The natural history of class I primate alcohol dehydrogenases includes gene duplication, gene loss, and gene conversion

Matthew A. Carrigan, Oleg Uryasev, Ross P. Davis, LanMin Zhai, Thomas Hurley, Steven A. Benner

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

Background: Gene duplication is a source of molecular innovation throughout evolution. However, even with massive amounts of genome sequence data, correlating gene duplication with speciation and other events in natural history can be difficult. This is especially true in its most interesting cases, where rapid and multiple duplications are likely to reflect adaptation to rapidly changing environments and life styles. This may be so for Class I of alcohol dehydrogenases (ADH1s), where multiple duplications occurred in primate lineages in Old and New World monkeys (OWMs and NWMs) and hominoids. Methodology/Principal Findings: To build a preferred model for the natural history of ADH1s, we determined the sequences of nine new ADH1 genes, finding for the first time multiple paralogs in various prosimians (lemurs, strepsirhines). Database mining then identified novel ADH1 paralogs in both macaque (an OWM) and marmoset (a NWM). These were used with the previously identified human paralogs to resolve controversies relating to dates of duplication and gene conversion in the ADH1 family. Central to these controversies are differences in the topologies of trees generated from exonic (coding) sequences and intronic sequences. Conclusions/Significance: We provide evidence that gene conversions are the primary source of difference, using molecular clock dating of duplications and analyses of microinsertions and deletions (micro-indels). The tree topology inferred from intron sequences appear to more correctly represent the natural history of ADH1s, with the ADH1 paralogs in platyrrhines (NWMs) and catarrhines (OWMs and hominoids) having arisen by duplications shortly predating the divergence of OWMs and NWMs. We also conclude that paralogs in lemurs arose independently. Finally, we identify errors in database interpretation as the source of controversies concerning gene conversion. These analyses provide a model for the natural history of ADH1s that posits four ADH1 paralogs in the ancestor of Catarrhine and Platyrrhine primates, followed by the loss of an ADH1 paralog in the human lineage.

Original languageEnglish
Article numbere41175
JournalPLoS One
Volume7
Issue number7
DOIs
StatePublished - Jul 31 2012

Fingerprint

Gene Conversion
gene conversion
Gene Duplication
Alcohol Dehydrogenase
alcohol dehydrogenase
gene duplication
Natural History
natural history
Primates
Genes
Lemur
Lemuridae
Hominidae
topology
genes
Strepsirhini
Topology
Platyrrhini
Databases
Cercopithecidae

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

The natural history of class I primate alcohol dehydrogenases includes gene duplication, gene loss, and gene conversion. / Carrigan, Matthew A.; Uryasev, Oleg; Davis, Ross P.; Zhai, LanMin; Hurley, Thomas; Benner, Steven A.

In: PLoS One, Vol. 7, No. 7, e41175, 31.07.2012.

Research output: Contribution to journalArticle

Carrigan, Matthew A. ; Uryasev, Oleg ; Davis, Ross P. ; Zhai, LanMin ; Hurley, Thomas ; Benner, Steven A. / The natural history of class I primate alcohol dehydrogenases includes gene duplication, gene loss, and gene conversion. In: PLoS One. 2012 ; Vol. 7, No. 7.
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