Jon Slate

Summary

Affiliation: University of Sheffield
Country: UK

Publications

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. doi request reprint Life history trade-offs at a single locus maintain sexually selected genetic variation
    Susan E Johnston
    Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
    Nature 502:93-5. 2013
  9. 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
  10. doi request reprint Genome-wide association mapping identifies the genetic basis of discrete and quantitative variation in sexual weaponry in a wild sheep population
    Susan E Johnston
    Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
    Mol Ecol 20:2555-66. 2011

Collaborators

Detail Information

Publications36

  1. 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...
  2. 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...
  3. 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...
  4. 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...
  5. 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...
  6. 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...
  7. 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...
  8. doi request reprint Life history trade-offs at a single locus maintain sexually selected genetic variation
    Susan E Johnston
    Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
    Nature 502:93-5. 2013
    ....
  9. 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
    ....
  10. doi request reprint Genome-wide association mapping identifies the genetic basis of discrete and quantitative variation in sexual weaponry in a wild sheep population
    Susan E Johnston
    Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
    Mol Ecol 20:2555-66. 2011
    ..This finding contrasts markedly from genome-wide association studies of quantitative traits in humans and some model species, where it is often observed that mapped loci only explain a modest proportion of the overall genetic variation...
  11. 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...
  12. doi request reprint Mining online genomic resources in Anolis carolinensis facilitates rapid and inexpensive development of cross-species microsatellite markers for the Anolis lizard genus
    Claire Wordley
    Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
    Mol Ecol Resour 11:126-33. 2011
    ..These markers will be a valuable resource for studies of population genetics, comparative mapping, mating systems, behavioural ecology and adaptive radiations in this diverse lineage...
  13. 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
    ....
  14. 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...
  15. doi request reprint Mitochondrial haplotype does not influence sperm motility in a UK population of men
    Jim A Mossman
    Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
    Hum Reprod 27:641-51. 2012
    ..Here, we tested whether mtDNA variation was associated with sperm motility in a large cohort of men from the UK, to test the robustness of previous studies and the reliability of mtDNA as a marker of poor sperm motility...
  16. doi request reprint The design and cross-population application of a genome-wide SNP chip for the great tit Parus major
    Nikkie E M van Bers
    Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, Wageningen, 6708 WD, The Netherlands
    Mol Ecol Resour 12:753-70. 2012
    ..More generally, the protocols and pitfalls encountered will be of use for those developing similar resources...
  17. 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
    ....
  18. 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...
  19. pmc Evolutionary analysis and expression profiling of zebra finch immune genes
    Robert Ekblom
    University of Sheffield, Department of Animal and Plant Sciences, Sheffield, UK
    Genome Biol Evol 2:781-90. 2010
    ..Several of the avian immune genes investigated here provide strong candidates for in-depth studies of molecular adaptation in birds...
  20. 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)...
  21. pmc Sperm speed is associated with sex bias of siblings in a human population
    Jim A Mossman
    Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912, USA
    Asian J Androl 15:152-4. 2013
    ..This observation suggests family composition is an important factor that needs to be considered in future epidemiological and clinical studies of human fertility...
  22. 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...
  23. doi request reprint Adaptation genomics: the next generation
    Jessica Stapley
    Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
    Trends Ecol Evol 25:705-12. 2010
    ..How many genes are involved in adaptation? What types of genetic variation are responsible for adaptation? Does adaptation utilise pre-existing genetic variation or does it require new mutations to arise following an environmental change?..
  24. doi request reprint Introgression and the fate of domesticated genes in a wild mammal population
    Philine G D Feulner
    Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
    Mol Ecol 22:4210-21. 2013
    ..Therefore, we demonstrate that introgression of domesticated alleles into wild populations can provide a novel source of variation capable of generating rapid evolutionary changes. ..
  25. doi request reprint Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population
    Anna W Santure
    Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
    Mol Ecol 22:3949-62. 2013
    ....
  26. 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
    ....
  27. doi request reprint Partitioning of genetic variation across the genome using multimarker methods in a wild bird population
    Matthew R Robinson
    Department of Animal and Plant Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
    Mol Ecol 22:3963-80. 2013
    ....
  28. 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
    ....
  29. doi request reprint Genetic mapping of the female mimic morph locus in the ruff
    Lindsay L Farrell
    Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
    BMC Genet 14:109. 2013
    ..Here, we use linkage analysis to map the chromosomal location of the Faeder locus, which controls development into the Faeder morph, and draw further conclusions about candidate genes, assuming shared synteny with other birds...
  30. doi request reprint Evidence of inbreeding depression but not inbreeding avoidance in a natural house sparrow population
    Anna M Billing
    Centre for Conservation Biology, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
    Mol Ecol 21:1487-99. 2012
    ..Despite this, birds did not seem to actively avoid mating with close relatives, perhaps as a consequence of constraints on mating possibilities in such a small population...
  31. 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
    ....
  32. 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
    ....
  33. 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...
  34. 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...
  35. 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
    ....
  36. 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...