AMOVA results.

<p>* = p < 0.05</p><p>** = p < 0.01.</p><p>Pairwise ϕ_ST values for the four breeding grounds [lower triangular matrix] and their significance values [upper triangular matrix]. Abbreviations: GS = southern Gulf, NL = Newfoundland and Labrador ice front, GS = Greenland Sea, WS = White Sea, NWA = GS and NL, NEA = GS and WS.</p

Calibration of intra-specific divergences among Harp Seal clades.

<p>(a) ML clock-corrected estimates of the molecular distances to the MRCA for four hominines with established divergence dates < 1 MYA follow a power curve relationship T = 1.886 x (d)^1.21 (r² = 0.9983), where T = KYA and d = linearized ML substitution rates (semi-log plot). Sources of homine mtDNA genomes are given in Methods: San2 is in the L1 haplogroup that is the basal divergence from other extant <i>Homo</i> [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134207#pone.0134207.ref001" target="_blank">1</a>], M vs N is the divergence between haplotypes in the U and A haplogroups, respectively [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134207#pone.0134207.ref009" target="_blank">9</a>]. (b) Dates of the MRCA of the major intra-specific <i>Pagophilus</i> clades estimated from the same power curve (linear plot).</p

Kolmogorov-Smirnov tests of differences among cumulative pairwise distributions.

<p>* = p < 0.05</p><p>** = p < 0.01</p><p>*** = p < 0.001.</p><p><b><i>D</i></b> values for pairwise comparisons among four breeding populations. <b><i>D</i></b> expresses the maximum difference between distributions weighted for sample size [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134207#pone.0134207.ref060" target="_blank">60</a>]. Significance was evaluated with the critical value <b><i>D</i></b>_{<b><i>a</i></b>} calculated by two alternative criteria, either the total number of pairwise comparisons in each samples ((<i>n</i>)(<i>n</i>-1)/2), or the sample size of each samples (<i>n</i>) (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134207#sec015" target="_blank">Materials and Methods</a>). The table gives the value of <b><i>D</i></b> and its significance based on the first criterion. None of the <b><i>D</i></b> values were significant by the second criterion.</p

Breeding and whelping areas of Harp Seals (<i>Pagophilus groenlandicus</i>) and the origins of samples used in this study (from [22]).

<p>The Dominion of Newfoundland was a separate nation until union with Canada in 1949, and its postage stamps often depicted wildlife, including Harp Seals. The stamp shows a “White Coat”, a neonatal seal prior to weaning at ca. 12 days of age.</p

Dispersal tree length decreases as phylogeography becomes more structured.

<p>Consider a dichotomously-branching mitogenomic tree of 16 individuals distributed among four geographic areas (red, orange, green, and blue), with one population (blue) designated as ancestral. (A) The most highly structured model, in which each of the three alternative areas corresponds to a separate clade originating by a single dispersal event, requires just L = 3 events. (B) The least structured model, in which clades are distributed uniformly among areas such that there is no correspondence between genetic relationship and population, requires L = 12 events. [Model drawn with delayed events, and terminal red / orange and green / blue pairs: alternative event distributions are possible]. Intermediate structures include: (C) Separate clades in the red and orange areas and in the green and blue areas, but uniform geographic distribution within those two clades (L = 9), (D) as in (C) but with minimal exchange between blue and green areas (L = 7), and (E) as in (C) but with complete separation of blue and green (L = 6). The models are drawn with delayed dispersal events: other event distributions are possible. Models C, D, & E are analogous respectively to a two-population Harp Seal model, a three-population mixed model with a uniform single Northwest Atlantic population and limited exchange between the Greenland and White Seas, and a pure three-population model with separate Greenland and White Sea populations (cf. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134207#pone.0134207.g008" target="_blank">Fig 8</a>).</p

AMOVA within and among breeding grounds of Harp Seals: alternative island models.

<p>* = p < 0.05</p><p>** = p < 0.01.</p><p>Four models were evaluated (I-IV), as described in Methods.</p

Results of Monte Carlo simulation of alternative phylogeographic models of Harp Seal dispersal.

<p>* = p < 0.05.</p><p>Abbreviations as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134207#pone.0134207.t002" target="_blank">Table 2</a>. For each model in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134207#pone.0134207.g008" target="_blank">Fig 8</a>, the table gives the dispersal cost (length L) required by the topology of the observed tree (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134207#pone.0134207.g002" target="_blank">Fig 2</a>), the frequency of that L class among 10,000 randomizations, the frequency of the tail of the distribution that includes that class, and the maximum, mode, and observed minimum among the randomizations.</p

Linearized maximum likelihood tree for mtDNA genome phylogeography of Harp Seals.

<p>(a) Rates of substitution per site are estimated from the clock model in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134207#pone.0134207.g005" target="_blank">Fig 5A</a>; confidence intervals (±95%) are indicated by bars. (b) Correlation of Holarctic temperature and glacial histories with times of clade origins. The temperature trend over the last 200 Kyr is taken from the Vostok ice core data, which are tied to analogous data from Greenland [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134207#pone.0134207.ref004" target="_blank">4</a>].</p

Bayes analysis of mtDNA genome phylogeography of Harp Seals.

<p>Tree rooted as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134207#pone.0134207.g002" target="_blank">Fig 2</a>. Nodes supported by posterior probabilities of p ≥ 0.95 are shown in black, those supported by 0.50 ≤ p < 0.95 are shown in red. All groups identified by > 95% of bootstraps in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134207#pone.0134207.g002" target="_blank">Fig 2</a> are supported with posterior probabilities p ~ 1.00, as are relationships within A. Differences in relationships within subgroup A4 are not strongly differentiated by bootstrap or posterior probabilities.</p

Mitochondrial DNA genome phylogeography of 53 Harp Seals.

<p>Neighbor-joining tree rooted with respect to the next most closely related species, the Ribbon Seal (<i>Histriophoca fasciata</i>) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134207#pone.0134207.ref025" target="_blank">25</a>]. Clusters supported by >67% of 10,000 bootstrap replications are indicated by numbers below the corresponding vertex; support >95% is indicated in red. Origins of samples from the four breeding areas (including separate Gulf and Front samples) are indicated by colored circles. The six primary groups / clades and their inter-relationships ([<b>F</b>+ [[<b>E</b> + <b>D</b>] + [<b>C</b> + [<b>B</b>+<b>A</b>]]]]) are all supported by >97% of NJ and MP bootstraps.</p