Gene tree discordance, phylogenetic inference and the multispecies coalescent.

By James H. Degnan, Noah A. Rosenberg. Trends in Ecology & Evolution, 2009

1,839 citations recorded by the source corpus.

Subfields: Ecology, Evolution, Behavior and Systematics, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/94d7e91666794ed25a26e1d5809f28872abaaeab

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Citations in the corpus

ASAP: assemble species by automatic partitioning (2020, methodology): “Although sometimes criticized because a single gene tree poorly represents the species tree (Degnan & Rosenberg, 2009; Nichols, 2001), these methods are widely used, as they are easy to apply on DNA-barcoding data sets, even large, and precisely because they do not necessitate pre-defined species…”
Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0) (2010, background): “These large error rates were probably due to the fact that mtDNA data correspond to a single locus and hence to a single gene genealogy subject to substantial stochastic variation [50].”
Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes (2011, background): “However, note that gene trees may often differ from the species tree (Galtier and Daubin 2008; Degnan and Rosenberg 2009).”
PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies (2019, methodology): “P hylo S uite is designed to address the global trend towards multi‐ gene‐based phylogenetic analyses (Degnan & Rosenberg, 2009; Rivera‐Rivera & Montoya‐Burgos, 2016): this software program incorporates and streamlines all steps included in such analyses, from data acquisition to phylogenetic tree…”
Phylotranscriptomic analysis of the origin and early diversification of land plants (2014, background): “This discordance was not unexpected and may be because of incomplete sorting of ancestral variation between speciation events represented by short internodes in the species phylogeny (63, 64) (Fig.”
Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees (2012, background): “Algorithms that capture duplication, transfer and ILS in a single, integrated model are of increasing importance (Degnan and Rosenberg, 2009).”
Error in Phylogenetic Estimation for Bushes in the Tree of Life (2013, result): “#is is in agreement with theory, which indicates that the expected time for two individuals within a population to coalesce is two coalescent units and that one can be 95% con&dent that any number of individuals within a population will have coalesced by &ve coalescent units [55,62,63].”
A DNA Sequence–Based Approach To the Identification of Shark and Ray Species and Its Implications for Global Elasmobranch Diversity and Parasitology (2012, background): “Such differential coalescence is best identified using a suite of multiple independent nuclear markers (Liu et al., 2009; Degnan and Rosenberg, 2009).”
Integrative taxonomy: a multisource approach to exploring biodiversity. (2010, background): “Sites & Marshall (57) reviewed 12 delimitation methods, and other formal criteria have been presented since, for example, for genetic (14, 46) and ecological data (48, 49, 60).”
Integrative taxonomy, or iterative taxonomy? (2011, background): “…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, 2007; reviewed in Degnan & Rosenberg, 2009).”
Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough (2011, background): “Future progress is expected (i) from the combination of various existing models [72], (ii) from the handling of other complexities, such as the heterogeneity of the substitution process over time, and (iii) from the handling of incomplete lineage sorting [11,73].”
The Utility of Single Nucleotide Polymorphism (SNP) Data in Phylogenetics (2017, background): “…on a chromosome Allelic dropout (ADO): biased sampling of alleles because of mutations at enzyme recognition sequences multiple independent genetic markers because any single locus is only a single sample from highly stochastic ancestral (or genealogical) processes (Degnan & Rosenberg 2009).”
The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves (2016, background): “Degnan & Rosenberg (2009) defined the anomaly zone as internodes where there is a higher probability of observing an anomalous gene tree than the actual species tree.”