Population Structure of Humpback Whales from Their Breeding Grounds in the South Atlantic and Indian Oceans

Although humpback whales are among the best-studied of the large whales, population boundaries in the Southern Hemisphere (SH) have remained largely untested. We assess population structure of SH humpback whales using 1,527 samples collected from whales at fourteen sampling sites within the Southwestern and Southeastern Atlantic, the Southwestern Indian Ocean, and Northern Indian Ocean (Breeding Stocks A, B, C and X, respectively). Evaluation of mtDNA population structure and migration rates was carried out under different statistical frameworks. Using all genetic evidence, the results suggest significant degrees of population structure between all ocean basins, with the Southwestern and Northern Indian Ocean most differentiated from each other. Effective migration rates were highest between the Southeastern Atlantic and the Southwestern Indian Ocean, followed by rates within the Southeastern Atlantic, and the lowest between the Southwestern and Northern Indian Ocean. At finer scales, very low gene flow was detected between the two neighbouring sub-regions in the Southeastern Atlantic, compared to high gene flow for whales within the Southwestern Indian Ocean. Our genetic results support the current management designations proposed by the International Whaling Commission of Breeding Stocks A, B, C, and X as four strongly structured populations. The population structure patterns found in this study are likely to have been influenced by a combination of long-term maternally directed fidelity of migratory destinations, along with other ecological and oceanographic features in the region

Chi-Square test for differences in haplotype frequencies for four breeding Regions (A, B, C and X) of Southern Hemisphere humpback whales.

<p>All strata based on sex of animals are shown. The P-value is the probability of a more extreme variance component or F-value than that observed, in comparison to a null distribution of these values on 1,000 random permutations of the data matrix. Significant values (p<0.05) are highlighted in bold.</p

AMOVA results for breeding areas A, B, C and X of Southern Hemisphere humpback whales using molecular distances (Φst) and haplotype frequencies (Fst).

<p>The AMOVAs (or ‘Global’ value) are shown for the entire dataset (All samples), animals of known sex from molecular sexing (M+F), females and males. The P-value is the probability of a more extreme variance component or F-value than that observed, in comparison to a null distribution of these values on 5,000 random permutations of the data matrix. Significant values (p<0.05) are highlighted in bold.</p

Pairwise measures of genetic divergence in various populations of Southern Hemisphere humpback whales, using all samples (Table 4), males + females (Table 5), females only (Table 6) and males only (Table 7).

<p>Pairwise Φst and Fst values are above and below the diagonal, respectively. Significant values are highlighted in bold.</p

Pairwise measures of genetic divergence in various populations of Southern Hemisphere humpback whales, using all samples (Table 4), males + females (Table 5), females only (Table 6) and males only (Table 7).

<p>Pairwise Φst and Fst values are above and below the diagonal, respectively. Significant values are highlighted in bold.</p

Sample location, size, mtDNA control region variability for breeding grounds and migratory corridors of Southern Hemisphere humpback whales.

<p>Region C1 groups samples from Mozambique (<i>M</i>) and Eastern South Africa (<i>ESA</i>), and Region C3 groups samples from Antongil Bay (<i>AB</i>) and Southern Madagascar (<i>SM</i>). Haplotype (h) and nucleotide (π) diversities, as well as their standard deviations are provided. Numbers of males and females do not always add up to the sample size, given that the dataset contains individuals sex. Duplicate samples were removed from the analysis.</p

Pairwise measures of genetic divergence in various populations of Southern Hemisphere humpback whales, using all samples (Table 4), males + females (Table 5), females only (Table 6) and males only (Table 7).

<p>Pairwise Φst and Fst values are above and below the diagonal, respectively. Significant values are highlighted in bold.</p

Pairwise measures of genetic divergence in various populations of Southern Hemisphere humpback whales, using all samples (Table 4), males + females (Table 5), females only (Table 6) and males only (Table 7).

<p>Pairwise Φst and Fst values are above and below the diagonal, respectively. Significant values are highlighted in bold.</p

Estimated number of migrants per generation (Nem) exchanged between neighbouring Southern Hemisphere humpback whale Breeding Regions, as estimated using the program MIGRATE.

<p>Magnitude and directionality are shown by reading the first row (ie A+) in the first place, and then matching the appropriate cell with regions listed in leftmost column. (*) Comparisons between Breeding Regions A or B vs. X, and A vs. C are omitted, as they are not neighbouring Breeding Stocks. Sub populations in Breeding Regions C1 and C3 were used for the MIGRATE analysis.</p

IWC boundaries for humpback whale breeding grounds and feeding areas in the South Atlantic and Indian Oceans.

<p>Sampling locations are indicated in parentheses and referred to in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007318#pone-0007318-t001" target="_blank">Table 1</a>.</p