2012/08/28 by Sen Song, Liang Liu, Scott V. Edwards +1 · 497 citations
Biochemistry, Genetics and Molecular Biology · Earth and Planetary Sciences · Mathematics · #Biology #Clade #Coalescent theory #Concatenation (mathematics) #Evolution and Paleontology Studies #Evolutionary biology #Gene #Genetic diversity and population structure #Genetics #Genomics and Phylogenetic Studies #Mathematics #Phylogenetic tree #Phylogenetics #Phylogenomics
paper · pdf · doi:10.1073/pnas.1211733109
published in Proceedings of the National Academy of Sciences 109(37), 14942-14947 (National Academy of Sciences)
openalex publication_date 2012/08/28 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
The reconstruction of the Tree of Life has relied almost entirely on concatenation methods, which do not accommodate gene tree heterogeneity, a property that simulations and theory have identified as a likely cause of incongruent phylogenies. However, this incongruence has not yet been demonstrated in empirical studies. Several key relationships among eutherian mammals remain controversial and conflicting among previous studies, including the root of eutherian tree and the relationships within Euarchontoglires and Laurasiatheria. Both bayesian and maximum-likelihood analysis of genome-wide data of 447 nuclear genes from 37 species show that concatenation methods indeed yield strong incongruence in the phylogeny of eutherian mammals, as revealed by subsampling analyses of loci and taxa, which produced strongly conflicting topologies. In contrast, the coalescent methods, which accommodate gene tree heterogeneity, yield a phylogeny that is robust to variable gene and taxon sampling and is congruent with geographic data. The data also demonstrate that incomplete lineage sorting, a major source of gene tree heterogeneity, is relevant to deep-level phylogenies, such as those among eutherian mammals. Our results firmly place the eutherian root between Atlantogenata and Boreoeutheria and support ungulate polyphyly and a sister-group relationship between Scandentia and Primates. This study demonstrates that the incongruence introduced by concatenation methods is a major cause of long-standing uncertainty in the phylogeny of eutherian mammals, and the same may apply to other clades. Our analyses suggest that such incongruence can be resolved using phylogenomic data and coalescent methods that deal explicitly with gene tree heterogeneity.