Genodive manual
Furthermore, recombination in multivalents can lead to sister chromatids segregating together, giving rise to AA, BB, CC, and DD alleles (‘Double reduction’, see discussion in Ronfort et al, 1998). Chromosomes either pair at random or form multivalents (described as ‘polysomic’ inheritance), such that a tetraploid individual carrying alleles ABCD can form gametes AB, AC, AD, BC, BD, and CD (reviewed by Bever and Felber, 1992 Olson, 1997 Ronfort et al, 1998). In newly formed autopolyploids, duplicated chromosomes do not have unique partners at meiosis. Polyploids can be further divided by their mode of inheritance. However, as species boundaries are rarely clear-cut, auto- and allopolyploidy actually represent opposite ends along a spectrum of intergenome differentiation, with ‘hybrids’ between differentiated lineages from within a single species forming the middle ground. Conversely, allopolyploids are derived from interspecific hybridisation, and therefore comprise two (or more) differentiated genomes. Autopolyploids are derived from the duplication of a single genome and – at least initially – there is no significant differentiation between duplicate genomes. Polyploids are often conceptually divided into two groups: autopolyploids and allopolyploids (reviewed by Ramsey and Schemske, 2002). Indeed, although polyploidy is particularly common among plants, fish, and amphibians, it is also found among birds, mammals, and many invertebrates ( Leitch and Bennett, 1997 Otto and Whitton, 2000 Legatt and Iwama, 2003). Although the utility of F ST may be limited for highly diverse loci (eg Nagylaki, 1998), and its interpretation in terms of simple population genetic models is questionable ( Whitlock and McCauley, 1999), F ST and related measures continue to be quoted almost universally in studies of population genetic structure.į ST and the other summary statistics cited above have been very widely employed to quantify patterns of genetic variation in diploid organisms. Several different methods have been used to quantify genetic differentiation among groups, most notably differentiation statistics related to F ST ( Wright, 1951 Weir and Cockerham, 1984). For molecular markers with a clear genetic interpretation such as microsatellites, isozymes and DNA sequences, widely used measures of diversity include allelic richness ( A), gene diversity ( H e – ‘expected heterozygosity’, see eg Hartl and Clark, 1997), and, for DNA sequence data, the proportion of pairwise site differences ( π). We illustrate the behaviour of these statistics using coalescent computer simulations that show that F′ ST behaves in a qualitatively similar way to F ST, thus providing a useful way to quantify population differentiation in allopolyploid species.Ī primary aim of population genetics is the measurement of genetic diversity and the characterisation of its hierarchical distribution among individuals, populations, or groups of populations. This statistic can be extended to a population differentiation measure ( F′ ST), which is analogous to F ST. Here, we propose the use of a simple allelic-phenotype diversity statistic ( H′) that measures diversity as the average number of alleles by which pairs of individuals differ. As a result, analysis of genetic diversity patterns in allopolyploids has tended to rely on the interpretation of phenotype frequencies, which loses information available from allele composition. In allopolyploids, the problem is compounded because genetically distinct isoloci frequently share alleles. This occurs because the presence of multiple alleles at each locus often precludes the measurement of genotype or allele frequencies. However, population genetic studies of polyploid organisms have been hampered by difficulties associated with scoring and interpreting molecular data. The analysis of genetic diversity within and between populations is a routine task in the study of diploid organisms.