ArticleGenetics2007
The neutral coalescent process for recent gene duplications and copy-number variants.
Article in Genetics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 29 citations in OpenAlex.
- ParaMask: a new method to identify multicopy genomic regions, corrects major biases in whole-genome sequencing data.Genome biology · 2025Article
- Effect of Collapsed Duplications on Diversity Estimates: What to Expect.Genome biology and evolution · 2018Article
- Strong phenotypic plasticity limits potential for evolutionary responses to climate change.Nature communications · 2018Article
- Reconciliation feasibility in the presence of gene duplication, loss, and coalescence with multiple individuals per species.BMC bioinformatics · 2017Article
- Convergent Balancing Selection on an Antimicrobial Peptide in Drosophila.Current biology : CB · 2016Article
- Human gene copy number variation and infectious disease.Human genetics · 2014Review
- Interplay of interlocus gene conversion and crossover in segmental duplications under a neutral scenario.G3 (Bethesda, Md.) · 2014Article
- New gene evolution: little did we know.Annual review of genetics · 2013Review
- Both positive and negative selection pressures contribute to the polymorphism pattern of the duplicated human CYP21A2 gene.PloS one · 2013Article
- Unified modeling of gene duplication, loss, and coalescence using a locus tree.Genome research · 2012Article
- The coalescent with selection on copy number variants.Genetics · 2012Article
- Chimeric genes as a source of rapid evolution in Drosophila melanogaster.Molecular biology and evolution · 2012Article
- High sequence variability, diverse subcellular localizations, and ecological implications of alkaline phosphatase in dinoflagellates and other eukaryotic phytoplankton.Frontiers in microbiology · 2012Article
- Balancing selection at the tomato RCR3 Guardee gene family maintains variation in strength of pathogen defense.PLoS genetics · 2012Article
- A worldwide analysis of beta-defensin copy number variation suggests recent selection of a high-expressing DEFB103 gene copy in East Asia.Human mutation · 2011Article
- Diversity-enhancing selection acts on a female reproductive protease family in four subspecies of Drosophila mojavensis.Genetics · 2011Article
- Molecular evolution of the three short PGRPs of the malaria vectors Anopheles gambiae and Anopheles arabiensis in East Africa.BMC evolutionary biology · 2010Article
- Duplication, selection and gene conversion in a Drosophila mojavensis female reproductive protein family.Genetics · 2009Article
- Arabidopsis thaliana genes encoding defense signaling and recognition proteins exhibit contrasting evolutionary dynamics.Genetics · 2009Article
- A survey of genetic simulation software for population and epidemiological studies.Human genomics · 2008Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
I describe a method for simulating samples from gene families of size two under a neutral coalescent process, for the case where the duplicate gene either has fixed recently in the population or is still segregating. When a duplicate locus has recently fixed by genetic drift, diversity in the new gene is expected to be reduced, and an excess of rare alleles is expected, relative to the predictions of the standard coalescent model. The expected patterns of polymorphism in segregating duplicates ("copy-number variants") depend both on the frequency of the duplicate in the sample and on the rate of crossing over between the two loci. When the crossover rate between the ancestral gene and the copy-number variant is low, the expected pattern of variability in the ancestral gene will be similar to the predictions of models of either balancing or positive selection, if the frequency of the duplicate in the sample is intermediate or high, respectively. Simulations are used to investigate the effect of crossing over between loci, and gene conversion between the duplicate loci, on levels of variability and the site-frequency spectrum.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.