title: Human population genetic structure and diversity inferred from polymorphic L1(LINE-1) and Alu insertions.
abstract: OBJECTIVE
  The L1 retrotransposable element family is the most successful self-replicating genomic parasite of the human genome. L1 elements drive replication of Alu elements, and both have had far-reaching impacts on the human genome. We use L1 and Alu insertion polymorphisms to analyze human population structure.
  
  
  METHODS
  We genotyped 75 recent, polymorphic L1 insertions in 317 individuals from 21 populations in sub-Saharan Africa, East Asia, Europe and the Indian subcontinent. This is the first sample of L1 loci large enough to support detailed population genetic inference. We analyzed these data in parallel with a set of 100 polymorphic Alu insertion loci previously genotyped in the same individuals.
  
  
  CONCLUSIONS
  The data sets yield congruent results that support the recent African origin model of human ancestry. A genetic clustering algorithm detects clusters of individuals corresponding to continental regions. The number of loci sampled is critical: with fewer than 50 typical loci, structure cannot be reliably discerned in these populations. The inclusion of geographically intermediate populations (from India) reduces the distinctness of clustering. Our results indicate that human genetic variation is neither perfectly correlated with geographic distance (purely clinal) nor independent of distance (purely clustered), but a combination of both: stepped clinal.
authors.affiliation: Department of Human Genetics, University of Utah Health Sciences Center, Salt Lake City, UT 84112-5330, USA. david.witherspoon@utah.edu
authors.forename: D J
authors.initials: DJ
authors.lastname: Witherspoon
authors.forename: E E
authors.initials: EE
authors.lastname: Marchani
authors.forename: W S
authors.initials: WS
authors.lastname: Watkins
authors.forename: C T
authors.initials: CT
authors.lastname: Ostler
authors.forename: S P
authors.initials: SP
authors.lastname: Wooding
authors.forename: B A
authors.initials: BA
authors.lastname: Anders
authors.forename: J D
authors.initials: JD
authors.lastname: Fowlkes
authors.forename: S
authors.initials: S
authors.lastname: Boissinot
authors.forename: A V
authors.initials: AV
authors.lastname: Furano
authors.forename: D A
authors.initials: DA
authors.lastname: Ray
authors.forename: A R
authors.initials: AR
authors.lastname: Rogers
authors.forename: M A
authors.initials: MA
authors.lastname: Batzer
authors.forename: L B
authors.initials: LB
authors.lastname: Jorde
mesh_terms: D020087:Alu Elements / Q000502:physiology*; D005787:Gene Frequency; D008040:Genetic Linkage; D014644:Genetic Variation; D005828:Genetics, Population; D015894:Genome, Human; D005838:Genotype; D006801:Humans; D020084:Long Interspersed Nucleotide Elements / Q000502:physiology*; D010802:Phylogeny; D011110:Polymorphism, Genetic; D044382:Population Groups / Q000208:ethnology