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Delimiting Coalescence Genes (C-Genes) in Phylogenomic Data Sets.

author

Mark S. Springer

published in: Genes

date of publication: 2018-02-26

main subject: phylogenomics

Cites articles 69

Date

Title

Authors

2018-01-01

Coalescent-based analyses of genomic sequence data provide a robust resolution of phylogenetic relationships among major groups of gibbons

Cheng-Min Shi
2017-08-14

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

Fu-Min Lei, Frank E. Rheindt
2017-01-01

Incomplete Lineage Sorting in Mammalian Phylogenomics

Celine Scornavacca
2016-11

A performance study of the impact of recombination on species tree analysis
2016-12-01

Challenges in Species Tree Estimation Under the Multispecies Coalescent Model

Yang Ziheng
2016-01

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

Bojian Zhong, Brant C. Faircloth, Scott V. Edwards, Emily Moriarty Lemmon, Alan R. Lemmon, Travis Glenn, Axel Janke, Charles Cavender Davis
2015-05-26

RDP4: Detection and analysis of recombination patterns in virus genomes
2015-07-31

The gene tree delusion

Mark S. Springer
2015-06-18

Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses

Siavash Mirarab, Bastien Boussau, Tandy Warnow
2015-06-01

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

Siavash Mirarab, Tandy Warnow
2015-04-14

Estimating phylogenetic trees from genome-scale data

Scott V. Edwards, Charles Cavender Davis
2015-03-25

On the Robustness to Gene Tree Estimation Error (or lack thereof) of Coalescent-Based Species Tree Methods.

Tandy Warnow
2014-12-11

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

Siavash Mirarab, Bastien Boussau, Tandy Warnow
2014-12-12

Whole-genome analyses resolve early branches in the tree of life of modern birds

Beth Shapiro, Eske Willerslev, Peter Houde, David Haussler, Joel Cracraft, Tandy Warnow, Per Alström, Bent Lindow, Toni Gabaldón, Ludovic Orlando, Thomas Sicheritz-Ponten, Klaus-Peter Koepfli, Jaime Huerta-Cepas, Hans Ellegren, Michael Bunce, Kasper Munch, Alexandros Stamatakis, Morgan Wirthlin, Nitish Narula, Alonzo Alfaro-Núñez, Claudia C Weber, Jason T Howard, Alexander Suh, Cai Li, Siavash Mirarab, Bent Petersen, Rute R. da Fonseca, Sankar Subramanian, Bastien Boussau, Paula F Campos, Francisco Prosdocimi, Brant C. Faircloth, Knud A. Jønsson, Guojie Zhang, Robb T. Brumfield, Edward L. Braun, Mads Frost Bertelsen, Mikkel Heide Schierup, Scott V. Edwards, Marcus Thomas Pius Gilbert, Michael W. Bruford, Erich Jarvis, Salvador Capella-Gutierrez, Richard Paul Scofield, Warren E. Johnson, Carsten Rahbek, Yinhua Huang, David M Lambert, Jun Wang, Yang Huanming, Jian Wang, Linnéa Smeds, Amy C. Driskell, Claudio V Mello, Peter V Lovell, Elizabeth Derryberry, David Mindell, Travis Glenn, Wesley C Warren, Jon Fjeldså, Andre J Aberer, Benoit Nabholz, Xiangjiang Zhan, Andrew Dixon, José Alfredo Samaniego Castruita, Zijun Xiong, Yongli Zeng, Oliver A. Ryder, Frank E. Rheindt, Gary R. Graves, Stephen J. O'Brien, Simon Y. W. Ho, Amhed M Vargas-Velazquez, Shiping Liu, Richard E Green, Polina L Perelman
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
2014-08-07

Quartet inference from SNP data under the coalescent model

Julia Chifman, Laura S Kubatko
2014-07-30

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

Charles Cavender Davis
2014-08-22

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

Mark S. Springer
2014-04-09

OrthoMaM v8: a database of orthologous exons and coding sequences for comparative genomics in mammals

Frédéric Delsuc, Emmanuel Douzery, Celine Scornavacca, Vincent Ranwez
2014-03-15

Land plant origins and coalescence confusion.

Mark S. Springer
2014-03-15

The multispecies coalescent model and land plant origins: a reply to Springer and Gatesy

Bojian Zhong
2013

Phylogenomics and coalescent analyses resolve extant seed plant relationships

Joshua S Rest, Charles Cavender Davis
2013

Using genes as characters and a parsimony analysis to explore the phylogenetic position of turtles
2013-11-04

A fine-scale recombination map of the human-chimpanzee ancestor reveals faster change in humans than in chimpanzees and a strong impact of GC-biased gene conversion

Kasper Munch, Julien Y Dutheil, Mikkel Heide Schierup
2013-11-18

Phylogenomic analyses elucidate the evolutionary relationships of bats

Georgia Tsagkogeorga, Elia Stupka, Joe Parker, James A. Cotton, Stephen J. Rossiter
2013-07-03

Great ape genetic diversity and population history

Peter H Sudmant, Jeffrey M. Kidd, Belen Lorente-Galdos, Ferran Casals, Kasper Munch, Asger Hobolth, Can Alkan, Mario Ventura, David Comas, Thomas Mailund, Mikkel Heide Schierup, Tomas Marques-Bonet, Lucinda Fulton, Christoph Theunert, Javier Prado-martinez, Laurie S. Stevison, Joanna L. Kelley, Gabriel Santpere, Simon Myers, Aida M Andrés, Aurora Ruiz-Herrera, Jaume Bertranpetit, Tiago Carvalho, Jessica Hernandez-Rodriguez, Marc Dabad, Hafid Laayouni, Marta Melé, Timothy D O'Connor, Felix Lankester, Ronald Bontrop, Beatrice H. Hahn, Marc Pybus, James C Mullikin, Michael Lachmann, Carlos D. Bustamante, Evan E. Eichler, Sarah Tishkoff, Christina Hvilsom, Hans Redlef Siegismund, Elizabeth V. Lonsdorf, David Reich, Kay Prüfer, Arcadi Navarro, Marcos Fernandez-Callejo, Joshua M. Akey, Fereydoun Hormozdiari, Maika Malig
2013-05-24

Origin of land plants using the multispecies coalescent model

Bojian Zhong
2013-04-14

One thousand two hundred ninety nuclear genes from a genome-wide survey support lungfishes as the sister group of tetrapods.
2013-03-04

Concatenation versus coalescence versus "concatalescence".

Mark S. Springer
2013-07-09

Naive binning improves phylogenomic analyses

Tandy Warnow
2012

A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species

Gerton Lunter, Kay Prüfer, Kasper Munch, Asger Hobolth, Julien Y Dutheil, Thomas Mailund, Mikkel Heide Schierup, Lars N Andersen
2012

Macroevolutionary dynamics and historical biogeography of primate diversification inferred from a species supermatrix

Christopher A. Emerling, Tanja Stadler, Daniel L. Rabosky, Mark S. Springer, William J Murphy

Article - wd:Q51150219

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