Mitogenomic Crocodylia phylogeny and population structure of Crocodylus porosus including the extinct Seychelles crocodile

Abstract This study investigates the phylogenetic relationships of extant crocodiles and the population structure of the saltwater crocodile (Crocodylus porosus). We combined mitochondrial genomes from museum specimens with genetic data from modern samples to reconstruct the evolutionary history of the saltwater crocodile and clarify the identity of the extinct Seychelles crocodile. Mitochondrial genomes were sequenced for 11 museum specimens of Crocodylus halli, C. niloticus, C. novaeguineae, C. palustris and C. porosus, including the Seychelles crocodile. In addition, the mitochondrial control and ND4 regions were analysed for 187 and 13 C. porosus individuals, respectively. This study provides the most comprehensive Crocodylus phylogeny to date, establishes the phylogenetic placement of the extinct Seychelles crocodile as a distant population of the saltwater crocodile and provides no mitochondrial support for C. halli as a distinct species from C. novaeguineae. Nineteen haplotypes were identified among C. porosus samples, showing no clear mitochondrial geographic structure. However, this probably reflects the limited resolution of mitochondrial DNA rather than true genetic homogeneity, consistent with nuclear genomic studies revealing strong regional differentiation. Our results highlight the need for conservation strategies that recognize the broad genetic connectivity of C. porosus populations rather than emphasizing subspecies distinctions.