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Map of the Garonne river basin (South–Western France) representing (1) sites where Parachondrostoma toxostoma was sampled for the genetic analyses (green circles) and (2) sites that have been selected for analyses of temporal trends in population abundances (black triangles).
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Prioritizing and making efficient conservation plans for threatened populations requires information at both evolutionary and ecological timescales. Nevertheless, few studies integrate multidisciplinary approaches, mainly because of the difficulty for conservationists to assess simultaneously the evolutionary and ecological status of populations. H...
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... We here focused on mean heterozygosity because, unlike metrics such as allelic richness, heterozygosity values are bound between 0 and 1, which facilitates comparison between case studies. Moreover, this metric is much more straightforward to calculate for managers than the actual effective population size, since the latter is notoriously difficult to estimate in complex landscapes (Paz-Vinas et al., 2013;Wang, 2005). Note also that the use of two different realistic mutation rates yielded two levels of H e across simulations (a low level at the low mutation rate and a high level at the high mutation rate; ...
Fragmentation by artificial barriers is an important threat to freshwater biodiversity. Mitigating the negative aftermaths of fragmentation is of crucial importance, and it is now essential for environmental managers to benefit from a precise estimate of the individual impact of weirs and dams on river connectivity. Although the indirect monitoring of fragmentation using molecular data constitutes a promising approach, it is plagued with several constraints preventing a standardized quantification of barrier effects. Indeed, observed levels of genetic differentiation GD depend on both the age of the obstacle and the effective size of the populations it separates, making comparisons of the actual barrier effect of different obstacles difficult. Here, we developed a standardized genetic index of fragmentation (FINDEX), allowing an absolute and independent assessment of the individual effects of obstacles on connectivity. The FINDEX is the standardized ratio between the observed GD between pairs of populations located on either side of an obstacle and the GD expected if this obstacle completely prevented gene flow. The expected GD is calculated from simulations taking into account two parameters: the number of generations since barrier creation and the expected heterozygosity of the populations, a proxy for effective population size. Using both simulated and empirical datasets, we explored the validity and the limits of the FINDEX. We demonstrated that it allows quantifying effects of fragmentation only from a few generations after barrier creation and provides valid comparisons among obstacles of different ages and populations (or species) of different effective sizes. The FINDEX requires a minimum amount of fieldwork and genotypic data, and solves some of the difficulties inherent to the study of artificial fragmentation in rivers and potentially in other ecosystems. This makes the FINDEX promising to support the management of freshwater species affected by barriers, notably for planning and evaluating restoration programs.
... We accordingly combined genetic and demographic datasets to assess the eco-evolutionary status of wild populations. For instance, we jointly analyzed data from a three-decade-long French National demographic survey (Poulet, Beaulaton, & Dembski, 2011) and from a snapshot assessment of genetic diversity in an endemic freshwater fish species (the threatened P. toxostoma) from the Garonne-Dordogne River basin ( Figure 2) to identify populations exhibiting high eco-evolutionary extinction risks and to propose conservation actions targeted toward these at-risk populations (Paz-Vinas, Comte, et al., 2013). Through multidisciplinary analyses including genetic structure assessment, genetic-based demographic change inference, species distribution modeling, and demographic trend analyses, we demonstrated that this species underwent a general decrease in effective population sizes over the last two to eight centuries and a significant decrease in its distribution range (13.1%) over the last three decades. ...
... We further evidenced ongoing demographic declines in five of the twelve rivers we analyzed. We accordingly drew a series of recommendations for prioritizing conservation actions toward populations exhibiting both signs of recent and significant decreases in abundance and small effective population sizes (Paz-Vinas, Comte, et al., 2013). As stated above (see section Patterns of intraspecific diversity in riverscapes: ...
Rivers are fascinating ecosystems in which the eco-evolutionary dynamics of organisms are constrained by particular features, and biologists have developed a wealth of knowledge about freshwater biodiversity patterns. Over the last ten years, our group used a holistic approach to contribute to this knowledge by focusing on the causes and consequences of intraspecific diversity in rivers. We conducted empirical works on temperate permanent rivers from Southern France, and we broadened the scope of our findings using experiments, meta-analyses and simulations. We demonstrated that intraspecific (genetic) diversity follows a spatial pattern (downstream increase in diversity) that is repeatable across taxa (from plants to vertebrates) and river systems. This pattern can result from interactive processes that we teased apart using appropriate simulation approaches. We further experimentally showed that intraspecific diversity matters for the functioning of river ecosystems. It indeed affects community dynamics, but also key ecosystem functions such as litter degradation. This means that losing intraspecific diversity in rivers can yield major ecological effects. Our work on the impact of multiple human stressors on intraspecific diversity revealed that-in the studied rivers systems-stocking of domestic (fish) strains strongly and consistently alters natural spatial patterns of diversity. It also highlighted the need for specific analytical tools to tease apart spurious from actual relationships in the wild. Finally, we developed original conservation strategies at the basin scale based on the systematic conservation planning framework that appeared pertinent for preserving intraspecific diversity in rivers. We identified several important research avenues that should further facilitate our understanding of patterns of local adaptation in rivers, the identification of processes sustaining intraspecific biodiversity-ecosystem function relationships, and the setting of reliable conservation plans.
... Biomass yields of fish from the African great lakes; Lake Malawi, Lake Victoria, and Lake Tanganyika have declined (Lowe-McConnell 2009). The declines have been attributed to overexploitation of natural water bodies due to increased demand for fish (Nankwenya et al. 2017;Zhou 2017), habitat degradation (Banda et al. 2005;Weyl et al. 2010;Christophe and Damien 2014), sedimentation and pollution of the water bodies (El-Sayed 2006;Malawi Government 2010) and climate change (Adams et al. 1998;El-Sayed 2006;De Silva and Soto 2009;Weyl et al. 2010;Paz-Vinas et al. 2013). In Malawi specifically, significant declines have been reported for large food fish species such as Bathyclarias spp., Copadichromis spp., Labeo spp., Opsaridium spp., and Oreochromis spp. ...
Oreochromis shiranus is an important cichlid both in capture fisheries and aquaculture. However, in Malawi, biomass yield for the species has declined. Sustainable strategies to increase in yield from capture fisheries and aquaculture would require sound knowledge of the population genetics of the species. In this study, 20 microsatellite markers developed from various Oreochromis spp. were used for cross-species amplification to evaluate allelic diversity, population structure and past demography of O. shiranus in the entire natural distribution range in Malawi. This study involved 306 fish sampled from Lake Malawi, Lake Malombe, Lake Chilwa, Lake Chiuta and the Lower Shire River. Thirty-eight fish from an experimental stock at Bunda College were also included. The study concluded that there were no significant differences in genetic diversity among and within the main water bodies which were also not different from the experimental population. Analysis of molecular variance (AMOVA), pairwise FST values, model-based clustering and multivariate discriminant analysis of principal components (DAPC) revealed that there was limited gene flow resulting in five meta-populations. There was evidence of population bottlenecks that corresponded to small effective population sizes (Ne < 500). The results emphasize that there is enough genetic diversity but management and conservation strategies of O. shiranus in Malawi should consider that the species is structured within the water bodies and possibly recovering from or experiencing genetic bottlenecks. In aquaculture, care should be taken when recruiting fish for breeding programmes to avoid mixing genetic material from different populations without proper regard.
... In river systems, movement is a very important and specific question (Fourcade et al., 2013;Paz-Vinas et al., 2013). For instance, the European Water Framework Directive (DCE, 2000) defines the objectives of the European Union to improve ecological status of water bodies. ...
Movements are a crucial aspect of ecology and evolution, as they determine population and community dynamics. Threats to these dynamics because of human perturbations are therefore a major concern for conservation. In this thesis, I studied movements in the Brown trout (Salmo trutta) in the context of stocking, i.e. the supplementation of wild populations with captive-bred strains from both, native and exogenous origin. For this purpose, I first developed a new genetic tool useful for detecting genetic structure in the brown trout, as well as hybridization with captive-bred strains, exhibiting high genotyping success and enabling to successfully identify patterns of isolation-by-distance. This tool was shown cost effective, and especially, should be useful for many population genetics studies on this species across its range. Then, I developed novel assignment approaches combining genetic data and stable isotopes, to study movements at the spatial scale of a river basin, which is of interest for applied matters such as management. This approach, based on machine learning, revealed high accuracy and power to discriminate and assign individuals to their population of origin. Further, I described the genetic effects of captive breeding on patterns of genetic diversity and differentiation, and found that captive-bred genotypes increased diversity and differentiation, and that expected natural patterns could be reversed in the case of higher frequency of captive-bred genotypes occurring at the level of populations. Then, I demonstrated that admixture between wild individuals and those carrying captive-bred ancestry affected dispersal patterns, that the two strains displayed different movement patterns in terms of propensity, distances, and direction, and that admixture between strains considerably reduced dispersal. Finally, I aimed at better understanding how individual, environmental and landscape related factors influence movements in natural populations; here I found that some determinants were universal across rivers, with larger individuals being more prone to movement for instance, or sites that are directly connected by the water flow, and those that are similar in terms of elevation and stream order exchanged more migrants. One the other hand, other drivers were context dependent, for instance the relations between movement patterns and position within riverscapes and habitat availability depended on the river basin considered. This thesis contributed to improve methods for studying movements, and to identify factors underlying patterns of movements at the scale of the river basin. The implications of my thesis are thus both fundamental and applied as a better understanding of movement patterns in the context of human perturbations is crucial for management and conservation.
... Similarly, given the importance of long-distance dispersal for metapopulation dynamics and structure (Trakhtenbrot, Nathan, Perry, & Richardson, 2005), greater consideration should be given to ways of mitigating effects of existing barriers to movement of riverine fishes (Olden, 2016). Nonetheless, prioritizing and making effective conservation plans require complementary information on both demographic and genetic aspects of population status (Paz-Vinas et al., 2013). As such, genetic-based approaches provide a powerful way to identify fine-scale population structure and to shed light on the processes shaping patterns of genetic diversity and functional connectivity, both of which are central concern to conservation and management (McRae & Beier, 2007;Schmidt & Schaefer, 2018). ...
Enhancing our understanding of fish dispersal is central to the success of modern‐day conservation efforts in freshwater ecosystems. However, methods seeking to estimate dispersal are diverse; ranging from direct estimation of individual movements, computation of dispersal kernels, to indirect assessment using measures of gene flow across riverscapes. An important question is whether results from these different approaches provide a consistent picture of the spatial scales of dispersal. Here, we performed a review and meta‐analysis of the literature reporting both individual movements and genetic data to characterize patterns of dispersal for riverine fishes globally. Across all the studies considered (Ndirect = 206; Nindirect = 205), our results suggest restricted magnitudes of dispersal for riverine fishes, but highlight a large heterogeneity among species, taxonomic orders and geographies. For instance, we found that the maximum parent–offspring dispersal distances varied from 69 m to 1,086 km (median = 12 km; Nspecies = 107), whereas the dispersal spread derived from isolation‐by‐distance slopes (σIBD) from genetic data ranged from 19 m to 250 km (median = 1 km; Nspecies = 56). Comparisons of species‐specific values also revealed significant and positive relationships between direct and indirect estimates of dispersal distances, indicating that organismal movement ability often translates into effective transmission of genes. Finally, this global overview pointed to important geographic and taxonomic disparities in the study of dispersal for riverine fishes. We thus encourage researchers to broaden the taxonomic and geographical scope of future investigations and identify emerging research frontiers where new scientific efforts are needed.
... Leuciscus burdigalensis is a recently described species that is experiencing both demographic and genetic bottlenecks in many populations [24,25]. Parachondrostoma toxostoma is a vulnerable species [26] listed in the IUCN Red List, in Annex II of the European Union Habitats Directive and in Appendix III of the Bern Convention [26]. ...
... Leuciscus burdigalensis is a recently described species that is experiencing both demographic and genetic bottlenecks in many populations [24,25]. Parachondrostoma toxostoma is a vulnerable species [26] listed in the IUCN Red List, in Annex II of the European Union Habitats Directive and in Appendix III of the Bern Convention [26]. ...
Intraspecific diversity informs the demographic and evolutionary histories of populations, and should be a main conservation target. Although approaches exist for identifying relevant biological conservation units, attempts to identify priority conservation areas for intraspecific diversity are scarce, especially within a multi-specific framework. We used neutral molecular data on six European freshwater fish species (Squalius cephalus, Phoxinus phoxinus, Barbatula barbatula, Gobio occitaniae, Leuciscus burdigalensis and Parachondrostoma toxostoma) sampled at the riverscape scale (i.e. the Garonne-Dordogne river basin, France) to determine hot- and coldspots of genetic diversity, and to identify priority conservation areas using a systematic conservation planning approach. We demonstrate that systematic conservation planning is efficient for identifying priority areas representing a predefined part of the total genetic diversity of a whole landscape. With the exception of private allelic richness (PA), classical genetic diversity indices (allelic richness, genetic uniqueness) were poor predictors for identifying priority areas. Moreover, we identified weak surrogacies among conservation solutions found for each species, implying that conservation solutions are highly species-specific. Nonetheless, we showed that priority areas identified using intraspecific genetic data from multiple species provide more effective conservation solutions than areas identified for single species or on the basis of traditional taxonomic criteria.
... Therefore, our objectives were to: (i) estimate genetic diversity within and among currently occupied streams in the Black Hills region and (ii) assess population genetic structure and gene flow throughout the species range in the Black Hills of South Dakota. In addition, we followed an approach similar to Paz-Vinas et al. (2013) and considered genetic results in light of contemporary demographic information to make inferences about levels of genetic diversity and connectedness to better inform mountain sucker recovery efforts in this disjunct peripheral population.Fig. 1). ...
... The combination of stream survey and genetic data for the Black Hills streams suggest that there are numerous opportunities for management aimed at enhancing persistence of local diversity in the face of large-scale environmental change. We anticipate that mountain sucker will be an interesting test case for future demo-genetic (sensu Paz-Vinas et al. 2013) studies and management of similarly small and shrinking disjunct peripheral populations of native fishes, particularly suckers (Family Catostomidae; Marlis Douglas pers. comm.). ...
A peripheral population of mountain sucker, Pantosteus jordani, located in the Black Hills of South Dakota, USA, represents the eastern-most range of the species and is completely isolated from other populations. Over the last 50 years, mountain sucker populations have declined in the Black Hills, and now only occur in 40 % of the historic local range, with densities decreasing by more than 84 %.We used microsatellite DNA markers to estimate genetic diversity and to assess population structure across five streams where mountain suckers persist. We evaluated results in the context of recent ecological surveys to inform decisions about mountain sucker conservation. Significant allele frequency differences existed among sample streams (Global FST = 0.041) but there was no evidence of isolation by distance. Regionally, genetic effective size, Ne, was estimated to be at least 338 breeding individuals, but Ne within streams was expected to be less. Despite almost complete demographic isolation and reduced population size, there appears to be little evidence of inbreeding, but genetic drift and local isolation due to fragmentation probably best explains genetic structure in this peripheral mountain sucker population. Recommended strategies for population enhancement include restoration of stream connectivity and habitat improvement. Moreover, repatriation and assisted movement (i.e., gene flow) of fishes should maximize genetic diversity in stream fragments in the Black Hills region.
... Frequent genetic monitoring is also crucial since it is known that there is a time lag between the action of factors causing genetic change and the change itself, i.e., changes or disturbances that impact populations may not be immediately reflected in genetic metrics (Epps & Keyghobadi, 2015). The combination of long term genetic and demographic surveys of threatened species should be the norm in conservation practices, as suggested by Paz-Vinas et al. (2013). The dataset produced under the scope of the FISHATLAS project is available to be used by managers, decision-makers and authorities not only in the present context of hydrological resources management aiming to minimize the effects of climate changes, but also for the implementation of conservation and management plans aiming to preserve native Iberian cyprinids. ...
Iberian cyprinids are currently highly endangered, with over 68% of the species raising some level of conservation concern. Population declines were reported in the last decades, however, it was unknown if it was coupled with the depletion of gene pools. In order to assess the genetic diversity distribution patterns of native cyprinid species, the Portuguese hydrographical network was extensively covered (all the 34 river basins and 47 sub-basins). A total of 188 populations belonging to 16 cyprinid species of Squalius, Luciobarbus, Achondrostoma, Iberochondrostoma, Anaecypris and Pseudochondrostoma were characterized, for a total of 3,678 cytochrome b gene sequences. We found differences among populations from the same species and between species with identical distribution areas. Factors shaping the contemporary patterns of genetic diversity were explored and the results revealed the role of latitude, inter-basin connectivity, migratory behaviour, species maximum size, species range and other species intrinsic traits in determining the genetic diversity of sampled populations. Contrastingly, drainage area and hydrological regime (permanent vs. temporary) seem to have no significant effect on genetic diversity. Species intrinsic traits, maximum size attained, inter-basin connectivity and latitude explained over 30% of the haplotype diversity variance and, generally, the levels of diversity were significantly higher for smaller sized species, from connected and southerly river basins.
... Frequent genetic monitoring is also crucial since it is known that there is a time lag between the action of factors causing genetic change and the change itself, i.e., changes or disturbances that impact populations may not be immediately reflected in genetic metrics (Epps & Keyghobadi, 2015). The combination of long term genetic and demographic surveys of threatened species should be the norm in conservation practices, as suggested by Paz-Vinas et al. (2013). ...
Background. Worldwide predictions suggest that up to 75% of the freshwater fish species occurring in rivers with reduced discharge could be extinct by 2070 due to the combined effect of climate change and water abstraction. The Mediterranean region is considered to be a hotspot of freshwater fish diversity but also one of the regions where the effects of climate change will be more severe. Iberian cyprinids are currently highly endangered, with over 68% of the species raising some level of conservation concern.
Methods. During the FISHATLAS project, the Portuguese hydrographical network was extensively covered (all the 34 river basins and 47 sub-basins) in order to contribute with valuable data on the genetic diversity distribution patterns of native cyprinid species. A total of 188 populations belonging to 16 cyprinid species of Squalius, Luciobarbus, Achondrostoma, Iberochondrostoma, Anaecypris and Pseudochondrostoma were characterized, for a total of 3,678 cytochrome b gene sequences.
Results. When the genetic diversity of these populations was mapped, it highlighted differences among populations from the same species and between species with identical distribution areas. Factors shaping the contemporary patterns of genetic diversity were explored and the results revealed the role of latitude, inter-basin connectivity, migratory behaviour, species maximum size, species range and other species intrinsic traits in determining the genetic diversity of sampled populations. Contrastingly, drainage area and hydrological regime (permanent vs. temporary) seem to have no significant effect on genetic diversity. Species intrinsic traits, maximum size attained, inter-basin connectivity and latitude explained over 30% of the haplotype diversity variance and, generally, the levels of diversity were significantly higher for smaller sized species, from connected and southerly river basins.
Discussion. Targeting multiple co-distributed species of primary freshwater fish allowed us to assess the relative role of historical versus contemporary factors affecting genetic diversity. Since different patterns were detected for species with identical distribution areas we postulate that contemporary determinants of genetic diversity (species’ intrinsic traits and landscape features) must have played a more significant role than historical factors. Implications for conservation in a context of climate change and highly disturbed habitats are detailed, namely the need to focus management and conservation actions on intraspecific genetic data and to frequently conduct combined genetic and demographic surveys.
... Étudier la diversité génétique est certes très important en biologie de la conservation, mais la diversité génétique ne représente qu'une seule facette de la biodiversité ; elle ne peut donc que participer partiellement au développement de mesures de conservation appropriées (Frankham 2010;Loss et al. 2011;Geist 2011 , 2014 37 existe souvent un temps de latence entre le moment où une population subit un changement démographique (par exemple, un goulot d'étranglement 38 ) et le moment où apparaissent les premières conséquences évolutives dans la population étudiée (par exemple, biaisée vers l'aval dans les rivières (Paz-Vinas et al. 2013b; cf. chapitre III), peuvent induire des erreurs lors de l'utilisation de ces méthodes. ...
... Dans de pareils cas, leur utilisation dans le contexte de la biologie de la conservation serait compromise. L'analyse de données génétiques simulées sous des modèles mimant ces patrons et processus particuliers est donc une étape essentielle pour tester la robustesse des méthodes analytiques (Chikhi et al. 2010;Girod et al. 2011;Hoban et al. 2013a;Paz-Vinas et al. 2013b ...
... bottlenecks) based on neutral genetic data (Chikhi et al., 2010;Girod et al., 2011;PazVinas et al., 2013a). Paz-Vinas et al. (2013b) used this method to reveal recent human- related bottlenecks on several populations of the critically endangered freshwater fish Parachondrostoma toxostoma, and thus detect the high risk of extinction of these populations. Such inference methods should be used carefully, since they are generally based on simple demographic models (e.g. ...
The objective of this thesis is to characterize the distribution of genetic diversity in dendritic networks. First, we identify a general spatial pattern of genetic diversity on these ecosystems, as well as the effects of asymmetric gene flow, differential in effective population sizes and colonization processes on this pattern. Second, we characterize patterns of genetic diversity of four freshwater fish species (Gobio occitaniae, Squalius cephalus, Barbatula barbatula and Phoxinus phoxinus) at the Garonne river basin, so as to identify priority areas to protect. Third, we explore the effects of gene flow asymmetry on the inference of populations’ demographic histories. Finally, we combine genetic and demographic approaches to evaluate the status of a threathened species (Parachondrostoma toxostoma).
