Phylogeographical analysis and phylogenetic inference based on the cytochrome b gene in the genus Caiman (Crocodylia: Alligatoridae) in Central and South America

Abstract

The genus Caiman is one of the most taxonomically conflictive among crocodilians due to different views about the phylogenetic position of Caiman crocodilus, which has four subspecies: Caiman crocodilus crocodilus, Caiman crocodilus fuscus, Caiman crocodilus chiapasius and Caiman crocodilus apaporiensis, but some studies recognize C. yacare as a subspecies of C. crocodilus or as a Caiman crocodilus/yacare complex. In Argentina, Caiman latirostris and Caiman yacare are present and included in sustainable use programs although they are scarcely studied at the genetic level. The present study had two main objectives: 1) to study the genetic diversity, structure, and phylogeny of C. yacare and C. latirostris in Argentina and, 2) to perform a phylogenetic analysis of the genus Caiman throughout its entire distribution. The results show high haplotype diversity for both species but low nucleotide diversity for C. latirostris. Phylogenetic analysis shows a clear separation between both species, but surprisingly, a well-differentiated clade belonging to the Chaco region is was observed. The phylogenetic analysis exhibited determined clades made up of the sequences of each Caiman species, with some inconsistencies: in the clade of C. crocodilus, one sequence of C. yacare is included, and one clade is observed including sequences from C. c. fuscus and C. c. chiapasius. These data indicate the need to undertake interdisciplinary studies to clarify the taxonomic status of these crocodilian species.