Genetic diversity and differentiation of sea trout (<Emphasis Type="Italic">Salmo trutta</Emphasis>) populations in Lithuanian rivers assessed by microsatellite DNA variation

The genetic diversity and differentiation of sea trout were studied in three river basins in Lithuania: Akmena-Dane, Bartuva, and Nemunas. A total of 282 individuals were genotyped at eight microsatellite loci. A similar level of genetic diversity was found in all of the populations studied: mean allelic richness ranged from 3.64 to 5.03, and average expected heterozygosity ranged from 0.588 to 0.721. Significant genetic divergence was observed among the different river basins as well as between populations within the drainages. All pairwise F _ST values were highly significant, ranging from 0.027 to 0.197. The analysis of molecular variance showed rather weak hierarchical population structuring within the Nemunas basin, which may be explained by extensive gene flow among different river basins or, alternatively, reflect the influence of artificial breeding. Information on genetic diversity and differentiation of the Lithuanian sea trout populations will be useful for future management decisions.     

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

1. The tiger shark (Galeocerdo cuvier) is a common widespread coastal–pelagic shark species whose population genetic structure has only recently been the object of genetic studies.
2. In this study, the tiger's shark mitochondrial DNA control region was sequenced for a sample of 172 individuals from the western Atlantic and from Australia's east coast in the Pacific Ocean.
3. The results show a moderate variation in genetic diversity (h = 0.615 ± 0.038, π = 0.00184 ± 0.00021) with a strong population structure between Atlantic areas (Φ_ST = 0.28141, P = 0.00001).
4. The maternal lineage has high site fidelity, which paradoxically is coupled with connectivity across open ocean stretches to Fernando de Noronha Archipelago, which is identified as an important hotspot for this species. These results help with the understanding of what drives the displacement of this shark, at intra‐ and/or inter‐ocean basins levels, and can help inform the implementation of future conservation and management measures.
5. We recommend that the conservation of genetic diversity should be maintained at a global level and its maintenance should be pursued diligently in all populations of tiger shark. As the Fernando de Noronha region in the western Atlantic appears to contain the largest global genetic diversity of the species, this area should be treated as a marine reserve or ecological refuge for the tiger shark.

     

Microsatellite and mitochondrial DNA analyses reveal no genetic difference between two pufferfish species torafugu <Emphasis Type="Italic">Takifugu rubripes</Emphasis> and karasu <Emphasis Type="Italic">T. chinensis</Emphasis>

It has been reported that the nucleotide sequences of the mitochondrial and nuclear genes of Takifugu pufferfish torafugu T. rubripes and karasu T. chinensis show 99–100% sequence identity, indicating a very close relationship between the two species. To further investigate this genetic relationship, we compared genetic variation at four microsatellite loci and at the mitochondrial control region (CR) (561 bp) between groups of T. rubripes caught at two locations [TrG, caught in the Genkai Sea off Tsushima Island in 2003 (n = 50); TrS, caught in the Suwo Sea off Kita-Kyushu in 2008 (n = 50)] and T. chinensis caught at one location (TcK, caught off the east coast of Korea in 2004; n = 50). Analyses using microsatellite loci showed that genetic diversity index values of the TrG, TrS and TcK groups were 0.9505, 0.9350 and 0.9335, respectively, while values of genetic distance and genetic differentiation between TrG and TcK (0.0543 and 0.0189, respectively) were smaller than those between TrG and TrS (0.0857 and 0.0194, respectively). Analyses using CR for the same specimens showed that genetic distances were consistent with those obtained using microsatellite loci. These results, together with our previous observations, suggest that T. rubripes and T. chinensis are very closely related and possibly can be regarded as the same species.     

The importance of spatial scales to analysis of fish diversity in Amazonian floodplain lakes and implications for conservation

The Amazon River Basin has the highest fish species diversity of any region in the world, but is under threat from anthropogenic perturbations including overharvesting, alien species and drought. We asked whether species diversity in this region is more a function of within‐lake species richness (i.e., α diversity) or differences among lakes (β diversity). Although many studies have reported on species richness and diversity in single habitats, the importance of measuring diversity at different spatial scales is not yet well established. We collected fish in 10 floodplain lakes along the Solimões River (Brazil), divided evenly between two lake types: those on islands in the river channel (island lakes) and those on the margins of the river (coastal lakes) during 2006. We partitioned fish diversity into three spatial scales: α = within each lake; β₁ = among lakes of the same type (coastal or island) and β₂ = between the two types of lakes, and compared their relative contributions to regional (γ) diversity. β₁ + β₂ contributed as much or more to γ diversity than did α. Although many of the 116 fish species were shared between lake types (S = 72), 32 species were found exclusively in coastal lakes and 12 species were found exclusively in island lakes. Coastal lakes, which were deeper and cooler than island lakes, consistently had higher fish species richness than island lakes. We suggest that it will be necessary to set areas large enough to contain multiple lakes of both types to preserve regional fish diversity.     

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

1. The night shark, Carcharhinus signatus, is a mesopelagic, semi‐oceanic shark species found only in the Atlantic Ocean. It is one of the most frequently caught sharks in pelagic longline fisheries and is classified as Vulnerable by the International Union for the Conservation of Nature (IUCN). Despite their prevalence in commercial fisheries, the population genetic structure of the night shark has not been assessed.
2. The present study investigated the genetic diversity, genetic connectivity, and phylogeography of the species throughout the western Atlantic Ocean, based on complete mitochondrial control region (mtCR) sequence data (n = 152) and genotypic data from nine nuclear microsatellites (n = 119).
3. The mtCR sequence revealed 19 haplotypes, with overall haplotype and nucleotide diversities of 0.74 (±0.027) and 0.0034 (±0.0019), respectively, whereas the nuclear microsatellite observed and expected heterozygosities were 0.408 and 0.421, respectively. There was significant population structure (Ф_ST = 0.429; P < 0.01) and isolation by distance (r = 0.65, P = 0.03) based on mtCR sequence data, but no genetic differentiation based on nuclear microsatellite analyses.
4. The phylogenetic analyses support the existence of two matrilineal lineages, which diverged during the Pleistocene. Mitochondrial demographic analyses indicated a historical bottleneck effect followed by population expansion during the Pleistocene, whereas nuclear microsatellites did not detect a recent or a strong bottleneck.
5. For conservation purposes, we advocate that the species should be considered to comprise at least two management units (MUs) in the western Atlantic Ocean. MU‐specific catch quotas should be implemented throughout the range of the species given its low genetic diversity and vulnerability to overexploitation.

     

Migration and movement profiles of a potadromous fish (Brachymystax lenok Pallas 1773) in a highly connected river system (Mongolia)

Understanding a species’ spatial and temporal movements along with the way these shift under extreme environmental conditions is vital for developing scientifically sound conservation and management strategies. The aim of this research was to describe and quantify the seasonal migration patterns and fine‐scale movement profiles of Brachymystax lenok, a threatened, potadromous salmonid that inhabits the highly connected, boreal river basins of Siberia and northern Asia. During this study 21 mature individuals were monitored over a 15 month period in the upper Eroo River basin, Mongolia, using passive acoustic telemetry. Mean (±SD) B. lenok home ranges were 19.1 ± 15.1 km (median = 11.5 km), with maximum longitudinal movements detected > 45.3 km. Two periods of increased movements were identified; the first in late summer/early autumn when 10 B. lenok moved into deeper, overwintering pools, with the second period occurring in late spring and early summer when nine B. lenok were detected entering the surrounding tributaries. Diel activity and depth typically increased during daylight hours followed by decreased activity or resting periods in shallower river sections at night. These results highlight the need to maintain a high level of river connectivity and adequate fishing season closures by implementing and enforcing an expansive spatiotemporal management plan that can better protect and recover the Mongolian B. lenok populations. Such measures should be transferable to other threatened, potadromous fish species residing throughout the world's boreal river basins.     

Empirical estimation of recreational exploitation of burbot,Lota lota,in the Wind River drainage of Wyoming using a multistate capture–recapture model

Burbot, Lota lota (Linnaeus), is a regionally popular sportfish in the Wind River drainage of Wyoming, USA, at the southern boundary of the range of the species. Recent declines in burbot abundances were hypothesised to be caused by overexploitation, entrainment in irrigation canals and habitat loss. This study addressed the overexploitation hypothesis using tagging data to generate reliable exploitation, abundance and density estimates from a multistate capture–recapture model that accounted for incomplete angler reporting and tag loss. Exploitation rate μ was variable among the study lakes and inversely correlated with density. Exploitation thresholds μ₄₀ associated with population densities remaining above 40% of carrying capacity were generated to characterise risk of overharvest using exploitation and density estimates from tagging data and a logistic surplus‐production model parameterised with data from other burbot populations. Bull Lake (μ = 0.06, 95% CI: 0.03–0.11; μ₄₀ = 0.18) and Torrey Lake (μ = 0.02, 95% CI: 0.00–0.11; μ₄₀ = 0.18) had a low risk of overfishing, Upper Dinwoody Lake had intermediate risk (μ = 0.08, 95% CI: 0.02–0.32; μ₄₀ = 0.18) and Lower Dinwoody Lake had high risk (μ = 0.32, 95% CI: 0.10–0.67; μ₄₀ = 0.08). These exploitation and density estimates can be used to guide sustainable management of the Wind River drainage recreational burbot fishery and inform management of other burbot fisheries elsewhere.     

When low genetic variability in feral and hatchery-reared tilapia becomes a vicious circle: Oreochromis niloticus from Oaxaca, Mexico

Several tilapia species in Mexican reservoirs have been used as food source for more than 40 years but little effort has been devoted to the conservation and genetic selection of those species. Our objective was to evaluate genetic variability in feral (n = 59) and hatchery-produced (n = 58) Oreochromis niloticus stocked in the Benito Juarez dam. Allozyme analyses for 13 enzymatic systems and general proteins yielded 27 genetic loci. Seventeen loci were polymorphic in at least one sample. The observed heterozygosity was lower than expected and the imbalance in the Hardy–Weinberg equilibrium in almost all loci was caused by heterozygote deficiency. The inbreeding coefficient was 84%. Although the evidence suggests moderate genetic differentiation, it is probable that a great proportion of the source of hatchery organisms is from feral organisms. According to our results, management of the hatchery strain is inadequate, therefore other breeding strategies are needed to increase the genetic variability of O. niloticus from Oaxaca.     

Conservation genetics of the Mary River turtle (Elusor macrurus) in natural and captive populations

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Larval traits of the Caribbean amphidromous goby Sicydium punctatum (Gobioidei: Sicydiinae) in Guadeloupe

Amphidromous fish are the biggest contributor to the diversity of fish communities in river systems of Caribbean islands. Among them, Sicydium punctatum Perugia, 1896, which is endemic to the West Indies, represents the vast majority of fish in these rivers. The otolith microstructure and the biometry of S. punctatum postlarvae from Guadeloupe were investigated to explore the dispersal modalities of this species through an appreciation of the growth pattern, the pelagic larval duration (PLD) and the size‐at‐recruitment. The study was made on one cohort of 83 recruited postlarvae, fished at the Capesterre River's mouth on 2 November 2011. The mean (±SD) size‐at‐recruitment of the postlarvae was 24.6 ± 1.3 mm (range of 20.5–28.1 mm, n = 83). We found a mean (±SD) PLD of 72.2 ± 10.5 days (range of 54–101.5 days, n = 67). The growth rate estimated from the otolith increments showed a globally decreasing pattern during the marine larval phase. Growth rates at the beginning of the larval stage were significantly different between hatching periods, suggesting a relation between the hatching period and the growth rate in S. punctatum. This study adds on to the general understanding of the life cycle of S. punctatum in Guadeloupe that will help implement strategies to manage amphidromous fish populations in the Caribbean region.     

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.

     

Improved detection sensitivity using an optimal eDNA preservation and extraction workflow and its application to threatened sawfishes

1. Pressures on coastal ecosystems are increasing and aquatic species that are restricted to these habitats are facing the threat of extinction. However, the true extent of many threatened and rare aquatic species, especially elasmobranchs, remains unclear due to high levels of data deficiency and poor efficacy of traditional survey methods. Sawfishes (Pristidae), a family of shark-like rays, are among the most threatened and rare elasmobranch species and are difficult to detect in turbid, coastal habitats. Reliable cost-effective tools to detect these species are urgently needed to increase their conservation potential.
2. Characterization of environmental DNA (eDNA) extracted from water samples has garnered significant appeal for detection of rare and threatened species. To assist conservation and monitoring efforts for sawfishes using eDNA, species-specific TaqMan quantitative polymerase chain reaction assays were developed and validated to detect 1.25–5 copies of a 12S rRNA gene fragment. Filter samples were collected in Northern Territory, Australia to assess the utility of the developed eDNA assays and compare the efficacy of preservation and extraction workflows for detecting rare species.
3. Dwarf sawfish (Pristis clavata) were detected in three of 20 sites, and there was a significant effect of preservation and extraction workflow on total eDNA yield and subsequent detection success. Longmire's preserved samples extracted using glycogen-aided precipitation yielded a significantly higher concentration of total eDNA (n = 60; β = 1.27, t(95) = 8.172, P < 0.0001) and yielded positive P. clavata eDNA detections compared to ethanol preserved samples extracted using QIAGEN DNeasy kit, which did not yield any positive detections.
4. The optimized eDNA assays were developed to support monitoring efforts for endangered sawfishes. Importantly, this study demonstrates that choice of preservation and extraction workflow requires careful consideration, especially when detection of rare or threatened species can have important management and conservation outcomes.

     

Polymorphisms of the growth hormone gene in domesticated red sea bream populations (Pagrus major) based on minisatellite genotypes and nucleotide sequences

The genetic diversity of the growth hormone gene in domesticated red sea bream (pmaGH) was evaluated using a minisatellite DNA marker located in intron 3 (pmaGH22) and nucleotide sequences. The number of alleles of pmaGH22 was largely decreased in domesticated strains of red sea bream, and the possibility of selection pressures was also detected based on the analysis of the Hardy–Weinberg equilibrium in some strains. However, each strain inherited a small number of alleles of pmaGH22, and the entire domesticated population (combining all strains) showed a large number of alleles (n = 17), similar to the allelic richness of the wild population (n = 18.5). Based on nucleotide sequencing analysis, three synonym mutations were found in the coding regions, and also several SNPs and indels were found in the noncoding regions. In addition, four genealogies of growth hormone haplotypes were identified based on principal coordinate analysis, and these genealogies of pmaGH partly reflected allele size ranges of pmaGH22. Several haplotypes shared alleles of pmaGH22, and also fragment size homoplasy in pmaGH22 was suspected. These alleles of pmaGH22 and the haplotypes will be a useful indicator for divergence of pmaGH and for broodstock individual selection with minimum inbreeding effect.     

Wild stock structure of <Emphasis Type="Italic">Girella punctata</Emphasis> in Japan revealed shallow genetic differentiation but subtle substructure in subsidiary distributions

Twelve populations of Girella punctata, from widespread locations of the species’ range in Japan and Korea, were screened for sequence variability within the mitochondrial DNA (mtDNA) control region (n = 128) and at five polymorphic microsatellite loci (n = 547) to determine the genetic structure maintaining population integrity. mtDNA variability of 132 variable sites within a 334-bp region reveals shallow genetic differentiation across populations. The weak differentiation of G. punctata was partly supported by the screening of five polymorphic microsatellite loci. However, hierarchical analysis of molecular variance and principal component analysis on the basis of allele frequencies in microsatellite loci extracted a subtle substructure in a subsidiary population and in near-subsidiary populations in the semi-enclosed Seto Inland Sea.     

Mangrove horseshoe crab (Carcinoscorpius rotundicauda Latreille, 1802) populations reveal genetic break in Strait of Malacca,with connectivity along southern coasts of Peninsular Malaysia

1. The mangrove horseshoe crab, Carcinoscorpius rotundicauda, has divergent populations between the east and west coasts of Peninsular Malaysia, with the southern coast acting as a land barrier. The actual position of such a genetic break along Peninsular Malaysia as well as the connectivity status of the southernmost C. rotundicauda populations with east and west coast populations remain unexplored, however.
2. The aim was to investigate the genetic diversity and structure of C. rotundicauda populations from the west (Kuala Sepetang in State Perak), east (Balok in State Pahang), and southern (Pendas in State Johor) coasts of Peninsular Malaysia. Haemolymph samples from adult C. rotundicauda specimens (n = 152) and eggs from their freshly deposited nests (n = 190) were collected monthly (from January 2016 to January 2017) for the sequencing of mitochondrial cytochrome c oxidase subunit I (COI).
3. Gene isolates of C. rotundicauda from the present study were compared with National Center for Biotechnology Information (NCBI) GenBank sequences to cover most of the range of the species in Asia. A neighbour-joining tree strongly supported two clades, separating the west-coast populations from the south- and east-coast populations, with further substructure patterns.
4. Both haplotype network and barrier analyses revealed a genetic break within the Strait of Malacca instead of the southern tip of Peninsular Malaysia. The southernmost samples from the Strait of Johor formed a haplotypic diverse gene pool that appeared only as a subclade of the eastern populations. In a detailed haplotype network of 347 individuals, individuals with similar COI sequences indicate connectivity between C. rotundicauda on the east and C. rotundicauda on south and south west of Peninsular Malaysia.
5. Overall, the genetic break between C. rotundicauda populations is better explained by the convergent ocean currents and available mangrove habitats on the west coast (i.e. Strait of Malacca), rather than the point of the Malay Peninsula acting as a land barrier alone.

     

Genetic relatedness and differentiation of hatchery populations of Asian seabass (Lates calcarifer) (Bloch, 1790) broodstock in Thailand inferred from microsatellite genetic markers

After more than 20 years of hatchery production of Asian seabass in Thailand, genetic information is still lacking for effective genetic management and a selective breeding programme. This study aimed to evaluate genetic status of existing hatchery populations and genetic consequences of a selective breeding attempt. We examined genetic relatedness in seven hatchery samples, including a selectively bred population (RACF‐F1), compared with three wild samples using 11 microsatellite loci. Genetic diversity and relatedness values within most hatchery samples, except for RACF‐F1, did not differ from those of wild populations (P > 0.05). RACF‐F1 had the lowest allelic diversity and effective population size (A_r = 6.99; N_e = 7.8) and highest relatedness values (mean r_xy = 0.075–0.204). Pairwise Φ_ST values, principal component analysis and model‐based cluster analyses revealed three genetically distinct hatchery groups: Eastern Thailand (CHN, RACF, NSCF and SKCF), Southern Thailand (NICA) and the Andaman Sea (STCF). Results suggest that exiting domestic populations capture reasonable amount of genetic variation and can be useful for a base population for genetic improvement programmes. In addition, given the rapid increase in relatedness that we observed in one selectively bred population, we recommend using selection methods and hatchery practices that reduce variability in family contribution in the subsequent generations.     

Variation in fatty acid composition among nine forage species from a southeastern US estuarine and nearshore coastal ecosystem

The fatty acid (FA) composition of nine potentially important forage species was determined (n = 330): red drum (Sciaenops ocellatus), spot (Leiostomus xanthurus), spotted seatrout (Cynoscion nebulosus), striped mullet (Mugil cephalus), pinfish (Lagodon rhomboides), Atlantic croaker (Micropogonias undulatus), star drum (Stellifer lanceolatus), striped anchovy (Anchoa hepsetus), and brief squid (Lolliguncula brevis). Samples were collected from estuarine and nearshore coastal waters around Charleston, South Carolina, USA, from March 2002–February 2003. Twenty-nine of 125 identified FAs were included in multivariate analyses of FA profiles. Despite existing intraspecific variation, the PRIMER routine analysis of similarity (ANOSIM) indicated each species was distinct, and discriminant function analysis correctly classified 99.5% of the training data set samples (n = 221) and 98.2% of the validation samples (n = 109). Most species could be characterized by distinctive levels of a suite of FAs. Our results indicated FA profiles can be used to reliably distinguish even closely related forage species in this southeastern US estuarine ecosystem. The information gained from this study not only provides insight into the biochemical composition of these important species but also provides fundamental information to support studies on the feeding ecology of local higher-level predators. The U.S. Government’s right to retain a non-exclusive, royalty-free license in and to any copyright is acknowledged.     

Cytogenetic analysis of hybrids and hybrid triploids between the river puffer,Takifugu obscurus,and the tiger puffer,Takifugu rubripes

Cytogenetic analyses of the river puffer, Takifugu obscurus, the tiger puffer, Takifugu rubripes and hybrids produced between female T. obscurus and male T. rubripes and their hybrid triploids (produced by cold shock treatment at 4°C) were performed. T. obscurus had 2n = 44 chromosomes and 1.84 ± 0.019 pg DNA/cell, T. rubripes had 2n = 44 and 2.64 ± 0.015, the hybrids had 2n = 44 and 2.15 ± 0.010 and the hybrid triploids had 3n = 66 and 3.22 ± 0.010. The erythrocyte values of the hybrids were more similar to those for T. obscurus, whereas the hepatocyte, midgut and proximal tubule kidney cell values of the hybrids fell down between those for the parental species (p < .05). The erythrocyte, proximal tubule, hepatocyte and midgut epithelial cell sizes for the hybrid triploids were 1.5‐fold larger than those for the hybrids (p < .05). The thickness of retina and each layer in the hybrid triploids were 1.1‐fold larger than those of the hybrids (p < .05) and did not differ significantly among T. obscurus, T. rubripes and the hybrids (p > .05); however, the hybrid triploids had fewer cell nucleus outer layers than the hybrids (p < .05). Gonad development in the hybrids and hybrid triploids was less matured than in T. obscurus and T. rubripes. The metaphase nucleolus organizer regions (NORs) and the gill cells of T. obscurus, T. rubripes and the hybrids contained two satellite telocentrics, whereas the hybrid triploids contained three satellite telocentrics.     

Genotypic diversity among Shewanella spp. collected from freshwater fish

Different Shewanella species are isolated both from healthy and from diseased fish. To date, contemporary methods do not provide sufficient insight to determine species and detail differentiation between tested strains. Bacteria isolated from cultured (n = 33), wild (n = 12) and ornamental (n = 6) fish, as well as several reference strains, were tested by 16S rRNA gene sequencing, ERIC‐PCR and pulsed‐field gel electrophoresis (PFGE) assays. Our study indicates that isolates collected from freshwater fish were genetically diverse. Based on 16S rRNA gene sequences, bacteria were clustered into groups S. putrefaciens, S. xiamenensis and S. oneidensis. Some isolates were classified only to genus Shewanella; thus, 16S rRNA gene analyses were not enough to determine the species. ERIC‐PCR revealed 49 different genotype profiles indicating that the method might be useful for differentiation of Shewanella isolates irrespectively to species identification, contrary to PFGE which is not suitable for Shewanella typing.