IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

By S. Edwards. Evolution; international journal of organic evolution, 2009

1,043 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/063e1efb8a52da7cbac4487aecf08a1c69e4e854

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Citations in the corpus

Phylogeography's past, present, and future: 10 years after Avise, 2000. (2010, background): “Yet in the context of the coalescent, a single genealogy is but one realization of a stochastic process and estimating a single geographically contextualized phylogeny of multiple unlinked loci is often a misleading exercise (Edwards, 2009; Maddison, 1997).”
Molecular phylogenetics: principles and practice (2012, methodology): “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.”
Applications of next-generation sequencing to phylogeography and phylogenetics. (2013, background): “More recently, statistical phylogeography (Knowles, 2009) and the emerging species-tree paradigm of phylogenetics (Edwards, 2009) provided convincing theoretical arguments for incorporating information from multiple loci into estimates of population and species history to account for random…”
Species Tree Inference with BPP Using Genomic Sequences and the Multispecies Coalescent (2018, background): “…genes or genomic regions may have different evolutionary histories (gene trees), due to several important biological processes, including the coalescent process in ancestral species, gene duplication, and horizontal gene transfer (introgression) (Maddison 1997; Nichols 2001; Edwards 2009).”
How to fail at species delimitation (2013, background): “The species tree paradigm enables the relationships among lineages and the membership of individual samples in these lineages to be evaluated in a rigorous statistical framework (Edwards 2009).”
Multi‐gene phylogenetic analysis of south‐east Asian pest members of the Bactrocera dorsalis species complex (Diptera: Tephritidae) does not support current taxonomy (2014, methodology): “…(313 specimens, 2221 bp) Dataset #1 was designed to allow testing of the variation between loci and to apply a species-tree reconstruction approach (Edwards 2008); however, due to the poor resolution in Datasets #1.2–1.4, the additional, concatenation-based data sets were produced (after Gatesy et…”
High-Throughput Genomic Data in Systematics and Phylogenetics (2013, background): “Consequently, model misspecification resulting from concatenation of unlinked loci can result in increased phylogenetic error (Degnan & Rosenberg 2006, Edwards et al. 2007, Kubatko & Degnan 2007, Edwards 2009, Heled & Drummond 2010, Leaché & Rannala 2011, Weisrock et al. 2012).”
ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes (2015, methodology): “We used SimPhy (https://github.com/adamallo/SimPhy) to simulate species trees and gene trees (produced in mutation units) and then used Indelible (Fletcher and Yang, 2009) to simulate nucleotide sequences down the gene trees with varying length and model parameters.”
Higher level molecular phylogeny of darkling beetles (Coleoptera: Tenebrionidae) (2014, background): “Despite the recent advances in DNA sequencing technologies and phylogenetic analyses (Delsuc et al., 2006; Edwards, 2009; Correspondence: Gael J. Kergoat, INRA, UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro), Campus de Baillarguet, 34988 Montferrier-sur-Lez, France.”
The BPP program for species tree estimation and species delimitation (2015, background): “Edwards (2009) has argued that species tree estimation under the MSC represents a paradigm shift in molecular phylogenetics.”
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model (2010, background): “A species tree represents the evolutionary pathway of species-usually the relevant goal in phylogenetic studies [35] - while a gene tree represents the evolutionary history of a single gene.”