Inferring phylogeny despite incomplete lineage sorting.

By Wayne P. Maddison, Andrea Knowles. Systematic Biology, 2006

1,147 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/4ab2b903efcb2060fb35f5e7f307758efbce3574

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

Citations in the corpus

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model (2010, methodology): “In contrast, most species tree methods either ignore branch lengths in gene and/or species trees [8] or estimated ultrametric species trees [71].”
Species Delimitation using Genome-Wide SNP Data (2013, background): “However, BF support for the true model in relation to the split model provides only marginal improvement with even up to 1000 SNPs (Table 1). methods can also gain information by including more individuals for each species Maddison and Knowles (2006).”
Phylogeography: its development and impact in Australo-Papuan ornithology with special reference to paraphyly in Australian birds (2009, background): “One can now estimate phylogenetic trees of populations and species from collections of gene trees, which are the real characters of trees at the level of species and populations (Maddison and Knowles 2006; Liu et al. 2008).”
Unveiling cryptic species of the bumblebee subgenus Bombus s. str. worldwide with COI barcodes (Hymenoptera: Apidae) (2012, background): “…precisely with those of their owner organisms, either because of incomplete lineage sorting of ancestral polymorphisms (Edwards & Beerli, 2000; Maddison & Knowles, 2006); or because copies become transferred to the nucleus as mitochondrial pseudogenes and show altered patterns of evolution…”
Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees (2012, methodology): “In fact, one parsimony criterion that considers ILS has been proposed: minimization of the number of extra gene lineages on a species branch due to Deep Coalescence (MDC) has been used as a criterion for tree inference (Maddison, 1997; Maddison and Knowles, 2006; Maddison and Maddison, 2011; Page, 1”
IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING? (2009, methodology): “Recent parsimony methods for inferring species trees, such as methods minimizing deep coalescence, appear promising, particularly given their implementation in powerful software packages such as Mesquite (Maddison and Knowles 2006).”
The new systematics of scleractinia: Integrating molecular and morphological evidence (2016, background): “However, different genes cannot be assumed to share the same evolutionary history, and the phylogeny reconstructed for every gene may differ from the actual species history (Maddison and Knowles 2006).”
High-Throughput Genomic Data in Systematics and Phylogenetics (2013, background): “Discordance across loci can be accommodated using species tree models that account for unlinked coalescent histories (Maddison 1997, Maddison & Knowles 2006, Edwards et al. 2007; and see below).”
Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. (2007, methodology): “Under this paradigm, gene trees are generally considered to be synonymous with species trees, except when forces causing discordance between gene and species trees are obvious, such as horizontal gene transfer, deep coalescence, or gene duplication (Maddi-son, 1997; Maddison and Knowles, 2006).”
DNA-based species delimitation in algae (2014, background): “The presence of ancestral polymorphism in closely related species (shared ancestral polymorphism) may result in gene tree – species tree incongruence (Maddison & Knowles, 2006) (see also Trans-species polymorphism).”
How to fail at species delimitation (2013, methodology): “Second, phylogenetic methods that estimate phylogeny while allowing for the action of some of these processes (Maddison & Knowles 2006; Liu et al. 2007; Kubatko et al. 2009; Heled & Drummond 2010) are increasingly applied to low-level phylogenetic systems.”
Discordance of Species Trees with Their Most Likely Gene Trees (2006, neutral): “Because many lineages from each species may persist reasonably far into the past, the chance of coalescences on a short branch is higher if many lineages are present [7,14,30].”
BEST: Bayesian estimation of species trees under the coalescent model (2008, positive): “It is widely accepted that the evolutionary history of species is a stochastic process and should be modeled in a statistical framework (Maddison and Knowles, 2006).”
Isolation with migration models for more than two populations. (2010, background): “The discernment of recent evolutionary history for closely related populations or species presents challenges that fall in the area of population genetics (Gillespie and Langley 1979; Pamilo and Nei 1988; Hudson 1992; Nielsen 1998; Rannala and Yang 2003; Degnan and Salter 2005), and evolutionary bio”