Sperm whale population structure in the eastern and central North Pacific inferred by the use of single‐nucleotide polymorphisms, microsatellites and mitochondrial DNA

Abstract

We use mitochondrial DNA (mtDNA) (400 bp), six microsatellites and 36 single-nucleotide polymorphisms (SNPs), 20 of which were linked, to investigate population structure of sperm whales (Physeter macrocephalus) in the eastern and central North Pacific. SNP markers, reproducible across technologies and laboratories, are ideal for long-term studies of globally distributed species such as sperm whales, a species of conservation concern because of both historical and contemporary impacts. We estimate genetic differentiation among three strata in the temperate to tropical waters where females are found: California Current, Hawai`i and the eastern tropical Pacific. We then consider how males on sub-Arctic foraging grounds assign to these strata. The California Current stratum was differentiated from both the other strata (P < 0.05) for mtDNA, microsatellites and SNPs, suggesting that the region supports a demographically independent population and providing the first indication that males may exhibit reproductive philopatry. Comparisons between the Hawai`i stratum and the eastern tropical Pacific stratum are not conclusive at this time. Comparisons with Alaska males were statistically significant, or nearly so, from all three strata and individuals showed mixed assignment to, and few exclusions from, the three potential source strata, suggesting widespread origin of males on sub-Arctic feeding grounds. We show that SNPs have sufficient power to detect population structure even when genetic differentiation is low. There is a need for better analytical methods for SNPs, especially when linked SNPs are used, but SNPs appear to be a valuable marker for long-term studies of globally dispersed and highly mobile species.

Depredating sperm whales in the Gulf of Alaska: local habitat use and long distance movements across putative population boundaries

“…SWsat10 headed into the Sea of Cortez, and SWsat8 bypassed the left turn to the Sea of Cortez and continued south to 14°N where transmissions ended. A genetics study by Mesnick et al (2011) investigated the population structure of North Pacific sperm whales and determined that GOA males likely are from multiple origins. That study included 30 GOA biopsy samples, of which 19 were from the SEASWAP study, all males, known to have engaged in depredation.…”

“…Currently, in US waters, 3 populations are recognized: (1) California Current, (2) Hawaii, and (3) Alaska. According to Mesnick et al (2011), sperm whales present in the California Current are differentiated genetically, whereas sperm whales from the Hawaiian Archipelago and the eastern tropical Pacific could not be fully differentiated. Their results were clear that the high-latitude male sperm whales in Alaska originated from not one but multiple populations.…”

“…Thus, a species with low genetic diversity and wide ranging movements, perhaps including males foraging in ocean basins apart from the females and immature whales, is culturally connected acoustically rather than geographically. Mesnick et al (2011) revisited the population structure for sperm whales in the North Pacific using single-nucleotide polymorphisms (SNPS) along with microsatellite genotyping and mitochondrial DNA methods. Currently, in US waters, 3 populations are recognized: (1) California Current, (2) Hawaii, and (3) Alaska.…”

Genetic and genomic monitoring with minimally invasive sampling methods

“…Mesnick et al, (2011) used 8 microsatellite loci and 38 Amplifluor SNP loci to investigate the population structure of North Pacific sperm whales (Physter macrocephalus).…”

Empirical comparison of single nucleotide polymorphisms and microsatellites for population and demographic analyses of bowhead whales

“…PHASE infers haplotypes even in the absence of genotype data, which can cause a bias in haplotype frequencies among populations. We per formed replicate analyses of summary statistics using the default PHASE function and by removing genotypes inferred when one or more of the linked genotypes were missing (see Mesnick et al 2011).SNPs were checked for evidence of divergent se lection among populations using the program Baye Scan (Foll & Gaggiotti 2008) based on allele frequency differences among the 3 stocks, using default Markov chain Monte Carlo parameters in the program. …”