Computer Note
R. G. Danzmann With the recent development of mini- and microsatellite DNA analysis, it is now possible to detect very high levels of variability at individual genetic loci compared to only a few years ago when genetic variability was examined in populations using allozyme markers. It is now feasible to discriminate family origins for randomly selected individuals from a population using only a few hypervariable satellite repeat loci. PROBMAX is a program designed to help researchers identify the parents of an individual sampled from a population mixture when the genetic variation at several loci is known in both the progeny mixture and in the parents. Although the most powerful discriminatory loci are currently of the satellite repeat type with verifiable Mendelian segregation, the program also allows input for dominant-recessive type variation (I.e., RAPD loci or DNA fingerprinting bands). Input for mini- and microsatellite loci may be entered as actual allelic base pair sizes and for allozymes as gel migration distances. Two columns are entered for each diploid locus. Dominantrecessive loci are entered as a single column, with the presence of a polymorphic band being scored as 2 and the absence of the band as a 1. Missing data for both codominant and dominant-recessive loci are entered as zero values. For dominantrecessive marker bands, it is not possible to accurately ascertain the genotype as being homozygous or heterozygous dominant. The program assumes both possibilities with respect to genotypic segregation.
PROBMAX was written and compiled in Visual Basic for DOS and requires the user to input three files. The progeny genotype file is always designated with a *.pro extension and contains the genotypic scorings of all the potential progeny. The parent file (which must have a *.par extension) contains the genotypic scorings for all the loci included in the progeny file, with the final column containing an identification number for each potential male or female parent. Females are all designated with the numbers 1001-1999, while males are designated as 2001-2999. Thus the program can accommodate mating designations between 999 different males and females, although several input files may be required to test all parental pairs since the present version of PROBMAX is limited to 32,700 array elements. A third file, designated with a *.cro extension contains information regarding which males are known to be or may potentially be mated to each female In the parental generation. Female numbers are listed first in each line followed by the known or potential mates for each female. The program then generates a table showing each potential combination of male and female parent that was designated In the *.cro file with an associated probability vector belonging to that particular parental combination for each individual progeny designated in the *.pro file. These values are grouped In rows of 10 values each, with columns 1-10 corresponding to progeny numbers 1-10, row 2, progeny numbers 11-20, row 3, progeny numbers 21-30, etc. A probability vector of 1.0 would indicate that all the genotypes in that individual could have been generated by the parental combination tested, while, for example, a value of 0.50 would Indicate that only half the loci examined possessed genotypes that could have been generated by that particular parental combination. A second file gives the total number of possible progeny that
could be generated for each parental pair listed In the left-hand column of the file and also tabulates the total number of possible parental pairs for each progeny tested. Progeny numbers are listed according to the order of progeny input from the *.pro file. A third output file lists a table of the genetic loci tested and gives a listing of the genetic matches in progeny genotype to possible genotypes generated by each parental combination. A final feature of the program is that it allows the researcher to retest the progeny matches at certain microsatellite loci by assuming there is a misscoring of the progeny genotypes by ±2 bp of the true base pair size. The program will prompt the user to designate which loci should be retested using the broader size range. A second program, PROBMAXG, is also provided that will allow the user to generate random progeny genotypic sets from the cross-combinations and genotypes specified in the *.cro and *.par files, respectively. This feature may be helpful In determining whether the specified number of genetic markers being tested will be able to discriminate the exact parentage of the progeny in the pool being examined or whether additional markers may be needed to fulfil this objective. These programs should be of potential utility to a wide range of biologists that have access to parental and progeny tissue for genotyping but are not quite sure "who came from whom." The programs may be obtained by sending a DOS formatted 3.5" disk to the author or by contacting the author by e-mail at
[email protected]. From the Department of Zoology, University of Guelph, Guelph, Ontario, Canada NIG 2W1. The Journal of Heredity 1997:88(4) Received June 3, 1996 Accepted September 19, 1996 Corresponding Editor Stephen J. O'Brien
333
Downloaded from http://jhered.oxfordjournals.org/ by guest on August 21, 2015
PROBMAX: A Computer Program for Assigning Unknown Parentage in Pedigree Analysis From Known Genotypic Pools of Parents and Progeny
