The Creole cattle from Guadeloupe (GUA) are well adapted to the tropical environment. Its admixed genome likely played an important role in such adaptation. Here, we sought to detect genomic signatures of selection in the GUA genome. For this purpose, we sequenced 23 GUA individuals and combined our data with sequenced genomes of 99 animals representative of European, African and indicine groups. We detect 17,228,983 single nucleotide polymorphisms (SNPs) in the GUA genome, providing the most detailed exploration, to date, of patterns of genetic variation in this breed. We confirm the higher level of African and indicine ancestries, compared to the European ancestry and we highlight the African origin of indicine ancestry in the GUA genome. We identify five strong candidate regions showing an excess of indicine ancestry and consistently supported across the different detection methods. These regions encompass genes with adaptive roles in relation to immunity, thermotolerance and physical activity. We confirmed a previously identified horn-related gene, RXFP2, as a gene under strong selective pressure in the GUA population likely owing to human-driven (socio-cultural) pressure. Findings from this study provide insight into the genetic mechanisms associated with resilience traits in livestock.

Despite their central economic and cultural role, the origin of cattle populations living in Indian Ocean islands still remains poorly documented. Here, we unravel the demographic and adaptive histories of the extant Zebus from the Mayotte and Madagascar islands using high-density SNP genotyping data. We found that these populations are very closely related and both display a predominant indicine ancestry. They diverged in the 16th century at the arrival of European people who transformed the trade network in the area. Their common ancestral cattle population originates from an admixture between an admixed African zebu population and an Indian zebu that occurred around the 12th century at the time of the earliest contacts between human African populations of the Swahili corridor and Austronesian people from Southeast Asia in Comoros and Madagascar. A steep increase in the estimated population sizes from the beginning of the 16th to the 17th century coincides with the expansion of the cattle trade. By carrying out genome scans for recent selection in the two cattle populations from Mayotte and Madagascar, we identified sets of candidate genes involved in biological functions (cancer, skin structure, and UV-protection, nervous system and behavior, organ development, metabolism, and immune response) broadly representative of the physiological adaptation to tropical conditions. Overall, the origin of the cattle populations from Western Indian Ocean islands mirrors the complex history of human migrations and trade in this area.

La Caraïbe a été peuplée par les espèces de ruminants domestiques à partir du XV ème siècle. Après les premières introductions de bétail ibérique, des apports variés ont occasionné de nombreux métissages. Ils ont pu être plus ou moins importants, allant jusqu’à l’utilisation de croisements systématiques se substituant aux populations Créoles d’origine. Des populations locales variées et originales se maintiennent, malgré des apports récents liés aux échanges commerciaux et aux progrès des méthodes modernes de reproduction. Ces populations animales contribuent fortement à l’élevage de la région, principalement dans des systèmes de production traditionnels ou familiaux où leurs qualités d’adaptation sont appréciées. Malgré leur faible spécialisation, elles révèlent également des aptitudes intéressantes de production. Elles constituent également un matériel biologique modèle pour l’étude de caractères d’adaptation, comme la résistance à certaines pathologies tropicales. Peu d’actions ont été mises en œuvre pour la conservation ou la gestion des populations locales dans la Caraïbe. Elles concernent principalement les Grandes Antilles, où quelques troupeaux d’animaux Créoles subsistent, mais aussi des races synthétiques de constitution plus récente et fortement organisées. Dans les Petites Antilles, seuls les départements français proposent une gestion des races locales in situ, avec des programmes de sélection concertés. Avec des effectifs réduits et dispersés, la Caraïbe rassemble de nombreuses ressources génétiques locales méconnues et peu exploitées. Des travaux récents relancent l’intérêt pour ces ressources, au sein de systèmes d’élevage durables. La mise en place d’une stratégie globale de gestion de ces populations dans la Caraïbe et l’Amérique Latine devrait renforcer les efforts des différents partenaires dans ce sens.

The feral cattle of the subantarctic island of Amsterdam provide an outstanding case study of a large mammalian population that was established by a handful of founders and thrived within a few generations in a seemingly inhospitable environment. Here, we investigated the genetic history and composition of this population using genotyping and sequencing data. Our inference showed an intense but brief founding bottleneck around the late 19th century and revealed contributions from European taurine and Indian Ocean Zebu in the founder ancestry. Comparative analysis of whole-genome sequences further revealed a moderate reduction in genetic diversity despite high levels of inbreeding. The brief and intense bottleneck was associated with high levels of drift, a flattening of the site frequency spectrum and a slight relaxation of purifying selection on mildly deleterious variants. Unlike some populations that have experienced prolonged reductions in effective population size, we did not observe any significant purging of highly deleterious variants. Interestingly, the population’s success in the harsh environment can be attributed to preadaptation from their European taurine ancestry, suggesting no strong bioclimatic challenge, and also contradicting evidence for insular dwarfism. Genome scan for footprints of selection uncovered a majority of candidate genes related to nervous system function, likely reflecting rapid feralization driven by behavioral changes and complex social restructuring. The Amsterdam Island cattle offers valuable insights into rapid population establishment, feralization, and genetic adaptation in challenging environments. It also sheds light on the unique genetic legacies of feral populations, raising ethical questions according to conservation efforts.

Structural variants play an important role in evolutionary processes. Besides, they constitute a large source of inter individual genetic variation that might represent a major factor in the aetiology of complex, multifactorial traits. Their importance in adaptation is becoming increasingly evident in literature. Yet, the characterization of the genomic landscape of structural variants in local breeds remains scarce to date. Herein, we investigate patterns and gene annotation of structural variants in the Creole cattle from Guadeloupe breed using whole genome sequences from 23 bulls representative of the population. In total, we detected 32821 ascertained SV defining 15258 regions, representing ~ 17% of the Creole cattle genome. Among these, 6639 regions have not been previously reported in the Database of Genomic Variants archive. Average number of structural variants detected per individual in the studied population is in the same order of magnitude of that observed in indicine populations and higher than that reported in taurine breeds. We observe an important within-individual variability where approximately half of the detected structural variants have low frequency (MAF < 0.25). Most of the detected structural variants (55%) occurred in intergenic regions. Genic structural variants overlapped with 7793 genes and the predicted effect of most of them is ranked as “modifier”. Among the structural variants that were predicted to have a high functional impact on the protein, a 5.5 Kb in length, highly frequent deletion on chromosome 2, affects ALPI, a gene associated with the interaction between gut microbiota and host immune system. The 6639 newly identified structural variants regions include three deletions and three duplications shared by more than 80% of individuals that are significantly enriched for genes related to tRNA threonylcarbamoyladenosine metabolic process, important for temperature adaptation in thermophilic organisms, therefore suggesting a potential role in the thermotolerance of Creole cattle from Guadeloupe cattle to tropical climate. Overall, highly frequent structural variants that are specific to the Creole cattle population encompass olfactory receptor and immunity genes as well as genes involved in muscle tone, muscle development and contraction. Beyond mapping and characterizing structural variants in the Creole cattle from Guadeloupe breed, this study provides valuable information for a better understanding of the potential role of chromosomal rearrangements in adaptive traits in cattle.

Heartwater is a tick-borne disease caused by Ehrlichia ruminantium and remains endemic in the Guadeloupe archipelago. While previous data from 1989 suggested a seroprevalence of 22 % in cattle, no updated figures were available for livestock, and certain islands such as Les Saintes were considered disease-free. This study aimed to update the sero-epidemiological status of heartwater in cattle and goats across Guadeloupe in 2024. Blood samples were collected from 261 cattle and 135 goats from all islands. Serological testing using the MAP1B ELISA was performed, and true seroprevalence was estimated using a simplified stochastic model that accounts for test sensitivity, specificity, and sample uncertainty. The mean cattle seroprevalence was estimated at 28 % (95 % CI [22-34 %]), with no significant differences between Basse-Terre, Grande-Terre, and Marie-Galante. Importantly, seropositive goats were identified on all major islands, including Les Saintes. Our findings suggest that heartwater remains endemically stable in Guadeloupe since the 1980s and reveal for the first time its serological presence in Les Saintes. These results emphasize the importance of strengthening regional surveillance systems, including veterinary reporting, serological monitoring, and coordinated efforts to prevent further spread across the Caribbean.