Temporal genetic stability and high effective population size despite fisheries-induced life-history trait evolution in the North Sea sole

Contrasting population genetic responses to migration barriers in two native and an invasive freshwater fish

Habitat fragmentation impacts the distribution of genetic diversity and population genetic structure. Therefore, protecting the evolutionary potential of species, especially in the context of the current rate of human-induced environmental change, is an important goal. In riverine ecosystems, migration barriers affect the genetic structure of native species, while also influencing the spread of invasive species. In this study, we compare genetic patterns of two native and one highly invasive riverine fish species in a Belgian river basin, namely the native three-spined stickleback (Gasterosteus aculeatus) and stone loach (Barbatula barbatula), and the non-native and invasive topmouth gudgeon (Pseudorasbora parva). We aimed to characterize both natural and anthropogenic determinants of genetic diversity and population genetic connectivity. Genetic diversity was highest in topmouth gudgeon, followed by stone loach and three-spined stickleback. The correlation between downstream distance and genetic diversity, a pattern often observed in riverine systems, was only marginally significant in stone loach and three-spined stickleback, while genetic diversity strongly declined with increasing number of barriers in topmouth gudgeon. An Isolation-By-Distance pattern characterizes the population genetic structure of each species. Population differentiation was only associated with migration barriers in the invasive topmouth gudgeon, while genetic composition of all species seemed at least partially determined by the presence of migration barriers. Among the six barrier types considered (watermills, sluices, tunnels, weirs, riverbed obstructions, and others), the presence of watermills was the strongest driver of genetic structure and composition. Our results indicate that conservation and restoration actions, focusing on conserving genetic patterns, cannot be generalized across species. Moreover, measures might target either on restoring connectivity, while risking a rapid spread of the invasive topmouth gudgeon, or not restoring connectivity, while risking native species extinction in upstream populations.

Reconciling seascape genetics and fisheries science in three codistributed flatfishes

Uncertainty hampers innovative mixed-fisheries management by the scales at which connectivity dynamics are relevant to management objectives. The spatial scale of sustainable stock management is species-specific and depends on ecology, life history and population connectivity. One valuable approach to understand these spatial scales is to determine to what extent population genetic structure correlates with the oceanographic environment. Here, we compare the level of genetic connectivity in three codistributed and commercially exploited demersal flatfish species living in the North East Atlantic Ocean. Population genetic structure was analysed based on 14, 14 and 10 neutral DNA microsatellite markers for turbot, brill and sole, respectively. We then used redundancy analysis (RDA) to attribute the genetic variation to spatial (geographical location), temporal (sampling year) and oceanographic (water column characteristics) components. The genetic structure of turbot was composed of three clusters and correlated with variation in the depth of the pycnocline, in addition to spatial factors. The genetic structure of brill was homogenous, but correlated with average annual stratification and spatial factors. In sole, the genetic structure was composed of three clusters, but was only linked to a temporal factor. We explored whether the management of data poor commercial fisheries, such as in brill and turbot, might benefit from population-specific information. We conclude that the management of fish stocks has to consider species-specific genetic structures and may benefit from the documentation of the genetic seascape and life-history traits.

Implications of size-selective fisheries on sexual selection

Fisheries often combine high mortality with intensive size selectivity and can, thus, be expected to reduce body size and size variability in exploited populations. In many fish species, body size is a sexually selected trait and plays an important role in mate choice and mate competition. Large individuals are often preferred as mates due to the high fecundity and resources they can provide to developing offspring. Large fish are also successful in competition for mates. Fisheries‐induced reductions in size and size variability can potentially disrupt mating systems and lower average reproductive success by decreasing opportunities for sexual selection. By reducing population sizes, fisheries can also lead to an increased level of inbreeding. Some fish species avoid reproducing with kin, and a high level of relatedness in a population can further disrupt mating systems. Reduced body size and size variability can force fish to change their mate preferences or reduce their choosiness. If mate preference is genetically determined, the adaptive response to fisheries‐induced changes in size and size variability might not occur rapidly. However, much evidence exists for plastic adjustments of mate choice, suggesting that fish might respond flexibly to changes in their social environment. Here, I first discuss how reduced average body size and size variability in exploited populations might affect mate choice and mate competition. I then consider the effects of sex‐biased fisheries on mating systems. Finally, I contemplate the possible effects of inbreeding on mate choice and reproductive success and discuss how mate choice might evolve in exploited populations. Currently, little is known about the mating systems of nonmodel species and about the interplay between size‐selective fisheries and sexual selection. Future studies should focus on how reduced size and size variability and increased inbreeding affect fish mating systems, how persistent these effects are, and how this might in turn affect population demography.

Time matters: genetic composition and evaluation of effective population size in temperate coastal fish species

Background

Extensive knowledge on the genetic characterization of marine organisms has been assembled, mainly concerning the spatial distribution and structuring of populations. Temporal monitoring assesses not only the stability in genetic composition but also its trajectory over time, providing critical information for the accurate forecast of changes in genetic diversity of marine populations, particularly important for both fisheries and endangered species management. We assessed fluctuations in genetic composition among different sampling periods in the western Portuguese shore in three fish species.

Methods

White seabream Diplodus sargus, sand smelt Atherina presbyter and shanny Lipophrys pholis were chosen, because of their genetic patterns in distinct ecological environments, insight into historical and contemporary factors influencing population effective size (N_e), and degree of commercial exploitation. Samples were obtained near Lisbon between 2003 and 2014 and screened for genetic variation with mitochondrial and nuclear markers. Analyses included genealogies, genetic diversities, temporal structures and contemporary N_e.

Results

For mtDNA no temporal structure was detected, while for nDNA significant differences were recorded between some sampling periods for the shanny and the sand smelt. Haplotype networks revealed deep genealogies, with various levels of diversification. The shanny revealed a smaller N_e/generation when compared to the other species, which, in turn, revealed no evidence of genetic drift for most study periods. These results highlight the fact that temporal variations in genetic pool composition should be considered when evaluating the population structure of fish species with long distance dispersal, which are more vulnerable to recruitment fluctuations.

Temporal trends in genetic data and effective population size support efficacy of management practices in critically endangered dusky gopher frogs (Lithobates sevosus)

Monitoring temporal changes in population genetic diversity and effective population size can provide vital information on future viability. The dusky gopher frog, Lithobates sevosus, is a critically endangered species found only in coastal Mississippi, with low genetic variability as a consequence of isolation and population size reduction. Conservation management practices have been implemented, but their efficacy has not been addressed. We genotyped individuals collected 1997-2014 to determine temporal trends in population genetic variation, structure, and effective size. Observed and expected heterozygosity and allelic richness revealed temporally stable, but low, levels of genetic variation. Positive levels of inbreeding were found in each year. There was weak genetic structure among years, which can be attributed to increased effects of genetic drift and inbreeding in small populations. L. sevosus exhibited an increase in effective population size, and currently has an estimated effective size of 33.0-58.6 individuals, which is approximately half the census size. This large ratio could possibly be explained by genetic compensation. We found that management practices have been effective at maintaining and improving effective size and genetic diversity, but that additional strategies need to be implemented to enhance viability of the species.

Coupling Demographic and Genetic Variability from Archived Collections of European Anchovy (Engraulis encrasicolus)

It is well known that temporal fluctuations in small populations deeply influence evolutionary potential. Less well known is whether fluctuations can influence the evolutionary potentials of species with large census sizes. Here, we estimated genetic population parameters from as survey of polymorphic microsatellite DNA loci in archived otoliths from Adriatic European anchovy (Engraulis encrasicolus), a fish with large census sizes that supports numerous local fisheries. Stocks have fluctuated greatly over the past few decades, and the Adriatic fishery collapsed in 1987. Our results show a significant reduction of mean genetic parameters as a consequence of the population collapse. In addition, estimates of effective population size (Ne) are much smaller than those expected in a fishes with large population census sizes (Nc). Estimates of Ne indicate low effective population sizes, even before the population collapse. The ratio Ne/Ne ranged between 10-6 and 10-8, indicating a large discrepancy between the anchovy gene pool and population census size. Therefore, anchovy populations may be more vulnerable to fishery effort and environmental change than previously thought.

The evolutionary legacy of size-selective harvesting extends from genes to populations

Size-selective harvesting is assumed to alter life histories of exploited fish populations, thereby negatively affecting population productivity, recovery, and yield. However, demonstrating that fisheries-induced phenotypic changes in the wild are at least partly genetically determined has proved notoriously difficult. Moreover, the population-level consequences of fisheries-induced evolution are still being controversially discussed. Using an experimental approach, we found that five generations of size-selective harvesting altered the life histories and behavior, but not the metabolic rate, of wild-origin zebrafish (Danio rerio). Fish adapted to high positively size selective fishing pressure invested more in reproduction, reached a smaller adult body size, and were less explorative and bold. Phenotypic changes seemed subtle but were accompanied by genetic changes in functional loci. Thus, our results provided unambiguous evidence for rapid, harvest-induced phenotypic and evolutionary change when harvesting is intensive and size selective. According to a life-history model, the observed life-history changes elevated population growth rate in harvested conditions, but slowed population recovery under a simulated moratorium. Hence, the evolutionary legacy of size-selective harvesting includes populations that are productive under exploited conditions, but selectively disadvantaged to cope with natural selection pressures that often favor large body size.

Temporal stability of genetic variability and differentiation in the three-spined stickleback (Gasterosteus aculeatus)

Temporal variation in allele frequencies, whether caused by deterministic or stochastic forces, can inform us about interesting demographic and evolutionary phenomena occurring in wild populations. In spite of the continued surge of interest in the genetics of three-spined stickleback (Gasterosteus aculeatus) populations, little attention has been paid towards the temporal stability of allele frequency distributions, and whether there are consistent differences in effective size (Ne) of local populations. We investigated temporal stability of genetic variability and differentiation in 15 microsatellite loci within and among eight collection sites of varying habitat type, surveyed twice over a six-year time period. In addition, Nes were estimated with the expectation that they would be lowest in isolated ponds, intermediate in larger lakes and largest in open marine sites. In spite of the marked differences in genetic variability and differentiation among the study sites, the temporal differences in allele frequencies, as well as measures of genetic diversity and differentiation, were negligible. Accordingly, the Ne estimates were temporally stable, but tended to be lower in ponds than in lake or marine habitats. Hence, we conclude that allele frequencies in putatively neutral markers in three-spined sticklebacks seem to be temporally stable - at least over periods of few generations - across a wide range of habitat types differing markedly in levels of genetic variability, effective population size and gene flow.

Estimating effective population size from temporally spaced samples with a novel, efficient maximum-likelihood algorithm

The effective population size Ne is a key parameter in population genetics and evolutionary biology, as it quantifies the expected distribution of changes in allele frequency due to genetic drift. Several methods of estimating Ne have been described, the most direct of which uses allele frequencies measured at two or more time points. A new likelihood-based estimator NB^ for contemporary effective population size using temporal data is developed in this article. The existing likelihood methods are computationally intensive and unable to handle the case when the underlying Ne is large. This article tries to work around this problem by using a hidden Markov algorithm and applying continuous approximations to allele frequencies and transition probabilities. Extensive simulations are run to evaluate the performance of the proposed estimator NB^, and the results show that it is more accurate and has lower variance than previous methods. The new estimator also reduces the computational time by at least 1000-fold and relaxes the upper bound of Ne to several million, hence allowing the estimation of larger Ne. Finally, we demonstrate how this algorithm can cope with nonconstant Ne scenarios and be used as a likelihood-ratio test to test for the equality of Ne throughout the sampling horizon. An R package “NB” is now available for download to implement the method described in this article.

De novo assembly, characterization and functional annotation of Senegalese sole (Solea senegalensis) and common sole (Solea solea) transcriptomes: integration in a database and design of a microarray

Background

Senegalese sole (Solea senegalensis) and common sole (S. solea) are two economically and evolutionary important flatfish species both in fisheries and aquaculture. Although some genomic resources and tools were recently described in these species, further sequencing efforts are required to establish a complete transcriptome, and to identify new molecular markers. Moreover, the comparative analysis of transcriptomes will be useful to understand flatfish evolution.

Results

A comprehensive characterization of the transcriptome for each species was carried out using a large set of Illumina data (more than 1,800 millions reads for each sole species) and 454 reads (more than 5 millions reads only in S. senegalensis), providing coverages ranging from 1,384x to 2,543x. After a de novo assembly, 45,063 and 38,402 different transcripts were obtained, comprising 18,738 and 22,683 full-length cDNAs in S. senegalensis and S. solea, respectively. A reference transcriptome with the longest unique transcripts and putative non-redundant new transcripts was established for each species. A subset of 11,953 reference transcripts was qualified as highly reliable orthologs (>97% identity) between both species. A small subset of putative species-specific, lineage-specific and flatfish-specific transcripts were also identified. Furthermore, transcriptome data permitted the identification of single nucleotide polymorphisms and simple-sequence repeats confirmed by FISH to be used in further genetic and expression studies. Moreover, evidences on the retention of crystallins crybb1, crybb1-like and crybb3 in the two species of soles are also presented. Transcriptome information was applied to the design of a microarray tool in S. senegalensis that was successfully tested and validated by qPCR. Finally, transcriptomic data were hosted and structured at SoleaDB.

Conclusions

Transcriptomes and molecular markers identified in this study represent a valuable source for future genomic studies in these economically important species. Orthology analysis provided new clues regarding sole genome evolution indicating a divergent evolution of crystallins in flatfish. The design of a microarray and establishment of a reference transcriptome will be useful for large-scale gene expression studies. Moreover, the integration of transcriptomic data in the SoleaDB will facilitate the management of genomic information in these important species.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-952) contains supplementary material, which is available to authorized users.

Variation in age and size in Fennoscandian three-spined sticklebacks (Gasterosteus aculeatus)

Average age and maximum life span of breeding adult three-spined sticklebacks (Gasterosteus aculeatus) were determined in eight Fennoscandian localities with the aid of skeletochronology. The average age varied from 1.8 to 3.6 years, and maximum life span from three to six years depending on the locality. On average, fish from marine populations were significantly older than those from freshwater populations, but variation within habitat types was large. We also found significant differences in mean body size among different habitat types and populations, but only the population differences remained significant after accounting for variation due to age effects. These results show that generation length and longevity in three-spined sticklebacks can vary significantly from one locality to another, and that population differences in mean body size cannot be explained as a simple consequence of differences in population age structure. We also describe a nanistic population from northern Finland exhibiting long life span and small body size.

Multidisciplinary population monitoring when demographic data are sparse: a case study of remote trout populations

The potential of genetic, genomic, and phenotypic metrics for monitoring population trends may be especially high in isolated regions, where traditional demographic monitoring is logistically difficult and only sporadic sampling is possible. This potential, however, is relatively underexplored empirically. Over eleven years, we assessed several such metrics along with traditional ecological knowledge and catch data in a socioeconomically important trout species occupying a large, remote lake. The data revealed largely stable characteristics in two populations over 2–3 generations, but possible contemporary changes in a third population. These potential shifts were suggested by reduced catch rates, reduced body size, and changes in selection implied at one gene-associated single nucleotide polymorphism. A demographic decline in this population, however, was ambiguously supported, based on the apparent lack of temporal change in effective population size, and corresponding traditional knowledge suggesting little change in catch. We illustrate how the pluralistic approach employed has practicality for setting future monitoring efforts of these populations, by guiding monitoring priorities according to the relative merits of different metrics and availability of resources. Our study also considers some advantages and disadvantages to adopting a pluralistic approach to population monitoring where demographic data are not easily obtained.

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.