title: Palaeophylogenomics of the vertebrate ancestor--impact of hidden paralogy on hagfish and lamprey gene phylogeny.
abstract: In dissecting the transition from invertebrates to vertebrates at the molecular level, whole-genome duplications are recognized as a key event. This gave rise to more copies of genes in jawed vertebrates (gnathostomes), such as the four Hox clusters in the human, compared to the single ancestral cluster in invertebrates. To date, as the most early-branching lineages in vertebrates, cyclostomes (hagfishes and lampreys) have been used for comparative analyses of gene regulations and functions. However, assignment of orthology/paralogy for cyclostomes' genes is not unambiguously demonstrated. Thus, there is a high degree of incongruence in tree topologies between gene families, although whole genome duplications postulate uniform patterns in gene phylogeny. In this review, we demonstrate how expansion of an ancient genome before the cyclostome-gnathostome split, followed by reciprocal gene loss, can cause this incongruence. This is sometimes referred to as 'hidden paralogy'.
authors.affiliation: Laboratory for Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78464 Konstanz, Germany. shigehiro.kuraku@uni-konstanz.de
authors.forename: Shigehiro
authors.initials: S
authors.lastname: Kuraku
mesh_terms: D000818:Animals; D019485:Bone Morphogenetic Proteins / Q000235:genetics; D000071616:CDX2 Transcription Factor; D019143:Evolution, Molecular; D018628:Gene Dosage; D020440:Gene Duplication; D016678:Genome; D006196:Hagfishes / Q000235:genetics*; D018398:Homeodomain Proteins / Q000235:genetics; D007798:Lampreys / Q000235:genetics*; D010802:Phylogeny; D018168:Receptors, Retinoic Acid / Q000235:genetics; D015534:Trans-Activators / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics; D000099260:Empty Spiracles Homeobox Proteins
chemical_list: D019485:Bone Morphogenetic Proteins; D000071616:CDX2 Transcription Factor; D018398:Homeodomain Proteins; D018168:Receptors, Retinoic Acid; D015534:Trans-Activators; D014157:Transcription Factors; D000099260:Empty Spiracles Homeobox Proteins