Hideki Innan

Summary

Affiliation: Graduate University for Advanced Studies
Country: Japan

Publications

  1. pmc QTL Map Meets Population Genomics: An Application to Rice
    Jeffrey A Fawcett
    Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
    PLoS ONE 8:e83720. 2013
  2. pmc Modified Hudson-Kreitman-Aguade test and two-dimensional evaluation of neutrality tests
    Hideki Innan
    Human Genetics Center, School of Public Health, University of Texas Health Science Center, Houston, Texas 77030, USA
    Genetics 173:1725-33. 2006
  3. pmc Detecting local adaptation using the joint sampling of polymorphism data in the parental and derived populations
    Hideki Innan
    Graduate University for Advanced Studies, Hayama, Kanagawa 240 0193, Japan
    Genetics 179:1713-20. 2008
  4. doi request reprint The evolution of gene duplications: classifying and distinguishing between models
    Hideki Innan
    Graduate University for Advanced Studies, Hayama, Kanagawa 240 0193, Japan
    Nat Rev Genet 11:97-108. 2010
  5. ncbi request reprint Population genetic models of duplicated genes
    Hideki Innan
    Graduate University for Advanced Studies, Hayama, Kanagawa, 240 0193, Japan
    Genetica 137:19-37. 2009
  6. ncbi request reprint Selection for more of the same product as a force to enhance concerted evolution of duplicated genes
    Ryuichi P Sugino
    University of Texas Health Science Center at Houston School of Public Health, Human Genetics Center, 1200 Hermann Pressler, Houston, TX 77030, USA
    Trends Genet 22:642-4. 2006
  7. pmc Estimating the time to the whole-genome duplication and the duration of concerted evolution via gene conversion in yeast
    Ryuichi P Sugino
    Human Genetics Center, School of Public Health, Unversity of Texas Health Science Center, Houston 77030, USA
    Genetics 171:63-9. 2005
  8. doi request reprint The linkage method: a novel approach for SNP detection and haplotype reconstruction from a single diploid individual using next-generation sequence data
    Eriko Sasaki
    Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
    Mol Biol Evol 30:2187-96. 2013
  9. ncbi request reprint Theories for analyzing polymorphism data in duplicated genes
    Hideki Innan
    Human Genetics Center, School of Public Health, University of Texas Health Science Center, 1200 Hermann Pressler, Houston, TX 77030, USA
    Genes Genet Syst 79:65-75. 2004
  10. pmc Statistical tests of the coalescent model based on the haplotype frequency distribution and the number of segregating sites
    Hideki Innan
    Human Genetics Center, School of Public Health, University of Texas Health Science Center, Houston, 77030, USA
    Genetics 169:1763-77. 2005

Detail Information

Publications45

  1. pmc QTL Map Meets Population Genomics: An Application to Rice
    Jeffrey A Fawcett
    Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
    PLoS ONE 8:e83720. 2013
    ..Our study shows that population genomic approaches and QTL mapping information can be used together to identify genes that might be of agronomic importance. ..
  2. pmc Modified Hudson-Kreitman-Aguade test and two-dimensional evaluation of neutrality tests
    Hideki Innan
    Human Genetics Center, School of Public Health, University of Texas Health Science Center, Houston, Texas 77030, USA
    Genetics 173:1725-33. 2006
    ....
  3. pmc Detecting local adaptation using the joint sampling of polymorphism data in the parental and derived populations
    Hideki Innan
    Graduate University for Advanced Studies, Hayama, Kanagawa 240 0193, Japan
    Genetics 179:1713-20. 2008
    ..Therefore, for detecting the signature of local adaptation in polymorphism data, it is important to evaluate the data from both parental and derived populations simultaneously...
  4. doi request reprint The evolution of gene duplications: classifying and distinguishing between models
    Hideki Innan
    Graduate University for Advanced Studies, Hayama, Kanagawa 240 0193, Japan
    Nat Rev Genet 11:97-108. 2010
    ..Setting out these predictions is an important step towards identifying the main mechanisms that are involved in the evolution of gene duplications...
  5. ncbi request reprint Population genetic models of duplicated genes
    Hideki Innan
    Graduate University for Advanced Studies, Hayama, Kanagawa, 240 0193, Japan
    Genetica 137:19-37. 2009
    ..In the first half, models assuming independent evolution of duplicated genes are introduced, and then the effect of gene conversion is considered in the second half...
  6. ncbi request reprint Selection for more of the same product as a force to enhance concerted evolution of duplicated genes
    Ryuichi P Sugino
    University of Texas Health Science Center at Houston School of Public Health, Human Genetics Center, 1200 Hermann Pressler, Houston, TX 77030, USA
    Trends Genet 22:642-4. 2006
    ..This observation can be explained by selection favoring more of the same product, which could enhance concerted evolution in dosage-sensitive genes...
  7. pmc Estimating the time to the whole-genome duplication and the duration of concerted evolution via gene conversion in yeast
    Ryuichi P Sugino
    Human Genetics Center, School of Public Health, Unversity of Texas Health Science Center, Houston 77030, USA
    Genetics 171:63-9. 2005
    ..cerevisiae and Kluyveromyces waltii, suggesting that the WGD occurred in very early stages after speciation or the WGD might have been involved in the speciation event...
  8. doi request reprint The linkage method: a novel approach for SNP detection and haplotype reconstruction from a single diploid individual using next-generation sequence data
    Eriko Sasaki
    Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
    Mol Biol Evol 30:2187-96. 2013
    ..The algorithm was implemented as the program "linkSNPs." ..
  9. ncbi request reprint Theories for analyzing polymorphism data in duplicated genes
    Hideki Innan
    Human Genetics Center, School of Public Health, University of Texas Health Science Center, 1200 Hermann Pressler, Houston, TX 77030, USA
    Genes Genet Syst 79:65-75. 2004
    ..The theoretical results are well in agreement with polymorphism data in duplicated genes. The effect of selection on the pattern of polymorphism is also considered...
  10. pmc Statistical tests of the coalescent model based on the haplotype frequency distribution and the number of segregating sites
    Hideki Innan
    Human Genetics Center, School of Public Health, University of Texas Health Science Center, Houston, 77030, USA
    Genetics 169:1763-77. 2005
    ..For larger samples, we consider simulation-based approaches. The utility of the HCT is demonstrated in simulations of alternative models and in application to data from Drosophila melanogaster...
  11. pmc Neofunctionalization of duplicated genes under the pressure of gene conversion
    Kosuke M Teshima
    The Graduate University for Advanced Studies, Hayama, Kanagawa 240 0193, Japan
    Genetics 178:1385-98. 2008
    ....
  12. pmc Population genomics in bacteria: a case study of Staphylococcus aureus
    Shohei Takuno
    Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
    Mol Biol Evol 29:797-809. 2012
    ..aureus genomes. Our results call for more research into the evolutionary role of homologous recombination in bacterial populations...
  13. doi request reprint Selection fine-tunes the expression of microRNA target genes in Arabidopsis thaliana
    Shohei Takuno
    Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
    Mol Biol Evol 28:2429-34. 2011
    ..Based on these results, we conclude that tuning via miRNA regulation has a strong impact on the evolution of target genes through which highly sophisticated regulation systems have been established...
  14. doi request reprint Natural selection on gene order in the genome reorganization process after whole-genome duplication of yeast
    Ryuichi P Sugino
    Department of Evolutionary Studies of Biosystems, Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
    Mol Biol Evol 29:71-9. 2012
    ..It is indicated that gene regulation would be one of the major factors to determine the order of coding genes...
  15. ncbi request reprint Very low gene duplication rate in the yeast genome
    Li Zhi Gao
    Human Genetics Center, School of Public Health, University of Texas Health Science Center, 1200 Hermann Pressler, Houston, TX 77030, USA
    Science 306:1367-70. 2004
    ..The average length of the period of concerted evolution and the gene conversion rate are estimated to be approximately 25 million years and approximately 28 times the mutation rate, respectively...
  16. ncbi request reprint The effect of gene flow on the coalescent time in the human-chimpanzee ancestral population
    Hideki Innan
    Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, USA
    Mol Biol Evol 23:1040-7. 2006
    ..The result is discussed in the view of the mode of speciation. Another ML method is developed to estimate the male-female ratio (alpha) of mutation rate, in which the coalescent process in the ancestral population is taken into account...
  17. pmc Pattern of polymorphism after strong artificial selection in a domestication event
    Hideki Innan
    Human Genetics Center, School of Public Health, University of Texas Health Science Center, Houston, TX 77030, USA
    Proc Natl Acad Sci U S A 101:10667-72. 2004
    ..These theoretical results are discussed in light of data collected from maize. Although the main focus of this article is on domestication, this model can also be generalized to describe selective sweeps from standing genetic variation...
  18. pmc Population genetics and molecular evolution of DNA sequences in transposable elements. I. A simulation framework
    T E Kijima
    Graduate University for Advanced Studies, Hayama, Kanagawa 240 0193, Japan
    Genetics 195:957-67. 2013
    ..It is demonstrated that the phylogeny of TE sequences could be informative to understand the dynamics of TE evolution. ..
  19. doi request reprint Evolution of complexity in miRNA-mediated gene regulation systems
    Shohei Takuno
    Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
    Trends Genet 24:56-9. 2008
    ..Furthermore, we show that the mode of selection to maintain the systems depend on their complexity levels...
  20. doi request reprint Simulation-based likelihood approach for evolutionary models of phenotypic traits on phylogeny
    Nobuyuki Kutsukake
    Department of Evolutionary Studies of Biosystems and Hayama Center for Advanced Studies, The Graduate University for Advanced Studies, Hayama, Kanagawa 240 0193, Japan
    Evolution 67:355-67. 2013
    ..Our method can be easily implemented in more computationally effective frameworks such as approximate Bayesian computation (ABC), which will enhance the use of computationally intensive methods in the study of phenotypic evolution...
  21. ncbi request reprint Modeling evolutionary growth of a microRNA-mediated regulation system
    Tetsuya Akita
    Graduate University for Advanced Studies, Hayama, Kanagawa 240 0193, Japan
    J Theor Biol 311:54-65. 2012
    ..Further development of such models would provide insights into the evolutionary growth of the complexity of biosystems...
  22. pmc An autosomal analysis gives no genetic evidence for complex speciation of humans and chimpanzees
    Masato Yamamichi
    Department of Evolutionary Studies of Biosystems, Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
    Mol Biol Evol 29:145-56. 2012
    ..We conclude that the simplest speciation model with instantaneous split adequately describes the human-chimpanzee speciation event, and there is no strong reason to involve complicated factors in explaining the autosomal data...
  23. pmc The coalescent with selection on copy number variants
    Kosuke M Teshima
    The Graduate University for Advanced Studies, Hayama, Kanagawa 240 0193, Japan
    Genetics 190:1077-86. 2012
    ..Because this effect of gene conversion is restricted only to the duplicated region, more power to detect selection is expected if a flanking region to the duplicated copy is used...
  24. pmc mbs: modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection
    Kosuke M Teshima
    Hayama Center for Advanced Studies, Graduate University for Advanced Studies, Hayama, Kanagawa 240 0193, Japan
    BMC Bioinformatics 10:166. 2009
    ..However, it has been difficult to incorporate natural selection into the coalescent framework...
  25. doi request reprint Potential of fish opsin gene duplications to evolve new adaptive functions
    Jun Gojobori
    Graduate University for Advanced Studies, Hayama, Kanagawa 240 0193, Japan
    Trends Genet 25:198-202. 2009
    ..This could be due to the difference in the potential to evolve new functions; middle-wave genes should have greater contribution to adaptive vision evolution through gene duplication...
  26. doi request reprint The role of gene conversion in preserving rearrangement hotspots in the human genome
    Jeffrey A Fawcett
    Graduate University for Advanced Studies, Hayama, Kanagawa 240 0193, Japan
    Trends Genet 29:561-8. 2013
    ..We show that the literature on copy number variants (CNVs) and genomic disorders, and also the results of additional analysis of CNVs, are all more consistent with the gene conversion model. ..
  27. pmc A two-locus gene conversion model with selection and its application to the human RHCE and RHD genes
    Hideki Innan
    Human Genetics Center, School of Public Health, University of Texas Health Science Center, Houston, TX 77030, USA
    Proc Natl Acad Sci U S A 100:8793-8. 2003
    ..The selection intensity is estimated on the basis of the theoretical result...
  28. ncbi request reprint Confounding factors in HGT detection: statistical error, coalescent effects, and multiple solutions
    Cuong Than
    Department of Computer Science, Rice University, Houston, Texas 77005, USA
    J Comput Biol 14:517-35. 2007
    ..Finally, we show, empirically, that the locality of incongruence between a pair of trees has an impact on the numbers of HGT and coalescent reconciliation scenarios...
  29. doi request reprint On the estimation of the insertion time of LTR retrotransposable elements
    T E Kijima
    Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
    Mol Biol Evol 27:896-904. 2010
    ..It is concluded that the divergence method to estimate the insertion time should be applied with special caution because at least some LTRs undergo gene conversion...
  30. pmc Distinguishing the hitchhiking and background selection models
    Hideki Innan
    Human Genetics Center, University of Texas Health Science Center, Houston, Texas 77030, USA
    Genetics 165:2307-12. 2003
    ..The method is applied to data from Drosophila melanogaster and two highly selfing tomato species...
  31. pmc Competition between the sperm of a single male can increase the evolutionary rate of haploid expressed genes
    Kiyoshi Ezawa
    The Graduate University for Advanced Studies, Hayama, Kanagawa 240 0193, Japan
    Genetics 194:709-19. 2013
    ..The theoretical result was applied to mammalian data to estimate the selection intensity on nonsynonymous mutations in sperm genes. ..
  32. pmc The power of QTL mapping with RILs
    Shohei Takuno
    Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
    PLoS ONE 7:e46545. 2012
    ..Because the cost to establish a number of RILs for many generations is enormous, this finding will cause a reduction in the cost of QTL mapping, thereby accelerating gene mapping in many species...
  33. pmc The extent of linkage disequilibrium and haplotype sharing around a polymorphic site
    Hideki Innan
    Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089 1340, USA
    Genetics 165:437-44. 2003
    ..The implications of our results for data analysis, and in particular for detecting selection, are discussed...
  34. pmc The probability and chromosomal extent of trans-specific polymorphism
    Carsten Wiuf
    Department of Statistics, University of Oxford, Oxford, OX1 3TG, United Kingdom
    Genetics 168:2363-72. 2004
    ..When trans-specific polymorphism is obvious, on the other hand, it may be reasonable to argue that selection must be acting on multiple sites or that recombination is suppressed in the surrounding region...
  35. pmc The effect of gene conversion on the divergence between duplicated genes
    Kosuke M Teshima
    Center for Genome Information, College of Medicine, University of Cincinnati, Cincinnati, Ohio 45267, USA
    Genetics 166:1553-60. 2004
    ..Finally, we discuss potential problems in genomic data analysis of duplicated genes when it is based on the molecular clock but concerted evolution is common...
  36. pmc The coalescent and infinite-site model of a small multigene family
    Hideki Innan
    Department of Biological Science, University of Southern California, Los Angeles, California 90089 1340, USA
    Genetics 163:803-10. 2003
    ..Using the coalescent simulation of duplicated genes, the applicability of statistical tests of neutrality to multigene families is considered...
  37. pmc The genealogy of sequences containing multiple sites subject to strong selection in a subdivided population
    Magnus Nordborg
    Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089 1340, USA
    Genetics 163:1201-13. 2003
    ..We focus in particular on the statistical power to detect balancing selection when it is present...
  38. ncbi request reprint Molecular population genetics
    Magnus Nordborg
    Department of Biological Sciences, University of Southern California, 835 W 37th St, SHS 172, Los Angeles, California 90089 1340, USA
    Curr Opin Plant Biol 5:69-73. 2002
    ..Furthermore, population genetics is becoming increasingly relevant to other fields of biology, for example to genetic epidemiology, because of disease gene mapping in general populations...
  39. pmc The direction of linkage disequilibrium: a new measure based on the ancestral-derived status of segregating alleles
    K Ryo Takahasi
    Population and Quantitative Genomics Team, Genomic Sciences Center, RIKEN, Yokohama 230 0045, Japan
    Genetics 179:1705-12. 2008
    ....
  40. pmc The pattern of polymorphism on human chromosome 21
    Hideki Innan
    Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
    Genome Res 13:1158-68. 2003
    ....
  41. pmc The evolutionary rate of duplicated genes under concerted evolution
    Shuhei Mano
    Graduate School of Natural Sciences, Nagoya City University, Nagoya, Japan
    Genetics 180:493-505. 2008
    ..We also argue about the applicability of the theoretical results to models of multigene families with more than two loci...
  42. ncbi request reprint Recombination or mutational hot spots in human mtDNA?
    Hideki Innan
    Molecular and Computational Biology, University of Southern California, CA 90089 1340, USA
    Mol Biol Evol 19:1122-7. 2002
    ..Thus, there appears to be no evidence for recombination in the mtDNA polymorphism data. In conclusion, we discuss the possibility of detecting recombination in mtDNA and the implications of its existence...
  43. pmc Preservation of a pseudogene by gene conversion and diversifying selection
    Shohei Takuno
    Laboratory of Plant Breeding and Genetics, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
    Genetics 180:517-31. 2008
    ....
  44. pmc A method for estimating the mutation, gene conversion and recombination parameters in small multigene families
    Hideki Innan
    Department of Biological Science, University of Southern California, Los Angeles, California 90089 1340, USA
    Genetics 161:865-72. 2002
    ..The gene conversion rate is estimated to be approximately 60-165 times higher than the mutation rate for synonymous sites...
  45. pmc Nonindependent domestication of the two rice subspecies, Oryza sativa ssp. indica and ssp. japonica, demonstrated by multilocus microsatellites
    Li Zhi Gao
    Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, People s Republic of China
    Genetics 179:965-76. 2008
    ..The results suggest that completely independent domestication of indica and japonica subspecies may not explain our data and that there is at least partial sharing of their ancestral populations and/or recent gene flow between them...