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.

     

Basin‐scale distribution and haplotype partitioning in different genetic lineages of the Neotropical migratory fish Salminus brasiliensis

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Genetic divergence in Indian populations of M. rosenbergii using microsatellite markers

Macrobrachium rosenbergii, known as the giant freshwater prawn or Malaysian prawn, is the sixth largest aquaculture species in Asia. Knowledge of genetic diversity of M. rosenbergii is important to support management and conservation programmes, which will subsequently help in sustainable production of this economically important species. This study aimed to analyse the genetic diversity and population structure of five M. rosenbergii populations using 11 microsatellite loci. In analysing 240 samples, the number of alleles, observed heterozygosity (H_O) and expected heterozygosity (H_E) ranged from 3 to 20, from 0.250 to 0.978 and from 0.556 to 0.944 respectively. The five stocks of M. rosenbergii displayed high level of genetic diversity. Both the F_ST and amova analyses showed that there was significant genetic differentiation among all populations. The UPGMA dendrogram based on Nei's genetic distance matrix revealed that the Narmada and Mahi populations were in one cluster and Mahanadi and Subarnarekha populations in another single major branch, whereas the Kerala population clearly showed a separate cluster. This information on genetic variation will be useful for genetic improvement and conservation of Indian populations of giant freshwater prawn M. rosenbergii.     

Genetic Diversity and Population Structure in the Heavily Exploited Korean Rockfish,Sebastes schlegeli,in Korea

The Korean rockfish, Sebastes schlegeli, is a valuable and intensively exploited species in Korea. We discuss the genetic diversity and genetic structure of four Korean rockfish populations using eight microsatellite loci. In total, 161 different alleles from 138 individuals were observed. Average allele number per locus ranged from 2.5 to 23 and allelic richness varied from 13.38 to 14.63 within a population. Despite a long history of stocking practices, we found very high levels of polymorphism (mean heterozygosity = 0.810), which is comparable to other congeneric species. No significant difference in genetic diversity and molecular genetic variance (F_ST and R_ST) was observed among four local samples (P > 0.1). Little indication of contemporary inbreeding (F_IS= 0.051) or population structure (K = 1) was detected. This absence of differentiation may reflect high levels of gene flow along the coast of Korea. Our study demonstrates that rockfish in Korea should be managed as a single unit. Currently, the species does not appear to be genetically threatened, but the potential for a rapid loss of genetic diversity remains. This information on the genetic characteristics of Korean rockfish populations has important implications for fisheries management and conservation efforts, and will aid in the sustainable exploitation of the fishing resources and the preservation of biodiversity.     

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.

     

Allelic losses and gains during translocations of a high conservation value fish,Coregonus lavaretus

1. The use of translocations to establish new or ‘refuge’ populations for species with high conservation value is controversial but widely used in conservation management. One of the risks of this approach is that an establishing population does not adequately capture the genetic diversity of the donor gene pool. This effect, rarely examined, is tested here.
2. In this study the genetic consequences of two conservation translocations after five generations (16 years) of the European whitefish, Coregonus lavaretus, were quantified. Both translocations were made using almost the same genetic groups and thus represent a partly replicated natural study.
3. Analysis of 12 informative microsatellites showed that expected heterozygosity, the mean number of alleles per locus and allelic richness did not differ between donor and translocated populations. There was also no loss of heterozygosity in the translocated populations, nor deviations from Hardy–Weinberg equilibrium expectations, nor signs of linkage disequilibrium.
4. All populations were genetically differentiated but pairwise F_ST values were low, indicating that the magnitude of divergence was small.
5. There was no evidence of inbreeding but there were significant differences in private allelic richness between donor and translocated populations. Of 50 alleles found in the donor population, 16% of the rarer alleles were lost in one translocated population and 8% in the other.
6. Allele loss without a reduction in heterozygosity strongly points to stochastic drift effects having occurred following translocation. The evidence indicates that alleles that were not detected in the donor population have arisen de novo in the translocated populations.
7. It is concluded that conservation translocations comprising even a modest number of propagules can successfully capture a high proportion of genetic variation of the host population, and that reduced genetic variation in the translocated population may be mitigated by the emergence of new variation over short time periods.

     

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.

     

Genetic diversity,population structure,and historical demography of a highly vagile and human-impacted seabird in the Pacific Ocean: The red-tailed tropicbird,Phaethon rubricauda

1. Many seabird breeding colonies have recovered from heavy anthropogenic disturbance after conservation actions. The widely distributed red-tailed tropicbird, Phaethon rubricauda, was used as a model species to assess potential anthropogenic impacts on the genetic diversity of breeding colonies in the Pacific Ocean.
2. Cytochrome c oxidase subunit I and control region sequences analyses were conducted across the range of the species in the Pacific Ocean. The study sites were at islands without human-related disturbance (non-impacted islands) and with human-related disturbance (impacted islands). We hypothesized that (i) breeding colonies of the red-tailed tropicbird on impacted islands have lower genetic diversity compared with colonies on non-impacted islands, and (ii) breeding colonies of the red-tailed tropicbird show significant fine and broad-scale genetic structure across the Pacific Ocean. Bayesian skyline analyses were conducted to infer past changes in population sizes.
3. Genetic diversity was similar between impacted and non-impacted islands. There was significant broad-scale genetic structure among colonies separated by over 6,000 km, but a lack of significant fine-scale genetic structure within Australasia and Hawai'i, although a significant level of differentiation was found within Chile with Φ_ST analyses. Skyline analyses showed that effective population sizes remained relatively constant through time, but experienced either a slight decrease or the end of an expansion event through the last 1,000 years. These changes may be related to the arrival of humans on Pacific islands.
4. Impacted islands may have received immigrants from other relatively close islands, buffering the loss of genetic diversity. However, it is also possible that colonies have retained ancestral variation or that a large effective population size coupled with a long generation time (13 years) has prevented the loss of genetic diversity in human-impacted islands. Future research using higher-resolution markers is needed to resolve the population genetic structure of the red-tailed tropicbird in an ecological time-scale.

     

Population structure,genetic diversity,and colonization history of the eastern pondmussel,Sagittunio nasutus,in the Great Lakes drainage

1. The eastern pondmussel, Sagittunio nasutus (Bivalvia: Unionida), has declined in abundance and distribution in eastern North America over the last few decades. The declines are predominantly the result of infestation by invasive dreissenid mussels and changes in habitat. The species is now considered imperilled across large portions of its distribution, especially in the Laurentian Great Lakes region.
2. The genetic diversity and structure of the remnant populations in the Great Lakes region were assessed using 10 newly developed microsatellite DNA loci for S. nasutus. Understanding the remaining populations can inform future management projects and determine whether the remnant populations have experienced a genetic bottleneck or a founder effect. We hope that this will inform the conservation of other species in regions founded by, and isolated from, a more genetically diverse source population or with disjointed geographical distributions.
3. Focusing on the Great Lakes region, samples (n = 428) from 62 collection sites in 28 water bodies were collected. Across the locations sampled for S. nasutus 11 genetic populations were identified, with significant genetic differentiation among them. The genetic structure of the species was assessed, with genetic similarities among populations compared and with geographical routes of colonization and gene flow evaluated.
4. Initial colonization from the Atlantic coast into Lake Erie and Lake Ontario is evident, followed by colonization events into nearby inland rivers and lakes. Analyses found evidence of inbreeding in all but one population and evidence of past genetic bottlenecks or strong founder effects in all but four populations. This study deepens our understanding of the genetic past and present of this imperilled species, providing conservation suggestions for the future management of the species.

     

A biogeography‐based management for Mytilus chilensis: The genetic hodgepodge of Los Lagos versus the pristine hybrid zone of the Magellanic ecotone

1. This study was intended to identify mussel species from the Magellanic ecotone, quantifying interspecific hybridization within Mytilus and depicting the genetic architecture of Mytilus chilensis in its South Pacific range.
2. The analysis comprises the sub‐Antarctic Magallanes Province as a rich ecotone of climates, ecosystems and admixed faunas embedded among the biogeographic regions of the Pacific, the Atlantic, and Antarctica.
3. Highly conserved molecular sequences within species were used to identify species, and polymorphic microsatellites were used to calculate the genetic architecture of M. chilensis. The absence of the invasive species Mytilus galloprovincialis from the M. chilensis range clarifies previous doubts on its expansion southward from the Arauco Gulf. The ubiquitous presence of the typical Glu‐5′‐Me‐15/16 PAP allele of Mytilus trossulus in the Northern Hemisphere might come from hull biofouling, but rather it seems to be an ancient polymorphism conserved in M. chilensis as occurs in blue mussels from other regions of the Southern Hemisphere. There is a very limited connectivity (F_ST = 0.167) between two latitudinal gene pools of M. chilensis that are highly divergent in composition, architecture, and ecological relevance.
4. Fifty years of aquaculture enhancement in Los Lagos explains its high diversity and genetic heterogeneity among patches, so its mussel management should seek a balance between exploitation and environmental sustainability.
5. The Magellanic ecotone bears a pristine M. chilensis × Mytilus edulis platensis hybrid zone around the Southern Cone, larger (450 km) than previously thought. Such a hybrid zone permeates one of the last remaining wilderness areas in the world (Cape Horn Biosphere Reserve) and is a natural laboratory for addressing introgression, hybridization, and evolution of Mytilus spp. genomes in their last southern frontier.

     

Newly developed microsatellite markers for the pan‐European duck mussel,Anodonta anatina: revisiting the main mitochondrial lineages

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Global-scale genetic structure of a cosmopolitan cold-water coral species

• 1. When considering widely distributed marine organisms with low dispersal capabilities, there is often an implication that the distribution of cosmopolitan species is an artefact of taxonomy, constrained by the absence of characters for delimiting either sibling or cryptic species. Few studies have assessed the relationship among populations across the global range of the species' distribution, and the presence of oceanographic barriers that might influence gene flow among populations are underestimated.
• 2. In this study, evolutionary and ecological drivers of connectivity patterns have been inferred among populations of the cold-water coral Desmophyllum dianthus, a common and widespread solitary scleractinian species, whose reproduction strategy and larval dispersal are still poorly unknown.
• 3. The genetic structure of D. dianthus was explored using 30 microsatellites in 347 specimens from 13 localities distributed in the Mediterranean Sea and Atlantic and Pacific Oceans.
• 4. Results clearly reveal genetically differentiated populations in the Northern and Southern Hemispheres (F_ST = 0.16, F_SC = 0.01, F_CT = 0.15, P-values highly significant), and Chilean and New Zealand populations with independent genetic profiles.
• 5. Marine connectivity patterns at different spatial scales are discussed to characterize larval dispersal and gene flow through the Northern and Southern Hemispheres.

     

Microsatellite analysis of genetic diversity and genetic structure of the Chinese freshwater mussel Solenaia carinata (Bivalvia: Unionidae)

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First microsatellite data on Proteus anguinus reveal weak genetic structure between the caves of Postojna and Planina

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Identification of microsatellite loci and examination of genetic structure for the endangered springsnails Juturnia kosteri and Pyrgulopsis roswellensis in the Chihuahuan Desert

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Colonization history and human translocations explain the population genetic structure of the noble crayfish (Astacus astacus) in Fennoscandia: Implications for the management of a critically endangered species

1. The noble crayfish (Astacus astacus) is an endangered freshwater species in Europe. The main threat is from lethal crayfish plague, caused by the oomycete Aphanomyces astaci that has been spread over Europe by introduced North American crayfish species, acting as chronic carriers of the disease.
2. Most of the remaining noble crayfish populations are found in the Baltic Sea area, and there is an urgent need to implement conservation actions to slow down or halt the extinction rate in this region. However, limited knowledge about the genetic structure of populations in this area has so far precluded the development of conservation strategies that take genetic aspects into consideration.
3. Key objectives of this large-scale genetic study, covering 77 locations mainly from northern Europe, were to describe the contemporary population genetic structure of the noble crayfish in the Fennoscandian peninsula (Sweden, Norway, and Finland), taking postglacial colonization history into account, and to evaluate how human activities such as stocking have affected the genetic structure of the populations.
4. Analyses of 15 microsatellite markers revealed three main genetic clusters corresponding to populations in northern, middle, and southern Fennoscandia, with measures of genetic diversity being markedly higher within populations in the southern cluster. The observed genetic structure probably mirrors two main colonizations of the Baltic Sea basin after the last glaciation period. At the same time, several deviations from this pattern were observed, reflecting past human translocations of noble crayfish.
5. The results are discussed in relation to the conservation and management of this critically endangered species. In particular, we recommend increased efforts to protect the few remaining noble crayfish populations in southern Fennoscandia and the use of genetic information when planning stocking activities, such as reintroductions following local extinctions.

     

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 structuring among populations of the great egret,Ardea alba egretta,in major Brazilian wetlands

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

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