Teshima, Kosuke M, Innan, Hideki
Abstract Background The pattern of single nucleotide polymorphisms, or SNPs, contains a tremendous amount of information with respect to the mechanisms of the micro-evolutionary process of a species....
Cuong Than, Derek Ruths, Hideki Innan, Luay Nakhleh
Prokaryotic organisms share genetic material across species boundaries by means of a process known as horizontal gene transfer (HGT). This process has great significance for understanding prokaryotic...
The Effect of Gene Flow on the Coalescent Time in the Human-Chimpanzee Ancestral Population (2006)
Innan, Hideki, Watanabe, Hidemi
The coalescent process in the human-chimpanzee ancestral population is investigated using a model, which incorporates a certain time period of gene flow during the speciation process. a is a...
The Effect of Gene Flow on the Coalescent Time in the Human-Chimpanzee Ancestral Population (2006)
Innan, Hideki, Watanabe, Hidemi
The coalescent process in the human-chimpanzee ancestral population is investigated using a model which incorporates a certain time period of gene flow during the speciation process. a is a parameter...
The Pattern of Polymorphism on Human Chromosome 21 (2003)
Innan, Hideki, Padhukasahasram, Badri, Nordborg, Magnus
Polymorphism data from 20 partially resequenced copies of human chromosome 21—more than 20,000 polymorphic sites—were analyzed. The allele-frequency distribution shows no deviation from the...
Recombination or Mutational Hot Spots in Human mtDNA? (2002)
Innan, Hideki, Nordborg, Magnus
Awadalla, Eyre-Walker, and Maynard Smith (1999) recently argued that there might be recombination in human mitochondrial DNA (mtDNA). Their claim was based on their observation of decaying linkage...
Relaxed selective pressure on an essential component of pheromone transduction in primate evolution
Liman, Emily R., Innan, Hideki
The vomeronasal organ (VNO) detects pheromones in many vertebrate species but is likely to be vestigial in humans. TRPC2(TRP2), a gene that is essential for VNO function in the mouse, is a pseudogene...
A two-locus gene conversion model with selection and its application to the human RHCE and RHD genes
A two-locus gene conversion model with selection is developed. Under the joint action of selection, mutation, gene conversion, recombination, and random genetic drift, approximate formulas for the...
The Pattern of Polymorphism on Human Chromosome 21
Innan, Hideki, Padhukasahasram, Badri, Nordborg, Magnus
Polymorphism data from 20 partially resequenced copies of human chromosome 21—more than 20,000 polymorphic sites—were analyzed. The allele-frequency distribution shows no deviation from the...
Pattern of polymorphism after strong artificial selection in a domestication event
The process of strong artificial selection during a domestication event is modeled, and its effect on the pattern of DNA polymorphism is investigated. The model also considers population bottleneck...
The Probability and Chromosomal Extent of trans-specific Polymorphism
Wiuf, Carsten, Zhao, Keyan, Innan, Hideki, Nordborg, Magnus
Balancing selection may result in trans-specific polymorphism: the maintenance of allelic classes that transcend species boundaries by virtue of being more ancient than the species themselves. At the...
Innan, Hideki, Zhang, Kangyu, Marjoram, Paul, Tavaré, Simon, Rosenberg, Noah A.
Several tests of neutral evolution employ the observed number of segregating sites and properties of the haplotype frequency distribution as summary statistics and use simulations to obtain rejection...
Sugino, Ryuichi P., Innan, Hideki
A maximum-likelihood (ML) method is developed to estimate the duration of concerted evolution and the time to the whole-genome duplication (WGD) event in baker's yeast (Saccharomyces cerevisiae). The...
A simple two-locus gene conversion model is considered to investigate the amounts of DNA variation and linkage disequilibrium in small multigene families. The exact solutions for the expectations and...
The coalescent and infinite-site model of a small multigene family.
The infinite-site model of a small multigene family with two duplicated genes is studied. The expectations of the amounts of nucleotide variation within and between two genes and linkage...
Nordborg, Magnus, Innan, Hideki
A stochastic model for the genealogy of a sample of recombining sequences containing one or more sites subject to selection in a subdivided population is described. Selection is incorporated by...
The extent of linkage disequilibrium and haplotype sharing around a polymorphic site.
Innan, Hideki, Nordborg, Magnus
Various expressions related to the length of a conserved haplotype around a polymorphism of known frequency are derived. We obtain exact expressions for the probability that no recombination has...
Distinguishing the hitchhiking and background selection models.
Innan, Hideki, Stephan, Wolfgang
A simple method to distinguish hitchhiking and background selection is proposed. It is based on the observation that these models make different predictions about the average level of nucleotide...
The effect of gene conversion on the divergence between duplicated genes.
Teshima, Kosuke M, Innan, Hideki
Nonindependent evolution of duplicated genes is called concerted evolution. In this article, we study the evolutionary process of duplicated regions that involves concerted evolution. The model...
Modified Hudson–Kreitman–Aguadé Test and Two-Dimensional Evaluation of Neutrality Tests
There are a number of polymorphism-based statistical tests of neutrality, but most of them focus on either the amount or the pattern of polymorphism. In this article, a new test called the...
Relaxed selective pressure on an essential component of pheromone transduction in primate evolution
Liman, Emily R., Innan, Hideki
The vomeronasal organ (VNO) detects pheromones in many vertebrate species but is likely to be vestigial in humans. TRPC2(TRP2), a gene that is essential for VNO function in the mouse, is a pseudogene...
A two-locus gene conversion model with selection and its application to the human RHCE and RHD genes
A two-locus gene conversion model with selection is developed. Under the joint action of selection, mutation, gene conversion, recombination, and random genetic drift, approximate formulas for the...
The Pattern of Polymorphism on Human Chromosome 21
Innan, Hideki, Padhukasahasram, Badri, Nordborg, Magnus
Polymorphism data from 20 partially resequenced copies of human chromosome 21—more than 20,000 polymorphic sites—were analyzed. The allele-frequency distribution shows no deviation from the...
Pattern of polymorphism after strong artificial selection in a domestication event
The process of strong artificial selection during a domestication event is modeled, and its effect on the pattern of DNA polymorphism is investigated. The model also considers population bottleneck...
The Probability and Chromosomal Extent of trans-specific Polymorphism
Wiuf, Carsten, Zhao, Keyan, Innan, Hideki, Nordborg, Magnus
Balancing selection may result in trans-specific polymorphism: the maintenance of allelic classes that transcend species boundaries by virtue of being more ancient than the species themselves. At the...
Innan, Hideki, Zhang, Kangyu, Marjoram, Paul, Tavaré, Simon, Rosenberg, Noah A.
Several tests of neutral evolution employ the observed number of segregating sites and properties of the haplotype frequency distribution as summary statistics and use simulations to obtain rejection...
Sugino, Ryuichi P., Innan, Hideki
A maximum-likelihood (ML) method is developed to estimate the duration of concerted evolution and the time to the whole-genome duplication (WGD) event in baker's yeast (Saccharomyces cerevisiae). The...
A simple two-locus gene conversion model is considered to investigate the amounts of DNA variation and linkage disequilibrium in small multigene families. The exact solutions for the expectations and...
The coalescent and infinite-site model of a small multigene family.
The infinite-site model of a small multigene family with two duplicated genes is studied. The expectations of the amounts of nucleotide variation within and between two genes and linkage...
Nordborg, Magnus, Innan, Hideki
A stochastic model for the genealogy of a sample of recombining sequences containing one or more sites subject to selection in a subdivided population is described. Selection is incorporated by...
The extent of linkage disequilibrium and haplotype sharing around a polymorphic site.
Innan, Hideki, Nordborg, Magnus
Various expressions related to the length of a conserved haplotype around a polymorphism of known frequency are derived. We obtain exact expressions for the probability that no recombination has...
Distinguishing the hitchhiking and background selection models.
Innan, Hideki, Stephan, Wolfgang
A simple method to distinguish hitchhiking and background selection is proposed. It is based on the observation that these models make different predictions about the average level of nucleotide...
The effect of gene conversion on the divergence between duplicated genes.
Teshima, Kosuke M, Innan, Hideki
Nonindependent evolution of duplicated genes is called concerted evolution. In this article, we study the evolutionary process of duplicated regions that involves concerted evolution. The model...
Modified Hudson–Kreitman–Aguadé Test and Two-Dimensional Evaluation of Neutrality Tests
There are a number of polymorphism-based statistical tests of neutrality, but most of them focus on either the amount or the pattern of polymorphism. In this article, a new test called the...
Molecular Evolution of Pathogenicity-Island Genes in Pseudomonas viridiflava
Araki, Hitoshi, Innan, Hideki, Kreitman, Martin, Bergelson, Joy
The bacterial pathogen Pseudomonas viridiflava possesses two pathogenicity islands (PAIs) that share many gene homologs, but are structurally and phenotypically differentiated (T-PAI and S-PAI)....
Neofunctionalization of Duplicated Genes Under the Pressure of Gene Conversion
Teshima, Kosuke M., Innan, Hideki
Neofunctionalization occurs when a neofunctionalized allele is fixed in one of duplicated genes. This is a simple fixation process if duplicated genes accumulate mutations independently. However, the...
The origins of the Asian cultivated rice Oryza sativa from its wild ancestor O. rufipogon have been debated for decades. The question mainly concerns whether it originated monophyletically or...
Takahasi, K. Ryo, Innan, Hideki
A new measure of directional linkage disequilibrium is developed for detecting epistatic selection on interacting genes. Simulations show that by orienting the direction of linkage disequilibrium on...
When a local colonization in a new niche occurs, the new derived population should be subject to different selective pressures from that in the original parental population; consequently it is likely...
The Evolutionary Rate of Duplicated Genes Under Concerted Evolution
The effect of directional selection on the fixation process of a single mutation that spreads in a multigene family by gene conversion is investigated. A simple two-locus model with two alleles, A...
Preservation of a Pseudogene by Gene Conversion and Diversifying Selection
Takuno, Shohei, Nishio, Takeshi, Satta, Yoko, Innan, Hideki
Interlocus gene conversion is considered a crucial mechanism for generating novel combinations of polymorphisms in duplicated genes. The importance of gene conversion between duplicated genes has...
Duplication and Gene Conversion in the Drosophila melanogaster Genome
Using the genomic sequences of Drosophila melanogaster subgroup, the pattern of gene duplications was investigated with special attention to interlocus gene conversion. Our fine-scale analysis with...
Takahashi, Yasuyuki, Teshima, Kosuke M., Yokoi, Shuji, Innan, Hideki, Shimamoto, Ko
Rice is a facultative short-day plant, and molecular genetic studies have identified the major genes involved in short-day flowering. However, the molecular mechanisms promoting the diversity of...