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The white-crowned Pigeon (WCPi), Patagioenas leucocephala, and the scaly-naped Pigeon (SNPi), P squamosa, are two Caribbean endemic species of patrimonial and cynegetic interest. Although both species are under the threat of habitat destruction and hunting pressure, population trends remain undocumented in a large part of their geographical range. Here, we used both the “auditory and visual” and “call-broadcast” census methods to assess the occurrence and relative abundance of both species in Guadeloupe (French West Indies). The call-broadcast method was found to be more efficient as it reduced the problem of “false absence” while increasing the probability of detection. Results from our surveys showed that both WCPis and SNPis were at low density and showed complete habitat segregation. SNPis were only encountered in rainforest, whereas WCPis could be observed at count stations located in dry and swamp forests, mangroves, agricultural lands and wet meadows. We recommend the use of the call-broadcast method for monitoring the two species on islands where they occur at low density, under which conditions distance sampling may be poorly reliable. The general relevance of the call-broadcast method to other species of pigeons and doves deserves further attention, especially to document population trends in elusive game species of conservation interest.

Sex-determination is of particular importance in avian ecology and conservation. However, many bird species show no conspicuous sexual dimorphism, such as the La Selle Thrush, Turdus swalesi, a vulnerable species endemic to Hispaniola. We captured individuals in southeastern Haiti, in 2019–2022. For each one, we collected contour feathers or blood samples for molecular sex identification based on the CHD-1 gene. In addition, we took body measurements of several captured individuals and recorded their weight. Out of a total of 65 birds, 45 were identified as males and 20 as females, indicative of a significantly male-biased sex ratio. However, analyses of first captures showed that the sex ratio at our study site was male-biased only outside of the breeding season, suggesting that females may disperse at that time while males remain on their territories. Sexual dimorphism was limited to wing chord length and tail length, with males being larger than females. Tail length was the best predictor of sex in a logistic regression model and correctly classified about 80% of individuals as male or female. We discuss our results in relation to previous studies of sex ratio and sexual dimorphism in turdid species and address their relevance for the conservation of avian species in one of the major protected forest areas in Haiti.

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.

In domesticated strains of the Nile tilapia, phenotypic sex has been linked to genetic variants on linkage groups 1, 20 and 23. This diversity of sex-loci might reflect a naturally polymorphic sex determination system in Nile tilapia, or it might be an artefact arising from the process of domestication. Here, we searched for sex-determiners in wild populations from Kpandu, Lake Volta (Ghana-West Africa), and from Lake Koka (Ethiopia-East Africa) that have not been subjected to any genetic manipulation. We analysed lab-reared families using double-digest Restriction Associated DNA sequencing (ddRAD) and analysed wild-caught males and females with pooled whole-genome sequencing (WGS). Strong sex-linked signals were found on LG23 in both populations, and sex-linked signals with LG3 were observed in Kpandu samples. WGS uncovered blocks of high sequence coverage, suggesting the presence of B chromosomes. We confirmed the existence of a tandem amh duplication in LG23 in both populations and determined its breakpoints between the oaz1 and dot1l genes. We found two common deletions of ~5 kb in males and confirmed the presence of both amhY and amh∆Y genes. Males from Lake Koka lack both the previously reported 234 bp deletion and the 5 bp frameshift-insertion that creates a premature stop codon in amh∆Y.

Caribbean rivers are inhabited by native macrofauna with a diadromous life cycle. The factors influencing the upstream migration of diadromous species are not well understood. Suggested primary factors include species density, habitat suitability and food availability. We hypothesized that food quality could be a key parameter in the upstream migration of macrocrustaceans. We sampled the main shrimp species and their potential food sources along an altitudinal gradient in the Grand Carbet River of Guadeloupe. Lipid analyses of the different food items reveal that biofilm and drifting organic matter are main sources of eicosapentaenoic acid (EPA). Biofilm is richer in EPA upstream, while drifting material is richer in EPA downstream. These opposed altitudinal gradients are reflected in shrimp lipids depending on whether they feed on biofilm or drifting organic matter. In addition, low EPA levels in shrimp suggest that dietary EPA could be a limiting factor in this system and that this differential altitudinal distribution of EPA could influence shrimp settlement.

The American eel (Anguilla rostrata) has long been regarded as a panmictic fish and has been confirmed as such in the northern part of its range. In this paper, we tested for the first time whether panmixia extends to the tropical range of the species. To do so, we first assembled a reference genome (975 Mbp, 19 chromosomes) combining long (PacBio and Nanopore and short (Illumina paired‐end) reads technologies to support both this study and future research. To test for population structure, we estimated genotype likelihoods from low‐coverage whole‐genome sequencing of 460 American eels, collected at 21 sampling sites (in seven geographic regions) ranging from Canada to Trinidad and Tobago. We estimated genetic distance between regions, performed ADMIXTURE‐like clustering analysis and multivariate analysis, and found no evidence of population structure, thus confirming that panmixia extends to the tropical range of the species. In addition, two genomic regions with putative inversions were observed, both geographically widespread and present at similar frequencies in all regions. We discuss the implications of lack of genetic population structure for the species. Our results are key for the future genomic research in the American eel and the implementation of conservation measures throughout its geographic range. Additionally, our results can be applied to fisheries management and aquaculture of the species.

Background The European trout ( Salmo trutta species complex) occurs across a very wide altitudinal range from lowland rivers to alpine streams. Historically, the major European river systems contained different, evolutionarily distinct trout lineages, and some of this genetic diversity has persisted in spite of extensive human-mediated translocations. We used AFLP-based genome scans to investigate the extent of potentially adaptive divergence among major drainages and along altitudinal gradients replicated in several rivers. Results The proportion of loci showing evidence of divergent selection was larger between drainages than along altitudinal transects within drainages. This suggests divergent selection is stronger between drainages, or adaptive divergence is constrained by gene flow among populations within drainages, although the latter could not be confirmed at a more local scale. Still, altitudinal divergence occurred and, at approximately 2% of the markers, parallel changes of the AFLP band frequencies with altitude were observed suggesting that altitude may well be an important source of divergent selection within rivers. Conclusions Our results indicate that adaptive genetic divergence is common both between major European river systems and along altitudinal gradients within drainages. Alpine trout appear to be a promising model system to investigate the relative roles of divergent selection and gene flow in promoting or preventing adaptation to climate gradients.

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. Genomes and transcriptomes of five distinct lineages of African cichlids, a textbook example of adaptive radiation, have been sequenced and analysed to reveal that many types of molecular changes contributed to rapid evolution, and that standing variation accumulated during periods of relaxed selection may have primed subsequent diversification. Signs of adaptive radiation in the cichlid genome The 2,000 or so species of cichlid fish, to be found in the lakes and rivers of Africa's Rift Valley, provide the classic example of adaptive radiations. This large-scale international collaboration has sequenced and analysed the genomes and transcriptomes of five distinct lineages of African cichlids. The data reveal an excess of gene duplications in comparison to other fish species. There is an abundance of non-coding element divergence; accelerated coding sequence evolution; expression divergence associated with transposable element insertions in orthologous gene pairs; and regulation by novel miRNAs. Sequencing data from sixty individuals from six closely related Lake Victoria species point to rapid cichlid speciation associated with genome-wide diversifying selection on coding and regulatory variants, and imply that ancient periods of relaxed purifying selection enabled the accumulation of standing variation, which may have been important in facilitating diversification.

Abstract 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) (RST = 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 (RST = 0.24 - 0.32). The lowest differentiations were observed among connected populations within a basin (RST = 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 ~ 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.

This study assessed the adult sex ratio and sexual dimorphism in body size in the vulnerable La Selle Thrush, Turdus swalesi, over a 26-month period, in Haiti. We found that the overall adult sex ratio was significantly male-biased. However, this was only true during the non-breeding season, suggesting that males may show more site tenacity than females, although true differences in adult survival between males and females cannot be ruled out. We observed a slight, albeit significant, sexual dimorphism in size, with males having, on average, both a longer wing chord and a longer tail than females. Tail length was the best predictor of sex in a logistic regression model, with about 80% of individuals being correctly assigned to their actual sex. Understanding the causes and consequences of the observed male-biased sex ratio might be important for the conservation of the La Selle Thrush, particularly in the face of ongoing severe deforestation in Haiti. Sex-determination is of particular importance in avian ecology and conservation. However, many bird species show no conspicuous sexual dimorphism, such as the La Selle Thrush, Turdus swalesi, a vulnerable species endemic to Hispaniola. We captured individuals in southeastern Haiti, in 2019–2022. For each one, we collected contour feathers or blood samples for molecular sex identification based on the CHD-1 gene. In addition, we took body measurements of several captured individuals and recorded their weight. Out of a total of 65 birds, 45 were identified as males and 20 as females, indicative of a significantly male-biased sex ratio. However, analyses of first captures showed that the sex ratio at our study site was male-biased only outside of the breeding season, suggesting that females may disperse at that time while males remain on their territories. Sexual dimorphism was limited to wing chord length and tail length, with males being larger than females. Tail length was the best predictor of sex in a logistic regression model and correctly classified about 80% of individuals as male or female. We discuss our results in relation to previous studies of sex ratio and sexual dimorphism in turdid species and address their relevance for the conservation of avian species in one of the major protected forest areas in Haiti.