43 genes support the lungfish-coelacanth grouping related to the closest living relative of tetrapods with the Bayesian method under the coalescence model

Abstract

BackgroundSince the discovery of the "living fossil" in 1938, the coelacanth (Latimeria chalumnae) has generally been considered to be the closest living relative of the land vertebrates, and this is still the prevailing opinion in most general biology textbooks. However, the origin of tetrapods has not been resolved for decades. Three principal hypotheses (lungfish-tetrapod, coelacanth-tetrapod, or lungfish-coelacanth sister group) have been proposed.FindingsWe used the Bayesian method under the coalescence model with the latest published program (Bayesian Estimation of Species Trees, or BEST) to perform a phylogenetic analysis for seven relevant taxa and 43 nuclear protein-coding genes with the jackknife method for taxon sub-sampling. The lungfish-coelacanth sister group was consistently reconstructed with the Bayesian method under the coalescence model in 17 out of 21 taxon sets with a Bayesian posterior probability as high as 99%. Lungfish-tetrapod was only inferred from BCLS and BACLS. Neither coelacanth-tetrapod nor lungfish-coelacanth-tetrapod was recovered out of all 21 taxon sets.ConclusionsOur results provide strong evidence in favor of accepting the hypothesis that lungfishes and coelacanths form a monophyletic sister-group that is the closest living relative of tetrapods. This clade was supported by high Bayesian posterior probabilities of the branch (a lungfish-coelacanth clade) and high taxon jackknife supports.

Olfactory Projections in the Lepidosirenid Lungfishes

“…Today, only three members of the lobe-finned fish radiation are still extant: coelacanths, lungfishes and the limbed vertebrates (tetrapods). Recent phylogenetic molecular data indicate that lungfishes are either the sister group of coelacanths [Zardoya et al, 1998;Shan and Gras, 2011] or that they are the sister group of limbed vertebrates [Tohyama et al, 2000;Venkatesh et al, 2001;Brinkmann et al, 2004]. Recent immunohistochemical and hodological data [González and Northcutt, 2009;Northcutt, 2009;González et al, 2010, Northcutt andWesthoff, 2011] reveal that the brains of lungfishes and limbed vertebrates share a large number…”

The Relationship between Branchiosomatic and Pulmosomatic Indices in the African Lungfish, Protopterus Annectens of Anambra River, Nigeria

“…Some evolved leg-like fins which they could use to crawl from one drying out pond into another that still had water in it. Thus, at this period, before the splitting of Pangaea, an extinct Crossopterygian group related to modern lungfish evolved into amphibians and eventually all tetrapods (Randall et al, 1981;Brinkmann et al, 2004;Shan and Gras, 2011). This helps to explain the homology between many organs of lungfish with those of amphibians, indicating a closer relationship between these two groups than can be revealed by palaeontological or other physiological or genetic studies (King et al, 2011;Shan and Gras,2011).…”

“…The Devonian period or the Age of Fishes was a time of violent alternation of seasons (Caroll, 1997;Ahlberg et al, 2003;King et al, 2011;Shan and Gras, 2011). There were wet seasons alternating with times of severe drought (Randall et al, 1981;Carroll, 1997).…”

Positive selection effects on the biochemical properties of fish pyroglutamylated RFamide peptide receptor (QRFPR)

“…The coelacanth Latimeria has been designated as a "living fossil" because the lineage disappeared from the fossil record in the Cretaceous period, about 80 million years ago (Pyron 2010). Together with the lungfishes, the coelacanth is considered the closest living relative of the tetrapods (Shan & Gras 2011). Thus, Latimeria harbours a key position in the evolution of vertebrates, including mammals.…”