Wednesday, July 31, 2013

700,000 year old horse DNA sequenced

Researchers have constructed the DNA from a 700,000 year old horse fossil from the far north west of Canada, which has challenged the accepted version of equine evolution.

Indeed, the widely accepted understanding of the horse's evolution is of a gradual increase in size from small forest-dwelling animals to the larger animals of today.

The fossil, found in the Klondike area of Yukon by  University of Alberta researcher Duane Froese, raised questions about this version of events. Not only was the  fossil considerably older than those commonly found in ice age deposits in the Yukon, Alaska and Siberia, it was also at least as large as many modern horses.

The layer of permafrost in which the fossil was found has been dated  by the volcanic ashes it contained as originating about 700,000 years ago. This puts it among the oldest known ice in the northern hemisphere.

An international research team, led by Ludovic Orlando, and colleagues at the University of Copenhagen, Denmark, managed to extract fragments of ancient DNA from the fossil. After several years work, they succeeded in constructing  a draft genome of the horse. This is by far the earliest genome sequence yet recorded. “Our data represent the oldest full genome sequence determined so far by almost an order of magnitude” they say in the report of their work, which is published in the journal Nature.

It is unlikely that the research would have been successful had the DNA not remained frozen over the past 700,000 years.

Having reconstructed the complete genome of the horse, the team compared it with DNA from a horse dating from the Late Pleistocene (about 43,000 years ago), and from five contemporary domestic horse breeds, a Przewalski's horse and a donkey.

By looking at differences between the DNA of the various horses, they could estimate the rate at which mutations occurred in the genetic code over time.

Analysis of differences between these genomes indicated the last common ancestor of all modern equids ( horses, zebras and donkeys ) would have lived about 4.0- 4.5 million years ago. This is about twice as far back than previously thought.

The results also indicated that Przewalski’s horse― an endangered subspecies native to the Mongolian steppes ― diverged from the lineage that gave rise to modern domesticated horses about 50,000 years ago.

More information at:

Tuesday, July 30, 2013

Genetics and tendon injury

Superficial digital flexor (SDF) tendon injury is a common cause of wastage in National Hunt Thoroughbred (TB) horses – leading to training and racing days lost and early retirement.

Recent research, funded by the Horserace Betting Levy Board, explored whether genetic susceptibility is a potential risk factor for SDF tendon damage in the TB racehorse.

The work, by Lucinda Tully and colleagues, compared the genotype of horses with and without SDF tendinitis in a case-control study.

Tully looked specifically at single nucleotide polymorphisms (SNPs) in seven genes that are involved in tendon structure, function, and remodelling or are known to be involved in Achilles tendinopathy (an equivalent condition in humans).

Genetic material for the study was derived from mane hair, or peripheral blood cells, collected from 270 horses with a history of SDFT strain, and 270 unaffected control samples, chosen at random from among the other horses on yards with affected cases.

The study's findings suggest that sequence variants in TNC and COL5A1 genes are associated with SDF tendinopathy in TB racehorses.

A SNP in COL5A1 significantly increased the odds of having SDF tendinitis. Racehorses having two copies of the COL5A1 COL5A1_01 variant allele were nearly 3 times more likely to have SDF tendinopathy than those homozygous for the wild-type allele.

Conversely , a SNP in the TNC gene was associated with significantly lower odds of SDFT injury. Racehorses heterozygous for the TNC BIEC2-696469 polymorphism were less likely to have SDF tendinopathy than those with two copies of the wild-type allele.

The research team conclude that variants in the TNC and COL5A1 genes are associated with SDF tendinopathy in a population of UK trained NH TB racehorses.

They suggest that further studies in a larger group of horses are needed to determine the significance of these findings at the population level.

In the future it may be possible to use genetic markers to identify horses at risk of SDF tendinopathy.

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Monday, July 29, 2013

Fishing for chips

Not only is chipping far more reliable for marking horses than traditional methods of branding, it also causes far less injury to the animals, according to research led by Christine Aurich at the University of Veterinary Medicine, Vienna.
With very few exceptions, it is now mandatory within the European Union to mark horses by means of transponders. Nevertheless, some sport-horse registries oppose the use of microchips because they believe that the rate of identification failure is unacceptably high.
Thus far, no systematic examinations to see whether chips are easy to decode, have been conducted. So Manuela Wulf in the group of Christine Aurich at the Vetmeduni Vienna has examined the readability of microchips in more than 400 horses. She tested each of the chips with three different scanners. The scanners differed in diameter and field strength. Both sides of the animals’ necks were tested.
The “best” scanner (equipped with a digital signal processing function that filters interfering signals) detected and read all chips correctly when it was placed on the side of the neck where the chip was implanted, and located nearly 90% of the chips even when it was on the other side of the neck. The other two scanners performed considerably less well, producing correct reads in around 90% of the cases when on the same side of the neck. On the opposite side of the neck, however, the success rate fell to between 20-25%.
It never took more than 25s to detect the microchip , and with the most effective scanner it took a maximum of 5 seconds. So the most effective scanner not only detected all the microchips , it did so in the shortest time.
As Wulf puts it, “It is important that the scanners find and read the chips correctly in every case. We can only recommend the top-of-the-range scanner, which should ideally be placed on the side of the horse’s neck where the chip was implanted.” However, Aurich adds, “Even the lowest quality scanner we tested, performed much better than traditional branding methods of horse identification.”
The major objection to the use of branding relates to the pain and long-term damage it inflicts on the animals. Wulf and her colleagues thus investigated whether the use of microchip markers was any better. She looked closely at the site of chip implantation in 16 horses of nine different breeds and of various ages that had been submitted to the Vetmeduni for post mortem examinations. In the vast majority of cases, the chips seemed to have caused absolutely no ill effects. Two animals that were moderately affected had probably only been chipped recently and the wound had not yet had time to heal.
Aurich sums up the findings, “Not only is chipping a far more reliable method for marking horses than traditional methods of branding, we also found that it causes far less injury to the animals.”
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Tuesday, July 23, 2013

Does the human voice calm horses?

In addition to being warned to move slowly around horses, many new riders are also instructed to speak in a soothing tone, in the belief that it can make the animal calm. A recent study presented at the 2013 conference of the International Society for Equitation Science investigated whether such advice actually had a beneficial impact on the horse.

According to Katrina Merkies of the University of Guelph, “Anecdotally, we know that horses respond better to calm and soothing tones, so our hypothesis is that speaking in a calm and pleasant voice will inspire calm behaviour in a horse.”

Merkies and other researchers from both the University of Guelph, Ontario, Canada and Agrocampus Rennes, Rennes, France set out to discover whether emotional tone and pitch of voice did have any effect on horses. For the study, eight draft horses were individually assessed in a 10 m round pen. Each horse was released into the pen, and baseline behaviour and heart rate (HR) readings were taken over a five minute period. Behaviours scored included: gait; head height position; ear and body position relative to the human.

After establishing baselines, a familiar human approached the pen, and one of four recorded voices was played for a 10 second duration: PL – pleasant voice low tone; PH – pleasant voice high tone; SL – stern voice low tone; SH – stern voice high tone.

Researchers found that the horses maintained the lowest head position when no human or sound was present, but all elevated their heads in the presence of a human or sound. The playing of a pleasant tone resulted in the horses positioning their bodies toward the human. While there was no treatment effect on ear position, the horses did orientate their ears more toward the sound if the human was present.

Horse HR did not increase solely in the presence of the human, but it did increase coupled with sound, with SL in particular resulting in the greatest effect. Results would indicate that fewer signs of behavioural distress are observed when a human speaks to the horse in a pleasant, low tone rather than a stern tone.

We’ve shown that horses do in fact display different physiological and behavioural responses to different tones and voice. So horses are able to discriminate between different tones or qualities of voice.”

Research often creates more questions than it answers, and based on the results obtained, additional research may be required: “However, it’s not clear if the horse is interpreting or responding to the tone of voice alone, or if it’s looked at in combination - both tone of voice and the human’s body language. Which is the more salient clue to the horse? That certainly warrants further study.”

Monday, July 22, 2013

Improving management of wild horses and burros

How to manage the feral horses and burros of the western United States has been the subject of heated debate for some time.

A recent scientific review found that the current practice of removing free-ranging horses is counter-productive. The review concluded that the current approach promotes a high population growth rate, and that maintaining horses in long-term holding facilities is both economically unsustainable and contrary to public expectations.

Most free-ranging horse populations are growing at 15 percent to 20 percent a year, meaning these populations could double in four years and triple in six years.

With no intervention by BLM (the U.S. Bureau of Land Management), the horse population will increase to the point of self-limitation, where both degradation of the land and high rates of horse mortality will occur due to inadequate forage and water. In addition, periodic droughts, many of them severe, in the western public lands cause immediate and often unpredicted impacts.”

The report noted that there is little, if any, public support for allowing such harm to come to either the horse population or the land itself. However, the current removal strategy used by BLM actually perpetuates the overpopulation problem by maintaining the number of animals at levels below the carrying capacity of the land. Although this protects the rangeland and the horse population in the short term, it results in continually high population growth and exacerbates the long-term problem.

To manage horse populations without periodic removals, the committee concluded that widespread and consistent application of fertility control would be required.

Here's a video in which Committee chair Dr. Guy Palmer of Washington State University shares key findings about using science to improve the BLM wild horse and burro program.

The full report is available online.