The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference

2016/01/05 by James E. Tarver, Mario dos Reis, Siavash Mirarab +10 · 1 citation
Earth and Planetary Sciences · Biochemistry, Genetics and Molecular Biology · #Evolution and Paleontology Studies #Genomics and Phylogenetic Studies #Genetic diversity and population structure #Biology #Xenarthra #Phylogenetic tree #Evolutionary biology #Phylogenetics #Molecular clock #Lineage (genetic) #Coalescent theory #Zoology #Genetics #Gene

paper · pdf · doi:10.1093/gbe/evv261

openalex publication_date 2016/01/05 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/06

Abstract

Placental mammals comprise three principal clades: Afrotheria (e.g., elephants and tenrecs), Xenarthra (e.g., armadillos and sloths), and Boreoeutheria (all other placental mammals), the relationships among which are the subject of controversy and a touchstone for debate on the limits of phylogenetic inference. Previous analyses have found support for all three hypotheses, leading some to conclude that this phylogenetic problem might be impossible to resolve due to the compounded effects of incomplete lineage sorting (ILS) and a rapid radiation. Here we show, using a genome scale nucleotide data set, microRNAs, and the reanalysis of the three largest previously published amino acid data sets, that the root of Placentalia lies between Atlantogenata and Boreoeutheria. Although we found evidence for ILS in early placental evolution, we are able to reject previous conclusions that the placental root is a hard polytomy that cannot be resolved. Reanalyses of previous data sets recover Atlantogenata + Boreoeutheria and show that contradictory results are a consequence of poorly fitting evolutionary models; instead, when the evolutionary process is better-modeled, all data sets converge on Atlantogenata. Our Bayesian molecular clock analysis estimates that marsupials diverged from placentals 157-170 Ma, crown Placentalia diverged 86-100 Ma, and crown Atlantogenata diverged 84-97 Ma. Our results are compatible with placental diversification being driven by dispersal rather than vicariance mechanisms, postdating early phases in the protracted opening of the Atlantic Ocean.

Citations

• Convenio de mugas en 1422 entre Ustés y Navascués
• Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses
• Eocene primates of South America and the African origins of New World monkeys
• A New Mammaliaform from the Early Jurassic and Evolution of Mammalian Characteristics
• A new scheme for the opening of the South Atlantic Ocean and the dissection of an Aptian salt basin
• Retroposed Elements as Archives for the Evolutionary History of Placental Mammals
• The Placental Mammal Ancestor and the Post–K-Pg Radiation of Placentals
• A web-database of mammalian morphology and a reanalysis of placental phylogeny
• Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
• The delayed rise of present-day mammals
• A Jurassic mammaliaform and the earliest mammalian evolutionary adaptations
• Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent
• Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals
• Transitional mammalian middle ear from a new Cretaceous Jehol eutriconodont
• Placental mammal diversification and the Cretaceous–Tertiary boundary
• PAML 4: Phylogenetic Analysis by Maximum Likelihood
• Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model
• Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
• Evolutionary Biology for the 21st Century
• Global continental and ocean basin reconstructions since 200Ma
• Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification
• Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny
• Has Vicariance or Dispersal Been the Predominant Biogeographic Force in Madagascar? Only Time Will Tell
• PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment
• A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera

Cited by

• Evolution of mammals [wikipedia]