Systematic conservation planning for intraspecific genetic diversity

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

Patterns of Epigenetic Diversity in Two Sympatric Fish Species: Genetic vs. Environmental Determinants

Epigenetic components are hypothesized to be sensitive to the environment, which should permit species to adapt to environmental changes. In wild populations, epigenetic variation should therefore be mainly driven by environmental variation. Here, we tested whether epigenetic variation (DNA methylation) observed in wild populations is related to their genetic background, and/or to the local environment. Focusing on two sympatric freshwater fish species (Gobio occitaniae and Phoxinus phoxinus), we tested the relationships between epigenetic differentiation, genetic differentiation (using microsatellite and single nucleotide polymorphism (SNP) markers), and environmental distances between sites. We identify positive relationships between pairwise genetic and epigenetic distances in both species. Moreover, epigenetic marks better discriminated populations than genetic markers, especially in G. occitaniae. In G. occitaniae, both pairwise epigenetic and genetic distances were significantly associated to environmental distances between sites. Nonetheless, when controlling for genetic differentiation, the link between epigenetic differentiation and environmental distances was not significant anymore, indicating a noncausal relationship. Our results suggest that fish epigenetic variation is mainly genetically determined and that the environment weakly contributed to epigenetic variation. We advocate the need to control for the genetic background of populations when inferring causal links between epigenetic variation and environmental heterogeneity in wild populations

Data from: Elucidating the spatio-temporal dynamics of an emerging wildlife pathogen using approximate Bayesian computation

Emerging pathogens constitute a severe threat for human health and biodiversity. Determining the status (native or non-native) of emerging pathogens, and tracing back their spatio-temporal dynamics, is crucial to understand the eco-evolutionary factors promoting their emergence, to control their spread and mitigate their impacts. However, tracing back the spatio-temporal dynamics of emerging wildlife pathogens is challenging because (i) they are often neglected until they become sufficiently abundant and pose socio-economical concerns and (ii) their geographical range is often little known. Here, we combined classical population genetics tools and approximate Bayesian computation (i.e. ABC) to retrace the dynamics of Tracheliastes polycolpus, a poorly documented pathogenic ectoparasite emerging in Western Europe that threatens several freshwater fish species. Our results strongly suggest that populations of T. polycolpus in France emerged from individuals originating from a unique genetic pool that were most likely introduced in the 1920s in central France. From this initial population, three waves of colonization occurred into peripheral watersheds within the next two decades. We further demonstrated that populations remained at low densities, and hence undetectable, during 10 years before a major demographic expansion occurred, and before its official detection in France. These findings corroborate and expand the few historical records available for this emerging pathogen. More generally, our study demonstrates how ABC can be used to determine the status, reconstruct the colonization history and infer key evolutionary parameters of emerging wildlife pathogens with low data availability, and for which samples from the putative native area are inaccessible

raw data genotypes

bi-allelic data (16 microsatellite markers) used to measure Fst values among population pairs

raw data Maze Guilmo et al PRSLB

This file summarizes data obtained during the common experiment described in the MS. Variables used to perform statistical models (LMMs and Qst/Fst) are provided

raw data Maze Guilmo et al PRSLB

This file summarizes data obtained during the common experiment described in the MS. Variables used to perform statistical models (LMMs and Qst/Fst) are provided

SampleDetails_Genotypes_MEC15-500

This file contais three sheets. The first sheet contains information on parasite individuals used in this study (site, river and basin of origin, GPS coordinates of the sampling site, the genetic cluster to which the individuals were assigned and the probability to belong to their genetic clusters). The second sheet contains information about the sampling sites covered in this study. The third sheet contains individual multilocus genotypes at the 16 microsatellite markers used in this study

Variations of fish composition and diversity related to environmental variables in shallow lakes in the Yangtze River basin

Variations in fish communities of shallow lakes in the Yangtze basins were investigated from September 2007 to September 2009. Six lakes were chosen for comparative study of species composition and diversity in relation to environmental variations. Lake heterogeneity was described with environmental physico-chemical variables, using principal component analysis. Sixteen families, composed of 75 species of fish were found in the studied lakes, Cyprinidae being the dominant group. Fish species were divided by habitat preference and trophic guild: benthopelagic and herbivorous fish were the most common guilds in all lakes. Species diversity and richness were significantly higher in spring, while the evenness, expressed by equitability of Simpson's index, was not significantly different among seasons. Species richness and diversity were significantly higher in vegetated lakes (e. g. Liangzihu Lake) than in non-vegetated lakes (e. g. Biandantang Lake), with the largest area (Liangzihu Lake) harbouring the largest species richness and the greatest diversity. The relationship between environmental variables and fish assemblage were analysed using canonical correspondence analysis (CCA). The dominant gradients describing species composition and abundance among the sampling sites were: total phosphorus, total nitrogen, chlorophyll a, transparency and water depth. Our study led to the following conclusions: 1) the water quality was better - i.e. high transparency, low total phosphorus (TP) and total nitrogen (TN) and chlorophyll a- in vegetated lakes than in unvegetated lakes; 2) vegetated lakes had higher fish diversity than unvegetated lakes; 3) fish relative abundance (CPUE: number of fish per fishing pass) was significantly related to water chemical parameters. Consequently, the details of the findings are useful and relevant for developing suitable conservation strategies to sustain the integrity of fish communities in these lakes

The importance of cancer cells for animal evolutionary ecology

Reciprocal interactions between hosts, their symbionts and their oncobiota (cancer cell communities) are yet to be studied in detail. Considering malignant cells in addition to the holobiont perspective allows greater understanding of the processes governing both host phenotypes and cancer dynamics

Temporal changes in the taxonomic and functional diversity of fish communities in shallow Chinese lakes: the effects of river-lake connections and aquaculture

1. Habitat modification by humans has severe impacts on the biotic and abiotic components of freshwater ecosystems. In China, shallow lakes in the Yangtze River basin are facing major habitat modification owing to the loss of their natural connections with rivers and the development of aquaculture. 2. In this study, temporal data (ranging from 1970 to 2010) from a set of lakes (n=8) were used to quantify the abiotic and biotic consequences (i.e. taxonomic and functional diversity of fish communities) of such human activities. There were significant abiotic changes that mainly occurred after the 1990s. Specifically, water transparency decreased and the total nitrogen content of the lakes increased considerably. 3. A trend (although not significant) was detected towards a decrease in fish species richness over the period studied. The taxonomic dissimilarity (i.e. beta-diversity) among fish communities decreased significantly over the years, indicating a strong homogenization of the fauna across the lakes. 4. In addition, it was found that fish functional diversity has decreased in most lakes since the 1970s. In particular most migratory fish species with long life-spans and large body size disappeared from the lakes, hence contributing substantially to the observed decrease in functional diversity. 5. Based on the findings, it is argued that both the abiotic and biotic integrity of the lakes were seriously affected after the lakes lost their connections to the rivers. It would therefore be helpful to reconnect the lakes to rivers with wise sluice-gate management, and regulate fishery activities in those lakes to restore fish diversity. Copyright (c) 2013 John Wiley & Sons, Ltd.1. Habitat modification by humans has severe impacts on the biotic and abiotic components of freshwater ecosystems. In China, shallow lakes in the Yangtze River basin are facing major habitat modification owing to the loss of their natural connections with rivers and the development of aquaculture