Characterization of five complete Cyrtodactylus mitogenome structures reveals low structural diversity and conservation of repeated sequences in the lineage

Mitochondrial genomes (mitogenomes) of five Cyrtodactylus were determined. Their compositions and structures were similar to most of the available gecko lizard mitogenomes as 13 protein-coding, two rRNA and 22 tRNA genes. The non-coding control region (CR) of almost all Cyrtodactylus mitogenome structures contained a repeated sequence named the 75-bp box family, except for C. auribalteatus which contained the 225-bp box. Sequence similarities indicated that the 225-bp box resulted from the duplication event of 75-bp boxes, followed by homogenization and fixation in C. auribalteatus. The 75-bp box family was found in most gecko lizards with high conservation (55–75% similarities) and could form secondary structures, suggesting that this repeated sequence family played an important role under selective pressure and might involve mitogenome replication and the likelihood of rearrangements in CR. The 75-bp box family was acquired in the common ancestral genome of the gecko lizard, evolving gradually through each lineage by independent nucleotide mutation. Comparison of gecko lizard mitogenomes revealed low structural diversity with at least six types of mitochondrial gene rearrangements. Cyrtodactylus mitogenome structure showed the same gene rearrangement as found in most gecko lizards. Advanced mitogenome information will enable a better understanding of structure evolution mechanisms

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

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

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.

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

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

<p>(a) Mean Ln P(<i>K</i>) graph. (b) STRUCTURE bar plots depict the model-based clustering results for inferred <i>K</i> = 13. 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 A–M, 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

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