J Slate

Summary

Affiliation: University of Sheffield
Country: UK

Publications

  1. pmc High-utility conserved avian microsatellite markers enable parentage and population studies across a wide range of species
    Deborah A Dawson
    Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
    BMC Genomics 14:176. 2013
  2. doi request reprint From beavis to beak color: a simulation study to examine how much qtl mapping can reveal about the genetic architecture of quantitative traits
    Jon Slate
    Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom
    Evolution 67:1251-62. 2013
  3. pmc Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing
    Anna W Santure
    Department of Animal and Plant Sciences, University of Sheffield, UK
    BMC Genomics 12:283. 2011
  4. pmc A comparison of SNPs and microsatellites as linkage mapping markers: lessons from the zebra finch (Taeniopygia guttata)
    Alexander D Ball
    Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
    BMC Genomics 11:218. 2010
  5. pmc Digital gene expression analysis of the zebra finch genome
    Robert Ekblom
    Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
    BMC Genomics 11:219. 2010
  6. ncbi request reprint Patterns of linkage disequilibrium in mitochondrial DNA of 16 ruminant populations
    J Slate
    AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
    Mol Ecol 12:597-608. 2003
  7. ncbi request reprint Understanding the relationship between the inbreeding coefficient and multilocus heterozygosity: theoretical expectations and empirical data
    J Slate
    AgResearch, Invermay Agricultural Centre, Mosgiel, Private Bag 50034, New Zealand
    Heredity (Edinb) 93:255-65. 2004
  8. pmc A genome scan for quantitative trait loci in a wild population of red deer (Cervus elaphus)
    J Slate
    AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
    Genetics 162:1863-73. 2002
  9. pmc Molecular evolution of the sheep prion protein gene
    Jon Slate
    University of Sheffield, Department of Animal and Plant Sciences, Sheffield, S10 2TN, UK
    Proc Biol Sci 272:2371-7. 2005
  10. pmc Robustness of linkage maps in natural populations: a simulation study
    Jon Slate
    Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
    Proc Biol Sci 275:695-702. 2008

Collaborators

Detail Information

Publications47

  1. pmc High-utility conserved avian microsatellite markers enable parentage and population studies across a wide range of species
    Deborah A Dawson
    Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
    BMC Genomics 14:176. 2013
    ..No other marker types are capable of enabling this. We therefore developed a set of avian microsatellite markers with enhanced cross-species utility...
  2. doi request reprint From beavis to beak color: a simulation study to examine how much qtl mapping can reveal about the genetic architecture of quantitative traits
    Jon Slate
    Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom
    Evolution 67:1251-62. 2013
    ..More generally, recommendations are made to how QTL mapping can be combined with other approaches to provide more accurate descriptions of a trait's genetic architecture...
  3. pmc Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing
    Anna W Santure
    Department of Animal and Plant Sciences, University of Sheffield, UK
    BMC Genomics 12:283. 2011
    ....
  4. pmc A comparison of SNPs and microsatellites as linkage mapping markers: lessons from the zebra finch (Taeniopygia guttata)
    Alexander D Ball
    Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
    BMC Genomics 11:218. 2010
    ..Linkage map marker order was validated by making comparisons to the assembled zebra finch genome sequence...
  5. pmc Digital gene expression analysis of the zebra finch genome
    Robert Ekblom
    Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
    BMC Genomics 11:219. 2010
    ..Here we investigate tissue specific gene expression patterns in the zebra finch (Taeniopygia guttata) with special emphasis on the genes of the major histocompatibility complex (MHC)...
  6. ncbi request reprint Patterns of linkage disequilibrium in mitochondrial DNA of 16 ruminant populations
    J Slate
    AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
    Mol Ecol 12:597-608. 2003
    ..The potential impact of these processes should be considered when using mtDNA as a tool in vertebrate population genetic, phylogenetic and forensic studies...
  7. ncbi request reprint Understanding the relationship between the inbreeding coefficient and multilocus heterozygosity: theoretical expectations and empirical data
    J Slate
    AgResearch, Invermay Agricultural Centre, Mosgiel, Private Bag 50034, New Zealand
    Heredity (Edinb) 93:255-65. 2004
    ..The relevance of these findings to the causes of heterozygosity--fitness correlations is discussed and predictions for other wild and captive populations are presented...
  8. pmc A genome scan for quantitative trait loci in a wild population of red deer (Cervus elaphus)
    J Slate
    AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
    Genetics 162:1863-73. 2002
    ..To our knowledge this is the first time that a QTL for any trait has been mapped in a wild mammal population. It is hoped that this study will stimulate further investigations of the genetic architecture of fitness traits in the wild...
  9. pmc Molecular evolution of the sheep prion protein gene
    Jon Slate
    University of Sheffield, Department of Animal and Plant Sciences, Sheffield, S10 2TN, UK
    Proc Biol Sci 272:2371-7. 2005
    ..If, as these data suggest, that assumption is wrong, eradication programs will disrupt this balancing selection, and may have a negative impact on the fitness or scrapie resistance of national flocks...
  10. pmc Robustness of linkage maps in natural populations: a simulation study
    Jon Slate
    Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
    Proc Biol Sci 275:695-702. 2008
    ..However, genotyping error can result in incorrect maps being built with very strong statistical support over the correct order. Future applications of linkage maps of natural populations are discussed...
  11. ncbi request reprint Admixture and patterns of linkage disequilibrium in a free-living vertebrate population
    J Slate
    Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
    J Evol Biol 20:1415-27. 2007
    ..Association mapping may be possible in this population, although a high 'baseline' level of LD could lead to false positive associations between marker loci and a trait of interest...
  12. ncbi request reprint Quantitative trait locus mapping in natural populations: progress, caveats and future directions
    Jon Slate
    Department of Animal and Plant Sciences, University of Sheffield, S10 2TN, UK
    Mol Ecol 14:363-79. 2005
    ....
  13. doi request reprint A localized negative genetic correlation constrains microevolution of coat color in wild sheep
    J Gratten
    Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
    Science 319:318-20. 2008
    ..This result demonstrates the importance of understanding the genetic basis of fitness variation when making predictions about the microevolutionary consequences of selection...
  14. doi request reprint The genetic basis of recessive self-colour pattern in a wild sheep population
    J Gratten
    Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
    Heredity (Edinb) 104:206-14. 2010
    ....
  15. doi request reprint A comparison of synteny and gene order on the homologue of chicken chromosome 7 between two passerine species and between passerines and chicken
    M C Hale
    Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, UK
    Cytogenet Genome Res 121:120-9. 2008
    ..Some evidence of heterochiasmy, i.e. a difference in the recombination rate between the sexes, was observed...
  16. doi request reprint Selection and microevolution of coat pattern are cryptic in a wild population of sheep
    J Gratten
    Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
    Mol Ecol 21:2977-90. 2012
    ..This highlights the importance of resolving the underlying genetic basis of phenotypic variation in explaining evolutionary dynamics...
  17. pmc Compelling evidence that a single nucleotide substitution in TYRP1 is responsible for coat-colour polymorphism in a free-living population of Soay sheep
    J Gratten
    Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
    Proc Biol Sci 274:619-26. 2007
    ..0001, LOD=110.20), and very tight linkage between Coat colour and TYRP1 (LOD=29.50)...
  18. doi request reprint Horn type and horn length genes map to the same chromosomal region in Soay sheep
    S E Johnston
    Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
    Heredity (Edinb) 104:196-205. 2010
    ..Understanding the maintenance of horn type and length variation will require an investigation of selection on genotypes that (co)determine both traits...
  19. doi request reprint 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
    Anna W Santure
    Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
    Mol Ecol 19:1439-51. 2010
    ..Our data suggest that using marker information to reconstruct the pedigree, and then calculating relatedness from the pedigree, is likely to give more accurate relatedness estimates than using marker-based estimators directly...
  20. pmc A linkage map of the zebra finch Taeniopygia guttata provides new insights into avian genome evolution
    J Stapley
    Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom
    Genetics 179:651-67. 2008
    ..This whole-genome map is the first for any passerine and a valuable tool for the zebra finch genome sequence project and for studies of quantitative trait loci...
  21. pmc Linkage disequilibrium in domestic sheep
    A F McRae
    AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
    Genetics 160:1113-22. 2002
    ..It is recommended that the statistical significance of LD is used in conjunction with coefficients such as D' to determine the true extent of LD...
  22. ncbi request reprint Global patterns of gene expression in rice cultivars undergoing a susceptible or resistant interaction with the parasitic plant Striga hermonthica
    P J Swarbrick
    Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
    New Phytol 179:515-29. 2008
    ..Up-regulated genes included nutrient transporters, enzymes of amino acid metabolism and some abiotic stress genes...
  23. doi request reprint Detecting genes for variation in parasite burden and immunological traits in a wild population: testing the candidate gene approach
    E A Brown
    Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
    Mol Ecol 22:757-73. 2013
    ..The significant SNPs identified in this study may still, therefore, merit further investigation...
  24. doi request reprint Inbreeding causes early death in a passerine bird
    N L Hemmings
    Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
    Nat Commun 3:863. 2012
    ....
  25. doi request reprint Mitochondrial haplotype does not affect sperm velocity in the zebra finch Taeniopygia guttata
    J A Mossman
    Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
    J Evol Biol 23:422-32. 2010
    ..Therefore, there is no evidence that in this system mitochondrial mutations have asymmetric fitness effects on males and females, leading to genetic variation in male fertility that is blind to natural selection...
  26. ncbi request reprint A novel form of resistance in rice to the angiosperm parasite Striga hermonthica
    A L Gurney
    Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
    New Phytol 169:199-208. 2006
    ..5 of a phenotypic standard deviation. Thus, they should be regarded as major genes and are likely to be useful in breeding programmes to enhance host resistance...
  27. pmc A deer (subfamily Cervinae) genetic linkage map and the evolution of ruminant genomes
    Jon Slate
    AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
    Genetics 160:1587-97. 2002
    ....
  28. doi request reprint Genome mapping in intensively studied wild vertebrate populations
    Jon Slate
    Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
    Trends Genet 26:275-84. 2010
    ..Here, we highlight the progress made in this area and define evolutionary genetic questions that have become tractable with the arrival of these new genomics technologies...
  29. doi request reprint No evidence of genetic differentiation between anoles with different dewlap color patterns
    Jessica Stapley
    Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
    J Hered 102:118-24. 2011
    ..Therefore, dewlap color variation in A. apletophallus appears to be a polymorphism rather than an indicator of 2 fully or partially reproductively isolated populations...
  30. doi request reprint Sperm morphology and velocity are genetically codetermined in the zebra finch
    Jim Mossman
    Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
    Evolution 63:2730-7. 2009
    ....
  31. doi request reprint A test and review of the role of effective population size on experimental sexual selection patterns
    Rhonda R Snook
    Department of Animal and Plant Sciences, Western Bank, University of Sheffield, Sheffield S10 2TN, United Kingdom
    Evolution 63:1923-33. 2009
    ....
  32. pmc Pronounced inter- and intrachromosomal variation in linkage disequilibrium across the zebra finch genome
    Jessica Stapley
    Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
    Genome Res 20:496-502. 2010
    ..The variability in LD between and within chromosomes has important implications for genome wide association studies in birds and for our understanding of the distribution of recombination events and the processes that govern them...
  33. ncbi request reprint Microsatellite measures of inbreeding: a meta-analysis
    D W Coltman
    Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom
    Evolution 57:971-83. 2003
    ..10) with reasonable statistical power (0.80). Very few published studies have used samples sizes approaching this value...
  34. ncbi request reprint A predicted microsatellite map of the passerine genome based on chicken-passerine sequence similarity
    Deborah A Dawson
    Sheffield Molecular Genetics Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
    Mol Ecol 15:1299-320. 2006
    ....
  35. doi request reprint Gene mapping in the wild with SNPs: guidelines and future directions
    Jon Slate
    Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
    Genetica 136:97-107. 2009
    ..Finally, the opportunity afforded by new generation sequencing and typing technologies to map fitness genes by genome-wide association studies is discussed...
  36. ncbi request reprint Gene order and recombination rate in homologous chromosome regions of the chicken and a passerine bird
    Deborah A Dawson
    Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, United Kingdom
    Mol Biol Evol 24:1537-52. 2007
    ....
  37. doi request reprint Multiplex SNP-SCALE: a cost-effective medium-throughput single nucleotide polymorphism genotyping method
    T Kenta
    Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK, Current address Sugadiva Montane, Experimental Center, University of Tsukuba, Ueda, 386 2204, Japan
    Mol Ecol Resour 8:1230-8. 2008
    ..This new protocol was validated for different types of SNPs. The method is cost- and time-effective for medium-scale evolutionary and ecological projects involving 10s to 100s of loci...
  38. doi request reprint Bias in studies of heterozygosity and mate choice
    Jon Slate
    Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
    Mol Ecol 18:1815-7. 2009
    ..They identify two forms of bias that may affect tests of the genetic compatibility hypothesis, and provide guidelines on how these biases may be avoided...
  39. pmc Simple sequence repeats in zebra finch (Taeniopygia guttata) expressed sequence tags: a new resource for evolutionary genetic studies of passerines
    Jon Slate
    Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
    BMC Genomics 8:52. 2007
    ..Here we describe a bioinformatic analysis of zebra finch expressed sequence tag (EST) Genbank entries...
  40. doi request reprint Sexual selection and interacting phenotypes in experimental evolution: a study of Drosophila pseudoobscura mating behavior
    Leonardo D Bacigalupe
    Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Sheffield, UK
    Evolution 62:1804-12. 2008
    ..Changes as a consequence of genetic drift were excluded. Our results show that although variable potential strengths of sexual interactions influence the evolution of interacting phenotypes, the influence may be nonlinear...
  41. doi request reprint A major QTL for resistance of rice to the parasitic plant Striga hermonthica is not dependent on genetic background
    Philip J Swarbrick
    Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, UK
    Pest Manag Sci 65:528-32. 2009
    ....
  42. ncbi request reprint Antler size in red deer: heritability and selection but no evolution
    E B Kruuk
    Institute of Cell, Animal and Population Biology, University of Edinburgh, United Kingdom
    Evolution 56:1683-95. 2002
    ....
  43. pmc Linkage mapping reveals sex-dimorphic map distances in a passerine bird
    Bengt Hansson
    School of Biological Sciences, University of Edinburgh, Institute of Evolutionary Biology, West Mains Road, Edinburgh EH9 3JT, UK
    Proc Biol Sci 272:2289-98. 2005
    ..2 cM) compared to females (237.2 cM; female/male map ratio: 2.15). The sex-specific recombination rates will facilitate the building of a denser linkage map and cast light on hypotheses about sex-specific recombination rates...
  44. ncbi request reprint Mapping quantitative trait Loci underlying fitness-related traits in a free-living sheep population
    Dario Beraldi
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
    Evolution 61:1403-16. 2007
    ..We discuss the prospects for refining estimates of QTL position and effect size in the study population, and for QTL searches in free-living pedigrees in general...
  45. ncbi request reprint Quantitative trait loci (QTL) mapping of resistance to strongyles and coccidia in the free-living Soay sheep (Ovis aries)
    Dario Beraldi
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
    Int J Parasitol 37:121-9. 2007
    ....
  46. pmc Development of a linkage map and mapping of phenotypic polymorphisms in a free-living population of Soay sheep (Ovis aries)
    Dario Beraldi
    Institute of Evolutionary Biology, University of Edinburgh, UK
    Genetics 173:1521-37. 2006
    ..These findings represent an advance in the dissection of the genetic diversity in the wild and provide the foundation for QTL analyses in the study population...
  47. ncbi request reprint Does reduced heterozygosity depress sperm quality in wild rabbits (Oryctolagus cuniculus)?
    Jon Slate
    Curr Biol 16:R790-1; author reply R791-2. 2006