NewHybrids
manual

NewHybrids version 1.1 beta (7. April 2003)
NewHybrids is a program for computing the posterior distribution that individuals in a sample fall into different hybrid categories.

• Mac
• Windows

• diploid
• AFLP
• MICROSAT
• Standard

• whitespace (spaces and or tabs) separated text file *.txt/*.dat
• first line: NumIndivs number of individuals
• second line: NumLoci number of loci
• third line: Digits number of digits used to denote a particular allele
• fourth line: Format Lumped (genotype at a single locus is given by a single number) or NonLumped
• next lines: LocusNames names of all loci separated by whitespace
• next lines: genotype data
  • first character: number of the individual (numbering must be serially)
  • next characters: genotypes (all on same line or on different lines)
    • Lumped format: two alleles are encoded as one number, Digits specify how many digits are used to represent each locus
    • NonLumped format: alleles at each locus are given by a consecutive pair of numbers that are white space seperated
    • Missing data: Lumped: encoded as 0, NonLumped: encoded as -1 (each allele at the missing locus must have a -1)

• Lumped format
• + band is present
• - band is absent
• 0 missing data

• data types can be mixed

• Lumped data file:

NumIndivs 2
NumLoci 6
Digits 1
Format Lumped
LocusNames sAAT1 sAAT2 sAAT3 ADA1 ADA2 ADH
1 11 11 11 0 11 32
2 21 11 21 11 11 12 

• NonLumped data file:

NumIndivs 2
NumLoci 6
Digits 1
Format NonLumped
LocusNames sAAT1 sAAT2 sAAT3 ADA1 ADA2 ADH
1 123 143 -1 -1 144 144 120 122 157 158 144 144 
2 135 135 134 140 144 144 120 122 161 161 144 144 

• AFLP data file (4 Microsat loci, 5 AFLP loci):

NumIndivs 2
NumLoci 9
Digits 1
Format Lumped
LocusNames m1 m2 m3 m4 A1 A2 A3 A4 A5
1 11 12 13 11 + + + - +
2 22 33 11 22 - - 0 - -
3 12 13 13 11 + - - - +

Anderson, E.C. and Thompson, E.A. (2002) A model-based method for identifying species hybrids using multilocus genetic data. Genetics 160: 1217-1229.