Genetic barcoding facilitates captive and wild management of three cryptic African crocodile species complexes

Abstract

AbstractManagement of threatened species with conserved morphology is hindered by misidentification and potential hybridization in captivity. African crocodiles of the genera Osteolaemus, Crocodylus and Mecistops were previously considered monotypic, but have recently been identified as consisting of three, two and two cryptic species, respectively. Mitochondrial cytochrome c oxidase subunit I (COI) new and published sequences from 310 wild‐caught specimens were compared with 71 US zoological specimens to identify (barcode) species. We also sequenced either nuclear lactate dehydrogenase A or an anonymous microsatellite flanking sequence in both wild and captive specimens to identify potential first‐generation intra‐generic hybridization in captive populations. The Osteolaemus COI barcoding gap was 7–9% sequence divergence. In contrast, the two African Crocodylus species had a 4.7% barcoding gap. These results, in addition to a previously published Mecistops barcoding gap (4.9%), support the use of barcoding as a tool for diagnosing African crocodile species in captive populations. Captive individuals from 14 collections in the US represented five of the seven putative African taxa. Nuclear heterozygosity at fixed polymorphisms differentiating species within genera suggested that 23% of the captive Osteolaemus samples were admixed O. tetraspis × O. sp. nov. cf. tetraspis – West Africa, while no ex situ hybrids were found for Crocodylus or Mecistops. Our results underscore the need to formally recognize divergent crocodile taxa, especially in light of regional threats, and for proper captive breeding management.