mtDNA Control Region Sequences Research Articles

Where east meets west: Phylogeography of the high Arctic North American brant goose.

Genetic variation in Arctic species is often influenced by vicariance during the Pleistocene, as ice sheets fragmented the landscape and displaced populations to low- and high-latitude refugia. The formation of secondary contact or suture zones during periods of ice sheet retraction has important consequences on genetic diversity by facilitating genetic connectivity between formerly isolated populations. Brant geese (Branta bernicla) are a maritime migratory waterfowl (Anseriformes) species that almost exclusively uses coastal habitats. Within North America, brant geese are characterized by two phenotypically distinct subspecies that utilize disjunct breeding and wintering areas in the northern Pacific and Atlantic. In the Western High Arctic of Canada, brant geese consist of individuals with an intermediate phenotype that are rarely observed nesting outside this region. We examined the genetic structure of brant geese populations from each subspecies and areas consisting of intermediate phenotypes using mitochondrial DNA (mtDNA) control region sequence data and microsatellite loci. We found a strong east-west partition in both marker types consistent with refugial populations. Within subspecies, structure was also observed at mtDNA while microsatellite data suggested the presence of only two distinct genetic clusters. The Western High Arctic (WHA) appears to be a secondary contact zone for both Atlantic and Pacific lineages as mtDNA and nuclear genotypes were assigned to both subspecies, and admixed individuals were observed in this region. The mtDNA sequence data outside WHA suggests no or very restricted intermixing between Atlantic and Pacific wintering populations which is consistent with published banding and telemetry data. Our study indicates that, although brant geese in the WHA are not a genetically distinct lineage, this region may act as a reservoir of genetic diversity and may be an area of high conservation value given the potential of low reproductive output in this species.

Exploring mtDNA Databases to Evaluate the Population Structure and Genetic Diversity of Tursiops truncatus in the Atlantic Ocean: Implications for the Conservation of a Small, Offshore Population

Inshore and offshore bottlenose dolphin, Tursiops truncatus, ecotypes were distinguished through genetics, distribution, diet, morphology, diversity, and social behaviors. Although T. truncatus is a widely studied species, few studies have focused on offshore populations. Offshore biodiversity is frequently neglected due to the difficulty of data collection, and therefore, it is challenging to assess how threatened these populations are. A small, offshore population of dolphins residing around the Saint Peter Saint Paul Archipelago (SPSPA) in the middle of the Atlantic Ocean has been monitored for several years, and a decrease in the number of dolphin sightings has recently been noticed. We analyzed a comprehensive mtDNA control-region sequence dataset for this species to infer the conservation status and better understand the relationships between the SPSPA population and other offshore populations. We assessed the genetic diversity and population structure of the bottlenose dolphin from inshore and offshore populations of the Atlantic Ocean. Offshore populations are more genetically diverse and have less variation between populations than inshore populations. The offshore populations share haplotypes, indicating potential gene flow. However, the SPSPA population presented the lowest levels of genetic diversity between populations. The conservation status of the SPSPA population is concerning, and it is necessary to apply effective management strategies to guarantee its protection.

The sacred deer conflict of management after a 1000‐year history: Hunting in the name of conservation or loss of their genetic identity

AbstractHuman–wildlife conflict involves diverse stakeholders with conflicting values. Resolving such conflicts necessitates the development of management plans rooted in scientific knowledge and establishing of social consensus. In Nara City, situated within the Japanese Archipelago, wild sika deer (Cervus nippon) hold sacred significance due to religious reasons and have been protected for over a millennium, resulting in a distinct genetic identity. However, the escalating deer population has caused significant agricultural damage in the areas surrounding the sanctuary. Consequently, a debate has arisen regarding the advantages and disadvantages of implementing lethal measures to address individuals that might be considered sacred deer but are regarded as pests in the vicinity of the sanctuary. Here, we used mitochondrial DNA (mtDNA) control region and nuclear simple sequence repeat (SSR) markers to detect the origin of deer in the areas neighboring the sanctuary (management areas). As a result, two genetic populations of deer were detected in Nara City. In the sanctuary, we detected only one specific mtDNA haplotype (S4). On the other hand, seven haplotypes, including S4, were detected in the management area. SSR analysis also suggested that the sika deer in the management area may be an admixed population of multiple origins from the sanctuary and out of Nara City. Interbreeding populations may expand into the sanctuary, and unique genetic populations for more than 1000 years may disappear. This study suggests that ordinary deer could soon replace the deer revered and protected by the people of Nara. Additionally, the proximity of sanctuary deer to tourists worldwide and the interaction with wild deer in other areas pose a potential risk of spreading zoonotic diseases. Urgent decisions are required to determine whether to advocate for extermination in managed areas for ‘conservation’ purposes or risk losing the genetic identity of the sacred deer.

Population genetic structure of the provincially endangered mainland Eastern Moose (<i>Alces americanus americanus</i>) in Nova Scotia, Canada

Eastern Moose (Alces americanus americanus (Clinton, 1822)) on mainland Nova Scotia (MNS) are declining and experience limited immigration across the Isthmus of Chignecto from the larger population in neighbouring New Brunswick. Provincially Endangered, the recovery strategy for MNS Moose involves mitigating various threats that may lead to local extirpation. We examine genetic diversity of MNS Moose using microsatellite markers and mitochondrial (mtDNA) control region sequences. Genetic similarities with the Alces a. americana population in New Brunswick and the introduced Northwestern Moose (Alces americanus andersoni (= Alces alces andersoni) Peterson, 1952) population on Cape Breton Island are also analysed. Observed heterozygosity for microsatellites for MNS Moose was low and there was also evidence of limited gene flow between Nova Scotia and New Brunswick across the narrow Isthmus of Chignecto that connects these provinces. Consistent with relatively recent colonization of North America by Moose dispersing across the Bering Land Bridge <15 000 years ago, mtDNA haplotypes of MNS Moose were identical or extremely similar to haplotypes found across North America. However, mtDNA diversity was lower in Nova Scotia and New Brunswick than in more central regions of the species’ range. Active measures to maintain habitat that promote connectivity across the Isthmus of Chignecto would likely be valuable for Moose in terms of maintaining genetic variation in the region and reducing inbreeding.

Molecular Characterization of Mare Families in the Serbian Population of the Lipizzan Horse

Summary The Lipizzan horse breed was established in the 16th century in Lipica and later spread throughout Central and Eastern Europe. In addition to six classical stallion lines, 17 classical mare family lines were established in the old Lipica stud. Additional 44 mare family lines, including local lines, were established in other Lipizzan studs. The founders of the classical Lipizzan mare family lines date back to the period between the 18th and 20th century and came from various breeds, including the Karst, Spanish, Italian, Kladruber and Arabian horses. The history of the Lipizzan mare family lines is well described and supported by the availability of 44 nucleotide sequences of the mtDNA control region. In this study, the mtDNA control region of 23 Serbian Lipizzans, representing the established Lippizan mare family lines, as well as the local mare family line Zora, have been sequenced. The objective of this study was to test whether the Zora mare family line could be distinguished from other Lipizzan mare family lines according to the mtDNA sequence. Sequences were aligned to the entire set of mtDNA control region sequences representing 44 Lipizzan mtDNA haplotypes. Based on the alignment, a median-joining network was constructed. The individuals in this study formed a cluster with the existing Lipizzan mare family lines. However, a total of ten individuals belonging to the local Zora mare family line formed a compact cluster close to the mtDNA haplotypes, representing the classical mare family lines Wera, Betalka, and Monteaura. Additional pedigree data are needed to clarify the origin of the mtDNA haplotype variant identified in this study.

Whole mitochondrial genome sequencing provides new insights into the phylogeography of loggerhead turtles (Caretta caretta) in the Mediterranean Sea

Population structure and phylogeography of the loggerhead sea turtle (Caretta caretta) have so far been assessed mainly by mitochondrial DNA (mtDNA) single-gene sequencing studies. However, phylogenetic relationships amongst matrilines, genetic characterisation of rookeries and mixed-stock analyses have suffered from the limited resolution obtained by comparison of relatively short sequences such as from the mtDNA control region. Whole mitogenome sequencing can significantly improve population genetics, particularly in marine organisms showing female natal philopatry. Despite mitogenomics becoming increasingly common in biodiversity monitoring and conservation, only a few complete mitogenomes are available for C. caretta. In this study, we sequenced the complete mtDNA of 61 loggerhead turtles sampled between 2008 and 2021 along the Italian coastline and central Mediterranean Sea. We assigned complete mtDNA haplotypes to dead embryos and bycatch samples, and introduced a first nomenclature for loggerhead mitogenomes. Analysis of mtDNA diversity, Maximum Parsimony and Bayesian phylogenetic reconstruction allowed improved resolution of lineages with respect to studies reporting on partial mtDNA control region sequence comparisons, and we were able to further inform previous analyses on loggerhead ancestry based on control region haplogroups. Overall, whole mitogenome analysis has potential for considerable improvement of evolutionary history and phylogeographic investigations as well as mixed-stock surveys of loggerhead turtles.

Genetic Analysis of Mingrelians Reveals Long-Term Continuity of Populations in Western Georgia (Caucasus).

To elucidate the population history of the Caucasus, we conducted a survey of genetic diversity in Samegrelo (Mingrelia), western Georgia. We collected DNA samples and genealogical information from 485 individuals residing in 30 different locations, the vast majority of whom being Mingrelian speaking. From these DNA samples, we generated mitochondrial DNA (mtDNA) control region sequences for all 485 participants (female and male), Y-short tandem repeat haplotypes for the 372 male participants, and analyzed all samples at nearly 590,000 autosomal single nucleotide polymorphisms (SNPs) plus around 33,000 on the sex chromosomes, with 27,000 SNP removed for missingness, using the GenoChip 2.0+ microarray. The resulting data were compared with those from populations from Anatolia, the Caucasus, the Near East, and Europe. Overall, Mingrelians exhibited considerable mtDNA haplogroup diversity, having high frequencies of common West Eurasian haplogroups (H, HV, I, J, K, N1, R1, R2, T, U, and W. X2) and low frequencies of East Eurasian haplogroups (A, C, D, F, and G). From a Y-chromosome standpoint, Mingrelians possessed a variety of haplogroups, including E1b1b, G2a, I2, J1, J2, L, Q, R1a, and R1b. Analysis of autosomal SNP data further revealed that Mingrelians are genetically homogeneous and cluster with other modern-day South Caucasus populations. When compared with ancient DNA samples from Bronze Age archaeological contexts in the broader region, these data indicate that the Mingrelian gene pool began taking its current form at least by this period, probably in conjunction with the formation of a distinct linguistic community.

Diversity of mitochondrial DNA in 3 species of great whales before and after modern whaling.

The 20th century commercial whaling industry severely reduced populations of great whales throughout the Southern Hemisphere. The effect of this exploitation on genetic diversity and population structure remains largely undescribed. Here, we compare pre- and post-whaling diversity of mitochondrial DNA (mtDNA) control region sequences for 3 great whales in the South Atlantic, such as the blue, humpback, and fin whale. Pre-whaling diversity is described from mtDNA extracted from bones collected near abandoned whaling stations, primarily from the South Atlantic island of South Georgia. These bones are known to represent the first stage of 20th century whaling and thus pre-whaling diversity of these populations. Post-whaling diversity is described from previously published studies reporting large-scale sampling of living whales in the Southern Hemisphere. Despite relatively high levels of surviving genetic diversity in the post-whaling populations, we found evidence of a probable loss of mtDNA lineages in all 3 species. This is evidenced by the detection of a large number of haplotypes found in the pre-whaling samples that are not present in the post-whaling samples. A rarefaction analysis further supports a loss of haplotypes in the South Atlantic humpback and Antarctic blue whale populations. The bones from former whaling stations in the South Atlantic represent a remarkable molecular archive for further investigation of the decline and ongoing recovery in the great whales of the Southern Hemisphere.

Small-scale population structure of eastern North Pacific harbour porpoises (Phocoena phocoena) indicated by molecular genetic analyses

Concern about the conservation and management of harbour porpoise (Phocoena phocoena) populations, which have experienced relatively large incidental fishery kills in localised areas throughout their range, has prompted research to better understand their population structure. Both mitochondrial and nuclear (microsatellites) DNA were used to examine the intra-specific structure of harbour porpoise inhabiting the eastern North Pacific Ocean. Null hypotheses of panmixia were tested after mitochondrial DNA (mtDNA) control region sequence data (402 base pairs; n = 249) and allele frequency data (9 polymorphic loci; n = 194) were sub-divided into geographic strata defined a priori. Strata were based on sampling discontinuities and not discontinuities in population distribution. The mtDNA and nuclear gene data revealed statistically significant genetic differentiation between most strata (a = 0.05) suggesting demographic independence of fairly small sub-units within the population. Since harbour porpoises are essentially continuously distributed in the eastern North Pacific, this degree of genetic differentiation was unexpected and needs to be considered in developing a sound management plan to protect them.

Genetic portrait of the Amazonian communities of Peru and Bolivia: The legacy of the Takanan-speaking people.

During the colonial period in South America, many autochthonous populations were affected by relocation by European missionary reductions and other factors that impacted and reconfigured their genetic makeup. Presently, the descendants of some "reduced" and other isolated groups are distributed in the Amazonian areas of Peru, Bolivia, and Brazil, and among them, speakers of Takanan and Panoan languages. Based on linguistics, these peoples should be closely related, but so far no DNA comparison studies have been conducted to corroborate a genetic relationship. To clarify these questions, we used a set of 15 short tandem repeats of the non-recombining part of the Y-chromosome (Y-STRs) and mitochondrial DNA (mtDNA) control region sequence data. Paternal line comparisons showed the Takanan-speaking peoples from Peru and Bolivia descended from recent common ancestors; one group was related to Arawakan, Jivaroan, and Cocama and the other to Panoan speakers, consistent with linguistics. Also, a genetic affinity for maternal lines was observed between some Takanan speakers and individuals who spoke different Amazonian languages. Our results supported a shared ancestry of Takanan, Panoan, Cocama, and Jivaroan-speaking communities who appeared to be related to each other and came likely from an early Arawak expansion in the western Amazonia of South America.

Major Cuban Green Turtle Rookeries: Identification of Management Units and Their Genetic Relationships with Other Greater Caribbean Populations

Genetic monitoring of highly migratory endangered species is fundamental for effective management, particularly when they are shared internationally, and their populations need to be identified. A prime example is the green turtle, Chelonia mydas, whose genetic structure has been extensively studied in the Western Atlantic. Nevertheless, the identification of Cuban management units has remained uncertain, despite representing regionally significant nesting assemblages and occurring within a strategically central position. Compared to previous work, the current study used 800 bp mtDNA control region sequences and larger sample sizes (n = 189 from four nesting sites in SW Cuba). Of the 23 resolved haplotypes, nine were novel, fourteen were reported in Cuba for the first time, and eleven were endemic. Even though the distribution of nesting grounds barely spans 300 km, three management units were identified: Guanahacabibes-San Felipe (GUCB; with most of the endemic haplotypes), Isla de la Juventud (IJCB; with a predominance of haplotype CM-A13.1), and Cayo Largo (CLCB; with a haplotype profile closely related to Southern Caribbean rookeries). We discuss how the geographic distribution of mtDNA variation has likely been shaped by local and regional oceanic current patterns or derived from formerly hyperabundant regional populations. Genetic characterization of Cuban management units represents a significant contribution, filling critical knowledge gaps that have hampered the comprehensive mixed-stock analyses required to guide effective regional conservation strategies.

Genetic analyses (mtDNA and microsatellites) of Okhotsk and Bering/Chukchi/Beaufort Seas populations of bowhead whales

Both North Pacific populations of bowhead whales (Balaena mysticetus) underwent heavy exploitation by commercial whalers in the 19th century, but their reduction in numbers was unequal and their contemporary population sizes differ by an order of magnitude. To investigate the genetic divergence of the different populations, tissue samples of bowhead whales representing the Okhotsk Sea (OS) population (25 samples) and the Bering/Chukchi/Beaufort Seas (BCBS) population (29 samples) were used to generate mtDNA control region sequences and genotypes for three microsatellite loci. There were 20 haplotypes represented in the contemporary BCBS samples and four in the OS samples, three of which were shared with the BCBS samples. The BCBS samples had a much greater haplotypic diversity (0.93) than the OS samples (0.61). Analyses of both types of data revealed significant genetic differences between the two populations, indicating that the populations represent discrete gene pools.

Genetic Evidence for Indo-Western Pacific Olive Ridley Sea Turtles in Mexican Waters

The olive ridley sea turtle is predominantly an epipelagic species with no apparent migration corridors. Research in feeding areas in other sea turtle species has identified aggregations of individuals from diverse backgrounds; however, no specific feeding areas have been identified for the olive ridley. We used mtDNA control region sequencing to identify the haplotype composition of 85 olive ridley turtles (adult and immature turtles from both sexes) captured and released in Central Mexican Pacific waters. Amplified fragments of the control region (751 bp) revealed the presence of 17 haplotypes (h = 0.5877 ± 0.0622 and π = 0.001698 ± 0.001185), and 16 of them were phylogenetically grouped within the lineage of the Eastern Pacific, but the haplotype Lo37 showed close evolutionary relationships with the lineage of the East Coast of India. Lagrangian drifter data showed that West–East transport from the Indo-Pacific to the tropical Eastern Pacific might be possible through passive drift. These results highlight the importance of more genetic studies offshore and the role of the ocean currents in the migratory behavior of olive ridleys, as well as the need to establish multinational strategies for the conservation and management of the species in international waters.

Multilocus phylogeography, population genetics and niche evolution of Australian brown and black-tailed treecreepers (Aves:Climacteris)

AbstractThe Carpentarian barrier across north-eastern Australia is a major biogeographic barrier and a generator of biodiversity within the Australian Monsoonal Tropics. Here we present a continent-wide analysis of mitochondrial (control region) and autosomal (14 anonymous loci) sequence and indel variation and niche modelling of brown and black-tailed treecreepers (Climacteris picumnus and Climacteris melanurus), a clade with a classic distribution on either side of the Carpentarian barrier. mtDNA control region sequences exhibited reciprocal monophyly and strong differentiation (Fst = 0.91), and revealed a signature of a recent selective sweep in C. picumnus. A variety of tests support an isolation-with-migration model of divergence, albeit with low levels of gene flow across the Carpentarian barrier and a divergence time between species of ~1.7–2.8 Mya. Palaeoecological niche models show that both range size as measured by available habitat and estimated historical population sizes of both species declined in the past ~600 kyr and that the area of interspecific range overlap was never historically large, perhaps decreasing opportunities for extensive gene flow. The relatively long divergence time and low opportunity for gene flow may have facilitated speciation more so than in other co-distributed bird taxa across the Australian Monsoonal Tropics.

Cryptic Lineage and Genetic Structure of Acanthopagrus pacificus Populations in a Natural World Heritage Site Revealed by Population Genetic Analysis

Recent studies have revealed extensive genetic differentiation among some populations of marine taxa that were previously believed to be essentially homogeneous because larvae are widely dispersed in ocean currents. Acanthopagrus pacificus is a commercially and ecologically important teleost fish that is endemic to shallow coastal waters and estuaries of some tropical and sub-tropical areas in the West Pacific Ocean. Here, we examined genetic structure and the inferred demographic history of A. pacificus populations from mtDNA control region sequence data. A 677–678 base-pair fragment was sequenced from 159 individuals sampled at three localities across the West Pacific Ocean. Haplotype diversity was high, ranging from 0.915 to 0.989, while nucleotide diversity was low to medium, ranging from 0.8% to 2.60%. Analysis of molecular variance (AMOVA) showed significant genetic subdivision (FST = 0.155, p < 0.05) among sampled populations while pairwise FST estimates also revealed strong genetic differentiation among populations indicating that gene flow was restricted. Two distinct cryptic lineages were identified that were estimated to have diverged during the Pleistocene. In summary, contemporary factors including regional oceanic currents and self-recruitment are considered to have played significant roles in producing the population structure in this fish. In particular, the genetic information generated in the current study will allow appropriate fisheries management and conservation strategies to be developed for this important local fish in the waters around Iriomotejima Island, a World Heritage site.

Eastern king prawn Penaeus plebejus stock enhancement-Genetic evidence that hatchery bred prawns have survived in the wild after release.

Eastern king prawn (Penaeus plebejus) is endemic to eastern Australia and is of high commercial and recreational value. As part of a recreational fisheries enhancement initiative, hatchery reared juveniles from Queensland were released into two, more Southern New South Wales (NSW) estuaries between 2014 and 2015. Responsible stock enhancement programs rely on knowledge of the population structure of the released species. Previously, in consideration of fisheries data, it was assumed the king prawn populations in Australia are one single breeding stock. In the present study, our first aim was to test this posit of no genetic differentiation using mtDNA control region (mtCR) sequences from the wild samples collected from four estuaries ranging from Queensland/NSW border (source of the stocked animals) to Southern NSW. The second objective was to test for signals of hatchery-released animals in the two stocked estuaries. All four surveyed populations had an extremely high level of haplotype diversity (average h = 99.8%) and low level of haplotype sharing between populations. Estimates of PhiPT values were <0.01 or close to zero and AMOVA test did not indicate any significant differences among populations. Further, phylogenetic analysis and principal coordinate analysis did not support division of samples by population. Collectively these results suggest that eastern king prawn populations along the NSW coast can be considered as a single stock and stocking from the Queensland samples will not necessarily impact the genetic composition of the overall stock. After stocking of two estuaries, sharing of haplotypes was moderate to very high in the stocked sites (>80% in some collections) but negligible in the two unstocked estuaries (≤2%, which is assumed to be background coancestry unrelated to the hatchery). Moreover, some haplotypes present in the hatchery broodstock were detected in stocked sites, but not in unstocked sites. The highest stocking signal was detected in the estuary which becomes isolated from the sea by sand barrier suggesting such "lakes" maybe more favourable for stocking than estuaries directly open to the sea. Findings in the current study should assist in designing and implementation of future prawn stocking programs.

Extremely Low mtDNA Diversity and High Genetic Differentiation Reveal the Precarious Genetic Status of Dugongs in New Caledonia, South Pacific.

New Caledonia is home to one of the largest remaining populations of dugongs (Dugong dugon) and is located at the southeastern limit of the species range. Local knowledge suggests that current levels of removal due to anthropogenic pressures are unsustainable, whereas trends suggest an ongoing decline in the population. Considering this unfavorable conservation context, this study aimed to assess the New Caledonian dugong population's resilience by determining its level of genetic diversity and degree of isolation relative to other populations. Mitochondrial DNA (mtDNA) control region sequences (n = 55) collected from live and dead dugongs in New Caledonia were compared with a global data set of previously published sequences (n = 631) representing dugong populations throughout the species range. The New Caledonian dugong population displayed the lowest level of mtDNA diversity documented worldwide (3 haplotypes with 1-bp difference), suggesting a recent origin of the current population through limited colonization events. Population structure analyses indicate a strong genetic differentiation with all the putative populations represented in the global data set, including large neighboring Australian populations. These results show that the dugong population in New Caledonia is particularly isolated, fragile, and vulnerable to anthropogenic threats and diseases with low potential for resilience through incoming gene flow. Our findings call for an instant conservation response and consideration for IUCN population assessment to support the long-term survival of the New Caledonian dugong population.

Resolving the phylogenetic relationship among recently diverged members of the rockfish subgenus Sebastosomus

Rapid speciation is an important aspect of adaptive radiations, but can obfuscate phylogenetic relationships among taxa. For recent radiations, there are challenges to reconstructing the relationships among the species due to often shorter branch lengths. Resolution of these relationships is further confounded when studies only use a few genetic markers. Double digest restriction-site associated DNA sequencing (ddRADseq) is a method of next generation sequencing that identifies many single nucleotide polymorphisms (SNPs) throughout the genome. This increases statistical power to resolve close phylogenetic relationships like those found within an adaptive radiation. We used this approach to understand the evolutionary history of the rockfishes of the genus Sebastes, which experienced an adaptive radiation between 3 and 5 mya. Here, we reconstructed the phylogenetic relationships among six species of rockfish within the subgenus Sebastosomus using over 11,600 SNPs. This reconstruction includes the two recently diverged species, Sebastes mystinus and S. diaconus, that were first described genetically in 2008 using mtDNA control region sequence data and six microsatellite loci. We confirmed the relationship of these cryptic species as sister-taxa and found evidence that S. melanops and S. flavidus were also sister-taxa. The latter contradicts prior studies but is supported by our reconstruction using nuclear DNA and measures of genetic differentiation tests and a discriminant analysis of principal components. The relationships between the species of Sebastosomus are further supported by morphological, biological, and ecological justifications.

Little Sharks in a Big World: Mitochondrial DNA Reveals Small-scale Population Structure in the California Horn Shark (Heterodontus francisci).

The California horn shark (Heterodontus francisci) is a small demersal species distributed from southern California and the Channel Islands to Baja California and the Gulf of California. These nocturnal reef predators maintain small home-ranges as adults and lay auger-shaped egg cases that become wedged into the substrate. While population trends are not well documented, this species is subject to fishing pressure through portions of its range and has been identified as vulnerable to overexploitation. Here, we present a survey of 318 specimens from across the range, using mtDNA control region sequences to provide the first genetic assessment of H. francisci. Overall population structure (ΦST = 0.266, P < 0.001) is consistent with limited dispersal as indicated by life history, with two distinct features. Population structure along the continuous coastline is low, with no discernable breaks from Santa Barbara, CA to Bahia Tortugas (Baja California Sur, Mexico); however, there is a notable partition at Punta Eugenia (BCS), a well-known biogeographic break between tropical and subtropical marine faunas. In contrast, population structure is much higher (max ΦST = 0.601, P < 0.05) between the coast and adjacent Channel Islands, a minimum distance of 19 km, indicating that horn sharks rarely disperse across deep habitat and open water. Population structure in most elasmobranchs is measured on a scale of hundreds to thousands of kilometers, but the California Horn Shark has population partitions on an unprecedented small scale, indicating a need for localized management strategies which ensure adequate protection of distinct stocks.

The Potential Distribution and Maternal Lineage of Two Cetaceans Species (Grampus griseus and Pseudorca crassidens) in the Subfamily Globicephalinae from the Thai Andaman Sea and the Gulf of Thailand

Although the existence of two cetacean species in and around Thai Seas from within the subfamily Globicephalinae, Risso’s dolphin Grampus griseus G. Cuvier, 1812, and false killer whale Pseudorca crassidens Owen, 1846, has been known for decades, current knowledge on the abundance, genetic diversity, and conservation status of these marine mammals is limited as these are rare oceanic species for Thailand’s territorial waters. Frozen skin tissue samples taken from six cetaceans (four Risso’s dolphins: two false killer whales) stranded along Thai coastlines were investigated. We aimed to identify the maternal lineage and connection of our samples throughout their distribution range. Accordingly, we analyzed the dataset of 110 and 50 mtDNA control region sequences of Risso’s dolphins and false killer whales, respectively. This dataset was retrieved from the online database of the National Center for Biotechnology Information (NCBI) and included six mtDNA sequences obtained from Thai Seas. Two unique haplotypes of Risso’s dolphins were found in the Thai Andaman Sea, whereas one haplotype identified as being from the Gulf of Thailand is a common haplotype shared with other regions of the Pacific Ocean. Two haplotypes were found for false killer whales from the Thai Andaman Sea, and these were also in common with other regions of the Indo Pacific Ocean. While shared haplotypes with other regions may imply inheritance from the same female ancestor, we speculate that distinct populations with unique genetic structures also exist in Thai Seas. Beneficially, our results could be used to monitor alterations of haplotypes or to assess the maternal genetic diversity of designated species in the future to establish baseline information for Thai Seas and adjacent waters.