Genetic Characterization of Caiman crocodilus (Crocodilia: Alligatoridae) on Gorgona Island, Colombia

Abstract

This study examines the genetic variation and structure of the spectacled caiman (Caiman crocodilus) on Gorgona Island, Colombia, compared to continental populations. We analyzed 178 partial Cytochrome b gene sequences, most of which were obtained from GenBank, and identified 23 haplogroups, with five of these specifically found on the Island. Phylogenetic analysis using maximum likelihood placed C. crocodilus, including the Gorgona Island population, in a distinct monophyletic group. Genetic structure analysis identified two main clusters, with Gorgona Island caimans primarily assigned to the Trans-Andean cluster. The haplogroup network illustrates the two major groups, with a maximum of 12 mutational steps between them. Additionally, Tajima's D statistic suggests an excess of rare alleles in the spectacled caiman. Genetic differentiation across regions suggests historical isolation, likely shaped by geographical barriers and limited gene flow. The distinct genetic patterns of island populations highlight their disparity in terms of evolutionary dynamics and conservation importance. Further genomic analysis is recommended to explore demographic history. Conservation strategies should prioritize the maintenance of genetic diversity to mitigate the effects of isolation, while also incorporating insights from the species' biogeographic history. Our findings highlight the unique contribution of the small population in Gorgona Island to the species' spatial genetic structure.

Keywords: genetic variation; haplogroups; island conservation; phylogenetic; spectacled caiman.

Figure 1

(a) Locations where partial mtDNA sequences were obtained for Caiman crocodilus (from our study and GenBank) Green: Mesoamerica, Red: Gorgona, Blue-Magenta: Cis-Andean (Perú, Brazil, Colombia: Palmarito), Yellow: Trinidad and Tobago, and Magenta: Trans-Andean (Colombia: Chocó-Magdalena). (b) Haplogroup network based on partial Cyt b gene sequences. In the network, each color corresponds to a DNA sequence found at a specific location on the map, and circle sizes are proportional to the sample size.

Figure 2

Spatial assignment of Caiman crocodilus mtDNA partial sequences based on posterior probabilities from Geneland analysis. The map illustrates the degree of individual assignment to the Pacific Domain biogeographic region (Trans-Andean), as defined by Morrone [27]. Darker shades of orange represent higher probabilities of assignment to this region.

Figure 3

Mean ratio of non-synonymous to synonymous substitutions (dN/dS) in the mitochondrial Cyt b gene fragment across five populations. Dashed line: value expected under neutrality. TRA: Trans-Andean, CIS: Cis-Andean, GOR: Gorgona island, MES: Mesoamerican, T&T: Trinidad and Tobago.

Figure 4

Gene tree reconstruction showing the relationships among partial Cyt b sequences from Caiman crocodilus individuals sampled across their distribution, from Mexico to Brazil, including the study population from Gorgona Island. The method employed here is maximum likelihood (ML), with bootstrap support for groupings indicated by coloration gradient as per the figure’s scale.