The power and promise of population genomics: from genotyping to genome typing

Population genomics has the potential to improve studies of evolutionary genetics, molecular ecology and conservation biology, by facilitating the identification of adaptive molecular variation and by improving the estimation of important parameters such as population size, migration rates and phylogenetic relationships. There has been much excitement in the recent literature about the identification of adaptive molecular variation using the population-genomic approach. However, the most useful contribution of the genomics model to population genetics will be improving inferences about population demography and evolutionary history.

[1]  W. Ewens The sampling theory of selectively neutral alleles. , 1972, Theoretical population biology.

[2]  R. Lewontin,et al.  Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. , 1973, Genetics.

[3]  J. Charles,et al.  A Sino-German λ 6 cm polarization survey of the Galactic plane I . Survey strategy and results for the first survey region , 2006 .

[4]  G. A. Watterson The homozygosity test of neutrality. , 1978, Genetics.

[5]  J. Endler Natural selection in the wild , 1987 .

[6]  R. Vrijenhoek,et al.  Let's Not Throw the Baby Out with the Bathwater: A Comment on Management for MHC Diversity in Captive Populations , 1991 .

[7]  L. Excoffier,et al.  Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. , 1992, Genetics.

[8]  R. Boutilier,et al.  Genetic population structure and gene flow in the Atlantic cod Gadus morhua: a comparison of allozyme and nuclear RFLP loci. , 1995, Genetics.

[9]  P. Vos,et al.  AFLP: a new technique for DNA fingerprinting. , 1995, Nucleic acids research.

[10]  M. Beaumont,et al.  Evaluating loci for use in the genetic analysis of population structure , 1996, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[11]  K. McLean,et al.  Genetic distribution of Bare–1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP) , 1997, Molecular and General Genetics MGG.

[12]  Rong‐Cai Yang,et al.  PopGene, the user-friendly shareware for population genetic analysis, molecular biology and biotechnology center , 1997 .

[13]  J. Gulcher,et al.  Population Genomics: Laying the Groundwork for Genetic Disease Modeling and Targeting , 1998, Clinical chemistry and laboratory medicine.

[14]  L. Waits,et al.  Noninvasive genetic sampling: look before you leap. , 1999, Trends in ecology & evolution.

[15]  Self-organized criticality in ecology and evolution. , 1999, Trends in ecology & evolution.

[16]  Richard Bellamy,et al.  An Empirical Exploration of the (Δμ)2 Genetic Distance for 213 Human Microsatellite Markers , 1999 .

[17]  M. Whitlock,et al.  Indirect measures of gene flow and migration: FST≠1/(4Nm+1) , 1999, Heredity.

[18]  C. Baer Among-locus variation in Fst: fish, allozymes and the Lewontin-Krakauer test revisited. , 1999, Genetics.

[19]  G Luikart,et al.  New methods employing multilocus genotypes to select or exclude populations as origins of individuals. , 1999, Genetics.

[20]  A. Long,et al.  The power of association studies to detect the contribution of candidate genetic loci to variation in complex traits. , 1999, Genome research.

[21]  P. Keim,et al.  DNA methylation and AFLP marker distribution in the soybean genome , 1999, Theoretical and Applied Genetics.

[22]  T. Kocher,et al.  Phylogeny of a rapidly evolving clade: the cichlid fishes of Lake Malawi, East Africa. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Genetics, Demography and Viability of Fragmented Populations: Applications of population genetics and molecular techniques to conservation biology , 2000 .

[24]  Andrew G. Young,et al.  Genetics, Demography and Viability of Fragmented Populations: Introductory concepts , 2000 .

[25]  F. Allendorf,et al.  Gene-centromere mapping of 312 loci in pink salmon by half-tetrad analysis. , 2000, Genome.

[26]  Philip W. Hedrick,et al.  Genetics, Demography and Viability of Fragmented Populations: Genetic population structure in desert bighorn sheep: implications for conservation in Arizona , 2000 .

[27]  R. Wayne,et al.  Natural selection mapping of the warfarin-resistance gene. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[28]  K. Crandall,et al.  Considering evolutionary processes in conservation biology. , 2000, Trends in ecology & evolution.

[29]  P. Sunnucks,et al.  Efficient genetic markers for population biology. , 2000, Trends in ecology & evolution.

[30]  F. Allendorf,et al.  CONCORDANCE OF GENETIC DIVERGENCE AMONG SOCKEYE SALMON POPULATIONS AT ALLOZYME, NUCLEAR DNA, AND MITOCHONDRIAL DNA MARKERS , 2000, Evolution; international journal of organic evolution.

[31]  R. Lacy Should we select genetic alleles in our conservation breeding programs , 2000 .

[32]  R. DeSalle,et al.  Adaptive Evolution of Genes and Genomes , 2000, Heredity.

[33]  Jon A Yamato,et al.  Usefulness of single nucleotide polymorphism data for estimating population parameters. , 2000, Genetics.

[34]  J. Schouten,et al.  TE-AFLP: combining rapidity and robustness in DNA fingerprinting. , 2000, Nucleic acids research.

[35]  M. Weiner,et al.  A microsphere-based assay for multiplexed single nucleotide polymorphism analysis using single base chain extension. , 2000, Genome research.

[36]  P. Donnelly,et al.  Inference of population structure using multilocus genotype data. , 2000, Genetics.

[37]  G. Davey,et al.  A survey of genes in the Atlantic salmon (Salmo salar) as identified by expressed sequence tags. , 2001, Gene.

[38]  J. Conner,et al.  How strong is natural selection? , 2001, Trends in ecology & evolution.

[39]  R. Butlin,et al.  Differential gene exchange between parapatric morphs of Littorina saxatilis detected using AFLP markers , 2001 .

[40]  M. Nachman,et al.  Single nucleotide polymorphisms and recombination rate in humans. , 2001, Trends in genetics : TIG.

[41]  P. Boursot,et al.  Interpretation of variation across marker loci as evidence of selection. , 2001, Genetics.

[42]  Chung-I Wu The genic view of the process of speciation , 2001 .

[43]  L. Cardon,et al.  Association study designs for complex diseases , 2001, Nature Reviews Genetics.

[44]  S. Liu-Cordero,et al.  The discovery of single-nucleotide polymorphisms--and inferences about human demographic history. , 2001, American journal of human genetics.

[45]  R. Nielsen Statistical tests of selective neutrality in the age of genomics , 2001, Heredity.

[46]  Pardis C Sabeti,et al.  Linkage disequilibrium in the human genome , 2001, Nature.

[47]  D. Goldstein,et al.  Population genomics: Linkage disequilibrium holds the key , 2001, Current Biology.

[48]  C. Baer,et al.  Population genomics: genome-wide sampling of insect populations. , 2001, Annual review of entomology.

[49]  A. Kilian,et al.  Diversity arrays: a solid state technology for sequence information independent genotyping. , 2001, Nucleic acids research.

[50]  W S Watkins,et al.  Population genomics: a bridge from evolutionary history to genetic medicine. , 2001, Human molecular genetics.

[51]  G. Gibson,et al.  Enabling population and quantitative genomics. , 2002, Genetical research.

[52]  O. Hardy,et al.  spagedi: a versatile computer program to analyse spatial genetic structure at the individual or population levels , 2002 .

[53]  E. Delong,et al.  Microbial population genomics and ecology. , 2002, Current opinion in microbiology.

[54]  C. G. van der Linden,et al.  Biodiversity assessment using markers for ecologically important traits , 2002 .

[55]  Christian Schlötterer,et al.  A microsatellite-based multilocus screen for the identification of local selective sweeps. , 2002, Genetics.

[56]  Justin C. Fay,et al.  Testing the neutral theory of molecular evolution with genomic data from Drosophila , 2002, Nature.

[57]  TESTING FOR GENETIC EVIDENCE OF POPULATION EXPANSION AND CONTRACTION: AN EMPIRICAL ANALYSIS OF MICROSATELLITE DNA VARIATION USING A HIERARCHICAL BAYESIAN MODEL , 2002, Evolution; international journal of organic evolution.

[58]  P. Landry,et al.  Deriving evolutionary relationships among populations using microsatellites and (deltamu)(2): all loci are equal, but some are more equal than others... , 2002, Genetics.

[59]  D. Balding,et al.  Approximate Bayesian computation in population genetics. , 2002, Genetics.

[60]  I. Thomas,et al.  Molecular genecology of temperature response in Lolium perenne: 2. association of AFLP markers with ecogeography , 2002, Molecular ecology.

[61]  P. Bork,et al.  Human non-synonymous SNPs: server and survey. , 2002, Nucleic acids research.

[62]  G. Luikart,et al.  Detecting Wildlife Poaching: Identifying the Origin of Individuals with Bayesian Assignment Tests and Multilocus Genotypes , 2002 .

[63]  R. Everitt,et al.  RED: the analysis, management and dissemination of expressed sequence tags , 2002, Bioinform..

[64]  M. Shriver,et al.  Interrogating a high-density SNP map for signatures of natural selection. , 2002, Genome research.

[65]  M. Stumpf,et al.  Population Genomics: Ageing by Association , 2002, Current Biology.

[66]  M. Nachman,et al.  Searching for evidence of positive selection in the human genome using patterns of microsatellite variability. , 2002, Molecular biology and evolution.

[67]  P. Taberlet,et al.  Holstein's milk detection in cheeses inferred from melanocortin receptor 1 (MC1R) gene polymorphism. , 2002, Journal of dairy science.

[68]  Ziheng Yang,et al.  Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci. , 2002, Genetics.

[69]  Seeking the Signs of Selection , 2002, Science.

[70]  Craig Moritz,et al.  Strategies to protect biological diversity and the evolutionary processes that sustain it. , 2002, Systematic biology.

[71]  Pierre Taberlet,et al.  Landscape genetics: combining landscape ecology and population genetics , 2003 .

[72]  M. Stephens,et al.  Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. , 2003, Genetics.

[73]  J. Ott,et al.  Mathematical multi-locus approaches to localizing complex human trait genes , 2003, Nature Reviews Genetics.

[74]  R. Nielsen,et al.  Correcting for ascertainment biases when analyzing SNP data: applications to the estimation of linkage disequilibrium. , 2003, Theoretical population biology.

[75]  Michael A. Banks,et al.  Which Genetic Loci Have Greater Population Assignment Power? , 2003, Bioinform..

[76]  S. Edwards,et al.  RECONCILING ACTUAL AND INFERRED POPULATION HISTORIES IN THE HOUSE FINCH (CARPODACUS MEXICANUS) BY AFLP ANALYSIS , 2003, Evolution; international journal of organic evolution.

[77]  NATURAL SELECTION ON PROTEIN POLYMORPHISM IN THE RODENT GENUS PEROMYSCUS: EVIDENCE FROM INTERLOCUS CONTRASTS , 2003, Evolution; international journal of organic evolution.

[78]  F. Ronquist,et al.  Taxonomy and biodiversity inventories: time to deliver , 2003 .

[79]  R. Wayne,et al.  Locus-specific genetic differentiation at Rw among warfarin-resistant rat (Rattus norvegicus) populations. , 2003, Genetics.

[80]  T. Matise,et al.  Linkage disequilibrium and inference of ancestral recombination in 538 single-nucleotide polymorphism clusters across the human genome. , 2003, American journal of human genetics.

[81]  Momiao Xiong,et al.  The effect of single nucleotide polymorphism identification strategies on estimates of linkage disequilibrium. , 2003, Molecular biology and evolution.

[82]  F. Bonhomme,et al.  Large discrepancies in differentiation of allozymes, nuclear and mitochondrial DNA loci in recently founded Pacific populations of the pearl oyster Pinctada margaritifera , 2003, Journal of evolutionary biology.

[83]  S. Lavery,et al.  www.DNA-surveillance: applied molecular taxonomy for species conservation and discovery , 2003 .

[84]  L. Rieseberg,et al.  Effects of genetic background on response to selection in experimental populations of Arabidopsis thaliana. , 2003, Genetics.

[85]  T. Mitchell-Olds,et al.  Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana. , 2003, Genome research.

[86]  Alex Lancaster,et al.  PyPop: A Software Framework for Population Genomics: Analyzing Large-Scale Multi-Locus Genotype Data , 2002, Pacific Symposium on Biocomputing.

[87]  D. Nickerson,et al.  The utility of single nucleotide polymorphisms in inferences of population history , 2003 .

[88]  S. P. Fodor,et al.  Large-scale genotyping of complex DNA , 2003, Nature Biotechnology.

[89]  J. Batley,et al.  Mining for Single Nucleotide Polymorphisms and Insertions/Deletions in Maize Expressed Sequence Tag Data1 , 2003, Plant Physiology.

[90]  M. Blaxter,et al.  Molecular taxonomics for biodiversity surveys: already a reality , 2003 .

[91]  Deborah A. Nickerson,et al.  Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans , 2003, Nature Genetics.

[92]  E. Wilson The encyclopedia of life , 2003 .

[93]  M. Bamshad,et al.  Signatures of natural selection in the human genome , 2003, Nature Reviews Genetics.

[94]  Richard J. Mural,et al.  Genome-wide single-nucleotide polymorphism analysis defines haplotype patterns in mouse , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[95]  J. Wall,et al.  Haplotype blocks and linkage disequilibrium in the human genome , 2003, Nature Reviews Genetics.

[96]  C. Schlötterer Hitchhiking mapping--functional genomics from the population genetics perspective. , 2003, Trends in genetics : TIG.

[97]  Arnaud Estoup,et al.  Genetic assignment methods for the direct, real‐time estimation of migration rate: a simulation‐based exploration of accuracy and power , 2004, Molecular ecology.