What does it mean to add genes?

@lvoss:

The numbers I have seen done by people in the breed shows that we have lost roughly 50% of our founders. That includes just from the new imports in 87/88, which is only just over 20 years ago, and already we have lost 50% of them and some only trace back to one or two breedings or 1 or 2 offspring.

This brings us back round to Clay's point, what good is it to open the stud book to foundation stock if there is no longer plan for incorporating them into the gene pool. If BCOA wants a successful native stock program then it should also include educational opportunities to learn how to best make use of the native stock otherwise people will just dip in once and then breed away from it and get the "feel good" sensation of doing something good for the breed when in fact they have done nothing.

Genetic diversity in the Basenji breed has long been an issue that interests me. I have often wondered what is really happening in our breed to reduce gene diversity? Does bringing in additional native stock actually impact the gene diversity of the breed?
lvoss has been asking similar questions in this thread.

We know that historically the Basenji breed has suffered significant bottlenecks that contribute to loss of diversity in the gene pool.

In the first 25 years of the establishment of a breed we call Basenji (between 1936- 1961), 18 individuals who contributed unequally to the gene pool were the foundation of the breed (9 dogs & 9 bitches). Three of these were outcrossed Liberian camp-dogs. The record reveals that the Liberian camp-dogs were subjected to a controlled breeding program for more than 12 years selecting for "Basenji" traits. Only then did the get of this intensive selection effort become recognized as outcross founders. In fact, the results of the breeding program produced dogs that were exported to Zambia to be bred with purebred, registered Basenji bitches (bred down from Congo native stock) brought from England. Then those get were imported to England by Elspet Ford and to the USA by Gwen Stanich. Although they are considered to be native dogs because they were whelped in Africa, they were actually only a percentage African stock.
There were no Liberian imports (native Liberian dogs) registered as Basenjis. By the time the dogs were imported, they were heavily blended with Congolese dogs BEFORE the progeny were included in the breed registry. This outcross was done simply because some members of the fancy wanted the dominant black coat color. Once the dominant black & white was bred with Basenjis from England, there were never any back-crosses to native Liberian stock.

This is a perfect example of the comments by lvoss. Her important premise is that in order to have a significant impact, new dogs have to be desirable to breeders and the fancy. They have to contribute something positive to the breed. In the example of above, the contribution from outcrossing to Liberian dogs was the dominant black coat color.
Similarly, the example of the Congo dogs registered in 1990. The contribution they made to the breed was the brindle coat pattern. Although subsequently we can say that they also provided new breeding opportunities to steer away from fanconi; we did not know that when the dogs were imported and that was not a goal of the importation effort in 1987/1988.

Anyway, the founder effect severely reduced the genome (frequency of genes in the population) of what had been the genetically diverse EFb geographic breed.
Drastically narrowed, only the genome of the dogs used to start the breed served as the genetic foundation of the dogs named Basenji by Westerners. In this way, a gene quite rare in the EFb population may have a much higher frequency in the Basenji population; conversely, genes common in the EFb population may be infrequent or even absent from the Basenji population. We can never know what we lost or what we disproportionately magnified in the genome of the Basenji compared to that of the EFb.

Of course, that wasn't the end of the story nor was the door closed on including other EFb genes. In 1990 and in the recent two years, additional native dogs have been added to the foundation gene pool. But, the Basenji genome is still based on a small number (subset) of individuals and can never represent the EFb genome.

Several years ago a breeder interested in finding unrelated lines to use with her own line did a pedigree analysis. By studying a sample of dogs that might be of interest and were "unrelated" to her own lines, she found three significant bottlenecks and extrapolated her findings to the wider gene pool of the breed.
First, from her sample she concluded that the US Basenji gene pool was approximately eight significant foundation individuals. The foundation stock who had contributed most to the breed were :
Bongo of Blean (male)
Amatangazig of the Congo (female)
Bereke of Blean (female)
Kindu (male)
Kasenyi (female)
Fula of the Congo (female)
Bokoto of Blean (female)
Wau of the Congo (male)
Second, Basenjis in the US show a second significant genetic bottleneck through disproportionate use of the OTC suffix (Of the Congo) dogs. During World War II Veronica Tudor-Williams was foremost in preserving the breed at a time when the Ministry of Home Security required the compulsory destruction of all dogs. There were a handful of other breeders that maintained lines, but it was VTW who bred prolifically and exported her OTC dogs to the USA.
Third, Basenjis in the US had a significant genetic bottleneck in the 1960's and 1970's due to the use of three popular sires, two of whom were sons of the third.

Without knowing about that analysis, a number of years ago I inquired about the Basenjis that were used as the basis to make conclusions about the Basenji Genome in all the genetic research into breed origins. From that information I was able to determine that genetically Basenjis are derived (for the purpose of research) from only six founders :
three foundation sires -
Avongara Gangura
Kindu
Wau of the Congo
and three foundation bitches -
Avongara N'Gondi
Avongara M'Bliki
Amatangazig of the Congo

And a couple years ago I initiated a game on one of the Basenji chat lists to track tail male and tale female lines. This was a simply and fun exercise to illustrate a singular aspect of founder loss in our current population (it does not reveal what is happening in the middle of a pedigree nor loss of genes on the autosomal chromosomes). So, it does have limitations. But it can reveal when a founder no longer has descendants; i.e., the founder is lost to the breed and all the unique genes the founder contributed. At that time it appeared to me that there were quite a few breeders who believe that each kennel name represents a distinct genetic line. The exercises was not only fun and easy with minimum instruction, but it illustrated to many that genetic diversity is NOT determined by the number of kennel names.

These examples give us important insight into the use of native stock in our breed; the overrepresentation of individuals in the breeding program, loss of some unique breeding lines, and illustrate how much our gene pool has narrowed.
Concerning the erosion of the gene pool, it is important to know how many founders are still represented in the current Basenji population and to consider the number of generations our current dogs are away from the founder. In genetically limited populations, a certain amount of unique genetic diversity is diluted with each reproductive event through the action of genetic drift, inbreeding and artificial selection. Thus, the number of generations away from the founder becomes an issue of concern. Genetic material can be rapidly narrowed, each generation carrying a reduced level of heterozygosity as it is permanently linked by the horizontal pedigree. The average time between one generation and the next is a convenient yardstick to help us realize the relative rate of genetic attrition.

So, I still wonder if admitting new native stock EFb into the Basenji gene pool will actually help gene diversity in the long run.
I keep going back to the article by Mary Lou Kenworthy, "WHAT IS DIVERSITY REALLY?" (The Modern Basenji Worldwide, Vol. 1, No. 2, Summer 2011, page 3) and Mary Lou's statement, " If breeders create and monitor their own lines, the breed, as a whole, will prosper. No breeder can maintain diversity by himself, and any attempt to do so will lead to disaster for the breeder and the breed. It takes a network of breeders working together with individual lines to maintain diversity. "
I think she is correct. 🙂

Jo,

Thanks for taking the time to provide so much thought provoking detailed information. I almost missed a meeting because I was so engaged reading all of it, lol. I know I have several questions but I'll have to wait until after work to ask them.

Clay

@Nemo:

Jo,

Thanks for taking the time to provide so much thought provoking detailed information. I almost missed a meeting because I was so engaged reading all of it, lol. I know I have several questions but I'll have to wait until after work to ask them.

Clay

Thanks Clay! Just in case your computer presented my two posts on different pages … I posted two long comments this morning. The first with an attached figure appeared on page 6 of this thread and my second this morning appeared on page 7.

I know the situation is different in the UK but I find this thread extremely interesting and of course much applies to our UK population.

I am having to print your posts - for my own information - Jo because I find it difficult to read off a computer - I hope I have your permission?

@Patty:

I am having to print your posts - for my own information - Jo because I find it difficult to read off a computer - I hope I have your permission?

Yes. Of course. 🙂

Thank you for this Jo. I will be rereading it until I am sure I "get" it all.

I think it might be useful to post some information about preserving land race breeds. My primary source when researching this over the years has been Dr Phil Sponenberg, a geneticist and professor at Virginia Tech’s vet school, who is a specialist on preserving rare and land race breeds.

I’ve also gotten useful insights from Species Survival Plans, but IMHO Sponenberg is both more applicable and presents more practical applications. FYI, Dr Sponenberg is scheduled to speak at the 2012 National, which should give Basenj fanciers a useful opportunity.

Sponenberg has advised many breeders, in many species, on how to preserve their breeds. One frequently asked question is what to include in the registered breeding pool. His principle is simple. Include as many animals as possible of that breed, and do not include those that are not of that breed. He has a fairly detailed discussion of this, with examples, in his last book, Managing Breeds for a Secure Future, which is available from Amazon and from the ALBC. See particularly pages 20-23.

As far as gene loss goes, Boyko’s work on genetic diversity in Basenjis versus village dogs shows very significant reduction in genetic diversity using microsatellite markers, with about .356 for Basenjis versus .553 to .684 for various populations of village dogs.

Bringing in new individuals from the same geographic areas does add new alleles (versions of genes – all dogs have the same genes - just different versions of them) and does contribute to genetic diversity. In many land race breed populations, all of the individuals may come from a relatively narrow area (Soay sheep, Shetland sheep, Fjord horses, and Icelandic horses all spring to mind) but there can be significant genetic diversity within the parent population in any given location, that requires a fairly large number to sample thoroughly.

In general, a minimum of 100 founders is given, and I have heard 200 bandied about as a more desirable minimum number. In practical discussions of preserving land race breeds, I have never seen an expectation that founders be unrelated – all members of a land race breed, or any breed, are expected to be related – but rather terminology used that founders are the individuals where known pedigrees stop.

Increasing diversity in the gene pool was a major driver in the 1980’s importations, per people who went. Dr Russ Brown, a geneticist from Virgina Commonwealth University, contributed to the petition to open the stud book, contributing from that perspective. Russ lived near where I worked, and was the breeder of my Ch JuJu’s Pistol Pete. I understand that some people do not realize these dogs were imported to expand the gene pool, but Russ was quite definite about it.

Avongaras have made a significant impact on the gene pool, and not in the sense of one cross and quickly breeding away from. A number of long time breeders breed straight Avongaras. I was able to come up with a dozen serious breeders that have recently bred full Af litters, plus probably half again that many people working with them (ie, own one or two Avongaras that they keep intact, and work with the group.) Plus the overseas people.

Of the dozen I thought of right off, they’re pretty much all working together to a greater or lesser degree. The goal is to maintain an outcross gene pool, of good type and quality, which does offer significant value to the breed.

Newly imported Avongara stock would be particularly useful in maintaining a viable outcross group for the longer term, and some of the newer Avongara imports have already been incorporated. Others (like the ones in the nice pix Katie and Ethel had) show a lot of promise.

Most of the breeders I know using Avongara blends are not using one outcross and then diluting – they are using significant percentages of Avongara stock. Good examples from my region include the #3 producing brood bitch of all time, Ch Eldorado’s Ooh La La (38.625% Avongara from 3 separate crosses that incorporate 5 different Avongara founders.)

Or you can look at a stud dog I have used, Ch Wakan MicCookie http://www.wakanbasenjis.org/Micki%20collage%20jpg.jpg 31.25% Avongara and his littermate Ch Wakan Sugar Cookie http://www.wakanbasenjis.org/SugarCollage.jpg

My own favorite brood bitch, Itzyu Good Golly Miss Molly (call name Sally, long story), is 50% Af – the result of breeding two good half Afs together – dam of some very nice pups, with one ready to go out and on my FB page, and two on deck. The latter two are about 35% Af, from breeding to a dog that is 19.3125% African, with pups that are about 35% Af. The pups go back in 5 different lines, with each line going to one or more of five different Avongaras (Gangura, Diagba, Zamee, Mbliki, and Ngola.) It’s not cross once and out – it’s blend, and blend back, and blend back again.

I have full Afs in my kennel that also go back to Kposi and Elly, plus breeding rights on a Tambura kid (or possibly kids, another long story) and Renzi is also represented in my part Afs and in a number of dogs in this area.

These dogs have pedigrees that have been, and are being, used by many different breeders. Of the 87/88 imports, most of what got lost, was lost the first generation (Wele died in an accident, Renzi went sterile after one litter although his kids were used and are in a good number of Virginia pedigrees, Nabodio was in a pet home and did not produce pups when he was used as an older dog, one was not bred by choice, and one had pups with bite issues and was not bred down from.)

Diagba, Gangura, Zamee, Mbliki, Ngola, Elly, and to a lesser extent Kposi are pretty well represented in the gene pool – even Kposi, which is the rarest of the bunch, has full Af descendents with some linebreeding to her going on. I have dogs here that are 25% or more Gangura, Zamee, or Elly – just lost a Kposi grandson who has multiple kids in the gene pool - and there are many dogs out there that are 25% or more Mbliki or Diagba.

@Itzyu:

Sponenberg has advised many breeders, in many species, on how to preserve their breeds. One frequently asked question is what to include in the registered breeding pool. His principle is simple. Include as many animals as possible of that breed, and do not include those that are not of that breed. He has a fairly detailed discussion of this, with examples, in his last book, Managing Breeds for a Secure Future, which is available from Amazon and from the ALBC. See particularly pages 20-23.

Itzyu, I'm glad you joined the discussion. 🙂 Without having easy access to the book to read about the bolded sentence, can you paraphrase what comments he has on how "animals of that breed" and "animals not of that breed" can be defined? I think that gets to the crux of some of the issues discussed here.

@Itzyu:

Avongaras have made a significant impact on the gene pool, and not in the sense of one cross and quickly breeding away from. A number of long time breeders breed straight Avongaras.

Diagba, Gangura, Zamee, Mbliki, Ngola, Elly, and to a lesser extent Kposi are pretty well represented in the gene pool ? even Kposi, which is the rarest of the bunch, has full Af descendents with some linebreeding to her going on.

Can you help me understand your definitions of the above? I think that would be a useful context to further the discussion. What is a "significant impact" or what is "well represented"? This would help me understand the different perspectives on this.

@Nemo:

Itzyu, I'm glad you joined the discussion. 🙂 Without having easy access to the book to read about the bolded sentence, can you paraphrase what comments he has on how "animals of that breed" and "animals not of that breed" can be defined? I think that gets to the crux of some of the issues discussed here.

It's really good to get the book - well worth buying and I strongly recommend it for anyone interested in Basenjis or any other land race breed of any species. See www.amazon.com or the ALBC website.

That said, ALBC has their books online at Google Books and you can read pages 20-23 at http://books.google.com/books?id=GmsDwDuuP2cC&pg=PT100&lpg=PT100&dq=sponenberg+preserving+breeds&source=bl&ots=6RiX-84Svh&sig=LZhXlf8_auMwBfmuShgk9nDfVTY&hl=en&ei=EWtMTti5Ls25tgelib28Cg&sa=X&oi=book_result&ct=result&resnum=1&ved=0CBYQ6AEwAA#v=onepage&q&f=false

Sponenberg says it better than I can, and the whole section - heck, the whole book - is worth reading.

@Itzyu:

It's really good to get the book - well worth buying and I strongly recommend it for anyone interested in Basenjis or any other land race breed of any species. See www.amazon.com or the ALBC website.

That said, ALBC has their books online at Google Books and you can read pages 20-23 at http://books.google.com/books?id=GmsDwDuuP2cC&pg=PT100&lpg=PT100&dq=sponenberg+preserving+breeds&source=bl&ots=6RiX-84Svh&sig=LZhXlf8_auMwBfmuShgk9nDfVTY&hl=en&ei=EWtMTti5Ls25tgelib28Cg&sa=X&oi=book_result&ct=result&resnum=1&ved=0CBYQ6AEwAA#v=onepage&q&f=false

Sponenberg says it better than I can, and the whole section - heck, the whole book - is worth reading.

Thanks, I can't preview those pages but I will definitely add it to my wish list.

@Nemo:

Can you help me understand your definitions of the above? I think that would be a useful context to further the discussion. What is a "significant impact" or what is "well represented"? This would help me understand the different perspectives on this.

I think that is going to differ depending on who you talk with - but to me, a significant impact is when dogs are recognized as being useful in the gene pool to enough people that they are likely to have a lasting influence.

Well represented, to me, means descendents are in multiple households, appear likely to breed on, and are not limited to one or two people or one or two small programs.

They tend to go together, for obvious reasons, but aren't exactly the same thing.

@Nemo:

Thanks, I can't preview those pages but I will definitely add it to my wish list.

Try using the right hand scroll bar - it should let you scroll all the way up. At least when I browsed it, I was able to read that section.

@Itzyu:

Try using the right hand scroll bar - it should let you scroll all the way up. At least when I browsed it, I was able to read that section.

It's just letting me preview a different section of the book, pages earlier in the book than 50 are "omitted from this book preview." Just bad luck with Google Books. The section I looked is very interesting though. Definitely looks like a good book.

@JoT:

[
This is a critical statement. The value of adding additional native dogs to access other EFb genes only comes from adding dogs within the EF biome from areas not already represented by current founders. To continue bringing in dogs from the same geographic area(s) within the EF biome does not add "new" genes or contribute to gene diversity.

Jo, my main question goes to this general statement. Practically, do these "areas not already represented by current founders" still exist and if so, are they accessible and relatively "un-compromised" (for lack of a better word) by dogs that may represent other areas in the EF biomes or elsewhere.](http://www.suite101.com/content/central-africas-dog--congo-origin-of-the-basenji-a224967)

@Itzyu:

I think that is going to differ depending on who you talk with - but to me, a significant impact is when dogs are recognized as being useful in the gene pool to enough people that they are likely to have a lasting influence.

Well represented, to me, means descendents are in multiple households, appear likely to breed on, and are not limited to one or two people or one or two small programs.

They tend to go together, for obvious reasons, but aren't exactly the same thing.

Thanks, I realize this all depends on perspective. It would be beneficial IMO if "significant impact to the breed" could be dimensioned in a more quantitative way. We seem to have ways to demonstrate "significant negative impacts" such as with the discussions of popular sires and their disproportionate contributions to the gene pool but "positive impacts" seems to be more nebulous to demonstrate.

@Nemo:

It's just letting me preview a different section of the book, pages earlier in the book than 50 are "omitted from this book preview." Just bad luck with Google Books. The section I looked is very interesting though. Definitely looks like a good book.

A brief summary of the relevant section - and please get a copy of the book if you can - what to include and what to exclude is the stickiest issue, and more difficult with land race breeds than any other. In general, one should look at phenotype and cultural setting. It can be misleading with individuals, but is indicative with populations.

History can be greatly of use. Phenotype is important. DNA can be useful (parenthetically, Boyko's DNA work showed that most African village dogs he sampled were either relatively pure or highly admixed, with villages having entirely or almost entirely one or the other.)

He has page after page of examples of applying this (it is also a frequent topic in his other writings.)

@Nemo:

Jo, my main question goes to this general statement. Practically, do these "areas not already represented by current founders" still exist and if so, are they accessible and relatively "un-compromised" (for lack of a better word) by dogs that may represent other areas in the EF biomes or elsewhere.

The South Sudan is newly accessible (although I don't know of any Basenji person who has gone yet) and is historically a major home of Basenjis. I have heard multiple people interested in going there - I do not know if a trip is planned yet but I would be surprised if it did not happen.

However, in bringing in new dogs, you do NOT want to avoid areas already represented by current founders. Unless you've already gotten 100-200 founders well represented in the gene pool, the area is likely to include very significant untapped genetic diversity. Additional genetic diversity is likely even if we had that many founders. We still have, last I checked, less than 50. And that genetic diversity is highly correlated with healthy long-term survival of a breed.

The principle used to preserve rare and land race breeds is basically "include as much genetic material that is of that breed as you can".

@Nemo:

Thanks, I realize this all depends on perspective. It would be beneficial IMO if "significant impact to the breed" could be dimensioned in a more quantitative way. We seem to have ways to demonstrate "significant negative impacts" such as with the discussions of popular sires and their disproportionate contributions to the gene pool but "positive impacts" seems to be more nebulous to demonstrate.

Significant impact isn't a quantitative measure. It's a qualititative one. It varies depending on your values, your breeding program, and what you are selecting for. Major questions are usually, which population, and what qualities do you consider significant.

Giving horse examples (because they are likelier to keep me out of trouble) - Nazeer has a significant impact on the Arabian class A halter population, as does El Shaklan, Bey El Bey, and Padron.

They have no significant influence on the CMK population (very popular as endurance, family, riding, and dressage horses.) You'll occasionally see a distant descendent of Nazeer via Ralvon Elijah, who is 90-odd percent Crabbet otherwise, but that's about it. On the other hand, Aurab, who you don't see a lot of in pedigrees in the Class A halter ring, is a major influence on Arabian dressage horses and a significant force in CMK pedigrees.

For Basenjis (treading carefully here), the new imports are being widely used, in significant percentages of pedigree (not once and out) in show dogs in my area and in other areas that I know. This includes dogs that are top Honor Roll producers (see previously mentioned #3 Brood Bitch of all time, dam of at least one BIS winner and a boatload of champions, who is about 40% Avongara), National Specialty Award of Merit winners, all-breed Best in show winners, and top performance competitors. The Honor Roll producers include at least a couple of Avongaras, dogs that I frequently see in pedigrees.

So I'm not sure I "get" the idea that the earlier imports have not been well-used. In general, I see better, not worse, overall conformation with full and part Afs - I may be seeing results of more successful selection, but the source dogs are the same. In particular, Afs and Af blends I see tend to have better substance. They avoid extremely upright and forward shoulders too common in domestics. All I have seen have better musculature than average.

The usage I am seeing is not "one and out" breeding as much as careful and ongoing blending over multiple generations.

The Avongaras are significant to these programs, and these breeders feel they are getting better dogs through them. They are winning enough, and having enough other people to use their dogs, that their impact on the overall breed is substantial.

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