Spatial heterogeneity in the Mediterranean Biodiversity Hotspot affects barcoding accuracy of its freshwater fishes.

Incomplete knowledge of biodiversity remains a stumbling block for conservation planning and even occurs within globally important Biodiversity Hotspots (BH). Although technical advances have boosted the power of molecular biodiversity assessments, the link between DNA sequences and species and the analytics to discriminate entities remain crucial. Here, we present an analysis of the first DNA barcode library for the freshwater fish fauna of the Mediterranean BH (526 spp.), with virtually complete species coverage (498 spp., 98% extant species). In order to build an identification system supporting conservation, we compared species determination by taxonomists to multiple clustering analyses of DNA barcodes for 3165 specimens. The congruence of barcode clusters with morphological determination was strongly dependent on the method of cluster delineation, but was highest with the general mixed Yule-coalescent (GMYC) model-based approach (83% of all species recovered as GMYC entity). Overall, genetic morphological discontinuities suggest the existence of up to 64 previously unrecognized candidate species. We found reduced identification accuracy when using the entire DNA-barcode database, compared with analyses on databases for individual river catchments. This scale effect has important implications for barcoding assessments and suggests that fairly simple identification pipelines provide sufficient resolution in local applications. We calculated Evolutionarily Distinct and Globally Endangered scores in order to identify candidate species for conservation priority and argue that the evolutionary content of barcode data can be used to detect priority species for future IUCN assessments. We show that large-scale barcoding inventories of complex biotas are feasible and contribute directly to the evaluation of conservation priorities.

Occurrence of priority and emerging organic compounds in fishes from the Rhone River (France).

The main objective of this study was to collect new data on the occurrence, levels of priority and emerging organic compounds in freshwater fish sampled in the Rhone River. The 34 studied contaminants included alkylphenols, bisphenol A, polybromodiphenylethers (PBDE), perfluorinated compounds, hexabromocyclododecanes (HBCD), hexachlorobenzene and hexachlorobutadiene (HCBD). About 50 fish samples (individual specimens or pooled fish) were collected from three sites located upstream and downstream of the Lyon metropolitan area in the Rhone River (France). Four species were caught at each site, namely: the barbel (Barbus barbus), the common bream (Abramis brama), the white bream (Blicca bjoerkna) and the chub (Squalius cephalus). Some contaminants were quantified in all the 32 fish samples analysed: 4-nonylphenol, α-HBCD, the six PBDE congeners (28, 47, 99, 100, 153, 154), perfluorooctanesulfonate (PFOS) and perfluorodecanoic acid. Twenty three of the 32 samples had a concentration of PFOS above the Environmental Quality Standards (EQS) (up to six times higher than the EQS), and all the 32 samples had concentrations of PBDE above the EQS (up to 4,000 times higher, with the sum of six PBDE varying from 4.5 to 182 ng/g dry weight). Clearly, the interest to consider PFOS and HBCD as new priority substances is confirmed. In contrast, the pertinence of a priority status for HCBD, which was never quantified in our study, might have to be reconsidered in the future.

Transfer of PCBs from bottom sediment to freshwater river fish: a food-web modelling approach in the Rhône River (France) in support of sediment management.

Since 2005, restrictions have been because of fish consumption along the Rhone River because of high polychlorobiphenyl (PCB) concentrations, which have resulted inadverse economic consequences for professional fisheries in affected areas. French environmental authorities have expended considerable efforts to research sediment remediation strategies and development of sediment quality guidelines designed to protect the health of humans consuming Rhône River fish. Here we: (1) develop a bioaccumulation food-web model that describes PCB concentrations in three common freshwater fish species of the Rhône River, using Bayesian inference to estimate the input parameters; (2) test the predictive power of the model in terms of risk assessment for fish consumption; and (3) discuss the use of this approach to develop sediment quality guidelines that protect the health of humans consuming Rhône River fish. The bioaccumulation model predictions are protective for human consumer of fish and are efficient for use in risk assessment. For example, 85% of the predicted values were within a factor of 5 of measured CB153 concentrations in fish. Using sensitivity analyses, the major role played by sediment and diet behaviors on bioaccumulation process is illustrated: the parameters involved in the respiratory process (contamination from water) have little impact on model outputs, whereas the parameters related to diet and digestion processes are the most sensitive. The bioaccumulation model was applied to derive sediment concentrations compatible with safe fish consumption. The resulting PCB sediment thresholds (expressed as the sum of seven PCB indicator congeners) that are protective for the consumption of the fish species ranged from 0.7 to 3 ng/g (dw).

Is PCBs concentration variability between and within freshwater fish species explained by their contamination pathways?

Many chemical, physiological, and trophic factors are known to affect bioaccumulation of polychlorinated biphenyls (PCBs) in biota. Understanding the primary factors affecting fish contamination is critical for predicting and assessing risks to upper-trophic level consumers, including humans. Here we identify PCB contamination pathways that could explain within- and between-species variability in fish concentration levels. Three freshwater river fish species (barbel, chub and bream) were sampled at three sites along the Rhone River (France) where fish consumption is partially prohibited because of PCB levels exceeding the European health-based benchmark. The trophic position was assessed using an innovative approach based on stable isotope analyses and Bayesian inference, which takes into account both isotope data variability and parameter uncertainty. The effect of foraging habitat on fish contamination was addressed using stable isotope mixing models. The fish trophic position and PCB concentrations were found to be unrelated while the exploitation of sediment detrital carbon as a food source appeared to be a critical factor affecting fish contamination. Fish length, PCB concentration of the sediment, and individual fish foraging habitat (exploitation of detrital versus planktonic carbon sources) explained 80% of within- and between-species variability observed in PCB concentrations. These results, obtained for species that have overlapping TPs and exploit different carbon sources, reveal that the important factor in fish PCB contamination is not only what fish consume, but also and essentially the feeding location.

Genetic analysis of potential postglacial watershed crossings in Central Europe by the bullhead (Cottus gobio L.).

Natural colonizations across watersheds have been frequently proposed to explain the present distributions of many freshwater fish species. However, detailed studies of such potential watershed crossings are still missing. Here, we investigated potential postglacial watershed crossings of the widely distributed European bullhead (Cottus gobio L.) in two different areas along the Rhine-Rhône watershed using detailed genetic analysis. The main advantage of studying bullheads vs. other freshwater fish species is that their distribution has been lightly influenced by human activities and as such, interpretations of colonization history are not confounded by artificial transplantations. The genetic analyses of eight microsatellite loci revealed strong genetic similarities between populations of both sides of the Rhine-Rhône watershed in the Lake Geneva area, giving strong evidence for a natural watershed crossing of bullheads from the upper Rhine drainage into the Rhône drainage in the Lake Geneva area likely facilitated by the retreat of the glaciers after the last glacial maximum some 20,000 years ago. Populations from the Lake Geneva basin were genetically more similar to populations from across the watershed in the upper Rhine drainage than to populations further downstream in the lower Rhône. In contrast, populations from Belfort, an area, which was not covered by ice during the last glacial maximum, showed strong genetic differentiation between populations of the upper Rhine and Rhône drainages. Based on our results on the bullhead, we propose that glacial retreat may have eased the dispersal of numerous European freshwater fish species across several geological boundaries.

Complex patterns of colonization and refugia revealed for European grayling Thymallus thymallus, based on complete sequencing of the mitochondrial DNA control region.

The complete mitochondrial DNA (mtDNA) control region (1043 base pairs) and 162-bp of flanking transfer RNA genes were sequenced in 316 European grayling, Thymallus thymallus, from 44 populations throughout the Western European range of the species. A total of 58 haplotypes were revealed with pairwise divergence ranging from 0.001 to 0.038. An inferred intraspecific phylogenetic tree revealed two well-supported clades within the Danube basin, one highly divergent clade in the Adriatic basin, and one large, diverse group representing most other populations. A deeply divergent haplotype fixed in the Loire basin in central France, more groups of haplotypes from distinct Danubian tributaries, and a relatively ancestral haplotype fixed in former tributaries of the Elbe in Denmark all suggest a complex pattern of interglacial and postglacial expansions originating from disjunct refugia throughout central Europe. Despite some evidence of human-mediated stock transfers, parsimony-network-based nested-clade analysis (NCA) supported specific inferences relating to corridors of postglacial expansion such as the lower Rhine (Moselle) and Elbe systems (Danish populations) serving as sources for expansion into the Baltic to the north as well as the upper Rhine and Danube to the south; and specific Rhine populations (Doller, Orbe and Reuss) serving as sources for colonization of the Rhone. The multiple divergent clades representing populations in the upper Danube, as well as the deeply divergent haplotypes found in the Adriatic and Loire basins (> 5% divergence from Asian outgroups) support the theory that European grayling have had a long history in Western Europe, pre-dating Pleistocene glacial cycles. The patterns of mtDNA divergence shown here support a perspective of rich inter- and intrabasin genetic diversity that should be protected from current trends to translocate brood stocks for rearing and release in response to declining populations, especially in southern European basins.

Phylogeography and postglacial dispersion of the chub (Leuciscus cephalus) in Europe.

A phylogeographic analysis of mitochondrial DNA variation was performed in order to test the hypothesis of a postglacial recolonization of mid- and north-European rivers from a Danubian refuge. Over 345 chub specimens from European rivers covering most of the species' native range were investigated using 600 bp of the cytochrome b gene. Chub in European rivers belong to four highly divergent mitochondrial groups (lineages) differing by mean divergence estimates from 5.2% to 7.89%. These four lineages have a largely allopatric distribution, implying four geographical sets: two Mediterranean, and two north-European sets. This pattern provided strong evidence for: (i) the eradication of this species from most of Europe during maximum ice extent; (ii) its survival in four refugia (Adriatic side of the Balkans, eastern Greece (Aegean Rivers), southern tributaries of the Danube, and periphery of Black and Caspian Seas); (iii) a differential postglacial recolonization of mid- and northern Europe from the last two refugia only; (iv) the occurrence of this recolonization in two steps for the Danubian (western) lineage that entered western Europe (Rhine-Rhone-Loire drainages) during the Riss-Würm interglacial period and survived the last glaciation there before colonizing Garonne, UK and German drainages up to the Elbe during the Holocene; and (v) the occurrence of this recolonization in a single step for the Ponto-Caspian (eastern) lineage that entered the Baltic area as far as the Oder in the Holocene. Both lineages came into contact in the River Elbe without evident mixing.

Genetic variability in sculpin (genus cottus) from southern france, with reference to the taxonomic status of an endemic species, C. petiti

The genetic variability of seven populations of Cottus sp. from southern France was analysed using starch-gel electrophoresis. Fourteen enzyme systems were screened revealing seven monomorphic and 12 polymorphic genetic loci. Low within-population allelic variation was observed, with frequent allelic fixations and a maximum of two polymorphic loci per population. By contrast, between-population variation was high, with several private alleles and a unique genotypic pattern for each population. A neighbour-joining tree clustering Nei distances showed three major clades corresponding to locations in the catchment area of the Loire, the Garonne and the Mediterranean. Within the Mediterranean group, the morphologically distinct population of the Lez river, described as C. petiti, was not more differentiated than the other populations on the basis of allozymes.