Data from: Genetic evidence of hybridization between the critically endangered Cuban crocodile and the American crocodile: implications for population history and in situ/ex situ conservation

Inter-specific hybridization may be especially detrimental when one
species is extremely rare and the other is abundant owing to the potential
for genetic swamping. The Cuban crocodile (Crocodylus rhombifer) is a
critically endangered island endemic largely restricted to Zapata Swamp,
where it is sympatric with the widespread American crocodile (C. acutus).
An on-island, C. rhombifer captive breeding program is underway with the
goals of maintaining taxonomic integrity and providing a source of
individuals for reintroduction, but its conservation value is limited by
lack of genetic information. Here we collected mtDNA haplotypic and
nuclear genotypic data from wild and captive C. rhombifer and C. acutus in
Cuba to: (1) investigate the degree of inter-specific hybridization in
natural (in situ) and captive (ex situ) populations; (2) quantify the
extent, distribution and in situ representation of genetic variation ex
situ; and (3) reconstruct founder relatedness to inform management. We
found high levels of hybridization in the wild (49.1%) and captivity
(16.1%), and additional evidence for a cryptic lineage of C. acutus in the
Antilles. We detected marginally higher observed heterozygosity and
allelic diversity ex situ relative to the wild population, with captive C.
rhombifer exhibiting over twice the frequency of private alleles. Although
mean relatedness was high in captivity, we identified 37 genetically
important individuals that possessed individual mean kinship (MK) values
lower than the population MK. Overall, these results will guide long-term
conservation management of Cuban crocodiles for maintaining the genetic
integrity and viability of this species of high global conservation value.