I had expected to post the following elsewhere but never finished it. Thought it might interest you anyway.
The ONLY possible significance of genetic material contained in mtDNA (thus carried by the female tail line) to affect thoroughbred performance is the potential that one family may (or may not) have to produce energy more efficiently, nothing else. There is so little left in mtDNA and the interaction between nuclear and mtDNA so inconsequential that it could only be a factor if some significant mutation were to take place. mtDNA is so stable that mutations can’t be expected any more frequently than once in 10,000 years (thus their reliability in determining female family and even human ancestry). I’ll assume that Ruffian was that mutation and sadly she never entered the gene pool. We’ll be long gone before we see another (her or a mutation).
Hi Pete,
That’s a VERY interesting (and depressing) idea about Ruffian...
Still, when you think about it, if only one important enhancing mitochondrial mutation has occurred in Thoroughbred History; it probably had a 50% chance of it happening in a male horse who couldn’t have passed it on even if he didn’t die prior to breeding like Ruffian did (though
if she had the mutation, she had the capacity to pass it on; which makes all the difference).
Still, Life tends to abhor doing something for no reason (after all, why do you think the Dodos lost the ability to fly?~), so maybe Mitochondrial Mutations (such as there are) are somehow avoided in Male Horses (still, it’s not like the egg “knows” whether it will be male or female at the most relevant point to mutations: namely meiosis).
Anyway, I have a feeling non-coding mitDNA might be Mutating at a higher rate than the coding and some recent speculation has centered on whether or not the so-called “Junk” DNA is actually just junk or not (once again, I here note that Life
abhors doing something for nothing and replicating a huge amount of Genetic Material almost everytime a Cell Divides is certainly doing something).
(Perhaps the "Cost" to the Lifeform of replicating this extra DNA is so tiny that ditching the so-called junk wouldn't provide an advantage?)
Nonetheless, the mitDNA is clearly more stable than Nuclear DNA and a lot of hot air has been released the last few years on the subject of certain female families and their supposed ability to still matter a gazillion generations after the founder died…
But Pete there’s one more thing; how come Adrian Parry is getting NEGATIVE results for female family inbreeding? (There are only two logical conclusions I can think of: one, AP’s study is somehow flawed; or two, the female lines of these horses are somehow having some kind of effect on them even if it’s only a negative one.)
Pete wrote:Goldmine G1:
There is a salient issue with looking at G1 races (only).
1 - The ideal is to breed G1 winners and that should be our intention as breeders.
2 - The quality of lesser stakes races is more suspect.
I always make a careful examination of the quality of competition for any stallion (or better brood mare) prospect. A listed or graded event is not credentials for quality of the competitors without scrutiny. The system itself is subjective and so must I be in my evaluations. There's little to stop any trainer / owner from entering their horse in a stakes, graded, listed or restricted.
Not all G1 races are the same but we can usually assume that any horse that wins one is a genuine stakes quality horse.
Thanks Pete,
That very nicely approximates what my thought process was in deciding to do it this way (and I especially like what you said about how the goal of Horse Breeders should be to breed G1Ws; also I share your justified skepticism on Stakes Races and Graded Stakes Races).
From what I know and what you’ve said, Goldmine current deals with Direct Affinities (nicks) - measuring the impact of mating a specific sire with the daughters of another specific sire that have produced G1 winners - the top level of racing?
Actually, the G1Goldmine can look up G1Ws with a cross of Stallion A and Stallion B in whatever position and just about any combination of positions you want. For instance, if you wanted to look up AP Indy as a sire with daughters of Mr Prospector you could; or if you wanted to look up AP Indy as a Grandsire with Mr Prospector anywhere on the damside you could as well.
Also, if wanted to look up all the G1 Winners with Mr Prospector on either side and AP Indy on the opposite (or Mr Prospector on the sireside and AP Indy on the opposite), you could do that and things like it as well.
However, the VGS Score generated by the G1Goldmine (in it's current form at least) looks at the overall impact of crossing Stallion A with Stallion B regardless of how many generations far back they are.
For instance, the score for the AP Indy / Mr Prospector nick includes horses with AP Indy as the sire and Mr Prospector as the damsire (see Mineshaft, etc); horses with AP Indy as the grandsire and Mr Prospector as the dam's Great-Grandsire (see Declan's Moon and Tapit), etc, etc.
Incidentally (or perhaps not…), the Overall VGS Score on this cross is
3.18 (which means it outperforms 1.00, or how ever many G1Ws it was predicted to get, by 218%).
An obvious problem is that G1 races are fewer and the bloodlines tend to be the most closely watched, evaluated and costly. I believe you could add great value and meaning to Goldmine if you were able to provide an examination of some affinity types that would have more meaning with sons and daughters of the expensive bloodlines (before they become high priced stock).
That is an excellent point Pete.
One example I can think of the affinity between AP Indy and Mr Prospector (from a pretty good sample size of 9 G1Ws it gets 218% more G1Ws than predicted).
And I call it an example as...
1. AP Indy
as a Sire crossed with Mr Prospector anywhere on the damside gets
361% more G1Ws than it was predicted to.
and...
2.
Sons of AP Indy crossed with Mr Prospector anywhere on the damside get
129% more G1Ws that it was predicted to.
Now when you consider that an unsurprisingly huge percentage (
5 out of the 9 G1Ws ) of the G1Ws by AP Indy sons are by sons of AP Indy (either Pulpit or Malibu Moon) themselves out of Mr Prospector mares; you understand that the 129% positive impact value on the AP Indy Son / Mr Prospector cross was accomplished running into a significant headwind of inbreeding avoidance (and even not taking that into account, the impact value is good enough that one might take it to mean that the strong nick AP Indy had with Mr Prospector is strong enough that it's getting inherited by his sons [or at least two of them]).
Also interestingly, we can note that both the G1Ws (Tapit and Declan's Moon) with AP Indy as the sire of the sire and Mr Prospector on the damside (in both cases on the damsire's sireline, perhaps not incidentally) were by sons of AP Indy who ALREADY had Mr Prospector.
Which suggests (I think) that piling more Mr P into an AP Indy sons who already have him is a good idea.
Any direct nick can be quantified and to me they’re the least interesting. Once you remove a generation on either or both sides of the pedigree you change the potential of the direct nick and need to substantiate any inheritance of the nick if it exists.
I
100% agree with you here, Pete.
Actually, one of my preferred method of using the G1Goldmine is to first find further back Bloodline Affinities such as the one between Storm Cat and Mr Prospector (which gets 144% more G1Ws than predicted) and than using the G1Goldmine Program to search through all the (in this case) 20 G1Ws with it to see which sources evidently inherited the nick, which didn't, and which sources don't produce enough data to draw conclusions on.
Looking at the Storm Cat / Mr Prospector cross we find that both his sons Giant's Causeway (who has
792% more G1Ws with Mr Prospector than predicted) and Tabasco Cat (who has
512% more G1Ws with Mr Prospector than predicted) both evidently share their pappy's affinity.
Of course, I don't like Giant's Causeway too much (at least for his currently absurdly high fee) and Tabasco Cat is (sadly) no longer with us.
Still, Hennessy (who is still alive and who I don't dislike) gets both his best Male Runner (the Champion Johannesburg) and
418% more G1Ws than predicted with Mr Prospector.
Pete, am I reading your statements on Inherited Affinities right in thinking that Hennessy's evidently inheriting an affinity from his sire Storm Cat indicates that Hennessy's sons are likely to inherit it in turn? (I have a feeling I might be wrong on what you meant but I'm not sure.)
In this context perhaps it is worthy of note that going back one generation from Storm Cat we find Storm Bird and Mr Prospector get 118% more G1Ws than they were predicted to (I’ll check how much of that is driven by Storm Cat tomorrow but given that Storm Cat’s score with Mr P ain’t that much higher at 144% better than predicted I doubt Storm Bird won’t get a very nice score even looking exclusively at sources of him aside from Storm Cat).
Looking at a cheaper son of Storm Cat, we find that Catienus gets
819% more G1Ws than he was predicted to and even though it's only based on a single G1W (who not incidentally is Catienus' only G1W: Dawn of War), this high score was accomplished in spite of undoubtedly intense inbreeding avoidance on account of:
1. Catienus being out of a Mr Prospector mare.
and...
2. Breeders avoiding inbreeding to Mr Prospector more than any other major stallion born in the time frame he was.
Still, any "affinity" based on only one horse could conceivably be a fluke (or perhaps the success of the horse was driven by some other aspect of the mare's pedigree besides Mr Prospector; though the more general affinity seems to make this unlikely...).
Why not quantify the removal of the nick, the inheritance – not necessarily for sire lines of the last 20 years – but long before. Inheritance of affinity is a cornerstone in pedigrees and ‘mapping’ inheritance of nicks I believe would be worth its weight in Gold(mine).
Why not quantify the removal of the nick, the inheritance
Do you mean I should (to use an example) figure out what the VGS Score on the AP Indy / Mr Prospector cross is excluding AP Indy as a sire and Mr Prospector as a damsire so I can see if it's a Inheritable Nick or not?
Because interestingly we (or at least I) find that while the overall AP Indy (anywhere)/Mr Prospector (anywhere) cross outperforms opportunity by 218%, the cross of AP Indy and Mr Prospector excluding the Direct Affinity (or nick) between AP Indy as the Sire and Mr Prospector as the damsire actually get a Much Higher Score of
669% more G1Ws than predicted.
not necessarily for sire lines of the last 20 years – but long before.
That is a very interesting idea Pete (though to be upfront with you the G1Goldmine currently only searches back to the 5th generation so that might limitate efforts to look really far back).
I think I did something similar to what I think you're talking about here a little while ago when I was looking up Mr Prospector / Hyperion in the VGS partly on account of your theories and found it gets (based on a very good sized sample size of 86.45 Predicted G1Ws)
26% LESS G1Ws than it was predicted to get.
Especially in this context, it's
very important to understand that the average Cross which doesn't entail inbreeding will get a VGS indicating it outperforms opportunity…
The reason is simply because the flipside of Inbreeding Avoidance unfairly depressing the scores of crosses involving inbreeding is that Outcrossing Selection will unfairly improve the score of crosses not involving inbreeding.
To illustrate, if a bloke with a Mr Prospector mare is less likely to go to a Mr Prospector line Stallion that means he's more likely to go to a Seattle Slew line Stallion, etc.
Therefore this bad result for the Mr Prospector/Hyperion cross is very most quite remarkable to me and very interestingly if I take Hyperion G1W descendants who got their Hyperion through Northern Dancer out of the equation the results in America (I haven’t checked the Whole World yet on account of me presently having to do this sort of thing by hand), are even worse for the Mr P / Hyperion cross as they’d
36% worse than predicted as opposed to the
27% worse than predicted impact value the cross gets in America without Northern Dancer getting taken out...
-llbean
I picked up a mare earlier today at the Keeneland sale and would like to choose a stallion to book her to as soon as possible.
,