Search

Sex-determining regions have been identified in the Nile tilapia on linkage groups (LG) 1, 20 and 23, depending on the domesticated strains used. Sex determining studies on wild populations of this species are scarce. Previous work on two wild populations, from Lake Volta (Ghana) and from Lake Koka (Ethiopia), found the sex-determining region on LG23. These populations have a Y-specific tandem duplication containing two copies of the Anti-Müllerian Hormone amh gene (named amhY and amhΔY). Here, we performed a whole-genome short-reads analysis using male and female pools on a third wild population from Lake Hora (Ethiopia). We found no association of sex with LG23, and no duplication of the amh gene. Furthermore, we found no evidence of sex linkage on LG1 or on any other LGs. Long read whole genome sequencing of a male from each population confirmed the absence of a duplicated region on LG23 in the Lake Hora male. In contrast, long reads established the structure of the Y haplotype in Koka and Kpandu males and the order of the genes in the duplicated region. Phylogenies constructed on the nuclear and mitochondrial genomes, showed a closer relationship between the two Ethiopian populations compared to the Ghanaian population, implying an absence of the LG23Y sex-determination region in Lake Hora males. Our study supports the hypothesis that the amh region is not the sex-determining region in Hora males. The absence of the Y amh duplication in the Lake Hora population reflects a rapid change in sex determination within Nile tilapia populations. The genetic basis of sex determination in the Lake Hora population remains unknown.

International audience; Caribbean island rivers are the home to migratory indigenous macro-fauna. Concurrently, they also serve as the main source of freshwater for human consumption. This production of drinking water involves the construction of a large number of structures across the riverbed, which can slow or even stop the migration of aquatic species. The resident river macro-fauna is composed of crustacean and fish species that all have a diadromous and mostly amphidromous life cycle, involving pro-larval drift downstream towards the sea, marine larval dispersal, followed by an upstream river migration to complete their growth and reproduction cycle. Our study compares, across three rivers on the island of Guadeloupe, the recruitment of five crustacean species and two fish species in the mouths of these rivers with species demographic distributions on either side of the major water withdrawal structure built along these rivers. Post-larval recruitment events were multispecific, discrete over time and their amplitude varied depending on the river. We show differential biological porosity of each obstacle according to species, revealing different specific crossing abilities. Our results also suggested that the impacts were not directly related to the height of the structure but that external, hydrological and environmental, conditions are involved. These achievements can be translated into operational measures such as the maintaining and monitoring of reserved minimal flows that are adapted to passways, as well as the setting up of protective measures for the natural environment.; Les rivières caribéennes sont le lieu de vie d’une macrofaune indigène migratrice et aussi le principal lieu de prélèvement pour la production d’eau potable pour la population humaine. Cette production d’eau potable impli-que la construction d’un grand nombre d’ouvrages en travers du lit des rivières, qui peuvent ralentir ou stopper la migration des espèces. La macrofaune résidente est composée d’espèces de crustacés et de poissons qui ont tou-tes un cycle de vie diadrome et majoritairement amphidrome, impliquant une dévalaison larvaire vers la mer, une dispersion larvaire marine puis une montaison en rivière pour terminer leur croissance et se reproduire. Notre étude porte sur la comparaison du recrutement de cinq espèces de crustacés et deux espèces de poissons dans les embouchures de trois rivières proches, ainsi que sur la distribution démographique des différentes espèces de part et d’autre de l’ouvrage majeur de ces trois rivières. Les recrutements sont multispécifiques, discrets dans le temps et leur importance est variable selon l’embouchure. La porosité biologique de chaque obstacle est diffé-rente en fonction des espèces révélant différentes capacités de franchissement. Nos résultats suggèrent aussi que les impacts ne sont pas directement liés à la hauteur de l’ouvrage mais qu’interviennent des conditions externes à celui-ci, hydrologiques et environnementales. Ces acquis peuvent se décliner en mesures opérationnelles comme l’importance du maintien et de la surveillance de débits réservés adaptés et maîtrisés au niveau des passes, ainsi que la mise en place de mesures conservatoires de la ripisylve et de l’environnement naturel proche

International audience

International audience

National audience

Interspecific hybridization leading to viable andfertile fishes in the Tilapia group (Pisces, Cichlidae) is readily obtainedin stock populations and occasionally occurs in natural populations. Tilapias thus provide a valuable model to investigate hybrid genome evolution in vertebrates. As part of an aquaculture development project, (Oreochromis niloticus x Sarotherodon melanotheron) hybrids were produced and propagated for three generations. As evidenced from karyotypic analysis, both parental species are endowed with a typical Tilapiini chromosomal formula (2n =44 ST) which was found to be conserved in hybrids. In order tocharacterize the structure ofthe 2 specific genomes classical cytogenetic methods (Chromomycin A3 staining, C-banding) as weIl as FISH (telomeric, ribosomal, and rex retro-transposons probes) were achieved. Furthermore we performed comparative genomic hybridization (CGH) in offspring of hybrids and pure specimens using genomic DNA from O. niloticus and S. melanotheron. CGH revealed a partial painting restricted to heterochromatic regions also characterized by positive C-banding and retro-transposon rich regions (i.e. the centromere and the short arms of aIl chromosomes and especially the distal part of the long chromosome arm of the first pair). Despite cross-hybridization of the probes we were able to trace each centromere back to the parental species and to show the occurrence ofrecombination events in thefirstchromosomepair. Moreoverthe firstlong pair was expected to be sex linked according to the study of synaptonemal complexes. This idea was supported by the results of CGH and especially FISH of transposons but the size heteromorphism ofthe long arm in the first pairwas 0 bserved in sorne males and sorne females as weIl. These results suggest that, although species exhibit an important eco-morphological diversity, genome organization is highly conserved among the Tilapiini apart sorne differences in heterochromatic structure and pattern of retro-transposons distribution. This could explain why hybrids are easily produced in this group when evolutionary barriers are disrupted. (Texte intégral)

Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.

When searching for loci possibly under selection in the genome, an alternative to population genetics theoretical models is to establish allele distribution models for each locus to directly correlate allelic frequencies and environmental variables like precipitation, temperature, or sun radiation for example. Such an approach implementing multiple logistic regression models in parallel was implemented within a computing programme named MATSAM. Recently, this application was improved in order to support qualitative environmental predictors as well as to permit the identification of associations between genomic variation and individual phenotypes, allowing the detection of loci involved in the genetic architecture of polymorphic characters. Here we present the corresponding methodological developments and compare the results produced by software implementing population genetics theoretical models (DFDIST, BAYESCAN) and allele distribution models (MATSAM) in an empirical context to detect signatures of genomic divergence associated with speciation in Lake Victoria cichlid fishes.

When searching for loci possibly under selection in the genome, an alternative to population genetics theoretical models is to establish allele distribution models (ADM) for each locus to directly correlate allelic frequencies and environmental variables such as precipitation, temperature, or sun radiation. Such an approach implementing multiple logistic regression models in parallel was implemented within a computing program named MATSAM. Recently, this application was improved in order to support qualitative environmental predictors as well as to permit the identification of associations between genomic variation and individual phenotypes, allowing the detection of loci involved in the genetic architecture of polymorphic characters. Here, we present the corresponding methodological developments and compare the results produced by software implementing population genetics theoretical models (DFDIST and BAYESCAN) and ADM ( MATSAM ) in an empirical context to detect signatures of genomic divergence associated with speciation in Lake Victoria cichlid fishes.

Background: Reconstructing the evolutionary history of a species is challenging. It often depends not only on the past biogeographic and climatic events but also the contemporary and ecological factors, such as current connectivity and habitat heterogeneity. In fact, these factors might interact with each other and shape the current species distribution. However, to what extent the current population genetic structure reflects the past and the contemporary factors is largely unknown. Here we investigated spatio-temporal genetic structures of Nile tilapia (Oreochromis niloticus) populations, across their natural distribution in Africa. While its large biogeographic distribution can cause genetic differentiation at the paleo-biogeographic scales, its restricted dispersal capacity might induce a strong genetic structure at micro-geographic scales. Results: Using nine microsatellite loci and 350 samples from ten natural populations, we found the highest genetic differentiation among the three ichthyofaunal provinces and regions (Ethiopian, Nilotic and Sudano-Sahelian) (R(ST) = 0.38 - 0.69). This result suggests the predominant effect of paleo-geographic events at macro-geographic scale. In addition, intermediate divergences were found between rivers and lakes within the regions, presumably reflecting relatively recent interruptions of gene flow between hydrographic basins (R(ST) = 0.24 - 0.32). The lowest differentiations were observed among connected populations within a basin (R(ST) = 0.015 in the Volta basin). Comparison of temporal sample series revealed subtle changes in the gene pools in a few generations (F = 0 - 0.053). The estimated effective population sizes were 23 - 143 and the estimated migration rate was moderate (m similar to 0.094 - 0.097) in the Volta populations. Conclusions: This study revealed clear hierarchical patterns of the population genetic structuring of O. niloticus in Africa. The effects of paleo-geographic and climatic events were predominant at macro-geographic scale, and the significant effect of geographic connectivity was detected at micro-geographic scale. The estimated effective population size, the moderate level of dispersal and the rapid temporal change in genetic composition might reflect a potential effect of life history strategy on population dynamics. This hypothesis deserves further investigation. The dynamic pattern revealed at micro-geographic and temporal scales appears important from a genetic resource management as well as from a biodiversity conservation point of view.

Cichlid fishes have evolved tremendous morphological and behavioral diversity in the waters of East Africa. Within each of the Great Lakes Tanganyika, Malawi, and Victoria, the phenomena of hybridization and retention of ancestral polymorphism explain allele sharing across species. Here, we explore the sharing of single nucleotide polymorphisms (SNPs) between the major East African cichlid assemblages. A set of approximately 200 genic and nongenic SNPs was ascertained in five Lake Malawi species and genotyped in a diverse collection of ∼160 species from across Africa. We observed segregating polymorphism outside of the Malawi lineage for more than 50% of these loci; this holds similarly for genic versus nongenic SNPs, as well as for SNPs at putative CpG versus non-CpG sites. Bayesian and principal component analyses of genetic structure in the data demonstrate that the Lake Malawi endemic flock is not monophyletic and that river species have likely contributed significantly to Malawi genomes. Coalescent simulations support the hypothesis that river cichlids have transported polymorphism between lake assemblages. We observed strong genetic differentiation between Malawi lineages for approximately 8% of loci, with contributions from both genic and nongenic SNPs. Notably, more than half of these outlier loci between Malawi groups are polymorphic outside of the lake. Cichlid fishes have evolved diversity in Lake Malawi as new mutations combined with standing genetic variation shared across East Africa., Molecular Biology and Evolution, 30 (4), ISSN:0737-4038, ISSN:1537-1719