Phylogenomics and the reconstruction of the tree of life

By Frédéric Delsuc, H. Brinkmann, Hervé Philippe. Nature reviews genetics, 2005

1,203 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/b99eb30dd0a39928ce161f1d41303e99eedcc911

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Citations in the corpus

A phylogeny of Drosophilidae using the Amyrel gene: questioning the Drosophila melanogaster species group boundaries (2007, background): “Delsuc et al. (2005) stated that A long-standing debate in phylogenetics is whether the greatest improvement in accuracy results from an increased number of characters (in this case, genes) or species.”
Detecting and overcoming systematic errors in genome-scale phylogenies. (2007, background): “The use of large multigene data sets to infer phylogenetic trees (phylogenomics) has been successfully applied to resolve evolutionary questions for which single-gene phylogenies failed (Bapteste et al., 2002; Delsuc et al., 2005, 2006; Madsen et al., 2001; Murphy et al., 2001; Philippe et al., 20”
Mapping the biosphere: exploring species to understand the origin, organization and sustainability of biodiversity (2012, background): “Although the availability of abundant, affordable molecular sequence data has complemented fossil, morphological and developmental data in resolving phylogenies, challenges persist (Delsuc et al., 2005).”
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. (2007, background): “However, for longer alignments, for example, those used in phylogenomic studies where several genes are concatenated (Delsuc et al., 2005; Jeffroy et al, 2006), there is enough total information so that selecting the best pieces with Gblocks using the stringent conditions allows to get closer to…”
Tunicates and not cephalochordates are the closest living relatives of vertebrates (2006, neutral): “This decrease can be interpreted as a probable LBA of the fast evolving tunicates towards the outgroup; the long branch of the outgroup is no longer broken by the sea-urchin, a phenomenon known to exacerbate the effect of LBA 17,22 .”
Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes (2011, background): “Evaluating branches inferred by supertree and supermatrix methods is currently emerging as a new research direction in phylogenetic reconstruction (Delsuc et al. 2005; Joly and Bruneau 2009; Ropiquet et al. 2009).”
Pitfalls in supermatrix phylogenomics (2017, neutral): “In the mid-2000s, multigene phylogenetics therefore turned into phylogenomics (Delsuc et al. 2005; Philippe et al. 2005a).”
Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space (2008, background): “The tree of life (Delsuc et al., 2005) presents a taxonomic hierarchy of organisms.”
The role of molecular genetics in sculpting the future of integrative biogeography (2008, methodology): “The emerging field of phylogenomics is a result of this explosive data boom, representing the study of complete genomes from many closely related species using an evolutionary perspective (Delsuc et al., 2005).”
The human phylome (2007, background): “Among these, the construction of super-trees and trees based on concatenated alignments are among the most widely used [32].”
Morphology should not be forgotten in the era of genomics—a phylogenetic perspective (2015, neutral): “… thus combined the 87 previous genomic data with a rapidly evolving set of multigene data sets derived from 88 expressed sequence tags (ESTs) (Delsuc et al., 2006; Delsuc et al., 2005; Lartillot and 89 Philippe, 2008; Philippe et al., 2007; Philippe et…”
BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics (2017, background): “Estimating true phylogenetic relationships among organisms is a prerequisite to almost any evolutionary study and usually employs mathematical methods to infer evolutionary histories based on evidence in the form of features from extant species (Delsuc et al. 2005).”
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions (2010, background): “phylogenomics (1), constitutes a powerful tool to address many relevant questions including, among many others, the reconstruction of evolutionary relationships across different species (2), the prediction of function of uncharacterized proteins (3) and the establishment of orthology and paralogy re”