ancient DNA

So, they've resurrected 45-million-year-old yeast from amber, and are using it to brew beer under the "Fossil Fuels" label:

The beer has received good reviews at the Russian River Beer Festival and from other reviewers. The Oakland Tribune beer critic, William Brand, says the beer has "a weird spiciness at the finish," and The Washington Post said the beer was "smooth and spicy."

Part of that taste comes from the yeast's unique metabolism. "The ancient yeast is restricted to a narrow band of carbohydrates, unlike more modern yeasts, which can consume just about any kind of sugar," said Cano.

I have this incredible compulsion to taste the stuff. Actually, I really like the entire idea of the taste qualities of these micro-adapted yeast strains -- which go into everything from San Francisco sourdough bread to the wild yeasts living on grape skins in Bordeaux.

But last week I went to a talk by Alan Moses, who's been working in "population genomics" -- essentially, comparative population genetics taken across the genome. The major model organisms for this work so far have been yeast -- the domesticated Saccharomyces cerevisiae and its wild relative Saccharomyces paradoxus. There were a lot of interesting things coming out of that work (not only about yeast, but also about people and mice).

One of the easiest analyses was a simple overlay of phylogeny on geography for the two yeast species, described in a preprint by Moses' collaborators on Nature Precedings. The wild S. paradoxus has a very clear population structure, with genetically distinct populations in Europe, America, East Asia, and Hawaii. These populations are easily pulled out of a STRUCTURE analysis, so there are a large set of distinctive alleles that characterize them.

In contrast, the domesticated S. cerevisiae has been extensively crossed, hybridized, and managed by humans. This has led to a population structure that does not clearly distinguish strains by their geographic locations -- and in fact, strains are not easily distinguished by their use (wine versus sake, for instance). The geographic structure has largely been smudged out of existence by human intervention and recombination between strains. Moreover, some changes of adaptive importance, such as nonsense or missense mutations in the galactase pathway, have been repeated more than once in these human-managed strains. That's a very clear contrast, and other aspects of the genomic variation bear the marks of selection.

To me, there is a practical import to these analyses. If the domesticated strains have tuned in countless ways to operate in our food, what are the chances that genuine "wild" strains of yeast have actually persisted for years and years in the face of this boundary-crossing contact between yeasts? We say that these are original wild yeasts, because a lump of starter has been replenished and renewed for years and years, or because the natural yeasts enter from the grape skins, or some other story. But that starter is not in a hermetically sealed chamber, and people don't put on bunny suits to work on it. Our gregarious domestic yeast strains have gotten in there, and they've probably replaced the original yeast strains many times over.

So, if we take yeast out of 45-million-year-old amber, what are the chances it's going to last long in culture? Maybe it will do surprisingly well. But this is a case where genetic barcoding might be in order.

References:

Carter D, Liti, G, Moses A and 22 others. Population genomics of domestic and wild yeasts. Preprint. Available at Nature Precedings

Mitochondrial phylogeography is a useful tool for the study of wild populations. But applying phylogeography to domestic species is more complicated....

A classic example of the use of mitochondrial DNA (mtDNA) diversity to infer the history of domestication refers to dogs (Canis familiaris). Four to six mitochondrial haplogroups (Hg) have been described in genetic studies of modern dogs, indicating recurrent domestication or backcrosses between domestic dogs and wild wolves (Canis lupus). Three of the major Hgs are distributed throughout the world, whereas one (D) is restricted to Europe, especially in breeds originating in Scandinavia. Similar patterns of fragmented genetic diversity have been used to argue for local domestication in other species. Such scenario could apply to dogs as they appear as early as 9000 years ago in Scandinavia, and as dogs and wolf remains have been found on the same sites (Malmström et al. 2008:4).

So, they sampled ancient DNA from Neolithic and medieval dog skeletons, to look for the D haplogroup, which would provide evidence that these ancient dogs had a unique and separate origin from other domesticated dogs elsewhere in the world.

Except, it wasn't there.

Our results indicate that Hg frequencies have been altered in Scandinavian dogs since their first arrival. Interestingly, while Hg C is overrepresented in our ancient material, there is a complete lack of the Scandinavian group D in our ancient dataset. Hg D is the one that could support a Scandinavian origin whereas Hg C is suggested to be of Asian origin. Thus, we find no obvious evidence for prehistoric canid domestication in Scandinavia. An external origin of Scandinavian dogs is supported by morphologic data, as even the oldest remains of dogs in Scandinavia were of smaller size than those of prehistoric and extant wolves. While canid domestication may have occurred in other parts of Europe, Scandinavian dogs were likely imported and had experienced a long period of morphological change under human control before they reached the Scandinavian peninsula (Malmström et al. 2008:7).

Fair enough -- the mitochondrial gene pool of Scandinavian dogs has rapidly changed under human influence during the last few thousand years. No word on where the D haplogroup that characterizes today's Scandinavian dogs has come from; whether introgression from local wolves or dogs elsewhere in Europe.

Why does this remind me of human evolution? Well, consider this 2005 paper by Wolfgang Haak and colleagues:

Here we present an analysis of ancient DNA from early European farmers. We successfully extracted and sequenced intact stretches of maternally inherited mitochondrial DNA (mtDNA) from 24 out of 57 Neolithic skeletons from various locations in Germany, Austria, and Hungary. We found that 25% of the Neolithic farmers had one characteristic mtDNA type and that this type formerly was widespread among Neolithic farmers in Central Europe. Europeans today have a 150-times lower frequency (0.2%) of this mtDNA type, revealing that these first Neolithic farmers did not have a strong genetic influence on modern European female lineages.

I discussed this paper when it came out, noting that one explanation for the results is selection, either in favor of the N1a type in Neolithic farmers or against it later. The change in frequency in post-Neolithic Europeans is clearly not consistent with drift. On the basis of other genetic loci, migration from other populations cannot explain the catastrophic decline in frequency of the N1a type, which the ancient DNA data show was widespread across central Europe. So, there would appear to have been local selection against N1a.

The Scandinavian dogs are showing the inverse pattern -- a now-common mtDNA type was formerly not present at a measurable frequency, at least in the available sample of ancient dogs. With dogs, of course, there is every reason to expect selection imposed by humans. The only question is whether the selection was directly on the mtDNA itself, or whether the mtDNA has been carried along fortuitously with other selected genes. The extreme inbreeding under recent intensive breeding would allow either scenario -- unlike in humans, where no extreme inbreeding occurred.

I want to point out the parallels and differences clearly, because I'm writing this week about effective population sizes and inbreeding. There are many geneticists who hold out the possibility of extreme degrees of inbreeding in post-Neolithic humans. Genetic, archaeological and historic data -- not to mention common sense -- weigh against this possibility. However, many prefer to maintain a strict view that natural selection occurs rarely, if ever.

(via Dienekes)

References:

Malmström H, Vilà C, Gilbert MTP, Storå J, Willerslev E, Holmlund G, Gotherstrom A. 2008. Barking up the wrong tree: Modern northern European dogs fail to explain their origin. BMC Evol Biol 8:71. doi:10.1186/1471-2148-8-71

Haak W, Forster P, Bramanti B, Matsumura S, Brandt G, Tänzer M, Villems R, Renfrew C, Gronenborn D, Alt KW, Burger J. 2005. Ancient DNA from the first European farmers in 7500-year-old Neolithic sites. Science 310:1016-1018. doi:10.1126/science.1118725

There's a fun paper in last month's Molecular Biology and Evolution by Georgina Bowden and colleagues, investigating whether the Viking influence on surnames in England is mirrored by Y chromosomes. This is one of those chapters in English history that people should know more about:

A useful test case to evaluate the potential of surname-based ascertainment is provided by the 1,000-year-old Viking settlement of the British Isles. The Viking age of raiding, exploration, trading, and colonization began in the late eighth century, with a series of attacks on the coasts of Britain, Ireland, and France. In England, a shift from raiding to permanent settlement began after AD 865. The modern consensus has moved from the earlier view of a mass migration of Viking settlers to a more geographically variable and gradual process, with much assimilation of local culture, under the administration of a Scandinavian elite (Richards 2004). Even though Viking rule in England came to an end nearly 1,000 years ago and the settlers were soon integrated linguistically and culturally, abundant evidence of Scandinavian influence remains today. Important archaeological findings exist, but the most striking evidence is linguistic and onomastic -- many words in Standard English and in local dialects, and many place-names, are of Scandinavian origin. In some areas of English counties that formed part of the Danelaw (fig. 1), the region under the administrative control of the Vikings from the late ninth century, up to 70% of major place-names are in this category, with endings such as "-by" and "-thorp(e)" (Bowden 2008:301-302).

What a word: "onomastic"!

The paper has a nice bit of this history. The general idea of the study was to assess whether a genetic sampling focusing on surnames that were present in the past can give an accurate picture of the genetic structure of the population in the past. To this end, they were able to exploit historical records that include lists of surnames present in northwest England more than 500 years ago.

Gene lineages erode out of populations over time. Every individual has a substantial chance (> 15%) of not having any children at all, and every time a person has no children, any unique gene lineages he carries will become extinct. Immigration can replace a population's ancient lineages with genes from elsewhere. So the genes that did characterize an ancient population disappear, while the genes that characterized other ancient populations may come to roost. Taken over enough time, everyone in every population is a descendant of immigrants, because human populations have emerged through mixture and dispersal. Anthropologists try to work out where and when the important dispersals and contacts happened. To do this, they sometimes try to reconstruct the ancient genetic structure of a population, attempting to see how it differs from the present genetic structure.

Information about the ancient structure of a population is hard to come by. By far the best source of information is ancient skeletons. Sample the DNA sequences from the ancient bones themselves and you can determine the genetic structure of their owners. But that's expensive and takes some luck -- you have to have enough ancient bones that preserve DNA and the right to grind them up.

If you had some kind of accurate indication of which people descend primarily from immigrants and which ones have mostly local ancestors, you might be able to sample the mainly local people's genes to get an idea of the genetic structure of the ancient population. This idea won't work well for most genes, because immigrants don't remain a separate, inbred population for long -- over the years (in this case, hundreds of years) they intermarry and blend into the population. People with immigrant surnames come to have the same genes as everyone else.

These authors propose that patrilineal English surnames let them reconstruct the genetic structure of Y chromosomes in the men of northwestern England more than 450 years ago. Over that time span, surnames have been conservative enough (and paternity confidence high enough) that most men who share a rare surname today also share closely related Y chromosomes. Hence, they may serve as a proxy for men who carried the same surname in the past. If you have a record of the surname proportions, you can substitute in today's Y chromosomes to estimate the past population structure.

They find that around 50 percent of northwest English men once descended from Viking patrilines. That's a surplus over today's value, which is under 40%:

The medieval sample from West Lancashire shows an increased proportion (51 ± 4%) of Scandinavian ancestry compared with its modern counterpart (38 ± 4%); the equivalent values for Wirral are 47 ± 5% and 38 ± 3%. These differences, revealed by our different sampling strategies, are likely to reflect a change in haplotype frequencies due to postmedieval immigration and are supported by genetic distances (FST) between the Norwegian sample and the Wirral and West Lancashire samples. FST between Norwegians and the West Lancashire modern sample is 0.130, whereas the value for the medieval sample is only 0.069; corresponding values for the Wirral samples are 0.162 and 0.096.

I don't want to oversell this study. The surname approach may work reasonably well for Y chromosomal diversity across a few hundred years, in strongly patrilineal societies. The idea starts to show weaknesses over longer time periods, as evidenced by the problems documenting the "Cohen modal haplotype" -- another Y chromosome-surname association. And it won't work at all for other genes, which are inherited from the mother as well as the father. The last paragraph of the study reflects on the limitations:

The use of patrilineal surnames in ascertainment provides both the power of our approach and its major limitation because any analysis of the structure or history of populations based on a single genetic locus, the Y chromosome, has inherently low power and population statistics calculated from Y data have high variance (Wilson et al. 2001). Furthermore, we can learn nothing about changes in the maternal genetic landscape, which is unfortunate, because the role of women in the Viking colonizations was as important as that of men (Jesch 1991). Nonetheless, in the absence of a time machine, the link between a haplotype and a cultural marker, the surname, may provide the only practical means to access the genetic composition of populations in the past. As well as allowing us to investigate the influence of migration and drift over the last few centuries in changing the population structure of Britain, the method should be applicable to other regions where surnames are patrilineal and suitable historical records survive.

Still, I wish that there were more papers like this, incorporating history with genetic information. Too many geneticists actively shun historical and archaeological evidence, preferring to rely on genes alone. Sure, at some superficial level they may tie their findings in to a "what everybody knows" version of history, but they don't report any history or archaeology in their papers, and they shelter their students from needing to learn any. That's a strategy for some pretty boring research, and these geneticists are leaving on the table some of the strongest evidence about recent human events.

References:

Bowden GR and 13 others. 2008. Excavating past population structures by surname-based sampling: The genetic legacy of the Vikings in northwest England. Mol Biol Evol 25:301-309. doi:10.1093/molbev/msm255

That's the strand of this LiveScience article:

Contamination from bacteria DNA generally make up 50 to more than 90 percent of the raw DNA extracted from the bone and muscles of ancient specimens, [University of Copenhagen reseracher Tom] Gilbert said. In contrast, more than 90 percent of the DNA extracted from hairs taken from woolly mammoth specimens in the new study belonged to the extinct mega-mammals themselves.

It sounds like this might make a difference to forensic work:

The new study overturns previous assumptions about where in hair DNA could be harvested. "When people thought of sequencing DNA from hair, the usual assumption was that the material must come from the hair root, which contains recognizable cells, because the hair shaft appears to be dead," said study team member Webb Miller of Pennsylvania State University.

That reminds me, CSI starts its fall season tonight. As if I needed reminding...

No Neanderhair, unfortunately. Of course, if we had real live Neanderthals, like that show that starts next week, I'd be after them like the OSI guys after Jaime Sommers. Or we could just send Hiro back in time to get a sample...

Nicholas Wade writes to answer the mammoth cloning question. I know, nobody cares about anything else. It's always, "Clone, clone, clone!"

Well, keep this in mind:

The reconstructed sequence of DNA units would then need to be turned into an actual mammoth genome. Mammalian genomes are made up of chromosomes of about 100 million DNA units in length and are beyond the capacity of current synthesis. Still, researchers at the Venter Institute in Rockville, Md., say they are close to synthesizing the genome of a bacterium that is 500,000 units long.

There's a lot of doing between a bacterium genome and a chromosome. Don't hold your breath.

And then, there's the picture:

Inspecting the baby mammoth carcass. Photo credit: Sergei Cherkashin/Reuters

Here's a piece of advice: If the room is warm enough for tank tops, it's too warm to preserve permafrost mammoth sperm.

No, that's not Henry Harpending. At least, I don't think it is...

It's another week, which means it's time for another of the mysteriously-not-yet-appeared PNAS papers. But this time, a friendly source sent me the paper (which should be here, when it appears).

You can see my comments on it in David Biello's article at Scientific American.

Basically, this is the analysis of DNA damage in the genome sequence coming out on the 454 sequencing platform. They show the damage as limited to two kinds of chemical changes, which generate spurious C->T and G->A substitutions. Also, the position of the nucleotide in the sequencing read makes a difference, as terminal nucleotides have more than 5 times as many spurious errors than some internal ones. There is a lot of detail in the paper about all of this.

The interesting part is near the end, where the paper discusses ways to quantify contamination and correct for misincorporated bases. Basically, one can quantify and correct all such problems with multiple coverage. The more copies of a given sequence are produced, the more it becomes possible to estimate the proportion of contaminant sequence -- at least in areas where the contaminant may be differentiated based on its sequence. But even where contaminants are possibly identical to the endogenous sequence, it may be possible to find them in various ways (for example, if three homologous sequences were present instead of two, or if a significant excess of some particular sequence were present. Likewise, misincorporations can be found and corrected with multiple reads.

The demonstration of these problems helps to increase confidence in the outcome: if we understand the errors, we can better evaluate results. The important (and unanswered) question is how much fossil grinding it will take to get good genomes.

References:

Briggs AW and 10 others. 2007. Patterns of damage in genomic DNA sequences from a Neandertal. Proc Nat Acad Sci USA (early)

An article by science writer Henry Nicholls in PLoS Biology covers a lot of ground. Most of the attention goes to Alan Cooper, with Svante Pääbo in a supporting role. There is this on the hobbits:

aDNA could also, in principle, be used to shed light on the evolutionary position of the 18,000-year-old "hobbit" recently unearthed on the Indonesian island of Flores [8]. Both Cooper and Pääbo have offered to have a go at isolating DNA from the "hominid" skeleton, but the early signs are that DNA has not survived. "The somewhat moist and tropical preservation conditions make the recovery of DNA improbable," says Peter Brown, the paleoanthropologist at the University of New England in Armidale, Australia, who led the hobbit study. Efforts to extract DNA from other bones collected at the same site as this tiny hominid have not produced results. "We have made attempts with Stegodon molars," he says, "but so far without success."

I am most impressed with studies that survey many ancient specimens to make conclusions about ancient population dynamics, such as local extinctions and recolonizations. The recent arctic fox paper is a great example. This article mentions two more: a study of ancient bison fossils from Beringia, and a study of arctic brown bears. Here's a paragraph about the bison study:

Cooper's latest work has analysed DNA from over 400 bison fossils from Beringia—the frozen wastes between eastern Siberia and the Canadian Northwest Territories [3]. "What we've done is carbon-date a shitload [JH --is that a metric shitload?] of bison and get DNA out of them." It's the largest aDNA study to date, he says (Figure 1). The icy conditions mean that good quality mitochondrial DNA could be extracted from most of the specimens. The bison could also be dated accurately. This allowed Cooper and his colleagues to trace the changes in the bison genetic diversity from 150,000 years ago to the present. It was even possible to predict the effective population size throughout this period of bison evolution. "Our analyses depict a large diverse population living throughout Beringia until around 37,000 years before the present, when the population's genetic diversity began to decline dramatically," they note.

The main drawback of these studies has been their limitation to mitochondrial DNA. The story of that one molecule is informative, but it is not the whole story -- and in particular, it may reflect selection associated with climate change, not just extinction and population expansion.

That is the main reason the Neanderthal genome is so important -- it allows us to compare the vast majority of the genome to find evidence of functional changes. Likewise, the ability to look at many genetic regions is a highlight of the described work on early maize domestication:

Pääbo's analysis suggests that the alleles typical of contemporary maize were already present in Mexican maize 4,400 years ago, so just a couple of thousand years after its initial domestication from the wild grass teosinte (Figure 3). "Quite early on, properties were selected that were not only the structure of the plant but also the biochemistry," he says.

There is really a light year of difference between the labs bringing out nuclear genomic sequences and those working exclusively with mtDNA. There is so much more information to be had from the full genome that these datasets will keep PhD's busy for decades.

But for the time being, labs that limit to mtDNA are able to bring out more and more sequences from different individuals. This adds the essential component of population variability, which is essential to understanding the dynamics of evolutionary change. So it's like we are getting a third of the story from each of these sides -- with the other third coming, of course, from traditional morphological comparisons.

References:

Nicholls H. 2005. Ancient DNA Comes of Age. PLoS Biol 3: e56. doi:10.1371/journal.pbio.0030056

What's behind the headline about "resurrecting an ancient virus"?

The study, which appears tomorrow in Science, focuses on Pan troglodytes endogenous retrovirus (PtERV1). More than 100 copies of inactive PtERV1 are sprinkled throughout the chimpanzee and gorilla genomes, whereas humans have none. "About 4 million years ago, this virus was active and independently infecting all these species, but not humans," says virologist Michael Emerman, who conducted the study with evolutionary biologist Harmit Malik and postgraduate student Shari Kaiser, all of whom work at the Fred Hutchinson Cancer Research Center in Seattle, Washington.

That's a pretty radical genome-wide difference between humans and the African apes. It's interesting that the chimpanzee and gorilla lineages were capable of exchanging viruses from early in their evolution. If they are right about the 4 Ma age, that is about halfway between the common ancestor of chimpanzees and gorillas (around 7--10 Ma) and today. Since they still exchange viruses today (including Ebola), you might think that it wouldn't be surprising that they did so in the Pliocene. But I think it's important because it establishes sympatry of the two apes: the ancestors of today's chimpanzees and gorillas lived in the same geographic region. If the two lineages originated in an allopatric speciation, then they had expanded their ranges by the Pliocene to overlap with each other. And sympatry means that they must have been adaptively differentiated by that time.

The now-extinct virus was interesting to this research group for another reason: apparently, a protein essential to HIV resistance in other primates lets humans down by being resistant to the extinct virus. This is a pretty tricky storyline, so I'll try to explain. The protein is named TRIM5α, it is key to the immune response to viruses. The human form of the protein does not do a good job of fighting HIV, and some other primates have a form that resists HIV infection must more effectively. So this protein has been a focus of HIV research.

When Kaiser and colleagues examined the sequences of the ancient retrovirus imprisoned in the chimpanzee genome, they found that one of the virus' genes interacts with TRIM5α. Prior work had established the variation among primates in TRIM5α's response to HIV. Now, they found that no known primate TRIM5α sequence provides an effective response to both HIV and the ancient chimpanzee virus.

In other words, this ancient chimpanzee virus, PtERV1, is like the immune system equivalent of Bizarro Superman -- it's just the opposite of the real thing.

In terms of hominid evolution, there is the obvious question of why humans never acquired the many endogenous copies of this viral genome. Clearly, ancient hominids did not have the virus in substantial enough numbers to result in its incorporation into our genome. But why not? In particular, did our TRIM5α sequence protect us?

Here's what Kaiser and colleagues have to say:

Although we cannot rule out the possibility that PtERV1 never infected human ancestors for other reasons (SOM Text, note 1), our data do suggest the possibility that TRIM5 was fixed in human populations because of its ability to confer protection against PtERV1 (Figs. 2 and 3) and that modern humans have descended from ancestors who resisted infection. Indeed, we know that there is very little diversity in the human population today in the part of TRIM5 that determines antiviral specificity (6, 16, 17). However, we find that chimpanzee TRIM5 is also capable of restricting PtERV1 and encodes an R332 (Fig. 3), yet chimpanzees contain multiple copies of PtERV1 in their genome and humans do not. Moreover, we find that R332 is monomorphic in the TRIM5 allele in all four subspecies of chimpanzees and in bonobos, which indicates that R332 is evolutionarily conserved through the chimpanzee radiation (in the past 1 to 2 million years). The most parsimonious explanation for the presence of R332 in humans and chimpanzees is that the mutation was fixed in our common ancestor, which presents a paradox because chimpanzee TRIM5 did not protect them against PtERV1. This suggests that TRIM5 alone does not determine retroviral invasion into the germline but that the combination of multiple retroviral restriction factors that are also rapidly evolving, such as the Apobec3 family (18), are necessary to explain ancient transmission events.

Well, no one can say for sure, but I think it seems pretty unlikely that the hominid TRIM5α gene is the result of selection against infection by this particular virus. The chimpanzee and gorilla genomes have more than 100 copies of the viral DNA in their genomes, which means that it was a long-term infectious agent in those lineages, and its genome was often incorporated into its hosts' germlines. It is probable that these viral genes evolved neutrally after being incorporated into the chimpanzee and gorilla genomes: if they were deleterious, they would be gone; if they were adaptive, they would probably be more highly conserved. Neither chimpanzees nor gorillas are known to carry the live virus today, which is therefore presumed to be extinct. If true, that means that both chimpanzees and gorillas lost the virus, probably sometime before 3 million years ago. This loss occurred either because of convergent genetic adaptations in both lineages (I say convergent because they may or may not have involved the same genes), or because of extreme bottlenecks during which the longtime viral parasites were lost by chance.

Now, consider some hypotheses:

Hypothesis 1: The virus was a longtime hominid pathogen, to which TRIM5α was an adaptation. If this were true, then the human genome ought to harbor at least some copies of the viral DNA. It has none. So this hypothesis probably isn't true.

Hypothesis 2: The virus was a severe short-term epidemic in ancient hominids, and we are descended from the only survivors, who happened to have a resistant TRIM5α allele. This is the hypothesis proposed in the quote above. If this were true, then we wouldn't necessarily expect to see copies of the viral genome in human DNA -- the infection and population crash may have happened too fast. But a single epidemic, or even a succession of several epidemics of the virus, would be unlikely to fix a variant allele. After all, neither the Black Death nor smallpox, nor any other historical epidemic has managed such a feat. And viruses with such exceptionally high death tolls do not tend to sustain epidemics through sparse populations like ancient hominids. Indeed, it seems likely that the virus' long survival in chimpanzees and gorillas implies that its hosts survived for a long time with the virus, and dispersed it as they encountered other individuals over time. If the virus let its hominid victims live a long time and thereby spread across low-density hominid populations, then there ought to be at least some copies of it in our genomes. And there aren't any. Also, the TRIM5α protein has a strong signature of positive selection in the human lineage, which means that there have been multiple selected substitutions. Multiple substitutions are very unlikely to have happened simultaneously; it is more likely that they occurred sequentially, taking a long time. So this hypothesis probably isn't true, either.

Hypothesis 3: The virus never infected hominids, who were, after all, allopatric from chimpanzees and gorillas. Instead, some other virus -- or more probably, several viruses -- infecting ancient hominids explain the evolution of the human TRIM5α gene.

I like hypothesis 3 the best; the data don't seem to reject it. Humans are not very susceptible to the PtERV1 virus. Indeed, our own TRIM5α variant, alone or with other genetic adaptations, have have helped to prevent the virus from infecting ancient hominids at all. Or maybe our ancestors never encountered the virus and our TRIM5α is a result of later events.

I should add, from a quick look at Sawyer et al. 2005, that chimpanzees and gorillas share at least one parallel amino acid subsitution in the rapidly-evolving SPRY domain of TRIM5α -- at position 340. The current paper (Kaiser et al. 2007) notes that humans and chimpanzees share a derived amino acid substitution at position 332. That position (332) is important because the biochemical work by Kaiser et al. 2007 and others has shown it is a critical site for human susceptibility to HIV:

For example, the amino acid at position 332 within this patch is a critical determinant of HIV-1 restriction (13). Humans and chimpanzees encode an arginine (R) residue at position 332, whereas the hominoid ancestral residue at this position is a glutamine (Q). Reversing this change (R332Q) had moderate effects on the ability of human TRIM5α to restrict MLV variants (fig. S2). Notably, changing the arginine to the ancestral glutamine abolished the ability of human TRIM5α to efficiently restrict PtERV1 infectivity (Fig. 2B). Unexpectedly, the R332Q mutation had the opposite effect on HIV-1, improving the ability of human TRIM5α to restrict this virus (15) (Fig. 2B). Thus, the R332Q mutation in human TRIM5α reveals a trade-off in TRIM5α's ability to restrict two retroviruses; a mutation that abolished restriction for PtERV1 results in a gain of restriction to other viruses such as HIV-1.

It would be interesting to see what difference the chimpanzee and gorilla alleles at position 340 make; perhaps their TRIM5α protein remains constrained by selection from yet another pathogen?

In any case, during the last few years we have learned a great deal about ancient selection in hominids associated with pathogens. And most of what has come out has been gross changes such as pseudogenization. In this instance, the key information comes from a genomic comparison showing the huge importance of an ancient pathogen in both chimpanzees and gorillas, but not humans.

It is hard to overstate just how glaring these comparisons are -- they are not at all subtle. If most genetic changes during human evolution have been like precision-aimed shots from a sniper rifle, these disease-associated adaptations we've been finding are like blasts from a cannon.

So there is a lot left to discover.

References:

Kaiser SI, Malik HS, Emerman M. 2007. Restriction of an extinct retrovirus by the human TRIM5α antiviral protein. Science 316:1756-1758. doi:10.1126/science.1140579

Sawyer SL, Wu LI, Emerman M, Malik HS. 2005. Positive selection of primate TRIM5α identifies a critical species-specific retroviral restriction domain. Proc Nat Acad Sci USA 102:2832-2837. doi:10.1073/pnas.0409853102

Ummm...

Daughters of Eve in DNA paintings

Artist Ulla Plougmand-Turner said the experience was "amazing"
An artist has created portraits of the "Seven Daughters of Eve" using paint containing reconstructed ancient DNA.

Danish artist Ulla Plougmand-Turner mixed sequences of ancient DNA, produced in an Oxford laboratory, into paint to create the images.

The pictures represent seven women, from whom it is thought the majority of Europeans can trace their DNA line.

Described as "a fusion of science and art", the paintings went on exhibition on Monday at Wolfson College, Oxford.

Uhh...

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)081<0223:SOAPBI>2.0.CO;2

Saw this today from The Onion, it's an oldie but a goodie:

Archaeologist Tired Of Unearthing Unspeakable Ancient Evils

...

Over the course of his career, Whitson has been frequently lauded by colleagues for his thorough, methodical examinations of ancient peoples. He has also been chased by the snake-bodied ophidian women of Al'lat in Israel, hunted down by Mayan coyote specters manifested out of lost time and shadow in the Yucatan, and hounded by the Arctic-sky-filling Walrus Bone Woman of the early Inuits.

"It's true, I've got to stop reading the inscriptions on ancient door seals out loud," Whitson said. "I also need to quit dusting off medallions set into strange sarcophagi, allowing the light to hit them for the first time in centuries. And replacing the jewels that have fallen from the foreheads of ancient frog-deity statues-that's just bad archaeological practice."

(via Savage Minds)

The story about blonde mammoths has been making the rounds, based on this paper by Holger Römpler and colleagues in Science. The abstract:

By amplifying the melanocortin type 1 receptor from the woolly mammoth, we can report the complete nucleotide sequence of a nuclear-encoded gene from an extinct species. We found two alleles and show that one allele produces a functional protein whereas the other one encodes a protein with strongly reduced activity. This finding suggests that mammoths may have been polymorphic in coat color, with both dark- and light-haired individuals co-occurring.

Missing from the story is this: it's the first insight about phenotypic variation that anyone has derived from ancient DNA.

It's a very short paper; the essential elements are that they found the polymorphism by trying to reconstruct the Mc1r sequence in an individual that turned out to be a heterozygote for three amino acid-coding sites. They then sequenced the polymorphisms in "additional specimens" including some homozygotes, which allowed them to work out the linkage among the polymorphisms. Sequencing of additional individuals helped to rule out the possibility that the candidate polymorphisms resulted from idiosyncratic DNA damage and not genuine biological variation. One of the three polymorphisms is frequently variable among other mammal species; two of them are highly conserved -- pointing to a possible important functional difference. They then constructed a model allele including these polymorphisms to see how it would be expressed in a cell culture; they found that one of the mammoth alleles showed only partial activity. From this they inferred that the polymorphism probably had phenotypic effects on pigmentation.

Of course it's a bit of a stretch from this conclusion to blonde hair; but they are helped in this by a little-known fact: frozen mammoths show variation in their fur coloration! So the genetic observations help to explain an already-known phenotypic variation.

Would they have had the confidence to make this argument if such pigment variations were not already known? Hard to say, but one consequence of this paper has to be an increase in the confidence in such conclusions for future studies, where phenotypes aren't already known.

I would say that the most important aspect of the paper is that it shows the importance of having sequences from multiple individuals. In this study, the sequencing of other individuals helped substantiate that the polymorphisms were not DNA damage. Since these sequences are broken into short pieces, reconstructing the alleles from a heterozygote is difficult if not impossible. So finding homozygotes among these individuals was necessary to reconstruct the two alleles, which gave the opportunity to assess their functional differences. And although this study didn't include a discussion of the origin of this polymorphism, reconstructing haplotypes is essential to that question also, another enterprise that is not possible without samples form multiple individuals.

So there is only a limited amount of information that can be obtained from a single individual, especially under circumstances where the DNA is fragmented or possibly damaged. Sampling multiple individuals helps these questions a lot -- even if it may introduce problems that haven't yet been considered.

And of course, from this work (undertaken in part at the Max Planck Institute for Evolutionary Anthropology) you can see some of the strategies that will ultimately be applied to the Neandertal genome. Mc1r is sort of an obvious candidate to look at, and they are certainly going to be trying to find FoxP2 polymorphisms also. But I anticipate that the story will be much deeper -- we may spend much more time figuring out the Neandertal genome than the 150 years since the Feldhofer cave discovery.

References:

Römpler H, and 8 others. 2006. Nuclear gene indicates coat-color polymorphism in mammoths. Science 313:62. DOI link

This strikes me as a problem:

Furthermore, we demonstrate that in this dataset, the damage rate of the old contaminant sequences is indistinguishable from that of the endogenous DNA sequences. As such, the commonly used argument that miscoding lesions observed among cloned aDNA sequences can be used to support data authenticity, is misleading in scenarios where the presence of old contaminant sequences is possible.

That's from the abstract of a new paper in MBE by María Lourdes Sampietro and colleagues (via Dienekes, who has some additional commentary).

References:

Sampietro ML, Gilbert MTP, Lao O, Caramelli D, Lari M, Bertranpetit J, Lalueza-Fox C. 2006. Tracking down human contamination in ancient human teeth. Mol Biol Evol (advance access) Abstract

I was reading through next month's Discover, and there is an article covering the work of Rodolfo Acuna-Soto, who has proposed that some of the most major epidemics that killed the Aztecs and other ancient American populations may have been caused by an indigenous hemorrhagic fever. This 2000 paper and this 2002 paper lay out the case.

The abstract of Acuna-Soto et al. (2000) describes the disease:

In 1545, twenty-four years after the Spanish conquest of the Aztec empire, an epidemic of a malignant form of a hemorrhagic fever appeared in the highlands of Mexico. The illness was characterized by high fever, headache, and bleeding from the nose, ears, and mouth, accompanied by jaundice, severe abdominal and thoracic pain as well as acute neurological manifestations. The disease was highly lethal and lasted three to four days. It attacked primarily the native population, leaving the Spaniards almost unaffected. The hemorrhagic fevers remained in the area for three centuries and the etiologic agent is still unknown. In this report we describe, and now that more information is available, analyze four epidemics that occurred in Mexico during the colonial period with a focus on the epidemic of 1576 which killed 45% of the entire population of Mexico. It is important to retrieve such diseases and the epidemics they caused from their purely historical context and consider the reality that if they were to reemerge, they are potentially dangerous.

There are several lines of evidence leading to this interpretation, including contemporary accounts of symptoms by doctors and priests, the lack of correspondence of these symptoms to known epidemics like smallpox, typhus, yellow fever, malaria and the other usual candidates, the fact that the indigenous people used a distinct word, cocolitzi to describe the epidemics, which was different from their description of smallpox (often assumed to have been the cause), and the association between epidemics and droughts.

The papers suggest that the transmission pattern is similar to the hantavirus that caused Four Corners disease: years of drought followed by rainfall, which caused an explosion of rodent populations and greatly increased human-rodent contacts. They substantiate the hypothesis with analysis of tree-ring data, which show a correspondence between drought years and plague years, as well as a massive drought and wet sequence associated with the largest epidemic in 1545.

A big problem with the hypothesis could be the fact that the cocolitzi epidemics did not greatly affect Spaniards, despite the expectation that they should have had no immunity to a native American disease. Acuna-Soto and colleagues propose that this is a reflection of their high status -- they would have been under less stress during droughts than the indigenous people, and they might not have had as extensive contact with rodents.

The 2002 paper speculates that the epidemic may derive from either a hantavirus or an arenavirus, both of which have caused rodent-borne disease in the New World, but no known species of either has been found in the right place. Perhaps the closest analogue would be the Machupo virus that causes Bolivian hemorrhagic fever. It's an awful disease.

Will it return?

Cocoliztli was an emerging disease of its time and it appeared at a time of intense social and ecologic change. The illness ran without control and caused catastrophic damage to the Indian population for at least a century. Today, there are no reported human or animal diseases resembling cocoliztli in the area. The disease has not been reported for a long time and the probability of an epidemic reemergence
remains unknown. As for potential risk factors, it is important to remember that poverty, a key element in the epidemic, remains prevalent in some areas formerly affected by the disease. In the small towns around the city of Tehuacan, in the state of Puebla where cocoliztli once flourished, the word cocoliztli is still used as synonymous with lethal disease. Perhaps it is only representative of a historical vestige, but if the word and the concept remain active, we may well wonder if the etiologic agent is also alive and waiting to emerge again (Acuna-Soto et al. 2000:737).

It makes a good detective story, with quotes from unpublished historical documents, dendrochronology, and all the rest.

References:

Acuna-Soto R, Romero LC, Maguire JH. 2000. Large epidemics of hemorrhagic fevers in Mexico 1545-1815. Am J Trop Med Hyg 62:733-739. PubMed

Acuna-Soto R, Stahle DW, Cleaveland MK, Therrell MD. 2002. Megadrought and megadeath in 16th century Mexico. Emerg Infect Dis 8:360-362. PubMed

A paper by Wolfgang Haak and colleagues in this week's Science sequenced ancient mtDNA in 24 Neolithic European skeletons.

A review by Martin Richards (2003) lays out the genetic evidence about population dynamics in Neolithic Europe, along with the likely scenarios. I recommend the paper, it clarified matters for me. During the past thirty years, Cavalli-Sforza and others have pushed a model called "demic diffusion" for Neolithic Europe -- essentially the idea that population growth resulted in the net movement of Near Eastern genes across Europe. But there are other models for population interactions as agriculture spread and populations became more dense -- including long-distance colonizations, elite dominance by one group or another, cultural diffusion without significant genetic movement, and so on.

The main question recently has been about the strength of net movement of genes into Europe. Some have claimed that the majority of present European genes can be traced to the Near East before 6000 years ago. Others have argued that the genetic influence of West Asian populations was substantially more minor, or at least had extended over a longer time from the Upper Paleolithic to the present, instead of being concentrated in the Neolithic revolution itself.

The current paper places itself in the frame of this ongoing debate, but raises an entirely new problem! The abstract:

The ancestry of modern Europeans is a subject of debate among geneticists, archaeologists, and anthropologists. A crucial question is the extent to which Europeans are descended from the first European farmers in the Neolithic Age 7500 years ago or from Paleolithic hunter-gatherers who were present in Europe since 40,000 years ago. Here we present an analysis of ancient DNA from early European farmers. We successfully extracted and sequenced intact stretches of maternally inherited mitochondrial DNA (mtDNA) from 24 out of 57 Neolithic skeletons from various locations in Germany, Austria, and Hungary. We found that 25% of the Neolithic farmers had one characteristic mtDNA type and that this type formerly was widespread among Neolithic farmers in Central Europe. Europeans today have a 150-times lower frequency (0.2%) of this mtDNA type, revealing that these first Neolithic farmers did not have a strong genetic influence on modern European female lineages. Our finding lends weight to a proposed Paleolithic ancestry for modern Europeans (Haak et al. 2005:1016).

Some observations:

1. This is the latest in a long line of ancient DNA results that depends on the strangeness of the observation to argue against contamination.

The observed distinct N1a types rule out the possibility of contamination with modern samples, which can be a problem in ancient human DNA studies. It is implausible that the five types are from five different modern contaminants, because the frequency of this type today is very low anywhere in the world, at about 0.2% (23Ð25) (fig. S1). It is also unlikely that the sequence variations seen within the five N1a types are the result of random postmortem DNA damage (26, 27), because three out of six sequence types that we have identified precisely match modern sequences previously published in the literature (table S2 and supporting references); finally, two further N1a types (HAL2 and UWS5) precisely fit into predicted but previously unobserved ancestral nodes in the N1a phylogeny (Fig. 2), underlining the authenticity of the ancient DNA.

It may be that there is just nothing else to be done, but it is troublesome from the perspective of hypothesis testing. Will we ever see a paper that says "ancient DNA demonstrates perfectly ordinary sequences in prehistoric people"? OK, I guess Caramelli et al. (2003) (which reported modern mtDNA sequences in some Upper Paleolithic Italian specimens) had that theme, but I have heard many people question that result for this precise reason.

2. The pattern here is a remarkable echo of the Neandertal mtDNA problem. Here we have a common variant in Europe only 7500 years ago that today is almost gone. With the Neandertals, we have a very common variant that today, after 40,000 years, is completely gone.

You might therefore expect that some clever geneticists would claim that the Neolithic farmers contributed little or no genetic ancestry to living Europeans. And that is precisely the hypothesis discussed by Haak et al. (2005):

These simulations reject the simple hypothesis in which modern Europeans are direct descendants of these first farmers and have lost N1a mainly by genetic drift. Hence the simulations confirm that the first farmers in Central Europe had limited success in leaving a genetic mark on the female lineages of modern Europeans. This is in contrast to the success of the Neolithic farming culture itself, which subsequently spread all over Europe, as the archaeological record demonstrates. One possible explanation is that the farming culture itself spread without the people originally carrying these ideas. This includes the possibility that small pioneer groups carried farming into new areas of Europe, and that once the technique had taken root, the surrounding hunter-gatherers adopted the new culture and then outnumbered the original farmers, diluting their N1a frequency to the low modern value. Archaeological research along the Western periphery of LBK and isotope studies of some of our sampled individuals seem to support the idea that male and female hunter-gatherers were integrated into the Neolithic communities (3, 10, 29). This hypothesis implies that N1a was rare or absent in Mesolithic Europeans, which may be a reasonable assumption given the rarity of the N1a type anywhere in the world (Fig. 3). An alternative hypothesis is a subsequent postÐearly-Neolithic population replacement in Europe, eliminating most of the N1a types. Archaeological evidence for such an event is as yet scant (Haak et al. 2005:1018).

Of course, this idea depends on several unknowns. It proposes that European hunter-gatherers who were contemporary with the LBK culture had very different mtDNA types -- indeed, that they had the types that are presently common. And it proposes that the intrinsic growth rate of agriculturalists was very small, so that their genes were flooded by hunter-gatherers transitioning to agriculture.

But if their genes were so flooded at every stage of their expansion, then the N1a mtDNA sequences shouldn't be there in the first place -- they should have been left behind in the Near East. So this is a very curious event -- an expanding population saw one of its major mtDNA variants greatly contract in frequency, so much so that today it is nearly gone.

3. Let's review the facts. The mysterious N1a mtDNA type is currently rare anywhere in the world. It is carried by only 0.2 percent of Europeans. But it has a high frequency among these Neolithic Europeans -- 25 percent of the samples, which means the true population frequency was likely between 8 and 42 percent (Haak et al. 2005:1017). The paper found that this great reduction in frequency within Europe cannot have been accomplished by genetic drift.

Can someone tell me why the word "selection" doesn't appear in this paper?

References:

Balter M. 2005. Ancient DNA yields clues to the puzzle of European origins. Science 310:964-965. Full text (subscription)

Haak W et al. 2005. Ancient DNA from the first European farmers in 7500-year-old Neolithic sites. Science 310:1016-1018. Full text (subscription)

Richards M. 2003. The Neolithic invasion of Europe. Annu Rev Anthropol 32:135-162. Full text