Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree.

By S. Gadagkar, M. Rosenberg, Sudhir Kumar. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 2005

470 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/63438a092856a0167ea331e10e005f2b023195f5

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Citations in the corpus

How to build phylogenetic species trees with OMA (2020, unknown): “As long as one takes the necessary precautions, notably selecting true orthologs for their comparisons, (see 3 for common pitfalls in phylogenomics), multilocus phylogenies are better resolved and more robust 4 .”
UFBoot2: Improving the Ultrafast Bootstrap Approximation (2017, methodology): “within each gene (gene-site resampling, invoked via “-bsam GENESITE” option) (Gadagkar et al. 2005).”
Cryptic speciation in Hymenoscyphus albidus (2011, unknown): “This approach produces more accurate results for inferring species phylogenies than the consensus phylogeny approach (Gadagkar et al. 2005).”
IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING? (2009, methodology): “…data from multilocus datasets—for example, consensus trees, majority rule trees, supertrees and supermatrices have been suggested as ways of combining data from multiple genes (de Queiroz 1993; de Queiroz et al. 1995; Wiens 1998; Steel et al. 2000; Gadagkar et al. 2005; Holland et al. 2005, 2006).”
MEGA12: Molecular Evolutionary Genetic Analysis Version 12 for Adaptive and Green Computing (2024, unknown): “This approach is effective in producing organismal relationships with high confidence (Gadagkar et al. 2005; Kumar et al. 2012a; Song et al. 2012; Kapli et al. 2020; Williams et al. 2020; Sharma and Kumar 2021).”
Discordance of Species Trees with Their Most Likely Gene Trees (2006, unknown): “The commonly used concatenation procedure [28,29]—in which the species tree is inferred by concatenating a set of loci and then employing the resulting sequence alignment to estimate a single gene tree—is not immune to the AGT problem (L.”
Inconsistency of phylogenetic estimates from concatenated data under coalescence. (2007, methodology): “…speciation events are separated by large time intervals relative to the effective population size, leading to high levels of congruence between individual gene trees, standard phylogenetic methods applied to concatenated multilocus data may still be expected to perform well (Gadagkar et al., 2005).”
Towards a new paradigm in mayfly phylogeny (Ephemeroptera): combined analysis of morphological and molecular data (2009, background): “Nevertheless, evidence supports the notion that combined data (morphology + molecular data) analysis provides a more robust estimate of phylogenetic relationships (Nixon & Carpenter, 1996; Gatesy et al., 1999, 2003; Gadagkar et al., 2005), particularly within the arthropods (Giribet et al.”