Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions.

By Liang Liu, Dennis K. Pearl. Systematic Biology, 2007

506 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/13443216c4bb3a25205a66df4e55c04c3230b6d4

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Molecular Biology

In Paleontology

Citations in the corpus

The impact of ancestral population size and incomplete lineage sorting on Bayesian estimation of species divergence times (2015, methodology): “4 Several Bayesian phylogenetic methods have been developed to perform inference under the multi-species coalescent (Rannala and Yang, 2003; Liu and Pearl, 2007; Liu, 2008; Heled and Drummond, 2010; Yang, 2015).”
BEST: Bayesian estimation of species trees under the coalescent model (2008, unknown): “The Bayesian hierarchical model that BEST implements consists of three components: sequences, gene trees and the species tree (Edwards et al., 2007; Liu and Pearl, 2007; Liu et al., 2008).”
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model (2010, methodology): “Several methods have been developed to accommodate the variability among gene trees when estimating species trees [6-11].”
STEM: species tree estimation using maximum likelihood for gene trees under coalescence (2009, methodology): “When phylogenetic trees representing the species history are of primary interest, it is therefore necessary to either modify standard phylogenetic methods to handle multi-locus data, or to develop new methods that explicitly model the source of discord (Ane et al., 2007; Liu, 2008; Liu and Pearl, 20”
Integrative taxonomy, or iterative taxonomy? (2011, methodology): “Other approaches such as those implemented in best (Edwards et al., 2007; Liu & Pearl, 2007) and *beast (Heled & Drummond, 2008), model the coalescent for sequence data across different input genes to estimate the species tree.”
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space (2012, methodology): “Bayesian phylogenetic inference of species trees from multiple gene trees was first accomplished in the Bayesian estimation of species trees (BEST) software using a complex computational machinery, in which MrBayes was one of the components (Edwards et al. 2007; Liu and Pearl 2007).”
The new systematics of scleractinia: Integrating molecular and morphological evidence (2016, methodology): “Thus, for species classifications, methods that use coalescent theory to jointly estimate gene trees and the species tree would be more appropriate (Liu and Pearl 2007; Liu 2008; Liu et al. 2008; Heled and Drummond 2010).”
Delimiting species without monophyletic gene trees. (2007, methodology): “…for delimiting species, even though the gene trees are not completely concordant— which is similar to recent studies on modeling evolutionary relationships probabilistically (e.g., Rannala and Yang, 2002; Rosenberg, 2002; Liu and Pearl, 2006; Carstens and Knowles, 2007a; Edwards et al., 2007).”
Quartet Inference from SNP Data Under the Coalescent Model (2014, unknown): “Much recent effort has been devoted to the development of methods to estimate species-level phylogenies from multi-locus data under the coalescent model (Bryant et al., 2012; Heled and Drummond, 2010; Kubatko et al., 2009; Liu and Pearl, 2007; Liu et al., 2009b; Than and Nakhleh, 2009).”
The BPP program for species tree estimation and species delimitation (2015, background): “…for addressing a number of important problems in evolutionary biology, such as species delimitation (Yang and Rannala, 2010; Rannala and Yang, 2013), species tree estimation (Edwards et al., 2007; Liu and Pearl, 2007; Heled and Drummond, 2010), and detection of hybridization and contamination.”
Marine dispersal as a pre‐requisite for Gondwanan vicariance among elements of the galaxiid fish fauna (2012, methodology): “…– the Galaxias vulgaris s.l. complex – Waters et al. (2010) has already performed analyses using more appropriate sampling (more individuals per species) and methods of phylogenetic inference that can accommodate discordance among gene trees owing to incomplete lineage sorting (Liu & Pearl, 2007).”
Species Delimitation using Genome-Wide SNP Data (2013, methodology): “1), and is equivalent in divergence times and population sizes to a species tree used in two other simulation studies Liu and Pearl (2007); Bryant et al. (2012).”