Basal Jawed Vertebrate Phylogenomics Using Transcriptomic Data from Solexa Sequencing

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.

Identification of Striatal and Pallidal Regions in the Subpallium of Anamniotes

“…Lungfishes comprise (along with the coelacanths) the only extant representatives of the lobe-finned fishes and are considered the closest living relatives of tetrapods [Brinkmann et al, 2004;Chen et al, 2012]. In a recent study, the organization of the telencephalon in lungfishes was analyzed by combined immunohistochemistry in specimens of Protopterus dolloi and Neoceratodus forsteri [González and Northcutt, 2009].…”

Conserved localization of Pax6 and Pax7 transcripts in the brain of representatives of sarcopterygian vertebrates during development supports homologous brain regionalization

“…In addition, data are presented for the first time on the distribution of these transcription factors in the brain of lungfishes ( Neoceratodus forsteri ), the closest living relatives of tetrapods (Brinkmann et al, 2004; Chen et al, 2012; Amemiya et al, 2013). We selected Pax6 and Pax7 because, as previously mentioned, several studies in different species had previously shown that they are widely expressed in distinct brain regions.…”

Ancient Grandeur of the Vertebrate Neuropeptide Y System Shown by the Coelacanth Latimeria chalumnae

“…Recent data suggest that the coelacanths are slightly more closely related to the lungfishes than either of these groups is to tetrapods (Shan and Gras, 2011). The Actinopterygii-Sarcopterygii divergence took place approximately 424 million years ago (Mya) according to a recent estimate based on molecular data (Chen et al, 2012). The coelacanth and tetrapod lineages may have parted only a few tens of millions of years later, well before the split of the amphibian and amniote lineages approximately 350 Mya.…”