Transthyretin gene (TTR) intron 1 elucidates crocodylian phylogenetic relationships

Abstract

Transthyretin (TTR) is an attractive candidate for use in phylogenetic analysis because it is a short, single-copy nuclear gene with regions that are highly conserved across evolutionarily-divergent organisms from Xenopus laevis to Homo sapiens. To explore its utility as a phylogenetic marker, the complete intron one region (789–805 bp) was sequenced in 22 crocodylian species. Detailed analyses of intron 1 resolved the three expected lineages, Alligatorids, Crocodylids, and Gavialids, and offered additional evidence for the utility of synapomorphic indels in elucidating higher-level phylogenetic relationships. When used in conjunction with other genetic and morphological data sets, intron 1 should be a valuable tool in the investigation of other closely-related taxa.

Complete mitochondrial genome sequences of three Crocodylus species and their comparison within the Order Crocodylia

“…The monophyly of genus Crocodylus was not supported by some analyses whereas the complete mitochondrial genome analyses show a strong statistical support for the monophyletic assemblage of genus Crocodylus. Previous crocodilian phylogenetic studies show a monophyletic assemblage of New World crocodiles including C. moreletii and also indicate the close relationship of C. niloticus to New World crocodilians (Brochu, 2000;Willis, 2009). Whereas, this study shows the sister relationship between C. niloticus and C. moreletii as observed in our previous analyses.…”

“…The Order Crocodylia is an excellent model for evolutionary studies as the extant species represent both ancient as well as recent divergences (Brochu, 2003;Willis, 2009). The order consists of 23 species and according to the present molecular data the crocodilians are represented by two families, Alligatoridae and Crocodylidae.…”

Strong correlation between cross‐amplification success and genetic distance across all members of ‘True Salamanders’ (Amphibia: Salamandridae) revealed by Salamandra salamandra‐specific microsatellite loci

“…Glenn et al (1996) observed a decrease in cross-species amplification success between phylogenetic divergent source-target species pairs when studying the allelic diversity in Alligator microsatellite loci compared to other crocodilian species. Although this study was mainly based on the taxonomic status of the species, the general phylogeny of the order Crocodylia has recently been confirmed also on molecular grounds (Roos et al 2007;Willis 2009).…”

A phylogenetic hypothesis for Crocodylus (Crocodylia) based on mitochondrial DNA: Evidence for a trans-Atlantic voyage from Africa to the New World

“…Second, crown-group Crocodylus is a relatively young clade thought to have diversified no earlier than the Miocene (Brochu, 2000). Given the moderate evolutionary rates of nuclear genes that have been applied to crocodylian relationships, relatively few phylogenetically informative sites are apparent within Crocodylus, and inferred relationships vary widely in different nuclear gene trees (McAliley et al, 2006;Willis et al, 2007;Willis, 2009;Meganathan et al, 2010). Third, for most published datasets, the sampling of Crocodylus species has been incomplete (e.g., McAliley et al, 2006).…”