"opening up" the stud book

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Pan Zareta
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Postby Pan Zareta » Sun Nov 12, 2006 1:46 pm

xfactor fan wrote:If the foundation of the Thoroughbred was Oriental blood stallions on native mares, the mtDNA would show Celtic mtDNA in many family lines. This doesn't match the research which indicates just the reverse.


How so? The map in Hill's report (2002) demonstrates that the mtDNA haplotypes identified within the TB and most other breeds are distributed throughout the clades. At present, this pretty much precludes being able to draw meaningful inferences in regard to whether TB taproot mares are of Arab or old English origin. The haplotype ('L') that Hill regarded as representative of the founder of family 5 is a singular exception because it resides in a branch of one of the least populous clades, the only other inhabitants of which are haplotypes found in the old European breeds.

Griff, how are you defining "original Quarter horse"?

PZ

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Postby halfpint23 » Sun Nov 12, 2006 6:12 pm

vineyridge wrote:Weren't the Hobbies gaited? Isn't that where we get "Hobby Horse" for rocking horse?
<SNIP>


Yes and yes.
Not gaited in the sense of being "only" gaited as the walking horses and more recent registry types are, but definitely so in that they were known and desired for their inbred lateral "travelling" gait.
It's been pretty much bred out of modern day QH lines and in the modern day descendents in Ireland, too - Irish Draught and Connemara being notable examples. I do remember back in my youth (a LONG time ago) riding a lot of oldtime ranchbred QH types that were very definitely lateral gaited, had what we called a "singlefoot" gait that really covered the miles and was easy to sit.

As to the American Quarter Horse being "bred down from Morgan blood on Mustangs" well I don't really think so..... The original Quarter Running Horses predate Justin Morgan by a little bit! and were usually the product of imported English race stallions on local mares of whatever breeding was running at the time. It's pretty well documented, though the bloodlines were often, well, not well recorded, shall we say?

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Postby griff » Sun Nov 12, 2006 8:10 pm

I used four of my mares and started clicking the tail female in the fifth beneration of this data base pedigree. In about two clicks every thing shown in the five generation pedigree was GB. In one case the tail femail ran to Tregeriwells Natural Barb Mare which was designated as Family # one.

the other three cases the tail femail trace ended in what appeared to be non orential mares; i.e [1] The Massey Mare or family # 5, [2] Davills Woodcock mare or Family #9 and [3] Layton Black mare.

Arabian or orential stallions are every where in those old foundation first five generation foundation pedigrees bit it appears only one of the four started with an arabial or orential mare.

Try clicking on the last tail female in each five geberation pedigree that pops up on your horse or horses and see what you find as the first tal female mare.

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Postby Pan Zareta » Sun Nov 12, 2006 10:45 pm

griff wrote:the other three cases the tail femail trace ended in what appeared to be non orential mares; i.e [1] The Massey Mare or family # 5, [2] Davills Woodcock mare or Family #9 and [3] Layton Black mare.


You do mean family 19, not 9, right? (The Davill's Woodcock Mare is considered the tap of 19.)

The haplotypes considered to be representative of families 4 (the Layton Barb Mare) and 19, like that of family 5, fall outside the most populous clade (the one in which is found the greatest number of haplotypes from all breeds incl. the TB). But even though they're less populous, the clades containing families 4 & 19 also contain haplotypes from breeds originating in the near & far east as well as Europe. Unfortunately, unlike family 5, phylogenetic location is of little use in discerning the recent origins of their founders.

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Postby griff » Mon Nov 13, 2006 7:00 am

Pam, you are way over my head.

All I wanted to point out was the Thoroughbred Pedigree Query data base can be used to trace any TB back to it's tail female foundation mare.

Also, when you get back there arabians and other orential stallions dominate the five generation pedigrees which seems to indicate that at the least the TB foundation stock was dominated by orential stallions with some help from orential mares.

Would that mean the TB is already an anglo-arab?

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Postby llbean » Mon Nov 13, 2006 4:32 pm

Would that mean the TB is already an anglo-arab?


A TB and a Anglo-Arab are two very different things and therefore the statement that the TB is a Anglo-Arab must be way off.

Let's say the TB is 60% Arab (very unlikely even in scenarios with little native English/Irish influence given the importance of Barbs)...

In that case a TB would be 60% Arab and 40% other things and in contrast an Anglo-Arab would be (on average) 80% Arab and 20% other things.

That's a big difference even if we for no good reason we ignore the importance of the powerful selective pressure that has shaped the Thoroughbred into what it is today.

Also, just because the "Arab" ancestors (Ancestor Group 1) of the TB were in the same breed as the "Arab" ancestors of an Arab (Ancestor Group 2) does not mean that there couldn't have been (and in all likliehood was) profoundly important differences between Ancestor Group 1 and Ancestor Group 2.

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Postby griff » Mon Nov 13, 2006 5:09 pm

Wow!1 A Thoroughbred is 60% arab and an anglo arab is 80% arab. Seems to me the plus/minus percentages in both cases would over shadow the 60% vs 80%,

How about a throughbred onto a real mustange, one from spanish horses. You think we might have another 60% vs 80% or maybe 60% vs 70% here???

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Postby llbean » Mon Nov 13, 2006 9:17 pm

Hi Griff,

Personally at least, I don't think Plus/Minus % is adequate to convey the differences.

For instance, the difference between a 60% Arab and a 80% Arab is probably more important than the difference between a 0% Arab and a 20% Arab as the first difference is big enough to push the Arab Gene Combinations into a securely dominant position.

In contrast, when you go from 0% to 20% and if the other 80% are from one breed, it won't push the Arab Blood into a securely dominant position by a long shot (of course, its a VERY complex question which is, for sure, the more important difference but my point is that there's a significant difference between the two differences that would be unduly ignored if I just reported the Plus/Minus %).

Anyway, what I'm trying to get at here is that Gene Effects are cumulative.

For instance, one "Arab Gene" is EXTREMELY unlikely to make a horse more like the typical Arab for the simple reason that to a great extent it is NOT Individual Genes that are unique to the races within a species but instead gene combinations that are.

For instance, lets say there was a Gene called SHYR-43 and that there were four variants in the Species under consideration: A, B, C, and D.

What we'd see with Arabs and even a unrelated Breed will almost certainly NOT be this:

Arabs = 40% Variant A

Arabs = 60% Variant B
Arabs = 0% Variant C
Arabs = 0% Variant D

Chinese Plow Horses (or whatever) = 0% Variant A
Chinese Plow Horses (or whatever) = 0% Variant B
Chinese Plow Horses (or whatever) =75% Variant C
Chinese Plow Horses (or whatever) = 25% Variant D


In THAT case, then yes, One Gene could tell you if a horse was an Arab or a Chinese Plow Horse. However, reality will be closer to something like this:

Arabs = 10% Variant A
Arabs = 20% Variant B
Arabs = 40% Variant C
Arabs = 30% Variant D

Chinese P.H. = 20% Variant A
Chinese P.H. = 35% Variant B
Chinese P.H. = 30% Variant C
Chinese P.H. = 15% Variant D


In this Scenario, you see, one gene won't be enough to determine breed origin to a meaningful degree of certainty.

Nonetheless though; these discrepancies are EASILY great enough to produce Gene Combinations unique to each of the two breeds and those Gene COMBINATIONS will produce very meaningful differences in Phenotype.

Therefore we can see that one (and even to an extent some numbers larger than one) Arab Gene(s) are not enough to really matter and as a result we can conclude that at least to an extent; the effects of Genes are cumulative.

How about a thoroughbred onto a real mustange, one from spanish horses. You think we might have another 60% vs 80% or maybe 60% vs 70% here???


I have a feeling the Mustangs are more Barb descended than Arab descended and as best I can tell (please correct me if I'm wrong), Barbs and Arabs are two essentially distinct breeds.

For this reason I don't think I have enough info at this point to make a meaningful attempt at an estimate.

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Postby llbean » Mon Nov 13, 2006 9:29 pm

Pan Zareta wrote:
xfactor fan wrote:If the foundation of the Thoroughbred was Oriental blood stallions on native mares, the mtDNA would show Celtic mtDNA in many family lines. This doesn't match the research which indicates just the reverse.


How so? The map in Hill's report (2002) demonstrates that the mtDNA haplotypes identified within the TB and most other breeds are distributed throughout the clades. At present, this pretty much precludes being able to draw meaningful inferences in regard to whether TB taproot mares are of Arab or old English origin. The haplotype ('L') that Hill regarded as representative of the founder of family 5 is a singular exception because it resides in a branch of one of the least populous clades, the only other inhabitants of which are haplotypes found in the old European breeds.

Griff, how are you defining "original Quarter horse"?

PZ


Really good post, Pan. Evidently you retained that Hill Study better than I did because I knew there was something wrong with some of the conclusions being drawn on this thread but couldn't put my finger on the precise reason they were off.

Also, you did a very good job of explaining it.

-llbean
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Postby xfactor fan » Mon Nov 13, 2006 11:17 pm

Just to clarify a point.

The discussion started with the idea that the origin of the TB was Arab stallions on "native" mares. There is only one female family that shows clear descent from the old european breeds.
If there was a pattern of upgrading oriental blood on a range of native breeds there should be at least a couple more of these european breed mtDNA families around.

Instead there are mtDNA families from other oriental clades. So there have to have been some oriental mares contributing this signature mtDNA somewhere along the line. These could have been mares introduced by the Romans, by horse buyers for King Arthur, or any other early military leader that was trying to upgrade their cavalry.

Hey, I've always seen more Turkoman influence in the modern TB than Arabian, which puts me in the minority in this debate.

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Postby vineyridge » Tue Nov 14, 2006 6:16 am

My ignorance is showing? Educate me please.

Aren't there only five types of horse from which all moderns descend? And aren't they mostly Asian? Don't I recall that there is a Western European Forest Horse, but all the rest came from the East?

Think about this. Almost all the migrations of peoples to Europe came from East to West, and almost all of them brought their horses with them, if they had horses. The Greeks, the Medes and Persians, the Turks, the Celts, the Teutons, the Norse, the Goths, the Vandals, the Gauls, and on and on--hell, even the Romans had a tradition of coming from Asia Minor. Indigenous peoples got stomped regularly.

Just because there aren't Old Forest horse families heavy in thoroughbred mtDNA wouldn't necessarily say anything about horse migrations to Europe in historic times--old historic times--that killed off native animals and replaced them with their own preferred stock, would it?

Isn't the Forest Horse one of the newest branches?

Kick me if I'm learning this wrong. :P
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Pan Zareta
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Postby Pan Zareta » Tue Nov 14, 2006 1:03 pm

xfactor fan wrote:Instead there are mtDNA families from other oriental clades. So there have to have been some oriental mares contributing this signature mtDNA somewhere along the line.


What clades are you referring to as 'oriental'? None of the clades mapped by Vila(2001) and Hill (2002) were or could be described as such. Hill's clade 'F' has only one or two haplotypes identified in old Euro breeds, otherwise it's near & far Eastern haplotypes in almost equal proportion. It's also the only clade that contained none of the haplotypes identified by Hill as representative of the TB founders. But in the context of the entire map that's essentially meaningless. It's obvious that representatives of several diverse (by mtDNA) aboriginal mares were present and well-dispersed geographically long before any sort of selection pressure was imposed on the domesticated horse population.

Non-recombinant DNA simply isn't useful for determining genetic relationship between domesticated horse breeds, but fwiw some work has been done toward that end by studying the frequency at which certain recombinant allelles occur in various contemporary breeds. Unfortunately, I can't recall a specific citation, but I'm pretty sure at least one report came out of UKy.