Consequences of recombination on traditional phylogenetic analysis.

By M. Schierup, Jotun Hein. Genetics, 2000

596 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/1b3fe162a90f1984282b2f0d08b71165c1fe34c2

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Citations in the corpus

RDP5: a computer program for analyzing recombination in, and removing signals of recombination from, nucleotide sequence datasets (2020, background): “…in virus genomic sequence datasets by these processes (which are here-after collectively referred to as recombination) can seriously un-dermine the accuracy of phylogenetics-based molecular evolution analyses (Schierup and Hein 2000a,b; Scheffler, Martin, and Seoighe 2006; Arenas and Posada 2010).”
Sex and virulence in Escherichia coli: an evolutionary perspective (2006, background): “If recombination were frequent in E. coli , it would blur phylogenetic signals (Holmes et al ., 1999; Schierup and Hein, 2000), reduce the degree of differentiation between groups and erase statistical support for any inferred branching patterns of trees.”
Bayesian Inference of Species Trees from Multilocus Data (2009, background): “The impact of this on species tree estimation under the multispecies coalescent has not been assessed; however, it is known that the presence of recombination can have a large biasing effect on estimated population sizes, if no recombination is assumed in the model (Schierup and Hein 2000).”
Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. (2003, methodology): “0), the accuracy of Bayes’ site prediction was very high Schierup and Hein (2000a) suggested that even low for M2 and M8, but slightly lower than predicted when levels of recombination can lead to biases in phyloge- data were analyzed using M3.”
A coalescent-based method for detecting and estimating recombination from gene sequences. (2002, unknown): “(Kingman 1982; Hudson 1991).”
Inference of Bacterial Microevolution Using Multilocus Sequence Data (2007, background): “These events are overweighted by nucleotide-based phylogenetic methods in comparison to pointmu-tations, which can lead to inaccurate genealogies being inferred (S chierup and H ein 2000).”
A Simple and Robust Statistical Test for Detecting the Presence of Recombination (2006, methodology): “Test statistic (Fw): The degree of genealogical correlation between neighboring sites is negatively correlated with the rate of recombination (Hudson and Kaplan 1985).”
Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects (2003, methodology): “…of recombination detection methods (e.g. Stephens 1985; Hudson & Kaplan 1988; Maynard Smith 1992; Hein 1993; Templeton & Sing 1993; Innan et al. 1996; Maynard Smith & Smith 1998; Wiuf & Hein 1999; McGuire et al. 2000; Schierup & Hein 2000; Xu 2000; Strimmer et al. 2001; reviewed in Posada 2002).”
Automated phylogenetic detection of recombination using a genetic algorithm. (2006, background): “Recombination can mislead the phylogenetic estimation procedure (Posada and Crandall, 2002) and distort subsequent inferences based on inferred phylogenies (Schierup and Hein, 2000a,b).”
RDP2: recombination detection and analysis from sequence alignments (2005, background): “In addition, recombination compromises the validity of several phylogenetic inferences one can make by examining trees (Schierup and Hein, 2000a,b).”
RDP4: Detection and analysis of recombination patterns in virus genomes (2015, background): “…itself, another important reason for analysing recombination patterns in virus genomes is to minimise the disruptive impact that recombination can have on other phylogeny-based analyses of molecular evolution (Schierup and Hein 2000b; Scheffler, Martin, and Seoighe 2006; Arenas and Posada 2010).”
The early spread and epidemic ignition of HIV-1 in human populations (2014, background): “Recombination may confound phylogenetic reconstructions and may adversely affect molecular clock estimates (58, 59).”