Australian sperm whales from different whaling stocks belong to the same population

1. Understanding the factors driving population structure in marine mammals is needed to evaluate the impacts of previous exploitation, current anthropogenic threats, conservation status, and success of population recovery efforts.
2. Sperm whales are characterized by a worldwide distribution, low genetic diversity, complex patterns of social and genetic structure that differ significantly within and between ocean basins, and a long history of being commercially whaled. In Australia, sperm whales from the (International Whaling Commission assigned) southern hemisphere ‘Division 5’ stock were very heavily exploited by whaling.
3. The present study assessed the potential effects of whaling on the genetic diversity of sperm whales in Australia and the population genetic structure of these whales within a global context. A combination of historical and contemporary sperm whale samples (n = 157) were analysed across six regions, from south-eastern Australia (‘Division 6’ stock in the Pacific Ocean) to south-western Australia (‘Division 5’ stock in the Indian Ocean).
4. Sperm whales sampled from the ‘Division 5’ and ‘Division 6’ stocks belong to the same population based on nuclear and mitochondrial DNA (mtDNA) analyses. Four novel sperm whale mtDNA haplotypes were identified in animals from Australian waters. Levels of genetic diversity were low in Australian sperm whales but were similar to those previously reported for populations in the Indian and Pacific Oceans.
5. Given the genetic distinctiveness of sperm whales in Australian waters from other regions in the Pacific and Indian Oceans, and the lack of recovery in population numbers, further scientific studies are needed to increase our understanding of population dynamics and the effectiveness of threat management strategies in this species.

     

Historical DNA as a tool to genetically characterize the Mediterranean sand tiger shark (Carcharias taurus,Lamniformes: Odontaspididae): A species probably disappeared from this basin

1. The sand tiger shark (Carcharias taurus) is a coastal species distributed in temperate and sub‐tropical waters, classified as ‘Vulnerable’ at global level and ‘Critically endangered’ in eastern Australia, south‐western Atlantic Ocean, and Mediterranean Sea. Six populations (north‐western Atlantic, Brazil, South Africa, Japan, eastern Australia, and western Australia) with low genetic diversity and limited gene flow were identified worldwide, but genetic information for many other geographic areas are still missing. Specifically, this species is listed in several reports as part of the Mediterranean fauna, even if there has been a lack of catches and sightings in recent years in this basin. To clarify the origin of C. taurus individuals caught in the past in the Mediterranean Sea, historical samples were genetically analysed.
2. Nine samples with certain Mediterranean origin were collected from different European museums. DNA was extracted and ~600 bp of the mitochondrial DNA control region were amplified using eight overlapping species‐specific primer pairs. Sequences obtained were aligned with all the haplotypes globally known so far.
3. Genetic analysis revealed the misidentification of one museum specimen. Among the remaining Mediterranean historical samples, three different haplotypes were recovered. Two of them previously observed only in South Africa and one described in both South African and Brazilian populations.
4. Results suggest a genetic relationship between Mediterranean sand tiger sharks and those from the western Indian Ocean. According to previous studies, we hypothesized that, during the Pleistocene, the cold Benguela upwelling barrier was temporarily reduced allowing the passage of C. taurus individuals from the Indian to Atlantic Ocean. After the restoration of this phylogeographic barrier some individuals were trapped in the Atlantic Ocean and probably migrated northward colonizing the western African coasts and the Mediterranean Sea.

     

Genetic structure of Orbicella faveolata population reveals high connectivity among a marine protected area and Varadero Reef in the Colombian Caribbean

1. The protection of ecosystems with high diversity, such as coral reefs, is not an approach that guarantees their conservation. Thus, maintaining connectivity among coral populations over the long term is a strategy that should be adopted in order to protect diversity and ecological processes. Although coral reefs in Colombia are highly diverse, the population genetics baseline data of keystone species such as Orbicella faveolata are limited.
2. To provide current information about the connectivity between populations of O. faveolata in the Colombian Caribbean, the genetic diversity and distribution of O. faveolata was evaluated with analysis of molecular variance (AMOVA), principal components, and migration estimations using 113 genets distributed in six populations. Also, a genetic structure analysis that included the available data for the Caribbean population was conducted, seeking to understand how the Colombian populations relate to the broader region.
3. According to the global fixation index (F_ST) for the Colombian Caribbean, there was no genetic structure (F_ST = 0.002). Discriminant analysis of principal components (DAPC) showed that Corales del Rosario Archipelago (CR), Este de Isla Fuerte (EIF), San Bernardo Archipelago (SB), and Varadero Reef (VR) were grouped with Oeste de Isla Fuerte (OIF), with Bushnell (BS) representing the most divergent cluster. Migration analysis showed relatively high migration from VR to CR and SB, highlighting the importance of VR as a genetic reservoir for the region. Structure analysis showed that the Colombian population presented a specific genetic identity (F_ST = 0.254), suggesting that the Colombian Caribbean population could be a peripheral population that contributes significantly to genetic variation and is connected through a complex connectivity process.
4. In conclusion, the estimated genetic connectivity reflects the influence of sea surface dynamics over the interpopulation exchange dynamics and the role of protected and nonprotected coral reef in the Colombian Caribbean. Thus, the Colombian Caribbean population of O. faveolata could be relevant to the conservation of genetic diversity on a larger scale.

     

Genetic structure,origin, and connectivity between nesting and foraging areas of hawksbill turtles of the Yucatan Peninsula: A study for conservation and management

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A modelling study of the role of marine protected areas in metapopulation genetic connectivity in Delaware Bay oysters

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Genetic connectivity of the South American fur seal (Arctocephalus australis) across Atlantic and Pacific oceans revealed by mitochondrial genes

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A new map of the tiger shark (Galeocerdo cuvier) genetic population structure in the western Atlantic Ocean: Hypothesis of an equatorial convergence centre

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Phylogeographic implications for release of critically endangered manatee calves rescued in Northeast Brazil

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Genetic diversity of immature Kemp's ridley (Lepidochelys kempii) sea turtles from the northern Gulf of Mexico

1. The Kemp’s ridley (Lepidochelys kempii) is the world’s most endangered sea turtle species. Predominately nesting at only one beach in Mexico, this species declined to an estimated 300 females in the mid-1980s. Conservation efforts in the United States and Mexico, including a head start programme in southern Texas in which hatchlings were reared in captivity for several months before being released into the wild, resulted in the recovery of this species.
2. Although genetic data have previously been used to assess the success of the head start programme and dispersal of individual adults, data on immature turtles sampled at foraging areas and adult females sampled at the main nesting beach in Mexico are lacking. Genetic characterization of immature individuals is important for understanding recruitment, survival, and population demography, while genetic data on individuals from Mexico are essential for understanding dispersal and overall genetic diversity in this species.
3. To address these gaps, mitochondrial DNA data were collected from 106 immature individuals sampled at four different foraging sites in the northern Gulf of Mexico and from 18 nesting females at the primary nesting beach in Mexico.
4. Two previously unknown mitochondrial DNA haplotypes were discovered among the immature individuals.
5. Except for these two new haplotypes, the genetic diversity of immature individuals in the northern Gulf of Mexico closely corresponds to that of adults sampled in Mexico, which suggests that much of the diversity within the nesting population can be found among immature animals dispersing to foraging grounds, including locations in the northern Gulf of Mexico.
6. Continued monitoring of the genetic variation of different life stages of this species across its distribution range will help assess the success of conservation programmes by ensuring the maintenance of genetic diversity and representation of this diversity across the species’ distribution range.

     

Genetic connectivity and phylogeography of the night shark (Carcharhinus signatus) in the western Atlantic Ocean: Implications for conservation management

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Conservation genetic assessment of the paleback darter,Etheostoma pallididorsum,a narrowly distributed endemic in the Ouachita Highlands,Arkansas, USA

1. The paleback darter, Etheostoma pallididorsum, is considered imperilled and has recently been petitioned for listing under the Endangered Species Act. Previous allozyme-based studies found evidence of a small effective population size, warranting conservation concern. The objective of this study was to assess the population dynamics and the phylogeographical history of the paleback darter, using a multilocus microsatellite approach and mitochondrial DNA.
2. The predictions of this study were that: paleback darter populations will exhibit low genetic diversity and minimal gene flow; population structure will correspond to the river systems from which the samples are derived; reservoir dams impounding the reaches between the Caddo and Ouachita rivers would serve as effective barriers to gene flow; and the Caddo and Ouachita rivers are reciprocally monophyletic.
3. Microsatellite DNA loci revealed significant structure among sampled localities (global F_st = 0.17, P < 0.001), with evidence of two distinct populations representing the Caddo and Ouachita rivers. However, Bayesian phylogeographical analyses resulted in three distinct clades: Caddo River, Ouachita River, and Mazarn Creek. Divergence from the most recent ancestor shared among the river drainages was estimated at 60 Kya. Population genetic diversity was relatively low (H_e = 0.65; mean alleles per locus, A = 6.26), but was comparable with the population genetic diversity found in the close relatives slackwater darter, Etheostoma boschungi (H_e = 0.65; A = 6.74), and Tuscumbia darter, Etheostoma tuscumbia (H_e = 0.57; A = 5.53).
4. These results have conservation implications for paleback darter populations and can be informative for other headwater specialist species. Like other headwater species with population structuring and relatively low genetic diversity, the persistence of paleback darter populations is likely to be tied to the persistence and connectivity of local breeding and non-breeding habitat. These results do not raise conservation concern for a population decline; however, the restricted distribution and endemic status of the species still renders paleback darter populations vulnerable to extirpation or extinction.

     

Weak connectivity and population cohesiveness in rudderfish Kyphosus sandwicensis (Teleostei: Kyphosidae) inhabiting remote oceanic islands

1. Population connectivity has a fundamental role in metapopulation dynamics, with important implications in conservation. Easter Island (EI) and Salas y Gómez Island (SG) in the Pacific Ocean are ideal for the study of population connectivity because they are separated by 415 km and isolated from other islands in the Pacific Ocean by >2,000 km.
2. Considering that dispersal processes could play a critical role in the persistence of its populations, the connectivity pattern of the rudderfish Kyphosus sandwicensis was evaluated between EI and SG using both a population genetics and a biophysical modelling approach.
3. The variability in the control region of the mitochondrial DNA did not show a significant phylogeographical pattern, and the variability in 16 microsatellite loci suggested that individuals of K. sandwicensis located at EI and SG belong to the same genetic population. However, historical migration showed that 0.2% of the recruits at EI come from SG and that 0.15% at SG come from EI per year.
4. Using simulated larval release during September and a larval development of 30 days in the plankton, biophysical modelling did not detect migration between the islands. Furthermore, self-recruitment shows interannual variation ranging from 5 to 10% of the total released larvae.
5. Whereas the genetic data showed a lack of population genetic structure but low connectivity of K. sandwicensis between EI and SG, the biophysical modelling showed null movement of particles between the islands. Stochastic movement of larvae or adults could explain the pattern observed, with rafting as an example. These low-frequency and stochastic movements may be important in maintaining the cohesiveness between EI and SG.

     

Phylogeography,genetic stocks,and conservation implications for an Australian endemic marine turtle

1. Identification of the geographic extent of population boundaries, the distribution of genetic lineages, and the amount of genetic exchange among breeding groups is needed for effective conservation of vulnerable marine migratory species. This is particularly true of the flatback turtle (Natator depressus), which only breeds in Australia but has extensive migrations that can include international waters.
2. This study investigated the phylogeography and genetic structure among 17 flatback turtle rookeries across their range by sequencing an 810 bp portion of the mitochondrial DNA in 889 samples and genotyping 10 microsatellite loci in 598 samples.
3. There was low phylogenetic divergence among haplotypes and evidence of recent population expansion, likely in the late Pleistocene. A predominant haplotype was found across all rookeries, but other haplotype groups were regionally specific.
4. In general, there was agreement in patterns of genetic differentiation in the mitochondrial DNA and microsatellite data, and in some pairwise comparisons a higher mutation rate of microsatellites provided stronger evidence of differentiation.
5. These results suggest natal philopatry operates in the choice of breeding locations for males as well as females.
6. Evidence of genetic connectivity among neighbouring rookeries led to the identification of seven genetic stocks. Geographic boundaries of rookeries used by genetic stocks varied widely (160–1,300 km), highlighting a need for field studies to better understand movement patterns.
7. Hierarchical analysis of molecular variance identified significant genetic differentiation based upon genetic stock, nesting phenology (summer vs. winter nesters), and a west–east discontinuity across Torres Strait. A pattern of isolation by distance was identified, which was most strongly observed in the microsatellite data.
8. In combination with tagging and telemetry studies, these results will allow better quantification of stock‐specific threats along migratory routes and in foraging habitats. Implications of climate change will be stock specific and may depend upon the extent of genetic connectivity between neighbouring stocks.

     

Population genetic divergence of bonnethead sharks Sphyrna tiburo in the western North Atlantic: Implications for conservation

1. Sharks are a priority for conservation because numerous species, including small-sized coastal species, are being heavily exploited by commercial and recreational fisheries. Understanding the genetic population structure of sharks is key to effective management, maximizing their evolutionary potential in a rapidly changing environment and preventing population declines.
2. Limited dispersal is an important factor promoting population divergence for several coastal shark species. The genetic variation in 14 microsatellite loci and 21,006 single nucleotide polymorphisms genotyped using restriction-site-associated DNA sequencing was analysed to assess the genetic structure of the bonnethead shark, Sphyrna tiburo, in the western North Atlantic.
3. Genetic differences were identified among three well-defined regions: the western Florida coast, the south-eastern US Atlantic coast, and the southern Gulf of Mexico. Results support previous studies based on mitochondrial DNA sequences in defining differences among these regions and suggest limitations of bonnethead sharks in routinely performing long-distance migrations.
4. The limited connectivity among regions explains the pattern of genetic divergence but also reported divergence at the species/subspecies level. These genetically discrete bonnethead populations have independent evolutionary histories that may include local adaptations to specific areas.
5. Bonnethead sharks are currently managed as two stocks in the USA owing to recent genetic, tagging, and life history studies; however, no stock assessments or management plans exist for Mexico. These results not only serve to reinforce US management strategies and provide critical data about the extent of gene flow and sex dispersal among populations, but also begin the process of effective management in the waters of Mexico to ensure the long-term productivity and resilience of this species. With an absence of gene flow between populations from US waters and the southern Gulf of Mexico, there is a need for management plans based upon independent biological and population dynamics data since limited or no opportunities for populations to interchange individuals may occur to re-establish population viability.

     

基于线粒体Cyt b基因序列的绿鳍马面鲀6个野生群体的遗传结构分析

利用线粒体细胞色素b(cytochrome b,Cyt b)基因分析了我国沿海绿鳍马面鲀(Thamnaconus septentrionalis)6个野生群体(大连、秦皇岛、蓬莱、日照、舟山和汕头)的遗传多样性和群体遗传结构。结果显示,在176个个体915 bp的Cyt b部分序列中共检测到32个变异位点和30个单倍型;6个群体的单倍型多样性为0.883~0.953,核苷酸多样性0.0032~0.0039;群体间固定指数较小,呈中低度分化;AMOVA分析表明,遗传变异主要来源于群体内,群体间遗传分化未达到显著水平。群体历史动态分析表明,绿鳍马面鲀在16.9万~42.2万年前经历种群扩张。总体上,各群体间的遗传分化较小,并未形成相应的地理支系,推测黑潮的输送作用以及绿鳍马面鲀的洄游习性维持了各群体间高强度的基因交流;中更新世中晚期的气候波动对绿鳍马面鲀的种群扩张以及地理分布格局可能具有重要影响。本研究结果加深了人们对于绿鳍马面鲀资源情况的认识,为绿鳍马面鲀资源的保护和合理利用提供了理论依据。     

Insights into population genetics,connectivity and demographic history of the longnosed skate Dipturus oxyrinchus (Linnaeus, 1758) in the western Mediterranean Sea

1. Genetic information is crucial for the conservation of Dipturus oxyrinchus (Linnaeus, 1758), a threatened large skate with declining populations over most of its geographical range. The main aim of the present study was to investigate the genetic structure, connectivity and demographic history of the longnosed skate in Sardinia (western Mediterranean Sea).
2. Patterns of population structure were assessed in 175 specimens from six sampling sites. Variation in two mitochondrial genes (cytochrome c oxidase subunit I (COI) and control region) highlighted high genetic diversity and low but significant genetic differentiation among sites, which clustered into three groups corresponding to the north‐west, north‐east and south Sardinian coasts.
3. The observed genetic structuring could presumably depend on a combination of past geological events, contemporary restrictions to dispersal and biological characteristics of the species (e.g. site‐fidelity, no pelagic larval stage, limited dispersal of juveniles and/or adults).
4. Demographic analyses showed signs of past population expansion, but substantial current stability of Sardinian populations. From a conservation perspective, these results are encouraging, and indicate that Sardinian populations are still large and stable, and seem not to have suffered negative side‐effects from the ever‐growing fishing pressure in the region.
5. The occurrence of genetic structuring strongly supported the close monitoring of populations to identify any erosion of their gene pool, and high genetic variability of the Sardinian D. oxyrinchus populations could thus represent priority populations for conservation purposes, providing potential sources for recolonization in cases of local extinctions in other areas of the distribution range of the species.
6. When the sequences from Sardinia were compared with those available from other areas, the data seem to exclude the possibility that the Atlantic and Mediterranean host totally isolated populations or even different species, as recently suggested. However, additional markers and a larger sampling sites are needed to confirm these findings.

     

Global population genetic structure of the sequential hermaphrodite,dusky grouper (Epinephelus marginatus)

1. The dusky grouper Epinephelus marginatus is a large epinephelid species that occurs in the eastern and south-western Atlantic and western Indian Oceans. Late maturity, protogynous hermaphroditism, site fidelity, and overfishing have all contributed to its demographic decline.
2. Connectivity and demography within a broad sampling of dusky grouper populations throughout its distribution were assessed. To do so, genetic variation at 11 polymorphic microsatellite loci and a partial sequence of the mitochondrial control region (mtCR) were evaluated.
3. Two major mtCR lineages with a sequence divergence of 1.6% were found. The magnitude of genetic differentiation for mtCR among north and south Atlantic and Indian Ocean populations was high, with Φ_ST = 0.528.
4. D_EST and results of discriminant analysis of principal component revealed significant microsatellite genetic differentiation between all collection areas. Significant pairwise D_EST showed moderate (0.084) to very great (0.603) differentiation. The effective population size was low for all localities, ranging between 25 (Azores Archipelago) and 311 (Rio Grande do Sul). The overall effective population size was estimated as 299 (confidence interval = 215–412), and there was no evidence of strong or recent bottleneck effects.
5. Local and regional genetic structuring among dusky grouper populations is the consequence of the species' site fidelity, distribution across multiple oceanographic boundaries, and probably also of sequential hermaphroditism that contributes to the intensity of random genetic drift.
6. The spatial pattern of genetic structuring of dusky groupers is such that fisheries management and conservation of population genetic integrity will have to be pursued at the local and regional scales.

     

Gene pool and connectivity patterns of Pinna nobilis in the Balearic Islands (Spain,Western Mediterranean Sea): Implications for its conservation through restocking

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Global phylogeography of the smooth hammerhead shark: Glacial refugia and historical migration patterns

1. Extreme climate changes during the Cenozoic Era strengthened different biogeographical barriers that decreased the connectivity among populations, triggering lineage diversification of different species worldwide.
2. The mitochondrial DNA control region was employed to explore the phylogeography of Sphyrna zygaena, a globally distributed species threatened by unsustainable, illegal, unreported and unregulated fisheries triggered by the international shark fin trade. It is listed as ‘Vulnerable’ by the IUCN Red List and its trade is regulated by CITES Appendix II.
3. Only 13 haplotypes were found with low genetic diversity levels (hd = 0.686 ± 0.014; π = 0.00206 ± 0.00004) compared with other species of the Sphyrnidae family. The species has a very strong phylogeographic population structure among the Atlantic, Indian and Pacific Oceans (Φ_ST = 0.79132). Worldwide, there are six distinct populations with some haplotype sharing.
4. These populations are probably connected by a stepping-stone dispersal of a small number of migrants per generation from the Indo-Pacific towards the Atlantic. Modelling suggests that S. zygaena diverged into two lineages around 6.96 million years ago which have been isolated in glacial refuges in the Atlantic and Indo-Pacific oceans; and after deglaciation, a population expansion probably permitted secondary contact.
5. Conservation plans to establish differentiated management units should be adopted in each of the identified populations. Among these, the Eastern Central Atlantic and West Indo-Pacific are the most important areas for the species considering the historical migration routes that act as a bridge connecting the Atlantic and Indo-Pacific Oceans while the Gulf of Guinea connects the Atlantic populations. Still, further studies are required to know if these populations are also linked with nursery areas for the species.
6. The results herein can help to delimit the main evolutionarily significant units to implement effective policies to establish differentiated management units as starting points to genetic monitoring programmes for Sphyrna zygaena.

     

河南境内四水系宽鳍鱲野生群体的遗传多样性

为准确掌握河南野生宽鳍鱲(Zacco platypus)群体遗传结构,本研究利用线粒体CO I基因检测了海河、黄河、淮河和长江水系宽鳍鱲群体的遗传多样性和种群分化情况。110个样品共检测出40个单倍型,平均单倍型多样性为0.92077,平均核苷酸多样性为0.02439。AMOVA分析显示,大多数遗传变异存在于宽鳍鱲群体间(60.59%),群体内的遗传变异为37.67%。系统发育树结果表明,长江水系宽鳍鱲群体遗传分化较大,一部分群体单独聚为一支,另外一部分群体与海河、黄河、淮河水系宽鳍鱲聚在一起,没有显示出明显的南北分化格局。种群历史动态结果推测宽鳍鱲群体经历过瓶颈效应,且该过程可能与第四纪中更新世气候波动有关。建议对河南境内的宽鳍鱲种群,特别是遗传多样性低的种群(海河水系)进行保护。