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Rooting the placental tree with better models and microRNAs (free pdf)



A new neontological paper that might be of interest to the list:

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 Biol Evol
doi:10.1093/gbe/evv261
http://gbe.oxfordjournals.org/content/early/2016/01/04/gbe.evv261.long

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.


Note that this is a long-awaited paper whose conclusions were
initially expected to be much more radical (at least by some of its
authors), as documented in the following Nature news article:

http://www.nature.com/news/phylogeny-rewriting-evolution-1.10885

-- 
David Černý