Control Region Sequences Research Articles

Population Genetic Structure with Mitochondrial DNA of the Chub Mackerel Scomber japonicus in Korean Coastal Waters

Scomber japonicus, commonly known as chub mackerel, is a fish species of economic significance in Korea, China, and Japan, whose natural abundance has reduced dramatically due to overfishing and environmental changes. To investigate the genetic differentiation and population structure of S. japonicus, a 359 base pair segment of the mitochondrial DNA (mtDNA) control region sequence was analyzed in 96 individuals sampled from three locations in Korean waters. Sixty-six haplotypes were recognized, of which 61 (92.42%) were population specific, whereas only five haplotypes were shared by multiple populations (8%). Two clades were revealed with low support values, and no specific genealogical branches were recognized according to geographical locations. Significant genetic differentiations, however, were detected among the three populations, with FST values (p < 0.05). These results indicate that populations of S. japonicus in Korean waters are genetically subdivided. Migration patterns, spawning site fidelity, and current temperature could be the possible causes of this subdivision. Consequently, it is thought that each of the genetically unique S. japonicus stocks found in Korean waters requires a different approach to management.

The genetic consequences of successful reintroduction of wild turkey (Meleagris gallopavo) in Nebraska

AbstractThe wild turkey (Meleagris gallopavo) recovered from near extirpation because of protection from unrestricted harvest and from introductions and translocations. In Nebraska, modern turkeys are descendants of introductions of domestic, Eastern, Merriam's, and Rio Grande wild turkeys. Whether introduced birds mated assortatively by plumage traits is unknown, and the effects of restoration efforts on the genetic integrity of the introduced birds are unclear. We analyzed variation in the mitogenome and nuclear genome of 16 turkeys selected to represent each subspecies. Analyses of mitochondrial DNA genomes suggest two clades, Gould's plus Merriam's, and a blended group of Eastern, Osceola and Rio Grande turkeys. Analysis of 58 birds from Nebraska for mtDNA control region sequences, plus birds from museums and domestic stock, did not recover any groupings consistent with subspecies or our mitogenome results. We extracted 8,554 single nucleotide polymorphisms (SNPs) from low‐coverage genomes, which resolved each subspecies albeit with some potential conflicts, but unlike the mtDNA pattern suggested that the Rio Grande was more closely related to individuals thought to represent Merriam's or Gould's subspecies. We designed 12 primers that bracketed subspecies‐specific/autapomorphic SNPs and used variation in these independent gene regions to assess genetic structure in birds from Nebraska, to evaluate genetically the known history of reintroductions. From 8,152 base pairs (bp) in the 12 gene regions flanking the subspecies‐specific/autapomorphic SNPs and after alignment and removal of sites with missing data, we created a data set (5,415 bp, 177 variable) of 57 birds from Nebraska including museum frozen tissue specimens identified to subspecies and 11 domestic birds. Our nuclear data suggested considerable blending of genetic distinctiveness among birds from Nebraska, as predicted by the history of reintroductions. Genetic data thus affirmed that Nebraska turkeys consisted mostly of birds of hybrid origin. The reestablishment of wild turkeys across North America has come at the cost of genetic admixing of originally distinct populations. Whether this is problematic depends on whether the goal of wild turkey management is to retain original genetic distinctiveness or harvestable populations of wild turkey irrespective of their genealogical background.

Persistence of Ancestral KhoeSan Mitochondrial Patterns in Contemporary South African Populations.

Southern Africa has been inhabited by hunter-gatherers for at least 20,000 years and has received diverse immigration flows in the last 2000 years. The original inhabitants have interacted with the pastoralist migrants from Eastern Africa (∼2000 ybp), followed by the southern Bantu migration arriving some 1000 ybp, and more recently with the European and Asian settlers after the 17th century. Many of the original Khoekhoe and San inhabitants have either become extinct or have disappeared through admixture in South Africa (SA), in a sex-biased manner involving KhoeSan women. In this study, we generated mitochondrial DNA (mtDNA) control region (CR) sequences for 247 South African individuals. The sampling effort was concentrated in regions and populations with historical links to the KhoeSan population groups: admixed (Coloured, Griqua), Nama (Khoekhoe) and Bantu in three provinces. Here we evaluate the composition and extent of connectivity between population groups and regions, and to assess the distribution of haplotypes for the practical application of mtDNA CR data in forensic identifications. The analysis of the newly generated sequences revealed 142 distinct haplotypes, of which 122 were unique. Haplogroup L0 was predominant (overall 71.7%). A high-frequency L0d2a haplotype dominated the pool of the admixed groups with 10%-12.5% incidence overall or per region. Comparative analysis with 545 extant mtDNA CR sequences from South African KhoeSan and admixed descendants revealed extensive population structure and high within-group haplotype sharing. The observed population and regional variations, combined with the prevalence of high-frequency haplotypes, align with patterns of matrilocality. These findings highlight the limitations of using mtDNA control region analysis for forensic applications in South Africa.

Unraveling migratory corridors of loggerhead and green turtles from the Yucatán Peninsula and its overlap with bycatch zones of the Northwest Atlantic.

Bycatch represents a conservation problem when endangered species are affected. Sea turtles are highly vulnerable to this threat as their critical habitats overlap with fishing zones in all regions of the world. We used sequences of the mitochondrial DNA control region obtained from loggerhead (Caretta caretta) and green (Chelonia mydas) turtles to determine the migratory routes between nesting habitats in the Yucatán Peninsula and their critical marine habitats in the Northwest Atlantic. Mixed Stock Analysis revealed that loggerheads from Quintana Roo migrated to foraging areas in the northwestern Atlantic. Migratory routes used by green turtles are determined by their natal nesting colony: (1) green turtles from the Gulf of Mexico migrate to foraging aggregations in Texas and the northern Gulf of Mexico, (2) Mexican Caribbean turtles travel to foraging grounds in Florida, and (3) a smaller proportion of individuals born in the Yucatán Peninsula display a local connectivity pattern. Our results suggest that the migratory corridors used by Mexican loggerheads overlap with longline fisheries in the mid-Atlantic where sea turtle bycatch is comprised predominantly of immature individuals. Green turtles from the Yucatán Peninsula migrate to critical habitats that overlap with shrimp trawl fisheries within the Gulf of Mexico. Bycatch data and the identification of migratory corridors used by loggerheads and green turtles suggests that shrimp trawl fisheries on the east coast of the U.S. and the Gulf of Mexico pose a serious threat to the conservation and recovery of Mexican sea turtle populations.

Mitochondrial control region sequences show high genetic connectivity in the brownstripe snapper, Lutjanus vitta (Quoy and Gaimard, 1824) from the east coast of Peninsular Malaysia

Mitochondrial control region sequences show high genetic connectivity in the brownstripe snapper, Lutjanus vitta (Quoy and Gaimard, 1824) from the east coast of Peninsular Malaysia

Potential Cryptic Diversity in the Genus Scoliodon (Carcharhiniformes: Carcharhinidae): Insights from Mitochondrial Genome Sequencing.

Scoliodon is a genus of small placental sharks living in offshore waters. For a long time, the genus was considered a monotypic genus until a valid species, Scoliodon macrorhynchos, was confirmed in 2010. However, S. muelleri in the same study was not widely recognized because of the lack of evidence. In this study, we obtained the complete mitochondrial genome of the genus Scoliodon from Ranong, Thailand, and tentatively named it Scoliodon sp. By comparing the complete mitochondrial genome with those of two other Scoliodon species and conducting phylogenetic and divergence time analyses, we determined that Scoliodon sp. diverged from the other species. These findings indicate the potential for a new cryptic species (Scoliodon sp.) in the Scoliodon genus. This conclusion was further supported by a subsequent analysis of the published S. laticaudus control region sequences from previous studies. Finally, based on these conclusions, we used machine learning to derive a new identification method for the cryptic species. This approach may be useful for the discovery of new species or cryptic species in other organisms.

Temporal and inter-specific population genetics analyses of Sebastiscus marmoratus and S. tertius provide novel implications for fishery management

ABSTRACT Understanding population genetic diversity and evolutionary dynamics of marine fish species can provide theoretical bases for fishery management and germplasm conservation, especially facing a changing environment. The rockfish species in genus Sebastiscus are economically important species for farming and sport fisheries in China, Japan and Korea. In this study, inter-annual and inter-specific comparisons on genetic diversity, population differentiation and historical demography of S. marmoratus and S. tertius collected from coastal waters of Zhangzhou, China were conducted using mitochondrial control region sequences. High levels of genetic diversity were observed in both species, indicating high adaptive potential to environmental changes. Demographic analyses detected recent population expansion in population S. tertius (Ste-2020) and population S. marmoratus collected in 2020 (Sma-2020), yet failed in population collected in 2016 (Sma-2016). Moreover, in population Sma-2020, novel haplotypes were detected and grouped into a separate sub-branch, revealed by neighbour-joining topology. Detected recent population expansion and novel haplotypes might be considered as a response to environmental changes. Besides, results of genetic differentiation analysis suggested high intra-specific genetic variation in both species. These genetic data and information will provide novel implications for strengthening the management of S. marmoratus and S. tertius fisheries in climate change scenarios.

Contrasting Patterns of Genetic Diversity in European Mammals in the Context of Glacial Refugia

Phylogeographic studies have been conducted on many different mammal species in order to track their recent demographic histories. The climatic fluctuations associated with the Last Glacial Maximum (LGM) appear to have had a profound influence on the geographic patterning of genetic diversity in mammals. However, most phylogenetic studies have focused on single species. Few have used a holistic approach covering multiple taxa to explore common patterns. Here, we conducted meta-analyses of mitochondrial DNA control region sequences, identifying haplotype diversity and private allelic richness patterns in a geographic context. Four general patterns emerged among European mammals: an east–west decline in variation, a Western-Central belt of the highest diversity, southern richness, and homogeneity with no geographic pattern. These patterns likely reflect the refugial origins of modern populations. The east–west variation decline suggests species with eastern LGM refugia; the Western-Central belt of the highest diversity may harbor taxa with cryptic northern refugia, while southern richness may correspond to traditional southern refugia. Species with homogeneity and no geographic pattern may have been panmictic without a specific refugium or may reflect the occurrence of both southern and cryptic northern refugia. Surprisingly, the “no pattern” phenomenon is seldom discussed and may frequently have been discounted. Our study emphasizes the importance of considering multiple taxa, providing valuable insights into the responses of European mammals to past climatic changes.

Genetic Variability and Population Genetic Structure of Marbled Flounder Pseudopleuronectes yokohamae in Korea and Japan Inferred from mtDNA Control Region Sequences

The marbled flounder (Pseudopleuronectes yokohamae) is a demersal flatfish species, widely distributed in the northwestern Pacific region. In the present study, the mitochondrial DNA (mtDNA) control region was used to determine the genetic diversity and population genetic structure of this species. We obtained a 380 bp segment of the mtDNA control region after the alignment of 78 individual sequences from P. yokohamae collected from two locations in Korea (Biungdo and Mukho) and one location in Japan (Tohoku) and 103 individual sequences from a previous study (Yokjido and Namhae). The overall haplotype diversity and nucleotide diversity were 0.983 ± 0.003 and 0.016 ± 0.008, respectively. The genealogical relationships of the mtDNA control region did not exhibit any specific genealogical association according to sampling location. The pairwise FST value indicated that the Biungdo (west coast of Korea) and Tohoku (Japan) populations showed genetically differentiated structures (but the Tohoku and Mukho populations did not). However, there was no discernible difference between the Mukho population from Korea’s eastern coast and the Yokjido and Namhae populations from the southern coast. The biological characteristics of P. yokohamae and oceanographic barriers may have contributed to producing genetically distinct populations.

Exploring the presence of tilapia species in a central western Mexican reservoir using mitochondrial DNA control region sequencing

Oreochromis niloticus is the most important aquacultural species worldwide. Several countries are interested in repopulating natural or artificial reservoirs with the fry of tilapia (Oreochromis sp.) to develop new fisheries or to enhance the existing ones. However, as tilapia is considered an invasive species, it is essential to check the existence of the species in the place before releasing any fry. Characterization of tilapia species with meristic is unreliable because of existing morphological similarities among species. In this work, the composition of the tilapia species of Laguna El Mastranzo (LEM), Nayarit, Mexico, was explored for the first time through a molecular method using the mitochondrial DNA control region. Three tilapia species (Oreochromis niloticus, O. aureus, and O. urolepis) were found in LEM, and it was confirmed that the two commercial strains (Aquamol and Spring) intended for repopulation were O. niloticus. Seven haplotypes of mitochondrial DNA control region sequences were obtained: three in LEM, three in Aquamol, and one in Spring strains. Before repopulating any reservoir, a molecular verification strategy is recommended to avoid spreading the species. The results of this work represent a glimpse into the genetic material of LEM, Nayarit, Mexico.

Mitochondrial DNA control-region and coding-region data highlight geographically structured diversity and post-domestication population dynamics in worldwide donkeys.

Donkeys (Equus asinus) have been used extensively in agriculture and transportations since their domestication, ca. 5000-7000 years ago, but the increased mechanization of the last century has largely spoiled their role as burden animals, particularly in developed countries. Consequently, donkey breeds and population sizes have been declining for decades, and the diversity contributed by autochthonous gene pools has been eroded. Here, we examined coding-region data extracted from 164 complete mitogenomes and 1392 donkey mitochondrial DNA (mtDNA) control-region sequences to (i) assess worldwide diversity, (ii) evaluate geographical patterns of variation, and (iii) provide a new nomenclature of mtDNA haplogroups. The topology of the Maximum Parsimony tree confirmed the two previously identified major clades, i.e. Clades 1 and 2, but also highlighted the occurrence of a deep-diverging lineage within Clade 2 that left a marginal trace in modern donkeys. Thanks to the identification of stable and highly diagnostic coding-region mutational motifs, the two lineages were renamed as haplogroup A and haplogroup B, respectively, to harmonize clade nomenclature with the standard currently adopted for other livestock species. Control-region diversity and population expansion metrics varied considerably between geographical areas but confirmed North-eastern Africa as the likely domestication center. The patterns of geographical distribution of variation analyzed through phylogenetic networks and AMOVA confirmed the co-occurrence of both haplogroups in all sampled populations, while differences at the regional level point to the joint effects of demography, past human migrations and trade following the spread of donkeys out of the domestication center. Despite the strong decline that donkey populations have undergone for decades in many areas of the world, the sizeable mtDNA variability we scored, and the possible identification of a new early radiating lineage further stress the need for an extensive and large-scale characterization of donkey nuclear genome diversity to identify hotspots of variation and aid the conservation of local breeds worldwide.

Population genetic structure and historical demography of the population of forest elephants in Côte d'Ivoire.

The population of forest elephant (Loxodonta cyclotis) has continuously declined in Côte d'Ivoire and, the remaining population largely consists of subpopulations that are fragmented and isolated. No data actually exist on the level of genetic diversity and population genetic structure of current forest elephant populations in Côte d'Ivoire. In this sense, determining genetic diversity and the underlying mechanisms of population differentiation is crucial for the initiation of effective conservation management. A total of 158 dung samples of forest elephants were collected at stage 1 of decompositions (dung pile intact, very fresh) in three Classified Forests (CF) (Bossématié, Dassioko and Port-Gauthier) in Côte d'Ivoire. A total of 101 sequences of the mitochondrial DNA control region measuring 600 base pair and 26 haplotypes were obtained. A haplotypic diversity ranging from 0.655 ± 0.050 at Bossématié and 0.859 ± 0.088 at Port Gauthier was obtained. Fifteen (15) out of 26 haplotypes observed were singletons and only the Dassioko and Port Gauthier CFs shared the same haplotypes. The strong genetic connectivity between forest elephant populations of the Dassioko and Port Gauthier CFs is supported by the grouping of these populations into a single cluster by Bayesian analysis. Although populations of L. cyclotis exhibit relatively high genetic diversity, habitat fragmentation could affect the genetic variability of current populations. Urgent measures including the reinforcement/establishment of genetic corridors and the strengthening of protection measures need to be undertaken to save the remaining populations of forest elephants in Côte d'Ivoire.

Are There Barriers Separating the Pink River Dolphin Populations (Inia boliviensis, Iniidae, Cetacea) within the Mamoré-Iténez River Basins (Bolivia)? An Analysis of Its Genetic Structure by Means of Mitochondrial and Nuclear DNA Markers.

The pink river dolphin, or bufeo, is one of the dolphins which lives in the rivers of the Orinoco and Amazon basins in South America. The Bolivian bufeo population is considered a differentiated species (Inia boliviensis) from the Amazon and Orinoco species (Inia geoffrensis). Until now, no study has completed an extensive population genetics analysis of the bufeo in Bolivian rivers. We analyzed 82 bufeos from different rivers from the Mamoré and Iténez (Guaporé) river basins for the mt control region (CR), nuclear microsatellites, and DQB-1 gene sequences to determine if the inner rapids of these Bolivian river basins have some influence on the genetic structure of this species. The first relevant result was that the genetic diversity for CR, and the microsatellites were substantially lower in the Bolivian bufeos than in the dolphins studied in other areas of the Amazon and Orinoco. However, the DQB-1 gene sequences yielded similar genetic diversity to those found in other areas. The second relevant result is the existence of some significant genetic heterogeneity among the bufeo populations within Bolivia, although in a small degree, but this differentiation is independent of the inner rapids of the Bolivian rivers we sampled. The third relevant result was the existence of significant isolation by distance for the CR, but not for microsatellites and DQB-1 gene sequences. This was related to differential gene flow capacity of females (philopatric) and males (less philopatric and more migrants) and, possibly, to different selective patterns affecting the molecular markers studied. The fourth relevant result was related to diverse demographic changes of these bufeos. At least two or three bottleneck events and one or two population expansions have occurred in the Bolivian bufeo population. The major part of these events occurred during the Pleistocene.

Selected Lark Mitochondrial Genomes Provide Insights into the Evolution of Second Control Region with Tandem Repeats in Alaudidae (Aves, Passeriformes).

The control region (CR) regulates the replication and transcription of the mitochondrial genome (mitogenome). Some avian mitogenomes possess two CRs, and the second control region (CR2) may enhance replication and transcription; however, the CR2 in lark mitogenome appears to be undergoing loss and is accompanied by tandem repeats. Here, we characterized six lark mitogenomes from Alaudala cheleensis, Eremophila alpestris, Alauda razae, and Calandrella cinerea and reconstructed the phylogeny of Passerida. Through further comparative analysis among larks, we traced the evolutionary process of CR2. The mitochondrial gene orders were conserved in all published lark mitogenomes, with Cytb-trnT-CR1-trnP-ND6-trnE-remnant CR2 with tandem repeat-trnF-rrnS. Phylogenetic analysis revealed Alaudidae and Panuridae are sister groups at the base of Sylvioidea, and sporadic losses of CR2 may occur in their common ancestor. CR sequence and phylogeny analysis indicated CR2 tandem repeats were generated within CR2, originating in the ancestor of all larks, rather than inherited from CR1. The secondary structure comparison of tandem repeat units within and between species suggested slipped-strand mispairing and DNA turnover as suitable models for explaining the origin and evolution of these repeats. This study reveals the evolutionary process of the CR2 containing tandem repeat in Alaudidae, providing reference for understanding the evolutionary characteristics and dynamics of tandem repeats.

Unusual Patterns of Lateral Scutes in Two Olive Ridley Turtles and Their Genetic Assignment to the Thai Andaman Sea Populations of Lepidochelys olivacea Eschscholtz, 1829.

Two stranded Lepidochelys-like sea turtles were rescued from the Thai Andaman Sea coastline by veterinarians of the Phuket Marine Biological Center (PMBC), one in May of 2019 and another in July of 2021. They were first identified as olive ridley turtles (Lepidochelys olivacea), as the external appearance of both turtles was closer to that species than the other four species found in the Thai Andaman Sea. In fact, when carefully examined, an unusual pattern of the lateral scutes on each turtle was observed, specifically symmetric 5/5 and asymmetric 5/6, both of which are considered rare for L. olivacea and had never been reported in the Thai Andaman Sea. In contrast, this characteristic was more common for the closely related species, Kemp's ridley (L. kempii), although this species is not distributed in the Indo-Pacific Ocean. Thus, we further investigated their genetic information to confirm species identification using two molecular markers, namely the mtDNA control region and nDNA RAG2. The results from the mtDNA control region sequences using the Basic Local Alignment Search Tool (BLAST) indicated that both individuals exhibited a higher percent identity with L. olivacea (99.81-100.00%) rather than L. kempii (94.29-95.41%) or any other species. A phylogenetic tree confirmed that these two turtles belonged to the L. olivacea clade. Moreover, the results of RAG2 also supported the mtDNA result, as both individuals shared the same RAG2 haplotype with L. olivacea. Thus, we have concluded that the two turtles with unusual lateral scute patterns exhibited genetic consistency with their original species, L. olivacea, which has brought attention to the importance of exploring rare phenotypes in sea turtle populations residing in Thai Seas.

Genetic diversity and shallow genetic differentiation of the endangered scaly-sided merganser Mergus squamatus.

Examining patterns of genetic diversity are crucial for conservation planning on endangered species, while inferring the underlying process of recent anthropogenic habitat modifications in the context potential long-term demographic changes remains challenging. The globally endangered scaly-sided merganser (SSME), Mergus squamatus, is endemic to a narrow range in Northeast Asia, and its population has recently been contracted into two main breeding areas. Although low genetic diversity has been suggested in the Russian population, the genetic status and demographic history of these individuals have not been fully elucidated. We therefore examined the genetic diversity and structure of the breeding populations of the SSME and investigated the relative importance of historical and recent demographic changes to the present-day pattern of genetic diversity. Using 10 nuclear microsatellite (SSR) markers and mitochondrial DNA (mtDNA) control region sequences, we found limited female-inherited genetic diversity and a high level of nuclear genetic diversity. In addition, analysis of both markers consistently revealed significant but weak divergence between the breeding populations. Inconsistent demographic history parameters calculated from mtDNA and bottleneck analysis results based on SSR suggested a stable historical effective population size. By applying approximate Bayesian computation, it was estimated that populations started to genetically diverge from each other due to recent fragmentation events caused by anthropogenic effects rather than isolation during Last Glacial Maximum (LGM) and post-LGM recolonization. These results suggest that limited historical population size and shallow evolutionary history may be potential factors contributing to the contemporary genetic diversity pattern of breeding SSME populations. Conservation efforts should focus on protecting the current breeding habitats from further destruction, with priority given to both the Russian and Chinese population, as well as restoring the connected suitable breeding grounds.

Population genetic structure and demographic history of short mackerel, Rastrelliger brachysoma, in the Gulf of Thailand

The short mackerel Rastrelliger brachysoma (Bleeker 1851) is an important fish in the Gulf of Thailand (GoT). The biology of this species has been intensively studied, but its genetic diversity is little known. The genetic diversity, population genetic structure, and demographic history of this species in the GoT were studied using complete mt control region sequences. The CR sequences of 455 mackerel samples collected from 23 localities at four fishing grounds revealed 333 haplotypes with haplotype diversity (h) per population, ranging between 0.8933 and 1.000, with an average of 0.9781. In turn, the nucleotide diversity (µ) ranged between 0.0119 ± 0.0060 and 0.0333 ± 0.0174, with an average of 0.0220 ± 0.00059.A haplotype network analysis showed that all sequences segregated into two subgroups named, clade I and clade II. Two clades were separated by 26 mutational steps. Each clade formed star-like clusters with many haplotypes derived from a common haplotype. Moreover, an analysis of molecular variance (AMOVA) revealed no significant differences among the studied localities, suggesting the presence of a single population in the GoT. Pairwise differences between samples from different fishing regions also indicated no population structure. Both Tajima’s D and Fu’s F S statistics were highly significant for the two clades but nonsignificant for the entire population according to a mismatch distribution analysis. These results confirmed that both clades experienced demographic expansion. The estimated expansion times for clade I and clade II were 1,542.307 years (1.5423 ka BP) and 7,602.541 (7.6025 ka BP) years, respectively.

New insights into population structure, demographic history, and effective population size of the critically endangered blue shark Prionace glauca in the Mediterranean Sea.

The blue shark, Prionace glauca, is the most abundant pelagic shark in the open ocean but its vulnerability remains poorly understood while being one of the most fecund sharks. In the Mediterranean Sea, the blue shark is listed as Critically Endangered (CR) by the International Union for Conservation of Nature. The species is facing a strong decline due to fishing, and scientific data regarding its genetic structure and vulnerability are still lacking. Here, we investigated the genetic diversity, demographic history, and population structure of the blue shark within the Mediterranean Sea, from samples of the Gulf of Lion and Malta, using sequences of the mtDNA control region and 22 microsatellite markers. We also compared our mitochondrial data to previous studies to examine the Atlantic-Mediterranean population structure. We assessed the blue shark's genetic vulnerability in the Mediterranean basin by modelling its effective population size. Our results showed a genetic differentiation between the Atlantic and the Mediterranean basins, with limited gene flow between the two areas, and distinct demographic histories making the Mediterranean population an independent management unit. Within the Mediterranean Sea, no sign of population structure was detected, suggesting a single population across the Western and Central parts of the sea. The estimated effective population size was low and highlighted the high vulnerability of the Mediterranean blue shark population, as the estimated size we calculated might not be sufficient to ensure the long-term persistence of the population. Our data also provide additional evidence that the Gulf of Lion area acts as a nursery for P. glauca, where protection is essential for the conservation strategy of the species in the Mediterranean.

Mixed stock analysis identifies natal origins of green turtles at foraging grounds in southeastern Australia

IntroductionIdentifying critical habitats for marine turtles and connectivity between genetic stocks and the foraging grounds they use is a conservation priority worldwide. Green turtles (Chelonia mydas) are impacted by a wide range of anthropogenic threats that can vary by geographic region and the ontogenetic stage of the individual. In Australia, the strengthening of the East Australian Current due to climate change is increasing ocean temperatures, particularly in southern New South Wales (NSW), which is having large-scale impacts on the distribution and abundance of marine resources. Green turtles are frequently observed in temperate southern NSW waters, but our knowledge of their habitat use, migration patterns and the impact of threatening processes is limited.MethodsTo assess the origins of green turtles from foraging grounds in southeastern Australia, samples were obtained from green turtles of all size classes (post-hatchlings to adults) that had stranded along an ~870 km expanse of the NSW coast and Lord Howe Island between 1997 and 2021. Mitochondrial DNA control region sequences for 283 individuals were compared to 25 potential source genetic stocks in the Indo-Pacific using mixed-stock analysis.ResultsA total of 26 haplotypes were identified in NSW, of which 14 had been previously observed at a rookery, eight had been identified previously, but not at a rookery (i.e. orphan haplotypes), and four were previously undescribed. Mixed-stock analysis revealed that NSW waters support multiple genetic stocks but are dominated by those of the southern Great Barrier Reef and New Caledonia genetic stocks. A small proportion of green turtles originated from more distant stocks in the Indo-Pacific region.DiscussionUnderstanding the connectivity between green turtle rookeries and foraging grounds provides an opportunity to assess the impact of anthropogenic threats to turtle stocks, and in turn, prioritize management actions for the conservation of green turtles across regional, national and international jurisdictions.

Does the Artificial Enhancement and Release Activity Affect the Genetic Diversity of Marbled Rockfish Sebastiscus marmoratus in Zhoushan Waters?

Artificial enhancement and release activity is an important method in the restoration of fishery resources. In order to understand the possible genetic effect of hatchery-released populations on wild populations during the artificial enhancement and release activities of Sebastiscus marmoratus in Zhoushan waters, we utilized mitochondrial DNA control region sequences to examine the genetic diversity in four S. marmoratus populations, including one farmed population, one released population and two wild populations. A total of 68 haplotypes from 123 individuals were detected, including 3 shared haplotypes. Haplotype diversity ranged from 0.944 to 0.980, with a mean of 0.966. The nucleotide diversity ranged from 0.020 to 0.025, with a mean of 0.022. Analysis of Molecular Variance (AMOVA) indicated that the primary genetic variation occurs within populations and the index of genetic differentiation between populations (FST) among the four populations showed no differentiation. The results indicate that the current artificial enhancement and release has not impacted the S. marmoratus population in Zhoushan waters. Continued long-term monitoring is essential to protect the high-quality germplasm resources of S. marmoratus.