Pedigree Query

when looking at progeny....you see a column that says family in this column there is a letter and a number I have tried to read up on it and just cant get it to set in can you give me a basic understanding or somewhere I can read about it...what is good?? or does it have anything to do with being good???thankyou for your time

This may help.

http://www.bloodlines.net/TB/Families/FamilyNumbers.htm

Hi Tammy,

Some recent mtDNA studies (like that of Dr. Steve Harrison) have found that perhaps 25% of all horses are incorrectly identified by female families.

The problem of course is that the errors multiple as the horse breeds.

Regards,

Pete

Pete wrote:Some recent mtDNA studies (like that of Dr. Steve Harrison) have found that perhaps 25% of all horses are incorrectly identified by female families.

The problem of course is that the errors multiple as the horse breeds.

Some lines are obviously misplaced. But it might be unwise to draw conclusions yet about lines that appear by haplotype to converge. Dr. Harrison's finding of functional diversity among individuals with the same D-loop haplotype suggests that further differentiation between the haplotypes identified in his study, as well as the one by Hill et al. (2002), may be possible.

PZ

Hi Pan,

Perhaps I'm missing something but what does functional diversity have to do with identifying female families? Can two unrelated horses have the same mtDNA?

We can only identify errors in perhaps a 50 year window because we don't have earlier DNA samples. It's probable that the percentage of errors increases as we go back in time.

It's probable too that most pedigrees contain a parentage error if you go back far enough. Female families go back a long way so I hope that the percentage of errors that Steve hypothesized is the worst of it.

Regards,

Pete

Sorry Pete, I was a bit unclear. By "functional diversity" I mean diversity in the regions of mtDNA that code for functions critical to energy production. As is noted in Harrison's report, the D-Loop region is "supposedly more hypervariable" than the functional regions. That's well-established by studies of other species that either mapped an entire mt genome, or directly sequenced a greater amount of D-Loop by percentage than did Hill 2002 and Harrison 2006. Either the equine is a notable exception to this, or direct sequencing and comparison of additional D-Loop bp's should yield additional segregating sites that would distinguish by D-Loop between Harrison's haplotypes II, III, and XV (reported as identical at ~400 D-Loop bp, but segregating at two functional loci).

Pete wrote:We can only identify errors in perhaps a 50 year window because we don't have earlier DNA samples.

But with non-recombinant (mt or y) DNA we effectively have those earlier DNA samples. Absent mutation (rare even in the hypervariable regions, and occurs at a predictable rate) the mtDNA we're 'looking' at today is exactly as it was many, many, dams ago. Given a large enough sample, representative of as many branches as possible, I think errors in the historic record considerably earlier than 50 years ago may be identified with a high degree of confidence. Anecdotally, in a few select cases hair or hoof from historic notables can be tested. Rumor has it that Eclipse should be adding luster to family 23, not 12, but I think provenance of the material sampled might be an issue.

(Note to Lucy - did you buy that hoof that was allegedly Alice Hawthorn's?)

No argument that the record is full of errors. Twenty five percent might turn out to be conservative. More than one haplotype and greater diversity between/among them than can be explained by simple, predictable, mutation apparently exists among contemporary representatives of most of the English founders.

Best,
PZ

Pan Zareta wrote:(Note to Lucy - did you buy that hoof that was allegedly Alice Hawthorn's?)

It was her tail. And no.

But boy, was I tempted.

Hi Pan,

simple, predictable, mutation apparently exists among contemporary representatives of most of the English founders.

Actually, mutation is random but its effective rate over a span of time can be surmised. In the past several years it’s been found that mtDNA mutates at a higher rate than was originally believed. This ‘discovery’ is the basis for some religious fundamentalists who believe that this can now prove that a common Eve (for humans) lived perhaps 6500 years ago and not @200,000 year ago as was originally hypothesized.

The most recent paper that I’ve read on the mutation variation in DNA was updated in 12/06: http://www.kerchner.com/dnamutationrates.htm

This report uses a mutation rate in mtDNA of 2.9 x 10^-5 or about 3 mutations per 100,000 generations so it’s possible that some horses have mtDNA that has mutated from its’ source but there aren’t going to be very many and even still they should be definable by family (as you suggest). After all, we’re discussing a breed that’s only 300-400 years old and not the dawn of mankind.

the mtDNA we're 'looking' at today is exactly as it was many, many, dams ago.

Then I think we agree and this I’ll take this as an answer to my original question that 2 horses can’t have the same mtDNA unless they’re related by female family. Now we’re left with the problem of trying to build the house from the top down and hoping that we have a solid foundation because the problem is not identifying mutations rather it’s the embedded errors that exist in the studbook.

About a year ago I criticized Steve Harrison’s report in which I asked the question of why is it necessary to use mtDNA to determine potential racing aptitude when pedigree serves the same purpose? If the pedigree is reliable it’s a reasonable question but any scientific endeavor of this type should be applauded, so my bad.

We can assume what the DNA of an ancestor might be from the descendants but we have the problem of the aforementioned errors, whether intentional or not and the further back the fewer checks that were in place to prevent them. Alice Hawthorn’s hoof notwithstanding, I’d question the authenticity of most any equine DNA source unless the horse was alive.

I think errors in the historic record considerably earlier than 50 years ago may be identified with a high degree of confidence.

Errors that exist in the designation of female families should be possible to be identified but it’s unlikely that the Jockey Club will allow the changes to be made to the Stud Book. Errors on the sire side will be harder to establish, if at all, and again I think we can assume that the records won’t be changed. The bottom line is that we have performance based on pedigree for most of the breed in the last 50 years that’s increasing in reliability. At the least the horse is the manifestation of the actual pedigree even if we don’t yet have it right.

Regards,

Pete

Pete wrote:Errors that exist in the designation of female families should be possible to be identified but it’s unlikely that the Jockey Club will allow the changes to be made to the Stud Book. Errors on the sire side will be harder to establish, if at all, and again I think we can assume that the records won’t be changed.

Wasn't DNA testing approved only after agreement that previously recorded pedigrees would not be corrected based upon errors incidentally identified when verification by DNA began?

Whether the registry is corrected or not, a dual system of classifying female families, by Lowe/B-Z, et al. #s and by haplotype, is emerging. Sorting out historic errors made obvious by discrepancy between the two is of academic interest to those of us with pedigree-related OCDs. From the standpoint of breeding tho', I'd like to see the more recent errors corrected, but I can also see why the JC wouldn't want to go there. That slope could be slippery.

PZ

Lucy wrote:It was her tail. And no.

But boy, was I tempted.

Had it been made into a fly switch, or what?

Pan Zareta wrote:Had it been made into a fly switch, or what?

Yes, exactly. Such an indignity!

Hi Pan,

Wasn't DNA testing approved only after agreement that previously recorded pedigrees would not be corrected based upon errors incidentally identified when verification by DNA began?

I don't know what the Jockey Club's position is and if there's a similar policy in England where Steve Harrison's study was done.

It is a slippery slope and I understand and would expect that the Jockey Club can't afford to make any changes. Corrections that can be made to the female families would help but it doesn't correct the problems that were propagated through stallions. We're just going to have to live with what we've got but it would be nice to know who the real sire of Son Of St. Crispin was. .

Regards,

Pete

I thought the real sire of Son of St. Crispin was Father of Son of St. Crispin.

Hi Geo,

The Father of Son of St. Crispin was his original name until it was realized that it contained too many characters so it was shortened to Son Of St. Crispin. So are you actually saying that Son Of St. Crispin is actually his own father? Then I'm impressed

Regards,

Pete

Oh my, that's what I call inbreeding, we should tell Louis immediately. Could Son of St. Crispin read, write and talk?