There are different views about the relationship and evolution of reptiles and depending on the datasets used different phylogenetic relationships are found. Historically, morphological data has been used most, but more recently DNA or protein sequence data is the preferred source of information for phylogenetic analysis. Unfortunately, different genes evolve at different rates and thus trees derived from different data sets may result in contradictory phylogenetic hypotheses. For example, certain taxa (e.g., teiids) show a significant codon bias coupled with an increased relative rate of evolution of C-mos sequences compared to other squamates. This seems to distort attempts to use C-mos in phylogenetic analyses, both across squamates and within teiids (Harris 2003). Therefore, combined dataset using many sequences and/or morphological characters are usually most reliable.
The trees below have been derived from the combined analysis of mitochondrial protein coding genes and tRNAs.
Optimal phylogenetic hypothesis for representative lineages of Reptilia using a Bayesian inference approach. For this figure, branch lengths have been calculated using a GTR+gamma model, with a dataset including 11 protein coding genes and 19 tRNAs from mitochondria. Numbers in bold at internodes are divergence time estimates in millions of years before the present. Asterisks designate calibration points from the fossil record (see Benton, 1993; Carroll, 1988). Numbers in italics are nonparametric bootstrapped Bayesian posterior probabilities (BPP) based on 100 replicates and 200,000 generations (see text). Bayesian posterior probabilities (PP) for nodes are underlined (from Rest et al. 2003).
Reptile Phylogeny
The mitochondrial genomes of the iguana (Iguana iguana) and the caiman (Caiman crocodylus): implications for amniote phylogeny.
Janke A,
Erpenbeck D,
Nilsson M,
Arnason U.
Department of Genetics, University of Lund, Sweden.
The complete mitochondrial genomes of two reptiles, the common iguana (Iguana iguana) and the caiman (Caiman crocodylus), were sequenced in order to investigate phylogenetic questions of tetrapod evolution. The addition of the two species allows analysis of reptilian relationships using data sets other than those including only fast-evolving species. The crocodilian mitochondrial genomes seem to have evolved generally at a higher rate than those of other vertebrates. Phylogenetic analyses of 2889 amino-acid sites from 35 mitochondrial genomes supported the bird-crocodile relationship, lending no support to the Haematotherma hypothesis (with birds and mammals representing sister groups).
The complete mitochondrial genome of Alligator mississippiensis and the separation between recent archosauria (birds and crocodiles)
A Janke and U Arnason
Department of Genetics, University of Lund, Sweden.
The complete mitochondrial genome of the alligator, Alligator mississippiensis, was sequenced. The size of the molecule is 16,642 nucleotides. Previously reported rearrangements of tRNAs in crocodile mitochondrial genomes were confirmed and, relative to mammals, no other deviations of gene order were observed. The analysis of protein-coding genes of the alligator showed an evolutionary rate that is roughly the same as in mammals. Thus, the evolutionary rate in the alligator is faster than that in birds as well as that in cold-blooded vertebrates. This contradicts hypotheses of constant body temperatures or high metabolic rate being correlated with elevated molecular evolutionary rates. It is commonly acknowledged that birds are the closest living relatives to crocodiles. Birds and crocodiles represent the only archosaurian survivors of the mass extinction at the Cretaceous/Tertiary boundary. On the basis of mitochondrial protein- coding genes, the Haemothermia hypothesis, which defines birds and mammals as sister groups and thus challenges the traditional view, could be rejected. Maximum-likelihood branch length data of amino acid sequences suggest that the divergence between the avianand crocodilian lineages took place at approximately equal to 254MYA
