Mitochondrial DNA Sequence Variation Research Articles

A new bat species of the genus Myotis with comments on the phylogenetic placement of M. keaysi and M. pilosatibialis

Molecular studies of Neotropical Myotis (Chiroptera, Vespertilionidae) in the last decade have uncovered substantial cryptic diversity. One example is M. keaysi pilosatibialis , which is characterized by a complex taxonomy derived from low morphological variation. Herein, we studied cryptic diversity of a high elevation clade from premontane and montane forest of Chiriqui Province (Panama), Cordillera Oriental (Ecuador), and Valle del Silencio (Costa Rica). Additionally, we disentangle relationships of M. k. keaysi and M. k. pilosatibialis by determining their phylogenetic placement within the Neotropical Myotis radiation. In the process, we identified a new lineage of species level hierarchy that is described herein. We used an integrative taxonomy approach, using a combination of linear morphometrics, qualitative morphology, molecular phylogenetics, and climatic analysis. The newly identified lineage is a sister species to M. pilosatibialis str., but differs from M. sp. (Quintana Roo, Mexico), M. keaysi str. , and M . oxyotus gardneri in size and other quantitative morphological characters in addition to both nuclear and mitochondrial DNA sequence divergence. Based on our phylogenetic analysis of partial cytochrome b sequence, the polyphyly of M . keaysi str. and M. pilosatibialis str. is resolved, with M . keaysi str. paraphyletic to M . ruber and M . simus . Myotis pilosatibialis is part of a monophyletic clade that is sister to the newly identified species. This report refines our understanding of taxonomy and systematics of the Myotis pilosatibialis complex of bats, identifies and describes a new species of Myotis, and more broadly it contributes to efforts to characterize species in this genus in Neotropical environments. Based on its distribution, we classified this newly described species as paramontane due to its restriction to premontane and montane forest of Chiriqui Province (Panama), Valle del Silencio (Costa Rica), and Cordillera Oriental (Ecuador). These habitats are susceptible to the effects of climate change, in addition to ongoing habitat destruction.

Paternal Origins and Migratory Episodes of Domestic Sheep

The domestication and subsequent global dispersal of livestock are crucial events in human history, but the migratory episodes during the history of livestock remain poorly documented [1-3]. Here, we first developed a set of 493 novel ovine SNPs of the male-specific region of Y chromosome (MSY) by genome mapping. We then conducted a comprehensive genomic analysis of Y chromosome, mitochondrial DNA, and whole-genome sequence variations in a large number of 595 rams representing 118 domestic populations across the world. We detected four different paternal lineages of domestic sheep and resolved, at the global level, their paternal origins and differentiation. In Northern European breeds, several of which have retained primitive traits (e.g., a small body size and short or thin tails), and fat-tailed sheep, we found an overrepresentation of MSY lineages y-HC and y-HB, respectively. Using an approximate Bayesian computation approach, we reconstruct the demographic expansions associated with the segregation of primitive and fat-tailed phenotypes. These results together with archaeological evidence and historical data suggested the first expansion of early domestic hair sheep and the later expansion of fat-tailed sheep occurred ∼11,800-9,000 years BP and ∼5,300-1,700 years BP, respectively. These findings provide important insights into the history of migration and pastoralism of sheep across the Old World, which was associated with different breeding goals during the Neolithic agricultural revolution.

Association of mitochondrial DNA content and displacement loop region sequence variations with cancer-related fatigue in breast cancer survivors receiving chemotherapy

Cancer-related fatigue (CRF) is characterized by a lack of energy, and mitochondrial dysfunction is postulated to contribute to its etiology. This prospective cohort study assesses the self-reported fatigue levels of early-stage breast cancer patients using the validated Multi-Dimensional Fatigue Symptom Inventory–Short Form (MFSI-SF) and blood samples drawn at three time points: before treatment, approximately 6 weeks, and 12 weeks after the initiation of chemotherapy. The aim of this study is to evaluate mitochondrial measures with CRF, over the course of chemotherapy using mitochondrial DNA (mtDNA content) and displacement loop (D-loop) region sequence variations at nucleotide positions 303, 489 and 514. The relative mtDNA copy number was determined via real-time quantitative polymerase chain reaction and compared between study time points and D-loop sequence variants. The association of mtDNA content with MFSI-SF total and sub-domain scores was analyzed in a sample of 155 patients (mean age ± SD: 51.7 ± 8.8 years). The median mtDNA content decreased over 12 weeks after the initiation of chemotherapy (p < 0.001). Baseline mtDNA content was lower for nucleotide position 303 in sequence variations than for the reference sequence (67.2 copies vs 79.1 copies, p = 0.03). Physical fatigue negatively correlated with mtDNA content in both unadjusted (β = −0.0075, p = 0.048) and adjusted models (β = −0.0062, p = 0.042), accounting for age, anxiety, insomnia, haemoglobin levels and body mass index. Our findings add to the literature indicating that mitochondrial function serves as an important target for mitigating CRF.

Mitochondrial lineages or discrete species? Assessing diversity within Timon tangitanus (Lacertidae) using mitochondrial and nuclear DNA sequences

Abstract Identification of extremely high levels of mitochondrial DNA (mtDNA) sequence divergence within reptiles from North Africa is commonplace. This high divergence often compares with interspecific levels among widely accepted species, leading to the hypothesis of the occurrence of species complexes. Indeed, in many examples, data from nuclear markers support such taxonomic recognition. Such is the case of two recently recognized ocellated lizard species of the genus Timon, T. nevadensis, from Spain, and T. kurdistanicus, from the Middle East, which both showed notable genetic differentiation from their sister taxa. In North Africa, highly divergent mtDNA lineages of Timon tangitanus were previously identified but not corroborated with nuclear markers. Here we expand geographic sampling across the range of Timon tangitanus and complement mtDNA sequences with data from nuclear markers (MC1R and ACM4). We identify four divergent mtDNA lineages, at a level similar to some reptile species. However, the nuclear markers show limited differentiation and lack of lineage sorting. This and some other recent assessments within reptiles discourage the use of mtDNA data alone as a proxy for taxonomic units, demonstrating once more the need for integrative taxonomic approaches.

Association between Mitochondrial DNA Sequence Variants and V˙O2 max Trainability.

We designed the study to determine whether mitochondrial DNA (mtDNA) haplogroup, sequence, and heteroplasmy differed between individuals previously characterized as low (LR) or high responders (HR) as defined by their maximal oxygen uptake response to a standardized aerobic exercise training program. DNA was isolated from whole blood in subjects from the HERITAGE Family Study that were determined to be either HR (n = 15) or LR (n = 15). mtDNA was amplified by long-range polymerase chain reaction, then tagged with Nextera libraries and sequenced on a MiSeq instrument. Different mtDNA haplogroup subtypes were found in HR and LR individuals. Compared with HR subjects, significantly more LR subjects had variants in 13 sites, including 7 in hypervariable (HV) regions: HV2 (G185A: 0 vs 6, P = 0.02; G228A: 0 vs 5, P = 0.04; C295T: 0 vs 6; P = 0.04), HV3 (C462T: 0 vs 5, P = 0.04; T489C: 0 vs 5; P = 0.04), and HV1 (C16068T: 0 vs 6, P = 0.02; T16125C: 0 vs 6, P = 0.02). Remaining variants were in protein coding genes, mtND1 (1 vs 8, P = 0.02), mtND3 (A10397G: 0 vs 5, P = 0.04), mtND4 (A11250G: 1 vs 8, P = 0.02), mtND5 (G13707A: 0 vs 5, P = 0.04), and mtCYTB (T14797C: 0 vs 5, P = 0.04; C15451A: 1 vs 8, P = 0.02). Average total numbers of heteroplasmies (P = 0.83) and frequency of heteroplasmies (P = 0.05) were similar between the groups. Our findings provide specific sites across the mitochondrial genome that may be related to maximal oxygen uptake trainability.

Geographic origin and timing of colonization of the Pacific Coast of North America by the rocky shore gastropod Littorina sitkana.

The demographic history of a species can have a lasting impact on its contemporary population genetic structure. Northeastern Pacific (NEP) populations of the rocky shore gastropod Littorina sitkana have very little mitochondrial DNA (mtDNA) sequence diversity and show no significant population structure despite lacking dispersive planktonic larvae. A contrasting pattern of high mtDNA diversity in the northwestern Pacific (NWP) suggests that L. sitkana may have recently colonized the NEP from the NWP via stepping-stone colonization through the Aleutian-Commander Archipelago (ACA) following the end of the last glacial 20,000 years ago. Here, we use multi-locus sequence data to test that hypothesis using a combination of descriptive statistics and population divergence modeling aimed at resolving the timing and the geographic origin of NEP populations. Our results show that NEP populations share a common ancestor with a population of L. sitkana on the Kamchatka Peninsula ∼46,900 years ago and that NEP populations diverged from each other ∼21,400 years ago. A more recent population divergence between Kamchatka and NEP populations, than between Kamchatka and other populations in the NWP, suggests that the ACA was the most probable dispersal route. Taking into account the confidence intervals for the estimates, we conservatively estimate that L. sitkana arrived in the NEP between 107,400 and 4,100 years ago, a range of dates that is compatible with post-glacial colonization of the NEP. Unlike other congeners that are relatively abundant in the Pleistocene fossil record of the NEP, only one report of L. sitkana exists from the NEP fossil record. Although broadly consistent with the molecular data, the biogeographic significance of these fossils is difficult to evaluate, as the shells cannot be distinguished from the closely-related congener L. subrotundata.

Mitochondrial DNA Inheritance in Humans: Mix, Match, and Survival of the Fittest

Mitochondrial DNA (mtDNA) sequence variation and maternal inheritance are valuable tools in assessing ancestry of different human populations and for clinical practice. A new study (Wei etal., 2019) reports that the fate of new mtDNA variants in the female germline is non-random as they report functional selection and matching to nuclear ancestry to shape human mtDNA variation.

Identification of genetic families based on mitochondrial D-loop sequence in population of the Tatra chamois (Rupicapra rupicapra tatrica)

The Tatra chamois is an endemic subspecies of Northern chamois, indigenous only in the Tatras, a wild animal genetic resource unique to Slovakia. The main goal of this study was to describe the distribution of mtDNA haplogroups in isolated populations inhabiting geographical areas in the Slovak part of the Tatras and the development of methodologies for reliable differentiation between the closely related Alpine and Tatra subspecies based on mitochondrial DNA (mtDNA) sequence variation. A partial sequence of the D-loop region was obtained to enable analysis of the mtDNA and subsequent estimation of the population haplotype structures. Despite the relatively short fragment of the D-loop region (final length 480 bp) analysed, reliable differentiation of the selected subspecies as genetically unique was obtained. Moreover, the study results indicated the occurrence of four haplotypes within the sampled population. Except for three previously published haplotypes, the analysis of the target mtDNA region suggested the occurrence of a new group, here noted as Tatra 10, indicating the existence of a new, unique haplotype. From the geographical point of view, this new haplotype, seems to be restricted to the area of the Western Tatras. Thus, our study provides new insight into the haplotype structure of the native Tatra chamois population in Slovakia and can be beneficial for the management of its conservation status. It should be emphasised that the Tatra chamois is regarded as a critically endangered species. Therefore, the systematic monitoring of genetic diversity, including the distribution of mtDNA haplotypes, is necessary to develop an appropriate conservation strategy.

Two Divergent Genetic Lineages within the Horned Passalus Beetle, Odontotaenius disjunctus (Coleoptera: Passalidae): An Emerging Model for Insect Behavior, Physiology, and Microbiome Research.

The horned passalus (Odontotaenius disjunctus) is one of the most extensively studied saproxylic beetles in the eastern United States. For several decades this species has been the subject of investigations into the behaviors associated with subsociality as well as physiological responses to stress, and, most recently, the composition of its gut microbiome has been closely examined. However, no published study to date has characterized this beetle’s broad-scale population genetic structure. Here, we conducted intensive geographic sampling throughout the southern Appalachian Mountains and surrounding areas and then assessed mitochondrial DNA (mtDNA) sequence variation among individuals. Unexpectedly, we discovered two divergent, yet broadly sympatric, mtDNA clades. Indeed, the magnitude of divergence between- vs. within-clades ranged from 5.9 to 7.5×, depending on the dataset under consideration, and members of the two lineages were often syntopic (i.e., found in the same rotting log). Given the potential implications for past and future studies on behavior, physiology, and the gut microbiome, we developed a simple cost-efficient molecular assay (i.e., polymerase chain reaction restriction fragment length polymorphism; PCR-RFLP) to rapidly determine mtDNA clade membership of O. disjunctus individuals. We suggest that the evolutionary processes that gave rise to the emergence and persistence of divergent sympatric lineages reported here warrant investigation, as this type of spatial-genetic pattern appears to be rare among southern Appalachian forest invertebrates.

Mitochondrial DNA sequence variations in populations of Sardinapilchardus(Walbaum 1792) along the Tunisian coasts

Sardine is a fish species of great economic importance to Tunisia. Knowledge of genetic diversity and population distribution is essential for an efficient management and sustainability of any regional fishery. This study aimed to assessing the genetic structure and to specify the stocks of the European sardine (Sardina pilchardus). To this end, 83 specimens were collected from three localities along the Tunisian coast and analysed using mitochondrial DNA sequences. The results of sequence analysis determined the existence of variations in 40 single nucleotide sites within the 307 bp fragment of the cytb gene examined and defined twenty different haplotypes. Genetic diversity, estimated by haplotypic diversity, was high in all samples. Tunisian S.pilchardus samples show some level of genetic structuring. First, genetic differentiation between localities (ΦST estimates) was significant for all comparison. Second, the analysis of molecular variance AMOVA indicates a high level of genetic variation (ΦST = 0.093; P&lt;0.001). The structural patterns identified can be explained largely in relation to the regional oceanographic features. In conclusion, this study provided initial genetic data in making inference of the genetic structure of S. pilchardus along the Tunisian coasts.

Analysis of 16S mitochondrial ribosomal DNA sequence variations and phylogenetic relations among some Serranidae fishes

Reconstruction of phylogenetic relations among certain Serranidae fish could be applied to detect the biodiversity that is needed to conserve these biological resources. This study was designed to provide information about the molecular variations within and among numbers of economically important fishes (42 fish species that belong to three genera), using a simple and effective barcoding system. A comparative genetic analysis was carried out among some 16S r-RNA sequences in various Serranidae fish genera ( Plectropomus , Cephalopholis and Epinephelus ). Nucleotide composition, sequence conservation, single nucleotide polymorphism (SNP), haplotype diversity and nucleotide diversity were calculated in all these fish species. All of these fish samples were differentiated by the barcoding system. Average genetic distance values within Plectropomus , Epinephelus and Cephalopholis were 0.03, 0.039 and 0.048, respectively. Plectropomus species were found to be distantly related to both Epinephelus and Cephalopholis . The DNA barcoding system should be used in fisheries and aquaculture to conserve aquatic genetic resources. Keywords: Epinephelus , Plectropomus , Cephalopholis , comparative, genetics

MtDNA haplotype analysis in Finnish families with leber hereditary optic neuroretinopathy.

The mitochondrial DNA (mtDNA) sequence variation of 24 Finnish Leber hereditary optic neuroretinopathy (LHON) probands was characterized by sequencing and restriction endonuclease analyses. All LHON-associated substitutions and Caucasoid haplogroup-specific mutations were screened in the families. Analysis of the mtDNAs revealed that the Finnish LHON families have two unique features: an absence of the ND6/14484 mutation and a high number of families (10/24) without the primary mutations ND1/3460 and ND4/11778. Furthermore, the LHON families showed considerable mtDNA heterogeneity: among 24 families 22 haplotypes were detected. Overall, the haplogrouping of LHON families was similar to other European populations. However, the frequency of ND4/11778-positive families in haplogroup J was high, which may indicate that background mutations in this haplogroup together with the ND4/11778 primary mutation promote the penetrance of LHON.

Mitochondrial DNA and Y chromosome-specific polymorphisms in the Seminole Tribe of Florida.

Mitochondrial DNA (mtDNA) sequence variation was examined in 37 Seminoles from Florida by polymerase chain reaction amplification and high resolution restriction endonuclease analysis. The Y chromosome TaqI restriction fragment length polymorphisms detected by the probes 49a, 49f, and 12f2 were examined in the 26 males of this group. Analysis of the mtDNA revealed that all four Native American haplogroups (A, B, C and D) were present in the Seminoles encompassing about 95% of the Seminole mtDNAs. No European mtDNAs were found among the Seminoles, but two mtDNAs (about 5%) were members of the African-specific haplogroup L1, thus indicating that a limited number of African women were incorporated in the Seminole tribe. Analysis of Y chromosome haplotypes supports the hypothesis that haplotypes 18 and 63 are the most likely founding Native American Y chromosome haplotypes from Asia. However, 11% of the Seminole Y chromosomes represented haplotypes generally attributed to Europeans, though none harbored standard African haplotypes. These findings support historical evidence that the Seminole tribe has integrated individuals of European and African ancestry, but suggests that the sex ratio of nonnatives from different continents may have varied.

Phylogeny and phylogeography of the genus Luciobarbus (Haeckel, 1843) in Algeria inferred from mitochondrial DNA sequence variation

Phylogenetic relationships and biogeographical patterns of the genus Luciobarbus in Algeria were investigated by analysing the complete cytochrome b sequence variation. With regard to species of the Maghreb Province and the Iberian Peninsula, phylogenetic analysis resulted in five strongly supported clades and a non-monophyletic origin for the Algerian populations. The present study supports the existence of two distinct lineages of L. setivimensis which could have diverged posterior to the emplacement of the Kabylides onto the African margin. Analysis of the 48 haplotypes detected within populations showed a clear phylogeographic structure strongly correlated with species’ geographical distribution. Two haplotypes were found to be shared between different species attesting the possibility that an introgression would have occurred within the genus Luciobarbus in Algeria. The divergence time estimate suggests a rapid radiation of the genus Luciobarbus in Algeria and a pattern of distribution of populations shaped under paleogeographic conditions such as the tectonic dynamics which have led to the change in the geographic configuration of North Africa at the end of Miocene, the formation of the current fluvial basins’ net in the Pliocene as well as the end of the Tell System building in the Pleistocene which seems to have played an important role in the speciation of this genus.

Identification of a novel mitochondrial DNA sequence variation within the human mitochondrial DNA Control Region in a population of Aegean population

Identification of a novel mitochondrial DNA sequence variation within the human mitochondrial DNA Control Region in a population of Aegean population

Phylogeography of the widespread creek chub Semotilus atromaculatus (Cypriniformes: Leuciscidae).

The extent and nature of genetic differentiation in Semotilus atromaculatus, one of the most abundant and widespread leuciscids in North America, were evaluated based on mitochondrial (mt) and nuclear DNA sequence variation. Phylogenetic relationships were first inferred based on a fragment of the cytochrome b (cytb) region and the nuclear intron s7 gene for S. atromaculatus and all other congeners as well as representative species from all other genera in the creek chub-plagopterin clade. The phylogeography of major haplogroups of S. atromaculatus was also assessed according to variation in a fragment of the mitochondrial cytb region from 567 individuals across its range. All analyses identified S. thoreauianus, S. lumbee and S. corporalis as reciprocally monophyletic groups. Analyses of nuclear sequence variation resolved S. atromaculatus as a single clade, where S. thoreauianus and S. lumbee were recovered as the sister group to S. atromaculatus, and S. corporalis was resolved as sister to all other species in the genus. Analyses of mtDNA sequence variation recovered S. atromaculatus as three well supported and differentiated monophyletic groups, with a widespread genetically homogeneous lineage extending across most of the current range of the species; a more geographically restricted and geographically structured lineage in the southern Appalachians, sister group to S. lumbee; and a geographically restricted lineage was identified from two Gulf Slope basins. Evidence of complex mito-nuclear discordance and phylogeographic differentiation within S. atromaculatus illustrates that further analysis of widespread species is warranted to understand North American freshwater fish diversity and distributions.

Meta-analysis identifies mitochondrial DNA sequence variants associated with walking speed.

Declines in walking speed are associated with a variety of poor health outcomes including disability, comorbidity, and mortality. While genetic factors are putative contributors to variability in walking, few genetic loci have been identified for this trait. We examined the role of mitochondrial genomic variation on walking speed by sequencing the entire mitochondrial DNA (mtDNA). Data were meta-analyzed from 1758 Lifestyle Interventions and Independence for Elders (LIFE) Study and replication data from 730 Health, Aging, and Body Composition (HABC) Study participants with baseline walking speed information. Participants were 69+ years old of diverse racial backgrounds (African, European, and other race/ethnic groups) and had a wide range of mean walking speeds [4-6m (0.78-1.09m/s) and 400m (0.83-1.24m/s)]. Meta-analysis across studies and racial groups showed that m.12705C>T, ND5 variant was significantly associated (p < 0.0001) with walking speed at both short and long distances. Replication and meta-analysis also identified statistically significant walking speed associations (p < 0.0001) between the m.5460.G>A, ND2 and m.309C>CT, HV2 variants at short and long distances, respectively. All results remained statistically significant after multiple comparisons adjustment for 499 mtDNA variants. The m.12705C>T variant can be traced to the beginnings of human global migration and that cells carrying this variant display altered tRNA expression. Significant pooled effects related to stopping during the long-distance walk test were observed across OXPHOS complexes I (p = 0.0017) and III (p = 0.0048). These results suggest that mtDNA-encoded variants are associated with differences in walking speed among older adults, potentially identifying those at risk of developing mobility impairments.

Mitochondrial DNA Sequence Variants Associated With Blood Pressure Among 2 Cohorts of Older Adults.

BackgroundAge‐related changes in blood pressure are associated with a variety of poor health outcomes. Genetic factors are proposed contributors to age‐related increases in blood pressure, but few genetic loci have been identified. We examined the role of mitochondrial genomic variation in blood pressure by sequencing the mitochondrial genome.Methods and ResultsMitochondrial DNA (mtDNA) data from 1755 participants from the LIFE (Lifestyle Interventions and Independence for Elders) studies and 788 participants from the Health ABC (Health, Aging, and Body Composition) study were evaluated using replication analysis followed by meta‐analysis. Participants were aged ≥69 years, of diverse racial backgrounds, and assessed for systolic blood pressure (SBP), diastolic blood pressure, and mean arterial pressure. After meta‐analysis across the LIFE and Health ABC studies, statistically significant associations of mtDNA variants with higher SBP (m.3197T>C, 16S rRNA; P=0.0005) and mean arterial pressure (m.15924A>G, t‐RNA‐thr; P=0.004) were identified in white participants. Among black participants, statistically significant associations with higher SBP (m.93A>G, HVII; m.16183A>C, HVI; both P=0.0001) and mean arterial pressure (m.16172T>C, HVI; m.16183A>C, HVI; m.16189T>C, HVI; m.12705C>T; all P's<0.0004) were observed. Significant pooled effects on SBP were observed across all transfer RNA regions (P=0.0056) in white participants. The individual and aggregate variant results are statistically significant after multiple comparisons adjustment for the number of mtDNA variants and mitochondrial regions examined.ConclusionsThese results suggest that mtDNA‐encoded variants are associated with variation in SBP and mean arterial pressure among older adults. These results may help identify mitochondrial activities to explain differences in blood pressure in older adults and generate new hypotheses surrounding mtDNA variation and the regulation of blood pressure.Clinical Trial Registration URL: http://www.ClinicalTrials.gov. Unique identifiers: NCT01072500 and NCT00116194.

Analysis of mitochondrial DNA sequence and copy number variation across five high-altitude species and their low-altitude relatives

High-altitude inhospitable environments impose a formidable life challenge for the local animals. Training and exposure to high-altitude environments produce both distinct physiological and phenotypic characteristics. The mitochondrion, an organelle crucial for the energy production, plays an important role in hypoxia adaptation. In this study, we investigated the mitochondrial DNA (mtDNA) polymorphism and copy number variation between the population pairs from distinct altitudes across the multi-species. Higher mitochondrial DNA control region’s genetic diversity is conspicuous in high-altitude animals versus low-altitude relatives. We also found an accordant decrease of mtDNA copy number in most of the tissues from high-altitude animals. Compared to mammals, chickens have significantly distinct mitogenomic characteristics, and more significant changes in the skeletal muscle mtDNA copy number between high- and low-altitude individuals. Our study catches a snapshot of the biological similarities and differences in the mitochondrial high-altitude acclimation across the species.

Deep-Sea Phylogeographic Structure Shaped by Paleoenvironmental Changes and Ongoing Ocean Currents Around the Sea of Japan in a Crangonid Shrimp, Argis lar.

The deep-sea crangonid shrimp, Argis lar, is a highly abundant species from the northern Pacific Ocean. We investigated its phylogeographic and demographic structure across the species' extensive range, using mitochondrial DNA sequence variation to evaluate the impact of deep-sea paleoenvironmental dynamics in the Sea of Japan on population histories. The haplotype network detected three distinct lineages with allopatric isolation, which roughly corresponded to the Sea of Japan (Lineage A), the northwestern Pacific off the Japanese Archipelago (Lineage B), and the Bering Sea/Gulf of Alaska (Lineage C). Lineage A showed relatively low haplotype and nucleotide diversity, a significantly negative value of Tajima's D, and a star-shaped network, suggesting that anoxic bottom-water in the Sea of Japan over the last glacial period may have brought about a reduction in the Sea of Japan population. Furthermore, unexpectedly, the distributions of Lineage A and B were closely related to the pathways of the two ocean currents, especially along the Sanriku Coast. This result indicated that A. lar could disperse across shallow straits through the ocean current, despite their deep-sea adult habitat. Bayesian inference of divergence time revealed that A. lar separated into three lineages approximately 1 million years before present (BP) in the Pleistocene, and then had been influenced by deep-sea paleoenvironmental change in the Sea of Japan during the last glacial period, followed by a more recent larval dispersal with the ocean current since ca. 6 kilo years BP.