Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics.


: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.


Mol Phylogenet Evol


Edwards SV,Xi Z,Janke A,Faircloth BC,McCormack JE,Glenn TC,Zhong B,Wu S,Lemmon EM,Lemmon AR,Leaché AD,Liu L,Davis CC




Has Abstract


2016-01-01 00:00:00




Pt A










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    pub_type: 杂志文章


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    pub_type: 杂志文章


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    pub_type: 杂志文章


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    更新日期:2004-06-01 00:00:00

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    pub_type: 杂志文章


    authors: Morando M,Avila LJ,Turner CR,Sites JW Jr

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    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章


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    更新日期:1992-09-01 00:00:00

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    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章


    authors: Zhang Z,Xing Y,Cheng J,Pan D,Lv L,Cumberlidge N,Sun H

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    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章


    authors: Iglésias SP,Lecointre G,Sellos DY

    更新日期:2005-03-01 00:00:00

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    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章


    authors: Holland BS,Hadfield MG

    更新日期:2004-08-01 00:00:00

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    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章


    authors: Martínez P,González EG,Castilho R,Zardoya R

    更新日期:2006-05-01 00:00:00

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    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章


    authors: Everaerts C,Maekawa K,Farine JP,Shimada K,Luykx P,Brossut R,Nalepa CA

    更新日期:2008-06-01 00:00:00

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    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章


    authors: Margos G,Becker NS,Fingerle V,Sing A,Ramos JA,Carvalho IL,Norte AC

    更新日期:2019-02-01 00:00:00

  • Ancient mitochondrial genomes clarify the evolutionary history of New Zealand's enigmatic acanthisittid wrens.

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    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章


    authors: Mitchell KJ,Wood JR,Llamas B,McLenachan PA,Kardailsky O,Scofield RP,Worthy TH,Cooper A

    更新日期:2016-09-01 00:00:00

  • Phylogeny of the Carnivora (Mammalia): congruence vs incompatibility among multiple data sets.

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    pub_type: 杂志文章


    authors: Flynn JJ,Nedbal MA

    更新日期:1998-06-01 00:00:00

  • Phylogeny and biogeography of the Poecilia sphenops species complex (Actinopterygii, Poeciliidae) in Central America.

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    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章


    authors: Alda F,Reina RG,Doadrio I,Bermingham E

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    pub_type: 杂志文章


    authors: Doosey MH,Bart HL Jr,Saitoh K,Miya M

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    pub_type: 杂志文章


    authors: Osborne MJ,Christidis L

    更新日期:2001-08-01 00:00:00

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    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章


    authors: Cadar D,Cságola A,Kiss T,Tuboly T

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    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章


    authors: Klitgaard Nielsen K,Arctander P

    更新日期:2001-03-01 00:00:00

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    pub_type: 杂志文章


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    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章


    authors: Fuentes-Bazan S,Mansion G,Borsch T

    更新日期:2012-01-01 00:00:00

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    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章


    authors: Budaeva N,Schepetov D,Zanol J,Neretina T,Willassen E

    更新日期:2016-01-01 00:00:00

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    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章


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    更新日期:2020-02-01 00:00:00

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    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章


    authors: Rahmatpour N,Perera NV,Singh V,Wegrzyn JL,Goffinet B

    更新日期:2021-01-01 00:00:00

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    pub_type: 杂志文章


    authors: Bollmer JL,Kimball RT,Whiteman NK,Sarasola JH,Parker PG

    更新日期:2006-04-01 00:00:00

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    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章


    authors: Yokoyama R,Goto A

    更新日期:2005-09-01 00:00:00

  • Phylogenetic analysis of the Argonaute protein family in platyhelminths.

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    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章


    authors: Zheng Y

    更新日期:2013-03-01 00:00:00

  • A multi-gene dataset reveals a tropical New World origin and Early Miocene diversification of croakers (Perciformes: Sciaenidae).

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    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章


    authors: Lo PC,Liu SH,Chao NL,Nunoo FK,Mok HK,Chen WJ

    更新日期:2015-07-01 00:00:00

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    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章


    authors: Wirchansky BA,Shain DH

    更新日期:2010-01-01 00:00:00

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    pub_type: 杂志文章


    authors: Tiemann-Boege I,Kilpatrick CW,Schmidly DJ,Bradley RD

    更新日期:2000-09-01 00:00:00