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Updated: Jul 11, 2026
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RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level
Published on: May 19, 2019
Human population genetic structure and diversity inferred from polymorphic L1(LINE-1) and Alu insertions.
D J Witherspoon1, E E Marchani, W S Watkins
1Department of Human Genetics, University of Utah Health Sciences Center, Salt Lake City, UT 84112-5330, USA. david.witherspoon@utah.edu
Human Heredity
|September 28, 2006
Summary
Human genomic parasites, LINE-1 (L1) and Alu elements, reveal population structure. Analysis of L1 and Alu insertion polymorphisms supports the recent African origin of humans and indicates stepped clinal variation.
Area of Science:
- Genomics
- Population Genetics
- Human Evolution
Background:
- LINE-1 (L1) retrotransposable elements are significant genomic parasites in humans.
- L1 elements are crucial for the replication of Alu elements, both impacting the human genome.
- Insertion polymorphisms of L1 and Alu elements offer insights into human population structure.
Purpose of the Study:
- To analyze human population structure using L1 and Alu insertion polymorphisms.
- To investigate the utility of L1 and Alu insertion polymorphisms for population genetic inference.
- To test the recent African origin model of human ancestry.
Main Methods:
- Genotyping of 75 polymorphic L1 insertions in 317 individuals across 21 sub-Saharan African, East Asian, European, and Indian subcontinent populations.
- Parallel analysis of 100 polymorphic Alu insertion loci previously genotyped in the same individuals.
- Application of a genetic clustering algorithm to discern population structure.
Main Results:
- Congruent results from L1 and Alu data support the recent African origin model.
- Genetic clustering algorithm identified distinct clusters corresponding to continental regions.
- A critical number of loci (over 50) is necessary for reliable population structure discernment.
- Inclusion of intermediate populations (India) reduced clustering distinctness.
Conclusions:
- Human genetic variation exhibits a stepped clinal pattern, combining both distance-dependent (clinal) and clustered components.
- The study validates the utility of retrotransposon insertion polymorphisms for human population genetics.
- Findings reinforce the model of human origins from Africa with subsequent migrations and population structuring.
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