Genome mapping in intensively studied wild vertebrate populations

Trends in Genetics

Volumn 26, Issue 6, 2010, Pages 275-284

  Slate, Jon ^a   Santure, Anna W ^a   Feulner, Philine G D ^a   Brown, Emily A ^a   Ball, Alex D ^a   Johnston, Susan E ^a   Gratten, Jake ^a  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

GENE LINKAGE DISEQUILIBRIUM; GENE MAPPING; GENETIC CONSERVATION; GENETIC SELECTION; GENETIC TRAIT; GENOMICS; GENOTYPE; HERITABILITY; NONHUMAN; PHENOTYPIC VARIATION; POPULATION GENETICS; PRIORITY JOURNAL; QUANTITATIVE GENETICS; QUANTITATIVE TRAIT LOCUS MAPPING; REVIEW; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; VERTEBRATE; WILD SPECIES;

ANIMALS; CHROMOSOME MAPPING; EVOLUTION, MOLECULAR; GENETICS, POPULATION; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; VERTEBRATES;

VERTEBRATA;

EID: 77953290833     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2010.03.005     Document Type: Review

References (71)

1. Kruuk L.E.B., Hill W.G. Introduction. Evolutionary dynamics of wild populations: the use of long-term pedigree data. Proc. R. Soc. B 2008, 275:593-596.
2. Kruuk L.E.B., et al. New answers for old questions: the evolutionary quantitative genetics of wild animal populations. Annu. Rev. Ecol. Evol. Syst. 2008, 39:525-548.
3. Merilä J., Sheldon B.C. Avian quantitative genetics. Curr. Ornithol. 2001, 16:179-255.
4. Kruuk L.E.B. Estimating genetic parameters in natural populations using the 'animal model'. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 2004, 359:873-890.
5. Merilä J., et al. Explaining stasis: microevolutionary studies in natural populations. Genetica 2001, 112:199-222.
6. Ellegren H., Sheldon B.C. Genetic basis of fitness differences in natural populations. Nature 2008, 452:169-175.
7. Slate J. QTL mapping in natural populations: progress, caveats and future directions. Molec. Ecol. 2005, 14:363-379.
8. Beraldi D., et al. Development of a linkage map and mapping of phenotypic polymorphisms in a free-living population of Soay sheep (Ovis aries). Genetics 2006, 173:1521-1537.
9. Slate J., et al. A genome scan for quantitative trait loci in a wild population of red deer (Cervus elaphus). Genetics 2002, 162:1863-1873.
10. Mardis E.R. The impact of next-generation sequencing technology on genetics. Trends Genet. 2008, 24:133.
11. Hudson M.E. Sequencing breakthroughs for genomic ecology and evolutionary biology. Mol. Ecol. Res. 2008, 8:3-17.
12. Metzker M.L. Sequencing technologies - the next generation. Nat. Rev. Genet. 2010, 11:31-46.
13. Vera J.C., et al. Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Molec. Ecol. 2008, 17:1636-1647.
14. Baird N.A., et al. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 2008, 3:7.
15. van Bers N., et al. Genome-wide SNP detection in the great tit Parus major using high throughput sequencing. Molec. Ecol. 2010, 19:89-99.
16. Ragoussis J. Genotyping technologies for genetic research. Annu. Rev. Genomics Hum. Genet. 2009, 10:117-133.
17. Beraldi D., et al. Quantitative trait loci (QTL) mapping of resistance to strongyles and coccidia in the free-living Soay sheep (Ovis aries). Int. J. Parasitol. 2007, 37:121-129.
18. Beraldi D., et al. Mapping QTL underlying fitness-related traits in a free-living sheep population. Evolution 2007, 61:1403-1416.
19. Johnston S.E., et al. Horn type and horn length genes map to the same chromosomal region in Soay sheep. Heredity 2010, 104:196-205.
20. Tarka M., et al. A strong quantitative trait locus for wing length on chromosome 2 in a wild population of great reed warblers. Proc. R. Soc. B 2010, doi:10.1098/rspb.2010.0033.
21. Flint J., Mackay T.F.C. Genetic architecture of quantitative traits in mice, flies, and humans. Genome Research 2009, 19:723-733.
22. Visscher P.M. Sizing up human height variation. Nat. Genet. 2008, 40:489-490.
23. Manolio T.A., et al. Finding the missing heritability of complex diseases. Nature 2009, 461:747-753.
24. Beavis W.D. The power and deceit of QTL experiments: lessons from comparative QTL studies. Proceedings of the forty-ninth annual corn and sorghum industry research conference 1994, 250-266.
25. Wilson A.J., et al. An ecologist's guide to the animal model. Journal Of Animal Ecology 2010, 79:13-26.
26. Hansson B., et al. Does linkage disequilibrium generate heterozygosity-fitness correlations in great reed warblers?. Evolution 2004, 58:870-879.
27. Slate J., Pemberton J.M. Admixture and patterns of linkage disequilibrium in a free-living vertebrate population. J. Evol. Biol. 2007, 20:1415-1427.
28. Coltman D.W., et al. Positive genetic correlation between parasite resistance and body size in a free-living ungulate population. Evolution 2001, 55:2116-2125.
29. Nussey D.H., et al. The evolutionary ecology of individual phenotypic plasticity in wild populations. J. Evol. Biol. 2007, 20:831-844.
30. Charmantier A., et al. Adaptive phenotypic plasticity in response to climate change in a wild bird population. Science 2008, 320:800-803.
31. Nussey D.H., et al. Selection on heritable phenotypic plasticity in a wild bird population. Science 2005, 310:304-306.
32. Reale D., et al. Genetic and plastic responses of a northern mammal to climate change. Proc. R. Soc. B. 2003, 270:591-596.
33. Qvarnström A., et al. Testing the genetics underlying the coevolution of mate choice and ornament in the wild. Nature 2006, 441:84-86.
34. Kirkpatrick M., Hall D.W. Sexual selection and sex linkage. Evolution 2004, 58:683-691.
35. Mank J.E., et al. Sex chromosomes and male ornaments: a comparative evaluation in ray-finned fishes. Proc. R. Soc. Lond. B. Biol. Sci. 2006, 273:233-236.
36. Foerster K., et al. Sexually antagonistic genetic variation for fitness in red deer. Nature 2007, 447:1107-1109.
37. Bonduriansky R., Chenoweth S.F. Intralocus sexual conflict. Trends Ecol. Evol. 2009, 24:280-288.
38. Poissant J., et al. Sex-specifc genetic variance and the evolution of sexual dimorphism: a systematic review of cross-sex genetic correlations. Evolution 2010, 64:97-107.
39. Knott S.A., et al. Methods for multiple-marker mapping of quantitative trait loci in half-sib populations. Theor. Appl. Genet. 1996, 93:71-80.
40. Rowe S.J., et al. Detecting parent of origin and dominant QTL in a two-generation commercial poultry pedigree using variance component methodology. Genet. Sel. Evol. 2009, 41:11.
41. Day T., Bonduriansky R. Intralocus sexual conflict can drive the evolution of genomic imprinting. Genetics 2004, 167:1537-1546.
42. Lander E., Kruglyak L. Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results. Nat. Genet. 1995, 11:241-247.
43. Dalziel A., et al. Linking genotypes to phenotypes and fitness: how mechanistic biology can inform molecular ecology. Molec. Ecol. 2009, 18:4997-5017.
44. Korsten P., et al. Association between DRD4 gene polymorphism and personality variation in great tits: a test across four wild populations. Molec. Ecol. 2010, 19:832-843.
45. Fidler A.E., et al. Drd4 gene polymorphisms are associated with personality variation in a passerine bird. Proc. R. Soc. Lond. B. Biol. Sci. 2007, 274:1685-1691.
46. Hoekstra H.E., Coyne J.A. The locus of evolution: evo devo and the genetics of adaptation. Evolution 2007, 61:995-1016.
47. Carroll S.B. Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution. Cell 2008, 134:25-36.
48. Gratten J., et al. Compelling evidence that a single nucleotide substitution in TYRP1 is responsible for coat-colour polymorphism in a free-living population of Soay sheep. Proc. R. Soc. B. 2007, 274:619-626.
49. Gratten J., et al. The genetic basis of recessive self-colour pattern in a wild sheep population. Heredity 2010, 104:206-214.
50. Gratten J., et al. A localized negative genetic correlation constrains microevolution of coat color in wild sheep. Science 2008, 319:318-320.
51. Hernández-Sánchez J., et al. Candidate gene analysis for quantitative traits using the transmission disequilibrium test: the example of the melanocortin 4-receptor in pigs. Genetics 2003, 164:637-644.
52. Hernández-Sánchez J., et al. A web application to perform linkage disequilibrium and linkage analyses on a computational grid. Bioinformatics 2009, 25:1377-1383.
53. Clutton-Brock T., Sheldon B.C. The seven ages of Pan. Science 2010, 327:1207-1208.
54. McRae A.F., et al. Modeling linkage disequilibrium in natural populations: the example of the Soay sheep population of St. Kilda, Scotland. Genetics 2005, 171:251-258.
55. Backström N., et al. Genetic mapping in a natural population of collared flycatchers (Ficedula albicollis): conserved synteny but gene order rearrangements on the avian Z chromosome. Genetics 2006, 174:377-386.
56. Backström N., et al. A gene-based genetic linkage map of the collared flycatcher (Ficedula albicollis) reveals extensive synteny and gene-order conservation during 100 million years of avian evolution. Genetics 2008, 179:1479-1495.
57. Backström N., et al. Levels of linkage disequilibrium in a wild bird population. Biol. Lett. 2006, 2:435-438.
58. Li M.H., Merilä J. Extensive linkage disequilibrium in a wild bird population. Heredity 2009, doi:10.1038/hdy.2009.150.
59. Jaari S., et al. A first-generation microsatellite-based genetic linkage map of the Siberian jay (Perisoreus infaustus): insights into avian genome evolution. BMC Genomics 2009, 10:1.
60. Hansson B., et al. Avian genome evolution: insights from a linkage map of the blue tit (Cyanistes caeruleus). Heredity 2009, 104:67-78.
61. Åkesson M., et al. Linkage mapping of AFLP markers in a wild population of great reed warblers: importance of heterozygosity and number of genotyped individuals. Molec. Ecol. 2007, 16:2189-2202.
62. Hansson B., et al. Linkage mapping reveals sex-dimorphic map distances in a passerine bird. Proc. R. Soc. B. 2005, 272:2289-2298.
63. Romanov M., et al. The value of avian genomics to the conservation of wildlife. BMC Genomics 2009, 10:S10.
64. Sargolzaei M., Schenkel F.S. QMSim: a large-scale genome simulator for livestock. Bioinformatics 2009, 25:680-681.
65. Morrissey M.B., Wilson A. pedantics: an r package for pedigree-based genetic simulation and pedigree manipulation, characterization and viewing. Mol. Ecol. Res. 2009.
66. Morrissey M.B., et al. A framework for power and sensitivity analyses for quantitative genetic studies of natural populations, and case studies in Soay sheep (Ovis aries). J. Evol. Biol. 2007, 20:2309-2321.
67. Falchi M, Borlino C. PowQ: a user-friendly package for the design of variance component multipoint linkage analysis studies. Bioinformatics 2006, 22:1404-1405.
68. Neuenschwander S., et al. quantiNemo: an individual-based program to simulate quantitative traits with explicit genetic architecture in a dynamic metapopulation. Bioinformatics 2008, 24:1552-1553.
69. Purcell S., et al. Genetic power calculator: design of linkage and association genetic mapping studies of complex traits. Bioinformatics 2003, 19:149-150.
70. Purcell S., et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 2007, 81:559-575.
71. George A.W., et al. Mapping quantitative trait loci in complex pedigrees: a two-step variance component approach. Genetics 2000, 156:2081-2092.