Genetic analysis of populations (part 2)

Genetic analysis of populations (part 2)

The Icelandic Sheepdog is what’s called a “landrace”. These are dogs that have been shaped by not just by function but also by their environment, because they are usually not purposely bred like purebred dogs in a studbook. Usually they are linked with a culture in which they play an important role in the lifestye of the humans they are associated with. So for instance, Basenjis are found in villages in central Africa, where they breed freely and are generally unmanaged, but select dogs are chosen to help with hunting. In the deserts of the Middle East, the Canaan dog lives in association with nomadic Bedouins, where it protects the livestock from predation, but likewise breeding is not arranged and the dogs largely fend for themselves. The Icelandic Sheepdog descended from Nordic dogs brought over from Europe centuries ago, and they are adapted to the harsh landscape and assist in managing livestock.You can read more about the breed HERE.
Landrace breeds usually have high genetic diversity and few health problems, because for the most part the animals receive little or no veterinary care or special husbandry, and natural selection ensures that only the fittest dogs survive. When these breeds attract the attention of breeders, a population of dogs is gathered that are then designated the “founders” of the registered breed, and they start a stud book that forms the permanent registration record of the new “purebred” dog breed. Once the studbook is closed to introduction of new animals, only offspring of registered parents can be entered into the studbook without special permission (in the US at least). From then, the doga are usually managed the same as any other registered breed.
Because landrace breeds begin with dogs that are likely to have relatively high genetic diversity, they present an interesting opportunity to see how the genetics of a population of dogs is changed by introduction into a closed stud book.
We’re going to look at an excellent study by Dr Pieter Oliehoek from The Netherlands. As in the study of Nova Scotia Duck Tollers and Lancashire Heelers, Oliehoek was able to create a pedigree database that extended from the living population back to the founding of the registered breed. With that, he was able to do the analyses that document the history of the breed as well as its current genetic status.
Oliehoek found that the Icelandic Sheepdog is like many other rare dog breeds -1) It was founded with a small number of dogs (36);2) It became a registered breed fairly recently (~1955);

3) For much of its history as a registered breed the total population was small (less than ~500 dogs until about 1990);

4) There has been a rapid increase in registrations in recent years as the breed has gained a following and been introduced to new countries (see Figure 1);

5) At the time of the study, the current population numbered about 2500 dogs, many times the size of the founding population.

This graph summarizes the population history of the breed from 1955 until 1997.
2014-11-17_1353
Knowing that breeding of Icelandic Sheepdogs had not been managed in any way as the breed grew in popularity, Oliehoek and his colleagues suspected that an analysis of the breed might reveal some evidence of significant inbreeding.They gathered together the pedigrees for all the registered dogs in the world back to founders (a total of 4680 current and ancestor dogs) and subjected them to special analyses that were able to reveal things about the breed that would have been difficult or impossible to learn any other way.

They found that not only were the dogs extremely inbred, but the situation of the breed was dire.

In just the first 10 years after registration, the breed lost more than 50% of its initial genetic diversity (Figure 2). In this graph, the breed starts with the genetic equivalent of 20 founders. The green line with crosshatch is the average MK (mean kinship), an index of genetic diversity, and you can see that it falls dramatically in the first decade (1950s) and continues to decline in the second (1960s). It levels off in the early 1970s at a level of about 2.2 (expressed as “founder genome equivalents”, which we defined in our discussion of Tollers and Heelers). In essence, the breed had been reduced in just 20 years to a population of animals with the genetic diversity of less than three dogs.

Picture

The astonishing decline in genetic diversity was a consequence of breeding practices that resulted in increasing levels of inbreeding (i.e., homozygosity) and kinship (relatedness of dogs to each other). When you see these two lines cross in this graph (below), it means that breeders where selectively breeding animals that were more closely related than average, which drives up the level of inbreeding faster than kinship. The average coefficient of inbreeding of 25% is equivalent to that produced by sib-sib matings. 

Picture

In essence, the entire breed population had the genetic diversity you would expect to find in less than 3 dogs that are as closely related as full siblings.

To save the breed from potential extinction as a consequence of inbreeding, the genetic diversity in the population(s) of breeding dogs needed to increase. How could they do this?

Using an analytical technique called “cluster analysis”, Oliehoek sorted the existing dogs into groups of individuals that were similar genetically. He was able to identify 8 groups: two large ones (green and purple), four of modest size, and two that were very small. You can see these in Figure 6 (below). Note that the longest bar is really 10 times longer than depicted – so it’s a VERY big group – in fact, 85% of the entire population.

What this means is that the breed population is not genetically homogeneous. That is, there are subpopulations of animals that carry alleles not found in the other groups. This non-random distribution of genetic diversity in a population is called “genetic structure”. It means that breeders could take advantage of this structure to improve the genetic diversity of the subpopulations and also ensure that the small ones do not go extinct.

Picture

Summary of Genetic Information
In the summary table below, the average degree of inbreeding (“F” in the table) in the population as a whole (“All”) was 26% (0.26). Average mean kinship within a cluster (mk) is the degree of relatedness of the animals; a value of 0.25 would be the equivalent of full siblings. The two statistics using founder genome equivalents (Nmk and NOC), indicate that the entire population has the genetic diversity that would be expected to result if there had been only two founders. NAD is a measure of allelic diversity (higher is better).
Picture

These data show that if the Icelandic Sheepdog breed was in a carefully managed breeding program, the little clusters of diversity in the subpopulations could be used to bring the overall genetic diversity in the breeding population from the equivalent of 2.2 founders up to as much as 4.7 – more than double, but is still extremely low.
The good news is that when this study was published, the Icelandic Sheepdog breeders used this information to modify breeding strategies to protect the smaller populations of genetically unique animals from extinction, and minimize the additional loss of genetic diversity from the breed.
You can download a copy of the original publication here -Oliehoek, PA, P Bijma, & A van der Meijden.  2009.  History and structure of the closed pedigreed population of Icelandic Sheepdogs.  (PDF download)