Discordance of Species Trees with Their Most Likely Gene Trees

By James H. Degnan, Noah A. Rosenberg. PLoS Genetics, 2006

944 citations recorded by the source corpus.

Because of the stochastic way in which lineages sort during speciation, gene trees may differ in topology from each other and from species trees. Surprisingly, assuming that genetic lineages follow a coalescent model of within-species evolution, we find that for any species tree topology with five or more species, there exist branch lengths for which gene tree discordance is so common that the most likely gene tree topology to evolve along the branches of a species tree differs from the species phylogeny. This counterintuitive result implies that in combining data on multiple loci, the straightforward procedure of using the most frequently observed gene tree topology as an estimate of the species tree topology can be asymptotically guaranteed to produce an incorrect estimate. We conclude with suggestions that can aid in overcoming this new obstacle to accurate genomic inference of species phylogenies.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/fda7a34733c8618fa533c6aae0ca136cbaa1e2cd

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

Error in Phylogenetic Estimation for Bushes in the Tree of Life (2013, background): “It is known that there are extreme situations (the “anomaly zone”) where the most common gene tree is discordant with the species tree [23].”
How to fail at species delimitation (2013, background): “As multilocus data became common, and as curious statistical results such as anomalous zones (Degnan & Rosenberg 2006) were discovered, the multispecies coalescent (i.e. species trees) became the default option for phylogeny estimation within phylogeographical investigations.”
Extensive introgression in a malaria vector species complex revealed by phylogenomics (2014, background): “Eitherway, standardphylogenomic practice entails some formof “majority rule,” based on the assumption that as the amount of data increases so will the probability of converging on the correct species branching order [apart from exceptional cases (26)].”
BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis (2010, neutral): “With x=0.6 and y=0.4, the population tree is outside the ‘anomaly zone’ described by Degnan and Rosenberg (2006) .”
Inconsistency of phylogenetic estimates from concatenated data under coalescence. (2007, methodology): “Degnan and Rosenberg (2006) have shown that the collection of (x, y) pairs can be partitioned into two regions: an anomaly zone in which P(S1) > P(MT) and a region where there are no AGTs (Fig.”
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis (2018, background): “Species trees with four or more ingroup species can have a region of their parameter space (the “anomaly zone” [83]) where most gene trees have a topology different to the one of the species tree.”
StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates (2016, background): “In the so-called “anomaly zone” of short branch lengths, the most probable gene tree topology will be different from the species tree, and estimated tree topologies will likely differ from the true species tree topologies (Degnan and Rosenberg, 2006; Kubatko and Degnan, 2007).”
ASTRAL: genome-scale coalescent-based species tree estimation (2014, background): “Furthermore, under some conditions, even the most probable gene tree topology may not be identical to the species tree topology (Degnan, 2013; Degnan and Rosenberg, 2006, 2009), a condition called ‘the anomaly zone’.”
Bayesian Inference of Species Trees from Multilocus Data (2009, background): “Please bear in mind that “species” above and in the rest of the text is not necessarily the same as a taxonomic rank, but designates any group of individuals that, after some “divergence” time, have no history of breeding with individuals outside that group.”
Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes (2011, background): “Most strikingly, for more than five taxa, the most probable reconstructed gene tree is distinct from the species tree (Degnan and Rosenberg 2006).”
Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies (2016, background): “While there has been substantial progress in developing methods that estimate a species tree given a collection of gene trees, less attention has been paid to fast and accurate methods of quantifying support.”