Rasmus Nielsen

Summary

Affiliation: University of Copenhagen
Country: Denmark

Publications

  1. pmc Patterns of positive selection in six Mammalian genomes
    Carolin Kosiol
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
    PLoS Genet 4:e1000144. 2008
  2. ncbi request reprint Demography: peopling the Americas
    Rasmus Nielsen
    Department of Biology, Center for Bioinformatics, University of Copenhagen, Universitetsparken 15, Copenhagen 2100 Kbh Ø, Denmark
    Eur J Hum Genet 13:1100-1. 2005
  3. ncbi request reprint Evolution. Why sex?
    Rasmus Nielsen
    Center for Bioinformatics and Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Kbh Ø Denmark
    Science 311:960-1. 2006
  4. ncbi request reprint Radiation and speciation of pelagic organisms during periods of global warming: the case of the common minke whale, Balaenoptera acutorostrata
    Luis A Pastene
    Institute of Cetacean Research, 4 5 Toyomi cho, Chuo Ku, Tokyo 104 0055, Japan
    Mol Ecol 16:1481-95. 2007
  5. pmc Reconstituting the frequency spectrum of ascertained single-nucleotide polymorphism data
    Rasmus Nielsen
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
    Genetics 168:2373-82. 2004
  6. pmc A scan for positively selected genes in the genomes of humans and chimpanzees
    Rasmus Nielsen
    Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
    PLoS Biol 3:e170. 2005
  7. pmc Genomic scans for selective sweeps using SNP data
    Rasmus Nielsen
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
    Genome Res 15:1566-75. 2005
  8. ncbi request reprint Molecular signatures of natural selection
    Rasmus Nielsen
    Center for Bioinformatics and Department of Evolutionary Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark
    Annu Rev Genet 39:197-218. 2005
  9. ncbi request reprint Maximum likelihood estimation of ancestral codon usage bias parameters in Drosophila
    Rasmus Nielsen
    Institute of Biology and Centre for Bioinformatics, University of Copenhagen, Copenhagen, Denmark
    Mol Biol Evol 24:228-35. 2007
  10. ncbi request reprint Evolutionary genomics: detecting selection needs comparative data
    Rasmus Nielsen
    Centre for Bioinformatics, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
    Nature 433:E6; discussion E7-8. 2005

Collaborators

Detail Information

Publications84

  1. pmc Patterns of positive selection in six Mammalian genomes
    Carolin Kosiol
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
    PLoS Genet 4:e1000144. 2008
    ..This study provides additional evidence for widespread positive selection in mammalian evolution and new genome-wide insights into the functional implications of positive selection...
  2. ncbi request reprint Demography: peopling the Americas
    Rasmus Nielsen
    Department of Biology, Center for Bioinformatics, University of Copenhagen, Universitetsparken 15, Copenhagen 2100 Kbh Ø, Denmark
    Eur J Hum Genet 13:1100-1. 2005
  3. ncbi request reprint Evolution. Why sex?
    Rasmus Nielsen
    Center for Bioinformatics and Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Kbh Ø Denmark
    Science 311:960-1. 2006
  4. ncbi request reprint Radiation and speciation of pelagic organisms during periods of global warming: the case of the common minke whale, Balaenoptera acutorostrata
    Luis A Pastene
    Institute of Cetacean Research, 4 5 Toyomi cho, Chuo Ku, Tokyo 104 0055, Japan
    Mol Ecol 16:1481-95. 2007
    ..Our hypothesis that prolonged periods of global warming facilitate speciation in pelagic marine species that depend on upwelling should be tested by comparative analyses in other pelagic species...
  5. pmc Reconstituting the frequency spectrum of ascertained single-nucleotide polymorphism data
    Rasmus Nielsen
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
    Genetics 168:2373-82. 2004
    ..Appropriate treatment of SNP ascertainment is vital to our ability to make correct inferences from the data of the International HapMap Project...
  6. pmc A scan for positively selected genes in the genomes of humans and chimpanzees
    Rasmus Nielsen
    Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
    PLoS Biol 3:e170. 2005
    ..The polymorphism analysis further supports the presence of positive selection in these genes by showing an excess of high-frequency derived nonsynonymous mutations...
  7. pmc Genomic scans for selective sweeps using SNP data
    Rasmus Nielsen
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
    Genome Res 15:1566-75. 2005
    ..Evidence for selective sweeps is also found in many other regions, including genes known to be associated with disease risk such as DPP10 and COL4A3...
  8. ncbi request reprint Molecular signatures of natural selection
    Rasmus Nielsen
    Center for Bioinformatics and Department of Evolutionary Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark
    Annu Rev Genet 39:197-218. 2005
    ..Particular attention is placed on issues relating to the analysis of large-scale genomic data sets...
  9. ncbi request reprint Maximum likelihood estimation of ancestral codon usage bias parameters in Drosophila
    Rasmus Nielsen
    Institute of Biology and Centre for Bioinformatics, University of Copenhagen, Copenhagen, Denmark
    Mol Biol Evol 24:228-35. 2007
    ..melanogaster lineage. For example, we also confirm previous results showing that the Notch locus has experienced positive selection for previously classified unpreferred mutations...
  10. ncbi request reprint Evolutionary genomics: detecting selection needs comparative data
    Rasmus Nielsen
    Centre for Bioinformatics, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
    Nature 433:E6; discussion E7-8. 2005
    ..We show here that this method is particularly sensitive to assumptions regarding the underlying mutational processes and does not provide a reliable way to identify positive selection...
  11. pmc Recent and ongoing selection in the human genome
    Rasmus Nielsen
    Center for Comparative Genomics, University of Copenhagen, Universitetsparken 15, 2100 Kbh Ø, Denmark
    Nat Rev Genet 8:857-68. 2007
    ..Although such studies will always be associated with some uncertainty, steps can be taken to minimize the effects of confounding factors and improve our interpretation of their findings...
  12. pmc Darwinian and demographic forces affecting human protein coding genes
    Rasmus Nielsen
    Department of Biology, University of Copenhagen, Copenhagen, Denmark
    Genome Res 19:838-49. 2009
    ..In accordance with previous studies, we find evidence for negative selection against mutations in genes associated with Mendelian disease and positive selection acting on genes associated with several complex diseases...
  13. pmc Assessing the evolutionary impact of amino acid mutations in the human genome
    Adam R Boyko
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
    PLoS Genet 4:e1000083. 2008
    ....
  14. ncbi request reprint Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios
    Andrew G Clark
    Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Science 302:1960-3. 2003
    ..In addition to suggesting adaptive physiological differences between chimps and humans, human-accelerated genes are significantly more likely to underlie major known Mendelian disorders...
  15. ncbi request reprint Natural selection on protein-coding genes in the human genome
    Carlos D Bustamante
    Department of Biological Statistics and Computational Biology, 101 Biotechnology Building, Cornell University, Ithaca, New York 14853, USA
    Nature 437:1153-7. 2005
    ....
  16. pmc Linkage disequilibrium and inference of ancestral recombination in 538 single-nucleotide polymorphism clusters across the human genome
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Am J Hum Genet 73:285-300. 2003
    ..This result is consistent with differences in the genealogical depth of local genomic regions, a finding that has direct bearing on the design and utility of LD mapping and on the National Institutes of Health HapMap project...
  17. doi request reprint Ancient human genome sequence of an extinct Palaeo-Eskimo
    Morten Rasmussen
    Centre for GeoGenetics, Natural History Museum of Denmark and Department of Biology, University of Copenhagen, Universitetsparken 15, DK 2100 Copenhagen, Denmark
    Nature 463:757-62. 2010
    ..This provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of that giving rise to the modern Native Americans and Inuit...
  18. pmc Proportionally more deleterious genetic variation in European than in African populations
    Kirk E Lohmueller
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nature 451:994-7. 2008
    ..Using extensive simulations, we show that this excess proportion of segregating damaging alleles in Europeans is probably a consequence of a bottleneck that Europeans experienced at about the time of the migration out of Africa...
  19. doi request reprint Species-specific responses of Late Quaternary megafauna to climate and humans
    Eline D Lorenzen
    Centre for GeoGenetics, University of Copenhagen, Øster Voldgade 5 7, DK 1350 Copenhagen K, Denmark
    Nature 479:359-64. 2011
    ....
  20. ncbi request reprint Detecting coevolving amino acid sites using Bayesian mutational mapping
    Matthew W Dimmic
    Department of Biological Statistics and Computational Biology, Cornell University Ithaca, NY 13101, USA
    Bioinformatics 21:i126-35. 2005
    ..A coevolutionary Markov model for codon substitution is also described, and this model is used as the basis of several test statistics...
  21. pmc Targets of balancing selection in the human genome
    Aida M Andres
    Department of Molecular Biology and Genetics, Cornell University, USA
    Mol Biol Evol 26:2755-64. 2009
    ....
  22. ncbi request reprint Evolution of genes and genomes on the Drosophila phylogeny
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nature 450:203-18. 2007
    ..These may prove to underlie differences in the ecology and behaviour of these diverse species...
  23. pmc Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites
    Wendy S W Wong
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
    Genetics 168:1041-51. 2004
    ..The parsimony method has a very low rate of false positives but very little power for detecting positive selection or identifying positively selected sites...
  24. pmc Radiation of extant cetaceans driven by restructuring of the oceans
    Mette E Steeman
    Centre for GeoGenetics, Natural History Museum of Denmark, 2100 Copenhagen, Denmark
    Syst Biol 58:573-85. 2009
    ..The results imply that paleogeographic and paleoceanographic changes, such as closure of major seaways, have influenced the dynamics of radiation in extant cetaceans...
  25. doi request reprint The effect of ancient DNA damage on inferences of demographic histories
    Erik Axelsson
    Department of Biology, Evolutionary Biology, Copenhagen University, Copenhagen, Denmark
    Mol Biol Evol 25:2181-7. 2008
    ..Our results suggest that population genetic analyses of aDNA sequences, which do not accurately account for damage, should be interpreted with great caution...
  26. ncbi request reprint Finding cis-regulatory modules in Drosophila using phylogenetic hidden Markov models
    Wendy S W Wong
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
    Bioinformatics 23:2031-7. 2007
    ..There are numerous methods available for solving this problem, however, very few of them take advantage of the increasing availability of comparative genomic data...
  27. doi request reprint Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse
    Ludovic Orlando
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5 7, 1350 Copenhagen K, Denmark
    Nature 499:74-8. 2013
    ..Such regions could correspond to loci selected early during domestication...
  28. pmc The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing
    Jonas Binladen
    Center for Ancient Genetics, Institute of Biology, University of Copenhagen, Copenhagen, Denmark
    PLoS ONE 2:e197. 2007
    ....
  29. pmc Ascertainment bias in studies of human genome-wide polymorphism
    Andrew G Clark
    Molecular Biology and Genetics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
    Genome Res 15:1496-502. 2005
    ....
  30. ncbi request reprint Bayesian and maximum likelihood estimation of genetic maps
    Thomas L York
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14850, USA
    Genet Res 85:159-68. 2005
    ..We also re-analyse a recently published set of data from the eggplant and show that the use of the MCMC-based method leads to smaller estimates of genetic distances...
  31. pmc A Bayesian multilocus association method: allowing for higher-order interaction in association studies
    Anders Albrechtsen
    Bioinformatics Centre, University of Copenhagen, 2100 Copenhagen, Denmark
    Genetics 176:1197-208. 2007
    ..It is computationally feasible even for a large number of possible interactions and differs fundamentally from most previous approaches by entertaining nonlinear interactions and by directly addressing the multiple-testing problem...
  32. pmc Bayesian estimation of genomic distance
    Richard Durrett
    Department of Mathematics, Cornell University, Ithaca, New York 14853, USA
    Genetics 166:621-9. 2004
    ..In the first case the most likely number of events is larger than the parsimony value. In the last two cases the parsimony solutions have very small probability...
  33. pmc Correcting estimators of theta and Tajima's D for ascertainment biases caused by the single-nucleotide polymorphism discovery process
    Anna Ramírez-Soriano
    Department of Biology, University of Copenhagen, 2100 Kbh Ø, Copenhagen, Denmark
    Genetics 181:701-10. 2009
    ..We reanalyze a human genomewide SNP data set and find substantial differences in the results with or without ascertainment bias correction...
  34. pmc Linkage disequilibrium as a signature of selective sweeps
    Yuseob Kim
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
    Genetics 167:1513-24. 2004
    ..However, the improvement made by including LD is rather small, suggesting that most of the relevant information regarding selective sweeps is captured by the spatial distribution and marginal allele frequencies of polymorphisms...
  35. pmc Simultaneous inference of selection and population growth from patterns of variation in the human genome
    Scott H Williamson
    Department of Biological Statistics and Computational Biology, 101 Biotechnology Building, Cornell University, Ithaca, NY 14853, USA
    Proc Natl Acad Sci U S A 102:7882-7. 2005
    ....
  36. pmc Ancient biomolecules from deep ice cores reveal a forested southern Greenland
    Eske Willerslev
    Centre for Ancient Genetics, University of Copenhagen, Denmark
    Science 317:111-4. 2007
    ..The results provide direct evidence in support of a forested southern Greenland and suggest that many deep ice cores may contain genetic records of paleoenvironments in their basal sections...
  37. pmc A method for detecting IBD regions simultaneously in multiple individuals--with applications to disease genetics
    Ida Moltke
    The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
    Genome Res 21:1168-80. 2011
    ..2-Mb region using SNP data from only five seemingly unrelated affected individuals. This would not be possible using classical linkage mapping or association mapping...
  38. pmc Identification of physicochemical selective pressure on protein encoding nucleotide sequences
    Wendy S W Wong
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
    BMC Bioinformatics 7:148. 2006
    ..However, they have been limited by not taking the physiochemical properties of amino acids into account...
  39. pmc Ascertainment biases in SNP chips affect measures of population divergence
    Anders Albrechtsen
    Department of Biostatistics, Copenhagen University, Copenhagen, Denmark
    Mol Biol Evol 27:2534-47. 2010
    ..We not only present a correction of the spectrum for the widely used Affymetrix SNP chips but also show that such corrections are difficult to generalize among studies...
  40. ncbi request reprint Patterns of mutation and selection at synonymous sites in Drosophila
    Nadia D Singh
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, USA
    Mol Biol Evol 24:2687-97. 2007
    ....
  41. pmc Localizing recent adaptive evolution in the human genome
    Scott H Williamson
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
    PLoS Genet 3:e90. 2007
    ..In general, we find that recent adaptation is strikingly pervasive in the human genome, with as much as 10% of the genome affected by linkage to a selective sweep...
  42. ncbi request reprint Detecting site-specific physicochemical selective pressures: applications to the Class I HLA of the human major histocompatibility complex and the SRK of the plant sporophytic self-incompatibility system
    Raazesh Sainudiin
    Department of Statistical Science, Cornell University, Ithaca, NY14853, USA
    J Mol Evol 60:315-26. 2005
    ..An empirical Bayes approach is used to identify sites that may be important for ligand recognition in these proteins...
  43. pmc Adaptive evolution of cytochrome c oxidase: Infrastructure for a carnivorous plant radiation
    Richard W Jobson
    Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA
    Proc Natl Acad Sci U S A 101:18064-8. 2004
    ....
  44. pmc Dependence of paracentric inversion rate on tract length
    Thomas L York
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, USA
    BMC Bioinformatics 8:115. 2007
    ..We develop a Bayesian method based on MCMC for estimating the relative rates of pericentric and paracentric inversions from marker data from two species. The method also allows estimation of the distribution of inversion tract lengths...
  45. pmc Estimation of 2Nes from temporal allele frequency data
    Jonathan P Bollback
    Department of Biology and Evolutionary Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark
    Genetics 179:497-502. 2008
    ..In our second example, we estimate the selection coefficient acting on a mutation segregating in an experimental phage population. We show that the selection coefficient acting on this mutation is approximately 0.43...
  46. ncbi request reprint Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA
    Rasmus Nielsen
    Department of Biometrics, Cornell University, USA
    Mol Biol Evol 20:1231-9. 2003
    ....
  47. pmc Natural selection and the distribution of identity-by-descent in the human genome
    Anders Albrechtsen
    Department of Biostatistics, University of Copenhagen, Copenhagen, 1014, Denmark
    Genetics 186:295-308. 2010
    ..As equilibrium overdominance does not tend to increase IBD, we argue that this type of selection cannot explain our observations...
  48. pmc Microsatellite mutation models: insights from a comparison of humans and chimpanzees
    Raazesh Sainudiin
    Department of Statistical Science, Cornell University, Ithaca, New York 14853, USA
    Genetics 168:383-95. 2004
    ..In general, models that allow chimps to have a larger per-repeat unit slippage rate and/or a shorter focal length compared to humans give a better fit to the human-chimp data as well as the human genomic data...
  49. ncbi request reprint Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques
    Ryan D Hernandez
    Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14850, USA
    Science 316:240-3. 2007
    ..15 at 10 kilobases) versus Indian (r(2) approximately 0.52 at 10 kilobases) macaque populations...
  50. ncbi request reprint Estimating effective paternity number in social insects and the effective number of alleles in a population
    Rasmus Nielsen
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
    Mol Ecol 12:3157-64. 2003
    ..It should also be of use in population genetic studies in which the effective number of alleles is of interest...
  51. doi request reprint Relatedness mapping and tracts of relatedness for genome-wide data in the presence of linkage disequilibrium
    Anders Albrechtsen
    Department of Biostatistics, Copenhagen University, Copenhagen, Denmark
    Genet Epidemiol 33:266-74. 2009
    ..The new IBD mapping method provides considerable improvement in mapping power in natural populations compared to standard association mapping methods...
  52. pmc Population genetic analysis of ascertained SNP data
    Rasmus Nielsen
    Department of Biological Statistics and Computational Biology, Cornell University, 439 Warren Hall, Ithaca, NY 14853 7801, USA
    Hum Genomics 1:218-24. 2004
    ..Several recently developed methods for correcting for the ascertainment bias will also be discussed...
  53. pmc Ancient DNA reveals late survival of mammoth and horse in interior Alaska
    James Haile
    Centre for GeoGenetics, University of Copenhagen, Copenhagen 2100, Denmark
    Proc Natl Acad Sci U S A 106:22352-7. 2009
    ....
  54. ncbi request reprint Statistical approaches for DNA barcoding
    Rasmus Nielsen
    Department of Biological Statistics and Computational Biology, Center for Bioinformatics, University of Copenhagen Universitetsparken 15, 2100 Copenhagen, Denmark
    Syst Biol 55:162-9. 2006
  55. pmc Evolution of the integral membrane desaturase gene family in moths and flies
    Douglas C Knipple
    Department of Entomology, New York State Agricultural Experiment Station, Cornell University, Geneva, New York 14456, USA
    Genetics 162:1737-52. 2002
    ....
  56. pmc Genes under positive selection in Escherichia coli
    Lise Petersen
    Bioinformatics Centre, University of Copenhagen, Copenhagen DK 2200, Denmark
    Genome Res 17:1336-43. 2007
    ..Based on structural evidence, we hypothesize that the selection acting on transposases is related to the genomic conflict between transposable elements and the host genome...
  57. pmc The population structure of African cultivated rice oryza glaberrima (Steud.): evidence for elevated levels of linkage disequilibrium caused by admixture with O. sativa and ecological adaptation
    Mande Semon
    Department of Plant Breeding, Cornell University, Ithaca, New York 14853, USA
    Genetics 169:1639-47. 2005
    ..The remaining three O. glaberrima subpopulations were significantly associated with specific combinations of phenotypic traits-possibly reflecting ecological adaptation to different growing environments...
  58. ncbi request reprint Bayesian estimation of the number of inversions in the history of two chromosomes
    Thomas L York
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
    J Comput Biol 9:805-18. 2002
    ..melanogaster comparison, the lower boundary of a 95% highest posterior density credible interval for the number of inversions is considerably larger than the most parsimonious number of inversions...
  59. pmc Population size changes reshape genomic patterns of diversity
    John E Pool
    Centre for Comparative Genomics, Institute of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
    Evolution 61:3001-6. 2007
    ..Consideration of this effect may improve the inference of population history and other evolutionary processes...
  60. ncbi request reprint Correcting for ascertainment biases when analyzing SNP data: applications to the estimation of linkage disequilibrium
    Rasmus Nielsen
    Department of Biometrics, Cornell University, 439 Warren Hall, Ithaca, NY 14853 7801, USA
    Theor Popul Biol 63:245-55. 2003
    ....
  61. pmc Detecting selection in noncoding regions of nucleotide sequences
    Wendy S W Wong
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
    Genetics 167:949-58. 2004
    ..Data analysis of both simulated and real viral data is presented. Using the new method we show that positive selection in viruses is acting primarily in protein-coding regions and is rare or absent in noncoding regions...
  62. doi request reprint Adaptionism-30 years after Gould and Lewontin
    Rasmus Nielsen
    Department of Biology, University of Copenhagen, 2100 Kbh Ø, Denmark
    Evolution 63:2487-90. 2009
    ..However, despite the difficulties in establishing scientific arguments in favor of specific historic evolutionary events, there is still much to learn about evolution from genomic data...
  63. ncbi request reprint Mapping mutations on phylogenies
    Rasmus Nielsen
    Department of Biological Statistics, Cornell University, 439 Warren Hall, Ithaca, New York 14853 7801, USA
    Syst Biol 51:729-39. 2002
    ..Applications include a method for testing for variation in the substitution rate along the sequence and a method for testing whether the d(N)/d(S) ratio varies among lineages in the phylogeny...
  64. pmc Rational design of DNA sequence-based strategies for subtyping Listeria monocytogenes
    Steven Cai
    Department of Food Science, Cornell University, Ithaca, New York 14853, USA
    J Clin Microbiol 40:3319-25. 2002
    ..Our specific results also show that inclusion of virulence gene target sequences in a DNA sequence-based subtyping scheme for L. monocytogenes is necessary to achieve maximum subtype differentiation...
  65. pmc A likelihood ratio test for species membership based on DNA sequence data
    Mikhail V Matz
    Whitney Laboratory for Marine Bioscience, Department of Molecular Genetics and Microbiology, University of Florida, 9505 Ocean Shore Blvd, Saint Augustine, FL 32080, USA
    Philos Trans R Soc Lond B Biol Sci 360:1969-74. 2005
    ....
  66. ncbi request reprint Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level
    Jianzhi Zhang
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, USA
    Mol Biol Evol 22:2472-9. 2005
    ..Bayes empirical Bayes identification of amino acid sites under positive selection along the foreground branches was found to be reliable, but lacked power...
  67. ncbi request reprint Using nuclear haplotypes with microsatellites to study gene flow between recently separated Cichlid species
    Jody Hey
    Department of Genetics, Rutgers The State University of New Jersey, Piscataway, NJ 08854, USA
    Mol Ecol 13:909-19. 2004
    ..An example using Cichlid fishes from Lake Malawi is described. The analysis suggests that the species have been exchanging genes since the time they began to diverge...
  68. pmc Genome-wide patterns of nucleotide polymorphism in domesticated rice
    Ana L Caicedo
    Department of Genetics, North Carolina State University, Raleigh, North Carolina, USA
    PLoS Genet 3:1745-56. 2007
    ....
  69. ncbi request reprint The cost of inbreeding in Arabidopsis
    Carlos D Bustamante
    Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA
    Nature 416:531-4. 2002
    ....
  70. ncbi request reprint Human genomics: disclosure of variation
    Rasmus Nielsen
    Nature 434:288-9. 2005
  71. ncbi request reprint Bayes empirical bayes inference of amino acid sites under positive selection
    Ziheng Yang
    Department of Biology, University College London, London, UK
    Mol Biol Evol 22:1107-18. 2005
    ..The results suggest that in small data sets the new BEB method does not generate false positives as did the old NEB approach, while in large data sets it retains the good power of the NEB approach for inferring positively selected sites...
  72. ncbi request reprint Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages
    Ziheng Yang
    Galton Laboratory, Department of Biology, University College London
    Mol Biol Evol 19:908-17. 2002
    ..Additional tests on several data sets suggest that the new models may be useful in detecting positive selection after gene duplication in gene family evolution...
  73. pmc Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution
    Stephen Richards
    Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston Texas 77030, USA
    Genome Res 15:1-18. 2005
    ..Overall, a pattern of repeat-mediated chromosomal rearrangement, and high coadaptation of both male genes and cis-regulatory sequences emerges as important themes of genome divergence between these species of Drosophila...
  74. ncbi request reprint Is haplotype block identification useful for association mapping studies?
    Weiwei Zhai
    Genet Epidemiol 27:80-3. 2004
  75. ncbi request reprint Exploring variation in the d(N)/d(S) ratio among sites and lineages using mutational mappings: applications to the influenza virus
    Weiwei Zhai
    Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720 3140, USA
    J Mol Evol 65:340-8. 2007
    ..Our results suggest that it may be more difficult to use inferences regarding the strength of selection on mutations to make predictions regarding viral epidemics than previously thought...
  76. pmc Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites
    Maria Anisimova
    Department of Biology, University College London, London WC1E 6BT, United Kingdom
    Genetics 164:1229-36. 2003
    ..Identification of sites under positive selection by the empirical Bayes method appears to be less affected than the LRT by recombination...
  77. ncbi request reprint Evolutionary and biomedical insights from the rhesus macaque genome
    Richard A Gibbs
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
    Science 316:222-34. 2007
    ..The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species...
  78. ncbi request reprint Stochastic mapping of morphological characters
    John P Huelsenbeck
    Section of Ecology, Behavior and Evolution, Division of Biology, University of California San Diego, La Jolla, California 92093 0116, USA
    Syst Biol 52:131-58. 2003
    ..Biol. 51:729-739) to the mapping of morphological characters under continuous-time Markov models and demonstrate here the utility of the method for mapping characters on trees and for identifying character correlation...
  79. pmc Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals
    Ines Hellmann
    Departments of Integrative Biology and Statistics, University of California, Berkeley, California 94720, USA
    Genome Res 18:1020-9. 2008
    ..Finally, we identify a number of genomic regions with increased or reduced diversity compared with the local level of human-chimpanzee divergence and the local recombination rate...
  80. pmc The impact of founder events on chromosomal variability in multiply mating species
    John E Pool
    Department of Integrative Biology, University of California, Berkeley, USA
    Mol Biol Evol 25:1728-36. 2008
    ..Investigating the potential of this process to account for sharply reduced X-linked diversity in European Drosophila melanogaster, we find that this model yields predictions that are compatible with the empirical data...
  81. pmc Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics
    Jody Hey
    Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08846, USA
    Proc Natl Acad Sci U S A 104:2785-90. 2007
    ..Several examples, including an application to the divergence of chimpanzee subspecies, are provided...
  82. pmc Adaptive genic evolution in the Drosophila genomes
    Joshua A Shapiro
    Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 104:2271-6. 2007
    ..Finally, we discuss the theories and data pertaining to the interpretation of adaptive evolution in genomic studies...
  83. ncbi request reprint Discerning between recurrent gene flow and recent divergence under a finite-site mutation model applied to North Atlantic and Mediterranean Sea fin whale (Balaenoptera physalus) populations
    Per J Palsbøll
    Ecosystem Science Division ESPM, University of California at Berkeley, 151 Hilgard Hall, 3110, Berkeley, California 94720 3110, USA
    Evolution 58:670-5. 2004
    ..Intensive commercial shore-based whaling during the 1920s removed substantial numbers of fin whales in the Strait of Gibraltar and this local population has seemingly since failed to recover...
  84. ncbi request reprint Maximum likelihood and Bayesian methods for estimating the distribution of selective effects among classes of mutations using DNA polymorphism data
    Carlos D Bustamante
    Mathematical Genetics Group, Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, UK OX1 3TG
    Theor Popul Biol 63:91-103. 2003
    ....