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Evolutionary origin and phylogeny of the modern holocephalans (Chondrichthyes: Chimaeriformes): A mitogenomic perspective


Inoue, JG and Miya, M and Lam, K and Tay, B-H and Danks, JA and Bell, JD and Walker, TI and Venkatesh, B, Evolutionary origin and phylogeny of the modern holocephalans (Chondrichthyes: Chimaeriformes): A mitogenomic perspective, Molecular Biology and Evolution, 27, (11) pp. 2576-2586. ISSN 0737-4038 (2010) [Refereed Article]

DOI: doi:10.1093/molbev/msq147


With our increasing ability for generating whole-genome sequences, comparative analysis of whole genomes has become a powerful tool for understanding the structure, function, and evolutionary history of human and other vertebrate genomes. By virtue of their position basal to bony vertebrates, cartilaginous fishes (class Chondrichthyes) are a valuable outgroup in comparative studies of vertebrates. Recently, a holocephalan cartilaginous fish, the elephant shark, Callorhinchus milii (Subclass Holocephali: Order Chimaeriformes), has been proposed as a model genome, and low-coverage sequence of its genome has been generated. Despite such an increasing interest, the evolutionary history of the modern holocephalans-a previously successful and diverse group but represented by only 39 extant species-and their relationship with elasmobranchs and other jawed vertebrates has been poorly documented largely owing to a lack of well-preserved fossil materials after the end-Permian about 250 Ma. In this study, we assembled the whole mitogenome sequences for eight representatives from all the three families of the modern holocephalans and investigated their phylogenetic relationships and evolutionary history. Unambiguously aligned sequences from these holocephalans together with 17 other vertebrates (9,409 nt positions excluding entire third codon positions) were subjected to partitioned maximum likelihood analysis. The resulting tree strongly supported a single origin of the modern holocephalans and their sister-group relationship with elasmobranchs. The mitogenomic tree recovered the most basal callorhinchids within the chimaeriforms, which is sister to a clade comprising the remaining two families (rhinochimaerids and chimaerids). The timetree derived from a relaxed molecular clock Bayesian method suggests that the holocephalans originated in the Silurian about 420 Ma, having survived from the end-Permian (250 Ma) mass extinction and undergoing familial diversifications during the late Jurassic to early Cretaceous (170-120 Ma). This postulated evolutionary scenario agrees well with that based on the paleontological observations. © 2010 The Author.

Item Details

Item Type:Refereed Article
Keywords:divergence time; Elasmobranchii; Holocephali; mitochondrial genome; model organism; article; codon; comparative genomic hybridization; fish; fossil; gene function; gene sequence; gene structure; maximum likelihood method; molecular evolution; Fishes
Research Division:Agricultural, Veterinary and Food Sciences
Research Group:Fisheries sciences
Research Field:Fish physiology and genetics
Objective Division:Environmental Management
Objective Group:Marine systems and management
Objective Field:Marine biodiversity
UTAS Author:Bell, JD (Dr Justin Bell)
ID Code:82461
Year Published:2010
Web of Science® Times Cited:148
Deposited By:Sustainable Marine Research Collaboration
Deposited On:2013-02-04
Last Modified:2013-06-06

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