Science News

[Steve]

http://www.the-scientist.com/blog/display/56279/

Researchers have delved back further than ever into the genetic history of humans, and found that the ancient population that gave rise to modern humans may have been nearly twice as genetically diverse than humans today, according a study published this week in Proceedings of the National Academy of Sciences.

Scientific reconstruction of a Homo erectus

Image: Wikimedia commons,

Lillyundfreya

While most studies on the genetics of ancient humans have focused on the last half million years, this study looks at particularly old areas of the genome, allowing the researchers to look at the more distant past, said molecular geneticist

Prescott Deininger of the Tulane Cancer Center in New Orleans, LA, who was not involved in the research. "This [study] is a little window to look back a little bit further," he said.

When examining genetic diversity, scientists often use a measure called the effective population size, which describes how big a population has to be to carry its level of genetic diversity. Modern humans have an effective population size of about 10,000 -- a relatively low level of diversity. Chimps and gorillas, for example, both have effective population sizes of greater than 20,000. This estimate of 10,000 has been regarded as stable for about 200,000 to 400,000, maybe "as far back as a million" years, said population geneticist Chad Huff of the University of Utah. But looking deeper into human history, Huff and his colleagues determined that before about 1.2 million years ago, the effective population size of our ancestral populations was actually around 18,500.

The researchers gained their insight by looking at mobile elements -- bits of DNA that can insert themselves into the genome -- known as Alus. Occurring in an estimated 1 in 21 to 22 births, Alus, which are about 300 base pairs long and the most abundant mobile elements in the human genome, insert into the genome at a rate at least three orders of magnitude rarer than the single nucleotide mutation rate. Because of this rarity, any particular Alu is likely to be much older than an average mutation. Furthermore, because the DNA just outside of these Alu inserts is closely linked to the mobile element, that surrounding DNA is also likely to be relatively old.

The researchers can thus "use these elements they call molecular fossils to dig down through the strata of the human genome and arrive at some conclusions about human origin," explained molecular biologist John Goodier of the University of Pennsylvania School of Medicine, who did not participate in the research.

Comparing these ancient areas of the human reference genome with the genome of a particular individual -- that of genomics guru Craig Venter, as it happens -- the team found that much of the DNA surrounding the Alu inserts was older than would be expected if the effective population size had always been 10,000. Based on their results, they concluded that the effective population size had been nearly double its current level before about 1.2 million years ago. While this is clearly a substantial difference, Huff said he was actually surprised the diversity of the ancient population wasn't even greater. "It is unusual that our [effective population size] is so small for so long," Huff said, especially given the success of our species. If our ancestors "really did live on three continents," he added, "you would expect a much larger [effective] population size."

"I also wouldn't have expected our [effective population size] to be 10,000 for so long," Huff added. The small effective population size of modern humans was attributed to a bottleneck event that eliminated a great deal of ancient diversity sometime in the last 400,000 years. But if humans have maintained such low diversity for more than a million years, "I'm wondering if maybe it hasn't been [a] series of bottlenecks or if it's always been relatively small," Huff said.

While the exact mechanisms shaping the diversity of ancient humans will undoubtedly require further research, this study makes a good start by identifying a potential tool that can be used to see further back into our history, Deininger said. "I'm always a little bit impressed by how sophisticated some of these population biology studies can be in terms of unraveling ancient details," he said. "It's fun to look at the dynamics of our history."

Related stories:

·

On Human Diversity

[24th October 2005]

·

The 0.1% Portrait of Human History

[30th June 2003]

·

Genetic Variation Illuminates Murky Human History

[24th July 2000]

[Monah]

This is facsinating stuff. I've had to study it and there were not only many types of human caucasian, asian etc. but other 'peoples' all at the same time. They used to think they were around during different periods, but they were here with 'us' and it appears that we killed them off in one way or another

As the world shrinks, we will become less diverse, pity.

[Steve]

Oh well at least then they wont need to blame chemicals and pollution or climate change for in breeding depressions.

[bet hargreaves]

Oh well at least then they wont need to blame chemicals and pollution or climate change for in breeding depressions.

Can I mention about the Bateson Report here in Britain and the In-Breeding Discussions taking place here at the moment?

Whether this fact is well known by Geneticists about our Cavalier King Charles Spaniel Breed I don't know.

In the 1930's the Cavalier Breed was created by Mother being mated to Son ,Father to Daughter , Brother to Sister.,

Unfortunately for the Cavalier Breed ,World War 2, started in 1939, and to keep the Cavalier Breed going, this same type of Matings were taking place,this was on top on the previous Matings ,I have described just 4-5 years previously.

In fact one Cavalier Bitch was mated to her Son ,and had 7 Litters ,39 Puppies

There is one Cavalier Pedigree with a 44.6% COI.

There was futher In-Breeding in Cavaliers in the 50's -60's - 70's and 80's.

Grand-Mother to Grand-Son ,Grand- Father to Grand -Daughter has been normal Breeding Practice by Cavalier Breeders for around 50 years.

Is it possible that the Cavalier Breed is different from other Dog Breeds ,in that their In-Breeding took place with- in such a short Space of Time.?

Mrs A. Pitt ,the Founder of the Cavalier Breed,wrote in a UK CKCS CLUB Magazine, in 1957, that because of that In-Breeding no Thought had been given by Cavalier Breeders as to the Future of Cavaliers.

With the two Serious Health Problems now afflicting Cavaliers ,are some of them now paying the price of their In-Bred Back-Ground?

Bet Hargreaves.

[GeckoTree]

The very fact we had racial prototypes and now races says so, I cant believe a gene study needed to point it out.

if someone wants to look at it in a micro scale just look at the diversity of pit cairn islanders to see howit happens on a world wide scale.

[mita]

This is facsinating stuff. I've had to study it and there were not only many types of human caucasian, asian etc. but other 'peoples' all at the same time. They used to think they were around during different periods, but they were here with 'us' and it appears that we killed them off in one way or another

'Tis indeed fascinating. I just read Traces of a Distant Past in the Scientific American, July, 2008. Their summary:

DNA from contemporary humans can be compared to determine how long an indigenous population has lived in a region.

The latest study surveys swathes of entire genomes & produce maps of human movement across much of the world. They also describe how people's genes have adapted to changes in diet, climate & disease.

Even more fascinating, added info:

The genetic record of human history may be bolstered by simply paging thro' a phone book for certain names.

A team led by Mark A, Jobling of the Uni of Leicester reported last year that men in north-western England with surnames that had been used there before 1600 had high levels of Scandanavian ancestry on their Y chromosones, a legacy of a Viking heritage.

Edited January 27, 2010 by mita

[asal]

Oh well at least then they wont need to blame chemicals and pollution or climate change for in breeding depressions.

:rofl: :rofl: :D :D :D :D

course not they will blame it on the "unethical" breeders/ parents of the next human generation surely?

[asal]

rather a long time ago, i wanted something that was not in existance in australia. a black guinea pig.

that bred true.

not a big ask u would think? but nope no such critter.

so i set out to create them. the gene base was 3 females and 2 males. 1 male was discovered to carry a lethal. so, to delete all his offspring would have me down to one foundation male, thanks to a genetist friend he mapped out for me how to delete the lethal by test mating any of his male descendants to females that had produced a lethal an no male that failed the test was kept only clear males used. in theory it should have taken minimum of 12 tested generations of males to eliminate the gene, luckily it was gone in 6.

one female was so outstanding she was bred to her son, that son to her and that son to her in all 4 "generations" all with the same mum. n better every time. no lethals surfaced, although a lilac gene showed up along with a chocolate one as well creating another two new colours.

the resulting progeny took out supreme champion at the initial interstate champion show.

15 years later and an awful lot of guinea pig generations later these descendants took out champion and supreme against the now dozens of imports since allowed into the country.

yet i was told by the successfull exhibitors that they found to add the imported lines or any other outcross resulted in losing quality. so the winners and champion were totally traceable solely back to those 5 animals.

a line that had at that stage went back 21 years to the original 5?

now some 27 years later i learnt they still exist.

so thats 49 years n still producing well with no lethals showing up

pity dog breeding cant achieve the same results. n no dna tests available in them thar days to take shortcuts

but it does take something thats pretty hard and very upsetting to do. totally ruthless in selection n culling.

an wont pretend there wernt tears on the way.

doubt i would have stuck it out without the guidance of old school breeders and my genetics friend now retired and known world wide for his genius in oat breeding research. he is the real brains behind them.

Edited January 27, 2010 by asal

[asal]

found this

"

Mr ADRIAN PICCOLI (Murrumbidgee) [7.49 p.m.]: I rise to speak about the Department of Primary Industries agriculture station at Temora. I refer particularly to the oat breeding program conducted at the field station at Temora. There has been some discussion about the future of the program since the current oat breeder, Mr Glen Roberts, announced his retirement a little while ago. Concerns were expressed that the winter breeding trials might be terminated at the end of 2008 to coincide with his retirement, and that has been pretty well confirmed. The Temora Agricultural Research and Advisory Station has bred high-quality wheat and oat varieties for the State's growers for over 75 years and it is a major component of New South Wales Agriculture's bred wheat program.

The ravages of the drought that we have endured for many years mean that it is now essential that varieties continue to be bred and trialled at Temora so that they can be refined not only for conditions that prevail at Temora but for those in the whole of the Western Riverina. With oats considered one of the healthiest cereals available to combat cholesterol, it seems unbelievable that the department is content to see oat breeding cease at Temora. The breeding program there is the only publicly funded program in New South Wales. The Temora Shire Council and the community have sought advice on the continuation of these programs. There is a feeling that it is essential that these crops continue to be bred and trialled at Temora to ensure that varieties are available to provide the best option for the farming community in Temora shire and across the State.

The Department of Primary Industries a few days ago issued a statement to say that the Temora Agricultural Research and Advisory Station would not be closed. Whilst I appreciate that it will not close for the time being, the value of stations such as Temora is dependent on the activities that are undertaken there. If we do not have an oat breeding program there and other grain breeding programs throughout the grain belt in Western New South Wales we will lose a great asset that this State has had for well over 100 years. If we are not breeding grains in the areas in which they are to grow and are instead relying on trials conducted in greenhouses in Canberra, the United States and Europe we will not get the varieties we need that are particularly relevant to our weather conditions. The varieties of grains that grow well in central and northern New South Wales do not necessarily grow well in the Riverina or in Victoria. We need site-specific trials and breeding of these different grain varieties.

With all the talk about world food shortages I think it is very unfortunate that over the past couple of decades grain breeding and the emphasis on research and development in agriculture have declined, particularly in western New South Wales. We will come to regret the downgrading of facilities at places such as Temora, Yanco and Deniliquin—two are in the Murrumbidgee electorate and Deniliquin used to be in my electorate—particularly Yanco with the TAFE training that was undertaken there, because of the world food shortages and the changes in climate being experienced across New South Wales. I can only call on the Department of Primary Industries to reconsider the funding cuts to all the agricultural research stations, but particularly the three in my electorate. I call on the department to reinstate some of the breeding programs so that we can continue to support our farmers to be the world's best in the growing and production of wheat and other grains.

Last modified 20/08/2008 16:10:15 :"

"

REGIONAL BREEDING PERSPECTIVES - AUSTRALASIA

Robyn McLean (i), Keith Armstrong (ii), John Oates (iii), Glen Roberts (iv), Leonard Song (v) and Pamela Zwer (vi)

(i)Agriculture Western Australia, Locked Bag 4, Bentley Delivery Centre, Western Australia 6983 Email: [email protected]

(ii)Crop and Food Research, Private Bag 4704, Christchurch, New Zealand. Email: [email protected]

(iii)University of Sydney, Plant Breeding Institute, Private Bag 11, Camden, NSW 2570 Email: [email protected]

(iv)NSW Agriculture and Fisheries, Agricultural Research and Advisory Station, PO Box 304, Temora, NSW 2666 Email: [email protected]

(v)Queensland Department of Primary Industries, Leslie Research Centre, PO Box 2282, Toowoomba, Queensland 4350 Email: [email protected]

(vi)SARDI, GPO Box 397, Adelaide, South Australia 5001 Email: [email protected]

Now is a time of considerable change in breeding programs generally throughout Australasia, and oat breeding is no exception. We are facing changes in research funding arrangements, breeding directions and priorities, changing market and end user quality requirements, and the integration of new breeding technologies into our programs.

It is also a time of exciting new prospects and opportunities to be seized by breeding programs. We have the opportunity to use new tools, such as marker technology, genetic engineering, doubled haploids, and others to improve our breeding programs and our ability to select superior lines. It is also a time in Australasia when we are starting to make significant advances in defining oat quality through our collaborations with end users and exporters. "

somehow i doubt the vets who have decided they know best and are getting so much media attention have a miniscule of the genetic knowledge of these people mentioned above, these are the real people dog breeders should be seeking for knowledge i think?

Edited January 27, 2010 by asal

[asal]

probably offended everyone insuinuating any connection between a furkid and an oat

[Jed]

That's really interesting about the guinea pigs, asal. Maybe you should send it off as scientific research to Sydney Uni?

The kids had guinea pigs, and due to the inability of the kids to correctly sex them (and my not checking), added to their unbelievable libidos, and a lack of morals, we had about 5 generations of inbred guinea pigs - all very hale and hearty!!

Bet Hargraves

Can I mention about the Bateson Report here in Britain and the In-Breeding Discussions taking place here at the moment?

Whether this fact is well known by Geneticists about our Cavalier King Charles Spaniel Breed I don't know.

In the 1930's the Cavalier Breed was created by Mother being mated to Son ,Father to Daughter , Brother to Sister.,

Unfortunately for the Cavalier Breed ,World War 2, started in 1939, and to keep the Cavalier Breed going, this same type of Matings were taking place,this was on top on the previous Matings ,I have described just 4-5 years previously.

In fact one Cavalier Bitch was mated to her Son ,and had 7 Litters ,39 Puppies

There is one Cavalier Pedigree with a 44.6% COI.

There was futher In-Breeding in Cavaliers in the 50's -60's - 70's and 80's.

Grand-Mother to Grand-Son ,Grand- Father to Grand -Daughter has been normal Breeding Practice by Cavalier Breeders for around 50 years.

Is it possible that the Cavalier Breed is different from other Dog Breeds ,in that their In-Breeding took place with- in such a short Space of Time.?

I would be interested in knowing the inbred lines of cavaliers.

When the breed was originated, it is generally believed that Welsh spaniels, cockers, the longer faced and flatter headed king charles spaniels and papillons were used to create the breed. It has been speculated that Ann's Son was sired by a Papillon, and indeed in a lot of photos he does resemble a Papillon (Phalene). That is hardly in breeding. That's outcrossing to the nth degree.

Amice Pitt, the breeder of Ann's Son who was the model for the standard was a very good breeder, with a lot of experience with Chow Chows previously.

In England during the war, it is well known that many dogs were destroyed as part of the war effort, and at the end of the war, when breeding resumed, some breeds were left numerically lean, and were closely mated to each other to keep the breed going. No frozen semen then, and no imports. Most breeds seem to have survived that quite well, and I cant see why Cavaliers would have been the only breed to have detrimental resuts from this, particularly considering the slew of breeds used to create the breed less than 20 years previously. The genetic pool would have been huge, I imagine, with all those breeds.

Grandmother x grandson, g/father x g/daughter etc is a valid way of setting a line in every species, and also a valid way of not allowing detrimental recessives into a line. Unless the dogs used had major faults, there should be no problems. because no detrimental genes are being introduced. And the pedigrees that I have researched of major dogs over the years don't show any degree of inbreeding.

A dog having a COI of 44.6% tells us nothing. Is he a good dog, or a bad dog? Was he bred from well conformed and healthy parents, or unhealthy dogs who were badly conformed? Is he healthy himself? These are the important questions, not what his COI is. Is he used at stud, or is he a pet?

COI is a tool, not a definitive answer.

The pedigree of Ch Alansmere Aquarius is basically an outcrossed pedigree, with not one dog the same to the 5th generation. After that, there is little influence. Most of the pedigrees of "good" dogs of the past I have read are similar. Some have a couple of crosses of Daywell Roger as the GG G/father, which is acceptable in all breeding programs, such as Crisdig Merry Matelot, who has 2 crosses of D. Roger, giving him 12.5% of Daywell Roger in his pedigree, which is hardly inbred. Most of the better known dogs of days past show similar pedigrees.

A very important line of Welsh Mountain ponies, which has survived the test of time was created by a mother / son mating, and produced some of the best pones of the day, which bred on. I am fortunate enough to own a mare who is a descendant of a son of that mating. She is nearly 36, is strikingly beautiful, and has never been ill for a second in her life. I owned another pony who was very closely line bred to a luminary of the breed, long dead when he was produced. On the 10th line of his pedigree, there was only one stallion. I am not too sure what the % of that cross was, but the actual results in terms of the horses produced, were outstanding.

It's not the closeness of the cross, it is the quality of the stock used in, and produced by, that cross which is important.

I would also suggest to you that in the case of the Cav. bitch mated to her son that from 39 pups, if there was a recessive gene in the line, it would have surfaced in one of those pups. I believe 40 pups is the scientifically accepted number to check for a recessive gene.

If it didn't, that is a good test case for the line being free of nasty recessives. Only a check of the 39 dogs and their health status would be important, not the cross itself. If none of those dogs were affected by anything, something worthwhile has been achieved. If not, something more worthwhile has been achieved.

We can be upset about line breeding, but to understand it, we need not just know the pedigree, but the dogs themselves. Conversely, there is no point in going for a totally outcrossed line, unless you know the health status of the dogs. With outcrossing, you continually introduce recessive genes into a line, and if you continue to outcross, it can take some time for those genes to surface, but as soon as a dog is mated to a carrier of the same recessive from another line which may be totally unrelated, you have a problem. and you have no way of backtracking to find where the gene came from, because the pedigree is so scrambled.

However, it is all speculation. Until there is a known mode of inheritance for MVD, no amount of speculation will change anything. Independent university studies show Syringomyelia tends to be found more often in the smaller breed dogs such as Pomeranians, Chihuahuas, Maltese and Poodles as well as Cavalier King Charles Spaniels, and it affects humans and cross bred dogs as well.

I don't believe there is any definite proof one way or another that syringo is hereditary, and speculation may lead to a great deal of harm being done.

With MVD, it is presumed to be hereditary, and breeders tend to check hearts to breed away from it, but with syringo, it is only believed that dogs with the chiari malformation are more at risk of producing dogs with syringo. Dogs who are clinically positive are not always affected, and the cysts in some dogs regress for no known reason, and I understand that dogs without symptoms of syringo, and without the chiari malformation, are siring affected pups.

This either means syringo is not hereditary, or it is due to a recessive or an autosomal recessive,, and test matings should be carried out with affected dogs to try to ascertain the mode of inheritance if there is one, as "scientific study" does not seem to be producing any results which breeders can use to avoid syringo, despite breeders from all over the world having poured an unconscionable amount of money into research.

Edited January 29, 2010 by Jed