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PMID: 15008405 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

Comprehensive analysis of two Alu Yd subfamilies.

Journal of molecular evolution ·Vol. 57 Suppl 1 ·2003-00-00 ·Pages S76-89

Xing J, Salem AH, Hedges DJ, Kilroy GE, Watkins WS, Schienman JE, Stewart CB, Jurka J, Jorde LB, Batzer MA

Abstract

Alu elements have inserted in the human genome throughout primate evolution. A small number of Alu insertions have occurred after the divergence of humans from nonhuman primates and therefore should not be present in nonhuman primate genomes. Most of these recently integrated Alu elements are contained with a series of discrete Alu subfamilies that are related to each other based upon diagnostic nucleotide substitutions. We have extracted members of the Alu Yd subfamily that are derivatives of the Alu Y subfamily that share a common 12-bp deletion that defines the Yd lineage from the draft sequence of the human genome. Analysis of the Yd Alu elements resulted in the recovery of two new Alu subfamilies, Yd3 and Yd6, which contain a total of 295 members (198 Yd3 and 97 Yd6). DNA sequence analysis of each of the Alu Yd subfamilies yielded age estimates of 8.02 and 1.20 million years old for the Alu Yd3 and Yd6 subfamilies, respectively. Two hundred Alu Yd3 and Yd6 loci were screened using polymerase chain reaction (PCR) assays to determine their phylogenetic origin and associated levels of human genomic diversity. The Alu Yd3 subfamily appears to have started amplifying relatively early in primate evolution and continued propagating albeit at a low level as many of its members are found in a variety of hominoid (humans, greater and lesser ape) genomes. Only two of the elements are polymorphic in the human genome and absent from the genomes of nonhuman primates. By contrast all of the members of the Alu Yd6 subfamily are restricted to the human genome, with 12% of the elements representing insertion polymorphisms in human populations. A single Alu Yd6 locus contained an independent parallel forward insertion of a paralogous Alu Sq sequence in the owl monkey. These Alu subfamilies are a source of genomic fossil relics for the study of primate phylogenetics and human population genetics.

MeSH Terms
Alu Elements Animals Base Sequence Evolution, Molecular Gene Conversion Genetic Variation Genome, Human Humans Molecular Sequence Data Multigene Family Polymorphism, Genetic Primates/genetics
Authors & Affiliations
10 authors, click to expand affiliations / ORCID
Xing Jinchuan
Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA.
Salem Abdel-Halim
Hedges Dale J
Kilroy Gail E
Watkins W Scott
Schienman John E
Stewart Caro-Beth
Jurka Jerzy
Jorde Lynn B
Batzer Mark A
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Article Info
Journal
Journal of molecular evolution
Abbr.
J Mol Evol
ISSN
0022-2844
DOI
10.1007/s00239-003-0009-0
Published
2003-00-00
Pages
S76-89
Language
English
Region
Germany
NLM ID
0360051
Subset
IM
Grants
NIGMS NIH HHS · R01 GM59290 · United States
NIGMS NIH HHS · R01 GM60760 · United States
External Links
PubMed source DOI: 10.1007/s00239-003-0009-0 View journal details
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