Basal jawed vertebrate phylogenomics using transcriptomic data from Solexa sequencing.

PloS One
Ming ChenShunping He

Abstract

The traditionally accepted relationships among basal jawed vertebrates have been challenged by some molecular phylogenetic analyses based on mitochondrial sequences. Those studies split extant gnathostomes into two monophyletic groups: tetrapods and piscine branch, including Chondrichthyes, Actinopterygii and sarcopterygian fishes. Lungfish and bichir are found in a basal position on the piscine branch. Based on transcriptomes of an armored bichir (Polypterus delhezi) and an African lungfish (Protopterus sp.) we generated, expressed sequences and whole genome sequences available from public databases, we obtained 111 genes to reconstruct the phylogenetic tree of basal jawed vertebrates and estimated their times of divergence. Our phylogenomic study supports the traditional relationship. We found that gnathostomes are divided into Chondrichthyes and the Osteichthyes, both with 100% support values (posterior probabilities and bootstrap values). Chimaeras were found to have a basal position among cartilaginous fishes with a 100% support value. Osteichthyes were divided into Actinopterygii and Sarcopterygii with 100% support value. Lungfish and tetrapods form a monophyletic group with 100% posterior probability. Bichir and two tele...Continue Reading

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Mar 10, 2015·Zoological Journal of the Linnean Society·Martin D Brazeau, Matt Friedman
Jun 27, 2017·The Journal of Comparative Neurology·Jesús M López, Agustín González
Mar 10, 2018·The Journal of Comparative Neurology·Ruth MoronaAgustín González
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Mar 13, 2014·Biological Reviews of the Cambridge Philosophical Society·Lauren C Sallan
Jun 1, 2021·Brain, Behavior and Evolution·Rudolf Nieuwenhuys

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Methods Mentioned

BETA
RNA-Seq

Software Mentioned

BioPerl
FigTree
GeneWise
Perl script
Ensembl
MUSCLE
Tracer
TreeAnnotator
TBLASTN
MrBayes

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