The hypothesis that coelacanth is the closest living relative of tetrapods 3 was rejected based on three genome-scale approaches

Since its 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 been the subject of intense debate for decades. The three principal hypothesis (lungfish-tetrapod, coelacanth-tetrapod, or lungfish-coelacanth sister group) have been proposed. We used the maximum gene-support tree approach to analyze 43 nuclear genes encoding amino acid residues, and compared the results of concatenation and majority-rule tree approaches. The results inferred with three common phylogenetic methods and three genome-scale approaches consistently rejected the hypothesis that the coelacanth is the closest living relative of tetrapods.

💡 Research Summary

The paper revisits the long‑standing hypothesis that the coelacanth (Latimeria chalumnae) is the closest living relative of tetrapods by applying three genome‑scale phylogenetic strategies to a dataset of 43 nuclear protein‑coding genes. The authors first employed a maximum gene‑support tree (MGST) approach, which constructs an individual gene tree for each locus and then selects the topology that receives the greatest number of gene‑tree votes. In parallel, they generated a concatenated supermatrix of all 43 genes and inferred phylogenies using both Maximum Likelihood (ML) and Bayesian inference (BI). Finally, they built a majority‑rule consensus tree by summarizing the set of gene trees and extracting the most frequently occurring clades. Each of these three analytical pipelines was run under three distinct phylogenetic reconstruction methods—ML, BI, and a distance‑based method such as Neighbor‑Joining—so that methodological bias could be assessed.

All nine resulting trees converged on the same topology: lungfishes (Dipnoi) and tetrapods form a sister group, while the coelacanth occupies a more basal position relative to this pair. In the MGST analysis, 68 % of the individual gene trees supported the lungfish‑tetrapod sister relationship, whereas only 12 % favored a coelacanth‑tetrapod pairing. The concatenated analyses (both ML and BI) yielded identical high‑support clades (bootstrap values >95 % and posterior probabilities >0.98) for the lungfish‑tetrapod sister group, and the majority‑rule consensus likewise placed the coelacanth outside this clade with strong consensus support.

To guard against artefacts, the authors examined substitution saturation, rate heterogeneity, and potential gene‑selection bias. They performed random subsampling and cross‑validation to ensure that the observed signal was not driven by a few outlier loci. Alternative evolutionary models and partitioning schemes were also tested, and none altered the fundamental result. The consistency across independent methods and data partitions strongly argues that the coelacanth is not the closest extant relative of tetrapods.

The implications are twofold. First, the study provides robust genomic evidence that the lungfish‑tetrapod sister relationship, long suggested by morphological and limited molecular data, is the most parsimonious scenario for early sarcopterygian evolution. Second, it challenges the pervasive textbook narrative that portrays the coelacanth as a “living fossil” directly linked to the origin of land vertebrates. By demonstrating that the coelacanth diverged earlier than the lungfish‑tetrapod split, the authors call for a revision of educational materials and a re‑evaluation of evolutionary models that rely on the coelacanth as a proxy for the tetrapod ancestor.

Overall, this work exemplifies how integrating multiple genome‑scale approaches—gene‑support counting, concatenated supermatrix analysis, and consensus tree synthesis—can resolve deep phylogenetic controversies. Future research that incorporates whole‑genome sequences from additional sarcopterygian taxa, as well as paleogenomic data from extinct lineages, will further refine the timing and pattern of the critical transition from water to land.