, RAT, NEAR and COMM, pooled; Arctic Canada = HB and MCV, pooled; Arctic Alaska = COL.</p

Map of peregrine falcon subspecies distributions in Alaska and Canada, and general sampling locales.

<p>Map of peregrine falcon subspecies distributions in Alaska and Canada, and general sampling locales.</p

Implications of the Circumpolar Genetic Structure of Polar Bears for Their Conservation in a Rapidly Warming Arctic

<div><p>We provide an expansive analysis of polar bear (<i>Ursus maritimus</i>) 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 (<i>U. arctos</i>) 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.</p></div

Assignment of individual polar bears (S11 Table) from their circumpolar range (19 subpopulations) to regional genetic clusters.

<p><b>a</b>. structure<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112021#pone.0112021-Pritchard1" target="_blank">[43]</a> assignment plot for microsatellite signatures (n = 2,899) of polar bears. Y-axis represents proportional membership each of three most-likely groups identified by program structure (Southern Canada [red dots], Canadian Archipelago [blue dots] and the Polar Basin [yellow dots]). Note, based on subsequent analysis (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112021#pone.0112021.s002" target="_blank">S2c Fig</a>., <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112021#pone.0112021.s012" target="_blank">S6 Table</a>) we discuss the Polar Basin cluster as two groups: the Eastern Polar Basin Western Polar Basin clusters. Individuals are organized (each represented by a single vertical line) along the X-axis according to subpopulation: East Greenland (EG), Barents Sea (BS); Kara Sea (KS); Laptev Sea (LP); Chukchi Sea (CS); Southern Beaufort Sea (SB); Northern Beaufort Sea (NB); Viscount Melville (VM); M'Clintock Channel (MC); Gulf of Boothia (GB); Lancaster Sound (LS); Norwegian Bay (NW); Kane Basin (KB); Baffin Bay (BB); Davis Strait (DS); Foxe Basin (FB); Western Hudson Bay (WH) and Southern Hudson Bay (SH). Individuals within each subpopulation are arranged according membership to one of the three clusters. <b>b</b>. Geographical locations of (n = 2,650) samples in the three genetic clusters.</p

Recent directional gene flow (ca. 3–10 generations) calculated on the basis of allelic frequencies (number of migrants, <i>m</i>) among polar bear clusters.

<p>Data generated using the program bayesass<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112021#pone.0112021-Wilson1" target="_blank">[47]</a>, examining gene flow relationships between the four clusters of polar bears (Southern Canada (SC; red), Canadian Archipelago (CA; blue), Eastern Polar Basin (EP; yellow) and Western Polar Basin (WP; green)), identified by program structure analysis of microsatellite data. Arrow widths represent only directional gene flow values that are significantly different from zero (no migration) and from the value for migration in the opposite direction.</p