Home LiteratureArticle Details
PMID: 23657479 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S. Review

Understanding the origin of species with genome-scale data: modelling gene flow.

Nature reviews. Genetics ·Vol. 14 ·No. 6 ·2013-06-00 ·Pages 404-14

Sousa V, Hey J

Abstract

As it becomes easier to sequence multiple genomes from closely related species, evolutionary biologists working on speciation are struggling to get the most out of very large population genomic data sets. Such data hold the potential to resolve long-standing questions in evolutionary biology about the role of gene exchange in species formation. In principle, the new population genomic data can be used to disentangle the conflicting roles of natural selection and gene flow during the divergence process. However, there are great challenges in taking full advantage of such data, especially with regard to including recombination in genetic models of the divergence process. Current data, models, methods and the potential pitfalls in using them will be considered here.

MeSH Terms
Animals Evolution, Molecular Gene Flow Gene Frequency Genetic Speciation Genome, Human Humans Likelihood Functions Linkage Disequilibrium Models, Genetic Polymorphism, Genetic
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Sousa Vitor
Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA.
Hey Jody
References (83)
83 references, click to expand
  1. Testing for ancient admixture between closely related populations.
    Mol Biol Evol. 2011 Aug;28(8):2239-52 PMID: 21325092
  2. Demographic inference using spectral methods on SNP data, with an analysis of the human out-of-Africa expansion.
    Genetics. 2012 Oct;192(2):619-39 PMID: 22865734
  3. Distinguishing migration from isolation: a Markov chain Monte Carlo approach.
    Genetics. 2001 Jun;158(2):885-96 PMID: 11404349
  4. Dating the age of admixture via wavelet transform analysis of genome-wide data.
    Genome Biol. 2011;12(2):R19 PMID: 21352535
  5. A draft sequence of the Neandertal genome.
    Science. 2010 May 7;328(5979):710-722 PMID: 20448178
  6. The genomic basis of adaptive evolution in threespine sticklebacks.
    Nature. 2012 Apr 04;484(7392):55-61 PMID: 22481358
  7. The power and promise of population genomics: from genotyping to genome typing.
    Nat Rev Genet. 2003 Dec;4(12):981-94 PMID: 14631358
  8. Linkage disequilibrium, gene trees and selfing: an ancestral recombination graph with partial self-fertilization.
    Genetics. 2000 Feb;154(2):923-9 PMID: 10655241
  9. Ancestral inference from samples of DNA sequences with recombination.
    J Comput Biol. 1996 Winter;3(4):479-502 PMID: 9018600
  10. A likelihood-based comparison of population histories in a parasitoid guild.
    Mol Ecol. 2012 Sep;21(18):4605-17 PMID: 22891657
  11. Population genetics models of local ancestry.
    Genetics. 2012 Jun;191(2):607-19 PMID: 22491189
  12. Haplotype phasing: existing methods and new developments.
    Nat Rev Genet. 2011 Sep 16;12(10):703-14 PMID: 21921926
  13. An accurate sequentially Markov conditional sampling distribution for the coalescent with recombination.
    Genetics. 2011 Apr;187(4):1115-28 PMID: 21270390
  14. Coalescent genealogy samplers: windows into population history.
    Trends Ecol Evol. 2009 Feb;24(2):86-93 PMID: 19101058
  15. A map of human genome variation from population-scale sequencing.
    Nature. 2010 Oct 28;467(7319):1061-73 PMID: 20981092
  16. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis.
    Genetics. 2004 Jun;167(2):747-60 PMID: 15238526
  17. The Bayesian revolution in genetics.
    Nat Rev Genet. 2004 Apr;5(4):251-61 PMID: 15131649
  18. Genetics in geographically structured populations: defining, estimating and interpreting F(ST).
    Nat Rev Genet. 2009 Sep;10(9):639-50 PMID: 19687804
  19. Maximum-likelihood estimation of demographic parameters using the frequency spectrum of unlinked single-nucleotide polymorphisms.
    Genetics. 2004 Nov;168(3):1699-712 PMID: 15579718
  20. Evolution in Mendelian Populations.
    Genetics. 1931 Mar;16(2):97-159 PMID: 17246615
  21. A fine-scale map of recombination rates and hotspots across the human genome.
    Science. 2005 Oct 14;310(5746):321-4 PMID: 16224025
  22. Bayesian inference of ancient human demography from individual genome sequences.
    Nat Genet. 2011 Sep 18;43(10):1031-4 PMID: 21926973
  23. Population genetic analysis of ascertained SNP data.
    Hum Genomics. 2004 Mar;1(3):218-24 PMID: 15588481
  24. Two-locus sampling distributions and their application.
    Genetics. 2001 Dec;159(4):1805-17 PMID: 11779816
  25. Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model.
    PLoS Genet. 2007 Feb 23;3(2):e7 PMID: 17319744
  26. Sequencing technologies - the next generation.
    Nat Rev Genet. 2010 Jan;11(1):31-46 PMID: 19997069
  27. The date of interbreeding between Neandertals and modern humans.
    PLoS Genet. 2012;8(10):e1002947 PMID: 23055938
  28. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics.
    Proc Natl Acad Sci U S A. 2007 Feb 20;104(8):2785-90 PMID: 17301231
  29. Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter-gatherers.
    Cell. 2012 Aug 3;150(3):457-69 PMID: 22840920
  30. Genotype and SNP calling from next-generation sequencing data.
    Nat Rev Genet. 2011 Jun;12(6):443-51 PMID: 21587300
  31. Maximum likelihood estimation of recombination rates from population data.
    Genetics. 2000 Nov;156(3):1393-401 PMID: 11063710
  32. Darwin's bridge between microevolution and macroevolution.
    Nature. 2009 Feb 12;457(7231):837-42 PMID: 19212402
  33. Inference of historical changes in migration rate from the lengths of migrant tracts.
    Genetics. 2009 Feb;181(2):711-9 PMID: 19087958
  34. A general method for calculating likelihoods under the coalescent process.
    Genetics. 2011 Nov;189(3):977-87 PMID: 21900266
  35. Simultaneous inference of selection and population growth from patterns of variation in the human genome.
    Proc Natl Acad Sci U S A. 2005 May 31;102(22):7882-7 PMID: 15905331
  36. Analysis of linkage disequilibrium in an island model.
    Theor Popul Biol. 1986 Apr;29(2):161-97 PMID: 3715765
  37. Phylogenies from molecular sequences: inference and reliability.
    Annu Rev Genet. 1988;22:521-65 PMID: 3071258
  38. A sequentially Markov conditional sampling distribution for structured populations with migration and recombination.
    Theor Popul Biol. 2013 Aug;87:51-61 PMID: 23010245
  39. Unified framework to evaluate panmixia and migration direction among multiple sampling locations.
    Genetics. 2010 May;185(1):313-26 PMID: 20176979
  40. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data.
    PLoS Genet. 2009 Oct;5(10):e1000695 PMID: 19851460
  41. Recombination as a point process along sequences.
    Theor Popul Biol. 1999 Jun;55(3):248-59 PMID: 10366550
  42. Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication.
    Nature. 2010 Apr 8;464(7290):898-902 PMID: 20237475
  43. A coalescent-based method for detecting and estimating recombination from gene sequences.
    Genetics. 2002 Mar;160(3):1231-41 PMID: 11901136
  44. Linkage disequilibrium--understanding the evolutionary past and mapping the medical future.
    Nat Rev Genet. 2008 Jun;9(6):477-85 PMID: 18427557
  45. INTERSPECIFIC HYBRIDIZATION, HETEROZYGOSITY AND GENE EXCHANGE IN PHLOX.
    Evolution. 1975 Mar;29(1):37-51 PMID: 28563279
  46. Evolutionary relationship of DNA sequences in finite populations.
    Genetics. 1983 Oct;105(2):437-60 PMID: 6628982
  47. Modern computational approaches for analysing molecular genetic variation data.
    Nat Rev Genet. 2006 Oct;7(10):759-70 PMID: 16983372
  48. Theory and speciation.
    Trends Ecol Evol. 2001 Jul 1;16(7):330-343 PMID: 11403865
  49. Demographic history and rare allele sharing among human populations.
    Proc Natl Acad Sci U S A. 2011 Jul 19;108(29):11983-8 PMID: 21730125
  50. Comparative and demographic analysis of orang-utan genomes.
    Nature. 2011 Jan 27;469(7331):529-33 PMID: 21270892
  51. Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data.
    Genetics. 2003 Dec;165(4):2213-33 PMID: 14704198
  52. Linkage disequilibrium: what history has to tell us.
    Trends Genet. 2002 Feb;18(2):83-90 PMID: 11818140
  53. Genome-wide genetic marker discovery and genotyping using next-generation sequencing.
    Nat Rev Genet. 2011 Jun 17;12(7):499-510 PMID: 21681211
  54. fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios.
    Bioinformatics. 2011 May 1;27(9):1332-4 PMID: 21398675
  55. The sequence and de novo assembly of the giant panda genome.
    Nature. 2010 Jan 21;463(7279):311-7 PMID: 20010809
  56. Genetic history of an archaic hominin group from Denisova Cave in Siberia.
    Nature. 2010 Dec 23;468(7327):1053-60 PMID: 21179161
  57. Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags.
    PLoS Genet. 2010 Feb 26;6(2):e1000862 PMID: 20195501
  58. Properties of a neutral allele model with intragenic recombination.
    Theor Popul Biol. 1983 Apr;23(2):183-201 PMID: 6612631
  59. Estimation of population parameters and recombination rates from single nucleotide polymorphisms.
    Genetics. 2000 Feb;154(2):931-42 PMID: 10655242
  60. Can one learn history from the allelic spectrum?
    Theor Popul Biol. 2008 May;73(3):342-8 PMID: 18321552
  61. Identity by descent between distant relatives: detection and applications.
    Annu Rev Genet. 2012;46:617-33 PMID: 22994355
  62. Molecular signatures of natural selection.
    Annu Rev Genet. 2005;39:197-218 PMID: 16285858
  63. Widespread genomic divergence during sympatric speciation.
    Proc Natl Acad Sci U S A. 2010 May 25;107(21):9724-9 PMID: 20457907
  64. The potential and challenges of nanopore sequencing.
    Nat Biotechnol. 2008 Oct;26(10):1146-53 PMID: 18846088
  65. The role of hybridization in evolution.
    Mol Ecol. 2001 Mar;10(3):551-68 PMID: 11298968
  66. The evolutionary genetics of speciation.
    Philos Trans R Soc Lond B Biol Sci. 1998 Feb 28;353(1366):287-305 PMID: 9533126
  67. Ascertainment bias in estimates of average heterozygosity.
    Am J Hum Genet. 1996 May;58(5):1033-41 PMID: 8651264
  68. Non-equilibrium allele frequency spectra via spectral methods.
    Theor Popul Biol. 2011 Jun;79(4):203-19 PMID: 21376069
  69. Gene flow and natural selection in the origin of Drosophila pseudoobscura and close relatives.
    Genetics. 1997 Nov;147(3):1091-106 PMID: 9383055
  70. Estimating divergence parameters with small samples from a large number of loci.
    Genetics. 2010 Feb;184(2):363-79 PMID: 19917765
  71. SOLUTION OF A PROCESS OF RANDOM GENETIC DRIFT WITH A CONTINUOUS MODEL.
    Proc Natl Acad Sci U S A. 1955 Mar 15;41(3):144-50 PMID: 16589632
  72. The ancestry of a sample of sequences subject to recombination.
    Genetics. 1999 Mar;151(3):1217-28 PMID: 10049937
  73. Estimating divergence time and ancestral effective population size of Bornean and Sumatran orangutan subspecies using a coalescent hidden Markov model.
    PLoS Genet. 2011 Mar;7(3):e1001319 PMID: 21408205
  74. Bayesian inference of fine-scale recombination rates using population genomic data.
    Philos Trans R Soc Lond B Biol Sci. 2008 Dec 27;363(1512):3921-30 PMID: 18852101
  75. Population genetic inference from genomic sequence variation.
    Genome Res. 2010 Mar;20(3):291-300 PMID: 20067940
  76. Sympatric speciation in animals: the ugly duckling grows up.
    Trends Ecol Evol. 2001 Jul 1;16(7):381-390 PMID: 11403871
  77. Adaptation genomics: the next generation.
    Trends Ecol Evol. 2010 Dec;25(12):705-12 PMID: 20952088
  78. Inference of human population history from individual whole-genome sequences.
    Nature. 2011 Jul 13;475(7357):493-6 PMID: 21753753
  79. Butterfly genome reveals promiscuous exchange of mimicry adaptations among species.
    Nature. 2012 Jul 5;487(7405):94-8 PMID: 22722851
  80. The hitch-hiking effect of a favourable gene.
    Genet Res. 1974 Feb;23(1):23-35 PMID: 4407212
  81. Recombination and speciation.
    Mol Ecol. 2005 Aug;14(9):2621-35 PMID: 16029465
  82. Statistical inferences in phylogeography.
    Mol Ecol. 2009 Mar;18(6):1034-47 PMID: 19207258
  83. Stepwise mutation likelihood computation by sequential importance sampling in subdivided population models.
    Theor Popul Biol. 2005 Jul;68(1):41-53 PMID: 15890376
Article Info
Journal
Nature reviews. Genetics
Abbr.
Nat Rev Genet
ISSN
1471-0064
Published
2013-06-00
Epub
2013-00-09
Pages
404-14
Language
English
Region
England
NLM ID
100962779
PMCID
PMC5568773
Subset
IM
Grants
NIGMS NIH HHS · R01 GM078204 · United States
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]