@article {R. McCune:2012:1389-2029:74,
title = "Using Genetic Networks and Homology to Understand the Evolution of Phenotypic Traits",
journal = "Current Genomics",
parent_itemid = "infobike://ben/cg",
publishercode ="ben",
year = "2012",
volume = "13",
number = "1",
publication date ="2012-03-01T00:00:00",
pages = "74-84",
itemtype = "ARTICLE",
issn = "1389-2029",
url = "https://www.ingentaconnect.com/content/ben/cg/2012/00000013/00000001/art00009",
doi = "doi:10.2174/138920212799034785",
keyword = "taxic homology, Gene regulatory networks, transformational homology, genomics, Phenotypic Traits, Character Identity Networks, Evolution, Next Gen Sequencing, Transformation, deep homology",
author = "R. McCune, Amy and C. Schimenti, John",
abstract = "Homology can have different meanings for different kinds of biologists. A phylogenetic view holds that homology, defined by common ancestry, is rigorously identified through phylogenetic analysis. Such homologies are taxic homologies (=synapomorphies). A second interpretation,
biological homology emphasizes common ancestry through the continuity of genetic information underlying phenotypic traits, and is favored by some developmental geneticists. A third kind of homology, deep homology, was recently defined as the sharing of the genetic regulatory
apparatus used to build morphologically and phylogenetically disparate features. Here we explain the commonality among these three versions of homology. We argue that biological homology, as evidenced by a conserved gene regulatory network giving a trait its essential identity
(a Character Identity Network or ChIN) must also be a taxic homology. In cases where a phenotypic trait has been modified over the course of evolution such that homology (taxic) is obscured (e.g. jaws are modified gill arches), a shared underlying ChIN provides evidence of this
transformation. Deep homologies, where molecular and cellular components of a phenotypic trait precede the trait itself (are phylogenetically deep relative to the trait), are also taxic homologies, undisguised. Deep homologies inspire particular interest for understanding the evolutionary
assembly of phenotypic traits. Mapping these deeply homologous building blocks on a phylogeny reveals the sequential steps leading to the origin of phenotypic novelties. Finally, we discuss how new genomic technologies will revolutionize the comparative genomic study of non-model organisms
in a phylogenetic context, necessary to understand the evolution of phenotypic traits. 
",
}