HICKORY

HICKORY
documentation

version 1.1
Software for analysis of geographic structure in genetic data. The software implements the Bayesian method described in Holsinger (1999) for estimating F-statistics co-dominant marker data and the method described in Holsinger et al. (2002) for estimating F-statistics from dominant marker data. It also includes routines to allow posterior comparisons as described in Holsinger and Wallace (2004).

• Windows
• Linux

• dominant markers
• co-dominant markers
• AFLP (amplified fragment length polymorphism)
• RAPD (random amplified polymorphic DNA)
• multi-allelic markers

files in NEXUS format

• need only an alleles block:

  #nexus
  begin alleles; [comments are surrounded by square brackets]
   dimensions newpops npops=2 nloci=3;
   format labels missing=? separator=/;
   locusallelelabels
    1 ’pgi 1’,
    2 ’pgi 2’,
    3 adh;
   matrix
    Embudo:
     indiv_1 A/A 100/110 slow/fast
     indiv_2 A/A 75 / 90 slow/slow
     indiv_3 A/a 75/100 fast/slow
     indiv_4 A/A 100/100 fast/fast,
    Black_Mesa:
     1 a/a 110/100 fast/slow
     2 a/A 75/100 slow/slow
     3 a/a 100/100 fast/fast
    ;
  end;

  • dimensions command:
    • nloci: number of loci scored
    • npops: number of populations scored
  • format command:
    • missing: character to be used for missing data (missing diploid genotype would thus be specified as ?/?)
  • locusallelelabels command:
    • optional (loci will simply be numbered)
    • comma-separated list of locus number and locus name pairs
  • matrix command:
    • The genotype for a diploid locus at a co-dominant locus takes the form A/a
    • forward slash (/) symbol serves as a separator symbol, making it clear which pairs of alleles belong to each locus
    • If the loci represent dominant genetic markers, do not use the slash and specify only one allele for each locus
    • phenotype for a dominant locus (dominant marker):
      • keyword dominant
      • dominant phenotype is scored as 1 (or +) or 0 (−) (default)
      • Hickory accepts the following alternatives:

        dominant;                 -> default         
        dominant all:1;           -> default
        dominant all:0;           -> dominant phenotype at all loci scored as 0 (recessive = 1) 
        dominant 1,2,3:1 4,5:0;   -> dominant phenotype at first 3 loci scored as 1 and at last 2 loci scored as 0
        dominant 1-3:1 4-5:0;     -> dominant phenotype at first 3 loci scored as 1 and at last 2 loci scored as 0

• the hickory block is optional:
  • you can set parameters governing the MCMC sampler

• Holsinger, K. E. 1999. Analysis of genetic diversity in geographically structured populations: a Bayesian perspective. Hereditas 130:245-255.
• Holsinger, K. E., P. O. Lewis, and D. K. Dey. 2002. A Bayesian approach to inferring population structure from dominant markers. Molecular Ecology 11:1157-1164.
• Holsinger, K. E., and L. E. Wallace. 2004. Bayesian approaches for the analysis of population structure: an example from Platanthera leucophaea (Orchidaceae). Molecular Ecology 13:887-894.
• Song, S., D. K. Dey, and K. E. Holsinger. 2006. Differentiation among populations with migration, mutation, and drift: implications for genetic inference. Evolution 60:1-12.