Population Genetics Report Fell Ponies Foal Immunodeficiency Syndrome Biology Essay


Enough horse fossils have been found so that archaeologists are able to trace the evolution of horses. The earliest fossil of a horse found was a dog sized Eohippus (Tyagi, 2009). This four toed Eohippus lived around 55 million years ago (Hall, 2010). The Equus mostly stayed the same with the exception of slight toe and teeth changes. During the Oligocene era about 34-34 million years ago the horse grew in size and 4 toes evolved into 3. Also in this time the horse had vanished from Europe, Africa and Asia and for the following million years the only place which was habitable for the horse was in the western part of North America (Rice, 2007). The Miocene era saw lush vegetation disappear and the land became a grassy plain. The horse was forced to adapt and evolve in order to survive in this new environment, for example its teeth needed to change so it was able to chew the new food, its toes changed into hooves which made it easier to get about the different landscapes. These horses are thought to have had a similar brain and molars to the modern horse of today (Kimball 2006).

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The only real wild horse, to compare to the domesticated horse is the Przewalski's horse, although this species is extinct in the wild, there are some captive in zoos which have saved the species from total extinction and are now being captive bred (Boyd 1994).

The Fell pony originates from the England/Scotland border. They are only a small breed around 14h maximum but are capable of carrying an adult man (Davis, 2008). They are a hard and sturdy breed and also versatile. The Fell pony matures late and will not breed often until as late as 7 years old. Most of the native Fells are left to roam free until the age of 2 or 3 and they aren't overfed. Mares shouldn't breed before the age of 3 or permanent damage could be done to the reproductive organs and the mares maturity and growth can be restricted (Fell pony society, 2006).

1.1 Environmental Factors

Survival of the fittest means that only the strongest most resourceful animals live to breed. In the bad winter of 1946-47 most of the pure bred native ponies survived, but cross-breeds died. This winter was so bad that all but one group of Fell ponies that were cut off by deep snow for 6 weeks also perished (Richardson, 2008)

The environment influences a horses characters, for example weight and muscle, these all depend on nutrition and exercise. The athletic ability and temperament also changes with different environmental factors. The size of the pony was due to the quality of grazing, ponies that were bigger than 13hh could not have survived on the moorland as their food intake would need to be greater than the smaller ponies (Mills, 2005).

Demographic profiling of horse domestication is hard. Mongol herds show the selective slaughter of stallions at 2 and half years old, leaving the mares to survive (Zeder, 2006).

A horse's breed typical behaviour is reflected on the combination of two forces- physical environment and humans. Temperament differences are often linked with blood temperature (Jensen, 2009)

1.2 Human intervention

In early history of the Fell Pony, their origins were from indigenous ponies of the region, and in the Roman period of Northern England the horses were cross-bred with horses which were introduced by foreign mercenaries. These horses from Friesland region have the pre-potency and characteristics still seen today in the Fell pony (Richardson, 2008)

There was also a mixture of Galloway blood, also Welsh cob from the stallion Comet. Small amount of Andalusian blood and finally Yorkshire trotter, which explains the larger 14.2hh ponies when the breed limit is 14hh (Fell pony Society, 2009). During the industrial revolution the Fell pony was used as a pack pony. They carried up to 16 stone of lead, iron ore, slate and coal from the mines. These ponies travelled 240 miles a week. From Kendal 300 Fells left to go over the country carrying cargo such as fish, grain, chickens and dairy products (Hamlets house, n.d.)

The Fell pony society was created in 1916 and has the Queen Elizabeth II as the patron (Fell pony society, 2003). During the depression of the 1930s along with mechanisation the Fell pony breed was threatened and in 1932 at a stallion show there was only 3 ponies that were shown. King George V saved the Fell pony breed with a large donation and also Beatrix Potter donated to save this breed (Richardson, 2008)

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Low breeding numbers can drastically reduce the gene pool in a breed, causing it to bottle neck. This happened to the Fell ponies. In 1914, 5 stallions were the direct descendant of the famous Blooming Heather. Homozygosity is 54% in British rare breed horses. (Richardson, 2008)

In today's terms, nature is taking out of the equation; there is no longer survival of the fittest among these horses. We provide them food and shelter, there is no longer natural selection (Richardson, 2008). Humans took horses from their environment in which they had evolved, and managed them under convenient conditions for us (Waran, 2007)

These days the Fell pony is used by man for showing, riding and driving. The Fell pony society regularly holds performance trials where the horse tackles different terrains such as boggy paths and water crossing. These horses are smart and need to be kept active (The Fell pony society, 2009).

2. Gene flow and polygenic inheritance of traits

Not all Fell ponies are black. There are also brown, bay and grey ponies. Black didn't become the main colour until the end of 20th century, before this time dark bay was just as common as the black ponies (Fell Pony Museum, 2010).

The two subspecies of wild horses are the Tarpan and Przewalski's horse. During domestication mares were crossed with stallions that had more desirable characteristics. It is assumed that mares from different regions were varied in morphology because of the adaptation to their environmental conditions. Gene flow (migration) is the main reason for lack of phylogeographic structure. As horses are so active migration levels are high. Two wild horses were found to have identical haplotypes from the Pleistocene era, one from Germany and the other Siberia (Kavar, 2008)

The colour of a horse is built on a base of two colours only, black- E and chestnut e. The colour of a horse is controlled by genes at 12 different loci (Thiruvenkadan, 2008). The two genetic loci: Extension and Agouti control the black or chestnut colour of a horse (Sponenberg, 2003). Black is dominant over chestnut, and chestnut is therefore recessive. A horse that carries 2 black genes EE will be homozygous- black, a horse that carries one black gene and one chestnut gene 'Ee' will also be black however it will be heterozygous, and finally a horse that carries two chestnut genes 'ee' will always be homozygous, chestnut.

If two heterozygous black horses are bred together 'Ee+Ee' there will be a 1 in 4 chance of producing a black homozygous 'EE' , 2 out of 4 chances of a black heterozygous 'Ee' and a 1 in 4 chance of a chestnut being produced (Wellman, 2009). See table 1.

Polygenic inheritance is seen in a variety of colour patterns in horses, such a shade and mane and tail colour. These might be due to influence of multiple genes (Thiruvenkadan, 2008).

Gene mapping has been used to assign numerous coat colour traits and disorders that are inherited to the horse chromosome. Molecular genetic studies for coat colour in horses have helped identify the genes and mutations which are responsible for coat colour variation. Microsatellite markers that linked to the trait were also found (Thiruvenkadan, 2008). Microsatellite loci tests across horse population showed that the highest observed heterozygosity of 0.0782 and highest diversity of 0.779 was the Fell pony, the lowest was in the Friesian horse (Luis, 2007). Microsatellites show high allelic diversity and are used to calculate genetic distance between the breeds (Mills, 2005).

Table 1. Common alleles at Agouti and extension loci.

Source: Sponenberg (2003).

Agouti genotype

Extension genotype

Colour phenotype

AA -



Aa Aa




Ee Ee

Chestnut (common)

Aa Aa

Ee Ee


Any horse breed existing today is an expression of the history of genetic drift and selection. The genotype for a breed will contain genes and combinations which code for specific characteristics, (such as good temperament and intelligence in Fells (Simper, 2003)).

Foal Pony Syndrome

Mutations that occur in a gene make it defective or somewhat unusual (Guttman et al 2002). This is seen as a deleterious gene in the Fell pony.

In the early 80's it became aware that new born foals were dying from an unknown disease which couldn't be cured by traditional medicines. After post-mortem examinations the conclusion came that is was most likely something of genetic origin (Brunt 2000).

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Fell pony foals get a condition called immunodeficiency disorder (Fell pony syndrome). Plate 1 shows a foal with the syndrome. It affects foals less than 3 years of age. Both sexes get it; the signs are diarrhoea, pneumonia, lymphopenia, ulcers on tongue, a curly coat which is unusually long and death (Higgins, 2006). Blood samples from the foals revealed that there is a low red blood cell count, low lymphocyte count and a high white cell count. A diagnosis can be made from a bone marrow sample taken from the breastbone. The syndrome causes severe anaemia, impaired immunity and is fatal with the foals usually being put down or dying by the age of 3-4 months. As the syndrome is only known in the Fell pony breed it is assumed that it's of genetic origin (Thomas, 2000).Foals usually fall ill around 4 weeks of age. This condition is possibly caused by an autosomal recessive deleterious gene which is inherited (Higgins, 2006)

FIS Pony http://upload.wikimedia.org/wikipedia/commons/2/2e/Shetland_pony_inbred.jpg

Plate 1. Plate 2

(Animal health trust, no date) (Wikipedia, inbreeding, 2008)

Due to the Fells small gene pool this syndrome is increasing at an alarming rate, as it is estimated that only 5000-6000 ponies are left worldwide. Selective breeding is better than the elimination of carriers when breeding to avoid a syndrome foal. If the syndrome is proved to be of genetic cause and the carriers can be found then they shouldn't eliminate the carrier ponies from the breeding stock as narrowing the small gene pool any further would have a devastating effect to the breed (Thomas, 2000). The level of FPS in the Fell pony population may be due to the history of the breed as after the Second World War there was a huge fall in numbers. This resulted in genetic bottleneck (Horse Trust, 2008).

It is likely that two- thirds of the Fell pony population is a carrier, and 10-20% of foals a year are syndrome foals. No affected foals have been known to survive (Thomas, 2000). The stem cells in bone marrow are generally missing in the syndrome foals. The bone marrow matrix might be failing to produce the stem cells and be deficient (Millard, 2000).The most likely cause of the syndrome beginning is thought to have been inbreeding/line breeding in the 1960s (Plate 2). The original carrier stallion isn't known but there is one heavily used stallion in the 1950s that is noticed in the pedigree of each known syndrome foal (Thomas, 2000)

The only way of getting rid of this genetic problem is with carefully managed breeding. Genetic disorders are common and the management of breeding has been seen in other animal breeds which have worked successfully for them (Brunt, 2000). The Fell pony society is performing constant genetic tests to try and eliminate the syndrome from the breed. The breeders are working with the society to preserve the Fell pony breed. Carries can still be bred to a test clear pony; this will stop the loss of desirable breed traits. The foals can be DNA tested to see whether they are a carrier or not. A veterinarian can collect samples and have them sent to a genetic lab to determine whether they are a carrier of the deleterious gene or not (Animal health trust, N.D)