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 teleost species form a monophyletic group with 100% support value. The previous tree, based on mitochondrial data, was significantly rejected by an approximately unbiased test (AU test, p = 0). The time of divergence between lungfish and tetrapods was estimated to be 391.8 Ma and the divergence of bichir from pufferfish and medaka was estimated to be 330.6 Ma. These estimates closely match the fossil record. In conclusion, our phylogenomic study successfully resolved the relationship of basal jawed vertebrates based on transtriptomes, EST and whole genome sequences.
Highlights
The traditional relationships among jawed vertebrates have been widely accepted by vertebrate zoologists for a long time
Our phylogenetic analysis supported the traditional view of relationships among basal jawed vertebrates (Figure 1a)
The lungfish–tetrapods divergence was estimated at 391.8 Ma when left unconstrained
Summary
The traditional relationships among jawed vertebrates have been widely accepted by vertebrate zoologists for a long time. (Figure 1a), extant jawed vertebrates (gnathostomes) were divided into Chondrichthyes (cartilaginous fishes) and the Osteichthyes (bony vertebrates). Osteichthyes are divided into Actinopterygii (rayfinned fishes) and Sarcopterygii (lobe-finned fishes and tetrapods) based on the attachment of their fins to their bodies. The fins of lobe-finned fishes are connected to the body via a single radial bone, which allows more flexible movement [2,3]. The Actinopterygii is the other major group of Osteichthyes. It comprises about half of all extant vertebrate species. The four major lineages of basal actinopterygians, Polypteriformes, Acipenseriformes, Lepisosteiformes, and Amiiformes are called ‘‘ancient fish’’. Polypteriformes is regarded as the most basal lineage of Actinopterygii [4,5,6,7]
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