High-resolution species trees without concatenation

By S. Edwards, Liang Liu, Dennis K. Pearl. Proceedings of the National Academy of Sciences of the United States of America, 2007

614 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/bd2a1f350c5a8e998d6bfe438996b5530ce43414

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Citations in the corpus

Phylogeography's past, present, and future: 10 years after Avise, 2000. (2010, background): “The coalescent has also become relevant and necessary for phylogeographers to estimate species-level phylogeny at low levels of divergence given data from multiple loci and multiple individuals per subspecies or populations (Edwards et al., 2007; Kubatko et al., 2009; Oliver, 2008).”
Error in Phylogenetic Estimation for Bushes in the Tree of Life (2013, methodology): “Moreover, methods that accommodate gene tree discordance do appear to improve the efficiency and accuracy of phylogenetic estimation [30], at least for some problems.”
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).”
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).”
Molecular phylogenetics: principles and practice (2012, background): “In species tree methods 2,18,19 , the gene trees at individual loci may not be of direct interest and may be in conflict with the species tree.”
IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING? (2009, methodology): “At the same time, other recent results are beginning to question the suitability of concatenation for all data types and time scales, in particular those from DNA sequences sampled from rapidly diverging clades (Edwards et al. 2007; Kubatko and Degnan 2007).”
The role of molecular genetics in sculpting the future of integrative biogeography (2008, methodology): “…reconstruction methods (e.g., computer algorithms and resources) may be a limiting factor (Delsuc et al., 2005), and the development of innovative analytical approaches will be required in order to take maximum advantage of these enormous datasets (e.g., Edwards et al., 2007; Li et al., 2007).”
Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. (2012, background): “This suggests that these loci conform to neutral coalescent expectations and are likely appropriate for use in phylogenetic analyses that model the coalescent, including species-tree analysis (Edwards et al. 2007).”
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.”
Discordant mitochondrial and nuclear gene phylogenies in emydid turtles: implications for speciation and conservation (2010, methodology): “Unfortunately, alternative methods designed to estimate species trees without concatenation (e.g. Edwards et al., 2007) would be problematic to apply here as a result of incomplete overlap in taxon sampling between genes.”
Phylogenetic Methods in Biogeography (2011, background): “Folding allele trees into species trees relies on extending the coalescent to multispecies contexts (Edwards et al. 2007, Heled & Drummond 2010).”
Integrative taxonomy, or iterative taxonomy? (2011, methodology): “…are more probable than matching gene trees, and concatenation would be expected to perform poorly in these situations (Carstens & Knowles, 2007; Edwards et al., 2007; © 2010 CSIRO Systematic Entomology © 2010 The Royal Entomological Society, Systematic Entomology, 36, 209–217 Kubatko & Degnan,…”
High-Throughput Genomic Data in Systematics and Phylogenetics (2013, methodology): “Species trees can be estimated directly from sequence alignments (e.g., BEST: Edwards et al. 2007; ∗BEAST: www.annualreviews.org • Genomic Data in Phylogenetics 113 A nn u.”