MolKin v2.0: a computer program for genetic analysis of populations using molecular coancestry information.

Recently different studies have formalized the way in which it is possible to obtain coancestry coefficients from molecular information (Caballero and Toro 2002; Eding and Meuwissen 2001) by applying Malécot’s (1948) definition of kinship to marker genes, though referring it to identity-by-state instead of identity-by-descent (Caballero and Toro 2002). The molecular coancestry between two individuals, i and j, is the probability that two randomly sampled alleles from the same locus in two individuals are identical by state. Because of its straightforward relationship with genealogical coancestry, this parameter has been shown to have interesting properties that may be used for conservation purposes (Eding et al. 2002; Toro et al., 2002; 2003). Moreover, molecular coancestry can be used to assess genetic diversity within and between populations (Eding and Meuwissen 2001). Using simulated data, Eding and Meuwissen (2001) showed that molecular coancestry has some interesting properties, namely that average kinship between populations becomes constant very quickly after population fission, causing between-population diversity to remain constant. This property allows researchers using molecular coancestry information to study the genetic relationships between populations (Álvarez et al. 2005; Caballero and Toro 2002; Fabuel et al. 2004). Despite the utility of molecular coancestry for conservation worth and evolutionary studies, no computer routines are available to facilitate the use of molecular coancestry information. MolKin (version 2.0) is a population genetics computer program that conducts several genetic analyses on multilocus information in a user-friendly environment. The program will help researchers or those responsible for population management to assess genetic variability and population structure at reduced costs with respect to dataset preparation. A previous version of MolKin (version 1.0) was available on request for research purposes (Álvarez et al. 2005). Following Bennewitz and Meuwissen (2005), who have recently suggested that bootstrapping could significantly improve kinship estimates, the main change included in the present version of MolKin (version 2.0) is the inclusion of a bootstrapping procedure to compute, when needed, molecular coancestry coefficients and most genetic distances calculated by MolKin with the corresponding standard errors. Following Felsenstein (1985), the bootstrapping procedure implemented in MolKin (version 2.0) involves creating new datasets by randomly sampling individuals with replacement, so that the resulting datasets have the same size as the original, but some genotypes have been left out and others are duplicated. The random variation of the results from analyzing these bootstrapped datasets can be shown statistically to be typical of the variation that you would get from collecting new datasets. Although written primarily as a program for research purposes, the new version of MolKin (version 2.0) improves the user’s environment and offers a number of features that may be of interest to teachers and students for developing an indepth understanding of concepts related to population genetic analysis.