Neandertals

Planting time has arrived in most of the country -- even here in zone 4 -- so you may be reading those seed packets carefully. This paragraph may catch your attention:

One anti-biotech group even managed to bamboozle some seed companies that cater to home gardeners into signing on to something called the Safe Seed Pledge: "We pledge that we do not knowingly buy or sell genetically engineered seeds or plants." This is fascinating because, with the sole exception of wild berries and wild mushrooms, all the fruits, vegetables and grains in North American and European diets have been genetically modified or engineered by one technique or another. This even includes 'heirloom' varieties of fruits and vegetables. Often, this genetic modification has involved radical changes at the level of DNA, including the movement of genes or even entire chromosomes across natural breeding barriers.

That's from a TCS Daily column by biotechnology analyst Henry Miller. This is a point that constantly amazes me -- do people not realize that it is unnatural to have purple potatoes and zebra-striped tomatoes, and all other manner of garden mutants? That, for the most part, it is unnatural for vegetables (i.e., non-fruit and non-seed plant parts) to be tasty and delicious? Plants don't want you to eat them!

Most of the column is devoted to reviewing some of the misleading parts of a recent report on international biotechnology trends by the Organization for Economic Cooperation and Development. It's a fair critique, but a little dry for light reading. Certainly it's valuable to have critics go through definitions in these international reports, because so much of the conclusions are essentially determined by the assumptions that go into compiling lists. Some countries look different than others, just because their regulatory agencies define things in different ways.

I approach this issue from the perspective of teaching the debate in my genetics course, and also as a way to examine how the debate around human genetic engineering may be framed in the future. After all, franken-people are bound to be a lot more interesting than franken-food.

Not to mention the possibility of Neander-people -- or, dare I suggest, NEANDER-FOOD!

I find the trend toward GMO production of pharmaceuticals to be a very interesting angle in the current biotechnology scene, because of the clear resonance of the issues with human genetic alteration. Both the opposition and promotion of GMOs have both involved heterogeneous groups of interests. Much of the muscle behind both positions has come from agriculture industry groups -- So far, the critics of GMO deployment have been successful when they frame their opposition in terms of risk of introgression into non-GMO crops or wild plants. They have also had success with the "natural food" frame.

A month or so ago, I referred to an article that discussed the potential of introgression by plants genetically engineered to produce pharmaceutical compounds. Quoted in the article, Norman Ellstrand asked, why not modify non-food plants, and thereby eliminate all risk of consumption?

In his article, Miller gives an answer to this question:

Although there is substantial and growing acreage of gene-spliced crops cultivated worldwide each year - 252 million acres in 2006 - more than 90 per cent of it is four large-scale commodity crops; largely because of the huge costs of meeting regulatory requirements, the application of the technology to fruits, vegetables and subsistence crops has been minimal, and disappointing.

In short, it is easier to get approval for altering one of the four major food crops, because they have a research history and are already grown on a immensely large scale. Introducing genetic modification on another kind of plant requires much more work to conform to regulations.

There is also the issue of a less-recognized mode of genetic modification; namely, Simpsons-style:

Currently, dozens of genetically improved varieties that are produced through hybridization, irradiation and other traditional methods of genetic improvement enter the marketplace and food supply each year without any governmental review or special labeling. A technique in use since the 1950s, induced-mutation breeding, involves exposing crop plants to ionizing radiation or toxic chemicals to induce random genetic mutations. These treatments most often kill the plants (or seeds) or cause detrimental genetic changes, but on rare occasions the result is a desirable mutation. For example, a mutation might produce a new trait in the plant that is agronomically useful, such as altered height, more seeds, larger fruit or enhanced resistance to pests.

On a large scale, these random mutations pose more potential of introgressing into wild plants, because they don't carry the baggage of a plasmid, and they might have unknown beneficial side effects on plant fitness. Plus, a strain bearing many random mutations might have some unintended ones along with the one that is strongly selected by subsequent breeding. This kind of induced-mutation breeding is really nothing more than ordinary breeding sped-up a little faster, but then, the only thing making trans-species gene transfer different is that you know in advance that the inserted gene works in some other organism.

In a previous column, Miller argued against legislation being considered to regulate the farming of gene-spliced plants in California. At the same time, he points out the harmful consequences that sometimes result from conventional breeding:

This measure is pointless. In the production of new plant varieties using conventional - that is, pre-gene-splicing - techniques, breeders, farmers and food producers lack knowledge of the exact genetic changes that produced the useful traits. More important, they have no idea what other changes have occurred concomitantly in the plant -- including those that could alter the ability to cause allergic reactions.

...

Only the molecular, gene-splicing methods allow breeders to identify and fully describe the changes that have been made in the progeny, so perhaps it isn't surprising that only the imprecise, trial-and-error techniques of conventional plant-breeding methods have led to food safety problems. Two conventionally bred varieties each of squash and potato and one of celery were found to contain dangerous levels of endogenous toxins and had to be barred from commercialization. Such mishaps are far less likely when genetic changes are wrought with the more precise and predictable gene-splicing techniques.

The difference is not mainly that the trans-species genes are predictable in effect, but that they are introduced only a few at a time. This is less likely to cause incidental side effects than altering the frequencies of many genes by conventional breeding. The point is that anything that we change may generate bad side effects, and we want to find ways to minimize these. One approach is not to change anything. But since nature changes things for us anyway, maybe best to change with science...

I found this passage in the discussion following T. Dale Stewart's paper, "The problem of the earliest claimed representatives of Homo sapiens," from the 1950 Cold Spring Harbor Symposium on Early Man.

DOBZHANSKY: The great variability of the Neanderthaloids, so ably described by Drs. McCown and Stewart [McCown's paper immediately preceded the one under discussion], bears upon one of the basic problems of human descent. It is now clear that the Neanderthaloids and the so-called sapiens type were at no time two reproductively isolated species, but rather component races of a single species. Some modern populations may carry genes that were present in the Neanderthaloids, and other moderns may not carry such genes. But this does not mean, of course, that mankind consists of races descended from Neanderthaloids and other races which came from the sapiens type contemporaneous with the Nenderthaoids. In general, the old anthropological alternative of monogenic versus polygenic descent of man ceased to exist when considered from the vantage point of the present evolution theory. Different populations (races) of a polytypic species may be descended largely from different races of the ancestral species and may differ in some genes in which these ancestral races differed. And yet, a polytypic species may still evolve as a single genetic system. Favorable mutants or gene combinations arrived at in one part (race) of such a species may, under the influence of natural selection, eventually spread to all other parts and thus become a common property of the entire species. Thus, local autonomy of the gene pools of racial populations does not preclude retention of a basic unity of the species as a whole. I would like to point out that this view agrees quite well with the conclusions reached by the late Weidenreich on basis of purely morphological analysis of pre-human populations. This is worth while [sic] stressing because Dr. Weidenreich has sometimes used expressions which seemed to put him close to the old-fashioned polygenist camp, which he actually rejected absolutely (Dobzhansky, following Stewart 1950:106-107).

I love these discussions, which often included exactly the people whose opinions you would like to see, and sometimes some surprising ones. For instance, after Dobzhansky in this particular discussion, Joseph Birdsell and Stewart had an exchange about the implications of the fluorine dating of Piltdown for interpreting variability within modern humans (Birdsell's point being that such an apelike jaw must extend the variability of Homo sapiens even further if it is actually recent! Ha!)

And they often jumped off on tangents, like the Piltdown tangent, which remind you of the other things that people cared about besides the immediate topic. I think it's the closest thing to science blogging that the 1940's and 1950's had to offer!

References:

Stewart TD. 1950. The problem of the earliest claimed representatives of Homo sapiens. Cold Spring Harbor Symp Quant Biol 15:97-107, comments following.

Elizabeth Pennisi has a news article in today's Science with the headline, "No Sex Please, We're Neandertals." It covers a couple of talks by Svante Pääbo at a Cold Spring Harbor meeting.

I'll get to the headline in a second; first I want to point out the more interesting paragraph at the end of the piece:

In a side project, Pääbo and his graduate student Johannes Krause have examined 30,000- to 38,000-year-old human fossils from Uzbekistan and the Atlai region of southern Siberia whose identities were a mystery. When the researchers compared the bones' mitochondrial DNA with that from more than a half-dozen Neandertals, they found that the Asian fossils were clearly Neandertal. "It tells us that Neandertals were much more widespread than we thought," says Pääbo.

It's not entirely unexpected that the biological population of central Asia was Neandertal-like during this time range; many researchers have long classified the Teshik-Tash child from present-day Uzbekistan as a Neandertal. I wouldn't go so far, but there are anatomical similarities between this specimen and European Neandertals that suggest gene flow right across central Asia.

What's interesting about the mtDNA result is that the Neandertal mtDNA lineage is defined by a number of distinctive mutations, all of which took some time to occur on that branch. The variation within Neandertals so far is quite limited -- much like the variation within recent humans is limited. And the date of separation of the Neandertal and recent human clades is also relatively recent -- between around 350,000 and 700,000 years ago.

So Neandertals were a population that was circumscribed to a small amount of mtDNA variation, like recent humans. This we already knew. But the large geographic extent of their mtDNA clade shows that they were a geographically widespread population -- from Spain to the border of China -- with a very small amount of mtDNA variation. Like recent humans.

And like recent humans, relatively rapid genetic dispersals appear to have been possible over long distances. That's not the stereotype of Neandertal population dynamics we're used to reading.

Now, about that interbreeding thing.

In one of last fall's Neandertal genome papers, Green and colleagues (2006) reported that the putative Neandertal sequence included an unusually high number of human-derived SNPs -- that is, polymorphisms in humans where both the Neandertal and some humans carried a derived mutation, while other humans carried the ancestral nucleotide.

These human-derived SNPs are important because they are likely to be relatively recent; and mutations that recently emerged in humans should be less likely to be found in a Neandertal. That is, unless Neandertals were interbreeding with the ancestors of living people. This isn't quite the same thing as Neandertals being the ancestors of living people; the comparison doesn't test for the direction of gene flow, which conceivably was one-way gene flow into Neandertals. Still, it was pretty striking evidence for Neandertal-human genetic interactions (as I pointed out in my FAQ post), if it was true.

But there was some doubt about the conclusion of gene flow. For one thing, the sequence might be contaminated by DNA from a recent human. There still is no way to tell from these sequencing techniques whether a given fragment of DNA from the fossil is actually endogenous to the fossil, or whether instead it is a contaminating sequence from some living (or recently dead) person. There's still no solution to this problem, beyond the claim that the sequence contains a small proportion (maybe less than 6 percent) of mtDNA contaminant sequences from recent humans. But 6 percent contamination could put a lot of human-derived SNPs in the sample, making it look like gene flow existed where none actually did.

The second reason for doubt was that databases of human SNPs are biased toward common alleles. That is, when people are looking for genetic markers (usually for medical research), they tend to exclude very rare polymorphisms and focus on ones where the alleles are nearer to 50 percent frequency. This is called an ascertainment bias. The bias is a problem for the Neandertal comparison because common alleles are more likely to be older than rare alleles. Which means that the human-derived SNPs in the human databases are probably somewhat older on average than theory would predict in the absence of this ascertainment bias.

In other words, these human-derived SNPs are interesting because they ought to be recent, but in fact the sample of SNPs that we have is likely to be older than they ought to be.

Now, this might make a difference to the hypothesis of Neandertal-human gene flow, or it might not. There is a pretty simple way to find out whether it makes a difference -- just work out the ages of the human-derived SNPs in humans.

Apparently, this isn't what the research did. Instead, they decided to limit the human comparison to two individuals -- attempting to zero-out the ascertainment bias.

So David Reich of Harvard Medical School in Boston and James Mullikin of the National Human Genome Research Institute in Bethesda, Maryland, have now compared SNPs in new Neandertal sequences to random SNPs obtained from one African and from one European. The result: "There's no indication of gene flow," Pääbo reported. Pääbo and his group got the same result when they examined variation in the Y chromosome, looking for signs of Homo sapiens DNA embedded in the Neandertal sequence.

It may never be possible to prove beyond doubt that interbreeding did not occur. "But if I were to make a guess, I would say more sequence will just confirm [these results]," says Noonan. "It convinces me."

The Y chromosome is expected; the recent human coalescent is so recent that a descendant sequence would be very unlikely to be found in this Neandertal.

Much depends on how the "random" SNPs were obtained, so I can't evaluate until I see more details. For example, if they were obtained by resequencing the same million base pairs in two humans as has been recovered from the Neandertal sequence, that would probably work. On the other hand, if they were obtained by bootstrapping already-existing SNPs from two HapMap individuals ... well, that's probably not the best idea.

And we are still left with the contamination problem. The thing is, contamination predicts that there ought to be an excess of these human-derived SNPs in the Neandertal sequence. Some of them should be in that sequence because of contamination, if for no other reason. So if they aren't finding any evidence of them in their comparisons, hmm...

In any event, none of these comparisons really address the most likely reason for gene flow from Neandertals into recent humans (or vice versa), which is selection. If the number of introgressing genes was relatively modest, we wouldn't expect to see a large number of human-derived SNPs in the Neandertal sequence, even though the gene flow between the two populations was highly important to their fitness. I've gone into this before, and of course it was the subject of one of my papers last year.

References:

Pennisi E. 2007. No sex please, we're Neandertals. Science 316:967. doi:10.1126/science.316.5827.967a

The NY Times gave a short writeup earlier this week to a paper about ancient DNA from arctic foxes:

"We wanted to know what happened with the Arctic foxes over the transition from the ice age to the current warm period," Dr. Dalen said. "When the tundra shifted up to Scandinavia and Siberia, did they move too?"

The researchers analyzed DNA from fossilized fox bones found at European ice age sites, and compared it with DNA from the current Scandinavian and Siberian populations. They found that there was no connection between the ancient and modern populations.

"They didn't move," Dr. Dalen said of the European animals. "That whole population is extinct."

The paper itself is a simple, 3-page read. The newsworthy element of the paper is its relationship to climate change -- with the implication that the current genetic diversity of many species will be lost if climate change restricts them to a limited part of their ranges. In the Pleistocene, habitat changes happened without humans getting in the way. So the observation that foxes didn't "track" the movement of their habitat as the glaciers receded means that today's species are very unlikely to do so, if climate zones move in the near future.

But I found a different implication to be more interesting. Arctic foxes that live in northern Scandinavia today are essentially occupying a refugium -- a shrunken fragment of their original habitat. The ancient DNA shows that foxes across northern France, Germany, and Russia were not mtDNA ancestors of today's Scandinavian foxes. While foxes occupy an interglacial refugium, we can look at their mirror image in the glacial refugia of European species; notably Neandertals.

During the height of the last glaciation, Neandertals appear to have been constrained to the southern tier of Europe -- possibly limited at some times to Iberia, Italy, Croatia and points further south. Usually, when people talk about these refugia, they mention northern European populations moving south. But Southern Europe was already full of Neandertals, and there probably was no moving south for the increasingly marginal populations of France, Germany, and other parts of northwest Europe when the climate deteriorated. If they followed the fox model, then northern Neandertal populations may have simply became extinct during each glacial maximum. Southern populations may have undergone substantial demographic turnover also, since glacial and interglacial conditions would have selected for different phenotypes for some characters.

There are many differences between arctic foxes and Neandertals in geographic range and life history, so it is certainly possible that Neandertals moving south maintained greater population continuity than the foxes moving north. Small mammals may grow their population faster than they can disperse over long distances. For Neandertals, that may be less true -- long-distance dispersal would certainly have been possible; the question is whether the population density of the southern refugia would have allowed it.

In general, I think the fox analogy is probably a good one, since carnivores have large home ranges and dispersal distances for their size. The home range size of arctic foxes today averages between 20 and 50 km² (Eberhardt et al. 1982; Landa et al. 1998), depending on the local habitat. Pups disperse outside their parents' home range for the most part, with a dispersal distance between 20 and 40 km (Strand 2000). The home ranges of Neandertals were larger,

The periodic reduction of Neandertals to glacial refugia in southern Europe would have set up a pattern of extinction and recolonization across most of Europe. This must have been a very important demographic force in Neandertal evolution -- since the continent underwent repeated episodes of climate change, possibly on a submillenial basis during the Late Pleistocene. During each range restriction, a nonrandom sample of southern European Neandertals survived and increased their relative gene frequencies compared to other Neandertals. Whenever conditions were suitable, this southern European population was the "first on the scene" to expand into the empty habitat of central and northwestern Europe. We can imagine some strong gene flow from outside Europe also, but the demographic growth of southern Europeans made their relative allele frequencies increase with a pulse every time the population expanded.

Hence, most of Europe was a pulsed population sink. Significant source populations in southern Europe may have maintained substantially distinct allele frequencies than contemporary populations outside Europe, both as a result of restricted gene flow during glacials and as a result of strong selection for dispersal and colonizing ability. These conditions would explain a relatively strong mtDNA distinction between Neandertals and some contemporaries, in comparison to relatively slight autosomal and X chromosomal differences. The mtDNA is much more strongly affected by restricted and temporally intermittent gene flow because of its smaller effective size. In a growing and shrinking population, the effective size of mtDNA would have made it more strongly affected by drift than other loci. In effect, it may be the strongest signature of this evolutionary pattern.

That's what seems to be the story with the foxes. The ancient mtDNA shows a lack of close relationship between today's arctic foxes in Scandanavia and Pleistocene populations further south. The range contraction had a strong effect on mtDNA. It will be of interest to see if autosomal genes show a similar effect, or whether instead they share the Neandertal-modern pattern of slight differences.

So far, so good. But there are a couple of kinks. More later.

References:

Dalén L and 8 others. 2007. Ancient DNA reveals lack of postglacial habitat tracking in the arctic fox. Proc Nat Acad Sci USA 104:6726-6729. doi:10.1073/pnas.0701341104

Eberhardt LE, Hanson WC, Bengtson JL, Garrott RA, Hanson EE. 1982. Arctic fox home range characteristics in an oil-development area. J Wildlife Management 46:183-190.

Landa A, Strand O, Linnell JDC, Skogland T. 1998. Home-range size and altitude selection for arctic foxes and wolverines in an alpine environment. Can J Zool 76:448-457.

Strand O, Landa A, Linnell JDC, Zimmermann B, Skogland T. 2000. Social organization and parental behavior in the arctic fox. J Mammal 81:223-233. doi:10.1644/1545-1542(2000)0812.0.CO;2