Supplementary file

Supplementary file includes supplementary figures and tables, which are relevant to publication. Please note that the supplementary tables included in this PDF are also uploaded separately, as .xlsx files

Snakes in this study

Snake samples (figure/species) used in this study

Table_S5

Frequencies of nonsynonymous/synonymous substitution ratios (Ka/Ks) in exon 11 of the CTNNB1 gene among eight snake species. The CTNNB1W gene is shown above the diagonal with the CTNNB1Z gene below the diagonal. Table is also available in PDF format in the "Supplementary file" PD

Table S1

Species and nucleotides sequences of the CTNNB1 gene used in this study. Table is also available in PDF format in the "Supplementary file" PD

Table_S4

Frequencies of synonymous and nonsynonymous substitutions in the exon 11 of female-derived CTNNB1Z sequences among eight snake species. Ks values are shown above the diagonal, and Ka values are shown below the diagonal. Standard errors are indicated in all values. Table is also available in PDF format in the "Supplementary file" PD

Table_S2

Pair-wise comparison of amino acid sequence identities (%) of CTNNB1W among eight snake species. Table is also available in PDF format in the "Supplementary file" PD

Population structure of Siamese and Saltwater crocodiles from 69 crocodile individuals.

<p>(a) Evanno's Δ<i>K</i> graph. (b) STRUCTURE bar plots depicting the model-based clustering results for inferred <i>K</i> = 2. Inferred genetic clusters are displayed as different colors. Each vertical bar on the <i>x</i>-axis represents an individual, and the <i>y</i>-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 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184526#pone.0184526.s002" target="_blank">S1 Table</a>.</p

Microsatellite-based phylogenetic relationships for 52 Siamese crocodiles and 17 Saltwater crocodiles generated by the unweighted pair group with arithmetic mean (UPGMA) clustering method.

<p>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 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184526#pone.0184526.s002" target="_blank">S1 Table</a>.</p

Observed distribution of pairwise relatedness for 52 Siamese crocodiles and 17 Saltwater crocodiles plotted against expected distributions.

<p>Observed distribution of pairwise relatedness for 52 Siamese crocodiles and 17 Saltwater crocodiles plotted against expected distributions.</p

High genetic diversity and demographic history of captive Siamese and Saltwater crocodiles suggest the first step toward the establishment of a breeding and reintroduction program in Thailand

<div><p>The Siamese crocodile (<i>Crocodylus siamensis</i>) and Saltwater crocodile (<i>C</i>. <i>porosus</i>) are two of the most endangered animals in Thailand. Their numbers have been reduced severely by hunting and habitat fragmentation. A reintroduction plan involving captive-bred populations that are used commercially is important and necessary as a conservation strategy to aid in the recovery of wild populations. Here, the genetic diversity and population structure of 69 individual crocodiles, mostly members of captive populations, were analyzed using both mitochondrial D-loop DNA and microsatellite markers. The overall haplotype diversity was 0.924–0.971 and the mean expected heterozygosity across 22 microsatellite loci was 0.578–0.701 for the two species. This agreed with the star-like shaped topology of the haplotype network, which suggests a high level of genetic diversity. The mean ratio of the number of alleles to the allelic range (<i>M</i> ratio) for the populations of both species was considerably lower than the threshold of 0.68, which was interpreted as indicative of a historical genetic bottleneck. Microsatellite markers provided evidence of introgression for three individual crocodiles, which suggest that hybridization might have occurred between <i>C</i>. <i>siamensis</i> and <i>C</i>. <i>porosus</i>. D-loop sequence analysis detected bi-directional hybridization between male and female individuals of the parent species. Therefore, identification of genetically non-hybrid and hybrid individuals is important for long-term conservation management. Relatedness values were low within the captive populations, which supported their genetic integrity and the viability of a breeding and reintroduction management plan. This work constitutes the first step in establishing an appropriate source population from a scientifically managed perspective for an <i>in situ</i>/<i>ex situ</i> conservation program and reintroduction of crocodile individuals to the wild in Thailand.</p></div