Literature DB >> 29078408

Reply to Gatesy and Springer: Claims of homology errors and zombie lineages do not compromise the dating of placental diversification.

Liang Liu1,2,3, Jin Zhang4, Frank E Rheindt5, Fumin Lei6, Yanhua Qu6, Yu Wang7,8, Yu Zhang7,8, Corwin Sullivan9, Wenhui Nie10, Jinhuan Wang10, Fengtang Yang11, Jinping Chen12, Scott V Edwards13,14,15, Jin Meng16, Shaoyuan Wu13,17.   

Abstract

Mesh：

Year:  2017        PMID： 29078408      PMCID： PMC5692603          DOI： 10.1073/pnas.1715371114

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN： 0027-8424            Impact factor:   11.205


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  9 in total

1.  Why would phylogeneticists ignore computerized sequence alignment?

Authors:  David A Morrison
Journal:  Syst Biol       Date:  2009-03-25       Impact factor: 15.683

Review 2.  Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics.

Authors:  Scott V Edwards; Zhenxiang Xi; Axel Janke; Brant C Faircloth; John E McCormack; Travis C Glenn; Bojian Zhong; Shaoyuan Wu; Emily Moriarty Lemmon; Alan R Lemmon; Adam D Leaché; Liang Liu; Charles C Davis
Journal:  Mol Phylogenet Evol       Date:  2015-10-27       Impact factor: 4.286

3.  Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds.

Authors:  Ziheng Yang; Bruce Rannala
Journal:  Mol Biol Evol       Date:  2005-09-21       Impact factor: 16.240

4.  Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary.

Authors:  Liang Liu; Jin Zhang; Frank E Rheindt; Fumin Lei; Yanhua Qu; Yu Wang; Yu Zhang; Corwin Sullivan; Wenhui Nie; Jinhuan Wang; Fengtang Yang; Jinping Chen; Scott V Edwards; Jin Meng; Shaoyuan Wu
Journal:  Proc Natl Acad Sci U S A       Date:  2017-08-14       Impact factor: 11.205

5.  Phylogenomic red flags: Homology errors and zombie lineages in the evolutionary diversification of placental mammals.

Authors:  John Gatesy; Mark S Springer
Journal:  Proc Natl Acad Sci U S A       Date:  2017-10-24       Impact factor: 11.205

6.  Resolving difficult phylogenetic questions: why more sequences are not enough.

Authors:  Hervé Philippe; Henner Brinkmann; Dennis V Lavrov; D Timothy J Littlewood; Michael Manuel; Gert Wörheide; Denis Baurain
Journal:  PLoS Biol       Date:  2011-03-15       Impact factor: 8.029

7.  trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.

Authors:  Salvador Capella-Gutiérrez; José M Silla-Martínez; Toni Gabaldón
Journal:  Bioinformatics       Date:  2009-06-08       Impact factor: 6.937

8.  Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies.

Authors:  Erfan Sayyari; Siavash Mirarab
Journal:  Mol Biol Evol       Date:  2016-04-15       Impact factor: 16.240

9.  Phylotranscriptomic consolidation of the jawed vertebrate timetree.

Authors:  Iker Irisarri; Denis Baurain; Henner Brinkmann; Frédéric Delsuc; Jean-Yves Sire; Alexander Kupfer; Jörn Petersen; Michael Jarek; Axel Meyer; Miguel Vences; Hervé Philippe
Journal:  Nat Ecol Evol       Date:  2017-07-24       Impact factor: 15.460
  9 in total
  5 in total

1.  Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation.

Authors:  Nathan S Upham; Jacob A Esselstyn; Walter Jetz
Journal:  PLoS Biol       Date:  2019-12-04       Impact factor: 8.029

2.  The effect of alignment uncertainty, substitution models and priors in building and dating the mammal tree of life.

Authors:  Yan Du; Shaoyuan Wu; Scott V Edwards; Liang Liu
Journal:  BMC Evol Biol       Date:  2019-11-06       Impact factor: 3.260

3.  Evolutionary Models for the Diversification of Placental Mammals Across the KPg Boundary.

Authors:  Mark S Springer; Nicole M Foley; Peggy L Brady; John Gatesy; William J Murphy
Journal:  Front Genet       Date:  2019-11-29       Impact factor: 4.599

4.  Comparative transcriptomics of ice-crawlers demonstrates cold specialization constrains niche evolution in a relict lineage.

Authors:  Sean D Schoville; Sabrina Simon; Ming Bai; Zachary Beethem; Roman Y Dudko; Monika J B Eberhard; Paul B Frandsen; Simon C Küpper; Ryuichiro Machida; Max Verheij; Peter C Willadsen; Xin Zhou; Benjamin Wipfler
Journal:  Evol Appl       Date:  2020-09-11       Impact factor: 5.183

5.  Genome-scale DNA sequence data and the evolutionary history of placental mammals.

Authors:  Shaoyuan Wu; Scott Edwards; Liang Liu
Journal:  Data Brief       Date:  2018-05-01
  5 in total

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