Genomic and environmental insights and conservation challenges for two hybridizing iconic crocodile species across Mexico: Crocodylus acutus and C. moreletii

Hybridization is of key relevance for conservation of wild species, and yet it is still one of the most controversial issues in conservation. Identifying historical and contemporary factors promoting the formation and maintenance of hybrids is crucial for the management of endangered species, as well as characterizing the environmental factors and patterns of habitat use among parental species and their hybrids. Crocodiles are a conservation priority group since all 23 species recognized worldwide are in a protected category and hybridization occurs between many of their species, particularly between Crocodylus acutus and C. moreletii. Their hybridization system encompasses a geographically extensive hybrid zone, where two distinct hybrids and two C. acutus lineages have diverged and only a few geographically isolated populations of both parental species remain. We used a combined approach of genome-wide sequencing and ecological niche modeling to discern the geographic and temporal patterns of introgression, migration, and demography, and to assess the ecological niches of the distinct lineages. Our approach enabled us to determine the spatial and temporal components of the divergence and admixture events of hybrids and non-admixed lineages, to describe the environmental characteristics and geographic extent of areas of sympatry, and to confirm human-mediated hybridization events. Our findings also showed overall distinct ranges and ecological niches among lineages, where hybrids presented a different set of environmental requirements from both parental species. This approach can be readily applied to different taxa and ecological contexts, providing species information on genetics and the environment with direct conservation relevance. We additionally describe the various conservation challenges that C. acutus and C. moreletii currently face, highlighting that these distinct crocodile species and hybrid lineages warrant recognition and need urgent conservation effort.