Fig 1.
Distribution (light blue) of beluga whales, Delphinapterus leucas, in the North Pacific Ocean.
The ten major nearshore concentration areas during the summer months are highlighted (dark blue). These areas along with a small resident group of beluga whales in the Gulf of Alaska are numbered according to Table 1.
Fig 2.
Migration routes and sampling locations of beluga whales from the major summer concentration areas in the Bering, Chukchi and Beaufort Seas and from the Gulf of Alaska.
Summering and wintering areas, and migration routes were inferred from a combination of satellite telemetry, aerial and shore based sightings, and Traditional Ecological Knowledge (TEK). Sampling sites are indicated by yellow circles and in the case of migration by triangles.
Table 1.
Sample sizes of beluga whales from fifteen geographic strata in the north Pacific: A resident population (Cook Inlet) and a separate small resident group (Yakutat Bay) in the Gulf of Alaska, six summering areas in the Bering, Chukchi, and Beaufort Seas, three summering areas in the Okhotsk Sea, and four locations along the northbound spring migration routes.
Some of these strata have previously been identified as demographically separate management stocks based on mtDNA. While almost all samples were screened for microsatellites sample numbers for these nuclear markers indicate only those samples that yielded genotypes at six or more loci.
Table 2.
Macrogeographic patterns of population differentiation in beluga whales in the north Pacific Ocean: (A) within mitochondrial DNA and (B) across eight microsatellite loci. Values for the frequency-based statistic, Fst, are below the diagonal, values for the distance-based statistic, Φst (mtDNA) and Rst (nDNA), are above the diagonal. All P-values from homogeneity tests, based on 50,000 permutations, were significant at p<0.0001. n denotes sample size.
Table 3.
Population differentiation within mitochondrial DNA (A) and across eight microsatellite loci (B) in Pacific beluga whales. Values for the frequency-based statistic, Fst, are below the diagonal. Values for the distance-based statistic, Φst (mtDNA) and Rst (nDNA), are above the diagonal. Corresponding p-values for homogeneity tests, based on 50,000 permutations, are represented by the following shading patterns: dark grey: p≤0.01, light grey: 0.01<p≤0.05, unshaded: p>0.05. Only strata with a sample size of n≥10 are reported, and the Beaufort Sea stratum is the Mackenzie and Point Hope strata combined (see text). Reported estimates of heterogeneity comprise the roughly two decade period from 1988–2010. See Table A and B in S7 Table for more details on temporal patterns of heterogeneity.
Fig 3.
Summary plots generated in Clumpak of model-based cluster analysis of population structure in Pacific beluga whales using STRUCTURE 2.3.4.
The major modes for K = 4 to 6 (based on five separate runs for each value of K) are presented for the analysis using prior sample group information and no admixture which revealed K = 5 clusters as the most likely (see panel 2). However, in a number of analyses K = 6 was the most or second-most likely resulting in the separation of Anadyr into a discrete cluster (see panel 3). Each genotyped individual is represented by a vertical line with estimated membership, Q, in each cluster denoted by different colors. The analysis was based on using all individuals (n = 1032) scored at 6 or more loci (nloci≥6).
Fig 4.
Mantel tests of the correlation between genetic differentiation (Fst) and geographic distance among summering and wintering grounds of beluga whales in the Bering, Chukchi and Beaufort Seas, for both (A) mitochondrial DNA and (B) microsatellite markers. Test p values are based on 10,000 permutations of the distance data.
Fig 5.
The likely population of origin of beluga whales on spring migration sampled at four locations in the Bering, Chukchi and Beaufort Seas.
Individual assignments are represented as the relative height of stacked bars to either of two baseline populations, the eastern Beaufort Sea (blue) or eastern Chukchi Sea (red) for mtDNA (dark shading) and nDNA (light shading). A: Maximun Likelihood assignments in Whichrun. B: Baysian assignments using prior sampling information and admixture models in Structure 2.3.4. C: Mixed-stock assignments in Bayes. Only individuals with complete mtDNA-nDNA profiles are shown. See Table 4 for more details.
Table 4.
The likely population of origin of beluga whales on spring migration sampled at four locations in the Bering, Chukchi and Beaufort Seas.
Maximum likelihood assignments to two candidate populations, the eastern Chukchi Sea (Kasegaluk Lagoon) and the eastern Beaufort Sea (Mackenzie-Amundsen), were conducted in Whichrun and are reported both as likelihood ratios (P(n)/P(max)) and the Log of these ratios (LOD) for each individual. Bayesian assignments, using prior sample group information (i.e., LOCPRIOR models), were made using STRUCTURE and are reported as the estimated ancestry, Q, in Clusters 1 (Chukchi) and 2 (Beaufort). Assignments of individual migrants were also estimated using the stock-mixture method in BAYES, summarized here as the proportion of times, P, an individual was assigned to each baseline population.
Fig 6.
The probability distribution of population proportions of groups of beluga whales sampled on northbound migration in spring.
Stock-mixture analysis was conducted in Bayes with the eastern Beaufort Sea (blue) and the eastern Chukchi Sea (red) as baseline populations and the migrating groups as the potential ‘mixtures’. The ordinate axis indicates the number of runs.
Table 5.
Genetic differentiation (Fst) between post-dispersal age cohorts of beluga whales from the eastern Chukchi (Kasegaluk Lagoon) and the Beaufort Seas (Mackenzie-Amundsen).
Pairwise estimates for mtDNA are below the diagonal and for microsatellites above the diagonal. Analyses were conducted on all adults (A) and on all large, and presumably older, adults (B). Sample sizes (n) for the mtDNA comparisons are in column 2 and for microsatellites in row 3. Estimates of age were based on the number of growth layer groups (GLGs) in sectioned teeth.
Fig 7.
The proportion of pairwise genealogical relationships estimated for beluga whales sampled within and between years across two decades near Kasegaluk Lagoon, Alaska.
Maximum likelihood estimates of four relationship categories were estimated from genotypic data using the program ml-relate. The stacked bars represent the proportions of distantly/unrelated individuals to closely related individuals (i.e., parent-offspring, full-sib and half-sib or equivalent) for a subset of the 20-year data set comprising the first three years (1988, 1993, 1994) and the last three years (2005, 2006, 2007).
Fig 8.
Test of differences in mean relatedness () among beluga whales within a single year compared to
between whales from two different years for the same summering ground using coancestry.
The graph depicts results for Kasegaluk Lagoon 1988 compared to 1988–2007 using the ML estimator TrioML of Wang (2007). If the observed difference (black line) falls outside the 90% (dotted lines), 95% (dashed lines), and 99% (green solid lines) confidence intervals from the bootstrap analysis distribution the difference is adjudged to be significant.