Fig 1.
Haplotype network based on sequence data for the mitochondrial DNA D-loop region of Siamese and Saltwater crocodiles constructed using statistical parsimony with the Templeton, Crandall, and Sing (TCS) algorithm.
The numbers of individuals that possessed a haplotype is indicated by the different colors inside the circles. Inferred but unsampled haplotypes are indicated by slashes. Missing haplotypes are indicated by a black circle. Detailed information for all crocodile individuals is presented in S1 Table.
Fig 2.
Phylogenetic relationships among mitochondrial DNA D-loop region sequences inferred using Bayesian inference analysis.
Support values at each node are the Bayesian posterior probability. Detailed information for all crocodile individuals is presented in S1 Table.
Fig 3.
Microsatellite-based phylogenetic relationships for 52 Siamese crocodiles and 17 Saltwater crocodiles generated by the unweighted pair group with arithmetic mean (UPGMA) clustering method.
Support values at each node are bootstrap values. “*” indicates a bootstrap value < 50%. The genetic similarity matrices are shown by Jaccard's coefficient. Detailed information for all crocodile individuals is presented in S1 Table.
Fig 4.
Principal component analysis of 69 crocodiles (52 Siamese crocodiles and 17 Saltwater crocodiles) using microsatellite data across 22 loci.
Blue diamonds indicate Siamese crocodile samples. Red diamonds indicate Saltwater crocodile samples. The yellow diamond indicates CSI17, which might be a Cuban crocodile or a hybrid between Siamese and Cuban crocodiles.
Fig 5.
Population structure of Siamese and Saltwater crocodiles from 69 crocodile individuals.
(a) Evanno's ΔK graph. (b) STRUCTURE bar plots depicting the model-based clustering results for inferred K = 2. Inferred genetic clusters are displayed as different colors. Each vertical bar on the x-axis represents an individual, and the y-axis presents the proportion of membership (posterior probability) in each genetic cluster. Recovered crocodile species, including clusters α and β, are superimposed on the plot, with black vertical lines indicating the boundaries. Detailed information for all crocodile individuals is presented in S1 Table.
Fig 6.
Population structure of Siamese and Saltwater crocodiles from 69 crocodile individuals.
(a) Mean Ln P(K) graph. (b) STRUCTURE bar plots depict the model-based clustering results for inferred K = 13. Inferred genetic clusters are displayed as different colors. Each vertical bar on the x-axis represents an individual, and the y-axis presents the proportion of membership (posterior probability) in each genetic cluster. Recovered crocodile species, including clusters A–M, are superimposed on the plot, with black vertical lines indicating the boundaries. Detailed information for all crocodile individuals is presented in S1 Table.
Fig 7.
Observed distribution of pairwise relatedness for 52 Siamese crocodiles and 17 Saltwater crocodiles plotted against expected distributions.