Insights into the population structure of blue whales in the Eastern North Pacific from recent sightings and photographic identification

Blue whales were widely distributed in the North Pacific prior to the primary period of modern commercial whaling in the early 1900s. Despite concentrations of blue whale catches off British Columbia and in the Gulf of Alaska, there had been few documented sightings in these areas since whaling for blue whales ended in 1965. In contrast, large concentrations of blue whales have been documented off California and Baja California and in the eastern tropical Pacific since the 1970s, but it was not known if these animals were part of the same population that previously ranged into Alaskan waters. We document 15 blue whale sightings off British Columbia and in the Gulf of Alaska made since 1997, and use identification photographs to show that whales in these areas are currently part of the California feeding population. We speculate that this may represent a return to a migration pattern that has existed for earlier periods for eastern North Pacific blue whale population. One possible explanation for a shift in blue whale use is changes in prey driven by changes in oceanographic conditions, including the Pacific Decadal Oscillation (PDO), which coincides with some of the observed shifts in blue whale occurrence.     

Assessment of genetic structure among eastern North Pacific gray whales on their feeding grounds

Although most eastern North Pacific (ENP) gray whales feed in the Bering, Beaufort, and Chukchi Seas during summer and fall, a small number of individuals, referred to as the Pacific Coast Feeding Group (PCFG), show intra‐ and interseasonal fidelity to feeding areas from northern California through southeastern Alaska. We used both mitochondrial DNA (mtDNA) and 12 microsatellite markers to assess whether stock structure exists among feeding grounds used by ENP gray whales. Significant mtDNA differentiation was found when samples representing the PCFG (n = 71) were compared with samples (n = 103) collected from animals feeding further north (F_ST = 0.012, P = 0.0045). No significant nuclear differences were detected. These results indicate that matrilineal fidelity plays a role in creating structure among feeding grounds but suggests that individuals from different feeding areas may interbreed. Haplotype diversities were similar between strata (h_PCFG = 0.945, h_Northern = 0.952), which, in combination with the low level of mtDNA differentiation identified, suggested that some immigration into the PCFG could be occurring. These results are important in evaluating the management of ENP gray whales, especially in light of the Makah Tribe's proposal to resume whaling in an area of the Washington coast utilized by both PCFG and migrating whales.     

Hierarchical structure of mitochondrial DNA gene flow among humpback whales Megaptera novaeangliae, world-wide

The genetic structure of humpback whale populations and subpopulation divisions is described by restriction fragment length analysis of the mitochondrial (mt) DNA from samples of 230 whales collected by biopsy darting in 11 seasonal habitats representing six subpopulations, or 'stocks', world-wide. The hierarchical structure of mtDNA haplotype diversity among population subdivisions is described using the analysis of molecular variance (AMOVA) procedure, the analysis of gene identity, and the genealogical relationship of haplotypes as constructed by parsimony analysis and distance clustering. These analyses revealed: (i) significant partitioning of world-wide genetic variation among oceanic populations, among subpopulations or 'stocks' within oceanic populations and among seasonal habitats within stocks; (ii) fixed categorical segregation of haplotypes on the south-eastern Alaska and central California feeding grounds of the North Pacific; (iii) support for the division of the North Pacific population into a central stock which feeds in Alaska and winters in Hawaii, and an eastern or 'American' stock which feeds along the coast of California and winters near Mexico; (iv) evidence of genetic heterogeneity within the Gulf of Maine feeding grounds and among the sampled feeding and breeding grounds of the western North Atlantic; and (v) support for the historical division between the Group IV (Western Australia) and Group V (eastern Australia, New Zealand and Tonga) stocks in the Southern Oceans. Overall, our results demonstrate a striking degree of genetic structure both within and between oceanic populations of humpback whales, despite the nearly unlimited migratory potential of this species. We suggest that the humpback whale is a suitable demographic and genetic model for the management of less tractable species of baleen whales and for the general study of gene flow among long-lived, mobile vertebrates in the marine ecosystem.     

What influences the worldwide genetic structure of sperm whales (Physeter macrocephalus)?

The interplay of natural selection and genetic drift, influenced by geographic isolation, mating systems and population size, determines patterns of genetic diversity within species. The sperm whale provides an interesting example of a long‐lived species with few geographic barriers to dispersal. Worldwide mtDNA diversity is relatively low, but highly structured among geographic regions and social groups, attributed to female philopatry. However, it is unclear whether this female philopatry is due to geographic regions or social groups, or how this might vary on a worldwide scale. To answer these questions, we combined mtDNA information for 1091 previously published samples with 542 newly obtained DNA profiles (394‐bp mtDNA, sex, 13 microsatellites) including the previously unsampled Indian Ocean, and social group information for 541 individuals. We found low mtDNA diversity (π = 0.430%) reflecting an expansion event <80 000 years bp, but strong differentiation by ocean, among regions within some oceans, and among social groups. In comparison, microsatellite differentiation was low at all levels, presumably due to male‐mediated gene flow. A hierarchical amova showed that regions were important for explaining mtDNA variance in the Indian Ocean, but not Pacific, with social group sampling in the Atlantic too limited to include in analyses. Social groups were important in partitioning mtDNA and microsatellite variance within both oceans. Therefore, both geographic philopatry and social philopatry influence genetic structure in the sperm whale, but their relative importance differs by sex and ocean, reflecting breeding behaviour, geographic features and perhaps a more recent origin of sperm whales in the Pacific. By investigating the interplay of evolutionary forces operating at different temporal and geographic scales, we show that sperm whales are perhaps a unique example of a worldwide population expansion followed by rapid assortment due to female social organization.     

Demography or selection on linked cultural traits or genes? Investigating the driver of low mtDNA diversity in the sperm whale using complementary mitochondrial and nuclear genome analyses

Mitochondrial DNA has been heavily utilized in phylogeography studies for several decades. However, underlying patterns of demography and phylogeography may be misrepresented due to coalescence stochasticity, selection, variation in mutation rates and cultural hitchhiking (linkage of genetic variation to culturally‐transmitted traits affecting fitness). Cultural hitchhiking has been suggested as an explanation for low genetic diversity in species with strong social structures, counteracting even high mobility, abundance and limited barriers to dispersal. One such species is the sperm whale, which shows very limited phylogeographic structure and low mtDNA diversity despite a worldwide distribution and large population. Here, we use analyses of 175 globally distributed mitogenomes and three nuclear genomes to evaluate hypotheses of a population bottleneck/expansion vs. a selective sweep due to cultural hitchhiking or selection on mtDNA as the mechanism contributing to low worldwide mitochondrial diversity in sperm whales. In contrast to mtDNA control region (CR) data, mitogenome haplotypes are largely ocean‐specific, with only one of 80 shared between the Atlantic and Pacific. Demographic analyses of nuclear genomes suggest low mtDNA diversity is consistent with a global reduction in population size that ended approximately 125,000 years ago, correlated with the Eemian interglacial. Phylogeographic analysis suggests that extant sperm whales descend from maternal lineages endemic to the Pacific during the period of reduced abundance and have subsequently colonized the Atlantic several times. Results highlight the apparent impact of past climate change, and suggest selection and hitchhiking are not the sole processes responsible for low mtDNA diversity in this highly social species.     

High genetic diversity in a small population: the case of Chilean blue whales

It is generally assumed that species with low population sizes have lower genetic diversities than larger populations and vice versa. However, this would not be the case for long‐lived species with long generation times, and which populations have declined due to anthropogenic effects, such as the blue whale (Balaenoptera musculus). This species was intensively decimated globally to near extinction during the 20th century. Along the Chilean coast, it is estimated that at least 4288 blue whales were hunted from an apparently pre‐exploitation population size (k) of a maximum of 6200 individuals (Southeastern Pacific). Thus, here, we describe the mtDNA (control region) and nDNA (microsatellites) diversities of the Chilean blue whale aggregation site in order to verify the expectation of low genetic diversity in small populations. We then compare our findings with other blue whale aggregations in the Southern Hemisphere. Interestingly, although the estimated population size is small compared with the pre‐whaling era, there is still considerable genetic diversity, even after the population crash, both in mitochondrial (N = 46) and nuclear (N = 52) markers (H_d = 0.890 and H_o = 0.692, respectively). Our results suggest that this diversity could be a consequence of the long generation times and the relatively short period of time elapsed since the end of whaling, which has been observed in other heavily‐exploited whale populations. The genetic variability of blue whales on their southern Chile feeding grounds was similar to that found in other Southern Hemisphere blue whale feeding grounds. Our phylogenetic analysis of mtDNA haplotypes does not show extensive differentiation of populations among Southern Hemisphere blue whale feeding grounds. The present study suggests that although levels of genetic diversity are frequently used as estimators of population health, these parameters depend on the biology of the species and should be taken into account in a monitoring framework study to obtain a more complete picture of the conservation status of a population.     

AN ACOUSTIC LINK BETWEEN BLUE WHALES IN THE EASTERN TROPICAL PACIFIC AND THE NORTHEAST PACIFIC1

Blue whale calls in the eastern North Pacific Ocean consist of a two-part call often termed the A-B call. This call has been described for regions offshore of Oregon, Washington, and California, USA and the Sea of Cortez, Mexico (reviewed in Rivers 1997). Data collected from moored hydrophones in the eastern tropical Pacific (ETP) indicate that the A-B pattern is common in this region as well. There is consistency in this call type throughout the eastern North Pacific and throughout the year. This acoustic evidence indicates continuity between blue whales in the ETP and those found west of North America. The acoustic data suggest that the population of blue whales generally referred to as the “Californi/Mexico” stock might better be termed the “northeast Pacific” stock of blue whales.     

Low genetic structure and diversity of Red-billed Tropicbirds in the Mexican Pacific

Understanding genetic structure and gene flow can elucidate the mechanisms of diversification and adaptation in seabirds and help define conservation and management units. From 2012 to 2016, we collected blood and feather samples from 156 Red-billed Tropicbirds (Phaethon aethereus) from seven colonies distributed along the Gulf of California and Mexican tropical Pacific to estimate genetic diversity, genetic structure, and gene flow using microsatellite markers and mitochondrial DNA (mtDNA; control region) sequences. Nuclear and mtDNA data revealed relatively low or null levels of genetic diversity, respectively, possibly the result of a founder effect in the eastern Pacific followed by a subsequent population expansion. Nuclear data revealed significant genetic structure among the colonies, but the differences were not associated with regional grouping (i.e., Gulf of California vs. Tropical Pacific). Greater gene flow was observed from the tropical Pacific toward the Gulf of California, possibly related to shared dispersal patterns during the non-breeding season (individuals traveling north to reach warm currents with abundant prey). With the exception of one colony in the Mexican tropical Pacific, we found no evidence of recent bottleneck events. Nonetheless, the overall reduced genetic diversity suggests a high intrinsic vulnerability and risk of extinction for this species.     

INTERCHANGE AND ISOLATION OF HUMPBACK WHALES OFF CALIFORNIA AND OTHER NORTH PACIFIC FEEDING GROUNDS

Humpback whales feed in several high-latitude areas of the North Pacific. We examined the interchange of humpback whales between one of these areas, off California, and those in other feeding grounds in the eastern North Pacific:. Fluke photographs of 597 humpback whales identified off California between 1986 and 1992 were compared with those off Oregon and Washington (29); British Columbia (81); southeastern Alaska (343); Prince William Sound, Alaska (141); Kodiak Island, Alaska (104); Shumagin Islands, Alaska (22); and in the Bering Sea (7). A high degree of interchange, both inter-and intrayear, was found among humpback whales seen off California, Oregon, and Washington., A low rate of interchange was found between British Columbia and California.: two whales seen near the British Columbia/Washington border were photographed off California in a different year, No interchange was found between California and the three feeding areas in Alaska. Humpback whales off California, Oregon, and Washington form a single intermixing feeding aggregation with only limited interchange with areas farther north. These findings are consistent with photographic identification studies in the North Atlantic and with genetic studies in both the North Atlantic and North Pacific.     

Genetic diversity and structure of circumtropical almaco jack,Seriola rivoliana: tool for conservation and management

The almaco jack, Seriola rivoliana, is a circumtropical pelagic fish of importance both in commercial fisheries and in aquaculture. To understand levels of genetic diversity within and among populations in the wild, population genetic structure and the relative magnitude of migration were assessed using mtDNA sequence data and single nucleotide polymorphisms (SNPs) from individuals sampled from locations in the Pacific and Atlantic Oceans. A total of 25 variable sites of cytochrome c oxidase subunit 1 and 3678 neutral SNPs were recovered. Three genetic groups were identified, with both marker types distributed in different oceanic regions: Pacific-1 in central Pacific, Pacific-2 in eastern Pacific and Atlantic in western Atlantic. Nonetheless, the analysis of SNP identified a fourth population in the Pacific coast of Baja California Sur, Mexico (Pacific-3), whereas that of mtDNA did not. This mito-nuclear discordance is likely explained by a recently diverged Pacific-3 population. In addition, two mtDNA haplogroups were found within the western Atlantic, likely indicating that the species came into the Atlantic from the Indian Ocean with historical gene flow from the eastern Pacific. Relative gene flow among ocean basins was low with _rm < 0.2, whereas in the eastern Pacific it was asymmetric and higher from south to north (_rm > 0.79). The results reflect the importance of assessing genetic structure and gene flow of natural populations for the purposes of sustainable management.     

Population genetic structure of Bryde’s whales (<Emphasis Type="Italic">Balaenoptera brydei</Emphasis>) at the inter-oceanic and trans-equatorial levels

Bryde’s whales (Balaenoptera brydei) differ from other typical baleen whale species because they are restricted to tropical and warm temperate waters in major oceans, and frequent trans-equatorial movement has been suggested for the species. We tested this hypothesis by analyzing genetic variation at 17 microsatellite loci (N = 508) and 299 bp of mitochondrial DNA (mtDNA) control region sequences (N = 472) in individuals obtained from the western North Pacific, South Pacific, and eastern Indian Ocean. Combined use of microsatellite and mtDNA markers allowed us to distinguish between contemporary gene flow and ancestral polymorphism and to describe sex-specific philopatry. A high level of genetic diversity was found within the samples. Both nuclear and mtDNA markers displayed similar population structure, indicating a lack of sex-specific philopatry. Spatial structuring was detected using both frequency-based population parameters and individual-based Bayesian approaches. Whales in the samples from different oceanic regions came from genetically distinct populations with evidence of limited gene flow. We observed low mtDNA sequence divergence among populations and a lack of concordance between geographic and phylogenetic position of mtDNA haplotypes, suggesting recent separation of populations rather than frequent trans-equatorial and inter-oceanic movement. We conclude that current gene flow between Bryde’s whale populations is low and that effective management actions should treat them as separate entities to ensure continued existence of the species.     

Social Affiliations within Sperm Whale (Physeter macrocephalus) Groups

We examined patterns of affiliation within groups of sperm whales ( Physeter macrocephalus ), particularly concentrating on how short-term spatio–temporal associations reflect long-term relationships. Female and immature sperm whales live in stable, and partially matrilineal, social units. Two or more social units may move together for periods of several days, forming a cohesive group of about 20 animals. We observed that sperm whales in the eastern tropical Pacific quite consistently associated with members of their own social unit more than they did with other animals in their group with whom they did not share a long-term relationship. There was little evidence for preferred, or avoided, affiliations within social units, except in two large and relatively unstable units. In two well-studied groups, individuals did not show consistently favoured positions in the foraging rank relative to other members of their social unit. These results indicate the importance of long-term relationships to female and immature sperm whales, but suggest that relationships are quite homogeneous within social units.     

Cephalopod remains from stomachs of sperm whales (Physeter macrocephalus) that mass‐stranded along the Oregon coast

On 16 June 1979, a herd of 41 sperm whales stranded near the mouth of the Siuslaw River in Florence, Oregon. The stomach contents from 32 whales were collected, identified to the lowest taxonomic level possible, enumerated, and measured. A total of 20,247 cephalopod lower beaks that represented 24 species from 14 different families were recovered. The most numerous species were Histioteuthis hoylei (25.9%), Taonius borealis (12.9%), Galiteuthis phyllura (11.2%), Gonatopsis/Berryteuthis type (10.9%), and Moroteuthis robusta (10.7%). Reconstructed estimates of mass indicated that M. robusta contributed almost 50% of the total mass of cephalopods consumed, followed by H. hoylei (19.3%), and T. borealis (7.0%). The most important species in the diet of stranded whales were M. robusta, H. hoylei, T. borealis, G. phyllura, Octopoteuthis deletron, and Gonatopsis/Berryteuthis type. There were significant differences in the diet of males and females, but no differences between sperm whales of different age groups. Overall, sperm whales primarily consumed small cephalopods that were likely eaten south of 45ºN in or near the California Current System. This study provides new estimates of the food habits of sperm whales in the northeast Pacific from one of the largest strandings of this species.     

Blue whale population structure along the eastern South Pacific Ocean: evidence of more than one population

Blue whales (Balaenoptera musculus) were among the most intensively exploited species of whales in the world. As a consequence of this intense exploitation, blue whale sightings off the coast of Chile were uncommon by the end of the 20th century. In 2004, a feeding and nursing ground was reported in southern Chile (SCh). With the aim to investigate the genetic identity and relationship of these Chilean blue whales to those in other Southern Hemisphere areas, 60 biopsy samples were collected from blue whales in SCh between 2003 and 2009. These samples were genotyped at seven microsatellite loci and the mitochondrial control region was sequenced, allowing us to identify 52 individuals. To investigate the genetic identity of this suspected remnant population, we compared these 52 individuals to blue whales from Antarctica (ANT, n = 96), Northern Chile (NCh, n = 19) and the eastern tropical Pacific (ETP, n = 31). No significant differentiation in haplotype frequencies (mtDNA) or among genotypes (nDNA) was found between SCh, NCh and ETP, while significant differences were found between those three areas and Antarctica for both the mitochondrial and microsatellite analyses. Our results suggest at least two breeding population units or subspecies exist, which is also supported by other lines of evidence such as morphometrics and acoustics. The lack of differences detected between SCh/NCh/ETP areas supports the hypothesis that eastern South Pacific blue whales are using the ETP area as a possible breeding area. Considering the small population sizes previously reported for the SCh area, additional conservation measures and monitoring of this population should be developed and prioritized.     

Genetic variation in blue whales in the eastern pacific: implication for taxonomy and use of common wintering grounds

Many aspects of blue whale biology are poorly understood. Some of the gaps in our knowledge, such as those regarding their basic taxonomy and seasonal movements, directly affect our ability to monitor and manage blue whale populations. As a step towards filling in some of these gaps, microsatellite and mtDNA sequence analyses were conducted on blue whale samples from the Southern Hemisphere, the eastern tropical Pacific (ETP) and the northeast Pacific. The results indicate that the ETP is differentially used by blue whales from the northern and southern eastern Pacific, with the former showing stronger affinity to the region off Central America known as the Costa Rican Dome, and the latter favouring the waters of Peru and Ecuador. Although the pattern of genetic variation throughout the Southern Hemisphere is compatible with the recently proposed subspecies status of Chilean blue whales, some discrepancies remain between catch lengths and lengths from aerial photography, and not all blue whales in Chilean waters can be assumed to be of this type. Also, the range of the proposed Chilean subspecies, which extends to the Galapagos region of the ETP, at least seasonally, perhaps should include the Costa Rican Dome and the eastern North Pacific as well.     

Following the rivers: historical reconstruction of California voles Microtus californicus (Rodentia: Cricetidae) in the deserts of eastern California

The California vole, Microtus californicus, restricted to habitat patches where water is available nearly year‐round, is a remnant of the mesic history of the southern Great Basin and Mojave deserts of eastern California. The history of voles in this region is a model for species‐edge population dynamics through periods of climatic change. We sampled voles from the eastern deserts of California and examined variation in the mitochondrial cytb gene, three nuclear intron regions, and across 12 nuclear microsatellite markers. Samples are allocated to two mitochondrial clades: one associated with southern California and the other with central and northern California. The limited mtDNA structure largely recovers the geographical distribution, replicated by both nuclear introns and microsatellites. The most remote population, Microtus californicus scirpensis at Tecopa near Death Valley, was the most distinct. This population shares microsatellite alleles with both mtDNA clades, and both its northern clade nuclear introns and southern clade mtDNA sequences support a hybrid origin for this endangered population. The overall patterns support two major invasions into the desert through an ancient system of riparian corridors along streams and lake margins during the latter part of the Pleistocene followed by local in situ divergence subsequent to late Pleistocene and Holocene drying events. Changes in current water resource use could easily remove California voles from parts of the desert landscape.     

Population structure of nuclear and mitochondrial DNA variation among humpback whales in the North Pacific

The population structure of variation in a nuclear actin intron and the control region of mitochondrial DNA is described for humpback whales from eight regions in the North Pacific Ocean: central California, Baja Peninsula, nearshore Mexico (Bahia Banderas), offshore Mexico (Socorro Island), southeastern Alaska, central Alaska (Prince Williams Sound), Hawaii and Japan (Ogasawara Islands). Primary mtDNA haplotypes and intron alleles were identified using selected restriction fragment length polymorphisms of target sequences amplified by the polymerase chain reaction (PCR–RFLP). There was little evidence of heterogeneity in the frequencies of mtDNA haplotypes or actin intron alleles due to the year or sex composition of the sample. However, frequencies of four mtDNA haplotypes showed marked regional differences in their distributions (Φ_ST = 0.277; P < 0.001; n = 205 individuals) while the two alleles showed significant, but less marked, regional differences (Φ_ST = 0.033; P < 0.013; n = 400 chromosomes). An hierarchical analysis of variance in frequencies of haplotypes and alleles supported the grouping of six regions into a central and eastern stock with further partitioning of variance among regions within stocks for haplotypes but not for alleles. Based on available genetic and demographic evidence, the southeastern Alaska and central California feeding grounds were selected for additional analyses of nuclear differentiation using allelic variation at four microsatellite loci. All four loci showed significant differences in allele frequencies (overall F_ST = 0.043; P < 0.001; average n = 139 chromosomes per locus), indicating at least partial reproductive isolation between the two regions as well as the segregation of mtDNA lineages. Although the two feeding grounds were not panmictic for nuclear or mitochondrial loci, estimates of long-term migration rates suggested that male-mediated gene flow was several-fold greater than female gene flow. These results include and extend the range and sample size of previously published work, providing additional evidence for the significance of genetic management units within oceanic populations of humpback whales.     

Contrasting population structure from nuclear intron sequences and mtDNA of humpback whales

Powerful analyses of population structure require information from multiple genetic loci. To help develop a molecular toolbox for obtaining this information, we have designed universal oligonucleotide primers that span conserved intron-exon junctions in a wide variety of animal phyla. We test the utility of exon-primed, intron-crossing amplifications by analyzing the variability of actin intron sequences from humpback, blue, and bowhead whales and comparing the results with mitochondrial DNA (mtDNA) haplotype data. Humpback actin introns fall into two major clades that exist in different frequencies in different oceanic populations. It is surprising that Hawaii and California populations, which are very distinct in mtDNAs, are similar in actin intron alleles. This discrepancy between mtDNA and nuclear DNA results may be due either to differences in genetic drift in mitochondrial and nuclear genes or to preferential movement of males, which do not transmit mtDNA to offspring, between separate breeding grounds. Opposing mtDNA and nuclear DNA results can help clarify otherwise hidden patterns of structure in natural populations.      

Sex-biased dispersal in sperm whales: contrasting mitochondrial and nuclear genetic structure of global populations

The social organization of most mammals is characterized by female philopatry and male dispersal. Such sex-biased dispersal can cause the genetic structure of populations to differ between the maternally inherited mitochondrial DNA (mtDNA) and the bi-parental nuclear genome. Here we report on the global genetic structure of oceanic populations of the sperm whale, one of the most widely distributed mammalian species. Groups of females and juveniles are mainly found at low latitudes, while males reach polar waters, returning to tropical and subtropical waters to breed. In comparisons between oceans, we did not find significant heterogeneity in allele frequencies of microsatellite loci (exact test; p = 0.23). Estimates of GST = 0.001 and RST = 0.005 also indicated negligible if any nuclear DNA differentiation. We have previously reported significant differentiation between oceans in mtDNA sequences. These contrasting patterns suggest that interoceanic movements have been more prevalent among males than among females, consistent with observations of females being the philopatric sex and having a more limited latitudinal distribution than males. Consequently, the typical mammalian dispersal pattern may have operated on a global scale in sperm whales.     

Population structure of chum salmon and selection on the markers collected for stock identification

Genetic stock identification (GSI) is a major management tool of Pacific salmon (Oncorhynchus Spp.) that has provided rich genetic baseline data of allozymes, microsatellites, and single‐nucleotide polymorphisms (SNPs) across the Pacific Rim. Here, we analyzed published data sets for adult chum salmon (Oncorhynchus keta), namely 10 microsatellites, 53 SNPs, and a mitochondrial DNA locus (mtDNA3, control region, and NADH‐3 combined) in samples from 495 locations in the same distribution range (n = 61,813). TreeMix analysis of the microsatellite loci identified the greatest convergence toward Japanese/Korean populations and suggested two admixture events from Japan/Korea to Russia and the Alaskan Peninsula. The SNPs had been purposively collected from rapidly evolving genes to increase the power of GSI. The largest expected heterozygosity was observed in Japanese/Korean populations for microsatellites, whereas it was largest in Western Alaskan populations for SNPs, reflecting the SNP discovery process. A regression of SNP population structures on those of microsatellites indicated the selection of the SNP loci according to deviations from the predicted structures. Specifically, we matched the sampling locations of the SNPs with those of the microsatellites and performed regression analyses of SNP allele frequencies on a 2‐dimensional scaling (MDS) of matched locations obtained from microsatellite pairwise F _ST values. The MDS first axis indicated a latitudinal cline in American and Russian populations, whereas the second axis showed differentiation of Japanese/Korean populations. The top five outlier SNPs included mtDNA3, U502241 (unknown), GnRH373, ras1362, and TCP178, which were identified by principal component analysis. We summarized the functions of 53 nuclear genes surrounding SNPs and the mtDNA3 locus by referring to a gene database system and propose how they may influence the fitness of chum salmon.