I'm worried about Neandertals. Not their bones, so much. Mainly their future.

We're living in a culture with Neandertal sitcoms and talk of cloning Neandertals from chimpanzee oocytes. The Renaissance brought back the ideas of classical Rome and Greece. Our age seems bent on bringing back the Mousterian.

But whether it's oversaturation or undercontextualization, certain Neandertal news is slipping through the cracks.

Last week, Carles Lalueza-Fox and colleagues reported that the Neandertals of El Sidron had blood type O. That's pretty interesting. Heck, five years ago it would have been big exciting news. Three years ago, a partial protein sequence from Neandertal bones was fairly big news, even though the sequence was identical to humans and had no new information.

This week, blood type O in Neandertals barely merited a mention in a single news story, which mainly focused on last year's news about MC1R and FoxP2 sequences in the same fossils.

Five years ago, finding blood type O in Neandertals would have been a Ph.D. project. Today, it's a short paper in BMC Evolutionary Biology. I applaud the authors for choosing the open source outlet, and getting the result out there rapidly. It's solid work. It just seems to have gotten easier.

Raw data about Neandertal genetics are quickly losing their novelty. Next year, with some luck we'll have a draft genome, no doubt reporting a lot more about Neandertal phenotypes. That will be big news. But will any other future sequencing effort be given as much attention or importance?

And will the next "next-generation" sequencing method make it easier to get ancient DNA sequences? The reads of 20 bp and less from the 454 method have allowed a huge breakthrough. But the longer read lengths from newer technologies don't seem as good a match to ancient DNA samples, where the original sequence is broken into very short fragments.

There may be a problem brewing here.

Neandertal genetic information is gaining more and more scientific value. Once we have a workable genome, we will be able to answer questions about Neandertal population demography and adaptation that would have simply been impossible before. This has the potential of creating a new frontier in paleoanthropology -- but only if the science can be replicated in many individuals. Many of the interesting hypotheses can be tested only by considering variation among many individuals. Every sequence must be obtained with the same care and attention, because when the data are necessarily sparse, a single outlier can exert a large influence on outcomes.

Sequencing a single Neandertal is a challenging task requiring the attention of many people. Some parts of the process have been automated, or at least standardized, but it takes a lot of tweaking, hands-on knowledge, and dedicated experience to yield results that anyone can trust. In the near future, we are going to need many specialists competent to shepherd Neandertal genetic results from bone to database. We are going to need lots of attention on this issue so that we can find ways to guarantee access, protect data from loss, and preserve precious specimens.

I'm a little worried that the topic may be poised to lose attention just at the moment that it should receive more intensive effort. What incentives will there be to generate data from Neandertals?

Today, we enjoy open access to genetic data from Neandertal specimens after they have been reported -- a wonderful situation compared to other kinds of data in paleoanthropology. But that policy is the product of a unique ecology -- one in which data are continually easier to obtain and replicate, and in which each technical advance gives a great payoff in terms of publications and attention.

Will the ecology continue? I don't have an answer. The current players in Neandertal genetics have done a wonderful job, and have advanced the ecosystem in a way that allows outside analysts -- like me -- to do good work.

But more than anything, I'm concerned that the sequencing technology will move away from methods that make ancient DNA easier and easier to obtain. For the past several years, ancient DNA and human genetics methods have moved in parallel. Neandertal genetics has benefited greatly from technologies that have been widely applied for humans and other organisms. But if these methods diverge, it may create a real bottleneck in terms of skillsets and methods for obtaining new data from Neandertal specimens.

References:

Lalueza-Fox C. Gigli E, de la Rasilla M, Fortea J, Rosas A, Bertranpetit J, Krause J. 2008. Genetic characterization of the ABO blood group in Neandertals. BMC Evol Biol 8:342. doi:10.1186/1471-2148-8-342

This week's Science includes a paper by M. K. Smith and colleagues, which assesses undergraduate learning in an introductory genetics course that uses "clickers" and small-group discussions.

The paper's authors include Carl Wieman, whose educational philosophy was a topic of one of my posts last summer.

In the current paper, Smith and colleagues examine the role of small group discussion as a component of the "interactive" strategy of lecturing:

Some instructors who use clicker questions skip peer discussion entirely, believing that instructor explanation of the correct reasoning will be more clear and accurate than an explanation by peers, and will therefore lead to more student learning. Although our current work does not directly compare the benefits of instructor versus peer explanation, research in physics has shown that instructor explanations often fail to produce gains in conceptual understanding (15). We have shown that peer discussion can effectively promote such understanding.

I wrote about physicist Eric Mazur's teaching philosophy in 2007, when he was profiled in the NY Times. He has an editorial accompanying the new report in Science, again emphasizing the small-group hands-on approach as a superior alternative to lectures:

I now structure my time during class around short, conceptual multiple-choice questions. I alternate brief presentations with these questions, shifting the focus between instructor and students. The questions address student difficulties in grasping a particular topic and promote thinking about challenging concepts. After posing the question, I give the students 1 to 2 minutes to think, after which each must commit to an individual answer. They do this by submitting their answers using handheld devices called "clickers" (see the figure). Because of the popularity of these devices, questions posed this way are now often referred to as "clicker questions." The devices transmit the answers to my computer, which displays the distribution of answers. If between 35% and 70% of the students answer the question correctly, I ask them to discuss their answers and encourage them to find someone in the class with a different answer. Together with teaching assistants, I circulate among the students to promote productive discussions and guide their thinking. After several minutes of peer discussion, I ask them to answer the same question again. I then explain the correct answer and, depending on the student answers, may pose another related question or move on to a different topic. This approach has two benefits: It continuously actively engages the minds of the students, and it provides frequent and continuous feedback (to both the students and the instructor) about the level of understanding of the subject being discussed (Mazur 2009:51).

I like many aspects of this approach, and I actually teach with a similar style. My lectures are divided into relatively short segments. I ask questions of the students, frequently calling on individual students for answers, and occasionally polling the class by a show of hands.

But what I really don't like in Mazur's description is the "multiple choice" formula. I know that the clickers don't really give an "open-ended" option, but many of my most interesting class presentations have come from using a completely open-ended approach. I react to student questions, bringing topics into the lecture that wouldn't otherwise have been covered. An open-ended approach allows me to show the application of methods outside the usual textbook canon. And it allows the engaged students to help direct the class content. An episodic series of multiple choice questions has to be completely stultifying for the bright students in the room.

Well, that's my opinion, anyway. I can't really imagine coming up with a series of multiple choice questions for each lecture. When I teach laboratories, I have an extensive set of questions ready to challenge students at each lab station, and I certainly have questions ready at the beginning of lectures. But the multiple choice format is demeaning. Or hokey -- kind of a "Who wants to be a millionaire?" approch.

And I sort of think that students could spend five minutes outside of class discussing the content, instead of being cheated out of five minutes of my time in class.

References:

Mazur E. 2009. Farewell, lecture? Science 323:50-51. doi:10.1126/science.1168927

Smith MK, Wood WB, Adams WK, Wieman C, Knight JK, Guild N, Su TT. 2009. Why peer discussion improves student performance on in-class concept questions. Science 323:122-124. doi:10.1126/science.1165919

Ronald Bailey opines about coming pressures for politicians to release their genetic test results:

Again, it's just as easy to obtain a DNA sample from a presidential candidate as it would be to get one from a celebrity like Winfrey. Green and Annas are most worried that competing campaigns might engage in "genetic McCarthyism." That is, campaigns will seek to obtain DNA from their adversaries and then release genetic data that suggests that their opponents are somehow unhealthy. Such a tactic could be used to confuse the public because genetic information is easy to misinterpret and to misrepresent. Consequently, Green and Annas argue that "future presidential candidates should resist calls to disclose their own genetic information. We recommend that they also pledge that their campaigns will not attempt to obtain or release genomic information about their opponents." They reject the idea of making it a federal crime to sequence a candidate's DNA without consent. Oddly, Green and Annas overlook the plausible scenario in which some media organization surreptitiously obtains DNA from candidates, and then sequences it and reports the results.

This last scenario, the sneaky approach, pretty much makes it inevitable that genetic test results for future candidates (or anyone else of sufficient interest) will be public. Congress could simply make it illegal to release any record of a person's genetic information. But this would extend the privacy right much further, with respect to publicly obtained information, than it currently goes -- and far into the territory where the First Amendment pushes back.

If it were only politicians, that would be trouble enough. But these kind of data may be used in the same manner as many kinds of "junk science" today. Imagine a custody battle, in which the father hires a private investigator to get a mother's genome. With two variants that yield a 15 percent higher risk of schizophrenia, will the mother's genetic risk be held against her? Or think of corporate boards, looking for a way to dismiss a CEO without paying that golden parachute. Could a genetic test result showing a higher risk for early Alzheimer's give them a reason to invoke a "health" clause in the contract?

Why does this entire topic look like "junk science?" I can think of a couple of reasons. First, genetic information today is essentially meaningless at the individual level. Consider Bailey's description of his own 23andMe results:

The genetic screening company reports that 24 out of 100 people with my genotype will get type 2 diabetes between the ages 20 and 79. The average risk is 21.9 per 100 people. With regard to macular degeneration, 9.5 out of 100 people with my genotype will get it between the ages of 43 and 79. The average risk for people of European ethnicity is 7 out of 100. And 0.94 out 100 people with my genotype will get Crohn's disease between the ages of 20 and 79. The average risk for people of European ethnicity is 0.43 out of 100. I will save for a future article the good news that I also have a number of genetic markers that indicate lower risks for many other conditions. This is the kind of risk information that genetic screening tests will reveal.

These "risks" are based on single genotypes, mostly replicated in more than a single study, but not analyzed with any combination of other genotypes. We simply don't have a way to predict a person's lifetime risk of chronic disease, based on the entire genome. A person who has one known risk allele may have any number of unknown protective alleles. So saying that a person has a XX risk for condition YY is highly misleading. At best, the strongest such variants suggest a higher relative risk, all other things -- including environment, diet, and past disease history -- being held constant.

Second, there is no natural limit to what a genetic test might be claimed to find. Genes affect health, sure, but they also affect personality, IQ, and behavior. Once a person's genetic data are made public, they are hostage to every future study that might show one (or more) genetic variants are associated with some trait.

This is not only about the candidate for President, where the public is judging their future health. This is about a sitting President, whose public genome data show a newfound association with a personality disorder.

Maybe, as George Church hopes, we are headed for a future where these things won't matter. But I think it will be a rough road.

Eric Konigsberg writes a long story in the NY Times with quirky stories about the joy or disenchantment with the results of pet cloning:

When Mr. Hawthorne recalls Missy, he tends to wax eugenic. “She was an amazing dog: superior intellect, incredibly beautiful, obedient, a phenomenal temperament,” he said. “I especially loved her majestic plume of a tail.” And in the clones, as he put it matter-of-factly, “all those qualities are represented.”

People who sell cloning services have a strong interest in portraying the clones as identical to the original pets. After all, if people just wanted a similar pet, they could get another pet of the same breed. For a price in the neighborhood of a Maserati, these buyers are looking for something a little more particular -- if not their dead pet reborn, at least a facsimile.

Or a science fair project for their grandkids:

Last spring, Skye completed a science project, “Cloning Grandma’s Dog” that included a behavioral comparison chart. Among other findings, the study concluded that Mira shares Missy’s fondness for broccoli and “lots of snuggles” — both dogs scored five out of five points in these categories, in addition to the one for “likes long walks.” (“Most dogs do,” Skye noted under “comments.”) Two key matters of variance were “Jumps into cars” (“Clone still learning which car is ours”) and “Hates camera flash” (“Clone did not respond to standard flash”).

The story at the end of the article, about the proud first owners of a cloned dog from this particular company, is creepy:

“Breathe, breathe,” Mr. Hawthorne said. “How does he look?”

“He looks like Neanderthal Man,” Mr. Otto called out from the background.

“No, he doesn’t,” his wife said.

“I can’t say he looks exactly like our other one,” Mr. Otto shouted.

“Yes, he does,” his wife said.

Oh, yes he does. This is reminding me of the BBC show that investigated people who adopted "real baby" dolls. Weird.

I've been out of e-mail range for the past week. In the meantime several people e-mailed me this new paper:

Neanderthal Extinction by Competitive Exclusion

Background: Despite a long history of investigation, considerable debate revolves around whether Neanderthals became extinct because of climate change or competition with anatomically modern humans (AMH).

Methodology/Principal Findings: We apply a new methodology integrating archaeological and chronological data with high-resolution paleoclimatic simulations to define eco-cultural niches associated with Neanderthal and AMH adaptive systems during alternating cold and mild phases of Marine Isotope Stage 3. Our results indicate that Neanderthals and AMH exploited similar niches, and may have continued to do so in the absence of contact.

Conclusions/Significance: The southerly contraction of Neanderthal range in southwestern Europe during Greenland Interstadial 8 was not due to climate change or a change in adaptation, but rather concurrent AMH geographic expansion appears to have produced competition that led to Neanderthal extinction.

OK, so should we believe it?

The authors are out to test the idea that climate killed the Neandertals (also covered by me in 2007, not to mention "The unbearable hotness" from last week).

The authors confine their analysis to a simple question: Were the European ecologies of the later times of Neandertal existence compatible with those that existed slightly earlier? If the climate deterioration is insufficient to explain the range reduction of late Neandertal sites, then we need some other factor. Competition with the non-Neandertal population would be a logical hypothesis, in this event.

Competitive exclusion is not a new concept applied to Neandertals. The novel element in the paper is its inclusion of paleoclimate models to support the hypothesis that Neandertals and modern humans actually would have competed in the same niche.

The authors applied an optimization algorithm to data. The data included:

1. Paleoclimate predictions for small areal units within Europe for three time periods between 43,000 and 35,000 (calibrated) years ago.

2. The locations and dates of archaeological sites dating to these periods, whether Mousterian, Châtelperronian, or Aurignacian. The first two are assumed Neandertal, the third modern human.

The algorithm tries to find shared paleoclimate features among the locations represented by archaeological sites. Once these are found, the algorithm finds other areas that fit the same paleoclimate parameters as those where archaeological sites were found. In other words, it is an attempt to determine the total ecological range of the populations represented by the sites.

For example, here are the results for the earliest of the three time periods, H4. This is a comparison of the maps of Europe for both the Mousterian-Châtelperronian (left) and Aurignacian (right) archaeological samples:

In this map, red areas are those predicted to be suitable for habitation by Mousterian-Châtelperronian (left) and Aurigacian (right) populations, respectively. One thing stands out: they have almost identical ecological tolerances. Modern humans were not using different ecological zones than Neandertals. The analysis of the later periods shows that the modern humans were not exploiting climate changes at the expense of Neandertals.

The key graph of the paper shows that during the latest time period, near 35,000 years ago, the paleoclimate models predict a very large area of Europe would have been suitable for Neandertal habitation -- at least, if their habitation were constrained only by climate. But the Neandertal sites during that time period are restricted to a very small area. So some additional factor is required. The authors promote the hypothesis that the important factor was the population growth of modern humans.

Now, should we doubt the results? I think this is a good test of the hypothesis that climate change killed the Neandertals. It didn't. They survived through an entire glacial cycle before 40,000 years ago. Without some other factor, they would still be here today.

The paper is stronger than many that have tried to make a similar argument -- that climate couldn't have killed various extinct megafauna. In large part, that is because both the American megafaunal disappearances and the entry and growth of human populations coincided with a period of rapid climate change. In the time frame of the last Neandertals, there were important climate changes, but the paleoclimate models indicate that these changes weren't enough to make Europe uninhabitable for either humans or Neandertals.

The paper is not a test of Neandertal genetic extinction. It takes Neandertal population disappearance as a given. Models that involve gene flow or cultural exchanges between Neandertals and other populations are not part of this paper's scheme.

In this sense, the assumption that the archaeological industries can be analyzed with methods developed for species seems questionable. The paper acknowledges this issue:

Our assumption is that human adaptive systems, defined here as the range of technological and settlement systems shared and transmitted by a culturally cohesive population within a specific paleoenvironmental framework, can be considered to operate as a ‘species’ with respect to their interaction with the environment. This does not imply, however, that human adaptive systems necessarily remained stable over time, as might be the case with animal species occupying narrow and stable niches. Humans can change their adaptive systems rapidly through technical and social innovations in response to environmental change. We know, however, that this was not the case during the late Middle and Upper Paleolithic, periods during which specific human adaptive systems spanned a number of climatic events. Thus, the method described in this study is particularly relevant for addressing issues of human adaptive system stability and eco-cultural niche stability (Banks et al. 2008:2).

But Neandertals during the span from 43,000 to 35,000 years ago were adopting various Upper Paleolithic technological elements. That seems to contradict the assumption that the "technological and settlement systems...operate as a 'species'." Instead, it seems to indicate that these systems changed significantly across the time frame modeled in the paper. I don't think that observation weakens the hypothesis that modern and Neandertal populations may have competed in the same ecological niche. If the Neandertals were using the same technical elements, it probably reinforces the hypothesis of competition.

But I think it is important to bear in mind what the paper tested. The analysis rejects the hypothesis that climate was sufficient to drive a range restriction of Mousterian and Châtelperronian. It doesn't provide additional information about the mode of such restrictions. With that in mind, I admire the paper and see some useful additional work that might be tackled with similar methods.

References:

Banks WE, d’Errico F, Peterson AT, Kageyama M, Sima A, et al. (2008) Neanderthal Extinction by Competitive Exclusion. PLoS ONE 3(12): e3972. doi:10.1371/journal.pone.0003972

I clicked on Webpages as Graphics (via Sandwalk), which is a Java applet that renders the HTML tags of a website as a tree.

If you haven't written any HTML from scratch, you may not be aware that a webpage has a treelike structure. The text and images of a page are encased in a <body> tag; the body itself may be divided into several <div> elements; each may contain many <p> (paragraph) elements and/or <img> (image), <table> (table) or <ul> (bullet list) elements. A paragraph will often contain links (<a>), italics (<i>) or other modifiers. Each element is contained in a higher-level element, up to the entire page.

So the "Webpages as Graphics" applet renders a webpage as a tree. Here's mine:

Hawks blog as tree. Key: green=div; orange=p; blue=a; purple=img; yellow=form elements; gray=all others (mostly i and b)

OK, so what is this? The big cluster at bottom left is the series of posts on the front page of the blog. Each post is a little cluster rooted on a div tag, with a varying number of orange p tags inside. Every post has at least one blue link, but most have several. There are few pictures. There is one small stem jutting toward the upper right that has a picture, that's the footer of the page.

The looser cluster at the upper right includes the right and left sidebars. The flowery structure at the extreme right is the blogroll, ordered into several lists, each with a link. The dense cluster of blue links is the tag cloud; the more diffuse pom with the gray center is the recent posts list. The purply umbel toward the left of this cluster is the Amazon zone. And the dangly vine with the yellow form tags is the search box.

So that's it. I think it's a nice way to look at a website and learn how it's put together. You can see that my daily writing consists of small clusters of tags containing text. The big clusters of links are separated from the daily (and changing) content, connected only by being contained on the same page.

Try it with a few sites -- the app takes a little while to optimize the spacing between links, but it's fascinating to watch it. For an extremely simple tree, try the map of Google's homepage. Scienceblogs is rather more complicated, with a big dandelion.

I commented on the movie version of the play, "Homo erectus," when I heard about it a couple of years ago, in a timeless post, titled "[Tom] Arnold will play Rog, a gay caveman."

Well, as might have been expected from a kooky caveman comedy featuring Gary Busey and porn star Ron Jeremy, "Homo erectus" failed to find an audience.

But not all the news is bad. Now the movie has been picked up by the masters of comedic judgment:

It’s hard to believe it’s been almost two years since we interviewed Adam Rifkin about his film Homo Erectus. Unfortunately, the caveman comedy never got a wide release, but there is hope for it on DVD - this is the kind of movie that smacks of becoming a cult favorite. Don’t look for it under the old name though. When the picture was picked up by National Lampoons, it received a title change - National Lampoon’s Stoned Age, which hits DVD on January 20th.

My first reaction to the title was that it sounds a lot more sophomoric than the cultural commentary Rifkin told me about during our interview. Then again, Homo Erectus wasn’t exactly a title that said “high class satire,” so if National Lampoons thinks this is a good title change, so be it - it’s not like they’ve been wrong before.

So at last, you can own it yourself. Here's National Lampoon's Stoned Age at Amazon:

But don't confuse it for the 1994 movie of a very similar title, The Stoned Age. Which you might actually prefer, if you tend to go for sleeper classics with bong humor:

Hey, whatever floats your boat. Just don't get either of them for me...

Paul Ham reports on developments which may force the relocation of rock art in northwestern Australia:

The world’s oldest depiction of a human face could be threatened if Australian mining companies are permitted to build an explosives factory on the remote Burrup peninsula in the northwest of the country.

A bulbous image of indiscernible sex, with huge eyes and sunken cheeks, the 10,000 year-old carving is chipped out of hard rock. Thousands of other carvings, mostly of plants and animals, which date back to beyond the last Ice Age, are scattered about the peninsula.

Archeologists believe that aboriginal tribes made the distinctive carvings up to 30,000 years ago. They could be nearly twice as old as the Lascaux cave paintings in the Dordogne, France.

The West Australian paper has this report on a December 20 rally:

A rally in Perth today marked the 200th global 'stand up' for Burrup Peninsula with a renewed call for World Heritage listing for the rock art site.

Since 2006, Friends of Australian Rock Art has organised 200 vigils for the Burrup rock art in more than 35 countries and in every continent except Antarctica.

FARA spokesperson Robin Chapple said that international pressure was mounting for Australia to include the Burrup on the UNESCO World Heritage List.

According to the Telegraph (UK), Neandertals became extinct because their mitochondria leaked excess heat:

Professor Patrick Chinnery, a neurogeneticist at Newcastle University, believes the differences in this mitochondrial DNA could have caused Neanderthals to be inefficient at producing energy, meaning their cells leaked heat.

He said: "The question is why did Neanderthals disappear? There are lots of explanations to do with changes in climate and the food supply.

"Differences in these mitochondrial DNA sequences might explain why modern humans were able to survive while Neanderthals were not.

So, is it true? Did Neandertals go panting into that long good night?

Well, Siberians may have mtDNA alleles that leak extra heat, and they're not extinct. It seems like a good idea if you don't live in the tropics and have enough food. Because it's not like Europeans lack opportunities to take off a layer to deal with the heat.

Plus, as the Neandertal morphology waned in Europe, the climate was getting colder, not warmer.

The real mistake here is assuming that the mtDNA necessarily shared the same fate as the rest of the genome. Sure, there aren't any living members of the Neandertal mtDNA clade, at least that we know of. But that suggests selection favoring human mtDNA, not necessarily Neandertal extinction. The idea of selection is supported by the finding of functional variations between human and Neandertal COX2, which I discussed in August.

The current research seems like it probably adds detail to this comparison, but that's not an argument for Neandertals going extinct in the heat.

I'm about to pull out my hair reading "supplementary information" for papers.

Two recent papers (by Mike Hammer's group and David Reich's group) attempt estimates of the diversity level of the X chromosome versus the autosomes. As discussed on Gene Expression this week, the two papers came to completely opposite results.

In the olden days, ten years ago, I would simply put the two papers side by side and find the discrepancies. But nooooo, we can't do that any more. Now, all the relevant parameters from one of the papers (you guessed it, the one published by the Nature Publishing Group) are hidden away in a supplement.

You'd think that might not be so bad, since I have the supplement. But I have to keep tracking the cross references to the paper to find out where the methods apply. It's a pain in the neck. Nobody else ever seems to complain. But that's because they simply don't read the papers! AAARGGGH!

So what's the discrepancy in this case? I'm still working through these darned things.

My first impression is that both papers use different methods to estimate the mutation rate on the X chromosome. It was Reich's group, after all, who claimed that the human-chimp divergence was followed by extended hybridization, a process that took over 4 million years in their estimation. The evidence was the X chromosome.

So, for their current paper, Keinan and colleagues (2008) try to correct for the recent divergence of human and chimpanzee X chromosomes. Simple enough -- rescale all X chromosome mutation events by the some ratio proportional to the human-chimp divergence discrepancies. In this case, they attempt to rescale to the human-macaque divergence. Since that divergence happened in the Oligocene, the discrepancies among chromosomes should slight compared to the overall divergence. I'd feel better if they actually tested this idea.

Meanwhile, Mike Hammer and colleagues scaled X chromosome diversity to the human-orangutan divergence. They claimed that this gave the same results as the human-chimpanzee divergence. Which, if true, would obviously give a different outcome than the procedure followed by Keinan and colleagues, which was predicated on the idea that the human-chimpanzee X divergence is the wrong number to use.

The human-chimpanzee divergence discrepancy, if it exists to the extent claimed by Patterson et al. (2006), is probably enough to explain the discrepancies in the results of these two papers, and clearly in the correct direction. By assuming a low divergence date for the human-chimp X chromosome comparison, Keinan et al. have assumed a low mutation rate for the X. That means that the X variation in humans represents relatively less time, and therefore lower genealogical diversity and a lower effective size, than estimated by Hammer et al.

But I don't think that's the end of the story. In fact, I think there are quite a few strange aspects of the results of both papers. Even though both papers explain their results in terms of demography, I don't think that avenue is very promising. The kinds of demographic changes that happened in the Late Pleistocene just don't look very much like those coming out of these papers. More on that later...

What the Keinan et al. paper is showing is some substantial differences in the derived/ancestral ratio between populations, and large discrepancies in X diversity across different regions of the X. Large discrepancies would be expected between small regions due to the intrinsic variability of the coalescent process. But these large discrepancies exist between regions 3 centimorgans in length -- large enough regions that there ought to be less dispersion among them. The Asian and European samples have a strong deficit of derived alleles at frequencies lower than 30 percent, but the African sample has a slight excess.

We'll apply some more simpleminded analysis to these data and see if anything interesting pops out. As they say, garbage in, garbage out -- but when the garbage consistently looks like banana peels, you can guess there's a monkey somewhere.

UPDATE (2008/12/21): More craziness -- this article from New Scientist includes a quote from David Reich:

However, the chance of finding archaeological evidence for these migrants is slim. "You're looking for a population that was there only a short period of time, perhaps only 10 generations, so the physical impact of that population in that environment wouldn't be enough to detect," Reich says.

Surely he's not talking about a bottleneck 10 generations long, which by the estimate in the paper would mean an effective size of around 50 individuals. Surely not. No. It's just a quote in an article.

Oh, heck. I think the point of all these recent papers that use "inbreeding ratio" instead of effective size and time as bottleneck parameters is to hide these kind of crazy numbers from peer review. We've got people out there who are talking about biblical models of human migration, like Noah-and-the-Flood level bottlenecks.

And archaeology makes no difference. All those archaeological sites you've got? Well, they're not the ones who founded the world's population. Our actual ancestors made no impact on the environment that we can detect today. They were invisible.

And hey, if results contradict each other? No worries. It's not like this is a refutationist science, after all:

Their analysis also challenges a study published earlier this year, which found that all humans descend from fewer numbers of males than females. The researchers suggested that polygyny, where few men procreate with many women, accounts for this result.

"It's possible, in principle, that both are true in some level," says Reich.

Polygyny that occurred over the last million years of human evolution could have left an imprint in our genomes, says Michael Hammer, a geneticist at the University of Arizona, who led that study.

Reich and Keinan, on the other hand, focused their analysis on the period when anatomically modern humans left Africa.

"We'll have to figure out this issue in future work," Reich says.

GAAAAAAAAHHHHHH! And you thought I was silly to be driven crazy by these papers! "It's possible, in principle, that both are true in some level."

Pfui.