Cross-species amplification of 41 microsatellites in European cyprinids: A tool for evolutionary, population genetics and hybridization studies

<p>Abstract</p> <p>Background</p> <p>Cyprinids display the most abundant and widespread species among the European freshwater Teleostei and are known to hybridize quite commonly. Nevertheless, a limited number of markers for conducting comparative differentiation, evolutionary and hybridization dynamics studies are available to date.</p> <p>Findings</p> <p>Five multiplex PCR sets were optimized in order to assay 41 cyprinid-specific polymorphic microsatellite loci (including 10 novel loci isolated from <it>Chondrostoma nasus nasus, Chondrostoma toxostoma toxostoma </it>and <it>Leuciscus leuciscus</it>) for 503 individuals (440 purebred specimens and 63 hybrids) from 15 European cyprinid species. The level of genetic diversity was assessed in <it>Alburnus alburnus, Alburnoides bipunctatus, C. genei, C. n. nasus, C. soetta, C. t. toxostoma, L. idus, L. leuciscus, Pachychilon pictum, Rutilus rutilus, Squalius cephalus </it>and <it>Telestes souffia</it>. The applicability of the markers was also tested on <it>Abramis brama, Blicca bjoerkna </it>and <it>Scardinius erythrophtalmus </it>specimens. Overall, between 24 and 37 of these markers revealed polymorphic for the investigated species and 23 markers amplified for all the 15 European cyprinid species.</p> <p>Conclusions</p> <p>The developed set of markers demonstrated its performance in discriminating European cyprinid species. Furthermore, it allowed detecting and characterizing hybrid individuals. These microsatellites will therefore be useful to perform comparative evolutionary and population genetics studies dealing with European cyprinids, what is of particular interest in conservation issues and constitutes a tool of choice to conduct hybridization studies.</p

Cinétique spatiale et temporelle de zones hybrides : unicité et diversité au sein du modèle Chondrostomes (Teleostei, Cyprinidés), : application pour la conservation d'espèces d'intérêt patrimonial.

Au sein de la famille des Cyprinidés (Téleostéens), Parachondrostoma toxostoma (le toxostome) et Chondrostoma nasus (le hotu) sont deux espèces (respectivement endémique et invasive) qui se rencontrent dans le sud de la France, formant deux zones hybrides distinctes : la zone de la Durance (un milieu fortement fragmenté) et la zone de l'Ardèche (un milieu non fragmenté). La présence de ces deux zones hybrides nous a donné l'opportunité de caractériser les parts respectives de la sélection exogène (l'environnement) et endogène (compatibilité génomique) permettant d'expliquer les patterns d'hybridation entre les deux espèces. Les travaux présentés dans le cadre de cette thèse illustrent parfaitement la complexité des phénomènes d'hybridation, chaque situation étant fortement dépendante du contexte d'étude et ce à l'échelle même de la station. Nous avons montré dans certaines stations que l'espèce endémique résiste à l'introgression de son génome par l'espèce invasive, dans d'autres cas nous avons des scénarios plus complexe d'admixture qui évoluent au cours du temps. Le potentiel évolutif engendré par les phénomènes d'hybridation est cependant indéniable et nous préconisons de prendre en compte ces processus d'hybridation dans les programmes de gestions et de conservation de la biodiversité.In the Cyprinidae family (Teleostei), Parachondrostoma toxostoma (the sofie) and Chondrostoma nasus (the nase) are respectively endemic and invasive species which are found in sympatry in the south of France. They form two distinct hybrid zones: the Durance River (a highly fragmented environment) and the Ardèche basin (an unfragmented area). The existence of these two different zones allow us to characterize the respective contributions of exogenous selection (environmental factors) and endogenous selection (genomic compatibility) to explain hybridization patterns between the two species.This PhD thesis highlights the complexity of hybridization phenomena. Each situation is highly dependent of the study context. We showed the resistance of the genome of the endemic species to introgression by the genome of the invasive species in some stations. In other cases, we demonstrated more complex scenarios of admixture that evolve over time. The evolutionary potential generated by hybridization is undeniable, and we recommend to take the hybridization process into account in management programs and conservation of biodiversity

When anthropogenic river disturbance decreases hybridisation between non-native and endemic Cyprinids and drives an ecomorphological displacement towards juvenile state in both species

International audienceUnderstanding the impact of non-native species on native species is a major challenge in molecular ecology, particularly for genetically compatible fish species. Invasions are generally difficult to study because their effects may be confused with those of environmental or human disturbances. Colonized ecosystems are differently impacted by human activities, resulting in diverse responses and interactions between native and non-native species. We studied the dynamics between two Cyprinids species (invasive Chondrostoma nasus and endemic Parachondrostoma toxostoma) and their hybrids in 16 populations (from allopatric to sympatric situations and from little to highly fragmented areas) corresponding to 2,256 specimens. Each specimen was assigned to a particular species or to a hybrid pool using molecular identification (cytochrome b and 41 microsatellites). We carried out an ecomorphological analysis based on size, age, body shape, and diet (gut vacuity and molecular fecal contents). Our results contradicted our initial assumptions on the pattern of invasion and the rate of introgression. There was no sign of underperformance for the endemic species in areas where hybridisation occurred. In the unfragmented zone, the introduced species was found mostly downstream, with body shapes similar to those in allopatric populations while both species were found to be more insectivorous than the reference populations. However, high level of hybridisation was detected, suggesting interactions between the two species during spawning and/or the existence of hybrid swarm. In the disturbed zone, introgression was less frequent and slender body shape was associated with diatomivorous behaviour, smaller size (juvenile characteristics) and greater gut vacuity. Results suggested that habitat degradation induced similar ecomorphological trait changes in the two species and their hybrids (i. e. a transition towards a pedomorphic state) where the invasive species is more affected than the native species. Therefore, this study reveals a diversity of relationships between two genetically compatible species and emphasizes constraints on the invasion process in disturbed areas

Plasticity of ontogenetic trajectories in cyprinids: a source of evolutionary novelties

International audienceResearch in evolutionary developmental (evo-devo) biology is making an increasingly important contribution to our understanding of the molecular mechanisms underlying the establishment of complex morphological traits. Deciphering the ontogenetic trajectories leading to the differentiation of sister species (and the existence of hybrids) is a new challenge in our understanding of speciation processes. In the present study, we characterized the ontogenetic trajectory of lower lip morphology in two cyprinid species and their hybrids. Chondrostoma toxostoma has an arched lower lip and a generalist diet. Chondrostoma nasus has a straight lower lip and a specialist diet. An analysis of 99 C. toxostoma, 99 C. nasus and 25 first-generation (F1) hybrid individuals demonstrated that the difference between arched and straight lip morphology was found to depend strongly on the height/width ratio of the lower lip. A comparison of the ontogenetic trajectories of these morphometric traits showed that the height of the lower lip was isometric to body length in both species, whereas developmental changes involving an acceleration and a hypermorphosis of the widening of the lower lip led to a straight lip morphology in C. nasus. F1 hybrids were characterized by an extreme phenotype resulting from a rate of lower lip widening slower than that in the two parent species. Therefore, we rejected a codominance hypothesis and concluded that the first stage of hybridization provides the foundations of evolutionary novelty. These results have important evolutionary implications because lower lip shape is linked to dietary behaviour in many fish species

Does invasive Chondrostoma nasus shift the parasite community structure of endemic Parachondrostoma toxostoma in sympatric zones?

International audienceBackground: The composition of parasite communities in two cyprinid species in southern Francenative and threatened Parachondrostoma toxostoma and introduced Chondrostoma nasuswas investigated. In sympatry, these two species form two hybrid zones in the Durance and Ardeche Rivers. Due to their different feeding preference and habitat positions in allopatry, we supposed a difference in parasite communities between fish species. We expected more similar parasite communities in sympatric zones associated with habitat overlap (facilitating the transmission of ectoparasites) and similar feeding (more generalist behaviour when compared to allopatry, facilitating the transmission of endoparasites) in both fish species. Finally, we investigated whether P. toxostoma x C. nasus hybrids are less parasitized then parental species. Methods: One allopatric population of each fish species plus two sympatric zones were sampled. Fish were identified using cytochrome b gene and 41 microsatellites loci and examined for all metazoan parasites. Results: A high Monogenea abundance was found in both allopatric and sympatric populations of C. nasus. Trematoda was the dominant group in parasite communities of P. toxostoma from the allopatric population. In contrast, the populations of P. toxostoma in sympatric zones were parasitized by Dactylogyrus species found in C. nasus populations, but their abundance in endemic species was low. Consequently, the similarity based on parasite presence/absence between the sympatric populations of P. toxostoma and C. nasus was high. Sympatric populations of P. toxostoma were more similar than allopatric and sympatric populations of this species. No difference in ectoparasite infection was found between P. toxostoma and hybrids, whilst C. nasus was more parasitized by Monogenea. Conclusions: The differences in endoparasites between P. toxostoma and C. nasus in allopatry are probably linked to different feeding or habitat conditions, but host-parasite evolutionary associations also play an important role in determining the presence of Chondrostoma-specific monogeneans. Our findings suggest that Dactylogyrus expanded with the source host C. nasus into introduced areas and that P. toxostoma became infected after contact with C. nasus. Although the genotype of P. toxostoma and recombinant genotypes of hybrids are susceptible to Dactylogyrus transmitted from C. nasus, the intensity of infection is low in these genotypes

Non-homogeneous combination of two porous genomes induces complex body shape trajectories in cyprinid hybrids

International audienceINTRODUCTION: Hybridization is a common phenomenon in fish and is considered to be a major source of diversification. Deciphering the remoulding of genomic regions and phenotypes in zones where hybrid specimens occur is of particular interest to elucidate the emergence of evolutionary novelties. This approach is particularly challenging because the first step of hybridization seems to be the most important stage in the emergence of hybrid lineages. However, the signal can be significantly altered after only a few generations. RESULTS: We studied 41 microsatellites and partial cytochrome b gene sequences in 970 specimens belonging to two fish species (Chondrostoma nasus and Parachondrostoma toxostoma) in allopatric/parapatric zones, hybrids between them in a natural sympatric zone: the Ardeche basin. We showed that the genomic architecture in hybrids presented pattern heterogeneity of selection for the different loci. Indeed, the upstream part of the river (Rosieres and Labeaume) presented an overdominant fitness of heterozygotes (12.20%) corresponding to a genomic compatibility, and underselection was observed for 4.88%-7.32% of the loci tested indicating a genomic incompatibility. Moreover the upstream station (Rosieres) presented a positive selection of invasive C. nasus homozygotes (17.07% to 21.95%) indicating that hybridization may increase the fitness of admixed individuals.We showed that hybrid morphology (body shape based on 21 landmarks) correlated with genomic dilution indicating a species fingerprint. However, we demonstrated that the hybrid morphology was not a linear modification between the two parental species but a trade-off between several correlated traits. CONCLUSIONS: Hybrid specimens present a mosaic of genomic combination, showing regions with genomic compatibility and others with genomic incompatibility between the two species. Positive selection (invasive advantage ranging from 9.76% to 21.95% of the loci) was evidenced in the upstream part of the Ardeche indicating that environmental selection makes a substantial contribution. Although the presence of a dam is known to impose heterogeneous hybrid zones between these two species, we demonstrated in this study that a natural environment can also generate a hybrid zone with a large number (and diversity) of hybrids. The combination of the two genomes in the hybrids results in complex ontogenetic trajectories (with different morphological traits evolving at different rates) that correspond to novel developmental pathways

Influence of group, environment, season and size on feeding behaviour.

<p>Distribution of the three classes of feeding behaviour (invertebrate eaters in purple, omnivores in orange and diatom eaters in deep green). Stacked bar chart showing the proportions of the various feeding behaviour classes by species and zone type in <b>A</b>), by season for each syntopic zone in <b>B</b>). Probability of GutVac (<i>y</i>-axis) as predicted by the multinomial model as a function of size in <b>C)</b> in which the <i>X</i>-axis corresponds to body size in cm, and we can read for example the longer specimens are more omnivor than herbivor.</p

Feeding behaviour.

<p>Molecular detection in the feces of the eight prey items analyzed by a principal component analysis of proportions. <b>A)</b> Principal plane of the PCA. The reference populations are represented by closed triangles for the Chée River (Cn. allopatry), open triangles for the Allier (Cn allopatry), closed diamonds for the Suran (Pt allopatry), and open diamonds for the Orbieu (Pt allopatry). The syntopic zones are indicated by a closed square for the Ardèche basin and a closed circle for the Durance basin. <i>C</i>. <i>nasus</i> is shown in green, <i>P</i>. <i>toxostoma</i> in red, hybrids in blue and <i>Barbus barbus</i> (insectivorous control) in grey. The size of the symbols for each specimen is proportional to the number of prey items detected. <b>B)</b> Non-parametric density estimation (Gaussian kernel) of the first axis co-ordinates. Each color corresponds to a category as follows: in purple, invertebrate eaters (i.e. only invertebrates detected in feces); in orange, omnivores (both invertebrates and diatoms detected); and, in deep green, diatom eaters (only diatoms were detected). The distribution density corresponding to <i>Barbus barbus</i> specimens is indicated by grey dashes.</p

Number of specimens considered, by analysis.

<p>K = coefficient of condition, Morpho = morphological analysis of the body, Diet = vacuity analysis and in parenthesis the DNA barcoding sub-sample. <i>Pt</i> = <i>P</i>. <i>toxostoma</i>, <i>Cn</i> = <i>C</i>. <i>nasus</i>, Sur = Suran, Ber = Berre, Orb = Orbieu, Che = Chée, All = Allier, Mir = Miribel, Ron = Roussillon, Ros = Rosières, Bau = Labeaume, Jus = Saint-Just, Bue = Buech, Man = Manosque, Per = Pertuis, Avi = Avignon, Spc = Serre-Ponçon. Data previously published are in italics [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0142592#pone.0142592.ref029" target="_blank">29</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0142592#pone.0142592.ref034" target="_blank">34</a>], new data are in bold.</p><p>All specimens were genotyped, and only subgroups of specimens were used in the various analyses, because size, weight measurements, images of the body or feces was unavailable.</p