Bend Or was Tadcaster?

[vineyridge]

PZ, in the Truth in The Bones article, there is a tree diagram.

Figure 2 Phylogenetic analysis. An unrooted maximum-likelihood tree of mitochondrial D-loop sequences from 12 historic Thoroughbred horses, including Eclipse and Bend Or and 296 living Thoroughbred horses. The HKY + gamma model of evolution was used, with 1000 bootstrap replicates.

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What the heck does this mean and how is the actual diagram to be read? I'm assuming this is where the Hyperion question originated. What do the little numbers scattered about mean?

[Pan Zareta]

PZ, in the Truth in The Bones article, there is a tree diagram.

Figure 2 Phylogenetic analysis. An unrooted maximum-likelihood tree of mitochondrial D-loop sequences from 12 historic Thoroughbred horses, including Eclipse and Bend Or and 296 living Thoroughbred horses. The HKY + gamma model of evolution was used, with 1000 bootstrap replicates.

.
What the heck does this mean and how is the actual diagram to be read? I'm assuming this is where the Hyperion question originated. What do the little numbers scattered about mean?

It just sets forth the mathematical models used to compute/draw the tree. I'm not sure what the little numbers indicate. The tree reflects the relative evolutionary distance between the various haplotypes, including that between Hyperion's and the other two haplotypes known from published report to occur in family 6. But more specific information may be had by comparing Hyperion's published sequence (GenBank, HM581898) with haplotypes "C" and "N" (Table 1, p. 288, Hill et al. 2002).

[xfactor fan]

Pan Zareta,

Would you make it easy for us, what haplotype Hyperion is? Since he's not "C" and "N".

[ElPrado]

You need the holotype, too.
Was he the Northern Dancer type, short coupled and burly...the Nijinsky type, long barreled and long legged?
He was the Northern Dancer holotype, from what I've seen of paintings of him.

[Pan Zareta]

Pan Zareta,

Would you make it easy for us, what haplotype Hyperion is? Since he's not "C" and "N".

Hyperion's sequence is a d-loop fragment inclusive of nps 15479-15819. It exhibits the following polymorphisms v. the CRS/HRS.

15483Adel*, 15491A>T*, 15494C, 15495C, 15496G, 15508insA*, 15534T, 15585A, 15602T, 15603C, 15649G, 15720A, 15771T

Asterisks indicate polymorphisms unique (among ~2000 E. caballus GenBank sequences defined by breed/type) to this particular sequence. They may or may not be valid markers. The other polymorphisms are sequence motif markers for sub-haplogroup L1 (Achilli et al. 2012, D1 in the nomenclature of Jansen et al. 2002).

Even if the unique markers are excluded this haplotype is an exact match for none of Hill's haplotypes. It does match, from nps 15479-15818, the published sequence (GenBank, 2008, EU580161) of Bower et al. defined as "TBG-8c". In the tree (Figure 2) Hyperion is in relatively close proximity to "Family 8c" (tho' far enough away that the unique markers were apparently not being ignored). Ormonde is just under "Family 8c". His mtDNA results were not precisely as expected either.

A couple of things to be mindful of -
These particular sequences are all in a haplogroup in which it is especially difficult to fully differentiate between/define haplotypes using HVS 1 d-loop (nps 15469-15834) alone.
The Ormonde and Hyperion samples came, obviously, from aged remains that may not have been stored in conditions ideal for DNA preservation.

[xfactor fan]

What is the mystery about Ormonde?

[Pan Zareta]

What is the mystery about Ormonde?

Sub-haplogroup D3/L3 (nomenclature of Jansen/Achilli) haplotype expected. D1/L1 found.

[xfactor fan]

Must have been a surprise. Any idea where that happened?

[Pan Zareta]

Must have been a surprise. Any idea where that happened?

The sequence for Ormonde is a short (440 bp) fragment from the most hypervariable area of the control region. Within that range the sequence motifs for sub-haplogroups D3/L3 and D1/L1 differ only at a single locus. More information is needed before drawing even a tentative conclusion that Ormonde's sequence is indicative of an error in the stud book record. Note that the "References" for the Eclipse/Bend Or paper indicate that an mtDNA paper has been submitted by Bower et al. to the 'Journal of Anim. Breeding & Genetics'. Let's hope that's published soon and puts their modern mtDNA samples (sequences published 2008) and the mtDNA sequences from the historic remains into more precise context.