All three polymorphisms may have undergone recurrent mutation (or gene conversion) in the past (Stead and Jeffreys 2002), so a given allele at each of these SNPs might be present on very different ancestral lineages.
Outer fragments are runs of unique sites that may be evidence of past gene conversion events that originated from outside of the alignment or else from within the alignment but such that evidence of the source has been destroyed by later mutation or gene conversion (see http://www.math.wustl.edu/∼sawyer/geneconv/gconvdoc.html#AssessSig).
This makes it likely that these additional two mutations are shared due to retrotransposition rather than parallel mutation or gene conversion, a non-reciprocal recombination process that affects Alu elements, so there may be two active source genes in this small subfamily.
Considering only the silent polymorphisms, to avoid confounding any effects of positive or balancing selection, we examined the probabilities of shared SNPs arising among the hsp70S genes via independent mutation or gene conversion using the method of Rozas and Aguade [ 26].
Genetically SMA is homogenous in that all forms of the disease are caused by homozygous deletion, rare subtle mutations, or gene conversion of the survival motor neuron-1 (SMN1) gene with concurrent retention of a linked paralog, survival motor neuron-2 (SMN2) [6], [7], [7].
In the absence of strong selection, MHC is expected to diverge over time between islands and populations due to drift, with the generation of new haplotypes through point mutations or gene conversion.
The source of tight double recombinations is still an open question; they could arise from biological phenomena such as mutations or gene conversions, or they could be (and experiments have shown that they are generally are) genotyping errors (Lincoln and Lander 1992; Dib et al. 1996; Broman et al. 1998; Broman and Weber 2000).
Such elements may have been generated by back mutation, gene conversion, or more likely a mixture of these two processes.
Assuming that the Scan genotypes are correct, and barring highly improbable mutation, gene conversion, or double recombination, then the granddaughter must have inherited the haplotypes shown and must carry the D allele.
