Sequencing the Denisovan genome

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There has been a good deal of publicity recently about the sequencing of the Denisovan genome by Svante Pääbo’s group at the Max Plank Institute (see here and here for examples). Using brand new technology for sequencing single strands of DNA (single strands as opposed to the normal double-strand), the group was able to achieve a sequencing rate of 30x–every position in the genome was sequenced 30 times. That’s comparable to sequencing modern genomes.

While some of the coverage has focused on what can be inferred about the individual from whom the DNA was recovered (female, dark skin, brown eyes and hair) what is much more interesting are the relationships of the Denisovans to various modern human populations and to Neandertals. Also interesting is the identification of genetic changes that have occurred in modern humans, a number of the changes having to do with genes associated with brain function and nervous system development,

Since John Hawks has discussed the paper in some detail, I won’t, but will direct you to Hawks’ review of the research. One quotation from that piece–the final sentence–is worth repeating:

Evolution really is the fundamental principle of biology, but using evolution to learn about biology sometimes requires traveling through time. Ancient DNA gives us a time machine bringing new insights into reach.

I can hear the echo of Ken Ham’s minions mindlessly shouting “Were you there???” No, but this is the next best thing.

97 Comments

No Ken, I wasn’t there and neither were you. But I can sequence DNA that was there. I can draw valid inferences from this data. You really ought to try it some time Ken. By the way, you can do the same thing with fossils.

The news about this sequencing and some of the conclusions drawn from it has proven to be a lot of fun and extremely interesting even to a layman like me. Technology and techniques are advancing so quickly that important findings are cropping up at a remarkable pace. We didn’t even suspect that there were Denisovans until about 2008, and we didn’t have good gene-based estimates for Neanderthal introgression until a short while later, and now we’re comparing all these genomes with the promise of even more interesting findings to come. That’s not to mention the findings of the dwarf Homo population of Flores, or the new Australopithecus finds like A. sediba. This has certainly been an exciting decade for the study of human origins.

RBH Wrote:

I can hear the echo of Ken Ham’s minions mindlessly shouting “Were you there???” No,

But Richard and I were. Scruffy we were. Hee hee. ;-)

Ha! Speak for yourself, geezer! :)

Mike Elzinga said:

RBH Wrote:

I can hear the echo of Ken Ham’s minions mindlessly shouting “Were you there???” No,

But Richard and I were. Scruffy we were. Hee hee. ;-)

(Which reminds me of a remark by the late Robert B. Parker, creator of the Spenser, Jesse Stone, and Sunny Randall series of mysteries. Asked why he was taking boxing lessons in his 70s, Parker replied that he was in training for a geezer-weight title match.)

Richard B. Hoppe said:

Ha! Speak for yourself, geezer! :)

Mike Elzinga said:

RBH Wrote:

I can hear the echo of Ken Ham’s minions mindlessly shouting “Were you there???” No,

But Richard and I were. Scruffy we were. Hee hee. ;-)

Heh; y’old coot. Done lost yer memry has yeh? Ah seed yeh thar; still had the same beard away back then yeh did. Jist as gray too.

Still hangin’ in there I see. Doin good work too! Bless ye.

I am amazed that Svante Paabo and his team were able to sequence the entire genome from that bone fragment. This is indeed - no pun intended - a stellar achievement. It’s also important since it has demonstrated that our understanding of hominid phylogeny is far more complicated than we had suspected.

As more genetic information accumulates relating to our ancient antecedents, it seems that there is, in fact, something to the multiregional hypothesis, at least for genetic content for many modern humans. We still are, all of us, African in most part. Travelling to Asia, 80,000 ya, carried different opportunities than it does today!

What gets me is that these were people. We know a fair amount of culture going back about 10k years but we know nothing about these guys. In the intervening 30k years think how many Gods were created and disappeared. How many stories of Heros real and imaginary have been lost to us. Were there any empires that we know nothing about over this time.

MichaelJ said:

What gets me is that these were people. We know a fair amount of culture going back about 10k years but we know nothing about these guys. In the intervening 30k years think how many Gods were created and disappeared. How many stories of Heros real and imaginary have been lost to us. Were there any empires that we know nothing about over this time.

These are fascinating insights, MichaelJ, which I didn’t thought of. They’re very good points, though I might add that empires don’t appear until thousands of years after we started farming in the Neolithic Period.

John said:

…empires don’t appear until thousands of years after we started farming in the Neolithic Period.

Oh yeah? How about the Hyborian Age and the Acheron Empire? We know way more about it than we do about “Eden” or “the land of Nod”!

The best media report of this research I’ve seen is in BusinessWeek.

Now this is really interesting: the Denisovans have the same chromosome 2 fusion as H. saps. John Hawks discusses it briefly here. Assuming that Neandertals also have the fusion (which we do not yet know), that pushes the date of the fusion back before the differentiation of H. saps, Neandertals, and Denisovans.

Richard B. Hoppe said:

Now this is really interesting: the Denisovans have the same chromosome 2 fusion as H. saps. John Hawks discusses it briefly here. Assuming that Neandertals also have the fusion (which we do not yet know), that pushes the date of the fusion back before the differentiation of H. saps, Neandertals, and Denisovans.

From a non-anthropology perspective, a question.

These are clearly distinguishable populations, but they were human, interbred quite freely with humans to produce fertile offspring, and are partly ancestral to modern human populations. How strong is the justification for designating different species?

This is a sincere question; any informed replies will be appreciated.

harold said: How strong is the justification for designating different species?

Svante Paabo clearly considers all three variations the same species.

[About Denisovians] “I would not call it a different species, but clearly different groups with a different history. I would not call the Neanderthals a different species from humans either, actually.”

its not the next best thing to being there. Yes its about looking back in time to things not now that way. All this genetic stuff still requires a constant state of motion on genetic change. Yet is the physics of DNA settled? I say it isn’t. The bible says people lived , even after the flood , for hundreds of years. So our genetics must of been more powerful. Likewise in all biology. So YEC creationists already can’t be persuaded that Dna is a trail for biological relationships. Whether diversity of time. All ideas on genetics is founded on a constant state. There is no reason to rule out other options about flexibility of genetic change. Evolutionists make a flaw of logic when saying genetic conclusions about biology can not be questioned on the great assumption of constant motion. Its not been included in these models the option for undiscovered flexibility of genetic change without ideas from evolution. It must include this option to be a tested hypothesis. Another whoops for evolutionary biology.

Robert,

I won’t even attempt to argue with your statements above. They speak for themselves.

But let me help you with a couple of things that maybe you could learn to correct, if you pay attention and are careful (I taught high school English).

Start your sentences with capital letters.

It’s not ‘must of’, it’s ‘must HAVE’. ‘Must of’ doesn’t even make sense.

When ‘its’ means ‘it is’, it always MUST have an apostrophe: it’s. You did it wrong three times in that short paragraph.

Avoiding some of those childish errors (and there are many more) won’t help your argument, but it will make readers less likely to dismiss your entry, after the first sentence, as the writing of a 5th grader.

Still spelling DNA with only one capital eh Robert? Well then, I guess everyone can see what an expert you are when you claim that the physics of Dna is not settled!! Perhaps you can enlighten us about exactly what is is you feel is still in question. Is it the mechanism of mutations? Is it the mutation rate? Is it the randomness of mutations?

Exactly how do you explain this evidence Robert? How can it possibly be reconciled with a young earth and immutable species? You make a flaw of logic when you say that others have ruled out undiscovered things. Exactly what undiscovered things should be considered? Why should they be considered if they haven’t been discovered yet? Could it be that you will just reject any conclusion that doesn’t agree with your preconceptions?

“So our genetics must have been more powerful.”

More powerful than what? A lawnmower? A speeding locomotive? A Saturn V rocket?

Enquiring minds want to know, Robert. Not your mind, of course.

Robert Byers said: The bible says people lived , even after the flood , for hundreds of years.

Well, Robert, that should be easy enough to establish.

Presumably, humans in the age of Methuselah grew to adulthood at the same rate (the Bible is full of old Jewish rituals and rules and the appropriate ages where these things apply, so we can make surmise that growth thru puberty into adulthood was about the same as it is today)

Since cranial sutures ossify at a known rate, we can identify the skulls (and dentition) of, say, a 10 year old as opposed to a 15 year old as opposed to a 20 year old.

And we know, roughly, what these people ate, and there are probably even modern populations with similar diets (though probably less gritty, because of better ways to grind grain) .

A little dento-archeology should quickly be able to compare and contrast teeth of known ages and establish a pretty good ruler for average wear rates.

it should be trivial to find and identify old jaws with 200 years of wear. Especially in an arid region like the Middle East, where bodies last a looooong time.

It’s also noteworthy that this region has been a hunting ground for Biblically-motivated archeology for centuries.

So… um.… where are all the really old skulls?

[crickets]

Indeed, Bob, people have actually done this sort of research, and guess what?

People died young back in the day. At 33 Jesus was verging on being an old man in his population when the Romans nailed him to a tree.

Life expectancy in the Bronze age and early iron age? 26 years. Though, in fairness, that is skewed a bit by an enormous infant mortality. If you were lucky enough to live through puberty you had decent odds of seeing your early 30’s.

Dave Luckett said: More powerful than what? A speeding locomotive?

Able to leap tall bullshit in a single bound.

stevaroni said:

People died young back in the day. At 33 Jesus was verging on being an old man in his population when the Romans nailed him to a tree.

Life expectancy in the Bronze age and early iron age? 26 years. Though, in fairness, that is skewed a bit by an enormous infant mortality. If you were lucky enough to live through puberty you had decent odds of seeing your early 30’s.

From a strictly Darwinian perspective, I’ve always wondered what modern medicine will do to the human race in an evolutionary sense. In the day, the people who “were lucky enough to live through puberty” were the ones who had lived long enough to breed. By that winnowing process, they were the hardy ones, the tough ones, the ones that the TOE would predict would pass on their genes to their offspring. Today? Not so much. I would have died from stomach ulcers before my 15th birthday. Without orthodontia, my teeth, and those of my son would have seriously compromised our ability to eat. Our son wouldn’t even have been born without IVF.

Yet here we are today, healthy contributing members of society. But our genes? Not so much, or at least not as much as 2,000 years ago. It’s looking like collective intelligence and technology is going to practically nullify the effects of “natural selection” on the human phenotype.

Oh, to come back in several thousand years, to live to see what the seeds we sew today have wrought! :-)

Scott F said:

From a strictly Darwinian perspective, I’ve always wondered what modern medicine will do to the human race in an evolutionary sense. In the day, the people who “were lucky enough to live through puberty” were the ones who had lived long enough to breed. By that winnowing process, they were the hardy ones, the tough ones, the ones that the TOE would predict would pass on their genes to their offspring. Today? Not so much. I would have died from stomach ulcers before my 15th birthday. Without orthodontia, my teeth, and those of my son would have seriously compromised our ability to eat. Our son wouldn’t even have been born without IVF.

Yet here we are today, healthy contributing members of society. But our genes? Not so much, or at least not as much as 2,000 years ago. It’s looking like collective intelligence and technology is going to practically nullify the effects of “natural selection” on the human phenotype.

Oh, to come back in several thousand years, to live to see what the seeds we sew today have wrought! :-)

We are just selecting for different things now, such as the ability to correctly judge the speed of an approaching vehicle. Our technology has changed the environment, but evolution is still tracking the changes.

Infant and childhood mortality were the real skews on the population statistics. A settled farming population with access to a good diet may live out what we would regard as a “normal” lifespan, with some respectable proportion of those who reach adulthood reaching sixty or seventy. Old people are repositories of knowledge in preliterate societies, and valuable for that reason, and so are usually supported past their ability to contribute with labour. At the same time, settlement removes the necessity for keeping up with the group as it forages. Hence the Biblical description of human life expectancy: “three score years and ten”.

The difficulty arises with intensive cultivation of grain. Given suitable land, cereal crops return the greatest number of calories per area, albeit at the cost of constant grinding labour. Land is converted to cereal farming by ploughing, drainage, ditching, irrigation and terracing. Woodland, wetland and hill pasture, sources of other foods, are reduced. Malnutrition appears as grain replaces them. At the same time, repetition and overuse injuries appear and become severe. So do dental caries.

All this tends to shorten life, except among the elite. But an elite is also a characteristic of settled agrarian populations.

The problem I suppose is one of biblical inerrency. If the bible says early humans had life spans of 900 plus years then they did, even if there is no fossil evidence for this scanario.

No matter how silly the claim, if the bible says it then Robert believes it.

It’s as simple as that.

Nearly everyone qualifies their belief in the primacy of the Bible. Very few people go along with Biblical heliocentrism, for example, even though for something like 2000 years it was the universal belief that the Sun orbited a fixed Earth, and agreed that the Bible said so. Most people today believe that the Earth is a planet of the Sun on the basis of modern science. (Even though few of them are able to give good reasons for that belief.) This is only one of the more striking examples of how people will qualify their trust in the Bible. (I dare say that the evidence for evolution is more accessible than the evidence for geocentrism.)

I’d agree with TomS. Even the godbots we get here don’t actually believe in Biblical inerrancy, not really. They say they do, of course, but any time the Bible doesn’t actually say what they want it to, they indulge in a little quiet metaphorisation, and hey presto!

And yes, to observe the retrograde motion of Venus and Mercury takes some doing, and a tremendous piece of insight to see how it is better explained by the Earth in motion rather than that it’s them doing loop-the-loops.

From a strictly Darwinian perspective, I’ve always wondered what modern medicine will do to the human race in an evolutionary sense. In the day, the people who “were lucky enough to live through puberty” were the ones who had lived long enough to breed. By that winnowing process, they were the hardy ones, the tough ones, the ones that the TOE would predict would pass on their genes to their offspring. Today? Not so much. I would have died from stomach ulcers before my 15th birthday. Without orthodontia, my teeth, and those of my son would have seriously compromised our ability to eat. Our son wouldn’t even have been born without IVF.

The impact of modern medicine on human selection is much less strong than you may think.

To some degree, it has an indirect effect, as the human traits being selected for right now are any alleles, if such exist, that are associated with extreme poverty, inadequate access to health care, and high childhood mortality. Those are the people with the “reproductive advantage” in today’s world. Those are the people who live in places where there is a strong net population growth.

Many of what we perceive as common “genetic” problems are environmental. For example, no pre-literate population ever has myopia to any significant degree. Myopia is common in all literate societies. Clearly, the alleles are there (possibly selected for in humans for some other reason or linked to something that was selected for), but the negative trait is only expressed in literate societies. A myopic hunter gatherer might be in trouble, but they don’t get myopia, because they aren’t exposed to the environmental risk factor. It’s much the same with many, many dental problems, not just caries.

Many premature deaths in the past were due to pathogens so virulent that any human has a good chance of dying from them, on first exposure, if untreated. Random chance plays a large role in populations with high exposure to virulent pathogens, and lack of adequate medical care.

Now, obviously, Eurasian populations of early modern times did have a relative resistance to Eurasian infectious disease, relative to Amerindian populations that is, for example, so there are long term trends, but such things may be more subtle than people think.

Scott F said:

stevaroni said:

People died young back in the day. At 33 Jesus was verging on being an old man in his population when the Romans nailed him to a tree.

Life expectancy in the Bronze age and early iron age? 26 years. Though, in fairness, that is skewed a bit by an enormous infant mortality. If you were lucky enough to live through puberty you had decent odds of seeing your early 30’s.

From a strictly Darwinian perspective, I’ve always wondered what modern medicine will do to the human race in an evolutionary sense. In the day, the people who “were lucky enough to live through puberty” were the ones who had lived long enough to breed. By that winnowing process, they were the hardy ones, the tough ones, the ones that the TOE would predict would pass on their genes to their offspring. Today? Not so much. I would have died from stomach ulcers before my 15th birthday. Without orthodontia, my teeth, and those of my son would have seriously compromised our ability to eat. Our son wouldn’t even have been born without IVF.

Yet here we are today, healthy contributing members of society. But our genes? Not so much, or at least not as much as 2,000 years ago. It’s looking like collective intelligence and technology is going to practically nullify the effects of “natural selection” on the human phenotype.

Oh, to come back in several thousand years, to live to see what the seeds we sew today have wrought! :-)

You are correct. It’s called relaxed selection and there is no doubt that modern technology is responsible far a substantial increase in the frequency of many deleterious alleles in the human gene pool. This can be quantified by estimating the number of lethal equivalents in the human genome, which are increasing due to modern technology.

But there are two things to remember about this effect. One is that as long as we retain modern technology, it may be OK to maintain a lot of this hidden variation. After all, alleles are only deleterious in a given environment. It may even prove to be beneficial if the environment changes in unexpected ways. Second, just because selection is relaxed for many traits, doesn’t mean that it doesn’t still operate for others. Currently, we seem to be under strong selection for genetic variation with regards to susceptibility to pandemics, resistance to side effects of pharmaceuticals, and resistance to the toxic effects of pollution. The fact that we have chosen to inflict these selection pressure on ourselves doesn’t make them any less real.

The interesting thing about ancient DNA analysis is that it can reveal evidence of selective sweeps in parts of the ancient human genome. This can help to determine the most important selection pressures in the past and can be used to predict possible responses to modern environmental challenges. So once again, modern evolutionary theory is central to studies of human health and planning for the future of the human race and creationism is till a nonstarter.

harold said:

A myopic hunter gatherer might be in trouble, but they don’t get myopia, because they aren’t exposed to the environmental risk factor. It’s much the same with many, many dental problems, not just caries.

My dental problems were the result of large teeth (dad’s) in a small jaw (mom’s). I wonder if that kind of variation would exist in small local populations or if that, too, is a result of our increased mobility since… well, since the wheel, I guess.

Byers thinks that teeth can be biologically stronger, whatever Byers means by “stronger”. Not that ‘stronger’ has any specific meaning at all in this context.

No, Bob. Wrong again. The teeth of ancient skulls have been minutely examined, and as has been explained patiently to you, those teeth are like ours, not “stronger”. Their tooth enamel was the same as ours, and its thickness the same as ours would be, if we ate the same foods as they did. The wear patterns show that people five, six, seven thousand years ago lived shorter, not longer lives than we do.

Them’s the facts, Bob. Suck it up.

Furthermore, Robert Byers still has not explained why no one has ever found any skull belonging to one of these legendary Biblical poly-centurions in the first place.

apokryltaros said:

Furthermore, Robert Byers still has not explained why no one has ever found any skull belonging to one of these legendary Biblical poly-centurions in the first place.

I hate to admit it, but in some ways Byers does me a favor with these senseless arguments of his.

When he babbles his nonsense, I often find myself wondering “well, what do we actually know about this?

Unlike him, I actually use the search bar on my browser to try to investigate it.

This week, like many times before, I’ve spent hours that I’d otherwise be wasting watching TV in looking up the things that Byers spouts of about - in this case reading paper after paper on forensic dental osteology in the Biblical Holy Lands.

Once again, I’m amazed how much excellent information is out there at your fingertips if you only look for it.

I compare and contrast this with my undergrad days when researching the simplest question required going to the university library and slogging through publication indexes for hours.

Now, you plug a search term like “dental archeology” into PubMed and get hundreds of interesting hits that take me hours to read. But hey - now I know about things like “Dental health in Northern Chile’s Atacama oases: evaluating the Middle Horizon (AD 500-1000) impact on local diet.”

Bob may be a purposely ignorant ass, but he reminds me constantly that we live in marvelous times.

Hell he can’t even click on the links that are provided for him. His nonsense is completely refuted by even the most trivial facts. He seems to think that if he refuses to look at it, it doesn’t exist. Kind of like a three year old playing hide and seek by covering his eyes.

The ice man lived 5300 years ago and died at the age of 40. His teeth were in really bad shape. He was no pre flood super human, that’s for sure. Bobby can’t explain it. So what? He can’t explain any of the evidence from genetics either.

Mike Elzinga said:

Some time back I gave some specifications for a deity detector.

Took me a while to find them again.

I think this is a good description and the more I think about this the more I realize that a living thing capable of reasoning could be this detector.

Marilyn said:

Mike Elzinga said:

Some time back I gave some specifications for a deity detector.

Took me a while to find them again.

I think this is a good description and the more I think about this the more I realize that a living thing capable of reasoning could be this detector.

As detectors, our signal to noise is terrible and we appear to be extremely imprecise (our detections are all over the map).

This assumes there aren’t an infinite number of contradictory gods. If that’s the case, then hey, maybe each detection is signal and what looks like imprecision is just individual accurate detection of different entities.

This assumes there aren’t an infinite number of contradictory gods. If that’s the case, then hey, maybe each detection is signal and what looks like imprecision is just individual accurate detection of different entities.

That reminds me of Heinlein’s novel Stranger in a Strange Land.

Henry

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This page contains a single entry by Richard B. Hoppe published on September 1, 2012 1:11 PM.

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