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Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
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DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.
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Transposons, or "jumping genes," are small mobile genetic elements (MGEs) that range from 700 to 40,000 base pairs in length. They are found in all organisms and can move within the same chromosome or transfer to different chromosomes. In some cases, transposons can also jump between different host DNA molecules, such as plasmids or viruses, contributing to genetic variability.Barbara McClintock first discovered these mobile genetic elements in the 1940s while studying maize genetics, and she...
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As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...
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LTR retrotransposons are class I transposable elements with long terminal repeats flanking an internal coding region. These elements are less abundant in mammals compared to other class I transposable elements. About 8 percent of human genomic DNA comprises LTR retrotransposons. Some of the common examples of LTR retrotransposons are Ty elements in yeast and Copia elements in Drosophila.
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The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
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Transposable element polymorphisms recapitulate human evolution.

Lavanya Rishishwar1, Carlos E Tellez Villa2, I King Jordan1

  • 1School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332-0230 USA ; PanAmerican Bioinformatics Institute, Cali, Valle del Cauca Colombia ; BIOS Centro de Bioinformática y Biología Computacional, Manizales, Caldas Colombia.

Mobile DNA
|November 19, 2015
PubMed
Summary
This summary is machine-generated.

Transposable elements (TE) provide a novel genome-wide dataset for human population genetics. This study reveals TE polymorphisms reflect human evolution and migration patterns, useful for ancestry and admixture analyses.

Keywords:
AdmixtureAluAncestry informative markersHuman ancestryL1PhylogeneticsPolymorphismPopulation geneticsSVATransposable elements

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Area of Science:

  • Human Population Genetics
  • Genomics
  • Molecular Anthropology

Background:

  • The human genome harbors active transposable elements (TEs) like Alu, L1, and SVA.
  • Germline TE transposition creates polymorphic TE (polyTE) loci, varying between individuals.
  • Previous studies used limited polyTE loci for ancestry, but genome-wide analysis was lacking.

Purpose of the Study:

  • To conduct the first human population genetic analysis using a comprehensive genome-wide polyTE dataset.
  • To assess the utility of polyTEs as markers for human ancestry and admixture.
  • To provide a resource of polyTE loci for developing new ancestry informative markers.

Main Methods:

  • Genotyped 16,192 polyTE loci across 2,504 individuals from 26 human populations.
  • Analyzed polyTE allele frequencies, geographic differentiation, and genetic diversity.
  • Computed allele sharing distances and compared polyTE-based relationships with SNP data.

Main Results:

  • PolyTEs, though at low frequencies, exhibit significant geographic differentiation and group-specific insertions.
  • African populations show the highest polyTE numbers and genetic diversity, with Alu being most prevalent.
  • PolyTE genotypes accurately reflect human evolutionary relationships, migration patterns, and continental ancestry/admixture.

Conclusions:

  • TE polymorphisms mirror established human evolutionary and migration patterns over the last 60-100,000 years.
  • Ensembles of polyTE loci are effective for both ancestry and admixture analyses.
  • PolyTE diversity patterns hint at potential links between genetic divergence and population-specific phenotypes.