puppies tool
 

Hi all, I think there was a tool here on wolfdog.org that allowed you to make theoretical puppies (pair a dog and a bitch) and see their combined pedigrees and calculate wright coefficient and such things. Anybody knows about it?

Are you talking about this?
http://www.wolfdog.org/forum/forumdisplay.php?f=60

Is it the one where you place the dogs database number where it says xxxx? I have a link to this tool in an old email, I can try to find it for you tomorrow.

Or are you talking about Elf's work?

:)
Marcy

I think its this one
http://www.wolfdog.org/php/modules.p...7654&DOG2=2066

But I dont have the link for the main page, where you choice the dogs by the name because I change it direct at the link by copy and paste the database ID of the dogs.

Here you are:
http://www.wolfdog.org/php/modules/WolfdogDB/dbase.php

this "tool" enables to match a male to a female, to see pedigrees and to calculate Wright's Coefficient of inbreeding.

Hello Sasha,

You can also use this (which gives also AVK etc): http://www.amicale-chien-loup-tcheco...#Mating%20tool

One interesting point is the ability to get a more accurate value of the wright coefficient, for exemple in the exemple gave Paula it gives 8.5937500000%, with the complete formula it gives 11.0303640366% ( http://www.amicale-chien-loup-tcheco...2B2066&depth=5 )

With "Ancestors statistics" you can have some stats on HD and occurence in bonitation code (same exemple): http://www.amicale-chien-loup-tcheco...2B2066&depth=5

Cheers

Thanks for all the fast answers!

Elf, that is great that you can use your tool that way, I should read the manuals it seems...

Am I the only one who can not make it work for some time allready? It still shows the combined pedigree, but not common ancestors :roll:

Hello Vaiva,

For several months I also can no longer use the tool, at least from this Site, which I regret too. I suppose it also has to do with the crash of a hard disk. I assume that this will undoubtedly soon be repaired too.

The tool Elf made available is about simmilar and perhaps even more complete. The only downside of it is that its measurement is is only on a limited number of generations (5). Regarding the COI: the more generations to be measured, the more objectively the outcome as we all know.

Greetings Robbert

No Vaiva, even for moderators it works the same at this moment! ;):lol:

But I expect everything will work fine in time :) !

Since now the WD tool doesn't work, and the tool Elf linked is only 5 generation, is there any other way to calculate COI for 10 generations, besides by hand?

Hi,

I the tool I set the limit to 8 generations (the server used is not very efficient that's why I needed to add this limit), value are filled by default to 5 but you can change it from 1 to 8.

A.

Thank you!!

The problem of measuring the COI on only a limited number of generations (even on 8 generations), is that most of the large inbreeding effect during the early years, which in particular Rep z Pohranièní stráze has brought, is simply being disregarded. In genetics, the most reliable figures regarding inbreeding are obtained if one measures the COI on as many generations as possible. In that respect it is regrettable that the COI measurement on ALL generations (temporarily?), is no longer possible on wolfdog.

Elf, being a fan of your statistic tool, does it ever get that possibility in the future?

Regards

It would require some optimization but unfortunately I have not much time lately for updates. But I think the best would be to plug the database of this site to a pedigree software (like Pedserve), this would unload some work and provide many features.

Yes, that is true, but some of the CW dogs I checked don't have compete pedigrees even in the 8th generation out. I have been reading about COI recently and came across this article. It doesn't talk about CW specifically but rather Australian Shepherds (some lines also don't have complete 10 generation pedigrees yet, like some CWs)..

Here is an excerpt:

"...The usual 3-5 generation pedigree won't give sufficient information for a useful calculation. For Australian Shepherds the author has found 10 generations to be the best indicator. Few Aussies have a complete 10-generation pedigree, so this will give you pretty much all there is to know. While some individual lines of descent may go back 20-30 generations, running the calculation for more than ten does not result in any significant change in the result. Running it for fewer than 10 frequently causes the number to drop, giving an incorrectly optimistic result...

Australian Shepherds are blessed with around 300 founders, so our background inbreeding is very low. However, our breed like most others has experienced historic inbreeding stemming from the choices made by recent generations of breeders who have used one sire more than others or frequently sought the output of a particular kennel. ...Even in working lines there are early sires and kennels whose names occur with considerable frequency."

I don't know if this is because Aussies have a larger foundation group (300), but if pedigrees for CW start to fray at around 8-9 generations back for some dogs, I think that an 8-10 generation COI is probably pretty accurate.

Still, I would like to be able to have the capability for all generations too! :)

http://www.ashgi.org/articles/breeding_incest.htm

ETA: Oh, wait.. I just reviewed some pedigrees again and the blanks in the 8th generations are those of the founder wolves. So then the question is.. how far back do the known pedigrees of the founding GSDs go?

Hello Yukidomari,

Very interesting post!
All Cvs have a complete pedigree at least to the base. I.e. up to the four wolves and the german shepherds they are crossed with; in some cases, even a limited number of ancestors of the founding German shepherds are included in the family tree. By measuring the COI on all generations I meant all the generations upon this base of the breeding. That is/was the way one could measure the COI on "all generations" with Wolfdog.org until recently.

If you measure the COI of old Cvs (or deceased) over 8 generations (or more), it can happen that you do indeed encounter a number of empty holes in the pedigree, but in any case it is complete upon the base of the breeding project, with exception of the "mixes".

I understand that Wolfdog is busy with adding the pedigrees of German Shepherds all the way to the base of the race; even to the dogs, Max von Stephanitz, the founder of the GSD, used (click here). This will give the measurement of the inbreeding coefficient on “all generations”, as specified above, another dimension of course, but from genetic point of view, it is very interesting.

Quote:

I don't know if this is because Aussies have a larger foundation group (300), but if pedigrees for CW start to fray at around 8-9 generations back for some dogs, I think that an 8-10 generation COI is probably pretty accurate

Partly true, depending on which Cvs you measure. If you measure the inbreeding coefficient of an older Cvs, then yes, as 8-10 generations in this case usually means that you measure all generations (to the base of the Breeding). If you do that for a young Cvs (newborn Cvs) it could mean that one simply disregard most part of the strong inbreeding effect of especially Rep z Pohranièní stráze.

Although we owe our beautiful breed in particular to Rep z Pohranièní stráze, it is unfortunate that large inbreeding with him was committed in an early stage and the initial gene pool quickly narrowed drastically. Therefore all our dogs are very much related to each other by him, with not really opportunities to outcrossing anymore. I don't know the initial breeding situation of the Australian shepherd, but apparently the basis of it consists from about 300 different dogs and the breed was probably not inbred right from such an early stage.This could explain the fact that the outcome of the inbreeding coefficient of 10 generations is not much different from that of more than 10 generations. This makes an important difference with our race, where extensive inbreeding in the beginning was committed. In regard to measurement accuracy, I therefore plead for measuring COI on all generations, at least to the base (> Rep z Pohranièní stráze included), as it was possible until recently. I have every trust is that soon it will be possible again.

Regards

Another point, currently WD calculate the COI assuming the COI of common ancestors is 0 [Sum (1/2)^n1+n2+1], if you're using the complete formula introducing COI of common ancestors [Sum (1/2)^n1+n2+1 * (1+Fa)], you will see that calculating the COI with complete formula on 8 generations gives often a higher value than calculating the COI with troncated formula on full pedigree.

Hi Buidelwolf, I have only one small note. Not all our dogs are related to Rep z Pohraniční stráže. We have 8 groups of males, but only 4 are based on him.
Yes, somewhere in mother side can be some Rep (or no) but in breeding we look at father lines.

What I do not quite understand cause the genes of the mother are as strong as the genes of the father and obviously there.

Ina

Of course. I thought, somebody will react. But in breeding of animals (horses, cows,....) we look at father lines more than on mother lines. But we must look at mother lines too.
But planning in breeding depends mor on father lines.

This is interesting Hanka because this is the way breeding groups work, but it's indeed a bit disconnect with reallity. For exemple, let's take a dog from group V: Ali Terespol. Look at it's inbreeding composition on 8 generations: http://www.amicale-chien-loup-tcheco...d=6671&depth=8

As you can see Rep comes first with 8.04901123047%. Atos Heol CS comes 2nd with 1.77384614945%, so far less. It's the same for all groups.

In the other hand, calculating COI on full pedigree is very interesting but it's a statistical footprint, it's difficult to make the difference between the "old influence and the new one" at genetic level as each generation bring it's new contribution with epigenetic changes (among others) that we know transmissible.

Well, I am just a beginner so sorry if now I will write a total nonsence, but... It is said, that when choosing a stud one should look to the mothers line of a male, to see if desired features are strong in it (line) :roll: Isn't this true?

As I have been breeding horses too and as a vet had to make an exam in breeding of animals I know that.
But if you want to avoid imbreeding instead of getting one attribute with a high probability in the offspring this is problematic. You could use a female with Rep as a father and still have a "Rep-free" line to give an extreme example.
If you look on features in breeding you have to look on both sides but there are always individuals that tend to give their features to all offspring, no matter what features the other side has. As a male individual can have much more offspring in a shorter time you give more weight on fathers and base a line in, for example race horses, on the fatherline cause you see the features of the offspring in a much higher amount in a much faster time. As a mare can only have one foal a year you talk of lines like Nothern Dancer or Secretarian but of course you also look for the mare if you are a good breeder.

Ina

But this not nesecerelly work with wolfdogs, when we have males with only one or two litters, and mostly females, used for breeding, have litters almost every year :roll: But if theoretically both male and female have the same amount of offsprings, are both sides equally important?

As both sides give the equal amount of genes apart from maybe some autosomal inherited genes they should be

Interestingly enough, the Bedouin and their breeding of their famed Arabian horses always believed that maternal lines were the determinators of genetic disposition, and that the male influence was only potent for the first couple of generations. In fact, Arabian horse pedigrees are traced by maternal lines and have been for hundreds of years.

Recently there have been some studies on mitochondrial DNA that suggest the lasting life of maternal DNA that male DNA did not have...

Of course, in a world of livestock and dog breeding, which was traditionally left to men, male animals were considered to have a stronger genetic make up, or a stronger influence on progeny.. this was even a idea that applied to humans, that females are just the 'vessels' in a which a male's 'seed' grew.

And of course, financially speaking, male animals are generally worth more because they can be bred more often and their genetic contributions can be sold piece-meal by artificial insemination, whereas a female animal could not.

Here is a good article regarding the subject.. it is in regards to pigeon breeding, but it is a good article nonetheless:

http://www.pipa.be/en/newsandarticle...-maternal-line

http://www.sport-horse-breeder.com/the-Mare.html

For example in horses, "The Thoroughbred industry has noted that sustaining traits for speed have come most reliably up the female lines.".. (second article)

Hi Hanka,

This is very interesting and totally new to me:

I can find no contemporary Cvs living today, without a heavy dose of Rep in its genes (even only from fathers' lines); can you give us some examples of Cvs' still alive without Rep in the genes?

I didn't understand a thing also :oops: Miss the good old puppies tool... It was so sweet and friendly :oops:

Yes, you are right, I forgot about that.

Yes, that's true, but the mitochondrial DNA only has the genes encoding proteins involved in the mitochondrial metabolism, and not all of them even. So mitochondrial DNA is great for genetical studies on evolution, population biology, speciation etc., but the DNA itself does not do much about the individual characteristics and absolutely nothing about the genetical variability of the population, it actually includes some of the most conserved genes there are - those are genes that are least changed as time goes and are very similar even in very unrelated species.

I forgot to add - there are of course regions of mitochondrial DNA that change quite rapidly, so can be different even between the individuals of the same species, or races or even families maybe, but those are non-coding regions, not the genes.

Oh, definitely!! The studies are not in the least conclusive..just exciting research on the differences on the inheritance of male and female genetics. Would definitely like to see if there are any other differences.

Just fascinating. I have a bitch (GSD) that throws her temperament every time regardless of the male. Same with size all her pups are large. Ive tried to carefully select studs with the genetic make up to get smaller animals but never had any luck.

Yes, all living CSV have a lot of Rep, no one without.