Journal
GENOME BIOLOGY AND EVOLUTION
Volume 8, Issue 2, Pages 330-344Publisher
OXFORD UNIV PRESS
DOI: 10.1093/gbe/evv261
Keywords
placental; phylogeny; mammalian; genome; microRNA; palaeontology
Categories
Funding
- Irish Research Council
- EU
- BBSRC [BB/J009709/1]
- Irish Research Council [GOIPG/2014/306]
- NERC [NE/L501554/1]
- Royal Society
- Leverhulme Trust
- U.S. National Institutes of Health [GM104318, GM103423]
- National Aeronautic and Space Agency
- U.S. National Science Foundation [1461364]
- Howard Hughes Medical Institute
- BBSRC [BB/J009709/1, BB/G006660/1, BB/J00538X/1] Funding Source: UKRI
- Biotechnology and Biological Sciences Research Council [BB/G006660/1, BB/J00538X/1, BB/J009709/1] Funding Source: researchfish
- Natural Environment Research Council [NE/C509974/1, 1374131] Funding Source: researchfish
- Direct For Biological Sciences
- Div Of Biological Infrastructure [1461364] Funding Source: National Science Foundation
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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 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 Bayesianmolecular 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.
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