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.publishedVersionUnit Licence Agreemen

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.publishedVersionUnit Licence Agreemen

Predicting fish community responses to environmental policy targets

The European Union adopted the Water Framework Directive (WFD) in the year 2000 to tackle the rapid degradation of freshwater systems. However, biological, hydromorphological, and physico-chemical water quality targets are currently not met, and identifying successful policy implementation and management actions is of key importance. We built a joint species distribution model for riverine fish in Flanders (Belgium) to better understand the response of fish communities to current environmental policy goals. Environmental covariates included physico-chemical variables and hydromorphological quality indices, while waterway distances accounted for spatial effects. We detected strong effects of physico-chemistry on fish species' distributions. Evaluation of fish community responses to simulated policy scenarios revealed that targeting a 'good' status, following the WFD, increases average species richness with a fraction of species (0.13-0.69 change in accumulated occurrence probabilities). Targeting a 'very good' status, however, predicted an increase of 0.17-1.38 in average species richness. These simulations indicated that riverbed quality, nitrogen, and conductivity levels should be the focal point of policy. However, the weak response of species to a 'good' quality together with the complexity of nutrient-associated problems, suggest a challenging future for river restoration in Flanders.Peer reviewe

Characterization and refinement of growth related quantitative trait loci in European sea bass (Dicentrarchus labrax) using a comparative approach

The identification of genetic markers for traits of interest for aquaculture, such as growth, is an important step for the establishment of breeding programmes. As more genomic information becomes available the possibility of applying comparative genomics to identify and refine quantitative trait locus (QTLs) and potentially identify candidate genes responsible for the QTL effect may accelerate genetic improvement in established and new aquaculture species. Here we report such an approach on growth related traits in the European sea bass (Dicentrarchus labrax), an important species for European aquaculture. A genetic map was generated with markers targeted to previously identified QTL for growth which reduced distance and improved resolution in these regions. A total of 36 significant QTLs were identified when morphometric traits were considered individually in maternal half sibs, paternal half sibs and sib-pair analysis. Twenty seven new markers targeted to the growth QTLs, obtained by comparative mapping, reduced the average distance between markers from 23.4, 9.1, and 5.8 cM in the previous map to 3.4, 2.2, and 5.2 cM, on linkage group (LG) LG4, LG6 and LG15 respectively. Lists of genes embedded in the QTL - 591 genes in LG4, 234 genes in LG6 and 450 genes in LG15 - were obtained from the European sea bass genome. Comparative mapping revealed conserved gene synteny across teleost fishes. Functional protein association network analysis with the gene products of the 3 linkage groups revealed a large global association network including 42 gene products. Strikingly the association network was populated with genes of known biological importance for growth and body weight in terrestrial farm animals, such as elements of the signaling pathways for Jak-STAT, MAPK, adipocytokine and insulin, growth hormone, IGFI and II. This study demonstrates the feasibility of a comparative genomics combined with functional gene annotation to refine the resolution of QTL and the establishment of hypothesis to accelerate discovery of putative responsible genes.Statement of relevance: This study demonstrates the feasibility of a comparative genomics approach, combined with functional annotation to refine the resolution of QTL and establishment of hypothesis to accelerate discovery of candidate genes. As production of genomic data is becoming more accessible, the implementation of this strategy will rapidly and efficiently provide the tools required for genetic selection in new candidate aquaculture species. (C) 2016 Elsevier B.V. All rights reserved

Development of EST-SSR Markers by Data Mining in Three Species of Shrimp: Litopenaeus vannamei, Litopenaeus stylirostris, and Trachypenaeus birdy

Abstract We report on the data mining of publicly available Litopenaeus vannamei expressed sequence tags (ESTs) to generate simple sequence repeat (SSRs) markers and on their transferability between related Penaeid shrimp species. Repeat motifs were found in 3.8% of the evaluated ESTs at a frequency of one repeat every 7.8 kb of sequence data. A total of 206 primer pairs were designed, and 112 loci were amplified with the highest success in L. vannamei. A high percentage (69%) of EST-SSRs were transferable within the genus Litopenaeus. More than half of the amplified products were polymorphic in a small testing panel of L. vannamei. Evaluation of those primers in a larger testing panel showed that 72% of the markers fit Hardy-Weinberg equilibrium, which shows their utility for population genetic analysis. Additionally, a set of 26 of the EST-SSRs were evaluated for Mendelian segregation. A high percentage of monomorphic markers (46%) proved to be polymorphic by singles-stranded conformational polymorphism analysis. Because of the high number of ESTs available in public databases, a data mining approach similar to the one outlined here might yield high numbers of SSR markers in many animal taxa

Evaluating genetic traceability methods for captive bred marine fish and their applications in fisheries management and wildlife forensics

Growing demands for marine fish products is leading to increased pressure on already depleted wild populations and a rise in the aquaculture production. Consequently, more captive bred fish are released into the wild through accidental escape or deliberate restocking, stock enhancement and sea ranching programs. The increased mixing of captive bred fish with wild conspecifics may affect the ecological and/or genetic integrity of wild fish populations. From a fisheries management perspective unambiguous identification tools for captive bred fish will be highly valuable to manage risks. Additionally there is great potential to use these tools in wildlife forensics (i.e. tracing back escapees to their origin and determining mislabelling of seafood products). Using SNP data from captive bred and wild populations of Atlantic cod (Gadus morhua L.) and sole (Solea solea L.), we explored the efficiency of population and parentage assignment techniques for the identification and tracing of captive bred fish. Simulated and empirical data were used to correct for stochastic genetic effects. Overall, parentage assignment performed well when a large effective population size characterizes the broodstock and escapees originate from early generations of captive breeding. Consequently, parentage assignments are particularly useful from a fisheries management perspective to monitor the effects of deliberate releases of captive bred fish on wild populations. Population assignment proved to be more efficient after several generations of captive breeding, which makes it a useful method in forensic applications for well-established aquaculture species. We suggest the implementation of a case by case strategy when choosing the best method

Tracing the genetic impact of farmed turbot Scophthalmus maximus on wild populations

The impact of escapees from aquaculture is of general concern for the sustainability of natural resources. Turbot Scophthalmus maximus is a marine flatfish of great commercial value whose land-based aquaculture started approx. 40 yr ago; hence, a low impact of escapees is expected on wild populations. However, enhancement of wild stocks using farmed turbot has been carried out along the Northeast Atlantic coasts in the last decades. Recently, a broad panel of single nucleotide polymorphism (SNP) markers (755 SNPs; 1 SNP Mb−1) has been used to evaluate the genetic structure of turbot throughout its distribution range, constituting the baseline to evaluate the impact of farmed fish in the wild. Two distinct origins were identified for farmed turbot (F_ORI1 and F_ORI2; FST = 0.049), which differentiated from wild populations after 5 generations of selection (average FST = 0.059), and consistent evidence of adaptation to domestication was de - tected. A notable proportion of fish of farmed ancestry was detected in the wild (15.5%), mainly in the North Sea, where restocking activities have taken place, determining genetic introgression in wild populations. Conversely, effects of land-based aquaculture appear negligible. A simulation exercise supported panels of 40 and 80 SNPs to identify fishes of F_ORI1 and F_ORI2 ancestry in the wild, respectively. Application to empirical data showed an assignment success (wild/farmed ancestry) of approx. 95% in comparison with the full SNP dataset. The SNP tools will be useful to monitor turbot of farmed ancestry in the wild, which might represent a risk, considering the lower fitness of farmed individualsThe project was funded by the 7th Framework Programme for research (FP7) under ‘Knowledge-Based Bio-Economy — KBBE’, Theme 2: ‘Food, Agriculture and fisheries, and Biotechnologies’ Project identifier: FP7-KBBE-2012-6-singlestage Grant agreement no.: 311920 ‘The development of tools for tracing and evaluating the genetic impact of fish from aquaculture: AquaTrace’ and the Spanish Regional Government Xunta de Galicia GRC2014/010. Ciência sem Fronteiras/CAPES − Brazil supported the fellowship for the stay of F.D.P. at USCS

Weak population structure and recent demographic expansion of the monogenean parasite Kapentagyrus spp. infecting clupeid fishes of Lake Tanganyika, East Africa

Author's accepted version (postprint).This is an Accepted Manuscript of an article published by Elsevier in International Journal for Parasitology on 08/04/2020.Available online: https://www.sciencedirect.com/science/article/pii/S0020751920300606?via%3DihubLake Tanganyika, East Africa, is the oldest and deepest African Great Lake and harbours one of the most diverse fish assemblages on earth. Two clupeid fishes, Limnothrissa miodon and Stolothrissa tanganicae, constitute a major part of the total fish catch, making them indispensable for local food security. Parasites have been proposed as indicators of stock structure in highly mobile pelagic hosts. We examined the monogeneans Kapentagyrus limnotrissae and Kapentagyrus tanganicanus (Dactylogyridae) infecting these clupeids to explore the parasites’ lake-wide population structure and patterns of demographic history. Samples were collected at seven sites distributed across three sub-basins of the lake. Intraspecific morphological variation of the monogeneans (n = 380) was analysed using morphometrics and geomorphometrics of sclerotised structures. Genetic population structure of both parasite species (n = 246) was assessed based on a 415 bp fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Overall, we observed a lack of clear geographical morphological differentiation in both parasites along a north–south axis. This lack of geographical population structure was also reflected by a large proportion of shared haplotypes, and a pattern of seemingly unrestricted gene flow between populations. Significant morphological and genetic differentiation between some populations might reflect temporal differentiation rather than geographical isolation. Overall, the shallow population structure of both species of Kapentagyrus reflects the near-panmictic population structure of both host species as previously reported. Morphological differences related to host species identity of K. tanganicanus were consistent with incipient speciation at the genetic level. Both parasite species experienced a recent demographic expansion, which might be linked to paleohydrological events. Finally, interspecific hybridisation was found in Kapentagyrus, representing the first case in dactylogyrid monogeneans.acceptedVersio

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.

ABSTRACT: A global genome database of all of Earth’s species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all ∼1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.info:eu-repo/semantics/publishedVersio