[HTML][HTML] Implementing and testing the multispecies coalescent model: a valuable paradigm for phylogenomics

SV Edwards, Z Xi, A Janke, BC Faircloth… - Molecular phylogenetics …, 2016 - Elsevier
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: theory and applications in phylogenetics

S Mirarab, L Nakhleh, T Warnow - Annual Review of Ecology …, 2021 - annualreviews.org
Species tree estimation is a basic part of many biological research projects, ranging from
answering basic evolutionary questions (eg, how did a group of species adapt to their …

Contentious relationships in phylogenomic studies can be driven by a handful of genes

XX Shen, CT Hittinger, A Rokas - Nature ecology & evolution, 2017 - nature.com
Phylogenomic studies have resolved countless branches of the tree of life, but remain
strongly contradictory on certain, contentious relationships. Here, we use a maximum …

[图书][B] Modern phylogenetic comparative methods and their application in evolutionary biology: concepts and practice

LZ Garamszegi - 2014 - Springer
Many evolutionary biologists are concerned with the tremendous amount of diversity of
species, and their phenotypes, that we can currently observe in nature, and one of the most …

Prehistoric genomes reveal the genetic foundation and cost of horse domestication

M Schubert, H Jónsson, D Chang… - Proceedings of the …, 2014 - National Acad Sciences
The domestication of the horse∼ 5.5 kya and the emergence of mounted riding, chariotry,
and cavalry dramatically transformed human civilization. However, the genetics underlying …

Evaluating summary methods for multilocus species tree estimation in the presence of incomplete lineage sorting

S Mirarab, MS Bayzid, T Warnow - Systematic Biology, 2016 - academic.oup.com
Species tree estimation is complicated by processes, such as gene duplication and loss and
incomplete lineage sorting (ILS), that cause discordance between gene trees and the …

Maximum likelihood inference of reticulate evolutionary histories

Y Yu, J Dong, KJ Liu, L Nakhleh - Proceedings of the …, 2014 - National Acad Sciences
Hybridization plays an important role in the evolution of certain groups of organisms,
adaptation to their environments, and diversification of their genomes. The evolutionary …

[HTML][HTML] The evolutionary history of bears is characterized by gene flow across species

V Kumar, F Lammers, T Bidon, M Pfenninger… - Scientific Reports, 2017 - nature.com
Bears are iconic mammals with a complex evolutionary history. Natural bear hybrids and
studies of few nuclear genes indicate that gene flow among bears may be more common …

[HTML][HTML] A maximum pseudo-likelihood approach for phylogenetic networks

Y Yu, L Nakhleh - BMC genomics, 2015 - Springer
Background Several phylogenomic analyses have recently demonstrated the need to
account simultaneously for incomplete lineage sorting (ILS) and hybridization when inferring …

The perfect storm: gene tree estimation error, incomplete lineage sorting, and ancient gene flow explain the most recalcitrant ancient angiosperm clade, Malpighiales

L Cai, Z Xi, EM Lemmon, AR Lemmon, A Mast… - Systematic …, 2021 - academic.oup.com
The genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life.
The development of the multispecies coalescent model and improved gene tree estimation …