Advances in the molecular analysis of fish population structure

Aquatic connectivity: challenges and solutions in a changing climate

The challenge of managing aquatic connectivity in a changing climate is exacerbated in the presence of additional anthropogenic stressors, social factors, and economic drivers. Here we discuss these issues in the context of structural and functional connectivity for aquatic biodiversity, specifically fish, in both the freshwater and marine realms. We posit that adaptive management strategies that consider shifting baselines and the socio-ecological implications of climate change will be required to achieve management objectives. The role of renewable energy expansion, particularly hydropower, is critically examined for its impact on connectivity. We advocate for strategic spatial planning that incorporates nature-positive solutions, ensuring climate mitigation efforts are harmonized with biodiversity conservation. We underscore the urgency of integrating robust scientific modelling with stakeholder values to define clear, adaptive management objectives. Finally, we call for innovative monitoring and predictive decision-making tools to navigate the uncertainties inherent in a changing climate, with the goal of ensuring the resilience and sustainability of aquatic ecosystems.

Lack of genetic structure in euryhaline Chelon labrosus from the estuaries under anthropic pressure in the Southern Bay of Biscay to the coastal waters of the Mediterranean Sea

Over the last decade, xenoestrogenic effects have been reported in populations of thicklip grey mullet Chelon labrosus from contaminated estuaries in the Bay of Biscay, resulting in intersex condition. To understand the level of gene flow in individuals of different Basque estuaries microsatellite markers were used to evaluate the population structure and connectivity of C. labrosus from estuaries of the Basque coast. 46 microsatellites were tested and 10 validated for the analysis of 204 individuals collected from 5 selected Basque estuaries and 2 outgroups in the Bay of Cadiz and Thermaic Gulf. The polymorphic microsatellites revealed 74 total alleles, 2-19 alleles per locus. The mean observed heterozygosity (0.49 ± 0.02) was lower than the expected one (0.53 ± 0.01). There was no evidence of genetic differentiation (F_ST = 0.0098, P = 0.0000) among individuals or sites. Bayesian clustering analysis revealed a single population in all sampled locations. The results of this study indicate widespread genetic homogeneity and panmixia of C. labrosus across the current sampling areas spanning the Atlantic and Mediterranean basins. The hypothesis of panmixia could therefore be well supported so individuals inhabiting estuaries with high prevalence of intersex condition should be considered as members of the same single genetic group as those inhabiting adjacent estuaries without incidence of xenoestrogenicity.

Phylogeography and population structure of - grypotus (Richardson, 1846) as revealed by mitochondrial control region sequences

The 137 individuals of Johniusgrypotus were collected from seven localities from the Bohai Sea to the East China Sea. A 549 base pair (bp) fragment of the hypervariable region of the mtDNA control region was sequenced to examine genetic diversity and population structure. The populations of J.grypotus showed high haplotype diversity (h) with a range from 0.7500 to 0.9740 and low nucleotide diversity (π) with a range from 0.0024 to 0.0067. Low and non-significant genetic differentiation was estimated among populations except for North Yellow Sea population, which has a significant genetic difference with other populations. The demographic history examined by mismatch distribution analyses and Bayesian skyline plot (BSP) analyses revealed that a sudden population expansion occurred almost 20 to 40 thousand years before. Relatively recent population expansion in the last glacial period, large dispersal of eggs or larvae carried by coastal current, and the homogeneity of living environment may have an important influence on the population genetic pattern.

Lack of Spatial Subdivision for the Snapper Lutjanus purpureus (Lutjanidae - Perciformes) from Southwest Atlantic Based on Multi-Locus Analyses

The Caribbean snapper Lutjanus purpureus is a marine species fish commonly found associated with rocky seabeds and is widely distributed along of Western Atlantic. Data on stock delineation and stock recognition are essential for establishing conservation measures for commercially fished species. However, few studies have investigated the population genetic structure of this economically valuable species, and previous studies (based on only a portion of the mitochondrial DNA) provide an incomplete picture. The present study used a multi-locus approach (12 segments of mitochondrial and nuclear DNA) to elucidate the levels of genetic diversity and genetic connectivity of L. purpureus populations and their demographic history. L. purpureus has high levels of genetic diversity, which probably implies in high effective population sizes values for the species. The data show that this species is genetically homogeneous throughout the geographic region analyzed, most likely as a result of dispersal during larval phase. Regarding demographic history, a historical population growth event occurred, likely due to sea level changes during the Pleistocene.

Demographic History and Reproductive Output Correlates with Intraspecific Genetic Variation in Seven Species of Indo-Pacific Mangrove Crabs

The spatial distribution and the amount of intraspecific genetic variation of marine organisms are strongly influenced by many biotic and abiotic factors. Comparing biological and genetic data characterizing species living in the same habitat can help to elucidate the processes driving these variation patterns. Here, we present a comparative multispecies population genetic study on seven mangrove crabs co-occurring in the West Indian Ocean characterized by planktotrophic larvae with similar pelagic larval duration. Our main aim was to investigate whether a suite of biological, behavioural and ecological traits could affect genetic diversities of the study species in combination with historical demographic parameters. As possible current explanatory factors, we used the intertidal micro-habitat colonised by adult populations, various parameters of individual and population fecundity, and the timing of larval release. As the genetic marker, we used partial sequences of cytochrome oxidase subunit I gene. Genetic and ecological data were collected by the authors and/or gathered from primary literature. Permutational multiple regression models and ANOVA tests showed that species density and their reproductive output in combination with historical demographic parameters could explain the intraspecific genetic variation indexes across the seven species. In particular, species producing consistently less eggs per spawning event showed higher values of haplotype diversity. Moreover, Tajima's D parameters well explained the recorded values for haplotype diversity and average γst. We concluded that current intraspecific gene diversities in crabs inhabiting mangrove forests were affected by population fecundity as well as past demographic history. The results were also discussed in terms of management and conservation of fauna in the Western Indian Ocean mangroves.

Contemporary population structure and post-glacial genetic demography in a migratory marine species, the blacknose shark, Carcharhinus acronotus

Patterns of population structure and historical genetic demography of blacknose sharks in the western North Atlantic Ocean were assessed using variation in nuclear-encoded microsatellites and sequences of mitochondrial (mt)DNA. Significant heterogeneity and/or inferred barriers to gene flow, based on microsatellites and/or mtDNA, revealed the occurrence of five genetic populations localized to five geographic regions: the southeastern U.S Atlantic coast, the eastern Gulf of Mexico, the western Gulf of Mexico, Bay of Campeche in the southern Gulf of Mexico and the Bahamas. Pairwise estimates of genetic divergence between sharks in the Bahamas and those in all other localities were more than an order of magnitude higher than between pairwise comparisons involving the other localities. Demographic modelling indicated that sharks in all five regions diverged after the last glacial maximum and, except for the Bahamas, experienced post-glacial, population expansion. The patterns of genetic variation also suggest that the southern Gulf of Mexico may have served as a glacial refuge and source for the expansion. Results of the study demonstrate that barriers to gene flow and historical genetic demography contributed to contemporary patterns of population structure in a coastal migratory species living in an otherwise continuous marine habitat. The results also indicate that for many marine species, failure to properly characterize barriers in terms of levels of contemporary gene flow could in part be due to inferences based solely on equilibrium assumptions. This could lead to erroneous conclusions regarding levels of connectivity in species of conservation concern.

Population genetics provides new insights into biomarker prevalence in dab (Limanda limanda L.): a key marine biomonitoring species

Bioindicators are species for which some quantifiable aspect of its biology, a biomarker, is assumed to be sensitive to ecosystem health. However, there is frequently a lack of information on the underlying genetic and environmental drivers shaping the spatiotemporal variance in prevalence of the biomarkers employed. Here, we explore the relative role of potential variables influencing the spatiotemporal prevalence of biomarkers in dab, Limanda limanda, a species used as a bioindicator of marine contaminants. Firstly, the spatiotemporal genetic structure of dab around UK waters (39 samples across 15 sites for four years: 2005–2008) is evaluated with 16 microsatellites. Two temporally stable groups are identified corresponding to the North and Irish Seas (average between basin = 0.007; = 0.022). Secondly, we examine the association between biomarker prevalence and several variables, including genetic structuring, age and contaminant exposure. Genetic structure had significant interactive effects, together with age and some contaminants, in the prevalence of some of the biomarkers considered, namely hyperpigmentation and liver lesions. The integration of these data sets enhanced our understanding of the relationship between biomarker prevalence, exposure to contaminants and population-specific response, thereby yielding more informative predictive models of response and prospects for environmental remediation.

Genetic divergence and molecular phylogenetics of Puntius spp. based on the mitochondrial cytochrome b gene

Puntius is an important genus of freshwater food and ornamental fish belonging to the family Cyprinidae. A total of 60 samples from twelve species of the genus Puntius were collected from eight sampling sites of eight Indian Rivers. Twelve species of Puntius (P. chola, P. sophore, P. filamentosus, P. fasciatus, P. vittatus, P. chelynoides, P. gonionotus, P. denisonii, P. ticto, P. gelius, P. conchonius and P. sarana) were investigated using 60 partial sequences of the mitochondrial cytochrome b (Cyt b, 1096 bp) gene to estimate genetic divergence and to establish the phylogenetic relationship. The average intraspecies diversity was estimated as 0.002, whereas the average interspecies diversity was estimated as 0.177. The sequence analysis of the Cyt b gene revealed four distinct groups, which are genetically distinct species and exhibited identical phylogenetic relationship. The present study validated the utility of the Cyt b gene in genetic diversity and phylogenetic studies.

Comparative analysis of AFLPs and SSRs efficiency in resolving population genetic structure of Mediterranean Solea vulgaris

The performance of different molecular markers in the assessment of population structure was tested using samples of Solea vulgaris collected in the Mediterranean within and outside the hypothetical dispersal ability of the species. A total of 172 individuals belonging to four population samples were analysed using 15 microsatellites [simple sequence repeats (SSRs)] and 153 amplified fragment length polymorphisms (AFLPs). Considering the global qualitative patterns, we found a correlation between SSRs and AFLPs in detecting genetic differentiation among samples. However, on a small geographical scale, AFLPs were able to discriminate individuals from neighbouring populations whereas SSRs were not, and the percentage of individuals correctly assigned to their population of origin was higher with AFLPs than with SSRs. The high number of loci analysed with the AFLP technique could increase the probability to include outlier loci in the analysis; however, the neutrality test performed on our data set did not show evidence of selection acting on the S. vulgaris samples. Even if the choice of the molecular marker depends mainly on the biological question to be addressed, the higher power of discrimination and the comparative technical ease of obtaining data from AFLPs with respect to SSRs suggest the use of AFLPs for many population genetics studies.

Microsatellite DNA variation reveals high gene flow and panmictic populations in the Adriatic shared stocks of the European squid and cuttlefish (Cephalopoda)

In the semienclosed Adriatic Sea, the shared stocks of the cephalopods Loligo vulgaris and Sepia officinalis represent important marine fisheries resources exploited by all coastal countries. The improving of knowledge on the demographic features of these shared stocks is internationally relevant for adopting responsible management and conservation of these marine resources. Analyses of microsatellite variation in geographical samples collected from all parts of the Adriatic Sea were performed using arrays of species-specific di-nucleotide and tri-nucleotide loci. In L. vulgaris the level of genetic variability was consistent with that observed in other loliginid species, whereas the S. officinalis stock showed a microsatellite variation markedly lower than that estimated for the Atlantic and Mediterranean populations collected around the Iberian peninsula. The weak spatial genetic differentiation, the discordant results of the genetic divergence estimators and the lack of any geographical cline in the spatial genetic differences suggest the occurrence of single genetically homogeneous populations within the Adriatic stocks of both species, recommending a coordinated management of the squid and cuttlefish by the Adriatic fishing countries. On the contrary, significant differences detected in temporal replicates of S. officinalis might suggest that allelic frequency can change relating to reproductive behaviour.

Genetic study of Coris julis (Osteichthyes, Perciformes, Labridae) evolutionary history and dispersal abilities

Microsatellite markers have been used to study the genetic variability of rainbow wrasse (Coris julis) Mediterranean and Atlantic populations. Differentiation tests failed to reveal any significant genetic differentiation among samples from continental Portugal and the Azores, despite more than 1800 km of geographical separation. Preliminary results tended to indicate a significant genetic differentiation among Atlantic and Mediterranean samples. It also supported the specific status of Cape Verde populations (Coris atlantica). We compare these results with previous mtDNA analyses and propose a biogeographic scenario that could explain our results.

Evidence of a hybrid-zone in Atlantic cod (Gadus morhua) in the Baltic and the Danish Belt Sea revealed by individual admixture analysis

The study of hybrid zones is central to our understanding of the genetic basis of reproductive isolation and speciation, yet very little is known about the extent and significance of hybrid zones in marine fishes. We examined the population structure of cod in the transition area between the North Sea and the Baltic Sea employing nine microsatellite loci. Genetic differentiation between the North Sea sample and the rest increased along a transect to the Baltic proper, with a large increase in level of differentiation occurring in the Western Baltic area. Our objective was to determine whether this pattern was caused purely by varying degrees of mechanical mixing of North Sea and Baltic Sea cod or by interbreeding and formation of a hybrid swarm. Simulation studies revealed that traditional Hardy-Weinberg analysis did not have sufficient power for detection of a Wahlund effect. However, using a model-based clustering method for individual admixture analysis, we were able to demonstrate the existence of intermediate genotypes in all samples from the transition area. Accordingly, our data were explained best by a model of a hybrid swarm flanked by pure nonadmixed populations in the North Sea and the Baltic Sea proper. Significant correlation of gene identities across loci (gametic phase disequilibrium) was found only in a sample from the Western Baltic, suggesting this area as the centre of the apparent hybrid zone. A hybrid zone for cod in the ecotone between the high-saline North Sea and the low-saline Baltic Sea is discussed in relation to its possible origin and maintenance, and in relation to a classical study of haemoglobin variation in cod from the Baltic Sea/Danish Belt Sea, suggesting mixing of two divergent populations without interbreeding.

Temporal and spatial genetic variation in spawning grounds of European hake (Merluccius merluccius) in the Bay of Biscay

Polymorphism at five microsatellite loci were screened to determine the genetic variability and the temporal stability of population structure in natural populations of European hake (Merluccius merluccius, L.) within the Bay of Biscay. In addition, the control region (900 bp) and two protein coding genes (ATPase, subunits 6 and 8, 842 bp and a partial sequence of the ND1, 800 bp) of the mitochondrial DNA (mtDNA) were sequenced from geographically distant populations from the extremes of the species range. One hundred individuals from either side of a supposed stock boundary within the bay were collected in autumn 1997. This sampling strategy was repeated during hake spawning seasons in late spring of 1998 and 1999. Low levels of population subdivision were found between putative populations within years. Similarly, low levels of differentiation were found between autumn 1997 northern samples and spring 1998 southern samples which were collected 7 months later on spawning grounds. These results are discussed in relation to ecological, behavioural and oceanographic information. Sampling effects, which may influence these results, are also discussed. Theta (theta) estimates were significantly different from zero in every other pairwise comparison between geographical areas (north and south of the Bay of Biscay) and between years within the same area (P<0.05). Hierarchical analysis of molecular variance (AMOVA) does not confirm the temporal persistence of population structure. These results are discussed in relation to variance in reproductive success, and temporal spawning patterns, which may exist within the bay. mtDNA variability was very low between geographically distant samples from Norway and the Mediterranean Sea with only 10 variable sites found in a total of 2542 bp of mtDNA, these differences being exclusively in the D-loop.