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.     

Population structure and conservation implications for the loggerhead sea turtle of the Cape Verde Islands

The Cape Verde Islands harbour the second largest nesting aggregation of the globally endangered loggerhead sea turtle in the Atlantic. To characterize the unknown genetic structure, connectivity, and demographic history of this population, we sequenced a segment of the mitochondrial (mt) DNA control region (380 bp, n = 186) and genotyped 12 microsatellite loci (n = 128) in females nesting at three islands of Cape Verde. No genetic differentiation in either haplotype or allele frequencies was found among the islands (mtDNA F _ST = 0.001, P > 0.02; nDNA F _ST = 0.001, P > 0.126). However, population pairwise comparisons of the mtDNA data revealed significant differences between Cape Verde and all previously sequenced Atlantic and Mediterranean rookeries (F _ST = 0.745; P < 0.000). Results of a mixed stock analysis of mtDNA data from 10 published oceanic feeding grounds showed that feeding grounds of the Madeira, Azores, and the Canary Islands, in the Atlantic Ocean, and Gimnesies, Pitiüses, and Andalusia, in the Mediterranean sea, are feeding grounds used by turtles born in Cape Verde, but that about 43% (±19%) of Cape Verde juveniles disperse to unknown areas. In a subset of samples (n = 145) we evaluated the utility of a longer segment (~760 bp) amplified by recently designed mtDNA control region primers for assessing the genetic structure of Atlantic loggerhead turtles. The analysis of the longer fragment revealed more variants overall than in the shorter segments. The genetic data presented here are likely to improve assignment and population genetic analyses, with significant conservation and research applications.     

Oceanographic Currents and Local Ecological Knowledge Indicate,and Genetics Does Not Refute,a Contemporary Pattern of Larval Dispersal for The Ornate Spiny Lobster,Panulirus ornatus in the South-East Asian Archipelago

Here we utilize a combination of genetic data, oceanographic data, and local ecological knowledge to assess connectivity patterns of the ornate spiny lobster Panulirus ornatus (Fabricius, 1798) in the South-East Asian archipelago from Vietnam to Australia. Partial mitochondrial DNA control region and 10 polymorphic microsatellites did not detect genetic structure of 216 wild P. ornatus samples from Australia, Indonesia and Vietnam. Analyses show no evidence for genetic differentiation among populations (mtDNA control region sequences Φ_ST = -0.008; microsatellite loci F_ST = 0.003). A lack of evidence for regional or localized mtDNA haplotype clusters, or geographic clusters of microsatellite genotypes, reveals a pattern of high gene flow in P. ornatus throughout the South-East Asian Archipelago. This lack of genetic structure may be due to the oceanography-driven connectivity of the pelagic lobster larvae between spawning grounds in Papua New Guinea, the Philippines and, possibly, Indonesia. The connectivity cycle necessitates three generations. The lack of genetic structure of P. ornatus population in the South-East Asian archipelago has important implications for the sustainable management of this lobster in that the species within the region needs to be managed as one genetic stock.     

Preliminary data on the variability of three microsatellite loci in Pacific <Emphasis Type="Italic">Gadus macrocephalus</Emphasis> and Atlantic <Emphasis Type="Italic">G. morhua</Emphasis> cod (Gadidae)

Variability of microsatellite DNA loci Gmo3, Gmo34, and Gmo35 is studied in samples of Pacific cod Gadus macrocephalus and Atlantic cod G. morhua. The results show high values of identity of the samples within the North Pacific basin (0.9766–0.9924) and within the Northeast Atlantic basin (0.9580). Based on the pairwise assessment of genetic differentiation, the F _ST values are significantly different in all variants between the samples of Pacific and Atlantic cod (F _ST = 0.5235–0.6719, p < 0.001). Within the basins, the significant differences in the frequencies of main alleles are revealed in the loci Gmo3 and Gmo34 for the samples from the Pacific and Atlantic oceans, respectively.     

Population Structure of the Giant Garter Snake, Thamnophis gigas

The giant garter snake, Thamnophis gigas, is a threatened species endemic to California’s Central Valley. We tested the hypothesis that current watershed boundaries have caused genetic differentiation among populations of T. gigas. We sampled 14 populations throughout the current geographic range of T. gigas and amplified 859 bp from the mitochondrial gene ND4 and one nuclear microsatellite locus. DNA sequence variation from the mitochondrial gene indicates there is some genetic structuring of the populations, with high F_ST values and unique haplotypes occurring at high frequency in several populations. We found that clustering populations by watershed boundary results in significant between-region genetic variance for mtDNA. However, analysis of allele frequencies at the microsatellite locus NSU3 reveals very low F_ST values and little between-region variation in allele frequencies. The discordance found between mitochondrial and microsatellite data may be explained by aspects of molecular evolution and/or T. gigas life history characteristics. Differences in effective population size between mitochondrial and nuclear DNA, or male-biased gene flow, result in a lower migration rate of mitochondrial haplotypes relative to nuclear alleles. However, we cannot exclude homoplasy as one explanation for homogeneity found for the single microsatellite locus. The mitochondrial nucleotide sequence data supports conservation practices that identify separate management units for T. gigas.     

Fine-scale population genetic structure in Alaskan Pacific halibut (<Emphasis Type="Italic">Hippoglossus stenolepis</Emphasis>)

Pacific halibut collected in the Aleutian Islands, Bering Sea and Gulf of Alaska were used to test the hypothesis of genetic panmixia for this species in Alaskan marine waters. Nine microsatellite loci and sequence data from the mitochondrial (mtDNA) control region were analyzed. Eighteen unique mtDNA haplotypes were found with no evidence of geographic population structure. Using nine microsatellite loci, significant heterogeneity was detected between Aleutian Island Pacific halibut and fish from the other two regions (F _ST range = 0.007–0.008). Significant F _ST values represent the first genetic evidence of divergent groups of halibut in the central and western Aleutian Archipelago. No significant genetic differences were found between Pacific halibut in the Gulf of Alaska and the Bering Sea leading to questions about factors contributing to separation of Aleutian halibut. Previous studies have reported Aleutian oceanographic conditions at deep inter-island passes leading to ecological discontinuity and unique community structure east and west of Aleutian passes. Aleutian Pacific halibut genetic structure may result from oceanographic transport mechanisms acting as partial barriers to gene flow with fish from other Alaskan waters.     

The Distribution and Host Shifts of Cotton-Melon Aphids in Northern China

Aphis gossypii Glover (Hemiptera: Aphididae) is a serious pest of cotton in northern China. A microsatellite analysis was used to characterize the genetic structure of A. gossypii populations from different geographic, host plant, and seasonal populations in 2014. Among 906 individuals, 507 multilocus genotypes were identified, with genotypic richness values of 0.07–1.00 for the populations. We observed moderate levels of genetic differentiation among geographic populations (F_ST = 0.103; 95% confidence interval: 0.065–0.145) and host plant populations (F_ST = 0.237; 95% confidence interval: 0.187–0.296). A Mantel test of isolation by distance revealed no significant correlations between Slatkin’s linearized F_ST and the natural logarithm of geographic distance. A Bayesian analysis of population genetic structures identified three clusters. An analysis of molecular variance revealed significant differences among the three clusters (F = 0.26596, P < 0.0001), among seasons (F = 0.04244, P = 0.00381), and among host populations (F = 0.12975, P = 0.0029). Thus, the A. gossypii populations in northern China exhibit considerable genotypic diversity. Additionally, our findings indicated that the 31 analyzed populations could be classified as one of three host biotypes (i.e., cotton, cucumber, and pomegranate biotypes). There were also clear seasonal effects on population genetic structure diversity among aphids collected from Anyang.     

Multiple ice‐age refugia in Pacific cod,Gadus macrocephalus

Pleistocene ice‐ages greatly influenced the historical abundances of Pacific cod, Gadus macrocephalus, in the North Pacific and its marginal seas. We surveyed genetic variation at 11 microsatellite loci and mitochondrial (mt) DNA in samples from twelve locations from the Sea of Japan to Washington State. Both microsatellite (mean H = 0.868) and mtDNA haplotype (mean h = 0.958) diversities were large and did not show any geographical trends. Genetic differentiation between samples was significantly correlated with geographical distance between samples for both microsatellites (F_ST = 0.028, r² = 0.33) and mtDNA (F_ST = 0.027, r² = 0.18). Both marker classes showed a strong genetic discontinuity between northwestern and northeastern Pacific populations that likely represents groups previously isolated during glaciations that are now in secondary contact. Significant differences appeared between samples from the Sea of Japan and Okhotsk Sea that may reflect ice‐age isolations in the northwest Pacific. In the northeast Pacific, a microsatellite and mtDNA partition was detected between coastal and Georgia Basin populations. The presence of two major coastal mtDNA lineages on either side of the Pacific Ocean basin implies at least two ice‐age refugia and separate postglacial population expansions facilitated by different glacial histories. Northward expansions into the Gulf of Alaska were possible 14–15 kyr ago, but deglaciation and colonization of the Georgia Basin probably occurred somewhat later. Population expansions were evident in mtDNA mismatch distributions and in Bayesian skyline plots of the three major lineages, but the start of expansions appeared to pre‐date the last glacial maximum.     

Population structure of North Atlantic and North Pacific sei whales (<Emphasis Type="Italic">Balaenoptera borealis</Emphasis>) inferred from mitochondrial control region DNA sequences and microsatellite genotypes

Currently, three stocks of sei whales (Balaenoptera borealis) are defined in the North Atlantic; the Nova Scotian, Iceland-Denmark Strait and Eastern North Atlantic stocks, which are mainly based upon historical catch and sighting data. We analyzed mitochondrial control region DNA (mtDNA) sequences and genotypes from 7 to 11 microsatellite loci in 87 samples from three sites in the North Atlantic; Iceland, the Gulf of Maine and the Azores, and compared against the North Pacific using 489 previously published samples. No statistically significant deviations from homogeneity were detected among the North Atlantic samples at mtDNA or microsatellite loci. The genealogy estimated from the mtDNA sequences revealed a clear division of the haplotypes into a North Atlantic and a North Pacific clade, with the exception of one haplotype detected in a single sample from the Azores, which was included in the North Pacific clade. Significant genetic divergence between the North Atlantic and North Pacific Oceans was detected (mtDNA Φ_ST?=?0.72, microsatellite Weir and Cockerham’s ? = 0.20; p?<?0.001). The coalescent-based estimate of the population divergence time between the North Atlantic and North Pacific populations from the sequence variation among the mtDNA sequences was at 163,000 years ago. However, the inference was limited by an absence of samples from the Southern Hemisphere and uncertainty regarding mutation rates and generation times. The estimates of inter-oceanic migration rates were low (Nm at 0.007 into the North Pacific and at 0.248 in the opposite direction). Although estimates of genetic divergence among the current North Atlantic stocks were low and consistent with the extensive range of movement observed in satellite tagged sei whales, the high uncertainty of the genetic divergence estimates precludes rejection of multiple stocks in the North Atlantic.     

Genetic differentiation and intraspecific structure of Eastern Tropical Pacific spotted dolphins,Stenella attenuata,revealed by DNA analyses

Mitochondrial DNA (mtDNA) control region sequences and microsatellite loci length polymorphisms were used to investigate genetic differentiation in spotted dolphins (Stenella attenuata) in the Eastern Tropical Pacific and to examine the intraspecific structure of the coastal subspecies (Stenella attenuata graffmani). One-hundred and thirty-five animals from several coastal areas and 90 offshore animals were sequenced for 455 bp of the mitochondrial control region, resulting in 112 mtDNA haplotypes. Phylogenetic analyses and the existence of shared haplotypes between the two subspecies suggest recent and/or current gene flow. Analyses using χ², F _ST (based on haplotype frequencies) and Φ_ST values (based on frequencies and genetic distances between haplotypes) yielded statistically significant separation (randomized permutation values P<0.05) among four different coastal populations and between all but one of these and the offshore subspecies (overall F _ST=0.0691). Ninety-one coastal animals from these four geographic populations and 50 offshore animals were genotyped for seven nuclear microsatellite loci. Analysis using F _ST values (based on allelic frequencies) yielded statistically significant separation between most coastal populations and offshore animals, although no coastal populations were distinguished. These results argue for the existence of some genetic isolation between offshore and inshore populations and among some inshore populations, suggesting that these should be treated as separate units for management purposes.     

Rolling stones and stable homes: social structure,habitat diversity and population genetics of the Hawaiian spinner dolphin (Stenella longirostris)

Spinner dolphins (Stenella longirostris) exhibit different social behaviours at two regions in the Hawaiian Archipelago: off the high volcanic islands in the SE archipelago they form dynamic groups with ever‐changing membership, but in the low carbonate atolls in the NW archipelago they form long‐term stable groups. To determine whether these environmental and social differences influence population genetic structure, we surveyed spinner dolphins throughout the Hawaiian Archipelago with mtDNA control region sequences and 10 microsatellite loci (n = 505). F‐statistics, Bayesian cluster analyses, and assignment tests revealed population genetic separations between most islands, with less genetic structuring among the NW atolls than among the SE high islands. The populations with the most stable social structure (Midway and Kure Atolls) have the highest gene flow between populations (mtDNA Φ_ST < 0.001, P = 0.357; microsatellite F_ST = ?0.001; P = 0.597), and a population with dynamic groups and fluid social structure (the Kona Coast of the island of Hawai’i) has the lowest gene flow (mtDNA 0.042 < Φ_ST < 0.236, P < 0.05; microsatellite 0.016 < F_ST < 0.040, P < 0.001). We suggest that gene flow, dispersal, and social structure are influenced by the availability of habitat and resources at each island. Genetic comparisons to a South Pacific location (n = 16) indicate that Hawaiian populations are genetically depauperate and isolated from other Pacific locations (mtDNA 0.216 < F_ST < 0.643, P < 0.001; microsatellite 0.058 < F_ST < 0.090, P < 0.001); this isolation may also influence social and genetic structure within Hawai’i. Our results illustrate that genetic and social structure are flexible traits that can vary between even closely‐related populations.     

Population stock structure of leatherback turtles (Dermochelys coriacea) in the Atlantic revealed using mtDNA and microsatellite markers

This study presents a comprehensive genetic analysis of stock structure for leatherback turtles (Dermochelys coriacea), combining 17 microsatellite loci and 763 bp of the mtDNA control region. Recently discovered eastern Atlantic nesting populations of this critically endangered species were absent in a previous survey that found little ocean-wide mtDNA variation. We added rookeries in West Africa and Brazil and generated longer sequences for previously analyzed samples. A total of 1,417 individuals were sampled from nine nesting sites in the Atlantic and SW Indian Ocean. We detected additional mtDNA variation with the longer sequences, identifying ten polymorphic sites that resolved a total of ten haplotypes, including three new variants of haplotypes previously described by shorter sequences. Population differentiation was substantial between all but two adjacent rookery pairs, and F _ST values ranged from 0.034 to 0.676 and 0.004 to 0.205 for mtDNA and microsatellite data respectively, suggesting that male-mediated gene flow is not as widespread as previously assumed. We detected weak (F _ST = 0.008 and 0.006) but significant differentiation with microsatellites between the two population pairs that were indistinguishable with mtDNA data. POWSIM analysis showed that our mtDNA marker had very low statistical power to detect weak structure (F _ST < 0.005), while our microsatellite marker array had high power. We conclude that the weak differentiation detected with microsatellites reflects a fine scale level of demographic independence that warrants recognition, and that all nine of the nesting colonies should be considered as demographically independent populations for conservation. Our findings illustrate the importance of evaluating the power of specific genetic markers to detect structure in order to correctly identify the appropriate population units to conserve.     

Conservation genetics of the short-beaked common dolphin (<Emphasis Type="Italic">Delphinus delphis</Emphasis>) in the Mediterranean Sea and in the eastern North Atlantic Ocean

Mediterranean Sea common dolphins have recently been listed as ‘endangered’ in the IUCN Red list, due to their reported decline since the middle of the 20th century. However, little is know about the number or distribution of populations in this region. We analysed 118 samples from the Black Sea, Mediterranean Sea and eastern North Atlantic at nine microsatellite nuclear loci and for 428 bps of the mtDNA control region. We found small but significant population differentiation across the basin between the eastern and the western Mediterranean populations at both nuclear and mtDNA markers (microsatellite F _ST = 0.052, mtDNA F _ST = 0.107, P values ≤ 0.001). This matched the differential distribution and habitat use patterns exhibited by this species in the eastern and the western parts of the Mediterranean Sea. The assignment test of a small number of samples from the central Mediterranean could not exclude further population structure in the central area of the basin. No significant genetic differentiation at either marker was observed among the eastern north Atlantic populations, though the Alboran population (inhabiting the Mediterranean waters immediately adjacent the Atlantic ocean) showed significant mtDNA genetic differentiation compared to the Atlantic populations. Directional estimates of gene flow suggested movement of females out of the Mediterranean, which may be relevant to the population decline. Phylogenetic analysis suggested that the observed population structure evolved recently.     

Phylogeography and population genetic structure of double-crested cormorants (Phalacrocorax auritus)

We examined the genetic structure of double-crested cormorants (Phalacrocorax auritus) across their range in the United States and Canada. Sequences of the mitochondrial control region were analyzed for 248 cormorants from 23 breeding sites. Variation was also examined at eight microsatellite loci for 409 cormorants from the same sites. The mitochondrial and microsatellite data provided strong evidence that the Alaskan subspecies (P. a. cincinnatus) is genetically divergent from other populations in North America (net sequence divergence = 5.85 %; Φ_ST for mitochondrial control region = 0.708; F_ST for microsatellite loci = 0.052). Historical records, contemporary population estimates, and field observations are consistent with recognition of the Alaskan subspecies as distinct and potentially of conservation interest. Our data also indicated the presence of another divergent lineage, associated with the southwestern portion of the species range, as evidenced by highly unique haplotypes sampled in southern California. In contrast, there was little support for recognition of subspecies within the conterminous U.S. and Canada. Rather than genetically distinct regions corresponding to the putative subspecies [P. a. albociliatus (Pacific), P. a. auritus (Interior and North Atlantic), and P. a. floridanus (Southeast)], we observed a distribution of genetic variation consistent with a pattern of isolation by distance. This pattern implies that genetic differences across the range are due to geographic distance, rather than discrete subspecific breaks. Although three of the four traditional subspecies were not genetically distinct, possible demographic separation, habitat differences, and documented declines at some colonies within the regions, suggests that the Pacific and possibly North Atlantic portions of the breeding range may warrant differential consideration from the Interior and Southeast breeding regions.     

Weak population genetic differentiation in the most numerous Arctic seabird,the little auk

Quantifying patterns of genetic diversity and differentiation among populations of Arctic birds is fundamental for understanding past and ongoing population processes in the Arctic. However, the genetic differentiation of many important Arctic species remains uninvestigated. Here, phylogeography and population genetics were examined in the worldwide population of a small seabird, the little auk (dovekie, Alle alle)—the most numerous avian species of the Arctic ecosystem. Blood samples or feathers were collected from 328 little auks (325 from the nominate subspecies and 3 from the A. a. polaris) in nine main breeding aggregations in the northern Atlantic and one location from the Pacific Ocean. The mtDNA haplotypes of the two subspecies were not segregated into separate groups. Also, no genetic structure was found within the nominate race based on microsatellite markers. The level of genetic differentiation among populations was low yet significant (mean F _ST = 0.005). Some pairwise F _ST comparisons revealed significant differences, including those involving the most distant Pacific colony as well as among some Atlantic populations. Weak population differentiation following the model of isolation by distance in the little auk is similar to the patterns reported in other high-Arctic bird species, indicating that a lack of distinct genetic structure is a common phenomenon in the Arctic avifauna.     

Population genetic structure of the common warthog (Phacochoerus africanus) in Uganda: evidence for a strong philopatry among warthogs and social structure breakdown in a disturbed population

Fine‐scale genetic structure of large mammals is rarely analysed. Yet it is potentially important in estimating gene flow between the now fragmented wildlife habitats and in predicting re‐colonization following local extinction events. In this study, we examined the extent to which warthog populations from five localities in Uganda are genetically structured using both mitochondrial control region sequence and microsatellite allele length variation. Four of the localities (Queen Elizabeth, Murchison Falls, Lake Mburo and Kidepo Valley) are national parks with relatively good wildlife protection practices and the other (Luwero), not a protected area, is characterized by a great deal of hunting. In the total sample, significant genetic differentiation was observed at both the mtDNA locus (F_ST = 0.68; P < 0.001) and the microsatellite loci (F_ST = 0.14; P < 0.001). Despite the relatively short geographical distances between populations, significant genetic differentiation was observed in all pair‐wise population comparisons at the two marker sets (mtDNA F_ST = 0.21–0.79, P < 0.001; microsatellite F_ST = 0.074–0.191, P < 0.001). Significant heterozygote deficiency was observed at most loci within protected areas while no significant deviation from Hardy–Weinberg expectation was observed in the unprotected Luwero population. We explain these results in terms of: (i) a strong philopatry among warthogs, (ii) a Wahlund effect resulting from the sampling regime and (iii) break down of social structure in the disturbed Luwero population.     

MITOCHONDRIAL DNA DIVERSITY IN THE SEA URCHINS STRONGYLOCENTROTUS PURPURATUS AND S. DROEBACHIENSIS

Restriction-fragment analysis was used to measure mitochondrial DNA (mtDNA) variability in 79 individuals of two species of temperate sea urchins. For the purple urchin Strongylocentrotus purpuratus, individuals were collected 1,500 km apart in 1985 and again from the same localities in 1988 (about one urchin generation). Twenty mtDNA genotypes belonging to four clades were found among 38 individuals. All four clades were found in both localities and in both years. Genetic structure was further tested by calculating the degree of interdeme genetic variation (G_ST) and comparing this value to the G_ST's from randomly shuffled data. No geographic structure was found. For S. droebachiensis, only six mtDNA genotypes were found among 41 individuals collected from the Pacific and Atlantic oceans. More than 80% of the individuals belonged to two genotypes. The genotype that dominated collections in the Pacific also occurred in the Atlantic; however, a common Atlantic genotype was never found in the Pacific. These two genotypes were identical at 64 of 65 restriction sites, and were only 0.2% divergent from each other. G_ST analysis confirmed that there were significant genetic differences between Atlantic and Pacific populations. The small divergence between genotypes suggests recent, but not continuous, migration. These marine species show smaller genotypic differences than terrestrial species over similar spatial and temporal scales. Both recruitment of adults from planktonic larval pools and the spread of sibling larvae over large distances from parents probably act as buffers to genetic differences in species with planktonic life-history phases.     

Genetic differentiation between humpback whales (Megaptera novaeangliae) from Atlantic and Pacific breeding grounds of South America

Humpback whales wintering in tropical waters along the Atlantic and Pacific coasts of the South American continent are thought to represent distinct populations or “stocks.” Here we present the first analysis of genetic differentiation and estimates of gene flow between these breeding stocks, based on both mitochondrial DNA (mtDNA) control region sequences (465 bp) and 16 microsatellite loci from samples collected off Brazil (n = 277) and Colombia (n = 148), as well as feeding areas near the western Antarctic Peninsula (n = 86). We found significant differentiation between Brazilian and Colombian breeding grounds at both mtDNA (F_ST = 0.058) and microsatellite (F_ST = 0.011) markers and corroborated previous studies showing genetic similarity between humpbacks from Colombia and those from Antarctic Peninsula feeding areas. Estimates of long‐term gene flow between Brazil and Colombia were low to moderate, asymmetrical, and mostly mediated by males. Assignment procedures detected some cases of interchange and individuals of admixed ancestry between breeding grounds, indicating limited mixing of individuals between these stocks. Overall, results highlight the differentiation of humpback whale breeding populations with adjacent feeding grounds. This appears to be a remarkable example of fidelity to seasonal habitat in the absence of any contemporary barriers.     

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.     

What Maintains the Central North Pacific Genetic Discontinuity in Pacific Herring?

Pacific herring show an abrupt genetic discontinuity in the central North Pacific that represents secondary contact between refuge populations previously isolated during Pleistocene glaciations. Paradoxically, high levels of gene flow produce genetic homogeneity among ocean-type populations within each group. Here, we surveyed variability in mtDNA control-region sequences (463 bp) and nine microsatellite loci in Pacific herring from sites across the North Pacific to further explore the nature of the genetic discontinuity around the Alaska Peninsula. Consistent with previous studies, little divergence (Φ_ST  = 0.011) was detected between ocean-type populations of Pacific herring in the North West Pacific, except for a population in the Yellow Sea (Φ_ST  = 0.065). A moderate reduction in genetic diversity for both mtDNA and microsatellites in the Yellow Sea likely reflects founder effects during the last colonization of this sea. Reciprocal monophyly between divergent mtDNA lineages (Φ_ST  = 0.391) across the Alaska Peninsula defines the discontinuity across the North Pacific. However, microsatellites did not show a strong break, as eastern Bering Sea (EBS) herring were more closely related to NE Pacific than to NW Pacific herring. This discordance between mtDNA and microsatellites may be due to microsatellite allelic convergence or to sex-biased dispersal across the secondary contact zone. The sharp discontinuity between Pacific herring populations may be maintained by high-density blocking, competitive exclusion or hybrid inferiority.