Salt-crossed lovers: A genomic investigation of adaptive potential in hybridizing saltwater and freshwater mesoamerican crocodiles (Crocodylus acutus and Crocodylus moreletii)

Abstract

Hybridization presents both a conservation challenge and an evolutionary opportunity – particularly where natural hybrid zones intersect with human-modified landscapes. Recent advances in genomics have reshaped our understanding of hybridization, revealing its role in facilitating adaptation and diversification, especially in dynamic environments. In this dissertation, I investigate the evolutionary and conservation implications of naturally occurring hybridization between two Mesoamerican crocodile species in Belize: Crocodylus acutus (American crocodile) and Crocodylus moreletii (Morelet’s crocodile). Using reduced-representation genomic data, I first characterized population structure, admixture dynamics, and demographic history. These analyses revealed widespread admixture, the presence of two genetically distinct C. acutus lineages in Belize, and evidence of both ancient and ongoing hybridization. Building upon this foundation, I examined the genetic architecture of salinity tolerance – a key ecological trait delineating species boundaries. Through genome-wide association scans (GWAS), I identified two candidate loci associated with environmental salinity gradients, including a previously uncharacterized sodium channel gene (SCN5A-like) in archosaurs. These findings suggest that introgressed variants may contribute to physiological adaptation in hybrid populations. Finally, I assessed the role of adaptive introgression in shaping hybrid genomes. By integrating genome-wide scans for recent positive selection with tests of interspecific gene flow and window-based introgression analyses, I identified introgressed genomic regions under selection enriched in genes linked to environmental stress response, osmoregulation, and metabolism. Notably, introgression patterns were asymmetric, with directional gene flow shaping distinct genomic regions through historical versus recent admixture. Together, these findings suggest that hybridization in crocodylians is not merely a consequence of anthropogenic disturbance but may serve as a mechanism of evolutionary innovation. This work deepens our understanding of hybridization in long-lived vertebrates and underscores the importance of recognizing hybrids as valuable contributors to biodiversity. By integrating genomic and ecological perspectives, this dissertation aims to inform conservation strategies for species affected by hybridization, particularly those subject to uneven legal protections and complex evolutionary trajectories.