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A comparative approach shows differences in patterns of numt insertion during hominoid evolution.
M I Jensen-Seaman1, J H Wildschutte, I D Soto-Calderón
1Department of Biological Sciences, Duquesne University, 600 Forbes Ave., Pittsburgh, PA 15282, USA. seamanm@duq.edu
Journal of Molecular Evolution
|May 28, 2009
Summary
Chimpanzees have significantly more nuclear mitochondrial DNA (numt) integrations than humans, suggesting differing integration patterns and repair mechanisms. These findings offer insights into numt evolution and hominoid phylogeny reconstruction.
Area of Science:
- Genomics
- Evolutionary Biology
- Molecular Biology
Background:
- Nuclear integrations of mitochondrial DNA (numts) are common in eukaryotes, but their prevalence varies across species.
- Previous numt evolution studies relied on single-species genomes or broad phylogenetic comparisons.
Purpose of the Study:
- To compare numt integration patterns between humans and chimpanzees to understand differences in numt evolution.
- To reconstruct preintegration sequences and identify nucleotide changes associated with numt integration.
- To investigate the mechanisms and evolutionary rates of numt insertions.
Main Methods:
- Comparative analysis of human and chimpanzee genome sequences.
- Identification and characterization of numts in both species.
- Quantification of small insertions, deletions, duplications, and microhomology at integration sites.
- Polymerase chain reaction (PCR)-based screening for numt insertions.
- Phylogenetic analyses using mitochondrial-numt alignments.
Main Results:
- Chimpanzees harbor more numts (66) than humans (37) since their divergence.
- Most numt integrations in both species involve microhomology and short indels, consistent with nonhomologous end-joining repair.
- Human-specific numts integrated into regions depleted of transposable elements, unlike in chimpanzees.
- Evidence suggests an increased rate of numt insertions in the common ancestor of humans and great apes.
- Phylogenetic analyses indicate optimal alignment lengths (>500 bp, preferably >1 kb) for accurate hominoid phylogeny reconstruction.
Conclusions:
- Human and chimpanzee numt integration processes show species-specific differences, particularly concerning transposable element association.
- The nonhomologous end-joining pathway is a primary mechanism for numt integration in both species.
- Numt insertion rates may have varied across hominoid evolutionary history.
- Precise alignment length is crucial for reliable phylogenetic inference using numt data.
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