Estimating quantitative genetic parameters in wild populations: A comparison of pedigree and genomic approaches

Molecular Ecology

Volumn 23, Issue 14, 2014, Pages 3434-3451

  Bérénos, Camillo ^a   Ellis, Philip A ^a   Pilkington, Jill G ^a   Pemberton, Josephine M ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

body size; genetic architecture; genomic relatedness; heritability; maternal genetic effect; SNP genotyping

Indexed keywords

OVIS ARIES;

MICROSATELLITE DNA;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; BODY SIZE; COMPARATIVE STUDY; ENVIRONMENT; FEMALE; GENETIC ARCHITECTURE; GENETICS; GENOMIC RELATEDNESS; GENOMICS; HERITABILITY; MALE; MATERNAL GENETIC EFFECT; METHODOLOGY; PEDIGREE; POPULATION GENETICS; SHEEP; SINGLE NUCLEOTIDE POLYMORPHISM; SNP GENOTYPING; UNITED KINGDOM;

BODY SIZE; GENETIC ARCHITECTURE; GENOMIC RELATEDNESS; HERITABILITY; MATERNAL GENETIC EFFECT; SNP GENOTYPING;

ANIMALS; BODY SIZE; ENVIRONMENT; FEMALE; GENETICS, POPULATION; GENOMICS; MALE; MICROSATELLITE REPEATS; MODELS, GENETIC; PEDIGREE; POLYMORPHISM, SINGLE NUCLEOTIDE; SCOTLAND; SHEEP;

EID: 84904035234     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.12827     Document Type: Article

References (69)

1. Åkesson M, Bensch S, Hasselquist D, Tarka M, Hansson B, (2008) Estimating heritabilities and genetic correlations: comparing the 'animal model' with parent-offspring regression using data from a natural population. PLoS ONE, 3, e1739.
2. Banos G, Wiggans GR, Powell RL, (2001) Impact of paternity errors in cow identification on genetic evaluations and international comparisons. Journal of Dairy Science, 84, 2523-2529. (Pubitemid 33613072)
3. Beraldi D, McRae AF, Gratten J, et al,. (2007) Mapping quantitative trait loci underlying fitness-related traits in a free-living sheep population. Evolution, 61, 1403-1416. (Pubitemid 46850689)
4. Bijma P, Wade MJ, (2008) The joint effects of kin, multilevel selection and indirect genetic effects on response to genetic selection. Journal of Evolutionary Biology, 21, 1175-1188.
5. Blanckenhorn WU, (2000) The evolution of body size: What keeps organisms small? Quarterly Review of Biology, 75, 385-407.
6. Blows MW, (2007) A tale of two matrices: multivariate approaches in evolutionary biology. Journal of Evolutionary Biology, 20, 1-8. (Pubitemid 44968143)
7. Charmantier A, Reale D, (2005) How do misassigned paternities affect the estimation of heritability in the wild? Molecular Ecology, 14, 2839-2850. (Pubitemid 41576965)
8. Clement V, Bibe B, Verrier E, et al,. (2001) Simulation analysis to test the influence of model adequacy and data structure on the estimation of genetic parameters for traits with direct and maternal effects. Genetics Selection Evolution, 33, 369-395. (Pubitemid 32822268)
9. Clutton-Brock TH, Pemberton JM, Coulson T, Stevenson IR, MacColl ADC, (2004) The sheep of St Kilda. In: Soay Sheep:Dynamics and Selection in an Island Population (eds, Clutton-Brock TH, Pemberton JM,), pp. 17-51. Cambridge University Press, Cambridge, UK.
10. Coltman DW, Smith JA, Bancroft DR, et al,. (1999) Density-dependent variation in lifetime breeding success and natural and sexual selection in Soay rams. American Naturalist, 154, 730-746. (Pubitemid 30071197)
11. Coltman DW, Pilkington J, Kruuk LEB, Wilson K, Pemberton JM, (2001) Positive genetic correlation between parasite resistance and body size in a free-living ungulate population. Evolution, 55, 2116-2125. (Pubitemid 34003831)
12. Csilléry K, Johnson T, Beraldi D, et al,. (2006) Performance of marker-based relatedness estimators in natural populations of outbred vertebrates. Genetics, 173, 2091-2101. (Pubitemid 44285687)
13. Dodenhoff J, Van Vleck LD, Kachman SD, Koch RM, (1998) Parameter estimates for direct, maternal, and grandmaternal genetic effects for birth weight and weaning weight in Hereford cattle. Journal of Animal Science, 76, 2521-2527. (Pubitemid 128439571)
14. Garant D, Kruuk LEB, (2005) How to use molecular marker data to measure evolutionary parameters in wild populations. Molecular Ecology, 14, 1843-1859. (Pubitemid 40772407)
15. Gay L, Siol M, Ronfort J, (2013) Pedigree-free estimates of heritability in the wild: promising prospects for selfing populations. PLoS ONE, 8, e66983.
16. Gilmour AR, Gogel BJ, Cullis BR, Thompson R, (2009) Asreml User Guide Release 3.0. VSN International Ltd, Hemel Hempstead, UK.
17. Goddard ME, Hayes BJ, (2009) Mapping genes for complex traits in domestic animals and their use in breeding programmes. Nature Reviews Genetics, 10, 381-391.
18. Goddard ME, Hayes BJ, Meuwissen THE, (2011) Using the genomic relationship matrix to predict the accuracy of genomic selection. Journal of Animal Breeding and Genetics, 128, 409-421.
19. Griffith SC, Owens IPF, Thuman KA, (2002) Extra pair paternity in birds: a review of interspecific variation and adaptive function. Molecular Ecology, 11, 2195-2212. (Pubitemid 35301894)
20. Hadfield JD, Richardson DS, Burke T, (2006) Towards unbiased parentage assignment: combining genetic, behavioural and spatial data in a Bayesian framework. Molecular Ecology, 15, 3715-3730. (Pubitemid 44564280)
21. Haile-Mariam M, Nieuwhof GJ, Beard KT, Konstatinov KV, Hayes BJ, (2013) Comparison of heritabilities of dairy traits in Australian Holstein-Friesian cattle from genomic and pedigree data and implications for genomic evaluations. Journal of Animal Breeding and Genetics, 130, 20-31.
22. Hayes B, Goddard M, (2010) Genome-wide association and genomic selection in animal breeding. Genome, 53, 876-883.
23. Henderson CR, (1984) Applications of Linear Models in Animal Breeding. University of Guelph Press, Guelph.
24. Hill WG, Weir BS, (2011) Variation in actual relationship as a consequence of Mendelian sampling and linkage. Genetics Research, 93, 47-64.
25. Israel C, Weller JI, (2000) Effect of misidentification on genetic gain and estimation of breeding value in dairy cattle populations. Journal of Dairy Science, 83, 181-187.
26. Jensen J, Su G, Madsen P, (2012) Partitioning additive genetic variance into genomic and remaining polygenic components for complex traits in dairy cattle. BMC Genetics, 13, 1-9.
27. Johnston SE, Gratten J, Berenos C, et al,. (2013) Life history trade-offs at a single locus maintain sexually selected genetic variation. Nature, 502, 93-95.
28. Kijas JW, Lenstra JA, Hayes B, et al,. (2012) Genome-wide analysis of the world's sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biology, 10, e1001258.
29. Kruuk LEB, (2004) Estimating genetic parameters in natural populations using the 'animal model'. Philosophical Transactions of the Royal Society B: Biological Sciences, 359, 873-890. (Pubitemid 38784077)
30. Kruuk LEB, Hadfield JD, (2007) How to separate genetic and environmental causes of similarity between relatives. Journal of Evolutionary Biology, 20, 1890-1903. (Pubitemid 47262852)
31. Kruuk LEB, Merila J, Sheldon BC, (2001) Phenotypic selection on a heritable size trait revisited. American Naturalist, 158, 557-571. (Pubitemid 34001755)
32. Kruuk LEB, Slate J, Wilson AJ, (2008) New answers for old questions: the evolutionary quantitative genetics of wild animal populations. Annual Review of Ecology Evolution and Systematics, pp. 525-548. Annual Reviews, Palo Alto.
33. Lande R, Arnold SJ, (1983) The measurement of selection on correlated characters. Evolution, 37, 1210-1226.
34. Larsson K, van der Jeugd HP, van der Veen IT, Forslund P, (1998) Body size declines despite positive directional selection on heritable size traits in a barnacle goose population. Evolution, 52, 1169-1184. (Pubitemid 28417895)
35. Lee C, Pollak EJ, (1997) Influence of sire misidentification on sire x year interaction variance and direct-maternal genetic covariance for weaning weight in beef cattle. Journal of Animal Science, 75, 2858-2863. (Pubitemid 127441616)
36. Lee SH, Goddard ME, Visscher PM, van der Werf JHJ, (2010) Using the realized relationship matrix to disentangle confounding factors for the estimation of genetic variance components of complex traits. Genetics Selection Evolution, 42, 22.
37. Lee SH, Yang J, Goddard ME, Visscher PM, Wray NR, (2012) Estimation of pleiotropy between complex diseases using single-nucleotide polymorphism-derived genomic relationships and restricted maximum likelihood. Bioinformatics, 28, 2540-2542.
38. Mackay TFC, Lyman RF, (2005) Drosophila bristles and the nature of quantitative genetic variation. Philosophical Transactions of the Royal Society B: Biological Sciences, 360, 1513-1527. (Pubitemid 43138553)
39. Meuwissen THE, Hayes BJ, Goddard ME, (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics, 157, 1819-1829. (Pubitemid 32298846)
40. Milner JM, Albon SD, Illius AW, Pemberton JM, Clutton-Brock TH, (1999) Repeated selection of morphometric traits in the Soay sheep on St Kilda. Journal of Animal Ecology, 68, 472-488. (Pubitemid 29247481)
41. Milner JM, Pemberton JM, Brotherstone S, Albon SD, (2000) Estimating variance components and heritabilities in the wild: a case study using the 'animal model' approach. Journal of Evolutionary Biology, 13, 804-813.
42. Morrissey MB, Wilson AJ, (2010) pedantics: an R package for pedigree-based genetic simulation and pedigree manipulation, characterization and viewing. Molecular Ecology Resources, 10, 711-719.
43. Morrissey MB, Wilson AJ, Pemberton JM, Ferguson MM, (2007) A framework for power and sensitivity analyses for quantitative genetic studies of natural populations, and case studies in Soay sheep (Ovis aries). Journal of Evolutionary Biology, 20, 2309-2321. (Pubitemid 47621900)
44. Morrissey MB, Parker DJ, Korsten P, et al,. (2012) The prediction of adaptive evolution: empirical application of the secondary theorem of selection and comparison to the breeder's equation. Evolution, 66, 2399-2410.
45. Overall ADJ, Byrne KA, Pilkington JG, Pemberton JM, (2005) Heterozygosity, inbreeding and neonatal traits in Soay sheep on St Kilda. Molecular Ecology, 14, 3383-3393.
46. Pemberton JM, (2008) Wild pedigrees: the way forward. Proceedings of the Royal Society B: Biological Sciences, 275, 613-621. (Pubitemid 351198036)
47. Purcell S, Neale B, Toddbrown K, et al,. (2007) plink: a tool set for whole-genome association and population-based linkage analyses. The American Journal of Human Genetics, 81, 559-575. (Pubitemid 47330214)
48. Rasanen K, Kruuk LEB, (2007) Maternal effects and evolution at ecological time-scales. Functional Ecology, 21, 408-421. (Pubitemid 46805016)
49. Ritland K, (1996) Marker-based method for inferences about quantitative inheritance in natural populations. Evolution, 50, 1062-1073.
50. Robinson MR, Santure AW, DeCauwer I, Sheldon BC, Slate J, (2013) Partitioning of genetic variation across the genome using multimarker methods in a wild bird population. Molecular Ecology, 22, 3963-3980.
51. Santure AW, De Cauwer I, Robinson MR, et al,. (2013) Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population. Molecular Ecology, 22, 3949-3962.
52. Sardell RJ, Keller LF, Arcese P, Bucher T, Reid JM, (2010) Comprehensive paternity assignment: genotype, spatial location and social status in song sparrows, Melospiza Melodia. Molecular Ecology, 19, 4352-4364.
53. Senneke SL, MacNeil MD, Van Vleck LD, (2004) Effects of sire misidentification on estimates of genetic parameters for birth and weaning weights in Hereford cattle. Journal of Animal Science, 82, 2307-2312. (Pubitemid 39103886)
54. Stanton-Geddes J, Yoder JB, Briskine R, Young ND, Tiffin P, (2013) Estimating heritability using genomic data. Methods in Ecology and Evolution, 4, 1151-1158.
55. Stopher KV, Walling CA, Morris A, et al,. (2012) Shared spatial effects on quantitative genetic parameters: accounting for spatial autocorrelation and home range overlap reduces estimates of heritability in wild red deer. Evolution, 66, 2411-2426.
56. Thomas SC, Coltman DW, Pemberton JM, (2002) The use of marker-based relationship information to estimate the heritability of body weight in a natural population: a cautionary tale. Journal of Evolutionary Biology, 15, 92-99. (Pubitemid 34175825)
57. Van Bers NEM, Santure AW, Van Oers K, et al,. (2012) The design and cross-population application of a genome-wide SNP chip for the great tit Parus major. Molecular Ecology Resources, 12, 753-770.
58. Van Der Jeugd HP, McCleery R, (2002) Effects of spatial autocorrelation, natal philopatry and phenotypic plasticity on the heritability of laying date. Journal of Evolutionary Biology, 15, 380-387. (Pubitemid 34523037)
59. Van Raden PM, (2008) Efficient methods to compute genomic predictions. Journal of Dairy Science, 91, 4414-4423.
60. Vattikuti S, Guo J, Chow CC, (2012) Heritability and genetic correlations explained by common SNPs for metabolic syndrome traits. PLoS Genetics, 8, e1002637.
61. Visscher PM, Medland SE, Ferreira MAR, et al,. (2006) Assumption-free estimation of heritability from genome-wide identity-by-descent sharing between full siblings. Plos Genetics, 2, 316-325.
62. Walling CA, Pemberton JM, Hadfield JD, Kruuk LEB, (2010) Comparing parentage inference software: reanalysis of a red deer pedigree. Molecular Ecology, 19, 1914-1928.
63. Wang J, Santure AW, (2009) Parentage and sibship inference from multilocus genotype data under polygamy. Genetics, 181, 1579-1594.
64. Wilson AJ, Coltman DW, Pemberton JM, et al,. (2005) Maternal genetic effects set the potential for evolution in a free-living vertebrate population. Journal of Evolutionary Biology, 18, 405-414. (Pubitemid 40350935)
65. Wilson AJ, Pemberton JM, Pilkington JG, et al,. (2007) Quantitative genetics of growth and cryptic evolution of body size in an island population. Evolutionary Ecology, 21, 337-356. (Pubitemid 46716738)
66. Yang J, Benyamin B, McEvoy BP, et al,. (2010) Common SNPs explain a large proportion of the heritability for human height. Nature Genetics, 42, 565-569.
67. Yang J, Lee SH, Goddard ME, Visscher PM, (2011a) gcta: a tool for genome-wide complex trait analysis. The American Journal of Human Genetics, 88, 76-82.
68. Yang J, Manolio TA, Pasquale LR, et al,. (2011b) Genome partitioning of genetic variation for complex traits using common SNPs. Nature Genetics, 43, 519-525.
69. Zaitlen N, Kraft P, Patterson N, et al,. (2013) Using extended genealogy to estimate components of heritability for 23 quantitative and dichotomous traits. PLoS Genetics, 9, e1003520.