Skeletal atavism

How skeletal atavism changes the bones in a pony’s legs

A horse’s limbs contain several bones whose size and relationships change during development. The ulna lies beside the radius in the forearm; the fibula lies beside the tibia in the lower part of the hind limb above the hock. In the usual horse skeleton, these structures are reduced or joined to neighboring bones depending on the location.

In skeletal atavism, the ulna and fibula can remain excessively developed and fail to join normally with adjacent bones. This disrupts balanced limb growth and produces angular or rotational deformities. Atavism refers to a resemblance to structures seen in ancestral equids.

References [1] · [3] · [5]

Why difficulty walking due to skeletal atavism can worsen as a pony grows

Possible findings include short or deviated limbs, abnormal alignment of the carpus, often called the front knee, and deformity of the hock. Hoof position and gait may be abnormal. Both front and hind limbs can be involved, although individual foals do not all look exactly alike.

Changes may be apparent at birth or during the first months, then worsen as the foal grows. A published miniature filly was examined at eight months of age, illustrating that a developmental disorder is not always identified immediately after birth. Pain and the ability to move comfortably matter more than simply comparing a foal’s height with its pasture companions.

References [1] · [3] · [4]

Which DNA fragments are missing in skeletal atavism linked to Del1 and Del2?

The 2016 research identified two large deletions that partly overlap. A deletion is a missing stretch of DNA. The Del1 deletion removes, among other sequences, the part of SHOX containing the instructions for making its protein; this gene contributes to skeletal development. The Del2 deletion removes a shorter stretch in the same region. Both deletions also remove sequences belonging to the neighboring CRLF2 gene.

This is a pseudoautosomal region, present on both X and Y sex chromosomes. Males and females each have two copies of the region, and the disorder follows a recessive pattern here. It is therefore different from the familiar pattern of an X-linked recessive disorder primarily affecting males. Testing concerns these identified deletions, rather than every genetic cause of short stature.

References [2] · [5]

Which populations have been studied for skeletal atavism and its variants?

The deletions were investigated in Shetlands, and laboratories also offer testing for American Miniature Horses. A clinical report in a miniature filly documented complete ulnae and fibulae with severe limb deformities. A case described before the DNA test was developed does not automatically establish a Del1 or Del2 result for that particular horse.

Being a Shetland, a miniature or simply small does not establish affected status. Friesian dwarfism and other growth disorders have different mechanisms. Carrier estimates from one sampled population are not figures for every country or breeding program. Ancestry helps frame a testing question but cannot replace a horse’s own identified result.

References [1] · [3] · [2] · [4]

How examination and X-rays help diagnose skeletal atavism

The veterinarian assesses limb alignment, progression and weight bearing. Radiographs reveal the bones, their proportions and their relationships. In the published miniature case, they demonstrated complete ulnae and fibulae. External limb appearance alone cannot provide the same anatomical information or establish every additional lesion that may be present.

DNA testing complements this assessment and identifies carriers without signs of this recessive condition. Limb deviation may also have another cause or accompany other lesions. A negative result therefore does not guarantee a normal skeleton, while an affected genetic result does not by itself measure pain or the ability to move comfortably.

References [3] · [1] · [4]

How to read the skeletal atavism genetic test for Del1 and Del2

N/N means neither tested deletion was detected. N/Del1 and N/Del2 describe unaffected carriers. Del1/Del1, Del2/Del2 and Del1/Del2 are the combinations associated with the condition. One copy of each deletion can therefore be as important as two copies of the same deletion.

The diagram below groups these possibilities to make a report easier to understand. Two diamonds represent two altered versions of the region, which can be identical or different. Considering Del1 alone while ignoring Del2 would be incomplete. The laboratory’s description establishes exactly which changes were tested, and its own instructions apply to collecting and identifying the sample.

References [1] · [2] · [5]

Assessing pain and quality of life in a pony with skeletal atavism

The deformities can cause substantial lameness and worsen as growth continues. Veterinary assessment considers weight bearing, pain, the ability to feed and move, and any additional abnormalities. Care or protective equipment designed for a different hoof problem cannot automatically solve a disorder of underlying bone development.

Severe cases described in clinical resources often have a poor prognosis and may require euthanasia at a young age for welfare reasons. Decisions concern the actual foal rather than a universal age deadline. Horses with only one deletion must not be equated with these cases: they can transmit the variant without having the recessive disorder described.

References [1] · [4] · [3]

A mare carrying Del1 and a stallion carrying Del2 can have a foal with skeletal atavism

Consider a N/Del1 mare and a N/Del2 stallion. The mare can pass on the Del1 deletion or a version of the region without a deletion; the stallion can pass on Del2 or a version without a deletion. At each conception, the foal therefore has a 25% chance of receiving Del1 from its mother and Del2 from its father and being affected, a 50% chance of receiving a deletion from only one parent and being an unaffected carrier, and a 25% chance of receiving neither deletion. The same risk applies when both parents each carry the same deletion. Four births need not follow that exact distribution.

If one parent carries Del1 or Del2 and the other is confirmed N/N for both deletions, the foal cannot receive a deletion from each parent. It will not have this form of skeletal atavism, although it may carry the deletion it inherits. A parent with two deletions, identical or different, always passes one of them to its offspring. Choosing a mating therefore requires both deletion results for both parents, alongside other health considerations and genetic diversity. Small size and absence of lameness do not identify every carrier.

References [1] · [2] · [4]

Questions about the condition: Skeletal atavism

Scientific sources about the condition: Skeletal atavism

This article brings together the research and the university and laboratory resources listed below. Numbers after each section link to the references used. Sources consulted in November 2026.

1. 1.
   Skeletal Atavism: Del1 and Del2 test interpretation

   UC Davis Veterinary Genetics Laboratory · Test documentation

2. 2.
   Rafati et al. (2016) — Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies

   G3: Genes, Genomes, Genetics · Uppsala / SLU · Research

3. 3.
   Tyson et al. (2004) — Skeletal atavism in a miniature horse

   Veterinary Radiology & Ultrasound · Research

4. 4.
   Gene test reveals severe skeletal disease in Shetland ponies

   Swedish University of Agricultural Sciences · University resource

5. 5.
   OMIA 002013-9796 — Skeletal atavism in the horse

   University of Sydney · Online Mendelian Inheritance in Animals · University resource