title: Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics.
abstract: In recent articles published in Molecular Phylogenetics and Evolution, Mark Springer and John Gatesy (S&G) present numerous criticisms of recent implementations and testing of the multispecies coalescent (MSC) model in phylogenomics, popularly known as "species tree" methods. After pointing out errors in alignments and gene tree rooting in recent phylogenomic data sets, particularly in Song et al. (2012) on mammals and Xi et al. (2014) on plants, they suggest that these errors seriously compromise the conclusions of these studies. Additionally, S&G enumerate numerous perceived violated assumptions and deficiencies in the application of the MSC model in phylogenomics, such as its assumption of neutrality and in particular the use of transcriptomes, which are deemed inappropriate for the MSC because the constituent exons often subtend large regions of chromosomes within which recombination is substantial. We acknowledge these previously reported errors in recent phylogenomic data sets, but disapprove of S&G's excessively combative and taunting tone. We show that these errors, as well as two nucleotide sorting methods used in the analysis of Amborella, have little impact on the conclusions of those papers. Moreover, several concepts introduced by S&G and an appeal to "first principles" of phylogenetics in an attempt to discredit MSC models are invalid and reveal numerous misunderstandings of the MSC. Contrary to the claims of S&G we show that recent computer simulations used to test the robustness of MSC models are not circular and do not unfairly favor MSC models over concatenation. In fact, although both concatenation and MSC models clearly perform well in regions of tree space with long branches and little incomplete lineage sorting (ILS), simulations reveal the erratic behavior of concatenation when subjected to data subsampling and its tendency to produce spuriously confident yet conflicting results in regions of parameter space where MSC models still perform well. S&G's claims that MSC models explain little or none (0-15%) of the observed gene tree heterogeneity observed in a mammal data set and that MSC models assume ILS as the only source of gene tree variation are flawed. Overall many of their criticisms of MSC models are invalidated when concatenation is appropriately viewed as a special case of the MSC, which in turn is a special case of emerging network models in phylogenomics. We reiterate that there is enormous promise and value in recent implementations and tests of the MSC and look forward to its increased use and refinement in phylogenomics.
authors.affiliation: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Electronic address: sedwards@fas.harvard.edu.
authors.forename: Scott V
authors.initials: SV
authors.lastname: Edwards
authors.affiliation: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Zhenxiang
authors.initials: Z
authors.lastname: Xi
authors.affiliation: Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.
authors.forename: Axel
authors.initials: A
authors.lastname: Janke
authors.affiliation: Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA.
authors.forename: Brant C
authors.initials: BC
authors.lastname: Faircloth
authors.affiliation: Moore Laboratory of Zoology, Occidental College, Los Angeles, CA 90041, USA.
authors.forename: John E
authors.initials: JE
authors.lastname: McCormack
authors.affiliation: Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA.
authors.forename: Travis C
authors.initials: TC
authors.lastname: Glenn
authors.affiliation: College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
authors.forename: Bojian
authors.initials: B
authors.lastname: Zhong
authors.affiliation: Department of Biochemistry and Molecular Biology & Tianjin Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China.
authors.forename: Shaoyuan
authors.initials: S
authors.lastname: Wu
authors.affiliation: Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA.
authors.forename: Emily Moriarty
authors.initials: EM
authors.lastname: Lemmon
authors.affiliation: Department of Scientific Computing, Florida State University, Tallahassee, FL 32306, USA.
authors.forename: Alan R
authors.initials: AR
authors.lastname: Lemmon
authors.affiliation: Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98195, USA.
authors.forename: Adam D
authors.initials: AD
authors.lastname: Leaché
authors.affiliation: Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
authors.forename: Liang
authors.initials: L
authors.lastname: Liu
authors.affiliation: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Charles C
authors.initials: CC
authors.lastname: Davis
mesh_terms: D000818:Animals; D003198:Computer Simulation; D019143:Evolution, Molecular; D049810:Genetic Speciation; D023281:Genomics / Q000379:methods*; D019684:Magnoliopsida / Q000145:classification / Q000235:genetics; D008322:Mammals / Q000145:classification / Q000235:genetics; D008957:Models, Genetic; D010802:Phylogeny; D011995:Recombination, Genetic