Worldwide mitochondrial DNA diversity and phylogeography of pilot whales (Globicephala spp.) (original) (raw)
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Molecular Ecology, 2019
Genomic phylogeography plays an important role in describing evolutionary processes and their geographic, ecological, or cultural drivers. These drivers are often poorly understood in marine environments, which have fewer obvious barriers to mixing than terrestrial environments. Taxonomic uncertainty of some taxa (e.g. cetaceans), due to the difficulty in obtaining morphological data, can hamper our understanding of these processes. One such taxon, the short-finned pilot whale, is recognized as a single global species but includes at least two distinct morphological forms described from stranding and drive hunting in Japan, the 'Naisa' and 'Shiho' forms. Using samples (n = 735) collected throughout their global range, we examine phylogeographic patterns of divergence by comparing mitogenomes and nuclear SNP loci. Our results suggest three types within the species: an Atlantic Ocean type, a western/central Pacific and Indian Ocean (Naisa) type, and an eastern Pacific Ocean and northern Japan (Shiho) type. mtDNA control region differentiation indicates these three types form two subspecies, separated by the East Pacific Barrier: Shiho short-finned pilot whale, in the eastern Pacific Ocean and northern Japan, and Naisa shortfinned pilot whale, throughout the remainder of the species' distribution. Our data further indicate two diverging populations within the Naisa subspecies, in the Atlantic Ocean and western/central Pacific and Indian Oceans, separated by the Benguela Barrier off South Africa. This study reveals a process of divergence and speciation within a globallydistributed, mobile marine predator, and indicates the importance of the East Pacific Barrier to this evolutionary process.
Marine Mammal Science, 2016
Correlations between morphological and genetic data provide evidence to delineate species or evolutionarily significant units, which then become the units to conserve in management plans. Here, we examine the distribution and genetic differentiation of two morphotypes of short-finned pilot whale (Globicephala macrorhynchus) in the Pacific Ocean. Mitochondrial control region sequences from 333 samples were combined with 152 previously published sequences to describe genetic variability globally and population structure in the Pacific. Although genetic variability is low, we found strong differentiation at both broad and local levels across the Pacific. Based on genetics, two types are distributed throughout the Pacific, one predominantly in the eastern Pacific and the other in the western and central Pacific. In the eastern Pacific Ocean, no correlation was found between distribution and sea surface temperature. The two types have broad latitudinal ranges, suggesting their distributions are likely driven by more complex factors, such as prey distribution, rather than sea surface temperature.
Molecular ecology resources, 2011
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 longterm studies of globally dispersed and highly mobile species.
2016
Genetic variation at 14 microsatellite DNA loci and mitochondrial DNA (mtDNA) control region sequences (275bp) was examined in right whales from the western North Pacific and Antarctic Area IV. Genetic analyses were based on biopsy samples collected during the surveys of the JARPNII in 2011 and 2012 (n=15), and JARPAII in 1993/94-2009/10 (n=67). The overall heterozygosity was 0.630 and 0.650 for North Pacific and southern right whales, respectively, while the nucleotide diversity/haplotype diversity were 0.0222/0.9048 and 0.0234/0.7743, respectively. Statistical tests found no evidence of deviation from the expected Hardy-Weinberg genotypic proportion in each of the oceanic basins. The Kimura’s two parameter net interpopulational distance was 0.0358 (mtDNA) while the Nei’s genetic distance (Da) was 0.7582 (microsatellite DNA), between North Pacific and southern right whale. A phylogenetic tree separated clearly mtDNA haplotypes of the North Pacific, North Atlantic and southern right...
Canadian Journal of Zoology-Revue Canadienne de Zoologie 73(9), 1995
We investigated the mitochondrial DNA (mtDNA) diversity of humpback whales, Megaptera novaeangliae, wintering off the Mexican Pacific coast and the Revillagigedo Islands. We amplified and sequenced a variable fragment of the mtDNA control region from skin samples of 65 whales and compared these with published sequences from whales in other regional habitats. Among the Mexican humpback whales, we distinguished eight haplotypes differing by 0.31 -3.75% along a consensus sequence length of 320 base pairs. A diagnostic restriction site outside the consensus sequence identified a ninth common haplotype. A phylogenetic reconstruction of the control region sequences revealed two main groupings: an AE group, which is common throughout the North Pacific, and a CF group, which is closely related to haplotypes from the southern hemisphere. We found a significant degree of geographic subdivision in the wintering grounds of the eastern North Pacific. Within Mexico, whales off the Revillagigedo Islands are weakly but significantly differentiated from those of the Mexican Pacific coast. Our data also suggest that mtDNA haplotypes are clinally distributed along the American Pacific coast and we hypothesize that the present distribution of these lineages among humpback whales in the eastern North Pacific is probably associated with weather changes after the last glaciation.
World-wide genetic differentiation ofEubalaena: questioning the number of right whale species
Molecular Ecology, 2000
Few studies have examined systematic relationships of right whales (Eubalaena spp.) since the original species descriptions, even though they are one of the most endangered large whales. Little morphological evidence exists to support the current species designations for Eubalaena glacialis in the northern hemisphere and E. australis in the southern hemisphere. Differences in migratory behaviour or antitropical distribution between right whales in each hemisphere are considered a barrier to gene flow and maintain the current species distinctions and geographical populations. However, these distinctions between populations have remained controversial and no study has included an analysis of all right whales from the three major ocean basins. To address issues of genetic differentiation and relationships among right whales, we have compiled a database of mitochondrial DNA control region sequences from right whales representing populations in all three ocean basins that consist of: western North Atlantic E. glacialis , multiple geographically distributed populations of E. australis and the first molecular analysis of historical and recent samples of E. glacialis from the western and eastern North Pacific Ocean. Diagnostic characters, as well as phylogenetic and phylogeographic analyses, support the possibility that three distinct maternal lineages exist in right whales, with North Pacific E. glacialis being more closely related to E. australis than to North Atlantic E. glacialis. Our genetic results provide unequivocal character support for the two usually recognized species and a third distinct genetic lineage in the North Pacific under the Phylogenetic Species Concept, as well as levels of genetic diversity among right whales worldwide .
2010
We investigated differences in mtDNA sequences and sex ratios in western North Pacific minke whales by combining information from samples collected in Korean market surveys (Korean 'bycatch', n=237) with three datasets made available courtesy of the Institute for Cetacean Research (ICR) through the IWC Data Availability Group on 8 January 2010 (version 1.0): Japanese 'bycatch' (n=832), 'coastal whaling' (n=481) and 'offshore whaling' (n=1238). An initial review of the Japanese datasets showed a large number of haplotypes (70 of 157) found in only a single individual (singletons), suggesting some error in sequencing of these samples. These concerns were communicated to ICR, which undertook re-sequencing and revision of the haplotype classification of some of these samples. In an effort to meet the agreed time frame of the Preliminary Implementation Assessment, we chose, in the interim, to focus on the analysis of 4 haplogroups, previously considered to be informative (although not diagnostic) of the 'J' and 'O' stocks. Although collapsing the haplotypes into haplogroups resulted in a substantial loss of resolution in mtDNA differentiation, it avoided the problems of categorical analyses posed by the singleton errors. The 'O-' and 'J-types' defined by the 4 mtDNA haplogroups showed a 93% concordance with samples assigned to the 'O-' and 'Jclusters' in the Structure analysis of microsatellite loci ).
Molecular Ecology, 2005
We present the first description of phylogeographic structure among Cuvier's beaked whales ( Ziphius cavirostris ) worldwide using mitochondrial DNA (mtDNA) control region sequences obtained from strandings ( n = 70), incidental fisheries takes ( n = 11), biopsy ( n = 1), and whale-meat markets ( n = 5). Over a 290-base pair fragment, 23 variable sites defined 33 unique haplotypes among the total of 87 samples. Nucleotide diversity at the control region was relatively low (π π π π = 1.27% ± ± ± ± 0.723%) compared to wide-ranging baleen whales, but higher than strongly matrifocal sperm, pilot and killer whales. Phylogenetic reconstruction using maximum likelihood revealed four distinct haplotype groups, each of which displayed strong frequency differences among ocean basins, but no reciprocal monophyly or fixed character differences. Consistent with this phylogeographic pattern, an analysis of molecular variance showed high levels of differentiation among ocean basins ( F ST = 0.14, Φ Φ Φ Φ ST = 0.42; P < 0.001). Estimated rates of female migration among ocean basins were low (generally ≤ ≤ ≤ ≤ 2 individuals per generation). Regional sample sizes were too small to detect subdivisions within oceans except in the North Atlantic, where the Mediterranean Sea ( n = 12) was highly differentiated due to the presence of two private haplotypes. One market product purchased in South Korea grouped with other haplotypes found only in the North Atlantic, suggesting a violation of current agreements banning international trade in cetacean species. Together, these results demonstrate a high degree of isolation and low maternal gene flow among oceanic, and in some cases, regional populations of Cuvier's beaked whales. This has important implications for understanding the threats of human impact, including fisheries by-catch, direct hunting, and disturbance or mortality from anthropogenic sound.