The interrelationships of placental mammals and the limits of phylogenetic inference

James E Tarver*, Mario dos Reis, Siavash Mirarab, Raymond Moran, Sean Parker, Joseph O'Reilly, Benjamin L. King, Mary J O'Connell, Robert J. Asher, Tandy Warnow, Kevin J Peterson, Philip C J Donoghue, Davide Pisani

*Corresponding author for this work

Research output: Contribution to journalArticle (Academic Journal)peer-review

136 Citations (Scopus)
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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 dataset, microRNAs, and the reanalysis of the three largest previously published amino-acid datasets, 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 datasets recover Atlantogenata + Boreoeutheria and show that contradictory results are a consequence of poorly fitting evolutionary models; instead, when the evolutionary process is better-modelled, all datasets 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.
Original languageEnglish
Pages (from-to)330-344
Number of pages15
JournalGenome Biology and Evolution
Issue number2
Early online date8 Jan 2016
Publication statusPublished - Feb 2016

Structured keywords

  • MSc Palaeobiology


  • placental
  • phylogeny
  • mammalian
  • genome
  • microRNA
  • palaeontology


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  • HPC (High Performance Computing) Facility

    Sadaf R Alam (Manager), Steven A Chapman (Manager), Polly E Eccleston (Other), Simon H Atack (Other) & D A G Williams (Manager)

    Facility/equipment: Facility

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