Literature DB >> 29078405

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

John Gatesy1, Mark S Springer2.   

Abstract

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Year:  2017        PMID： 29078405      PMCID： PMC5692601          DOI： 10.1073/pnas.1715318114

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


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  7 in total

1.  The gene tree delusion.

Authors:  Mark S Springer; John Gatesy
Journal:  Mol Phylogenet Evol       Date:  2015-07-31       Impact factor: 4.286

2.  Toothed whale monophyly reassessed by SINE insertion analysis: the absence of lineage sorting effects suggests a small population of a common ancestral species.

Authors:  Masato Nikaido; Oliver Piskurek; Norihiro Okada
Journal:  Mol Phylogenet Evol       Date:  2006-08-17       Impact factor: 4.286

3.  Earliest Mysticete from the Late Eocene of Peru Sheds New Light on the Origin of Baleen Whales.

Authors:  Olivier Lambert; Manuel Martínez-Cáceres; Giovanni Bianucci; Claudio Di Celma; Rodolfo Salas-Gismondi; Etienne Steurbaut; Mario Urbina; Christian de Muizon
Journal:  Curr Biol       Date:  2017-05-11       Impact factor: 10.834

4.  Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification.

Authors:  Robert W Meredith; Jan E Janečka; John Gatesy; Oliver A Ryder; Colleen A Fisher; Emma C Teeling; Alisha Goodbla; Eduardo Eizirik; Taiz L L Simão; Tanja Stadler; Daniel L Rabosky; Rodney L Honeycutt; John J Flynn; Colleen M Ingram; Cynthia Steiner; Tiffani L Williams; Terence J Robinson; Angela Burk-Herrick; Michael Westerman; Nadia A Ayoub; Mark S Springer; William J Murphy
Journal:  Science       Date:  2011-09-22       Impact factor: 47.728

5.  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

6.  Waking the undead: Implications of a soft explosive model for the timing of placental mammal diversification.

Authors:  Mark S Springer; Christopher A Emerling; Robert W Meredith; Jan E Janečka; Eduardo Eizirik; William J Murphy
Journal:  Mol Phylogenet Evol       Date:  2016-09-19       Impact factor: 4.286

7.  ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes.

Authors:  Siavash Mirarab; Tandy Warnow
Journal:  Bioinformatics       Date:  2015-06-15       Impact factor: 6.937
  7 in total
  9 in total

1.  Rolling of the jaw is essential for mammalian chewing and tribosphenic molar function.

Authors:  Bhart-Anjan S Bhullar; Armita R Manafzadeh; Juri A Miyamae; Eva A Hoffman; Elizabeth L Brainerd; Catherine Musinsky; Alfred W Crompton
Journal:  Nature       Date:  2019-02-13       Impact factor: 49.962

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

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:  2017-10-24       Impact factor: 11.205

3.  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

4.  Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Nonreversible Models for Mammals.

Authors:  Suha Naser-Khdour; Bui Quang Minh; Robert Lanfear
Journal:  Syst Biol       Date:  2022-06-16       Impact factor: 9.160

5.  Contradictory Phylogenetic Signals in the Laurasiatheria Anomaly Zone.

Authors:  Liliya Doronina; Graham M Hughes; Diana Moreno-Santillan; Colleen Lawless; Tadhg Lonergan; Louise Ryan; David Jebb; Bogdan M Kirilenko; Jennifer M Korstian; Liliana M Dávalos; Sonja C Vernes; Eugene W Myers; Emma C Teeling; Michael Hiller; Lars S Jermiin; Jürgen Schmitz; Mark S Springer; David A Ray
Journal:  Genes (Basel)       Date:  2022-04-26       Impact factor: 4.141

6.  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

7.  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

8.  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

9.  The soft explosive model of placental mammal evolution.

Authors:  Matthew J Phillips; Carmelo Fruciano
Journal:  BMC Evol Biol       Date:  2018-07-03       Impact factor: 3.260
  9 in total

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