Cristina Pomilla; Ana R. Amaral; Tim Collins; Gianna Minton; Ken Findlay; Matthew S. Leslie; Louisa Ponnampalam; Robert Baldwin; Howard Rosenbaum

“ The switching of a non-migratory population to a Northern Hemisphere breeding cycle is an interesting biological conundrum and while this is beyond the scope of our research, it is tempting to hypothesize an adaptive response of the ASHW to the Arabian Sea seasonal cycle of temperature and productivity in connection to the monsoon seasons. ”

“ A small, non-migratory population of humpback whales in the Arabian Sea is classified as “Endangered” on the IUCN Red List of Threatened Species, an assessment constrained by a lack of data, including limited understanding of its relationship to other populations. We analysed 11 microsatellite markers and mitochondrial DNA sequences extracted from 67 Arabian Sea humpback whale tissue samples and compared them to equivalent datasets from the Southern Hemisphere and North Pacific. Results show that the Arabian Sea population is highly distinct ”

“ Raggedness statistics (rg = 0.2566 p = 0.009) significantly rejected a population expansion.
Results from bottleneck indicate an excess of heterozygosity (one-tailed Wilcoxon test for heterozygosity excess, P <0.05) , which suggests a recent reduction in effective population size of the ASHW. However, an analysis of the allele frequency distribution revealed an L-shaped distribution, which is expected for a population that has not experienced a recent bottleneck that affected genetic variability [76] . ”

“ In order to estimate effective migration rates and divergence times between ASHW and other areas we analysed mtDNA data using the program Mdiv [56] , which uses a MCMC method within a likelihood framework to estimate the posterior distributions of the migration rate per gene per generation [M = (2 Nem) ] , the time in generations since the two populations diverged scaled by the effective population size [T = (t/2 Ne) ] , and the parameter theta (θ) , which is a product of the effective population size and the mutation rate per generation of the studied gene region [θ = (4 Neμ) ] . ”

“ If we consider K = 2 as the most likely number of clusters in our dataset, within the Arabian Sea population only a few individuals have probabilities around 0.5 of being assigned to the other cluster (Figure 4b) . For all other sampling locations individuals have equal probabilities of belonging to any of the two clusters. ”

“ Humpback whales (Megaptera novaeangliae) were among those species heavily impacted by whaling, particularly in the Southern Hemisphere [12] . Distributed worldwide, they typically undertake long migrations between high latitude feeding grounds and low latitude breeding grounds, to which they show a high degree of site fidelity (e.g. [13] ) . Frequently coastal in their distribution, they were a preferred whaling target with all populations heavily impacted [6] , [12] . ”

“ The current estimates for population size (82 individuals using mark-recapture data and 90–142 individuals using genetic data) and bottleneck timing are compatible with an 80% reduction. Additionally, our evidences of ongoing population decline indicate that while whaling has ceased, other underlying, and less understood causes of decline are still continuing. ”

“ The recovery rate of M is positively correlated with post-reduction population size, but that recovery occurs in both small and large populations, indicating that M can distinguish between populations that have been recently reduced in size and those that have been small for a long time. ”

“ While the first method is based on random linkage disequilibrium that arises by chance each generation in finite population, the second method is based on the observation that when the number of breeders is very small, an excess of heterozygotes is expected in the progeny. ”

“ A more recent bottleneck is further supported by tests of population expansion, which suggest the population may still be in decline, as is clearly seen in the BSP plot. This finding is of special concern if we consider several lines of evidence that suggest this population is spatially, genetically and demographically isolated from other breeding populations. ”

“ Its uniqueness is comparable to another relict population, the eastern North Pacific right whale [8] , a population that was drastically reduced by illegal Soviet whaling during the same period as potentially the ASHW and whose effective population size has remained low or declined over the last few decades [84] .
Scarring analyses for ASHW identified in Oman in 2003 indicated that ∼30–40% of examined whales were likely to have been entangled in fishing gear [80] . ”

“ Different bottleneck estimates were obtained with microsatellites (20-6,450 ya) and with mtDNA (15,000 ya) , which may reflect marker characteristics; mtDNA is likely showing an older signal than the microsatellites. A primary productivity collapse occurred ∼15,000 ya, coinciding with the apparent signal of population decline in the mtDNA BSP. ASHW feed in monsoon-driven upwelling areas of Oman, Pakistan and India [28] , [80] , and a decline in food availability could be responsible for initiating a population decline. ”

“ However, populations of these species have larger estimated population sizes (∼500 North Atlantic right whales [86] and ∼130 Western gray whales [83] ) and migrate between feeding and breeding grounds. The effective population size estimate for the ASHW obtained in this study suggests a population size of around 100 animals, which is in agreement with the census estimate of 82 individuals obtained for the area off Oman using mark-recapture data [20] . ”

“ Burgeoning anthropogenic threats in the Arabian Sea, including entanglement in fishing gear and ship strikes [6] , [94] , are known limitations to demographic recovery (e.g. [11] ) . Future studies should be aimed at understanding in detail which processes have led (or are leading) to the high observed genetic differentiation and more importantly, to the decline of this unique whale population.
Supporting Information Figure S1 Arabian Sea Humpback whales photographed in Dhofar, Southern Oman. Photo credits: T. Collins and D. MacDonald. (TIF)
Click here for additional data file. ”

“ The BSP was constructed using Beast v. 1.7.4 [68] , with MCMC runs of up to 10 million steps that yielded effective sample sizes (ESS) of at least 200. A mutation rate of 5.2% per million years was used [69] .
In order to estimate contemporary effective population size (Ne) for the ASHW using the microsatellite data, we used two methods as implemented in the program NeEstimator V2 [70] : a method based on linkage disequilibrium (LD) [71] and the heterozygote-excess method [72] . ”

“ The sequences were adjusted for multiple substitutions using the Kimura 2-parameter model [48] . A fin whale sequence from GenBank was used as an outgroup. Four simultaneous Markov chain Monte Carlo (MCMC) chains were run for 7 × 106 generations, with trees sampled at intervals of 1,000 generations. ”

“ Oman's humpback whales ( Megaptera novaengliae ) . Journal of Oman Studies 11:11–18 .↑ Van Bressem M-F, Antonio Raga J, Di Guardo G, Jepson PD, Duignan PJ, et al. (2009) Emerging infectious diseases in cetaceans worldwide and the possible role of environmental stressors. Diseases of Aquatic Organisms 86:143–157 . pmid:19902843↑ VanBressem MF, VanWaerebeek K (1996) Epidemiology of poxvirus in small cetaceans from the Eastern South Pacific. Marine Mammal Science 12:371–382 .↑ Bouzat JL (2010) Conservation genetics of population bottlenecks: the role of chance, selection, and history. ”

“ Effective population size/adult population size ratios in wildlife: a review. Genetical Research 66:95–107 .↑ Luikart G, Allendorf FW, Cornuet JM, Sherwin WB (1998) Distortion of allele frequency distributions provides a test for recent population bottlenecks. Journal of Heredity 89:238–247 . pmid:9656466↑ Jackson JA, Steel DJ, Beerli P, Congdon BC, Olavarría C, et al.. (2014) Global diversity and oceanic divergence of humpback whales (Megaptera novaeangliae) . ”