*long read*

The key aim of SPARKS is to help reduce the depletion of genetic diversity that can pose a serious threat to the existence of small populations. 

SPARKS - Single Population Analysis and Records keeping system - is a computer-based breed analysis system originally designed to promote genetic health of captive zoo-based populations of wild animals. Used in conjunction with the GENES genetic analysis programme, it can help breeders choose the optimum oairing of male and female for the maintenance of genetic diversity.

Andy, a biology teacher, came to the development of SPARKS through his passion for horses and as a breeder of Cleveland Bays. His work on SPARKS formed the basis of his Mhil/PhD in Equine Conservation Biology and, in fourteen years if its use by the Cleveland Bay Horse Society, its impact has stemmed the rapid rate of increase n inbreeding faced by the breed since the 1920s. It has brought year-on-year improvement to Effective Population Size (the globally recognised measure of genetic health of a population), taking it from a non-viable 22 in 2004, through the red line of 50 in 2013 and onwards to 68 in 2018.

Genetic drift

One of the main problems for small populations is that they lose genetic diversity more quickly than large populations. Genetic drift - the loss of genetic material - is a natural process which has little effect in large populations but can  be devasting when only small amounts of genetic material are available in the first place, as happens in small populations. Inbreeding, which occurs if a mother and father share a common ancestor, is a major contributor to loss of genetic diversity. This leads to loss of vigour and fertility and increases the probability of expression of deleterious traits. Small population breeds losing genetic diversity risk entering the 'Extinction Vortex', which sees them becoming increasingly small. 

On inbreeding, Andy says: 'Inbreeding is a problem shared by all ring-fenced populations. Generation on generation, diversity is lost, and the breed will accumulate inbreeding. You can't stop inbreeding, but you can control it and the key is to have the right information to base you breeding decisions on.

'Breeders have their individual likes and dislikes in terms of physical attributes - phenotype - but if they complement that knowledge by understanding the full value of the genetic constitution - genotype - of a particular animal, they can make positive decisions that can contribute to the long-term genetic health of the breed'.

Taking a lead from zoos

In developing SPARKS for the Cleveland Bays, Andy 'looked to the people who deal with really rare animals'. He took his lead from zoological organisations which, for decades, had been using the original SPARKS single population analysis programme to centrally manage populations of zoo animals separated by miles or even continents. This genetic software has played a key role in reviving endangered populations including the Przewalski horse which bordered on extinction when the last 12 horses were captured in Mongolia and brought into captivity.

The key requirement, he discovered, was a digitised stuff book. He says 'An electronic studbook is gold dust. You can't physically cope with more than an 8-generation pedigree on paper. The kitchen table isn't big enough and, even then, you won't necessarily identify common ancestors deep in the pedigree. The Cleveland Bay studbook goes back over 32 generations and on paper that size of pedigree would need a football pitch!'

Having, after a great deal of struggle, succeeded in digitising the Cleveland Bay Stud Book, Andy was able to integrate the Cleveland Bay's complete genealogy to achieve globalised genetic information sheets for all the Cleveland Bay breeders.

The output of SPARKS is a complete set of datasheets, updated annually, which lists the status of every current breeding Cleveland Bay. The data sheets have been produced every year since 2004 as an aid to mare owners when selecting prospective stallions. They emphatically do not address physical attributes, rather their significance is that they provide a calculation of mean kinships for every known pure-bred Cleveland Bay registered in the stud book.

Kinship coefficient

For any endangered population, the most important information provided by the combination of SPARKS and GENES software is the mean kinship coefficient, widely accepted as a conservation method within zoos. It is a measure of the genetic importance of an animal, calculated by its relatedness with the entire current population. This coefficient is a number between 0 and 1 that measures how related a particular animal is to the rest of the population of its pure breed. Those with very rare bloodlines have mean kinships closer to 0 and are considered priority breeders. Those with more common blood have mean kinships closer to 1 and are considered less important.

When considering mean kinship, it is also important to realise that an animal’s mean kinship status is not static. It might change over time with population changes and will increase each time an animal produces progeny – hence the importance of updating SPARKS data sheets annually.

The SPARKS analysis for Cleveland Bay horses calculates mean kinships for every known pure-bred mare in the global population registered in the CBHS stud book. It also calculates the potential inbreeding resulting from every male/female pairing within the population. The data sheets provide a mean kinship figure for each named mare and assigns them to one of seven mean kinship bands. The table also names every licensed stallion and orders them by their location, their own mean kinship band and the kinship coefficient, which quantifies the degree of relationship between two individuals, of the progeny of mating with a named mare. Essentially, the data sheets help breeders choose pairings that will give the progeny a lower inbreeding coefficient than both the parent animals whilst discouraging the pairing of animals of very different mean kinships.

Traffic lights
A significant recent development in the SPARKS datasheets for Cleveland Bays followed discussions with the RBST conservation team and breeders. 

In 2018, a new ‘traffic light’ categorisation was introduced, making the interpretation of the tables clearer and more straightforward. All possible matings are ranked into one of four tiers and colour coded. Tier 1 – green – represents the best genetic pairings which are encouraged, while tier 4 would result in highly inbred matings, which increase the fixation of alleles (increasing homozygosity) and the
probability of deleterious traits being expressed in future generations.

Commenting on this, Andy says: “We would stress that this tiering is an assessment of the merit of the pairing of two animals, and is not an endorsement or criticism of the genetic makeup or quality of either of the animals. Breeders will always have their personal preferences and we must respect that. However, we are approaching this from the perspective of the long-term genetic health of a
rare breed – that is, its survival. By adopting the system, we hope to prevent the loss of genetic diversity and the increasing levels of inbreeding that are inherent problems with rare breeds. This, in turn, should help avoid future problems of increasing infertility, offspring mortality, deformity and other genetically linked phenomena. “Certainly from the point of view of selecting suitable stallions for collection for the RBST Gene Bank, we need to use information from SPARKS and prioritise animals with the lowest mean kinship as they are the ones least well represented in the population, with the genes at greatest risk of being lost.”