vineyridge wrote:The reason that I asked about 5-e and 10-e is that both have a good history of mares who pass on very high quality jumping talent through generation after generation. If 5-e is a family that descends from Northern European mares rather than Oriental mares, I was sort of wondering if the same were true of 10-e. One sample from the whole family isn't really enough to make any call from, though.
Although the map (Fig. 2, p.292, Hill et al. in Animal Genetics, 2002) was somewhat suggestive of a geographic association between Northern European stock and haplotype L (found in all samples from fam. 5 exclusive of desc. of Hag 1744), Jansen's findings (PNAS 99:16 10905-10910, 2002) indicate greater geographic diversity in that area of the phylogenetic network. Haplotype M (found in desc. of Hag, and identical betw bp 15476-15818 to the 2008 submission defined as TB-5e) was not mapped, but would be nearer A than L.
Ref. GenBank sequences associated w/ the aforementioned study by Jansen et al., the TB is not alone in conserving Hill's haplotype F in two forms, one w/ a deletion betw bp 15528-32. By ignoring all indels the reports by Hill et al. 2002 and Harrison/Turrion-Gomez 2006 were faithful to the phylogenetic model of evaluating non-recombinant DNA, but that model is a pretty blunt instrument with which to analyze the matrilineages of a breed only ~350 yrs. old. Personally, I think that by ignoring the deletion a major point of segregation was overlooked. It's quite plausible that this is responsible for the superficially singular finding of diversity in functional mtDNA among groups "identical" by d-loop reported by Harrison/Turrion-Gomez.
Additionally, the relatively few GenBank accessions of longer d-loop sequences, for example those submitted by Flannery & Cothran, UKy 2006 (unassociated w/ any published report) show numerous segregating sites above bp 15827 (the high end of the sequence used by Hill et al. to analyze the TB haplotypes). None of these are meaningful from the broader phylogenetic viewpoint, but a handful of them look like they might be helpful in distinguishing betw TB families, imho.
