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The gene tree delusion

author

Mark S. Springer

published in: Molecular Phylogenetics and Evolution

date of publication: 2015-07-31

Cites articles 87

Date

Title

Authors

2015-05-19

Coalescence vs. concatenation: Sophisticated analyses vs. first principles applied to rooting the angiosperms
2014-01

Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals

Mario Dos Reis, Philip Donoghue
2014-08-22

Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum

Mark S. Springer
2014-11-04

Applying species-tree analyses to deep phylogenetic histories: challenges and potential suggested from a survey of empirical phylogenetic studies

Lacey Knowles
2014-11-26

Coalescent methods are robust to the simultaneous effects of long branches and incomplete lineage sorting

Charles Cavender Davis
2014-09-01

ASTRAL: genome-scale coalescent-based species tree estimation

Siavash Mirarab, Tandy Warnow
2014-12-11

Statistical binning enables an accurate coalescent-based estimation of the avian tree.

Siavash Mirarab, Bastien Boussau, Tandy Warnow
2014-03-15

Land plant origins and coalescence confusion.

Mark S. Springer
2014-11-11

Phylotranscriptomic analysis of the origin and early diversification of land plants

Gane Ka-Shu Wong, Saravanaraj Ayyampalayam, Regina Baucom, Michael Melkonian, Jim Leebens-Mack, Joshua P. Der, Norman J. Wickett, Siavash Mirarab, Matthew A Gitzendanner, Jun Wang, Pamela S. Soltis, Lisa Pokorny, Xiaolei Wu, Megan M Augustin, Naim Matasci, Tandy Warnow, Juan Carlos Villarreal Aguilar, Douglas E. Soltis, Hervé Philippe, Claude W dePamphilis, Eric J Carpenter, Sean P. Graham, Dennis William Stevenson, Barbara Surek, Michael Deyholos, Michael S. Barker, Carl J. Rothfels, Eric K Wafula, Sarah Mathews, Lisa DeGironimo, Béatrice Roure
2014-07-30

Coalescent versus concatenation methods and the placement of Amborella as sister to water lilies

Charles Cavender Davis
2014-10-17

BBCA: Improving the scalability of *BEAST using random binning

Siavash Mirarab, Tandy Warnow
2013

Conventional simulation of biological sequences leads to a biased assessment of multi-Loci phylogenetic analysis

Carlos G Schrago
2013-07-09

Naive binning improves phylogenomic analyses

Tandy Warnow
2013-03-04

Concatenation versus coalescence versus "concatalescence".

Mark S. Springer
2013-01-01

Retrophylogenomics place tarsiers on the evolutionary branch of anthropoids

Wojciech Makalowski, Jürgen Schmitz, Jürgen Brosius
2013-04-01

Coalescent-based genome analyses resolve the early branches of the euarchontoglires

Vikas Kumar, Axel Janke
2013-09-21

How low can you go? The effects of mutation rate on the accuracy of species-tree estimation

Lacey Knowles
2013-04-14

One thousand two hundred ninety nuclear genes from a genome-wide survey support lungfishes as the sister group of tetrapods.
2013-09

Heterogeneous models place the root of the placental mammal phylogeny

Davide Pisani, James O. McInerney
2013-02-08

The placental mammal ancestor and the post-K-Pg radiation of placentals

Marcelo Weksler, Paúl M. Velazco, Fernando A. Perini, Nancy B. Simmons, Jonathan I. Bloch, Guillermo W Rougier
2013

Error in Phylogenetic Estimation for Bushes in the Tree of Life

Edward L. Braun
2013-06-29

Less is more in mammalian phylogenomics: AT-rich genes minimize tree conflicts and unravel the root of placental mammals

Frédéric Delsuc, Emmanuel Douzery, Vincent Ranwez
2013-05-09

STRAW: Species TRee Analysis Web server

Travis Glenn
2013-11-18

Phylogenomic analyses elucidate the evolutionary relationships of bats

Georgia Tsagkogeorga, Elia Stupka, Joe Parker, James A. Cotton, Stephen J. Rossiter
2013

Phylogenomics and coalescent analyses resolve extant seed plant relationships

Joshua S Rest, Charles Cavender Davis
2013-05-24

Origin of land plants using the multispecies coalescent model

Bojian Zhong
2012-03-14

Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis

Noah Rosenberg, Joseph Felsenstein
2012

Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)

Frédéric Delsuc, Ylenia Chiari
2012-09-07

Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny

Mario Dos Reis, Jun G Inoue, Philip Donoghue
2012-01-02

Is recombination a problem for species-tree analyses?

Lacey Knowles
2012-04

Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis

Patricia Adair Gowaty, Travis Glenn, Brant C. Faircloth
2012-09

Resolution of the laurasiatherian phylogeny: evidence from genomic data

Mariana F Nery, Federico G. Hoffmann, Juan C. Opazo

Article - wd:Q38978053

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