Sunday, 18 March 2012

Breeds in danger of extinction in the UK

The English Setter - on the road to nowhere?

Soon after Pedigree Dogs Exposed, the Kennel Club announced a five-year commitment to fund a new Genetics Centre at the Animal Health Trust (AHT) in Newmarket - its mission to continue developing new DNA tests, to develop new breeding tools/strategies and to assess genetic diversity in KC breeds.

Overall, the partnership  has been fruitful.  Much-heralded Estimated Breeding Values (EBVs) to help Cavalier breeders breed away from syringomyelia and mitral valve disease may have failed to appear (and would seem to be moth-balled due to lack of breeder support) but EBVs for hip and elbow dysplasia are on the way.

Mate Select, another product of the partnership, has been a success and will get better - a boon to owners, breeders (and to television producers checking breeder claims re inbreeding).

So what about the promised assessment of genetic diversity and, in particular, a commitment to look at the effective population sizes of individual breeds (essentially a measure of genetic diversity)?

Last August, the Kennel Club Genetics Centre at the AHT  published what it called its "mid-term report" marking the half-way point in the five-year partnership between the KC and the AHT and here's what it said:

Population structures and inbreeding 
Inbreeding is one of the risk factors for inherited disease in purebred dogs. It is important to understand how the population structure of breeds may be contributing to an increased rate of inbreeding. Analysis of the population structure and rate of inbreeding for all 211 Kennel Club recognised breeds is currently underway.
Kennel Club pedigree records are being used to calculate the rate of inbreeding for each breed over the last 30 years. The rates show how fast inbreeding is accumulating in a breed and indicates the effective population size. This gives a measure of how many individuals are contributing genetically to the population and is a measure of the size of the gene pool in any UK breed.
The analysis also examines how much close inbreeding there is in the breed, and produces other descriptive statistics such as how many dogs are used for breeding and their average number of offspring.
So far we have analysed 38 breeds and published results for the following:
Bearded Collie, Bloodhound, Great Dane, Irish Red and White Setter, Miniature Bull Terrier, Otterhound and Tibetan Terrier.
Generally, our results show that most breeds have an effective population size below the recommended minimum to maintain a sustainably low rate of inbreeding. In many cases there is evidence that inbreeding rates could be much lower, if appropriate breeding strategies were adopted.
Such strategies might include reducing the degree of line breeding used, managing the use of popular sires to reduce their future impact on inbreeding, and using more individuals as sires and dams.

Now the paragraph I have bolded above was an exciting one for me. And that's because, in 2008, Imperial College London, using Kennel Club data, published a paper (Calboli et al) that examined the population structure of 10 KC breeds.  In particular, it assessed the individual breeds' effective population size.  Bearing in mind that anything lower than 100 is considered critical by conservationists and anything under 50 as being a one-way ticket to extinction, here is what Imperial found:

Akita Inu - 45
Boxer - 45
Bulldog - 48
Chow Chow - 50
Rough Collie - 33
Golden Retriever - 67
Greyhound - 17
German Shepherd - 76
Labrador - 114
English Springer Spaniel - 72

When I first saw this data, I was horrified, believing it had to be an enormous wake-up call for everyone in dog-breeding. In fact, its publication (in May 2008) changed the course of the first Pedigree Dogs Exposed. And yet despite the Kennel Club being co-authors and the findings known to the them for months before PDE,  there was no mention of it anywhere by the Kennel Club - and certainly no obvious action had been taken to address the paper's concerns.

In fact, Pedigree Dogs Exposed commisisoned the Imperial researchers to look at a further three breeds for us - the Flatcoated Retriever, Pug and Cavalier King Charles Spaniel and the figures for them were:

Flatcoat - 52
Pug -  38
CKCS - 68

A big worry.

So the announcement last August that the KC Genetics Centre had studied a further 38 breeds and published the results for eight of them was of real interest. I called the AHT to ask for a copy of the published findings - to be told that the results were going to be published on the KC website in a couple of weeks' time.

Nothing appeared. I left it for a while but when, by December, there was still no sign of the findings, I contacted Caroline Kisko at the Kennel Club who replied: ".... unfortunately these are not yet available.  There are some 48 breeds in hand at present and many of these will be going on the KC web site soon but I can’t be certain exactly when."

I chased a couple more times before we finished Pedigree Dogs Exposed - Three Years On with no success.  I presumed it was because the findings were dreadful and that the KC didn't want us highlighting them in the film.

Three days before the film, I got a call from a writer for the Sunday Times telling me he'd got an exclusive from the Kennel Club regarding these figures, asking for my input and for contacts in  various breeds. I gave him both - in exchange for the data. And here's what I wrote to him in an email:
I have battled - and failed - since last September to get the genetic diversity data that you have managed to get. That's when the KC released a report which indicated that the data had been published. 
To put it into some kind of perspective, what this data reveals is that these five breeds are more criticially endangered genetically than the Giant Panda.

If I'd known these figures even a week ago, I would have scrambled to get them in Pedigree Dogs Exposed - Three Years on because they could not be worse news for dogs.

In effect, 140 years of Kennel Club breeding has brought these breeds - and others - to their knees. The data should be an enormous wake-up call that something must be done before it is too late. We do have a precious resource in our pedigree dogs but we are frittering them away from being wedded to the idea that the more pure dogs are, the better. We know this isn't true, and that trapping dogs within ever-decreasing gene pools is destroying them.

The frustrating thing is that it doesn't have to be that way. We now have the knowledge to do it differently.

The story appeared in the Sunday Times two days later. It wasn't much more than a re-hash of the KC announcement that was officially released on the same day and it contained no mention of the role that KC breeding practices have played in reducing some breeds to genetic ghosts of their former selves.  It was way too late for us to include the new findings in the film - which aired the next day.

So the KC has finally released some of the data, but not all of it. And as the announcement seems to have got lost in the general melee around the film and then Crufts, I am returning to it now.

As suspected, it does make grim reading. (NB: the figures relate to the UK population of these breeds only).

There are five breeds with effective population sizes under 30. They are:

Irish Red and White Setter  - 28
English Setter  - 27
Manchester Terrier  - 20
Lancashire Heeler - 25
Otterhound - 29

The KC has also released the figures for five breeds they have found so far with effective population sizes over 100:

Saluki - 107
Newfoundland - 181
American Cocker Spaniel 189
Standard Poodle - 377
Bernese Mountain Dog - 762.

I confess that I am totally thrown by the effective population size found for the BMD - it seems impossibly high and so does the Standard Poodle's given the Wycliffe bottleneck. I will ask the AHT for some input.

And where are the others? The mid-term report mentioned Bearded Collie, Bloodhound, Great Dane, Miniature Bull Terrier and Tibetan Terrier. And what about the other 30 or so breeds they say they've looked at?  Hopefully they'll be be forthcoming soon.

Meanwhile, the KC says it will be talking to the breed clubs of the most compromised breeds about outcrossing.  In fact, the Irish Kennel Club has already endorsed an outcross programme between the IRWS and the working Red Setter

How will this go down with the breed clubs? I was heartened to see Judith Ashworth,  the health rep for the Otterhound Club say: “This new research, in addition to the World Health Survey of the entire breed, which we carried out with the Kennel Club and the Animal Health Trust in 2009, is crucial in helping us to develop breeding strategies that will protect the health of the breed that we love.

 “Outcrossing is certainly one option that we are very keen to look at, because we do need to increase the number of dogs that are contributing genetically to the very small population of dogs within our breed. We look forward to working with the Kennel Club and the Animal Health Trust to find solutions that will protect our breed in the future.”

I imagine there will be more resistance from others. But to hear the KC talk so proactively about outcrossing as one means of increasing genetic diveristy is encouraging. Let's hope the talk is followed by some action. And let's hope it doesn't trigger yet more accusations that the Kennel Club has been infiltrated by animal rights activists.

The picture at the top of this post, by the way, is of a young field-bred English Setter from Ireland that my rescue rehomed last year. She is called Orla and she is beautiful. She is spayed now but it's a reminder that there is a potential genetic resource outside of the confines of the Kennel Club without necessarily having to outcross to a different breed.

111 comments:

  1. Other than the greyhound, are there any of these breeds that also have significant non-KC registered populations?

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    1. Thank you for bringing us back to some serious thinking after all the silliness and hysteria around Crufts
      This is a very significant move forward by the KC in bringing attention to the effects of inbreeding , and how gene pools are reduced at a frightening speed. But the KC announcement was overlooked , coming just before Crufts, just as the significance of the Calboli research , one of the key moments in recent dog history, also got largely ignored.
      The Irish Red and White Setters UK have a convenient neighbouring gene pool in the working IRWS of Ireland, with which there has not been much exchange since the revival of the breed in the 1970s. In the UK the breed has developed largely as a show dog, while in Ireland it remains almost entirely a working and field trial dog. I have imported four working/FT bred IRWS from Ireland since 2000, with another one arriving shortly, and that has worked very well for me, but there is a reluctance in some quarters in the breed in the UK to consider using the working dogs of Ireland, having spent the last 30 years "improving" the UK breed type for the show ring. Fortunately some UK breeders are more open minded, and at Crufts 2012 , both CC winners in the breed have Irish field trial dogs close behind in their pedigrees, which suggests the show breeders have little to worry, either concerning type or health, about when using the Irish gene pool to widen diversity. But the Irish gene pool is also quite inbred, so one needs to be looking beyond this longterm to other lines in the breed worldwide or to outcrossing, as the IKC have done

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    2. Of course there are non-KC registered populations.

      What'smore, those effective population figures are for the UK. The world is full of dogs and AI is a useful tool in this area.

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  2. If the number for Bernese Mountain Dogs is as high as you claim, then how do you explain the very high incidence of genetic disease (esp. cancer and heart disease) in the breed? Very few of them live to reach double digits. This would not seem to uphold your theory.

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    1. This isnt Jemima's theory. These are figures produced by the KC Genetics centre at the AHT, based on the programme developed by Calboli et al at Imperial College, and using 30 years of the KC registration data

      And yes, the Bernese Mountain Dog figure looks very strange.

      Just as an aside, can somebody tell me why , if the Genetics Centre researchers have 30 years of data to work from, why doesnt Mate Select use the same number of generations? Many breeds, including IRWS, have found Mate Select gives COI figures based on less than 10 generations, which usually makes the COIs look lower than they would be on 10 generations

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    2. The effective population for BMD is distorted by the number of imports, this also applies to American Cockers and probably others which are well over 100. I would assume that the figures have not all been released by the Canine Genetics unit because some further explanation is needed on these points. This would be an example where more than a number needs to be provided. I believe that they will be released with supporting articles as soon as the genetics unit gets it all ready to be published. It is somewhat disingenuous of the KC to release such skewed figures, no doubt they have a reason....hmmm I wonder what it could possible be.

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    3. To answer Dalriach:

      I posed that question to Tom Lewis ( Ithink that is his name) and the rather unsatisfacory answer which I got was that only the data from KC registered dogs were available. They apparently have at least 15 generations for Labradors.

      Cooperation with other registries worldd wide might be a future opetion.

      I would suggest you send an email to the KC and/or the AHT.

      You can contact us using the following details.

      Telephone
      0844 463 3980 - open 9.00 to 17.00 Monday to Friday (excludes Bank Holidays)

      Email
      info@thekennelclub.org.uk

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    4. Thanks for asking the KC. I think the COIs given by Mate Select will improve with every additional generation, but will still be skewed where there are imported dogs not far back, unless they can find a way to use data from other registries. With IRWS , the most reliable COIs are worked out using the breed's own data base run by Eileen Walker, but this data base is far from complete. It's pretty comprehensive for the more show bred dogs worldwide, and shows the COI for each dog listed, based on available generations (up to 10?), and goes back to the revival of the breed and beyond, but contains few of the working and FT IRWS
      Maybe , with the current interest in a strategy for the healthy future of the breed, we should be putting out an international appeal for every possible dog to be included in Eileen's data base? Which would give us a more accurate picture of the state of the breed, while also opening up more options for breeding
      I'm just a practical breeder, who struggles with some of the genetic research available . Maybe , as well as an abstract , methodology and conclusions, some research papers could try to make a more understandable link showing the relevance of their research to actual breeding?
      Meanwhile a very comprehensive international data base for a breed , with COIs or EBVs , is one of the best tools we have

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  3. Effective Population Size is only as good as the data, specifically how far back the stud books go. If you're looking at a breed in a registry that is not the country of origin, you're going to get inflated numbers because imported dogs from the COO are most likely coming in without pedigree.

    Another one that is high is the Cavs. Breed history suggests that the entire bred is the result of only a small handful of already related dogs. I'm curious if that is taken into account in the analysis.

    Like pedigree analysis, the resulting numbers need to be given context with raw data because limited data usually makes the numbers look BETTER than they really are.

    If you only look at the last few generations for both COI and EPS, you're massively inflating the actual diversity that is present.

    This is what Claire Wade did with her "our Australian dogs aren't inbred" study. She truncated pedigrees.

    Berners might not have information that leads back to the founding.

    For example, if I wanted to calculate the effective population size of a breed that had this population over 5 years:

    # of dogs per year:
    5, 10, 20, 40, 500

    The EPS is just over 13. See, that 5 has much more impact on effective population size than 500.

    Let's replace that 5 with 500.
    500, 10, 20, 40, 500

    The EPS is still only 28. The crash down to 10 dogs has more impact than starting and ending with 500 dogs.

    Now, let's continue the example. Let's say two different registries are looking at Berners. One has 5 generations, the other has only the last 4 generations. This is what the population size has been:

    10, 200, 200, 200, 200

    The first registry which looks at all 5 generations will come up with an EPS of 42 dogs.

    The second registry which can only see the last 4 generations will claim that the EPS is 200.

    EPS is an upper limit given the data available. There isn't an associated way to make the numbers go the other way. You can't make the number look too small unless your data is false (i.e. you counted 10 animals in one generation when there were really 20 who were breeding).

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    1. yeah but those nasty backyard breeders regularly add cocker , springer and anything else to cavaliers then register them under false pedigree's.

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    2. With the problems the Cavaliers have got, one might find some of the "Cavaliers" which allegedly result from illicit outcrossing with other spaniels , are rather more healthy, could even be free of SM/Chiari or MVD. I like Cavaliers, wouldnt personally have a problem with a crossbred small spaniel type dog that has the looks and temperament of the Cavalier, without the health problems

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    3. I've noticed some of the so called " clear" lines ,dogs who supposedly live to 18 and dont have sm look very cocker like.

      The show types are going the way they did 100 years ago , domed heads and short noses ( and very short legs for some reason)

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    4. BorderWars, where do you get your data? Can you cite a source please? I am just curious so NBD if you don't know.

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    5. http://www.uwyo.edu/dbmcd/molmark/lect07/lect7.html

      If you are talking about the effective population size numbers, those are calculations, not data. Look at equation 7.4 from the above link for a sample calculation.

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    6. Not really:

      http://en.wikipedia.org/wiki/Effective_population_size

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    7. Anon @ 5:46 AM -

      The "data" I used in my example is of my own creation / calculation using the harmonic mean method of calculating EPS. You can learn more about this method by searching the internet or finding a good entry level population genetics textbook. It involves taking the inverse of the average of the inverse of the population sizes.

      This method is more crude that the one the Calboli paper used which took into account detailed pedigree analysis.

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    8. Ohhh I see, you masde it up :)

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    9. Anon @ 3:52 PM - Yes. I made up an example to demonstrate how one method of calculating EPS works, highlighting the the major effect of the smallest data point in the series.

      The math is correct, the formula is used correctly. I demonstrated that even a very fast growing breed that starts very small will still have a very low EPS.

      What is your problem with my example? Do you not understand that it's demonstrating a relevant concept, not reporting actual breed data?

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    10. I understood what you were doing... I wanted to make sure others reading this knew it as well. So often people look at a post online and just take it a the truth. That's all. I have actually spent a good ammount of time recently cross checking a lot of the "facts" on Borderwars. I wish you would dig deep in the American line GSD's. It's more horrifying than the Collies, Pam

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    11. Apologies.

      Of course you are right! I did not understand the way you gave the figures of the populations: ie 5, 10, 20, 40, 5oo; 500, 10, 20, 40, 500.

      Now I get it!

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    12. It is a shame that Christopher studied engineering instead of animal science where he may have received some basic instruction in the estimation of effective population size. Had he done so he would realize that his ridiculous method is not the standard method for caculating effective population size and that in populations with declining rates of inbreeding effective population size is actually increasing. Dog breeds are not species and should not be treated as such. Given world-wide population sizes of dog breeds, the idea of extinction is obviously ill founded. Breed extinction is far more threatened by fashion than anything controlled by the registries.

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    13. @ Anon 3:51 AM. Thanks for fact checking my blog, but I haven't noticed any errors submitted by you yet so I'll take it that my stuff is pretty good, no? If you do find errors, do tell, I like keeping up to date and accurate.

      I've made several posts about GSDs. I have several more lengthy drafts, but they depress me and it's hard to finish essays when it's all bad news.

      German Shepherd Dog Posts

      I'll note that I do have to update my Brackett's Formula posts (related to GSDs because Brackett was a GSD breeder of note) because my analysis deals with a direct reading of the formula, but apparently Brackett was not a master of clarity and his method is actually MORE inbred than I had calculated. Scary thought. But it's this MORE inbred method that Battaglia uses, so I'll have to update my analysis when I get a chance to run the numbers and see what pops out.

      Thanks for reading.

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    14. @ Anon 1:03 AM

      Please read more carefully. I NEVER stated that the most simplistic and crude harmonic mean method was "standard." It's simply the most approachable by the lay person and easiest to use to make an educational example.

      The example highlights that the value of any model is determined by the fit of the algorithm to reality and the quality of the data. I was highlighting the issue of data quality.

      The fit of the algorithm is certainly up for debate, that's why I ASKED for both the algorithm and the data for the KC published numbers, as we don't have that information.

      I'm WELL AWARE that the harmonic mean method is only used when better data is not available, such as in studying historical populations where DNA is unavailable or impractical to reconstruct pedigree structure, and where generational data can be obtained with more accuracy as a simple count.

      Before cheap DNA testing of feces and other markers, the harmonic mean method was absolutely used. So why would you call it "ridiculous" ?

      Simplistic, sure. Rudimentary, of course. But the best place to start to introduce these concepts to readers on a blog like this? I contend YES. If people can't understand the HM method, how are you ever going to give them an intuitive understanding of the more complex calculations?

      You're a FOOL for thinking my engineering background isn't directly applicable to this. I can guarantee you that an industrial engineer spends more time deconstructing a Poisson distribution than a population geneticist. Industrial Engineering is ALL ABOUT modeling real life data using more elegant calculation methods including differential equations and probability analysis.

      I'm sure many of the PhDs who publish papers have pawned off the data analysis to engineers or to software written by engineers. It's clear to me that PhDs like Claire Wade don't have a firm grasp of the underlying math involved or else a callous disregard for representing it accurately.

      In fact, the interdisciplinary nature of my study meant that the genetics and bioscience courses I took were within my major, not a side project.

      Now, to nail the coffin shut on your criticism, I'll direct you to my comment which you clearly failed to read. I'm well aware of the multiple means of calculating EPS and the applications and downfalls of each:

      "This method is more crude than the one the Calboli paper used which took into account detailed pedigree analysis."

      and

      "The Calboli paper is one I'm familiar with, and the caveat here is that they spend a good deal of the paper describing their algorithm for the calculations. If this wasn't followed by the KC, then the numbers are not comparable.

      The Calboli algorithm takes into account population structure and inbreeding. The KC data might not. If the KC data just looks at the harmonic mean of population sizes, it could be a very different number than Calboli.

      I'd really need to see the raw KC data and what their method was.

      For example, the GSD is 76 measured as "inbreeding effective population size of breed calculated from the average increase in f over generations 1–5" ... I'm sure if we only looked at raw generation numbers, we would have a number much higher, given that the harmonic mean method will never spit out a number lower than the smallest population size recorded, and I'm sure in the last 5 generations of GSDs no generation was smaller than 100 in raw numbers.

      Is the KC method or raw data available?"

      Is it not clear that I'm well aware of the variance in F method as I specifically pointed out the Calboli paper used and specifically note that the KC method could be more crude if they used either truncated data or another algorithm such as the HM method?

      Please read what I wrote, ALL of what I wrote, before you make such shameful accusations.

      Game. Set. Match.

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    15. Borderwars you are an imbecile. The only thing that is game, set, match is that you have an over inflated view of your own intelligence. You offer nothing to the betterment of pedigreed dog health.

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    16. Math is hard. Let's go to the mall!

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    17. Anonymous @ 1:03 AM

      What you are missing is that under-educated breeders insist that dog breeds should be treated like endangered species because the majority of them fall into the trap of believing each group is somehow genetically unique which cannot interbreed with others.

      Furthermore, if you actually followed the history of rare breeds, such as the Norwegian Lundehunds, many of them has been advised by conservation biologists and population geneticists before.

      Anonymous @ 04:46 PM

      Actually considering this person did take conservation biology, he is on the mark.

      Sorry he used too many big words and you got confused in the process.

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    18. Anon @ 4:46 PM

      I'm disappointed that you're entirely unable to have a simple conversation with civility and honesty.

      You're so outclassed and unprepared for even a simple example, you've resorted to insults, the last bastion of the intellectually inadequate.

      As for my intelligence, I'd explain the meaning of more than three standard deviations above the mean to you, but your reading comprehension is demonstrably poor and I suspect that your numerical aptitude is likewise dodgy.

      Fortunately your assessment of what I have to offer the world of pedigree dog health is not shared by the hundreds of thousands of people who have read my blog.

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  4. Anonymous - She's saying that the Bernese Mountain Dog's high number is questionable. I would have to agree given the high incidence of cancer alone. I would expect it to be lower given how overbred they are and inbred they seem to be.

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  5. Exactly, Anon 7:39...not only that, but all the breeds listed above 100, with the exception perhaps of the Saluki, have very significant health issues. I personally know several breeders of BMD's who've gotten out of the breed because they couldn't take their puppies dying at age 6 or 7.

    So much for low COI being the answer to perfect health. Next easy (incorrect) answer, Jemima?
    Linda

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    1. perhaps it is related to selecting dogs for certain traits.
      you can unknowingly select dogs who look a certain way due to a health problem ( perhaps a problem with hormones that makes them too large or too small and also causes other defects ) though the dogs are unrelated

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    2. No one ever said that low COI = perfect health in one dog. Low COI is for better health of breeds in the future. A good, caring, ethical, thoughtful breeder should know this and strive for the good of the health of the breed as a WHOLE ! I am fed up of the nay sayers who keep inbreeding without a care in the world for the breeders of the future. If the KC spent a bit of time on decent education programmes for breeders that might help to dispel a few myths surrounding COIs .......sigh

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  6. @ Border Wars: have a look at the Immperial paper. As you say, if you only go back a certain number of generations, your figures are unlikely to be accurate. However, Imperial only went back to the start of the KC's e-database (no more than 40 years) and despite finding an inordinate number of founders (over 15,000 for rhe GSD for instance, which of course is not right in reality) it still found very low effective population sizes - despite treating all those founders as unrelated.

    So I think Imperial and the AHT must be calculating it differently. I'll check.

    As for the Berners, as it happens there is an absolutely fantastic genetic resource for the breed in the Berner-Garde Foundation (http://www.bernergarde.org). And if you haven't already seen it, have a look at this presentation on inbreeding and longevity in the breed using the BG data:

    www.berner-iwg.org/upload/garda/BG%202009%20Final.ppt

    (there's a pedigree schematic in there that you will like, Christopher...)

    The headline findings:

    • Average COI (for dogs where at least 8 generations of data is available): 17.8%

    • A slight decrease in inbreeding in recent years

    • Inbreeding affects the longevity of Bernese Mountain Dogs.
    1% inbreeding results on average in a loss of 20 days of longevity for dogs dying after 2 years of age. Nine days for those dying before 2 years of age.

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    1. The Calboli paper is one I'm familiar with, and the caveat here is that they spend a good deal of the paper describing their algorithm for the calculations. If this wasn't followed by the KC, then the numbers are not comparable.

      The Calboli algorithm takes into account population structure and inbreeding. The KC data might not. If the KC data just looks at the harmonic mean of population sizes, it could be a very different number than Calboli.

      I'd really need to see the raw KC data and what their method was.

      For example, the GSD is 76 measured as "inbreeding effective population size of breed calculated from the average increase in f over generations 1–5" ... I'm sure if we only looked at raw generation numbers, we would have a number much higher, given that the harmonic mean method will never spit out a number lower than the smallest population size recorded, and I'm sure in the last 5 generations of GSDs no generation was smaller than 100 in raw numbers.

      Is the KC method or raw data available?

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    2. here in America must have a scary high COI. Most American line GSD's go back to 3 top sires, Lance in the late 60's early 70's, Bear in the 80's and Dallas. You can't find an American line GSD without at least 2 of those dogs in it's pedigree multiple times.

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    3. IDK what happened with the above post...
      It SHOULD have said "GSD's here in America"...
      Sorry, Pam

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    4. Sorry to repeat myself but I think this comment applies here too:

      Because North American dogs are generally descended from dogs that were imported from other countries, they would logically be descended from an even smaller subset of the greater population. North American breeders use the same breeding practices as those in other countries with the same result: a reduced gene pool. Thus, it is entirely possible that North American dogs have a similar and possibly worse rate of genetic diversity than dogs in Europe, even if there are more individuals per breed.

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  7. Anon at 7.39: I don't think the AHT data is reflective of the true picture fo BMDs because of limited pedigree info. But even if it was, it doesn't prove or disprove anything. There are many shades of grey in genetics. One has to look at the overall picture and, of course, it isn't "my theory" that low effective population size = a problem. It's the theory of conservation geneticists. It also doesn't mean that breeds with high EPS necessarily equals health - although there is likely some correlation.

    NB: careful not to confuse COI with Effective Population Size. They are not one and the same.

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  8. Wow Linda, no one is pitching easy answers.

    I've been working on a post called "Measures of Genetic Diversity" for several months now, a little bit here and there, fact checking, trying to distill the spectrum of measures out there into something understandable by the lay person.

    Off the top of my head I've tried to define: Coefficient of Inbreeding, Empirical Heterozygosity, MHC/DLA testing, Effective Founder Genomes, Sire and Dam Lines, Effective Population Size, Individual Gene tests, Coat Color Genetics, etc.

    There are A LOT of ways to describe populations and no ONE measure answers all questions.

    Inbreeding is different from founder effects, but both can lead to the same result: loss of diversity, intensification of disease expression, etc.

    Use these as TOOLS not as gospel. They are meant to inform, not to guarantee. If you don't appreciate the greater issues, why bother learning what the individual tools can tell you?

    One of these days I'll finish my post but you're welcome to investigate the math and science behind population genetics in the mean time.

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  9. I am hoping that the effective breeding population of the Greyhound is not including the racing Greyhound, but simply the show Grey? Although a racing Greyhound database mentioned that racing Greys worldwide are likely related to one another(!) This could be linked to their high incidence of bone cancer.

    I would really like to know the Whippet one when it comes out.

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    1. I'm also interested in the Whippet data as I have a rescue Whippet - although she is from working/racing lines and not a show dog, but still I hope she isn't inbred.

      Gloria

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    2. The whippet's effective population is just 43 (this is from the canine genetics unit at AHT)

      Just reflect that this is a hugely popular breed with around 2000 pups a year registered.
      Inbreeding is not uncommon in the show world.

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    3. I don't think I've seen the whippet figure before. Has it been published?

      Jemima

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    4. There's a genetic resource available in the racing whippets, presumably? Is that - or other options - being explored?

      Jemima

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    5. @ Gloria dont fallin to the trap thinking that show dogs are inbred, indeed a non show non KC registered whippet has a great chance of being inbred (after all NO record of its family background was recorded was it?) as for show dogs imports to the gene pool are quite common and indeed the show population is very wide...............do look at the dogs and dont make judgements based on rumour and not FACTS

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    6. WRT to Whippets:

      Pedigree racing whippets are registered by the KC, so presumably, their numbers were taken into account when the effective population size was measured. (It is 43 BTW.)

      Non-ped racing whippets have a pedigree, usually stemming back many decades, but are not recognised by the KC. They have a regular injection of NGRC Greyhound blood (at least they used to back in the 60s, so I hope this hasn't changed). As the Greyhounds' pedigrees are also known, it's debatable whether the KC will allow an outcross to these dogs and also whether show breeders would be willing to use them.

      Delete
  10. The EPS for the greyhound is purely for the show version of the breed; nothing at all to do with the racing Greys.

    Jemima

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  11. I am angry that the KC only released this data just before Crufts - it's like they wanted it to be lost amongst the excitement of Crufts. If they really were serious about dog health, they should have released these figures for PDE2 - that would have made the breeders sit-up and take notice.

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  12. These figures, are they reached by analysing the pedigree history of the breeds? If so, is there a way of cross referencing this with some kind of genetic analysis of the breeds to see if the genetic diversity is similar to what the pedigree analysis suggests?

    Are many non-KC registered dogs that are typey of a particular breed get brought into KC breeding? If the dogs are properly health tested then surely encouraging this is essential to widening the gene pools and outcrossing in cases where there isn't a healthy non registered population.

    Pamela

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  13. on your comment about being able to check health results of dogs i would like to point out a major flaw in this. the kc/bva only accept results from certain labs. All my dogs are genetically tested for the appropriate illnesses but none of these appear on mate select because i used a slovakian lab (good enough for the exhibitors on the continent but not good enough for the kc) i don't really care if the general public cant find my dogs health test results on mate select. i publish all results on my website and these are used BY ME and other people in my breed in order to make the right decisions when breeding opur dogs. so i will warn anyone ready to accuse someone of lying about health results to check before they go shooting their mouthy off.

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  14. Katariina Mäki found worldwide effective population size of Lancashire Heelers to be 28-30.

    Here's the reference: Mäki, K. 2010. Population structure and genetic diversity of worldwide Nova Scotia Duck Tolling Retriever and Lancashire Heeler dog populations. J. Anim. Breed. Genet. 127(4): 318-326.

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    Replies
    1. Thanks for posting that ref, Maija. So the UK population data do seem to reflect the WW findings for the Heeler, at least.

      Jemima

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    2. We need many more studies like Katariina Mäki's. She really did right by the data versus cherry picking.

      Delete
    3. The KC closed the LHC register in 1989 when there were still farms dogs that could have been registered. There is still an untapped reservoir of unregistered Heelers still being bred on farms and it is possible for them to be health tested and certified to be typical specimens and included on the KC register, although of course there would be no way of knowing whether they were closely related to dogs already registered. However I believe Kateriina Maki has stated that even if ancestors are common after five generations the genetic diversity is wide enough to not cause a problem.

      Delete
  15. Yes, I agree this is an issue. Now not all testing or DNA labs are equal. But I think am right in saying the KC only publish DNA test results done by AHT and Optigen and, clearly, there are other reputable labs out there, too.

    It could be argued that the benchmark for inclusion on the Health Test Finder should be whether the data is published in a peer-reviewed journal. But then there are labs that are perfectly reputable that don't publish for understandable reasons - once a mutation is made public, it's a free-for-all commercially. And of course, even peer-reviewed science is overturned from time to time.

    I am not sure what the answer is on this one.

    Jemima

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    1. I was under the impression that Mate Select was only for UK, KC registered dogs with, as Jemima says, tests by certain laboratorries. I believe that Laboklin is now cooperating with the AHT, but I would be surprised if any UK owner would use them.

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    2. KC accept results from all labs which have the proper accreditation in place this include hose done by optigen and AHT but also those done by Laboklin and through Idexx and some other labs. Yes, there have been question marks over one of those labs...
      VP

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  16. And, by the way, the ES pictured here is NOT a good example of the breed, cowhocked, lacks substance etc. While she may be a perfectly delightful pet, she is not one I would like to see added to any gene pool because of her obvious conformational defects.

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    Replies
    1. I think you mean she doesnt look like a show bred English Setter? Conformational differences rather than defects? In English Setters the breed split into show and working dogs well over a hundred years ago, and became effectively two different breeds, but still all registered as English Setters. The working ES descended from the Llewellins and the show ES from the Laveracks. The working ES are much smaller and lighter built dogs. This one could be a twin sister to a field trial champion bitch from Donegal in the west of Ireland that I have seen at field trials
      Where else do you think the English Setters of the UK should look for an outcross?
      I havent heard of any reaction yet from the English Setter Club to the KCs anouncement about the five endangered breeds. Does anybody know if they have put out any statement?

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    2. Even owners of Pet dogs that have no intention of going near a show ring want a dog that looks like the breed. This working dog does not and therfore would not apeal to those who want an English Setter

      Carol

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    3. personally i prefer the look of the working dog

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    4. This post is a real facepalm moment. Firstly, how can one poor photo from a weird angle have you decide that this dog has "conformational defects?" What she has is a look that you don't like. There's no mention here of her health, her temperament or her working ability.
      Second, in this long and thoughtful blog post, full of information talking about how such a tiny gene pool is basically making your chosen breed extinct, you decide that this bitch couldn't possible be of value to you because you don't like the way she works. You know nothing about her but what you see in this photo but her "lack of substance" makes her worthless to you as potential genetic diversity.

      Delete
    5. "because you don't like the way she works."
      Thats a typo. I should have written "because you don't like the way she looks."

      Delete
    6. Presumably a dog who has the correct nature, working instincts etc would "appeal to those who want an English Setter" whether or not it had the prescribed amount of substance.

      I've never heard any pet owner saying "well, my dog fetches like a champ, is a joy at the dog park, gets on great with the kids, but he just doesn't have enough bone."

      It's not something pet owners generally care about, for the obvious reason that it's not important in the life of the dog or for any practical purpose.

      Even for working dogs, a good mind and good training/care and fitness can overcome lots of conformational defects; certainly more easily than can be done with a good-looking dog without the right mind or temperament. Have a look at human runners: you see all kinds of gait abnormalities and deficiencies of the lower limbs there.

      Unless a dog is doing very heavy work or has a very serious abnormality conformation is unlikely to affect it.

      If the dog isn't doing heavy work, but has seemingly perfect conformation, then that conformation has not been tested and it's very possible there are 'invisible' problems. So if you're looking for perfect conformation, inspect, test, and work the dog. If you're looking for 'good-enough' conformation, then you look for hip dysplasia, laxity etc.

      Either way you'll need some less subjective criteria for breeding than a look you don't like.

      Delete
  17. Excellent, I don't profess to understand all the language, but this is certainly much better for dog health than b*tching about a BIS winner........

    If someone could do a laymans version of this I'd be most appreciative I can't even pretend to understand some of the math and science.

    Jemima - keep on this track, much more helpful and for the good of dogs - maybe even try and 'translate' for a simpleton like me = respect earnt once more :)

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  18. There must be a mistake with the BMT. According to Spengler's 1994 article Population und genetischer Fortbestand des Rassehundes on Hundewelt 7/94 (cited by Katariina Mäki), the effective population size of BMT i Germany seemed at first to be a promising 172. This was achieved by counting the number of dogs used for breeding. When you add in the fact that most of these dogs were related, the effective population size was reduced to just 70. I find it highly unlikely that the BMT is so much more robust in Britain than in Germany.

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  19. As I understand it, to compute effective population size correctly (also COI), the pedigree database needs to go all the way back to founders. This is because these calculations assume the individuals in the first generation of the pedigree data are founders and all UNRELATED. If the calculations are done using 10 (or whatever number) generations, all of the individuals in that first generation will be considered to be founders and unrelated. This will likely result in an underestimate of inbreeding and overestimate of effective population size

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    1. BTW, for breeds with many generations of pedigree data, these calculations are not trivial to do. Ideally, they should use the worldwide population of registered dogs, which will entail consolidating the records of the kennel clubs worldwide; this is going to take some effort. This is why the zoos of the world got together some years ago and formed ISIS, which maintains the consolidated database for all of their captive animals, allowing them to identify genetically appropriate mates for an animal anywhere in the world. We need to do this for dogs.

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    2. Absolutely, Carol.

      An ISIS for dogs would be amazing.

      Jemima

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    3. Yes but the further back you go the less genetic contribution there is per individual.

      50%, 25%, 12.5% 6.25%, and so forth.

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  20. I think there is a huge need for breeders to have access to and understand this information. I'm not a geneticist, but to this end I've started a dog genetics journal club. The first paper I've chosen for us to read has been hugely useful to me in understanding what population genetics has to offer dog breeders.

    I'm not expert on this, also learning as I go. So gene-heads are especially welcome to help us all with the tricky stuff.

    It's a place to start. Everybody is welcome. Read about it here -

    http://bit.ly/doggenes_reading_club

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    1. carol beuchat18 March 2012 22:56

      @BorderWars - please join us. Your expertise is most welcome!

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    2. Thanks, have printed off the paper to read , looks interesting

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    3. Count me in. I've just read the paper and it looks fantastic.

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    4. What a brilliant idea! I'm off to download and get reading :)

      Thank you.

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  21. RE - Worldwide database
    There's no reason it can't happen. It would take some bodies to do data management and the computer resources. The expertise is available. Once everything is compiled, new registrations can be added to update the database continuously. Bob Lacy (Chicago Zool Society & IUCN) developed many of these statistical techniques and the software for ISIS. Info about him and downloads of his pubs are available from here -

    http://www.vortex9.org/lacypubs.html

    All that's needed to make it happen is some $$$$$.

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  22. oops, did I include link to Lacy's website???

    http://www.vortex9.org/

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  23. Carol, I contacted Bob Lacy and his team when we were making PDE and asked if they might be interested in having a look at dogs. They were, but there wasn't enough time, unfortunately, to get something done in time for the programme.

    Jemima

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    Replies
    1. but you had THREE YEARS.................so not enough time ?!?

      Delete
    2. I didn't go looking for conservationists until I heard about the Calboli et al paper in early 2008. Given Bob Lacy and his team's commitments, that made it all too late for PDE1.

      Jemima

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    3. I should say, too, that it would be a big endeavour that would require a lot of goodwill and collaboration between kennel clubs and holders of individual breed databases.

      One that should be attempted, though, in my view.

      Jemima

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  24. If it is the halfway point of a five year plan, how can you say anything has 'failed to appear'?

    Surely you have to wait until the five year point to make this comment?

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    1. Don't think it's a huge big secret that the Cavalier situation is complex and there hasn't been much support from breeders for the EBVs. As such, there is a lack of data (ie. MRI scans), making it impossible at the moment for the researchers to come up with robust EBVs for the breed.

      Hopefully that will change, but with other breeds with other problems more eager and willing to help, I guess there comes a point when the researchers turn their attention elsewhere.

      Jemima

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    2. Are you a politician in disguise?

      The question was simple, but you avoid answering it.

      If there is a five year plan, surely you cannot answer until the end of five years.

      Delete
  25. I'm confused a little bit Jemima. Can you just summarize what this post is for me please? (-: Where are you getting at?

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    1. It's a plea for the Kennel Club, AHT and breeders to panic a bit more about the dwindling genetic diversity in individual breeds.

      The effective pop size of many breeds is extremely low. It spells trouble for many because low diversity often leads to (further) inbreeding and leaves a breed vulnerable to low fertility, reduced vigour and a compromised immune system.

      An injection of new blood - either from a different population of the same breed, or from another one - will be needed sooner or later to ensure the long-term survival of breeds like the English Setter.

      Jemima

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    2. I hope in the future, if possible, there can be a deal between all kennel clubs worldwide that can find ways to continue with all breeds without resorting to inbreed the dogs. I don't want any of them going extinct. :-( There are many healthy breeds out there. Breeders just need to search very high and very low for their breed. English Setters are one of my most favorite breeds along with the Great Danes. But hearing about the fate of my favorite breed, it's made my day a downer. I plan to continue to have this breed to be a part of the rest of my life. I still have three english setters and one very great dane, which are amazing dogs I have in my life.

      Delete
  26. The English Setter Association have a statement on their website by their chair about the KC announcement that the ES is one of the five most endangered breeds. Not a mention of how low their their EPS is, not a mention of the KC's recommendations of outcrossing, importing new dogs and limiting the use of popular sires, in fact no concern at all except that it will be harder to get a stud book number and judges are finding it difficult to get enough hands on dogs experience to progress their judging careers. She does mention bitches are "missing" and litters small, but only as an explanation for falling registrations, not otherwise a matter for concern apparently. However , not to worry, now they are are a vulnerable breed they wont lose any more CCs even if the show entries fall further
    Here is the statement

    ENGLISH SETTERS JOIN THE VULNERABLE NATIVE BREEDS.


    The Kennel Club Press Office did their job well and the press release headed English Setter Risks Extinction for the first time was over the top but it caught the eye of the National Papers, local news stations and the BBC. Local breeders were bombarded with requests from local radio stations to talk and BBC Breakfast featured Fran Grimsdell (of course she answered the question in a reassured sensible way and was helped by some of the canine variety Tattersetts).

    Well let’s look at the facts (which the press release also cited). The English Setter joins another twenty four breeds on the Kennel Club's Vulnerable Native Breeds (VNB) list. A breed is deemed at risk when less than 300 puppies are registered in a year. English Setters numbered 234 registrations last year a 33% decline on 2010. There has been a decline of almost two thirds in the number of English Setters to-day compared to ten years ago. The PR seems to be so certain that people are moving into buying Designer Dogs and in some instances maybe this is so. The Telegraph put in a pro British native breeds piece in which KC Secretary Caroline Kisko also blamed the trend for status dogs. The Guardian Pass Notes column also was horrified that people were deserting the Native British breeds so attractive in every way for breeds they felt had little appeal.

    One reason for the lack of English Setter puppies is that most well known English Setter breeders have strong lists of prospective buyers but only a limited number of puppies to fulfill their orders with sometimes small litters or bitches missing. Another reason is the English Setter is not the dog for every family home and most breeders are very responsible and careful to whom they sell. This reflects in the fact why very few of the breed need to be re-homed. Jenny Penna runs a very good Rescue service and is fortunately not overwhelmed. A salient point is VNB's do not lose CCs of which we have been doing of late. This is good because if the ideal English Setter purchaser wanted to go to a show and see the breed, with no class's there would be no dogs to look at. The latest to lose CCs is Blackpool which always drew a good entry and serviced a part of the country that is isolated. I wonder if the Canine Activities Dept that works out the Breeds CC allocation have gone to check breeds that are moving near NVB status and held back removing the CCs until they have the full years figures. Not in the case though of English Setters but maybe they will now. The KC can move fast at times.

    At the Kennel Club the Health & Breeder Services Dept compile the Breed Registration lists from the KC Data Base. Now we may have a change of Stud Book Bands. English Setters were Band D and now might go down to Band C or lower and this has a change for KCSB Qualifications and also for the number of 'hands’ on dogs for the Judges of A3 & B & C lists. This means more work for the overworked Joint ES Breed Clubs Joint Judges Committee and because they have to save money due to the current financial climate more work for the Clubs underpaid club officials.

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  27. And no reaction from the IRWSCGB so far, not even acknowledging the statement on their website. Asking other IRWS owners at Crufts what they thought about the KC announcement , mostly brought a blank response, they knew nothing about it. One concerned IRWS owner (not me) wrote to the KC after they announced the five endangered breeds, and asked if the KC had been in any consultation with the breed club over the possibility of outcrossing mentioned in the statement , and got a letter back last week saying they had had no contact with the breed club over this statement.

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  28. I dont think people who would want a large breed like an English setter would move over to a small fluffy cross breed.

    An English setter would not even come into my head when thinking of a dog breed, firstly the show type are odd looking. the head shape , the odd coat colour and style , the deep chest.
    They are large
    I know nothing of their temperment ( But I know the other setter breeds can be hard work)
    For a rare hard to find breed you would really have to fall in love with it to travel hundreds of miles.

    Most people buy a breed because a friend or relative has one and like the temperment and look of it.
    some see a picture and fall in love with that ( not a good idea as the temp may be unsuitable) or they choose the first breed they see advertised in the paper. I dont think an English setter falls into any of those catagories

    ReplyDelete
  29. GENES software for pedigree analysis and management can be downloaded free for individual use

    http://www.vortex9.org/genes.html

    Is anybody using this ? Any comments? Recommendations? I still have Jim Seltzer's old programme, worked well for me, but no longer available

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  30. I've just come into this.

    Regarding the KC's Mate Select breed average COIs, I spoke with Sarah Blott (AHT) and Aimee Llewellyn (KC) about the discrepancies in the COIs. I suggested that alongside each one they should add the number of generations that the average figure is based on. They agreed that they would do this. The big question is when this will be done. However it is in the plan to revise the COIs on a regular basis so that we can see if the breed averages are coming down.

    Carol Fowler

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    1. Carol, If you look up the COI of an individual dog by name on Mate Select, then scroll down to the bottom right of the screen, you will see a heading About This Calculation, and it tells you how many generations are available, and how many of these are complete. I just looked one up (my dog Tullamore Troubador) for which the records go back 17 generations, but only seven COMPLETE generations

      Delete
    2. Carol, my mistake, you were talking about the breed average, not the individual dog

      Delete
    3. The KC are at present working on the Cesky Terrier database, and in a short while, will have every dog traced back to the breed founders. This is a pilot project, and when it is finished they will turn their attention to other breeds.

      Delete
    4. Can you tell us a bit more about this initiative and its aims, Sheila? It sounds really interesting.

      It is just for UK reg'd dogs or will it be incorporating data from overseas, too? You have an excellent CT database anyway, I think?

      I know that Mate Select does not accurately reflect the COI of your CTs compared to the breed database. Was it this that triggered the pilot project?

      Jemima

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    5. Quite simply, the KC IT department are using my database (which is verified by online information from Swedish and Finnish KCs and printed records from the Czech Breed club) to extend the pedigrees of all the imported dogs back to the original Scottie/Sealyham cross.

      It's a fairly simple, if time-consuming process, but once they have tackled our relatively small breed they will look to do the same with other breeds. The main stumbling block was the question as to whether the records held by an individual could be considered to be as accurate as those of a national KC, but I think we have overcome that.

      Yes, you are quite right - because we have so many imported dogs, the COIs shown on MateSelect are nonsensical and it is virtually impossible to compare like with like as the number of generations under consideration is very variable.

      Sheila

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    6. Excellent, Sheila. Really pleased to hear this. And yes, heard from Sarah Blott yesterday that they are hoping to extend the pedigree data for all imported dogs. Good news.

      Jemima

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  31. When you think about the numbers of breeds being churned out in huge volumes (and poor quality) by puppy farmers, the Bichons, Westies, Yorkies, Cavs and Jack Russells being just a few examples - a lot of which are registered by the Kennel Club, it's not that surprising that we have certain pedigree breeds looking endangered. When was the last time anyone could claim to have seen a puppy farmed English Setter? If the commercial volume puppy farm breeding situation can't be sorted out as a priority then we are guaranteed a bleak outcome for those on the endangered list.

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  32. Anon, its not only the low registration numbers the KC are worried about in these five breeds, its also the levels of inbreeding. While some buyers may prefer to buy a Labradoodle rather than a setter, reducing the demand for setters (I've not seen any evidence of this), the low EBS has been caused entirely by the behaviour of breeders themselves , with their use of inbreeding and popular sires

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  33. "With 20 thousand English Setter pups whelped per year in Italy alone, and another 5000 or so each in France and Spain, not to mention the thousands bred in North America and elsehwere, there is absolutely no threat of extinction, but we may see the disappearance of a great breed from its native land." Chiendog

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  34. Interesting and slightly worrying data for my breed here (ESS) but I'm not so surprised....almost all working pedigres go back to a few famous FTCH sires. It's good this is being investigated but there are no easy answers, even outcrossing has it's potential pitfalls!

    An open question on the 'vulnerable' breeds though...should we try to save them? I think the Otterhound is a fabulous dog but.....ho needs Otterhounds in the 21st century? They just don't fit in so should we allow them to die out to be replaced ith more suiatable breeds and crossbreeds?
    (Just an open question, don't accuse me of being any sort of 'hater'!)

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  35. More detailed information on the Akita Inu from the study shows that they are actually doing very well despite low EPS, they have low levels of inbreeding. Akita Inu breeders are well aware of the small gene pool (as a new breed in the UK it is to be expected), but work hard to make he absolute best use of those available, as shown by the study.

    "The Akita Inu is also special in that the breed was introduced into the UK since the advent of electronic records, and so the pedigree analysed here spans the entire history of the breed in the UK."

    "Other than the Greyhound, the Akita Inu has the most even distribution of reproductive success: the lowest proportion of popular sires (1%) and the highest proportion (13%) of male dogs that are sires."

    "In contrast, the Akita Inu have a higher
    mean kinship at 0.023, reflecting their small population size, yet this breed has relatively 11
    low values of f, which could reflect a pattern of inbreeding avoidance by Akita Inu breeders."

    "The estimate of Ψ ranged between 0.10 in Akita Inu, to 0.55 in Springer Spaniel -- For comparison, among three widely separated human populations investigated in the International Hap Map project was estimated at 0.12."

    "The Akita Inu showed the least evidence of population structure and also a low level of inbreeding relative to its small size. Popular sires are evident in all breeds except the Greyhound, and are most common in the Golden Retriever."

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  36. I would have liked to see some more discussion of possible strategy for survival of any of these five breeds . The KC suggests outcrossing, importing new dogs and limiting the use of popular sires? Any body got any comments, suggestions about any one of the five breeds? Would the same strategies work for all of the, or are they different?
    I find it hard to believe that owners and breeders of these five breeds seem so uninterested in the KC statement

    ReplyDelete
  37. Border Wars and Carol are the stars of this comment section.

    They both have excellent and practical ideas for DOing something. Assessing the state of dog breeds should be a worldwide effort. It should include village dogs, crossbreeds, working dogs and all landrace dogs, too. Plus mutts.

    If Facebook can do it with people, then it should only be a matter of money to set up the proper format to do this. Any dog owner should be able to input data about their own dogs, including if they are registered,their health records, their pedigrees as known, then even purebred dogs that were never registered can be identified.

    Before the naysayers sound off, they really need to think about the facts that Border Wars and Jemima present. Neither one has an agenda other than the overall welfare of purebred dogs.

    I notice that at about the same time, the royalty stopped inbreeding, for the sake of their children, the dog world took up the practice with the same disastrous results in less than 150 years.

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  38. Statistical models, such as that used to compute the Estimated Population Size, and indices, such as the Coefficient of Inbreeding, produce numbers based on a series of assumptions, and may err due to the quality of the data being fed in.

    Almost all statistical methods/models assume data are independent. Mating decisions are not. In the wild, natural selection culls the unfit; in the pedigree world, those who depart from the breed standard tend to be neutered, and those with the best show potential, and hopefully, health tests, get bred. Furthermore, some genes are linked, so the sorting of genes during mitosis is not entirely random. Some genes are linked, which weakens the models ability to predict the health implications of high COI or low EPS. It's hard to quantify the errors imparted by the lack of independence in data, but they could be large. It would be interesting to see some experimental studies on how large the errors may imparted by assuming data are independent when they are correlated, eg, by bootstrapping.

    The core concern, however, is not the degree of inbreeding, but the extent to which inbreeding shows up as in the DNA as homozygous pairing, particularly in chromosomal regions that affect health. For example, the canine major histocompatability complex (MHC/DLA), concentrates genes that are critical in causing the hereditary component of cancer, allergy, and many other health problems.

    It would be far better to move from statistical modelling to deterministic analysis. As genetics improves and the cost of sequencing declines, we are increasingly able to focus on what is actually in the DNA (as we now do for a handful of factors), and analysis of pedigrees will be relegated to the task of predicting where problems, or strengths, are likely to be found.

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  39. The low EPS for Rough Collie in Britain is especially worrying since the Kennel Club does not allow Rough collies being bred to Smooths, as some other kennel clubs in Europe do.

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  40. Is low UK EPS really such a problem? Dalriach's comment about overseas stock surely applies not only to Irish setters. We breed standard poodles; our first one's sire was Swedish, our current stud dog's sire Dutch, other poodlers we know have imported from the USA. No doubt the same applies in other breeds. Have ICL never heard of globalisation?

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  41. I presume the BMD's absurd claim is calculated on imports-as-founders, which is just bad science. The swedish breed club calculates the current EPS as 100-200, and i can trace my nor/swe BMD back to the actual founding stock (which is deplorably low, of course).

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