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

Gray whale SNP genotypes

The data include SNP genotypes from gray whales for genic regions

Data from: Genetic data reveal mixed-stock aggregations of gray whales in the North Pacific Ocean

Gray whales (Eschrichtius robustus) in the Western Pacific are critically endangered whereas in the Eastern Pacific they are relatively common. Holocene environmental changes and commercial whaling reduced their numbers, but gray whales in the Eastern Pacific now outnumber their Western counterparts by more than 100-fold. Herein, we investigate the genetic diversity and population structure within the species using a panel of genic SNPs. Results indicate the gray whale gene pool is differentiated into two substocks containing similar levels of genetic diversity, and that both our Eastern and Western geographic samples represent mixed-stock aggregations. Ongoing or future gene flow between the stocks may conserve genetic diversity overall but admixture has implications for conservation of the critically endangered Western gray whale

Influence of Holocene habitat availability on Pacific gray whale (<i>Eschrichtius robustus</i>) population dynamics as inferred from whole mitochondrial genome sequences and environmental niche modeling

Abstract Environmental changes since the Pleistocene and commercial whaling in the last few centuries have drastically reduced many whale populations, including gray whales in the North Pacific. Herein we use complete mitogenome sequences from 74 individuals to evaluate gray whale phylogeography and historical demography, then use environmental niche modeling to assess how habitat availability has changed through time for Pacific gray whales. We identify a large degree of haplotype sharing between gray whales sampled in Russian and Mexican waters, coupled with very limited matrilineal population structure. Confirming previous studies, our environmental niche models showed a decrease in available habitat during the Last Glacial Maximum, but we find no genetic signals of recent population declines in mitochondrial genomes despite both sustained habitat loss and a commercial whaling bottleneck. Our results illustrate the complex dynamics of baleen whale biogeography since the Holocene as well as the difficulty in detecting recent demographic bottlenecks from mitochondrial DNA sequences.</jats:p

Additional file 1: of The inference of gray whale (Eschrichtius robustus) historical population attributes from whole-genome sequences

Table S1. Information on raw reads filtering statistics. Paired-end libraries were sequenced on an Illumina HiSeq 2500. Table S2. Environmental variables used in AQUAMAPS to generate maps of suitable habitat for gray whales during the Holocene. Table S3. The D–test statistic evaluates the number (n) of ABBA and BABA sites (D = (nABBA - nBABA) / (nABBA + nBABA)) and D < 0 means that P1 is more closely related to P3 than to P2, whereas D > 0 indicates that P2 is more closely related to P3 than P1. The significance of the D test was evaluated with a Z-score, where |Z-scores| > 3 was used as the critical value for a significant test. Figure S1. Inferred effective population sizes (Ne) over time. Estimates are averages based on 11 autosomal scaffolds larger than 30 Mb. A substitution rate of a) 10 × 10− 10 bp− 1 year− 1 and b) 1.5 × 10− 10 bp− 1 year− 1 were used. (DOCX 446 kb