The interrelationships of placental mammals and the limits of phylogenetic inference

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

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)330-344
Number of pages15
JournalGenome biology and evolution
Volume8
Issue number2
DOIs
StatePublished - Jan 1 2016

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Mammals
mammal
mammals
phylogenetics
Dasypodidae
phylogeny
Elephantidae
Metatheria
Crowns
microRNA
Atlantic Ocean
Sloths
Xenarthra
nucleotides
Armadillos
Marsupialia
amino acids
genome
vicariance

Keywords

  • Genome
  • Mammalian
  • MicroRNA
  • Palaeontology
  • Phylogeny
  • Placental

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

Tarver, J. E., Dos Reis, M., Mirarab, S., Moran, R. J., Parker, S., O'Reilly, J. E., ... Pisani, D. (2016). The interrelationships of placental mammals and the limits of phylogenetic inference. Genome biology and evolution, 8(2), 330-344. https://doi.org/10.1093/gbe/evv261

The interrelationships of placental mammals and the limits of phylogenetic inference. / Tarver, James E.; Dos Reis, Mario; Mirarab, Siavash; Moran, Raymond J.; Parker, Sean; O'Reilly, Joseph E.; King, Benjamin L.; O'Connell, Mary J.; Asher, Robert J.; Warnow, Tandy; Peterson, Kevin J.; Donoghue, Philip C.J.; Pisani, Davide.

In: Genome biology and evolution, Vol. 8, No. 2, 01.01.2016, p. 330-344.

Research output: Contribution to journalArticle

Tarver, JE, Dos Reis, M, Mirarab, S, Moran, RJ, Parker, S, O'Reilly, JE, King, BL, O'Connell, MJ, Asher, RJ, Warnow, T, Peterson, KJ, Donoghue, PCJ & Pisani, D 2016, 'The interrelationships of placental mammals and the limits of phylogenetic inference', Genome biology and evolution, vol. 8, no. 2, pp. 330-344. https://doi.org/10.1093/gbe/evv261
Tarver JE, Dos Reis M, Mirarab S, Moran RJ, Parker S, O'Reilly JE et al. The interrelationships of placental mammals and the limits of phylogenetic inference. Genome biology and evolution. 2016 Jan 1;8(2):330-344. https://doi.org/10.1093/gbe/evv261
Tarver, James E. ; Dos Reis, Mario ; Mirarab, Siavash ; Moran, Raymond J. ; Parker, Sean ; O'Reilly, Joseph E. ; King, Benjamin L. ; O'Connell, Mary J. ; Asher, Robert J. ; Warnow, Tandy ; Peterson, Kevin J. ; Donoghue, Philip C.J. ; Pisani, Davide. / The interrelationships of placental mammals and the limits of phylogenetic inference. In: Genome biology and evolution. 2016 ; Vol. 8, No. 2. pp. 330-344.
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