The Share of Human Genomic DNA under Selection Estimated from Human-Mouse Genomic Alignments
Abstract
Draft sequences covering most euchromatic parts haverecently become available for two mammalian genomes,human (Lander et al. 2001; Venter et al. 2001) and mouse(Waterston et al. 2002). This raises the possibility of using comparative genomics to estimate what fraction ofthe human genome evolves under purifying selection.Lacking genomes of other mammals, this comparativeexercise is still in its preliminary stages. However, arough estimate has been made that ~5% of the humangenome is in short segments that appear to be under selection based on comparison with mouse (Waterston et al.2002). Here, as a basis for future refinements, we presentthe computational strategy that led to this estimate, providing details on scoring functions, data preparation, andstatistical techniques. We also describe stability analyses,control experiments, and tests for the effects of artifactsthat were performed to establish robustness of our results,and discuss possible alternate interpretations...
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About 5% or more of bases in mammalian genomes are under purifying selection.
“Analyses of human and rodent genomes (Mouse Genome Sequencing Consortium 2002;Chiaromonte et al. 2003;Roskin et al. 2003;Cooper et al. 2004;Rat Genome Sequencing Project Consortium 2004) indicate that about 5% or more of bases in mammalian genomes are under purifying selection”
From Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes (2005) · cites this paper as Chiaromonte et al. 2003
The vertebrate coverage is similar to recent estimates of 5%-8% for the share of the human genome under purifying selection.
“Note that the vertebrate coverage is similar to recent estimates of 5%-8% for the share of the human genome that is under purifying selection”
From Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes (2005) · cites this paper as Chiaromonte et al. 2003
The composition of vertebrate conserved elements agrees with bulk statistical estimates of the share of the human genome under selection and with an analysis of conserved elements in the CFTR region.
“These numbers are in good agreement both with bulk statistical estimates, based on genome-wide human/mouse and human/ mouse/rat alignments, of the share of the human genome that is under selection (Chiaromonte et al. 2003;Roskin et al. 2003;Cooper et al. 2004), and with an analysis of conserved elements in the region of the CFTR gene (Margulies et al. 2003;Thomas et al. 2003).”
From Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes (2005) · cites this paper as Chiaromonte et al. 2003
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Self-citation
- Authors
- CHIAROMONTE, F., WEBER, R. J., ROSKIN, K. M., DIEKHANS, M., KENT, W. J., & HAUSSLER, D.
- Affiliations
- Pennsylvania State University (US)
- Venue
- Cold Spring Harbor Symposia on Quantitative Biology
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2003-01-01
- Volume
- 68
- Issue
- 0
- Pages
- 245-254
- ISSN
- 0091-7451 (ISSN-L)
- 1943-4456
- OpenAlex
- W2091656649
- Cited by
- 64
- References
- 0
- Citations by year
- 2026: 1 · 2024: 1 · 2023: 1 · 2022: 1 · 2021: 1 · 2018: 1 · 2017: 1 · 2015: 3 · 2014: 3 · 2013: 1 · 2012: 4
- Type
- posted content
- Language
- en
- Open access
- closed
- Locations
- Cold Spring Harbor Symposia on Quantitative Biology (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Human Genome Research Institute (HG 02238, P41HG002371, R01HG002238)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- purifying selection, human genome, mouse genome, comparative genomics, genome alignment, scoring functions, stability analysis, human-mouse comparison
- MeSH terms
- Animals, DNA, Humans, Repetitive Sequences, Nucleic Acid, Selection, Genetic, Species Specificity, Genome, Human, Sequence Alignment, Conserved Sequence, Evolution, Molecular, Mice
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