Publications

Slate Group - University of Sheffield

Publications

Where possible PDFs are provided. Otherwise follow the link to the full content or abstract. If that fails, email Jon Slate for a copy.

2013 and In Press

98) PGD Feulner*, JGratten*, JW Kijas, PM Visscher, JM Pemberton & J Slate (In Press) Introgression and the Fate of Domesticated Genes in a Wild Mammal Population. Molecular Ecology
* Joint First Authors

97) MR Robinson, AW Santure, I De Cauwer, BC Sheldon & J Slate (In Press) Partitioning of genetic variation across the genome using multi-marker methods in a wild bird population. Molecular Ecology

96) AW Santure*, I De Cauwer*, MR Robinson, J Poissant, BC Sheldon & J Slate (In Press) Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population. Molecular Ecology
* Joint first authors

95) CJ Garroway* R Radersma*, I Sepil, AW Santure, I De Cauwer, J Slate & BC Sheldon (2013) Fine-scale genetic structure in a wild bird population: the role of limited dispersal and environmentally-based selection as causal factors. Evolution DOI: 10.1111/evo.12121
* Joint First Authors

94) MP Heaton, TS Kalbfleisch, DT Petrik, B Simpson, JW Kijas, ML Clawson, CG Chitko-McKown, GP Harhay, KA Leymaster & The International Sheep Genomics Consortium (2013) Genetic Testing for TMEM154 Mutations Associated with Lentivirus Susceptibility in Sheep. PloS One 8(2): e55490.

93) RL Andrew, L Bernatchez, A Bonin, CA Buerkle, BC Carstens, BC Emerson, D Garant, T Giraud, NC Kane, SM Rogers, J Slate, H Smith, VL Sork, GN Stone, TH Vines, L Waits, A Widmer & LH Rieseberg (2013). A road map for molecular ecology. Molecular Ecology 22: 2605-26

92) DA Dawson, AD Ball, LG Spurgin, D Martin-Galvez, IRK Stewart, GJ Horsborough, J Potter, M Molina-Morales, AWJ Bicknell, SAJ Preston, R Ekblom, J Slate & T Burke (2013) High-utility conserved avian microsatellite markers enable parentage and population studies across a wide range of species. BMC Genomics 14:176

91) IJ Hagen, AM Billing, B Rønning, SA Pedersen, H Pärn, J Slate & H Jensen (2013). The easy road to genome-wide medium density SNP screening in a non-model species: development and application of a 10K SNP-chip for the house sparrow (Passer domesticus). Molecular Ecology Resources 13:429-439

90) J Slate (2013). From Beavis to Beak Colour: A simulation study to examine how much QTL mapping can reveal about the genetic architecture of quantitative traits. Evolution 67: 1251-1262

89) JA Mossman, J Slate, TR Birkhead, HD Moore & AA Pacey (2013) Sperm speed is associated with sex bias of siblings in a human population. Asian Journal of Andrology 15:152–154

88) S Alfadala, DA Dawson, GJ Horsburgh, JM Behnke, AB Eman, ME Mohallal, S Zalat & J Slate (2013). Large-scale isolation of Eastern spiny mouse Acomys dimidiatus microsatellite loci through GS-FLX 454 titanium sequencing. Conservation Genetics Resources 5:519-524

87) EA Brown, JG Pilkington, DH Nussey, A Watt, AD Hayward, R Tucker, AL Graham, S Paterson, D Beraldi, JM Pemberton & J Slate (2013). Detecting genes for variation in parasite burden and immunological traits in a wild population: testing the candidate gene approach. Molecular Ecology 22:757-773

2012

86) NL Hemmings, J Slate & TR Birkhead (2012). Inbreeding causes early death in a passerine bird. Nature Communications 3:863

85) JI Hoffman, R Tucker, MS Clark, J Forcada & J Slate. (2012) Rates of assay success and genotyping error when SNP genotyping in non-model organisms: a case study in the Antarctic fur seal. Molecular Ecology Resources 12: 861-872

84) NEM van Bers*, AW Santure*, K van Oers, I De Cauwer, BW Dibbits, C Mateman, RPMA Crooijmans, BC Sheldon, ME Visser, MAM Groenen & J Slate (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
* Joint First Authors

83) J Gratten, JG Pilkington, EA Brown, TH Clutton-Brock, JM Pemberton & J Slate (2012) Selection and microevolution of coat pattern are cryptic in a wild population of sheep. Molecular Ecology 21: 2977-2990

82) JA Mossman, J Slate, TR Birkhead, HD Moore & AA Pacey (2012). Mitochondrial haplotype does not influence sperm motility in a UK population of men (2012). Human Reproduction 27: 641-651

81) R Ekblom, J Slate, GJ Horsburgh, TR Birkhead & Terry Burke (2012) Comparison between normalised and un-normalised 454-sequencing libraries for small-scale RNA-seq studies. Comparative and Functional Genomics Volume 2012, Article ID 281693. doi:10.1155/2012/281693

80) AM Billing, AM Lee, S Skjelseth, ÅA Borg, MC Hale ,J Slate, H Pärn, TH Ringsby, B-E Sæther & H Jensen (2012) Evidence of inbreeding depression but not inbreeding avoidance in a natural house sparrow population. Molecular Ecology 21: 1487-1499.

79) JW Kijas, JA. Lenstra, B Hayes, S Boitard, LR Porto Neto, M San Cristobal, B Servin, R McCulloch, V Whan, K Gietzen, S Paiva, W Barendse, E Ciani,H Raadsma, J McEwan, B Dalrymple & other members of the International Sheep Genomics Consortium (2012). Genome Wide Analysis of the World’s Sheep Breeds Reveals High Levels of Historic Mixture and Strong Recent Selection. Plos Biology 10: e1001258. doi:10.1371/journal.pbio.1001258

2011

78) AW Santure, J Gratten, JA Mossman, BC Sheldon & J Slate (2011). Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing. BMC Genomics 12: 283

Highly Accessed

77) A Bretman, R Rodriguez-Munoz, C Walling, J Slate & T Tregenza (2011). Fine-scale population structure, inbreeding risk and avoidance in a wild insect population. Molecular Ecology 20: 3045-3055

76) SE Johnston, JC McEwan, NK Pickering, JW Kijas, D Beraldi, JG Pilkington, JM Pemberton & J Slate (2011). Genome-wide association mapping identifies the genetic basis of discrete and quantitative variation in sexual weaponry in a wild sheep population. Molecular Ecology 20: 2555-2566

75) R Ekblom, J Stapley, AD Ball, T Birkhead, T Burke & J Slate (2011). Genetic mapping of the major histocompatibility complex in the zebra finch (Taeniopygia guttata). Immunogenetics 63: 523-530

74) AJ Osborne, R Brauning, JK Schultz, MA Kennedy, J Slate & NJ Gemmell (2011). Development of a predicted physical map of microsatellite locus positions for pinnipeds, with wider applicability to the Carnivora. Molecular Ecology Resources 11: 503-513

73) J Stapley, C Wordley & J Slate (2010). No evidence of genetic differentiation between anoles with different dewlap color patterns. Journal of Heredity. 102: 118-124

2010

72) R Ekblom, L French, J Slate & T Burke (2010). Evolutionary Analysis and Expression Profiling of Zebra Finch Immune Genes. Genome Biology and Evolution 2: 781-790

71) J Stapley*, J Reger*, PGD Feulner, C Smaja, J Galindo, R Ekblom, C Bennison, AD Ball, AP Beckerman & J Slate (2010). Adaptation Genomics: the next generation. Trends in Ecology and Evolution 25: 705-712
* joint first authors

70) J Gratten, AJ Wilson, AF McRae, D Beraldi, PM Visscher, JM Pemberton & J Slate (2010). No evidence for warming climate theory of coat colour change in Soay sheep: a comment on Maloney et al. Biology Letters 6: 678-679

69) R Rodríguez-Muñoz, A Bretman, J Slate, CA Walling & T Tregenza (2010). Natural and sexual selection in a wild insect population. Science 328: 1269-1272

68) WC Warren, DF Clayton, H Ellegren, AP Arnold & 56 others, J Stapley, J Slate, R Ekblom, T Birkhead, T Burke & 17 Others (2010) The genome of a songbird. Nature 464: 757-762

67) C Wordley, J Slate & J Stapley (2010) Mining online genomic resources in Anolis carolinensis facilitates rapid and inexpensive development of cross-species microsatellite markers for the Anolis lizard genus. Molecular Ecology Resources DOI: 10.1111/j.1755-0998.2010.02863.x

66) J Slate, AW Santure, PGD Feulner, EA Brown, AD Ball, SE Johnston & J Gratten (2010) Genome mapping in intensively studied wild vertebrate populations. Trends in Genetics 26: 275-284

65) J Stapley, TR Birkhead, T Burke & J Slate (2010) Pronounced inter and intra-chromosomal variation in linkage disequilibrium across the zebra finch genome. Genome Research 20:496-502

64) R Ekblom, CN Balakrishnan, T Burke & J Slate (2010) Digital gene expression analysis of the zebra finch genome. BMC Genomics 11:219

Highly Accessed

63) AW Santure, J Stapley, AD Ball, TR Birkhead, T Burke & J Slate (2010) On the use of large marker panels to estimate inbreeding and relatedness: empirical and simulation studies of a pedigreed zebra finch population typed at 771 SNPs. Molecular Ecology 19:1439-51

62) AD Ball, J Stapley, DA Dawson, TR Birkhead, T Burke & J Slate (2010) A comparison of SNPs and microsatellites as linkage mapping markers: lessons from the zebra finch (Taeniopygia guttata). BMC Genomics 11:218

Highly Accessed

61) JA Mossman, J Slate & TR Birkhead (2010) Mitochondrial Haplotype Does Not Affect Sperm Velocity in the Zebra Finch Taeniopygia guttata. Journal of Evolutionary Biology 23:422-432

60) J Slate (2010). Gems from the Heredity Archive: Scrapie genetics before the discovery of prions. Heredity. 104:122-123

59) SE Johnston, D Beraldi, AF McRae, JM Pemberton & J Slate (2010). Horn type and horn length genes map to the same chromosomal region in Soay sheep. Heredity 104:196-205

58) J Gratten, JG Pilkington, EA Brown, D Beraldi, JM Pemberton & J Slate (2010). The genetic basis of recessive self colour pattern in a wild sheep population. Heredity 104: 206-214

2009

57) JA Mossman, J Slate, S Humphries & TR Birkhead (2009) Sperm Morphology and Velocity are Genetically Co-determined in the Zebra Finch. Evolution 63:2730-2737

56) JR Chapman, S Nakagawa, DW Coltman, J Slate & BC Sheldon (2009) A Quantitative Review of Heterozygosity-Fitness Correlations in Animal Populations. Molecular Ecology 18:2746-2765

55) RR Snook, L Brustle & J Slate (2009) A test and review of the role of effective population size on experimental sexual selection patterns. Evolution 63: 1923-1933

54) J Slate (2009) Perspective: Bias in studies of heterozygosity and mate choice. Molecular Ecology 18: 1815-1817

53) PJ Swarbrick, JD Scholes, MC Press & J Slate (2009) A major QTL for resistance of rice to the parasitic plant Striga hermonthica is not dependent on genetic background. Pest Management Science 65: 528-532

52) J Slate, J Gratten, D Beraldi, J Stapley, M Hale & JM Pemberton (2009). Gene mapping in the wild with SNPs: guidelines and future directions. Genetica 136: 97-107

2008

51) LEB Kruuk, J Slate & AJ Wilson (2008). New answers for old questions: the evolutionary quantitative genetics of wild animal populations. Annual Review of Ecology, Evolution and Systematics 39: 525-548

Available free here

50) T Kenta, J Gratten, NS Haigh GN Hinten, J Slate, RK Butlin & T Burke (2008) Multiplex SNP-SCALE: a cost-effective medium-throughput SNP genotyping method Molecular Ecology Resources 8:1230-1238

49) LD Bacigalupe, HS Crudgington, J Slate, AJ Moore and RR Snook (2008) Sexual selection and interacting phenotypes in experimental evolution: a study of Drosophila pseudoobscura mating behavior. Evolution 62:1804-1812

48) PJ Swarbrick, K Huang, G Liu, J Slate, MC Press, T Zhu and JD Scholes (2008) Global patterns of gene expression in rice cultivars undergoing a susceptible and resistant interaction with the parasitic plant Striga hermonthica. New Phytologist 179:515-529

47) MC Hale, H Jensen, TR Birkhead, T Burke & J Slate (2008) A comparison of synteny and gene order on the homologue of chicken chromosome 7 between two passerine species and between passerines and chicken. Cytogenetic and Genome Research 121:120-129

46) J Stapley, TR Birkhead, T Burke and J Slate (2008) A linkage map of the zebra finch Taeniopygia guttata provides new insight into avian genome evolution. Genetics 179:651-667

45) J Gratten, AJ Wilson, AF McRae, D Beraldi, PM Visscher, JM Pemberton and J Slate (2008) A localized negative genetic correlation constrains microevolution of coat color in wild sheep. Science 318:319-320

44) J Slate (2008). Robustness of linkage maps in natural populations: a simulation study. Proc. R. Soc. Lond B 275:695-702

43) JE Lane, S Boutin, MR Gunn, J Slate & DW Coltman (2008) Female multiple mating and paternity in free-ranging North American red squirrels Animal Behaviour 75:1927-1937

2007

42) DA Dawson, M Akesson, T Burke, JM Pemberton J Slate, & B Hansson (2007) Gene order and recombination rate in homologous chromosome regions of the chicken and a passerine bird Molecular Biology and Evolution 24:1537-1552

41) J Slate, MC Hale & TR Birkhead (2007). Simple sequence repeats in zebra finch (Taeniopygia guttata) expressed sequence tags: a new resource for evolutionary genetic studies of passerines. BMC Genomics 8:52.

40) J Slate & JM Pemberton. (2007). Admixture and patterns of linkage disequilibirum in a free-living vertebrate population. Journal of Evolutionary Biology 20:1415-1427

39) D Beraldi, AF McRae, J Gratten, J Slate, PM Visscher & JM Pemberton (2007). Mapping QTL underlying fitness-related traits in a free-living sheep population. Evolution 61: 1403-1416.

38) J Gratten, D Beraldi, BV Lowder, AF McRae, PM Visscher, JM Pemberton & J Slate (2007). Compelling evidence that a single nucleotide polymorphism in TYRP1 is responsible for coat colour polymorphism in a free-living population of Soay sheep. Proc. R. Soc. Lond B. 274: 619-626

Available Free Here

37) JE Lane, S Boutin, MR Gunn, J Slate & DW Coltman (2007) Genetic relatedness of mates does not predict patterns of parentage in North American red squirrels. Animal Behaviour 74:611-619

36) GN Hinten, MC Hale, J Gratten, JA Mossman, BV Lowder, MK Mann & J Slate (2007). SNP SCALE: SNP scoring by colour and length exclusion. Molecular Ecology Notes 7: 377-388

[Excel Macro For Automated Genotype Assignment][Instructions]

35) MR Gunn, K Hartnup, SA Boutin, J Slate & DW Coltman (2007)A test of the efficacy of whole-genome amplification on DNA obtained from low-yield samples. Molecular Ecology Notes7: 393-399

34) D Beraldi, AF McRae, J Gratten, JG Pilkington, J Slate, PM Visscher and JM Pemberton (2007) Quantitative trait loci (QTL) mapping of resistance to strongyles and coccidia in the free-living Soay sheep (Ovis aries) International Journal for Parasitology 37:121-129

2006

33) NJ Gemmell & J Slate (2006). Heterozygote advantage for fecundity PLoS One 1(1) e125 doi:10.1371/journal.pone.0000125

32) J Slate & JM Pemberton (2006) Does reduced heterozygosity depress sperm quality in wild rabbits (Oryctolagus cuniculus)? Current Biology 16: R790-792

Available Free Here

Authors’ Response

31) JA Mossman, TR Birkhead & J Slate (2006). The whole mitochondrial genome sequence of the zebra finch (Taeniopygia guttata). Molecular Ecology Notes 6:1222-1227

30) D Beraldi, AF McRae, J Gratten, J Slate, PM Visscher & JM Pemberton (2006) Development of a Linkage Map and Mapping of Phenotypic Polymorphisms in a Free-living Population of Soay Sheep (Ovis aries). Genetics 173: 1521-1537

29) DA Dawson, T Burke, B Hansson, J Pandhal, MC Hale, GN Hinten & J Slate (2006) A predicted microsatellite map of the passerine genome based on chicken-passerine sequence homology. Molecular Ecology 15: 1299-1320 [Appendix 1][Appendix 2]

28) AL Gurney, J Slate, MC Press & J. D. Scholes (2006) A novel form of resistance in rice to the angiosperm parasite Striga hermonthica. New Phytologist 169: 199-208

2005

27) J Slate (2005) Molecular evolution of the sheep prion protein gene. Proc. R. Soc.Lond. B. 272: 2371-2377 [supplementary info.]

Available Free Here

26) B Hansson, M Äkesson, J Slate & JM Pemberton (2005) Linkage mapping reveals sex-dimorphic map distances in a passerine bird. Proc. R. Soc.Lond. B. 272: 2289-2298

Available Free Here

25) MR Gunn, DA Dawson, A Leviston, K Hartnup, CS Davis, C Strobeck, J Slate & DW Coltman (2005) Isolation of 18 polymorphic microsatellite loci from the North American red squirrel, Tamiasciurus hudsonicus (Sciuridae, Rodentia), and their cross-utility in other species Molecular Ecology Notes 5: 650-653

24) J Slate (2005). QTL mapping in natural populations: progess, caveats and future directions Molecular Ecology 14: 363-379

2004

23) J Slate & NJ Gemmell (2004). Eve 'n' Steve: Recombination of human mitochondrial DNA. Trends in Ecology and Evolution. 19: 561-563

22) J Slate, P David, KG Dodds, BA Veenvliet, BC Glass, TE Broad & JC McEwan (2004). Understanding the relationship between the inbreeding coefficient and multilocus heterozygosity: theoretical expectations and empirical data. Heredity 93: 255-265

Available Free Here

New Scientist Feature here

2003

21) DW Coltman & J Slate (2003) Microsatellite measures of inbreeding: a meta-analysis. Evolution 57: 971-983

20) J Slate & S Phua (2003) Patterns of linkage disequilibirum in mitochondrial DNA of sixteen ruminant populations. Molecular Ecology 12: 597-608

19) LEB Kruuk, J Slate, JM Pemberton & TH Clutton-Brock (2003) Fluctuating asymmetry in a secondary sexual trait: no associations with individual fitness, environmental stress or inbreeding, and no heritability. J. Evolutionary Biol. 16: 101-113

Available Free Here

2002

18) J Slate, PM Visscher, S MacGregor, DR Stevens, ML Tate & JM Pemberton (2002) A genome scan for QTL in a wildÂ population of red deer (Cervus elaphus). Genetics. 162: 1863-1873

17) LEB Kruuk, J Slate, JM Pemberton, FE Guinness & TH Clutton-Brock. (2002). Antler size in red deer: heritability and selection, but no evolution. Evolution 56: 1683-1695

16) TC Marshall, DW Coltman, JM Pemberton, J Slate et al. (2002) Estimating the prevalence of inbreeding from pedigrees. Proc. R. Soc. Lond., B. 269: 1533-1539

Available Free Here

15) J Slate, T van Stijn, R Anderson, KM McEwan et al. (2002) A deer (subfamily Cervinae) genetic linkage map and the evolution of ruminant genomes. Genetics 160: 1587-1597

14) A McRae, JC McEwan, KG Dodds, T Wilson, AM Crawford & J Slate (2002) Linkage disequilibrium in domestic sheep. Genetics 160:1113-1122

13) J Slate & JM Pemberton (2002) Comparing molecular measures for detecting inbreeding depression. J. Evolutionary Biology15:20-31

Available Free Here

2001

12) J Slate, AF McRae & JC McEwan (2001) Prospects for linkage disequilibrium mapping in domestic sheep. Proc. Assoc. Advmt. Anim. Breed. Genet. 14: 86-89

2000

11) J Slate, LEB Kruuk, TC Marshall, JM Pemberton & TH Clutton-Brock (2000) Inbreeding depression influences lifetime breeding success in a wild population of red deer (Cervus elaphus). Proc. R. Soc. Lond., B 267:1657-1662

Available Free Here

10) J Slate, T Marshall & J Pemberton (2000) A retrospective assessment of the accuracy of the paternity inference program CERVUS. Molecular Ecology 9:801-808

9) LEB Kruuk, TH Clutton-Brock, J Slate, JM Pemberton, S Brotherstone & FE Guinness (2000) Heritability of fitness in a wild mammal population. PNAS 97: 698-703

Available Free Here

1995-1999

8) T Coulson, S Albon, J Slate & J Pemberton (1999) Sex dependent responses to inbreeding and outbreeding in red deer calves. Evolution 53:1951-1960

7) J Slate, JM Pemberton & PM Visscher (1999) Power to detect QTL in a free-living polygynous ruminant population. Heredity 83: 327-336

Available Free Here

6) J Slate, DW Coltman, SJ Goodman, I Maclean, JM Pemberton & JL Williams (1998) Bovine microsatellite loci are highly conserved in red deer, sika deer and Soay sheep. Animal Genetics 29:307-315

5) TC Marshall, J Slate, LEB Kruuk & JM Pemberton (1998) Statistical confidence for likelihood-based paternity inference in natural populations. Molecular Ecology 7:639-655

Available Free Here

4) TN Coulson, JM Pemberton, SD Albon, MA Beaumont, TC Marshall, J Slate, FE Guinness & TH Clutton-Brock (1998) Microsatellites measure inbreeding depression and heterosis in red deer. Proc. R. Soc. Lond., B265:489-495

Available Free Here

3) TN Coulson, SD Albon, JM Pemberton, TH Clutton-Brock, J Slate & FE Guinness (1998) Genotype by environment interactions in winter survival in red deer. J. Anim. Ecol. 67: 434-445.

2) JM Pemberton, JA Smith, TN Coulson, TC Marshall, J Slate et al. (1996) The maintenance of genetic polymorphism in small island populations: Large mammals in the Hebrides. Phil. Trans. R. Soc. Lond., B 351: 745-752.

Available Free Here

1) JM Pemberton, J Slate, DR Bancroft & JA Barrett (1995) Nonamplifying alleles at microsatellite loci: a caution for parentage and population studies. Molecular Ecology 4: 249-252.

Book Chapters/Conference Proceedings

4) JM Pemberton, D Coltman, TC Coulson & J Slate (1999) Using microsatellites to measure the fitness consequences of inbreeding and outbreeding. In: Microsatellites: Evolution and Application. eds. DB Goldstein & C Schlotterer. Oxford University Press.

3) J Slate, & JM Pemberton (1998) Mapping genes for birth weight in a natural population of red deer. In Fourth International Congress of the Biology of Deer. Kaposvar, Hungary.

2) JM Pemberton, JA Smith, TN Coulson, TC Marshall, J Slate, S Paterson, SD Albon (1998). The maintenance of genetic polymorphism in small island populations: Large mammals in the Hebrides. In: Evolution on Islands ed. P Grant. Cambridge University Press.

1) JM Pemberton & J Slate (1994)Genetic studies of wild deer populations: a technical revolution. In Third International Congress on the Biology of Deer, ed. JA Milne, Edinburgh.

Other

J Slate (2010) Terry Burke - recipient of the 2009 Molecular Ecology Prize. Molecular Ecology 19: 23-24