Circumpolar Diversity and Geographic Differentiation of mtDNA in the Critically Endangered Antarctic Blue Whale (Balaenoptera musculus intermedia)

To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work.\ud This is the publisher’s final pdf. The published article is copyrighted by the Public Library of Science and can be found at: http://www.plosone.org/home.action.The Antarctic blue whale (Balaenoptera musculus intermedia) was hunted to near extinction between 1904 and 1972, declining from an estimated initial abundance of more than 250,000 to fewer than 400. Here, we describe mtDNA control region diversity and geographic differentiation in the surviving population of the Antarctic blue whale, using 218 biopsy samples collected under the auspices of the International Whaling Commission (IWC) during research cruises from 1990-2009. Microsatellite genotypes and mtDNA sequences identified 166 individuals among the 218 samples and documented movement of a small number of individuals, including a female that traveled at least 6,650 km or 131 degrees longitude over four years. mtDNA sequences from the 166 individuals were aligned with published sequences from 17 additional individuals, resolving 52 unique haplotypes from a consensus length of 410 bp. From this minimum census, a rarefaction analysis predicted that only 72 haplotypes (95% CL, 64, 86) have survived in the contemporary population of Antarctic blue whales. However, haplotype diversity was relatively high (0.968 +/- 0.004), perhaps as a result of the longevity of blue whales and the relatively recent timing of the bottleneck. Despite the potential for circumpolar dispersal, we found significant differentiation in mtDNA diversity (F-ST = 0.032, p<0.005) and microsatellite alleles (F-ST = 0.005, p<0.05) among the six Antarctic Areas historically used by the IWC for management of blue whales

Circumpolar Diversity and Geographic Differentiation of mtDNA in the Critically Endangered Antarctic Blue Whale (Balaenoptera musculus intermedia)

The Antarctic blue whale (Balaenoptera musculus intermedia) was hunted to near extinction between 1904 and 1972, declining from an estimated initial abundance of more than 250,000 to fewer than 400. Here, we describe mtDNA control region diversity and geographic differentiation in the surviving population of the Antarctic blue whale, using 218 biopsy samples collected under the auspices of the International Whaling Commission (IWC) during research cruises from 1990-2009. Microsatellite genotypes and mtDNA sequences identified 166 individuals among the 218 samples and documented movement of a small number of individuals, including a female that traveled at least 6,650 km or 131 degrees longitude over four years. mtDNA sequences from the 166 individuals were aligned with published sequences from 17 additional individuals, resolving 52 unique haplotypes from a consensus length of 410 bp. From this minimum census, a rarefaction analysis predicted that only 72 haplotypes (95% CL, 64, 86) have survived in the contemporary population of Antarctic blue whales. However, haplotype diversity was relatively high (0.968 +/- 0.004), perhaps as a result of the longevity of blue whales and the relatively recent timing of the bottleneck. Despite the potential for circumpolar dispersal, we found significant differentiation in mtDNA diversity (F-ST = 0.032, p<0.005) and microsatellite alleles (F-ST = 0.005, p<0.05) among the six Antarctic Areas historically used by the IWC for management of blue whales

The inference of gray whale (Eschrichtius robustus) historical population attributes from whole-genome sequences

Commercial whaling caused extensive demographic declines in many great whale species, including gray whales that were extirpated from the Atlantic Ocean and dramatically reduced in the Pacific Ocean. The Eastern Pacific gray whale has recovered since the 1982 ban on commercial whaling, but the Western Pacific gray whale-once considered possibly extinct-consists of only about 200 individuals and is considered critically endangered by some international authorities. Herein, we use whole-genome sequencing to investigate the demographic history of gray whales from the Pacific and use environmental niche modelling to make predictions about future gene flow.Our sequencing efforts and habitat niche modelling indicate that: i) western gray whale effective population sizes have declined since the last glacial maximum; ii) contemporary gray whale genomes, both eastern and western, harbor less autosomal nucleotide diversity than most other marine mammals and megafauna; iii) the extent of inbreeding, as measured by autozygosity, is greater in the Western Pacific than in the Eastern Pacific populations; and iv) future climate change is expected to open new migratory routes for gray whales.Our results indicate that gray whale genomes contain low nucleotide diversity and have been subject to both historical and recent inbreeding. Population sizes over the last million years likely peaked about 25,000 years before present and have declined since then. Our niche modelling suggests that novel migratory routes may develop within the next century and if so this could help retain overall genetic diversity, which is essential for adaption and successful recovery in light of global environmental change and past exploitation

Sremba_AntBmu_410_52

Alignment of 52 Antarctic blue whale mtDNA control region haplotypes described from 410 bp in Sremba et al. 2012. File contains key for lab ID codes and GenBank codes for each haplotype not described in LeDuc et al. 2007

Pairwise differentiation (F_ST italicized below and φ_ST above) of mtDNA control region sequences among three populations of blue whales in the Southern Hemisphere: the Antarctic blue whale of the Southern Ocean, as presented in this study, and the pygmy blue whales of the Indian Ocean and South-east Pacific, as reported by LeDuc et al. [15].

<p>Sample sizes are listed for each region. Significance values were based on a permutation test in Arlequin.</p

Summary of microsatellite loci used to identify likely replicate samples in Antarctic blue whale samples, with test for Hardy Weinberg equilibrium (HWE) and test of differentiation.

<p>Locus name, number of samples genotyped, number of identified alleles (k), probability of identity (p(ID)), number of individuals genotyped, probability of Hardy Weinberg equilibrium (** notes loci out of HWE after a sequential Bonferonni correction), F_ST and significance (p-value) and original reference (Ref.) are listed for each loci. Overall F_ST and p values for 7 and 16 loci are listed. Asterisks (*) denote microsatellite loci included in LeDuc et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032579#pone.0032579-LeDuc1" target="_blank">[15]</a>.</p

Locations of biopsy samples collected from Antarctic blue whales during IDCR/SOWER cruises from 1990 and 2009.

<p>Solid lines demarcate IWC management Areas (I–VI). Dashed line depicts inferred movement of an Antarctic blue whale between Areas over an elapsed time of 4 years based on genotyped recapture locations (Z-51452).</p

Frequencies of mtDNA haplotypes for individual Antarctic blue whales spanning IWC management Areas I–VI (n = 184) and genetic sex information if available (f = female, m = male).

<p>Asterisks (*) denote haplotypes found in JARPA samples included from LeDuc et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032579#pone.0032579-LeDuc1" target="_blank">[15]</a>.</p

Pairwise differentiation (F_ST italicized below and φ_ST above) of Antarctic blue whale mtDNA haplotypes in IWC management Areas I–VI.

<p>Sample sizes are listed for each IWC management Area and p-values are listed under the φ_ST or F_ST values. Upper p-values were based on 5,000 permutations of the data matrix and lower p-values were based on an exact test of differentiation (for F_ST only) as implemented in Arlequin. F_ST and p-values are bolded if significant at p<0.05. Significant pairwise comparisons after a sequential Bonferroni correction are noted with an asterisk (*). Area I is reported for clarity but sample size was not considered sufficient for statistical tests.</p

Number of biopsy samples of Antarctic blue whales collected between 1990 and 2009 (n = 218) on IDCR/SOWER cruises.

<p>Frequency of samples collected in each Area and year are listed as well as within Area (I–VI) and yearly totals. ‘Year’ is referenced to the end-date of the annual surveys, e.g., 1990 refers to the 1989/1990 austral summer. Zeros indicate Areas that were surveyed but in which no biopsy samples were collected that year.</p