The external branch length is the number of unique genotypes from either intermediate ancestor Y or Z to any of the 4 descendant children A, B, C, or D. We generate sequences that evolve subject to natural selection using Avida.
The following Supporting Information is available in the online version of this article – File S1. 28 unique genotypes from 61 R. ponticum individuals in Irish populations identified by 4 SSR markers.
In this nest, we detected six maternal genotypes; three females with shared genotypes between the two broods, two unique female genotypes from the early brood, and one unique female genotype from the late brood (Table 2).
The internal branch length of this 4 taxa topology is the number of unique genotypes in the phylogeny from the intermediate ancestor Y to the intermediate ancestor Z, one of which is the ultimate ancestor X.
The frequency distribution of the pairwise number of allele differences of all MLGs was plotted as a genetic distance metric to address the possibility that not all unique genotypes stem from sexual events but also from allele scoring errors or somatic mutations within asexual lineages [ 41, 42].
Although all clones had unique genotypes, the four regenerated clones showed a greater genetic distance from the donor clone CP 92-1666 (mean GD 0.4) than to one another (mean GD 0.03).
Identification of additional unique genotypes in the studied population adds to the existing knowledge of KIR genotypes.
Although we phenotyped and genotyped 94 progeny, genotyping revealed only 61 unique genotypes; the presence of clones among progeny has been previously reported in Cryptococcus neoformans [48], [49].
This method relies on several assumptions, namely: (1) unique genotypes originate from a zygote rather than by mutation of an existing genotype; (2) mating is random [this may be violated in clonal populations (Cook, 1983)]; and (3) genotypes at separate loci are independent.
Frequency data for AI, AES and LSC were obtained from ramets of 569 unique genotypes (150 plants from 65 accessions, 300 F2, 119 RIL).
