Genome of Extinct Human Reveals Brown-Eyed Girl

(LiveScience) - The genome of a recently discovered branch of extinct humans known as the Denisovans that once interbred with us has been sequenced, scientists said today (Aug 30).

Genetic analysis of the fossil revealed it apparently belonged to a little girl with dark skin, brown hair and brown eyes, researchers said. All in all, the scientists discovered about 100,000 recent changes in our genome that occurred after the split from the Denisovans. A number of these changes influence genes linked with brain function and nervous system development, leading to speculation that we may think differently from the Denisovans. Other changes are linked with the skin, eyes and teeth. "This research will help [in] determining how it was that modern human populations came to expand dramatically in size as well as cultural complexity, while archaic humans eventually dwindled in numbers and became physically extinct," said researcher Svante Paabo at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. Future research may turn up other groups of extinct humans in Asia "in addition to Neanderthals and Denisovans," Paabo told LiveScience.

Although our species comprises the only humans left alive, our planet was once home to a variety of other human species. The Neanderthals were apparently our closest relatives, and the last of the other human lineages to vanish. [10 Mysteries of the First Humans] However, scientists recently revealed another group of extinct humans once lived at the same time as ours. DNA from fossils unearthed in Denisova Cave in southern Siberia in 2008 revealed a lineage unlike us and closely related to Neanderthals. The precise age of the Denisovan material remains uncertain -- anywhere from 30,000 to 80,000 years of age. "The Denisovan genome is particularly close to my heart, because it was the first time that a new group of extinct humans was discovered and defined just from DNA sequence evidence and not from the morphology of bones," Paabo said.

Denisovan genes unzipped
Now, based on only a tiny sample of genetic material from a finger bone, scientists have sequenced the complete genome of the Denisovans (pronounced deh-NEESE-so-vans), as they are now called. To make the most of what little genetic material they had, the researchers developed a technique that unzipped the double strands of DNA in the bone, doubling the amount of DNA they could analyze. This enabled them to sequence each position in the genome about 30 times over, generating an extremely thorough genome sequence. [See Photos of Denisovan Fossils] "We have very few errors in the sequences, even less errors than we often have when you sequence a person today," Paabo said. "With just a few technical reservations, there is actually today then no difference in what we can learn genetically about a person that lived 50,000 years ago and from a person today, provided that we have well-enough preserved bones."

Comparing the Denisovan genome with ours confirmed past research suggesting the extinct lineage once interbred with ours and lived in a vast range from Siberia to Southeast Asia. The Denisovans share more genes with people from Papua New Guinea than any other modern population studied. In addition, more Denisovan genetic variants were found in Asia and South America than in European populations. However, this likely reflects interbreeding between modern humans and the Denisovans' close relatives, the Neanderthals, rather than direct interbreeding with the Denisovans, researchers said.

Denisovans began to diverge from modern humans in terms of DNA sequences about 800,000 years ago. Among the genetic differences between Denisovans and modern humans are likely changes that "are essential for what made modern human history possible, the very rapid development of human technology and culture that allowed our species to become so numerous, spread around the whole world, and actually dominate large parts of the biosphere," Paabo said. Eight of these genetic changes have to do with brain function and brain development, "the connectivity in the brain of synapses between nerve cells function, and some of them have to do with genes that, for example, can cause autism when these genes are mutated," Paabo added.

What makes humans special?
It makes a lot of sense to speculate that what makes us special in the world relative to the Denisovans and Neanderthals "is about connectivity in the brain," Paabo said. "Neanderthals had just as large brains as modern humans had -- relative to body size, they even had a bit larger brains. Yet there is, of course, something special in my mind that happens with modern humans. It's sort of this extremely rapid technological cultural development that comes, large societal systems, and so on. So it makes sense that, well, what pops up is sort of connectivity in the brain." The fact that differences are seen between modern humans and Denisovans in terms of autism-linked genes is especially interesting, because whole books have been written "suggesting that autism may affect sort of a trait in human cognition that is also crucial for modern humans, for how we put ourselves in the shoes of others, manipulate others, lie, develop politics and big societies and so on," Paabo said.

The genetic diversity suggested by this Denisovan sample was apparently quite low. This was probably not due to inbreeding, the researchers say -- rather, their vast range suggests their population was initially quite small but grew quickly, without time for genetic diversity to increase as well. "If future research of the Neanderthal genome shows that their population size changed over time in similar ways, it may well be that a single population expanding out of Africa gave rise to both the Denisovans and the Neanderthals," Paabo said.

Intriguingly, comparing the X chromosome, which is passed down by females, to the rest of the genome, which is passed down equally in males and females, revealed "there is substantially less Denisovan genetic material in New Guinea on the X chromosome than there is on the rest of the genome," researcher David Reich at Harvard Medical School in Boston told LiveScience. One possible explanation "is that the Denisovan gene flow into modern humans was mediated primarily by male Denisovans mixing with female modern humans," Reich said. "Another possible explanation is that actually there was natural selection to remove genetic material on the X chromosome that came from Denisovans once that entered the modern human population, perhaps because it caused problems for the people who carried it."

These current Denisovan findings have allowed the researchers to re-evaluate past analysis of the Neanderthal genome. They discovered modern humans in the eastern parts of Eurasia and Native Americans actually carry more Neanderthal genetic material than people in Europe, "even though the Neanderthals mostly lived in Europe, which is really, really interesting," Reich said. The researchers would now like to upgrade the Neanderthal genome to the quality seen with the Denisovan genome. The genetic techniques they used could also be employed in forensic investigations, and in analyzing other fossil DNA, said researcher Matthias Meyer, also at the Max Planck Institute for Evolutionary Anthropology.
Article originally Published in the Journal Science. Submitted by Village. Thank you!


RBTC said...

this is really amazingly interesting - thank you !!!

Jamie Delaney said...

I <3 anthropology!!!! Thank you!

Village said...

If anyone is interested in this, I encourage you to read the entire article, as this is just a portion of it.

I thought it was groundbreaking on the origins of autism. The article suggests that austism related genes were present LONG before our intellectual jumps. It's also interesting to note that the genes were passed down through the xx chromosome, which to my mind goes a long way toward explaining why mostly boys get it, and why the age of the father matters. But the elephant in the living room is, if these genes have been present all along, WHY ARE THEY BEING EXPRESSED NOW?

Years ago when autism was making a surge, I reviewed the raw data on the number of cases per year. I came away from that believing 1994 was the year the cases began expanding expotientially. Several years later I stumbled across a graph outlining when different foods were genetically modified. From that graph, I learned that the first genetically modified foods entered the American food supply chain in 1994.

Personally, I have long suspected that austism was DNA based, when people were laughing at such a notion. But it was the only thing that made sense to me for such a profound syndrome. But genes have to be "switched on", so what is triggering the austism genes that have remained dormant for so long, which this article suggests is a VERY long time? I find it hard to believe it is just the age of the fathers, because old men have been having children with young mothers since the beginning of time.

RBTC said...

and you are a layman? lol

do you think vaccinations play a part

MissMannah said...

RBTC, please tell me you're joking.

Village, I am not nearly as smart as you are. I will readily admit I couldn't comprehend a lot of that article so I won't be reading the longer one. But I do have a question for you: do you believe people have always had autism (as seems to be suggested) but because of more thorough psych evals now, we're only just diagnosing so many cases? Perhaps people who were truly autistic years ago were written off as antisocial or rude?

RBTC said...

mannah - i do not want to even get into a direct disagreement with you because the last time you disagreed with me and vice versa it resulted in a blow up on here

village has presented some really really good research - let's enjoy it not criticize it

thank you again village - i really disagree with genetically screwed up food on many levels - i agree with you

i am also now reading in the newspaper more detailed info about what you are helping us learn about - obviously your parents are teachers and so are you ;)

RaleighWorld said...

Too long; Don't read.

Jamie Delaney said...

BIG GMO protest NATION WIDE on Sept 17th! Look up Occupy Monsanto and be there if you care!!! And THANKS VILLAGE! Excellent !

EastBay Nanny

i seriously loathe you... said...

RBTC can you ever just STFU? Mannah was asking Village a question. It isn't YOUR place to answer it NOR comment on it. Asshat.

unejeunefille said...

RBTC is doing what she claims she hates other posters doing. Following them around from post to most starting drama.

I assure you she will claim she is just defending someone.

She loves the attention and the drama. I suggest we all ignore her from now on and she'll find another blog to troll.

RBTC said...

hey - all you guys - have a very nice day - and i am not "joking" lol !

Village said...

RTBC I don't like to speculate. It's too important an issue. Until we map the genes of autism and find the "on switch" genes, we have no way of knowing why long dormant genes have now awakened.

I have already speculated I think the answer lies in GM food. BIG AGRA is splicing DNA pesticide genes (poison that kills things) into the food we eat. No good can come from that. And just to be clear, when we eat these DNA pesticide genes, they get into OUR DNA. And that doesn't address the massive amounts of antibiotics we are consuming through our food.

Could the presence of the autism genes coupled with the ingestation of pesticide DNA coupled with the administration of a large number of vacs close together, coupled with who know what else be the culprit? It's all speculation. But remember, 99% of kids who get vacs don't get austism. And in research, you have to get above 15% to begin to find a result, so 99% is out of the ballpark. It can't be vacs alone. BUT I'M SPECULATING. NO ONE KNOWS.

Vi said...

MissMannah. No, I do not. And don't confuse the presence of the genes with the expression of the genes. It's two entirely different things. 100% of us carry the austism gene. 1% of us present with the spectrum, up from .001 not that long ago.

And I don't think I'm smarter that you. I just read a lot.

RBTC was making a joke. That's dangerous around here. Trust me. I know.

Village said...

Again, spell correction got me. Now I'm Vi. Village

Village said...

NOT A TEACHER. I would have to kill myself first. I worship excellent teachers, but couldn't be one.

I want to speak to GM food, and more importantly how I avoid it. I eat NO processed food. ALL processed food in America is GM. I eat no cows or pigs. I eat organic fruits and veggies, free range, antibiotic free chickens, and European chocolate. USA chocolate is at least 15% wax, and GM. If I want a cookie, I get them from Germany or Belgium.

I no longer eat seafood. When a prominent commercial fisherman said our choice in seafood is between radioactive or oil laden, I quit. The oceans are poisoned. (There's that word again.)

RBTC said...

thank you village - there is a movement to have all GM food have a label - it's a crime it does not yet

Village said...

100% of boys carry the gene. 100% of boys carry the gene, not girls. A main point in the article was it's carried on the xx chromosome.


MissMannah said...

RBTC, I was asking both you and Village legitimate questions. I read your post asking about autism being linked to vaccinations and I was horrified. How am I to know that you are joking unless I ask?

Village, now I'm totally confused. You just said that 100% of boys carry the gene but that it is carried on the XX chromosome. Doesn't that contradict each other?

I also agree that all genetically modified foods should be required to carry a warning label. I don't know if GMs are linked to autism or any other brain disorders, but I think it is very apparent that they can cause endocrine disorders.

Village. said...

I need a freakin' editor. Xy boys, xx girls. I know better. Good catch. I was on my way to correct. All great minds.

OceanBlue said...


Dod you happen to be a scientist in a previous career life?

Village said...

One more thing. I'm not a teacher. See?

The article suggests that the austism genes are only on the boy chromosome, xy. Just because they did not find the autism genes in the girls where they found it in the boys doesn't mean that it won't be found somewhere else in the girls. It just means THESE autism genes aren't found in girls at THIS location. And that doesn't address the undisclosed location of the switches, or what is throwing them.

Prader Willi is a devastating syndrome that can range from constant hunger and lack of puberty, to profound mental retardation. It has been discovered that both parents can pass on Prader Willi, with one parent passing the mild forms, while the other parent passes the profound spectrum.

Maybe my slip up was my subconscious. I don't think it's just boys. I think we are going to find that while the boys carry a broad spectrum of genes, the girls may carry a fraction of those in number, but more profound genes. We'll see. (Austism is 80/20, boy/girl. Symptoms in boys can range from correctable to non verbal. Girls tend to have the more serious syndrome. Lab scientists sometimes don't see clinical details through a microscope.) I also suspect, while the boy autism genes are mind blowingly old, the girls may get theirs, if they get them at all, much later. (The older the DNA, the busier it is as it has been mutating longer.)

A huge portion of the genome study at one point was trying to map the genes from mom and the genes from dad. I could picture the scientists tying pink and blue ribbons to the genes as they were sourced.

RBTC said...

our genes are relatively new, we apparently bottle-necked about 30,000 years ago, as opposed to monkeys who have much older dna

why are there SO many mutations in us? compared to other animals

( so if you are not a teacher you are a "help people learner" lol)

Village said...

Money honey. I worked for hedge funds for 10 years out of college, then started my own company and sold caviar for 28 years. I retired this year.

Science is an avocation for me.

(Just for the record, there was a time when hedge funds actually underwrote their deals, and didn't just criminally steal. Imagine that.)

Village said...

RBTC There is nothing correct in your statement. Our oldest genes are 4.5 million years old. We are descended from lizards, when they branched from birds. Bottle neck?? 30,000?? I don't know what you could mean. And great apes R Us, without the 8 brain leaps, and the hair loss gene we acquired 110,000 years ago. Great apes have close to 99% of our DNA. (Not monkeys: they are not primates.)

Wanna know how we figured out when we lost our body hair? The genome of body lice is 110,000 years old. No exposed skin, no body lice. A girl scientist did that research. It was considered a major find.

Why do you think there are more mutations in us than animals? Much, much, much to the surprise of scientists, our genome is about 30,000 genes, as is just about everything else. Scientists expected us to have about 100,000, and lesser animals and plants to have lesser, but that wasn't the case. There isn't a huge gap in genomes. Don't quote me, but I think a carrot has 80% of our genome. Maybe not a carrot, but something equally as surprising. A pig is in the 90s. That's why pigs valves can be successfully implanted in humans.

DNA discoveries are being made daily. It sounds like you just might not be up to date. I know I'm not.

MissMannah said...

This is just my hypothesis, so take it with a grain of salt, but it seems to me that animals don't have fewer mutations than we do. Take the domestic dog, for example. ALL breeds were from the wolf at some point but we have hundreds of different breeds now. And they all look so different. Yes, I understand many were bred to look or act a certain way, but it also stands to reason that there were a lot of genetic mutations going on there, especially if you compare the mind of a dog to that of a wolf. Dogs are a lot smarter and able to be trained, why is that?

Of course I believe the same of rats, because I have them and believe they are just as smart as dogs (even though the wild rat is a different species than the domestic and not yet able to be trained). Incidentally, a rat has 90-something percent of our genome also, which is why scientists do so many drug testing on them, to see if we will react the same way.

RBTC said...

i may not have been using the right terminololgy - there are websites and articles which say that the chimpanzees have more genetic diversity than humans which points to more stability and less inbreeding over a longer period of time

the toba disaster happened about 70ooo years ago and caused a genetic bottle neck

also there is mitichodrial " eve" from about 200,000 years from whom we all descend

what i have read seems to say that humans are descended from probably a few dozen families

i was just wondering if that makes a difference in mutations

it's a constant learning process

Village said...

Miss Mannah - Dogs have been bred by humans forever, as have mice and rats. Scientists don't study man made species or animals in zoos. The dog genome is being sourced for economic purposes.

RCTB - The more genetic diversity the more fucking around. I don't know how else to put it. The African genome is stuffed full, while the Caucasian genome comparatively is practically empty. We have long stretches of Causasian DNA that is so empty, scientists used to refer to it as "junk DNA," again a scientific snobbery that if they don't know what it is, it must not exist. (The junk DNA was later determined to be switches.)

RCTB I really don't know how to respond. We starting mutating 4.5 million years ago. Yes there was a Eve, probably several of them, something in the teens, that goes back about 200,000 years. Once we thought that number was 30,000, so we have come a long way in our discoveries. But as for quality and quantity of muatations, I refer you to The Origin of the Species, by Darwin. He can answer that far better than I can.

aregular said...

I am descended from unicorns.

Seriously though, the "studies" that linked autism to vaccines have been thoroughly discredited. It was all over the news fairly recently. It is very likely that, like others have pointed out, our means of diagnosing autism have improved over time which is part of why it looks like the numbers have jumped. Previous, many kids who would now be labeled autistic were just considered mentally retarded or otherwise developmentally disabled.

This is a compelling discussion however... really liking this thread.

nycmom said...

Such a complicated topic and the bottom line is we still do not know what causes Autism Spectrum Disorders. It remains an area of intense debate and research. There is not doubt from heritability studies that genetics play a big part, but environment must also be a factor or we would see 100% concordance in monozygotic twins. Heritability estimates have ranged from 50s-90%, but there is no doubt other factors are at play also.

I do think it is very important not to place all our eggs in one basket here. Just like with the MMR debacle, it is unlikely we will isolate a single causative environmental insult. Yes, ASD rates began to increase in the mid 1990s and GMFs also became mainstream then. However, 1994 is also when the DSM-IV was released which dramatically altered the way we were allowed to diagnosis, code, bill, and help our patients acquire EI services. To discount any of these factors would be unreasonable. To attribute rising ASD diagnostic rates to any one factor with such scant evidence would be equally unreasonable.

Increasing rates of autism have been *mostly* attributed to differences in diagnosis, coding, availability of services and a concurrent drop in diagnostic rates of mental retardation. Nonetheless, there are a few studies mostly out of CA which suggest a potential genuine increase in the rate of ASD. Again, I think the jury is still out on a definitive answer here.

To clarify, we do not all carry the "Autism Gene" in the sense that we have not isolated the cause of autism to a single gene mutation, translocation, deletion, etc. Most of us carry the same basic set of genes, but most of us do not have a mutation causing ASD. Many genes implicated in Autism are also suspected to cause other illnesses. The male:female ration is likely due to increased penetrance among males, not a sole sex chromosome linkage. Certainly mutations on the Y chromosome are one likely potential trigger, but there are many others that have been identified too.

Same with multiple contributing environmental insults: birth order, age of father, exposure to toxins, prenatal insults. Is it possible that GM foods are a factor? Absolutely. It is very likely that various environmental exposures in an already susceptible prenatal infant can increase the risk for developing ASD. The data remains very inconclusive on postnatal exposures. I think that warrants caution, especially during early pregnancy, but the vaccine debacle should also help us stay mindful of the potential downside of advocating for a simple answer with so little evidence.

RBTC said...

thank you nycmom - i read every word

MissMannah said...

"Increasing rates of autism have been *mostly* attributed to differences in diagnosis, coding, availability of services and a concurrent drop in diagnostic rates of mental retardation."

This is exactly what I think, and not only about autism but many mental disorders. To put it in layman's terms, we know what to look for now and at an earlier age so we can start intervention.