Out with the old, introgression with the new: Signals of ancient and recent admixture in hybridizing Mesoamerican crocodiles (Crocodylus acutus x Crocodylus moreletii)

A central aim of conservation is to preserve existing biodiversity and
understand the ecological and evolutionary processes that support it.
Inter- and intra-specific hybridization in wildlife has been recognized as
a common and naturally occurring phenomenon that facilitates species
adaptation and evolution. However, hybridization still constitutes one of
the most challenging problems for legal protection and species management
due to its perceived biological risk, lack of regulatory oversight, and
different case-by-case impacts. When considering rare or threatened
hybridizing species with unequal legal protection, management strategies
risk being inaccurate or unsuccessful unless contextualized with an
informed understanding of the species' genetic and evolutionary
backgrounds. We investigated hybridization dynamics and genetic diversity
of American crocodiles (Crocodylus acutus) and Morelet’s crocodiles
(Crocodylus moreletii) from Belize to ascertain whether genetic exchange
through admixture displayed signs of evolutionary significance. Using
genomic reduced representation (3RAD) datasets from 242 wild crocodile
samples, we found evidence of population structure among C. acutus, as
well as ancient bidirectional gene flow that had occurred between C.
acutus and C. moreletii. Notably, we also found evidence of high levels of
recent admixture along the coastal Crocodylus populations in areas with
extensive habitat modification due to human impact. These findings as well
as a discovered disconnect between morphological and genetic species
assignments used to identify populations have implications for
conservation management practices and suggest a range of additional
genetic investigations to understand the natural and anthropogenic role of
hybridization in large long-lived tropical predators that span marine and
terrestrial ecosystems.