Mate Select - good but no cigar (just yet)

Yesterday, the Kennel Club launched Mate Select - over-ambitiously hailing it as a breeding tool that will "transform" the health of pedigree dogs. (KC blurb here)

It does irritate the life out of me when the KC makes such bold claims and this one is on a par with one recent press release claiming that KC funding of the KC Genetics Centre at the Animal Health Trust would assist in the "eradication" of genetic disease.  Clearly nonsense. I was concerned, too, to read the AHT's Sarah Blott being quoted in the KC press release saying that Mate Select would "prevent" the decline of genetic diversity in pedigree dogs.  Mate Select will do nothing of the sort.

Indeed, in answer to one breeder's questions yesterday, Dr Blott replied that the hope for Mate Select is that it would "help to manage the rate of inbreeding - the percentage by which it climbs - to no more than 0.5% per generation."  Inherent in this reply is the acknowledgment that this is the best that one can hope for given the way pedigree dogs are being bred currently- which is never (or very rarely) to allow new blood in to halt the inexorable loss of genetic diversity.

I understand that the KC wants some positive headlines out of the launch of Mate Select - and it deserves some as it is a step forward. But the KC  must resist overstating the case in this way.

So does that make Mate Select a bad thing? No, it doesn't. It's actually a pretty good thing - and it has the potential to grow into something quite powerful. It's just that it's important to be aware of its flaws and its current limitations.

But first, let's look at the good bits:

Mate Select in its current form allows you to do three things:

• look up the co-efficient of inbreeding (COI) of a particular dog (ie how inbred it is) and compare it to the breed average.
• find the published health test results for an individual dog
• do a virtual mating. This is intended for use by breeders who already have a shortlist of potential mates for their dog to find out which would produce the least-inbred litter.

Now this is a facility that breeders in Finland have had available (in a rather different form) for some time thanks to a particularly progressive Kennel Club there. But, I have to say that Mate Select's "front-end" has been well-designed and it is extremely easy to use - and it is streets ahead of what is offered by some other Kennel Clubs (notably the American Kennel Club which should be making much more effort to tackle this issue).

Indeed, when you think back to where we were three years ago,  Mate Select is nothing short of a revelation. Then, there was very little recognition that inbreeding was a problem; barely anyone knew what a COI was, and there was very little understanding of why genetic diversity was so important - or why the lack of it was such a threat to pedigree dogs.  This despite the Kennel Club knowing the devastating findings of the Imperial College study that found, in the 10 dogs breeds they looked at, that most had lost 90 per cent of their unique genetic variants in just six generations. (Calboli et al, 2007)

We have, then, come a long way. I know too, that there has been a huge amount of effort put into the development of Mate Select and it is good to note the genuine excitement about it emanating not just from the team at the Animal Health Trust that has put so many hours into developing it,  but also from the Kennel Club itself. I hope they're enjoying the warm glow that comes from initiating (even it if was under duress originally) something that is genuinely a good idea.

Mate Select is free, too, and available to anyone with a computer.  And the goodness doesn't stop there - the team at the AHT (which includes Sarah Blott and the lovely Tom Lewis) clearly wants to improve it and is open to suggestions on how to make it better or more useful to breeders (see below for details of how to contact them).

Which brings me to the not-so-good bits.

Yesterday, there was a flurry of breeders, owners and researchers trying out Mate Select, both in the UK and abroad. And it had many scratching their heads, with the most common comment being: "The breed average COIs are much lower than I expected."

• Mate Select throws up an inbreeding average of  just 4.2% for Standard Poodles, for instance.  The much more comprehensive Standard Poodle Database, however, finds that it is around 17%. 

• Mate Select's inbreeding calculation for Irish Red and White Setters throws up a breed average of 16%.  But using a more complete breed database, the 10-generation COI for a typical IRWS is over 25%.

• Mate Select finds a breed average inbreeding of 2.4% for Nova Scotia Tolling Retrievers - but the worldwide breed database, which goes back to the handful of founders, shows that the true figure (for Tollers registered between 1999 and 2008) is 26%, making a Toller more than a full sibling to any other Toller.

In at least some breeds, then, Mate Select seriously under-reports the level of inbreeding.

So what's going on?

There are a number of reasons for the discrepancies. First,  Mate Select uses the Kennel Club's electronic database as its raw material. The database was not computerised until 1980 and and the very earliest dogs recorded in it (picked up from the pedigree data for those early dogs) were born in the 1960s.  Mate Select treats the first dogs in the database as unrelated founders - ie. of having a COI of 0% - when that will almost never be the case.

This is, in fact, the flaw with any COI program unless the data includes the true breed founders.  The Imperial study mentioned above was similarly handicapped. As you can see from the table below, it found that there were over 15,000 founders for the GSD, for example - crazy when the reality is that German Shepherds descend from just a handful of original dogs.

Click to enlarge

Mate Select also treats the furthest-back dogs in the pedigrees of imported dogs (between three and five generations are recorded) as having a COI of 0% which, except perhaps in the case of a new breed, is never going to be the case. In fact, those dogs that Mate Select marks down as having a COI of 0% could (and in many cases do) go back to original UK stock and in reality could be extremely inbred.  That Mate Select does not include this missing data means that the inbreeding data it generates is flawed - quite severely in some cases, and particularly in breeds where there have been a lot of imports.

Another reason some of Mate Select's breed-average COIs are low is because it is based on the COIs of registered dogs from the last year for which complete records are held (currently 2010). This, in fact, makes some sense as the current inbreeding levels are probably the most relevant. However, again, it does not reflect the true level of inbreeding and the figure could be very skewed in breeds with few litters registered per annum. A rolling mean of five years would, perhaps, be a better idea.

Although some breeders on the canine genetic lists have welcomed Mate Select, others have expressed concern that people will be falsely reassured as to the extent of inbreeding/level of genetic diversity in their breed. A low breed average COI suggests there is no need to panic when the reality is that some breeds are in dire straits. The very low genetic diversity in Tollers, for instance, recently prompted Finnish researcher, Dr Katariina Maki to call for an outcross to another breed (pdf of Dr Maki's statement here).

The other concern was that it will be impossible in some cases for breeders to breed litters with a COI below the breed average because of the way it is worked out.  Mate Select suggests that its breed average for Malinois is 2.2% (almost certainly because of very few litters, many sired by imports) - but a breeder on one show list yesterday said that it would impossible to do a mating using their dogs that would get anywhere near this low a figure. This makes it unnecessarily awkward for breeders - and confusing for puppy-buyers.

So do we write off Mate Select then? Well, no. It has its uses. Although it should not be seen as a measure of a breed's extant genetic diversity, COIs of individual dogs will be fairly accurate, at least in terms of recent inbreeding, unless there are imports in the pedigree (and in many UK breeds there may be none). More health/genetics data will be added in time. There is, I understand, a plan for the system to flag up when individual dogs have been over-used at stud, which would be very welcome (and long overdue) given the enormous damage popular sires can do. I hope there is a plan to include effective population sizes too - a more useful measure of genetic diversity than COI alone.

For experienced breeders, nothing will replace in-depth pedigree analysis (something that is impossible to do with Mate Select as it gives no pedigree information at all) and they will undoubtedly continue to use alternative breed databases, which are very often mantained by the most dedicated of breed enthusiasts.

But, for casual breeders and pet owners, Mate Select offers a really simple, intuitive way to find out a bit of info on individual dogs, encouraging them to think about genetic diversity and, particularly, to breed for lower COIs without all the hassle and hard work of trawling through endless pedigree information.

For that reason, it gets the PDE Blog's seal of approval. Albeit one with caveats. Another one being, incidentally, that the person who wrote Mate Select's guide to genetic diversity should be shot. It starts: "At any single gene, diversity can be measured as the degree of homozygosity (the inheritance of the same version of a gene from both dam and sire) which is observed.  The more homozygous a population the less diverse it is.  One of the main factors leading to increased homozygosity or loss of diversity is inbreeding. "

As Pat Burns ("Terrierman") observed in a private email to me yesterday:

One of the ways you can tell an expert is thay they do not feel the need to toss around four-syllable words to a lay audience.  Picasso, in the end, could draw a raging bull with one line.

An old sailor, who knows how to teach sailing, does not talk about port and starboard, bow and aft, pintles and gudgeons, rodes and stays.  He talks about left and right, front and back, hinges, ropes, and cables.  Paint it simple, say it simple.   And the more important the message the simpler it needs to be.

I quote the Bible when I talk about inbreeding. This is an ancient wisdom and even the illiterate pagans know it is wrong to lie with their sisters.

Fucking your sister?  Not a good game plan for humans OR dogs.  Said plain, and easy to remember, eh?

Now there's a strapline.

To help make Mate Select better, write to mateselect@thekennelclub.org.uk