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Mol Phylogenet Evol. 2009 Nov;53(2):479-91. doi: 10.1016/j.ympev.2009.06.018. Epub 2009 Jul 3.

A mitogenomic perspective on the phylogeny and biogeography of living caecilians (Amphibia: Gymnophiona).

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Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720-3160, USA.


The caecilians, members of the amphibian Order Gymnophiona, are the least known Order of tetrapods, and their intra-relationships, especially within its largest group, the Family Caeciliidae (57% of all caecilian species), remain controversial. We sequenced thirteen complete caecilian mitochondrial genomes, including twelve species of caeciliids, using a universal primer set strategy. These new sequences, together with eight published caecilian mitochondrial genomes, were analyzed by maximum parsimony, partitioned maximum-likelihood and partitioned Bayesian approaches at both nucleotide and amino acid levels, to study the intra-relationships of caecilians. An additional multiple gene dataset including most of the caecilian nucleotide sequences currently available in GenBank produced phylogenetic results that are fully compatible with those based on the mitogenomic data. Our phylogenetic results are summarized as follow. The caecilian family Rhinatrematidae is the sister taxon to all other caecilians. Beyond Rhinatrematidae, a clade comprising the Ichthyophlidae and Uraeotyphlidae is separated from a clade containing all remaining caecilians (Scolecomorphidae, Typhlonectidae and Caeciliidae). Within this large clade, Scolecomorphidae is the sister taxon of Typhlonectidae and Caeciliidae but this placement did not receive strong support in all analyses. Caeciliidae is paraphyletic with regard to Typhlonectidae, and can be divided into three well-supported groups: Caeciliidae group 1 contains the African caeciliids Boulengerula and Herpele; Caeciliidae group 2 contains Caecilia and Oscaecilia and it is the sister taxon of Typhlonectidae; Caeciliidae group 3 comprises the remaining species of caeciliids. The mitochondrial genome data were also used to calculate divergence times for caecilian evolution using the penalized likelihood method implemented in the program R8S. The newly obtained dating results are compatible with (but a little older than) previous time estimates mainly based on nuclear gene data. The mitogenomic time tree of caecilians suggests that the initial diversification of extant caecilians most probably took place in Late Triassic about 228 (195-260) Ma. Caeciliids currently distributed in India and the Seychelles diverged from their African and American relatives most probably in Late Jurassic about 138 (112-165) Ma, fairly close to the time (approximately 130Ma) when Madagascar-India-Seychelles separated from Africa and South America. The split between the Indian caeciliid Gegeneophis and Seychellean caeciliids occurred about 103 (78-125) Ma, predated the rifting of India and the Seychelles (approximately 65Ma).

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