Phylogenetic analysis of colubrid snakes based on 12S rDNA reveals distinct lineages of Dendrelaphis pictus (Gmelin, 1789) populations in Sumatra and Java

Abstract

Nugraha FAD, Fatchiyah F, Smith EN, Nia Kurniawan N. 2018. Phylogenetic analysis of colubrid snakes based on 12S rDNA reveals distinct lineages of Dendrelaphis pictus (Gmelin, 1789) populations in Sumatra and Java. Biodiversitas 19: 303-310. The phylogenetic relationship among the major colubrid snakes, particularly those of the subfamily Colubrinae, has been the subject of much debate. Also, there was limited data on the molecular relationships of Sundaland colubrid snakes. This study aimed to examine the relationships among colubrid snakes from Sumatra and Java based on fragments of 12S rDNA gene. We sequenced 17 specimens of colubrid snakes representing 5 genera and 2 subfamilies: Colubrinae and Ahaetullinae. We used maximum likelihood, maximum parsimony and Bayesian inference methods for inferring phylogenetic relationships. The result of our phylogenetic analyses is in line with the previous findings for the separation between Colubrinae and Ahaetullinae. Interestingly, we found two distinct clades of Dendrelaphis pictus species with the high genetic divergence between them where D. pictus from Sumatra and West Java separated from Central and East Java clade. Our divergence time estimation showed that the differentiation between these clades of D. pictus occurred in the late Miocene epoch (8.9 Ma) when Sumatra and Java separated after being inundated in the early Miocene epoch.

First record of Ahaetullamycterizans (Linnaeus, 1758) (Serpentes: Colubridae) from the Lesser Sunda region, Indonesia, based on molecular and morphological identification

“…The divergence time estimates indicated that the genus Ahaetulla started to diverge as A. prasina and A. mycterizans in the late Oligocene, approximately 24.9 Ma. Our results were in agreement with those of Nugraha et al (2018) that the subfamily Ahaetullinae diversified during the late Oligocene, at about 24 Ma. The late Oligocene was the period when Sunda Shelf lakes were connected to the sea and were brackish, which may have facilitated many migrations of terrestrial fauna (Hall, 2013).…”

“…Malang, East Java KY700863 (Nugraha et al, 2018) Ptyas mucosa Malang, East Java KY700867 (Nugraha et al, 2018) using MrBayes software (Ronquist and Huelsenbeck, 2003) using Markov Chain Monte Carlo (MCMC) estimated for 5 million generations. The most appropriate sequence evolution models were selected using Akaike Information Criterion (AIC) for ML and BI.…”

“…The divergence time was estimated by using BEAST (Drummond et al, 2012) software under the Hasegawa-Kishino-Yano model of DNA evolution with the uncorrelated log-normal relaxed clock rate model (Drummond et al, 2006). The estimated time divergence between C. ornata and P. mucosa at 23.1 Mya and between P. mucosa and D. pictus at 37.6 Mya (Nugraha et al, 2018) were used for the external calibration. The estimated time divergence of West Java and Lampung separation was employed for the internal calibration.…”

“…Figueroa et al (2016) used mitochondrial DNA including the 12S-rDNA gene as barcodes to determine the phylogenetic relationship among 1592 snakes of the Colubridae family. Furthermore, the phylogenetic analysis of the snake species of the family Colubridae has not only contributed to the evaluation of snake diversity, but also to the evaluation of geological history through studies on estimated genetic divergence time (Takeuchi et al, 2011;Nugraha et al, 2018). This is the first study of the genus Ahaetulla in Sundaland and the Lesser Sunda region using the 12S-rDNA gene to analyze phylogenetic relationships, to construct the haplotype network, and to estimate the time of divergence.…”

First Insights on the Karyotype Diversification of the Endemic Malagasy Leaf-Toed Geckos (Squamata: Gekkonidae: Uroplatus)

“…A notable exception is represented by the specimens GA 328 and GA 329, which are here reported as U. prope guentheri ( Table 1 ) based on their maximum identity score (96.8%) with a previously deposited homologous sequence of U. guentheri , (AN EU596688). Considering the pairwise distance threshold usually used for species identification in squamates for the 12S (3–4%) see e.g., [ 30 , 31 ], it is therefore possible that the samples GA 328 and GA 329 represent an undescribed lineage of Uroplatus , but more focused morphological and molecular analyses employing a combination of mitochondrial and nuclear markers should be performed to better assess the taxonomic placement of these samples. This result is not surprising considering the significant number of newly described Uroplatus species in the last years and the molecular identification of different undescribed lineages (e.g., [ 20 , 23 ]).…”