Homology a personal view on some of the problems.

By W. Fitch. 2000

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Citations in the corpus

The topology of the possible: formal spaces underlying patterns of evolutionary change. (2001, unknown): “Di!erent characters in two species are homologous if they have evolved from the same character in a common ancestor (Fitch, 2000).”
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy (2015, background): “0/ (for example, if gene A is an orthologue of gene B, and gene B is an orthologue of gene C, it is not necessarily true that gene A is an orthologue of gene C) [4].”
Orthologs, Paralogs, and Evolutionary Genomics 1 (2005, background): “come the subject of intense debate and numerous misunderstandings with the advent of molecular evolution and, subsequently, evolutionary genomics (24, 25, 40, 46, 76, 80, 81, 97).”
Choosing BLAST options for better detection of orthologs as reciprocal best hits (2008, background): “Orthologs are defined as genes that have diverged after a speciation event (Fitch, 2000).”
Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough (2011, background): “One possibility is to assess whether branches receiving high statistical support from every single gene tree are congruent with the species tree [18].”
Evolution of proteins and proteomes: a phylogenetics approach (2005, background): “In other words, they are considered to be homologous proteins (Fitch 1970, 2000).”
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes (2004, background): “The two principal classes of homologs are orthologs and paralogs [8-11].”
Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes (2007, background): “Homologous proteins share a common ancestry, and may be characterized as either orthologs (which evolve by speciation only) or paralogs (which arise by gene duplication) [1,2].”
OrthoMCL: identification of ortholog groups for eukaryotic genomes. (2003, methodology): “Orthologs and paralogs constitute two major types of homologs: The first evolved from a common ancestor by speciation, and the latter are related by duplication events (Fitch 1970, 2000 .”