Study Detects Recent Instance of Human Evolution

The New York Times is running a Sunday article regarding new evidence about 'recent' human evolution. A research team at the University of Maryland has done some work looking at the rise of lactose tolerance in the human populations of Africa. From the article: "The principal mutation, found among Nilo-Saharan-speaking ethnic groups of Kenya and Tanzania, arose 2,700 to 6,800 years ago, according to genetic estimates, Dr. Tishkoff's group is to report in the journal Nature Genetics on Monday. This fits well with archaeological evidence suggesting that pastoral peoples from the north reached northern Kenya about 4,500 years ago and southern Kenya and Tanzania 3,300 years ago ... Genetic evidence shows that the mutations conferred an enormous selective advantage on their owners, enabling them to leave almost 10 times as many descendants as people without them. The mutations have created 'one of the strongest genetic signatures of natural selection yet reported in humans,' the researchers write. "

Comments

Re:They don't explain WHY

[MichaelSmith]

I really don't think it mattered if humans drank milk or not.

It lets another species do the hard work of converting grass to usable nutrients. Milk is a great source of calcium, with helps keep bones strong.

Why is it always "mutation"

[$RANDOMLUSER]

I realize that this is popular press and all, but why is mutation always mentioned, but crossover, never so?
Generally speaking, mutation is almost always fatal, crossover is almost never so. Crossover keeps you "in the genome", where mutation is just as likely to kick you out of it. My own theory is that mutation is the driver behind speciation, while crossover is the driver behind evolution.
I've run lots of GAs with mutation turned off, letting crossover do all the work. Crossover, not mutation, is what lets a population do that slow walk/hillclimb, over time, through the genetic landscape.

Re:Why is it always "mutation"

[kshort]

I'm a geneticist, and we typically use the terminology 'mutation' to describe any change in DNA which escapes the cell's natural ability to inhibit external of internal modification of the genome, typically using 'proofreading' mechanisms, or all the way through to cellular apoptosis to delete entire cells with certain (what the cell thinks are) detrimental mutations. Such simple changes, if they escape correction or deletion, most definitely have the ability to cause major problems, but on the flip side those mutations have the ability to modify the activities of proteins which can be advantageous (and others may do nothing at all). Whilst examples of advantageous mutations are few and far between on timescales that we can appreciate in concordance with a human lifetime, in the evolution of a species such mutations are seen to occur rather rapidly. Crossover is never a term I have come across in the definition of these terms, unless you're talking about recombination, which is another thing entirely.

Re:Why is it always "mutation"

[Guillermito2]

why is mutation always mentioned, but crossover, never so?

You're right. Point mutations (like a bit flipping in geekspeak) are only one kind of evolution mechanism, although it can be caused by several mechanisms (error during copy of the genome, which in fact happens all the time, 1 or 2 per billion base pair per duplication if I remember, a rate that would never be tolerated in computers, it's like 1 bit flipping every 125 Mb, also chemicals, cosmic rays, etc). But to participate in evolution, it has to be transmitted to the germline. So the mutation has to happen in your balls, in other terms.

Generally speaking, mutation is almost always fatal

In fact, no. There are many point mutations between human beings, they are called SNPs (Single Nucleotide Polymorphism) and there is a big worldwide project that mapped many of them them. Most of them are silent, or at least do not have a black and white effect (but it sometimes unfortunately happens : one single mutation in 3 billions nucleotides and you will suffer a painful and slow death). Remember that people used to say that most of the human genome is junk (this junk actually seems to be more and more important, but it's mainly "apart from defined genes - a few percent - we have no idea what the rest is doing here").

A point mutation in a primate genome would be like flipping a random bit in an overbloated Visual Basic application. It's very likely the program will still be funtional. As opposed to changing a random bit in a very size optimized assembler program, which is almost certainly going to crash.

My own theory is that mutation is the driver behind speciation, while crossover is the driver behind evolution.

I'm not sure it's supported by facts, although it's an interesting theory. Don't forget that there are even other ways to modify a genome. An important one is polyploidy : suddenly for some reason an organism doubles the number of chromosomes (a cell that duplicate the genome but fails to separate into two daughter cells). As you suddenly have twice the number of redundant genes, then the new genome is like a playground for other kinds of mutation, as time and random can play around with the copies of the genes without much effect, as long as there is one functional copy.

Another mechanism, as opposed to point mutation or whole genome doubling, is deletions or copies (in tandem, or inverted, or somewhere else, or in the middle of another gene) of huge portions of the genome (several thousands of nucleotides). In fact, there was a paper in Nature two or three weeks ago that compared the chimp and the human genome for this type of big chunk mutation.

A last one is through the action of transposons which may be some old retrovirus succesfully inserted in the genome. For some reason, sometimes a transposon get excited, wakes up and it will excise itself from its current location and jump somewhere else in the genome. But this process is never perfect, and the jump removes or leaves a few nucleotides that are going to induce a mess if it's inside a gene.

There are others ways to fuel evolution at the genome level, but that were the ones that came on top of my head quickly. Plus I need a coffee.

Re:Ooh, how precise!

[Sparr0]

significant figures. I would say that "2700-6800" signifies certainty between 2650 and 6850 years ago, with slightly less (but consistent) certainty that it is between 2750 and 6750 years ago.

Re:Micro vs Macro

[Sirch]

We have documented proof that Americans have gotten taller for instance. I believe (no sources) that that is most likely down to better nutrition (in the US? Hah! etc), rather than evolution.

Re:No way!

[bigtomrodney]

It was a tongue in cheek comment, I actually said Jebus to avoid that interpretation. It was only making fun of the crazies who use his name. I agree it shouldn't have been modded insightful, but hey it certainly wasn't flamebait.

Re:Micro vs Macro

[solanum]

It's not actually that simple. For example, the increase in height in Westerners isn't micro-evolution it's simply diet. When man went from hunter-gather (the state to which we evolved), to an agrarian lifestyle, the quality of diet went down, it hit rock bottom in Europe in the middle ages where teh majority of the population were quite severly malnourished and therefore short. The heights we are currently reaching (pun intended) are basically those of our hunter-gatherer forefathers, because as a population the quality of our diet over the last 50 years has improved so much. Of course we're probably heading down the path of too much now...

So my point is, that it's not easy to define or prove 'micro-evolution'. Just to clarify, I am a biologist by trade and am quite comfortable with the punctuated-equilibrium model of evolution, I'm certainly not arguing that evolution doesn't happen, just that we have to be careful with our conclusions.

Re:They don't explain WHY

[Monty_Lovering]

Mmmm... I think saying "I really don't think" is quite honest of you, although it is already painfully obvious to most of us here.

Humans originally didn't have the enzymes to digest cow lactose; why should they? It serves no purpose in a hunter-gatherers genome.

Most infants can digest lactose well enough to get by as they are expressing genes at that age to aid in the digestion of human milk, but by age 5 cow milk normally makes a lactose intolerent person puke mucus.

Occasionally through mutation some did have the right enzymes to digest cow lactose through adulthood, but as humans did not keep cows those people had no advantage over other people without the mutation, so the mutation was lost as it had no benefit.

When humans started to keep cows they had access to a new food source, milk.

This would have been used to feed infants to replace or suppliment the mother's milk, probably as part of the weaning process.

As those infants grew older those with tolerence to lactose had access to a renewable food resource denied to those who were intolerent to lactose. Those lactose intolerent infants whose parents kept feeding them milk would have been sickly and malnourished.

There would be such a big ebenfit to lactose tolerence that somethng called 'runaway evolution' took place. It's a bit like how mudskippers evolved; if ten fish of a species in a river survive a drought survive because of x charecteristics only they (in that species) have, after that drought all members of that species have x characteristic.

Similarly with human lactose tolerance the stronger, better fed, healthier members of the population with lactose tolerence would have had way more offspring then those who didn't have the genes for it, and those offsrping would fare better.

If 5% increase in genetic transfer through natural selection can make a new characteristic spread throughout a population in less than 200 generations, think how more quickly one with a much higher advantage might spread.

Guns are part of an extended phenotype, and are NOT subject to genetic transmission. Idiot.

Re:where's the mutation?

[arun_s]

So I read the article and it sounded like there was never a time they could point to and say 'here's when the mutation occured'.

It doesn't usually work that way. Evolution is a continuous process, like, for instance, hair growth. Consider a random population of 1000 short haired people. At what instance does the average length cross 3 cm? There really isn't a distinct time when it happens, since several may visit the barber on different days, making the average shuffle up and down (although maintaining a noticeable upward trend all the way). You could only conclude that, after say, 2 months, the average length in that sample was comfortably over 3 cm, although there might not necessarily have been a single instant when the change occured.
Alright that wasn't a very good analogy, but I hope you get the point: In evolution, the average trends in the gene pool are what are considered rather than a specific instance of change. (IANAEB (I'm not an evolutionary biologist), so please correct me if I'm wrong)

Re:They don't explain WHY

[raverman]

Milk is generally THOUGHT to be a good source of calcium, but in fact is not: http://www.afpafitness.com/articles/MILKDOC.HTM
The information in the above source seems reasonable enough, and well-backed with scientific reports. Please read it, I assure it is worth it.

Re:where's the mutation?

[i_should_be_working]

I think you missed what I was saying. Natural selection by itself is not evolution. If you have a species with many different traits and some outside influence makes some of those traits more desirable while others less so, the dying out of the less desirable traits is not evolution. No new trait has been introduced into the gene pool. It's not evolution anymore than if some freak disease killed off all the green eyed people in the world.

So, 5000 years ago natural selection occurred. But the gene that allowed the digestion of lactose may have been around for millions of years, before we were even human.

Evolution is the combination of the mutation that created the gene and the natural selection that made for the proliferation of the gene. But that process may have to include a time span of millions of years, from the creation of the gene to the domestication of animals, not just ~5000 years ago.

Why is only Africa brought up?

[Jugalator]

- About only 2% of Swedes are lactose intolerant.
- About 20-60% of Africans are lactose intolerant.

I can personally see a much stronger signature of these genetic traits in Scandinavia? Is the difference that this evolution was not "recent"? Because surely it has to be some form of natural selection causing this in Scandinavia too, perhaps trigged earlier for some reason?

Some useful links:
- Lactose intolerance by human groups.
- World map with lactose intolerance distribution.

Re:No way!

[eboot]

Because the very existence of religion creates extremism, and if you want evidence of this then, well, you've got basically the whole of human existence to choose from. More moderate people like you perpetrate the myth that religion can be balanced and forward thinking and therefore religion is allowed to continue existing. In fact for this simple reason alone you are more dangerous than the extremists and however deluded they might be you are more so. To them you are the public face, they are the necessary guards of the core values. And in a sense they are right, you have deluded yourself into believing in a god who is kind, just and fair when your own texts say that there was a lot of 'fire and brimstone' behind him. The true face of religion is divided in half, like that Batman villain, with one half being a serene, kind and gentle visage and the other half a snarling beast. But make no mistake, they are the same entity.

Re:They don't explain WHY

[molarmass192]

I read the article, I'm not the Breast Surgery Chief but I do have a fairly solid background in biology. The thing that made my bullshit meter go into the red is when he tried to discredit pasteurization. Also, he uses very weak arguments and then doesn't back them up. You can't just say milk has bacteria, bacteria makes people sick, therefore milk is bad ... it's simply too broad a brush to use in biological terms. If you want to talk about scary stuff, look at all the recent fecal coliform contaminated vegetables in this county. If this author took a stance on that subject, it would read like this: fertilizer and reclaimed water used to irrigate vegetable fields contain fecal coliforms, fecal coliforms make people sick, therefore vegetables are bad. Disconnected facts do not an argument make.

"Baby" ... that means ~1 year old.

[Ihlosi]

LD occurred in 38.5% of children in the 3-5 yearage group,

The article you quoted does not mention babies. If anything, it mentions toddlers. By the age 3, kids should have started to eat solids (and be able to walk, and talk). In fact, it's not unusual for them to stop nursing before they're two years old.

Re:No way!

[MECC]

Nowhere in the Bible does it say that non-believers should be made to follow the law

Correct, it doesn't. It says they'll go to hell.

Biblically, you don't get saved by following the law (or rather, you would, but nobody ever manages to keep it 100%). You get saved by following Jesus.

According to your group's interpretation of the collection of literary works that comprise the christian 'bible'. The original authors (the real ones - you know the jews whose 'spiritual' inheritance christians claim a part of) of the vast majority of those literary works (the OT) would disagree with that interpretation to say the very least. Quote the NT to them all you want - they don't believe it is the 'word of god' in the way you do, and they wrote all the parts that christians interpret as validating the divine nature of jesus.

And, for the open minded parent poster above, the christian 'bible' clearly states that homosexuality is an abomination (Lev. 18:22), for which you get to go to hell (Rom. 1:26-28). And I have to wonder, what is gay marriage without gay sex? Don't get me wrong, I applaud such open mindedness, but if you're a christian who believes that every word in the English christian bible was explicitly arranged by god, its pretty hard to reconcile open mindedness about such issues with the 'word of god'.

If it's an issue of morality, then it should be in the hands of the church (as the rules of the church apply only to its followers).

So, if you're not a member of a church, then you're free?

Re:They don't explain WHY

[HaggiZ]

All you needed was a reference to germs in that last sentence and you would have the name of an excellent book on the topic. I suspect it might not be a coincidence though.

Guns, Germs and Steel - Jared Diamond

Re:They don't explain WHY

[Mr. Slippery]

Milk is a great source of calcium, with helps keep bones strong.

Not so much. Despite milk marketing propaganda, higher milk consuption actually seems to be correlated with higher risk of osteoporosis.

Why? Protien. Consuming animal protein causes the blood to become slightly acidic; to balance the pH, your body pulls calcium from the bones (which function not just to keep you from being a blob, but as mineral storehouses).

There seems to be a move afoot to fortify milk with extra calcium to compensate, but more and more people are coming to realize that cow's milk just should not play a significant role in the human diet.

Re:No way!

[Anonymous Coward]

There are no passages in the Bible that "very clearly condemn homosexuality" as each passage can be interpreted in several different ways, as the parent suggested

You'll have to do some pretty radical interpretation to change for example these passages into something approving of homosexuality:

"Thou shalt not lie with mankind, as with womankind: it is abomination." - Leviticus 18:22

"If a man also lie with mankind, as he lieth with a woman, both of them have committed an abomination: they shall surely be put to death; their blood shall be upon them." - Leviticus 20:13

I don't really think anyone honest would claim these are anything else than condemnation of homosexual activities.

You will also find most of those passages up for debate are from the Old Testament, which isn't from the teachings of Jesus. You will find much in the New Testament that directly contradicts the Old Testament.

So? You will find passages also in New Testament that clearly state engaging in sex with the same gender is a grave sin:

"In the same way the men also abandoned natural relations with women and were inflamed with lust for one another. Men committed indecent acts with other men, and received in themselves the due penalty for their perversion.

...
Although they know God's righteous decree that those who do such things deserve death, they not only continue to do these very things but also approve of those who practice them." - Romans 1:27-32

I snipped part of it away to make it shorter but you can verify, if you so please, that the context is not changed and the end snippet does still talk about the same thing.

Let's finish this off with one last item from the New Testament:

"Do you not know that the wicked will not inherit the kingdom of God? Do not be deceived: Neither the sexually immoral nor idolaters nor adulterers nor male prostitutes nor homosexual offenders" - 1 Corinthians 6:9

Re:They don't explain WHY

[masklinn]

Why does natural selection favor lactase?

It doesn't, NS isn't a conscious process, it doesn't "favor" anything.

It's just that, in a not-so-distant past, people who could absorb dairies had a higher chance of survival during famines and such (because they didn't have to slaughter the cattle outright), therefore had a higher chance to reproduce and spread their lactase-tolerance to the next generation.

6000 years ago, in some parts of the world, lactase tolerance was a survival advantage. That's all there is to it.

Re:where's the mutation?

[arkanes]

You're subscribing to a common misconception of 'evolution'. Evolution is not the process of "bettering", where there's some ultimate "perfect" form. It's just a process of change. A disease which kills everyone with green eyes will select against people with green eyes and green eyes will disappear from the gene pool. That's evolution in action - the gene pool has changed. If the "green eye" gene is linked to something that is important, like the "digest milk" gene, it probably won't be eliminated entirely and if the disease is eradicated green eye color will resurface.

Remember, individuals don't evolve. *Populations* evolve, when pressures (there are more mechanisms than natural selection at work, too) cause certain traits to be selected for or against. Negative pressure is still pressure.

Shens!

[Bryansix]

There was an article in the LA Time Magazine called West that talked about Raw Milk. That is it talked about milk that was not pasteurized. It mentions that there are enzymes naturally occurring in milk that allow people to digest milk. That means that the ability to tolerate Lactose is not a very big deal since people thousands of years ago presumably were not pasteurizing milk.

Re:They don't explain WHY

[1ntegral]

I just wanted to add a note on the milk digression, I suppose. There are huge nutritional differences between pasteurized and raw milk, in terms of health benefits to humans. The live enzymes present in raw milk (phosphatase for cascium absorbtion, lipase for fat digestion, lactase/-ose, galactase/-ose, catalase, diastase, peroxidase, etc) are destroyed to a large extent by the pasteurization process. In raw milk, all 22 amino acids are present as well, whereas in pasteurized milk, the polypeptides lysine and tyrosine are changed by the heating process such that they are not as easily metabolized (meaning your body can't use the proteins as readily or as easily). Vitamins A, F, E, and D are lost to a large degree by the heating process as well, as is Vitamin C (though to a lesser degree). B6 and B12 are pretty much destroyed all together. Also, raw milk is seriously tasty. If you ever to a taste comparison, there's really no contest. It's a full, earthy flavor, whereas the flavors of pasteurized milk and milk products are shallow and less complex. Obviously, drinking raw milk has its risks. It's important to know where your raw milk is coming from and the process by which it's being produced. If the cows are fed what cows are supposed to be fed (grass, pasture plants, etc) and if the conditions on the farm are clean and natural (no anti-biotics, no hormones, no cows being fed other cows, no over-crowding), there shouldn't be a problem with pathogenic bacteria in the raw milk and it should be safe for human consumption. The beneficial bacteria, as the dominant culture, will prevent the growth of harmful bacteria (whereas in pasteurized milk, a sterile medium, there is no active culture of good bacteria to prevent bad bacteria growth). Going to the farm yourself is the best bet, although there are many states in which it's illegal for farms to sell raw milk due to the risks involved with sub-par milk production (factory farms, etc) and so raw milk purchases, even at all-natural organic farms, have to be made rather on the down low. It's good, though, for people to be involved more in their food, to know where it's coming from, to take an active role in their health and diet through awareness of the production process and its results. Also, a last thought: I don't think that relying on milk as a sole source of calcium would be good, but then, relying on any one thing for nutrition is probably not wise. Moderation and diversity are most likely the best routes to take. Go team Human.

Re:They don't explain WHY

[Mr. Slippery]

I'll stick to searching 'pubmed.org' for "milk, osteoporosis" and seeing the randomized control trials, thank you.

Culling out publications from obviously biases sources such as the "Journal of Dairy Science", can you find a randomized controled trial showing that unfortified dairy products have a protective impact on osteoporosis?

Such a result would be surprising given the findings of a study published in the American Journal of Public Health which followed 77,761 women and found no protective impact of dairy products on fractures.

A PubMed search will find this meta-analyis from Pediatrics on osteoporosis, or this article on the increased risk for prostate cancer from dairy consumption from the American Journal of Clinical Nutrition. This study from the same journal notes "Over the years, doubts have arisen concerning the use of milk as a calcium source in the prevention of osteoporosis, particularly because of potential offsetting effects of protein and phosphorus." This letter in that same journal points out that living in countries with a high dairy consumption is a risk factor for osteoporosis.

This page from PCRM give citations to several studies on the health impact of dairy consumption.

See also this analysis in Public Health Nutrition which states, "Regarding associations relating the consumption of dairy products with chronic diseases, in Western societies consumption of dairy products has traditionally been linked to cardiovascular diseases (arteriosclerosis) and osteoporosis owing to their saturated fatty acids and calcium content, respectively. While the association between saturated fat intake and risk of arteriosclerosis is well established, the association between calcium from dairy products, together with vitamin D, and osteoporosis is less clear."

Re:Life Changing information!

[TheNicestGuy]

ultimately evolution is something which happens over millions of years, so it's unlikely to see any other real notes / changes in my lifetime

The length of time it takes natural selection to shift the predominate traits in a population depends on a number of things, including the (in)stability of its habitat, how "important" whatever changes occur are to the organisms' survival and reproduction, and the length of the species' generation. Yes, we've generally seen noticeable changes take many thousands, if not millions of years, but it's not a foregone conclusion. Take, for example, the classic peppered moth. An entire population underwent a dramatic change in coloration in less than one hundred years, due to a sudden and perilous change in their habitat from industrial pollution.