Molecular Evolution and Phylogenetics

By Ardavan F. Oskooi. 2008

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Citations in the corpus

Colletotrichum gloeosporioides is not a common pathogen on tropical fruits (2010, methodology): “Maximum parsimony (MP) trees were obtained using the CloseNeighbor-Interchange algorithm (Nei and Kumar 2000) with search level 1, in which the initial trees were obtained with the random addition of sequences (10 replicates).”
Tree of Life Reveals Clock-Like Speciation and Diversification (2014, result): “Although coalescence of alleles may lead to overestimates of time (Nei and Kumar 2000), those times were interpreted as population and species splits, not allelic splits, in the published studies reporting them.”
Eurythoe complanata (Polychaeta: Amphinomidae), the ‘cosmopolitan’ fireworm, consists of at least three cryptic species (2010, methodology): “Pairwise genetic distances were estimated using Kimura’s two-parameters (K2P) method (Nei and Kumar 2000) for neighbor-joining tree reconstruction and estimation of divergence time between branches.”
DNA barcoding reveals new insights into the diversity of Antarctic species of Orchomene sensu lato (Crustacea: Amphipoda: Lysianassoidea) (2011, methodology): “, 2007) and sequence divergences were calculated using the Kimura 2-parameter (K2P) distance model (Kimura, 1980), the best metric system when distances are low (Nei and Kumar, 2000) (see supplementary material available at doi:10.”
Building phylogenetic trees from molecular data with MEGA. (2013, methodology): “A phylogenetic tree is an estimate of the relationships among taxa (or sequences) and their hypothetical common ancestors (Nei and Kumar 2000; Felsenstein 2004; Hall 2011).”
Automated Reconstruction of Whole-Genome Phylogenies from Short-Sequence Reads (2014, background): “…and ecology is to understand the evolutionary relationships between different taxa (Preston et al. 1998; Gill et al. 2005; Ishii et al. 2006; Chun et al. 2009; Ogura et al. 2009; Harris et al. 2010), which are typically quantified by constructing phylogenetic trees (Nei and Kumar 2000).”
Undisciplined thinking: morphology and Hennig’s unfinished revolution (2008, background): “In its place is a newfound confusion of pattern with process, as in maximum likelihood assumptions, hailed as progress (Nei & Kumar, 2000).”
MTML-msBayes: Approximate Bayesian comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity (2011, background): “Because the divergence with migration model is generally applied to taxa that have split in the last 10 My, these models should be sufficient [40].”
MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences (2008, methodology): “Many novel methodological and algorithmic developments, combined with a manifold increase in the computing power on average desktops, have made it possible to carry out computationally intensive statistical methods of phylogenetic analysis based on the Maximum Likelihood (ML) principle [3, 5, 6].”
Barcoding's next top model: an evaluation of nucleotide substitution models for specimen identification (2012, methodology): “Hebert et al. were presumably referring to the following passage in Nei & Kumar (2000): ‘Even the p distance becomes very similar to other distance measures when p £ 0Æ1.”
Are Convergent and Parallel Amino Acid Substitutions in Protein Evolution More Prevalent Than Neutral Expectations? (2015, background): “Potential discordances between gene trees and species trees were ignored due to low probabilities (P< 3 10 5 based on parameters pertaining to the species used; Nei and Kumar 2000).”
Molecular phylogeny of Juglans (Juglandaceae): a biogeographic perspective (2007, background): “25, as in the present case, and distances based on sophisticated models of evolution are not necessarily efficient for obtaining correct topology (Nei and Kumar 2000).”
Hyperbolic Geometry of Complex Networks (2010, background): “This mapping represents the tree-like hierarchy among the disks.”
MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. (2011, methodology): “Model Selection for Nucleotide and Amino Acid sequences MEGA5 now contains facilities to evaluate the ﬁt of major models of nucleotide and amino acid substitutions, which are frequently desired by researchers (Posada and Crandall 1998; Nei and Kumar 2000; Yang 2006) (ﬁg.”
MEGA12: Molecular Evolutionary Genetic Analysis Version 12 for Adaptive and Green Computing (2024, unknown): “MEGA assesses 6 primary nucleotide substitution models to determine the optimal mod - el: general time reversible (GTR), Hasegawa–Kishino–Yano (HKY), Tamura–Nei (TN93), Tamura 3-parameter (T92), Kimura 2-parameter (K2P), and Jukes–Cantor (JC); see Nei and Kumar (2000) for a review.”
IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING? (2009, background): “…core approaches of phylogenetic systematics have evolved into a suite of methodologies that focus on amassing character data to build these trees (Nei and Kumar 2000; Felsenstein 2003; Delsuc et al. 2006), and the leading role of DNA sequences in providing these characters over the past several…”