Anyone engaging in a Fred Reed impersonation, that is, talking about shit they know nothing about shamelessly and without any humility in light of their ignorance, will now be deleted at my discretion.

Posted by razib at 12:53 AM

Mitochondrial DNA haplogroup K is associated with a lower risk of Parkinson’s disease in Italians:

It has been proposed that European mitochondrial DNA (mtDNA) haplogroups J and K, and their shared 10398G single-nucleotide polymorphism (SNP) in the ND3 gene, are protective from Parkinson’s disease (PD)…However, the frequency of haplogroup K was significantly lower in PD. Stratification by sex and age indicated that the difference in the distribution of haplogroup K was more prominent in >50year old males. In spite of the common 10398G SNP, haplogroups J and K belong to widely diverging mitochondrial clades, a consideration that may explain the different results obtained for the two haplogroups in our cohorts. Our study suggests that haplogroup K might confer a lower risk for PD in Italians, corroborating the idea that the mitochondrial oxidative phosphorylation pathway is involved in the susceptibility to idiopathic PD.

Of course Parkinson’s disease effects the old so selection pressure probably isn’t that great (though older family members can have fitness effects down the generations).

Posted by razib at 11:24 PM

Over the past two weeks I’ve been reading three books on my spare time, some short takes now that I’ve finished all three.

Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom, by Sean Carroll, basically says it all in the title. “Evo-Devo” seems like a pretty “hot” field right now, and it is a decent introduction for laymen. As I’ve said elsewhere I’m an amateur, but, I really didn’t need another rehash of the lac operon system. But, if “lac operon” doesn’t ring any bells, this book is worth it. The author starts out from the basics of gene regulation in prokaryotes, shifts toward eukaryotic combinatorial control and steps into high gear with a lot of focus on the hox genes. I found the historical interpretation of Evo-Devo as a culmination of Darwin’s own thinking somewhat peculiar, I have a personal bias toward the author’s integration of new findings from developmental and molecular biology within the framework of the gradualism of the Modern Synthesis, but, if you read books by those who take a less “orthodox” Darwinian tack you will find that they see in Evo-Devo a way to overthrow the Neo-Darwinian paradigm. I don’t think the “radicals” are correct, but if you read this book you won’t get the impression that non-gradualism has any traction within academia (though the author is pained by the tendency toward saltationism in the press).Mutants : On Genetic Variety and the Human Body is a really dense and rich book. Of the three I read this is the most entertaining and data packed, unlike Carroll Armand Leroi, also an evolutionary developmental biologist (or developmental geneticist), doesn’t really lay a lot of groundwork, but cuts straight to the good stuff. By necessity Leroi focuses on very deleterious single locus mutations, but the whole text is riddled with allusions to Leroi’s interest in polygenic and quantitative traits which are extremely salient in our perception of human phenotype. This bears fruit in his epilogue, the “race and beauty” chapter. The ideas that Leroi has exposed in his recent essays take the step beyond mutants and asks what exactly the range of “normal” variation is. Seeing as how Leroi is now one of John Brockman’s pet projects I expect a steady stream of Dawkins quality popularizations in the future.William Calvin’s latest work, A Brief History of the Mind: From Apes to Intellect and Beyond is probably his most uneven. Its format is almost reminiscent of diary entries, and he tries to cover too much ground in less than 200 pages. Much of the book is focused on Calvin’s hypothesis that our motor control, in particular our incredible eye hand coordination, is at the heart of the changes that characterized the homonid brain over the last 2 million years. Calvin comes rather close to asserting that other aspects of our nature, like language, are pleitropic side effects of our increased motor skills. He also tacks back and forth between standard congitive science lingo and new theories about neurological plasticity, without really coming to any conclusion. Additionally, he was obviously hampered by a issue I have brought up before, that we seem to be in the midst of paradigm shifts in our understanding of Homo sapiens evolution and our relationship to other hominid groups (the current lingo is “hominin,” but I like it old school). Calvin admits this several times in the text, and I did note that he has his finger in the wind and is clearly part of a tendency to re-humanize Neandertals. Those who criticize science as just another historically contingent social enterprise could use the Neandertal as the exemplar of this sort of process, going from brute, to man, to brute, to man, many a time. Calvin should have waited a few years until the controversies died down and a new stable state asserted itself, but I suppose he had publication deadlines. Posted by razib at 05:03 PM

In a September 2004 interview at Front Page Magazine, Bat Ye’or defines Eurabia as follows.

Eurabia represents a geo-political reality envisaged in 1973 through a system of informal alliances between, on the one hand, the nine countries of the European Community (EC) which, enlarged, became the European Union (EU) in 1992 and on the other hand, the Mediterranean Arab countries. The alliances and agreements were elaborated at the top political level of each EC country with the representative of the European Commission, and their Arab homologues with the Arab League’s delegate. This system was synchronised under the roof of an association called the Euro-Arab Dialogue (EAD) created in July 1974 in Paris. A working body composed of committees and always presided jointly by a European and an Arab delegate planned the agendas, and organized and monitored the application of the decisions.

There are many problems with Bat Ye’or’s thesis. Most immediately, quite apart from assuming unrealistic motivations for everything from European foreign policy to immigrant demographics, she severely overestimates the functionality of the international organizations that she cites.

For instance, searching on Google for the keywords “Euro-Arab Dialogue” returns a bit over four thousand, up from under a thousand the last time I checked, back in 2002. There’s even a two references to the Euro-Arab Dialogue in the top 10 hits returned by Google which aren’t Ye’or’s endlessly copied articles. This compares to 33.5 million hits for “European Union,” 439 thousand for “Commonwealth of Independent States,” a bit over three million for “ASEAN,” 3.7 million for NAFTA, and almost 1.4 million hits for “Mercosur” or “Mercosul.” I’d have expected that such an important group as the Euro-Arab Dialogue–the central body behind Eurabia, after all–would have a bit of a higher presence outside of Ye’or’s literature than it does. Surely more people would have noticed by now?

Then again, reading the various non-Ye’or descriptions of what the Euro-Arab Dialogue is supposed to do and what it has actually done, I begin to suspect that accepting Ye’or’s thesis about the Euro-Arab Dialogue is something like believing that the Canada-Taiwan Parliamentary Friendship Group is actually a mechanism intended to ensure Canadian military participation in Taiwan’s upcoming war of independence against China. As for the Arab League, I fear that it has lost whatever tenuous coherence it once had once Egypt decided to break with the League and sign the Camp David Accords. It isn’t as if the Arab League has ever been as capable a body as the European Union, mind, as the failure to unify the Arab states in any meaningful way demonstrates.

This thesis also misreads the balance of power between the European Union on the one hand and the Arab states on the other. Yes, (some) Arab states have oil. The European Union is the $US 12 trillion First World economy that is a preferred destination for immigrants from the Arab world and a necessary source of much of the civilian and military technology used in the Arab world. The European Union is a global economic power with significant cultural and political influence worldwide, hence, numerous partners apart from the Arab world: Russia, South America, China, India. If any side is the hegemon in this relationship, it’s the European Union.

While other policies–those relating to the Middle East peace process, those relating to the Persian Gulf–play a role, the European Union’s relationship with the Arab world is dominated by the Euro-Mediterranean Partnership. The Euro-Mediterranean Partnership’s stated goals are threefold: establishing “a common area of peace and stability through the reinforcement of political and security dialogue”; building “a zone of shared prosperity through an economic and financial partnership and the gradual establishment of a free-trade area” by 2010; and, encouraging a “rapprochement between peoples through a social, cultural and human partnership aimed at encouraging understanding between cultures and exchanges between civil societies.” Unfortunately, the Partnership’s lofty hopes, as Hüseyin Isiksal notes in his paper (“Security, Globalisation, and Problems within the Euro-Mediterranean Partnership in the post Cold War Era”) (PDF format) may go unfulfilled. The implementation of the Partnership has gone slowly, with declining foreign investment in the Arab world and a rather fraught relationship generally between Europe and the Muslim world generally boding ill. The goal of establishing a free-trade zone by 2010 seems to be as realizable as the European Union’s Lisbon strategy to become the world’s most competitive economy by 2010.

Central Europe has easily beaten the Middle East and North Africa into the ranks of the European Union. More, it’s quite possible that the former Soviet Union will follow the central European trajectory, with countries like Ukraine, Moldova, and Georgia hoping to become member-states. The Eurabia thesis would seem to predict that the Middle East and North Africa would do rather better than either of these two regions. Even Turkey, a country with a long history of participation in European institutions, might well not get in. Although it is
as developed economically (PDF format) as the poorest entrants and has a fairly vibrant civil society, its effort could still fail given ungrounded fears of mass immigration, skepticism about the durability of Turkish democracy, and the fact that Turkey is homogeneously Muslim.

Such potential candidates as Morocco and Tunisia can expect to be eternally outside of the Union’s gates, to say nothing of such implausible candidates as Algeria, Libya, Syria, and Egypt. Quite apart from the fact of not being geographically European (and, it must be added in this era of civilizational clashes, culturally European). none of these states as yet meets any of the political, economic, or social preconditions for European Union membership. Arguably, radical republican dictatorships, conservative republican dictatorships, and conservative traditional monarchies are incapable of participating in structures like those of the European Union, lacking the flexibility and the transparency and the functionality of democratic regimes. Free-trade regimes are a different thing–China has notably achieved economic success in the past-quarter century despite its dictatorship–but as the various Arab Human Development Reports suggest, most of the non-oil economies of the Arab world are at best able to keep pace with population growth.

So. The European Union, contrary to the arguments of the Eurabia hypothesis, isn’t rushing into an ill-thought subordination under Arab rule. If anything, it’s decidedly relucta
nt to involve itself with the Arab world at all, favouring trade with China and immigration restrictions against the Third World and mandatory government assimilation programs. The most readily testable plank of the Eurabia argument is unsound.

I wrote back in January that one major failing of the Eurabia argument is its sheer danger. If it’s impossible for Europeans to agree with Arabs (or Muslims; there’s always some semantic slippage) on certain principles of foreign policy, or for Europeans and Arabs to enjoy mutually beneficial trade or to enter into grand political projects or to engage in a “dialogue of civilizations” (whatever that is), or for Arabs (and other Muslims) to be loyal citizens or honest partners, then the implications are both vast and obvious. Genocide and ethnic cleansing are two methods which have been used to control inconvenient or threatening populations within a state’s frontiers; aggressive war and colonization are two methods which have been used to control inconvenient or threatening populations outside of a state’s frontiers. If ever the peoples of the European Union bought the Eurabia thesis–if any nation-state did–we could expect bad times ahead.

Granted that Eurabia is a concept that lends itself easily to racism, people who accept it are not automatically racist. Myself, I admit that before I completed my post last year on the demographics of French Muslims, demonstrating that, in fact, they are assimilating, I thought it at least possible that Europe might become substantially Muslim and that some parts of Europe could become Muslim-majority. Fortunately, I think that there’s a litmus test that can be applied.

In the mid-2010s, a series of peaceful democratic revolutions and negotiated transitions establishes fairly secure and generally secular regimes throughout the Middle East and North Africa. Things are shaky, but no more shaky than they were in Argentina or Brazil in the mid-1980s, or in Poland and South Africa in the first half of the 1990s. The new governments respect human rights reasonably well, religious pluralism is put on a strong footing, and the rights of women are acknowledged as realities. In an environment where the fears of a threat to Europe from its southern neighbours are no longer remotely plausible in the presence of peaceful regimes, would it be a good idea for the European Union to relaunch the Euro-Mediterranean Partnership or not?

The idea behind the Euro-Mediterranean Partnership makes sense. The ideal of balanced and reciprocal relations between the two sides of the Mediterranean is a good one. Fernand Braudel was right: There really is a Mediterranean community, having transcended barriers of nationality and language and religion to form a single whole for at least a millennium. This community isn’t going to do well when everyone’s girding themselves for Huntington’s clashes of civilizations. When people aren’t afraid that their neighbours are going to descend on them and murder them, why stop this community from forming? Rules-based systems tend to produce better results than anarchical systems, after all.

Fearing and hating the idea of a takeover of Europe by Muslims is one thing. Fearing and hating all Muslims indiscriminately is quite another. Sometimes, reading Bat Ye’or and the other die-hard proponents of the Eurabia thesis say about the 21st century, I worry that they think that Europeans and Arabs should have anything to do with each other at all. Bigotry is never a good foundation for scholarship, or for policy.

Posted by randymac at 11:12 AM

I grew up a 10-15 minute walk from theHoar Bird Sanctuary, where I spent many a happy childhood hour wandering. In that sanctuary, grew astunted, blighted American Chestnut tree:

American chestnut was once the most important tree of the Eastern North American hardwood forest. One fourth of this forest was composed of native chestnut. According to a historical publication "many of the dry ridge tops of the central Appalachians were so thoroughly crowded with chestnut that, in early summer, when their canopies were filled with creamy-white flowers, the mountains appeared snow-capped."

The nut was a central part of eastern rural economies. Communities enjoyed eating chestnuts and their livestock was fattened by the nut. And what wasn’t consumed was sold. Chestnut was an important cash crop for many Appalachian families. Holiday nuts were railed to New York and Philadelphia and other big cities where street vendors sold them fresh-roasted.

What happened?

A chestnut disease was first introduced to North America through New York City in 1904. This chestnut blight, caused by a fungus and presumably brought in from eastern Asia, was first found in only a few trees in the New York Zoological Garden. The blight spread with a vengeance and in its wake left only dead and dying stems.

By 1950, Castanea dentata had disappeared except for shrubby root sprouts the species continually produces (and which also quickly become infected). Like many other pest introductions, blight had quickly spread into its new – and defenseless – host causing wholesale destruction throughout the entire range of the chestnut.

Believe it or not, as a child I dreamed of breeding a blight-resistant American Chestnut. Though I didn’t pursue it, others did. Now, it seems, theirefforts have paid off (viaInstapundit):

The tree planted Friday came from a research farm in Virginia, where blight resistance was bred into the native chestnut with the help of the Chinese chestnut.

The American chestnut, prized for its timber and its crop of glossy dark nuts, once dominated Eastern forests from Maine to Georgia. The graceful trees were virtually wiped out by blight starting at the turn of the 20th century.

That loss, Case said, "was the greatest environmental disaster in the Western Hemisphere since the Ice Age."

Now, after years of breeding, cloning and crossbreeding, the U.S. Department of Agriculture is ready to reintroduce disease-resistant chestnuts to Eastern forests next year.

How did they do it?

For decades, plant pathologists and breeders tried to create a blight-resistant tree by crossing our own species with the resistant Chinese chestnut and other chestnut species from Asia, but always with unsatisfactory results. Now, advances in our understanding of genetics have shown us where those early researchers went wrong.

Old science told us that resistance is controlled by numerous genes running a very complex system. Scientists simply flooded chestnut progeny with Chinese chestnut genes by crossing their Chinese-American hybrids with other promising Chinese-American hybrids. The result was consistently a blight-resistant but very Chinese chestnut-like chestnut tree.

New techniques are now being used. By an elaborate and time consuming system of backcrossing and intercrossing, TACF’s breeding program is attempting to develop a chestnut that will exhibit virtually every American characteristic. The desired tree is one that is fully resistant and when crossed, the resistant parents will breed true for resistance.

The method of breeding entails crossing the Chinese and American trees to obtain a hybrid which is one-half American and one-half Chinese. The hybrid is backcrossed to another American chestnut to obtain a tree which is three-fourths American and one-fourth Chinese, on average. Each further cycle of backcrossing reduces the Chinese fraction by a factor of one-half.

The idea is to dilute out all of the Chinese characteristics except for blight resistance down to where trees are fifteen-sixteenths American, one-sixteenth Chinese. At that point of dilution, most trees will be indistinguishable by experts from pure American chestnut trees.

Once a significant number of blight-free trees are produced, new crosses could potentially restore the full genetic diversity of the American Chestnut tree, with blight-resistance. Maybe we’ll get our American Chestnut forests back. I can’t wait!

(Cross-posted atRishon Rishon.)

Posted by David Boxenhorn at 07:24 AM

Will leave this new one up for about a day. Say yay or nay in the comments.

Update: If you think you have a cool logo design for gnxp’s header, email it to me at contactgnxp – at – gmail.com. Small images with transparent backgrounds preferred (so a GIF). Will take submissions for a few weeks.

Update II: Changed it back. Send me new logos if you want though. Might test them out.

Posted by razib at 11:52 PM

A week ago a mildly positive profile of the doyen of the Intelligent Design movement, Phillip Johnson, appeared in The Washington Post. I was going to comment on the relationship between Johnson’s positive comments about Critical Legal Studies and the Anabaptist takeover of Munster in 1534 until other time sensitive tasks came to pressing attention, nevertheless I want to take a moment and point something out that I noticed. Note:

William Provine, a prominent evolutionary biology professor at Cornell University, enjoys the law professor’s company and has invited Johnson to his classroom. The men love the rhetorical thrust and parry and often share beers afterward. Provine, an atheist, also dismisses his friend as a Christian creationist and intelligent design as discredited science.

Here is Provine’s research project as listed on his website:

I am working on four disparate research projects: (1) a history of the theories of neutral molecular evolution (Kimura, Ohta, King, Jukes, and many others); (2) a history of geneticists’ attitudes toward human race differences and race crossing; (3) implications of modern biology for free will, moral responsibility, and the foundations of ethics; and (4) a history of ideas about speciation from 1963 to the present.

The point is that anyone who is in-the-know would recognize William Provine as a prominent historian and philosopher of biology, not an evolutionary biologist, though he is based out of the ecology and evolution department at Cornell. Provine wrote a great intellectual biography of Sewall Wright, where he argues that the University of Chicago biologist was the most influential evolutionist of the 20thcentury.1 I think Provine’s status as a student of “meta-biology” (since he focuses on history and philosophy of biology) explains his excitement in debating Johnson, for rhetoric and disputation scaffolded by logic would likely come naturally to him as a tool of the trade. Not so for real scientists who are busy focusing on the minutiae of lab work or the esoterica of mathematical models.

As I have noted before the sophisticates who man the turrets in the Intelligent Design movement are skewed toward philosophers and other like-minded disciplines (though there are a smattering of natural scientists like Michael Behe). That is why I oppose the argument that bringing Intelligent Design into the classroom will aid in the understanding of evolution in any way, it is in essense a philosophical challenge to methodological naturalism, not an alternative research program. Until proponents of Intelligent Design start up an alternative nuts & bolts laboratory based research program (see what Michael Behe focuses on in his day job as a biochemist, his technical papers have little to do with Intelligent Design, those are all to be found in debate-focused books and philosophical and essay oriented journals) meta-biologists like Michael Ruse and William Provine are their true adversaries, not the scientists. Seeing as how most high school students aren’t even familiar with the basic foundations of Western philosophy I find the intellectual arguments for exploring the frontiers and margins of modern philosophy of science uncompelling (the political arguments are a different matter, since they can start from so many different axioms).

1 – This is a defensible assertion, seeing as how Wright lived for 99 years and was the primary theoretical influence on thinkers based in America like Dobzhansky and Mayr (and you can connect many evolutionary biologists in the United States to these two individuals). Nevertheless, I think one can not underestimate the prodding influence that R.A. Fisher had on Wright’s exploration of the mathematical geography of evolutionary genetics (see both Provine’s book and R.A. Fisher, the Life of a Scientist). Without R. A. Fisher there might never have been a Sewall Wright as we remember him today.

Posted by razib at 07:54 PM

Well, maybe not so noble……

If you search through the GNXP archives, you’ll see periodic references to how media, in general, negatively portray math/science (e.g., it is often the “evil villains” who are the geniuses). A colleague at the Clinic I work brought me a videotape of a show called Numb3rs to watch (at work). 1 After watching the part of the season he brought me, I have to say I am almost impressed.2 Instead of the evil-mad-scientist caricature, they have a very positive slant on math/science, with a genius-can-help-the-commoner caricature (perhaps due to the show’s consulting firm). Of course, they do portray the genius-in-residence as somewhat aloof and out of touch, but when you decide to devote a whole show to regression-to-the-mean, what can you expect? Still, the fella gets the last laugh, as his mentee-come-girlfriend is kinda cute (see below)

Ms. Rawat:

1. I am one of the 2% of Americans who refuse to buy a television.

2. The (forensic) psychology is hokey. Truthfully, I’ve yet to see a 1/2 accurate portrayal of a (non-psychoanalytic) psychologist.

Posted by A. Beaujean at 05:01 PM

Dienekes recently drew attention to an important forthcoming article on altruistic punishment. The article has now appeared: James H. Fowler: Altruistic punishment and the origin of cooperation, Proc. National Academy of Sciences, May 10 2005, vol. 102, 7027-49. It is available as a free pdf download here.

So what is altruistic punishment and why is it important?

One of the central problems of human evolution is to explain the widespread existence of cooperation. Such cooperation often produces a benefit for social groups as a whole, but at a cost to the cooperating individuals. So there is an advantage for ‘free-riders’ who take the benefits but avoid the costs. Why then does cooperation not break down?

The problem can obviously be solved if free-riders are punished. But those who do the punishing incur a cost in doing so (e.g. the risk of retaliation), greater than their individual gain, hence the term ‘altruistic punishment’. So why should anyone punish?

Again there is an obvious solution if failure to punish is itself punished. We can avoid an infinite regress of special rules about punishment by adopting a general social rule to the effect ‘punish all breaches of social rules’. Since this is itself a social rule, failure to punish is also a breach of a social rule, which must therefore be punished, and so on.

Such a rule is an evolutionarily stable strategy provided a large enough proportion of the population are already following it. But it is difficult to see how the rule could become established in the first place. Several theorists have resorted to an explanation by group selection: in small groups a large proportion of ‘punishers’ may be established by chance, and these groups then spread at the expense of other groups.

Group selection should be regarded as an explanatory last resort. The importance of Fowler’s paper is that it provides an alternative explanation of altruistic punishment based on individual selection. If the only strategies allowed are ‘cooperate’, ‘free ride’, and ‘cooperate and punish’, then ‘cooperate and punish’ will be more costly than the alternatives when it is rare, and it cannot spread by individual selection. The crucial feature of Fowler’s model is that it allows another strategy: individuals can opt out of group activities when the benefit of cooperation is lower than that of individual activity. If there are too many free-riders, more individuals will opt out and ‘do their own thing’. But when most of the population have opted out, the strategy of ‘cooperate and punish’ may have an advantage over ‘opt out’, which allows it to spread even when it is rare. The strategy ‘cooperate’ (but not punish) will spread more quickly at first, but once ‘cooperate and punish’ has passed a certain critical frequency (which depends on the parameters) it gains over ‘cooperate’ until it becomes the prevalent strategy. So ‘cooperate and punish’ cannot spread when it is rare in a population consisting only of ‘cooperators’ and ‘free-riders’, but the existence of the ‘opt-out’ strategy gives it an entry point.

Fowler considers a number of possible objections to his model. I am not sure that the model is very plausible, but it is no worse in this respect than the group-selectionist alternatives. It does at least mean that the groupies can no longer claim there is no alternative.

Personally I think that both approaches are misconceived. The basic flaw is encapsulated in the first sentence of Fowler’s paper: ‘Human beings frequently cooperate with genetically unrelated strangers whom they will never meet again, even when such cooperation is individually costly’.

Well, no, they don’t. Even in modern, well-regulated societies such cooperation is unusual. (When did you last do it?) In hunter-gather societies, which prevailed for most of human evolutionary history, it is practically unknown. But I will expand on my objections in another post.

Posted by David B at 11:56 AM

Genomics refutes an exclusively African origin of humans. This is a long and complex paper, but intelligible with close reading. I have cut & pasted the introduction and discussion below. But I want to highlight one point:

…Many, even most, functional loci globally surveyed…MC1R…show deep structure both geographically and temporally, with coalescence times for non-African variation extending to much earlier time periods than the first emergence of modern humans in Africa. This strongly suggests that archaic assimilation affected these loci….

The point about assimilation of the MC1R alleles from archaic populations matches what a GNXP commentor postulated earlier today. Please note that model presented above matches (down to semantics) what was outlined in Dragon Bone Hill, though with far greater clarity and precision.

(via Dienekes)

Introduction

Since the discovery of apparent signals of strong late Pleistocene population expansions (Rogers and Harpending, 1992 and Harpending et al., 1993) in human mitochondrial DNA (mtDNA), a number of studies have sought similar signs in other genetic polymorphisms. Among the data so analyzed have been nuclear sequences, short tandem repeat polymorphisms (STRs), and single nucleotide polymorphisms (SNPs). While mtDNA shows signals of recent expansions in almost every human population, it has by now become clear that the nuclear data do not present an unambiguous picture regarding population expansion associated with the spread of anatomically modern humans. For example, various analyses of STR data using different statistics have given contradictory signals of expansions, their timing, and the sub-populations involved (Di Rienzo et al., 1998, Reich and Goldstein, 1998, Kimmel et al., 1998 and Zhivotovsky et al., 2000). The first detailed evidence from the nuclear genome also showed no evidence at all of expansion (Harris and Hey, 1999).

To explain low interpopulation diversity in humans, it has been suggested that humans passed through a bottleneck (Haigh and Maynard Smith, 1972). It has also been proposed that there was a bottleneck associated with the emergence of modern humans in Africa and their spread throughout the world (Jones and Rouhani, 1986). For example, SNP haplotype block data show a signature of bottlenecks at vastly differing times in the prehistory of African and non-African populations (Reich et al., 2001 and Gabriel et al., 2002), even if their cause as yet remains unclear. These bottlenecks would need to have been of extraordinary severity and/or duration to explain some of the data, e.g., for Europeans, Reich et al. (2001) suggested a pre-expansion bottleneck size of 50 individuals for 20 generations (or any size and duration of the same ratio), while Marth et al. (2003) obtained their best fit with size-duration ratios between 1000 to 2500 individuals for, respectively, 240 to 550 generations. Yet, single locus studies (e.g., Harding et al., 1997, Harding et al., 2000, Zhao et al., 2000, Yu et al., 2001 and Yu et al., 2002) often find at most mild bottlenecks, or none, in non-Africans, resulting in an overall picture that is puzzling. A recent study by Marth et al. (2003) used 500,000 SNPs to conclude that the dominant population history of humans was a Pleistocene population collapse followed by a mild post-Pleistocene recovery. The importance of these varied signals of bottlenecks and expansions is the subject of this paper.

The significance of genetic signatures of late Pleistocene population expansions is that they directly address the contrasting theories of modern human origins that have been the subject of much debate since the 1980s. The recent African origin model (Cann et al., 1987 and Stringer, 1992) proposes that anatomically modern humans arose in Africa around 130,000 years ago as a new species, which subsequently spread across the world, replacing all non-African archaic humans. In contrast, the multiregional evolution model proposes that modern humans emerged across the world from regional archaic human populations that were always linked by gene flow (Wolpoff et al., 1984).

Genetic evidence to date has been interpreted as giving far greater support to the recent African origin (RAO) model than to the multiregional evolution (MRE) one. Signs of population expansions in human mtDNA have seemed to confirm the RAO model [albeit in a modified “weak” form that suggests multiple bottlenecks and then expansions; Harpending et al. (1993)], as the African expansion seems to clearly pre-date the Asian and European ones. These signals have been seen as indicating the rise of modern humans in Africa and their subsequent expansion into the other continents.

It is now routinely assumed that such signals of expansions support the most controversial of the claims of the strict RAO model—that all non-African “archaics” were replaced and all living people are descended exclusively from African modern humans (Manderscheid and Rogers, 1996). For this to be true, the entire extant human genome has to be derived from recent Africans. Therefore, if the signals of expansions in mtDNA, for example, indicate a population history rather than merely the history of a single genetic locus, the same signals should be discernable at all genetic loci.

Others have proposed models intermediate between the strict RAO and MRE models (Smith, 1985, Relethford, 2001 and Templeton, 2002). Relethford called his version “mostly out of Africa” because in it there is actual movement of populations from Africa. These newly arrived Africans mostly replace the local archaics, but there is some degree of admixture. On the other hand, in our model, there is no long distance movement of populations at all; change is driven entirely by local gene exchange among demes and natural selection. This model has the advantage of parsimony and simplicity, and it will be important to disentangle the effects of selection and long range migration from the archaeological and fossil records. For example, if there were long range population movements with local hybridization, then signatures of that hybridization should persist and be discernible in the fossil record and in populations today. In contrast, our model posits that there are hybrids essentially only at the wavefront. Since this front is moving at something more than 3 km per generation, it would take about 30 generations, or 750 years, to travel 100 km. We would then expect to find hybrid-looking fossils only within this small temporal window.

Templeton’s (2002) paper was an ambitious attempt to trace ancient gene flow from molecular markers. He examined the geographic distribution of subclades of several markers with an intuitively appealing logic that allowed him to date major movements to and from Africa. There are, however, several problems. His algorithm is regarded with skepticism by population geneticists (Felsenstein, 2003). Moreover, even if his algorithm were to identify real movements between ancestral populations, there is no information about where those populations were at the time. For example, a signature of movement between African and Asian ancestors several hundred thousand years ago might have been a movement between Africa and Asia under MRE, but a movement between adjacent river valleys, for example, under RAO since those ancestral populations would have been in Africa at the time. Templeton’s findings provided almost no evidence for distinguishing among models
of modern human origins.

A strongly negative value (e.g., ≤ −1.5) of the Tajima D statistic (TD; Tajima, 1989) for a single locus likely indicates a selective sweep at that locus, while many such values obtained at independent loci would suggest a population expansion. Przeworski et al. (2000), analyzing data from 16 independent loci, found nearly evenly distributed positive and negative TD-values, thus offering no support for putative population expansions. Stephens et al. (2001), analyzing data from 313 genes, found that 90% had negative values, but only a fraction of these were statistically significant.

In the RAO model, all loci should have strongly negative TD-values, comparable to that shown in non-African mtDNA [TD = −2.28; Ingman et al. (2000)]. Thus, the nuclear data do not consistently signal expansion, and when they do, the signal is of a mild expansion, perhaps reflecting only post-Pleistocene population growth associated with the spread of agriculture.

Alternative explanations for the puzzling features of the genetic data discussed above may be found in a recently proposed theory of modern human origins. Arguing along the lines of Sewall Wright’s (1932) “shifting balance” theory, Eswaran (2002) suggested that the African transition to anatomical modernity may not have been a speciation event, but was rather a “character change” involving alleles at multiple loci that cooperated to confer a co-adapted genetic advantage to modern humans. Given small random movements of hunter-gatherer groups (demic diffusion), and under the condition of a low rate of interbreeding between modern and archaic humans, such an advantageous gene combination could spread as a wave of advance, or a “diffusion wave,” of anatomical modernity (Eswaran, 2002).

One can visualize this process as that of the region of modern humans expanding at a steady rate into the region of archaic humans, the two regions being separated by a moving “wavefront” where the modern and archaic populations overlap. Only at the wavefront would both human types coexist; therefore, all hybridization and all selection favoring the moderns against the archaics—and thus all expansions in the modern population—would occur there.

According to this theory, the progress of the wave could be accompanied by considerable hybridization at the wavefront. Even so, the assimilation of archaic human genes into the modern populations would be low if the advantageous modern gene combination were complex enough that hybrids, with no selective advantage from their incomplete complement of modern genes, rarely became fully modern. Under such circumstances, the wave would essentially be an expansion of the modern humans at the wavefront. Further, as the small wavefront modern population would at any time be principally derived from previous wavefront moderns, the wavefront modern population would become severely bottlenecked over the thousands of generations that the wave took to travel from Africa to the far corners of Asia and Europe.

However, as all new modern populations would be created principally by the small wavefront modern population, the bottleneck would be followed by a continuous “rolling” expansion in the wake of the wave. As the signs of the wavefront bottleneck and the subsequent expansion would be passed on to the emergent modern populations, this theory offers an explanation for the bottleneck-and-expansion signature seen in so much human genetic data. It also explains why the expansions in Asia and Europe could have occurred tens of thousands of years after the African one (Harpending et al., 1993), for the wave would have traveled at about 3 km per generation, given the empirical evidence of the spread of modern humans.

Under conditions of a limited rate of archaic assimilation, only a few polymorphisms would survive at each locus in the bottlenecked wavefront modern populations. So, it is possible that African alleles often spread with the wavefront across the world. Such loci would then show signs of an expansion of a previously small set of African polymorphisms into a worldwide population. However, given a non-zero rate of assimilation from archaic populations, it is also possible that the wavefront moderns would, at some point along their spread, assimilate archaic human alleles (at loci unassociated with the functional advantages of modernity), which would then “surf” the wavefront and spread along with anatomical modernity. Thus, at these loci, the final modern world populations would have African/“modern” alleles, as well as alleles assimilated from archaic populations. The latter loci would show a considerable time depth and a corresponding lack of signs of expansions. This seems the most plausible explanation for the inconsistent signals of expansions obtained from various STR statistics (Eswaran, 2003), as well as the weak and variable signs of expansion in humans nuclear SNPs and the correlation among loci between Tajima’s D and nucleotide diversity (Stephens et al., 2001).

Missing signs of expansions at many genetic loci would be correlated with assimilation at those loci from non-African archaic populations. Such assimilation would obviously also be compatible with evidence of great time depth in present-day non-Africans and of ancient and uniquely non-African polymorphisms (Harding et al., 1997, Harding et al., 2000, Zhao et al., 2000, Yu et al., 2001 and Yu et al., 2002). It would also explain why significant geographical structuring (presumably ancient, and with partly archaic roots) is often seen at such loci, but not in others like mtDNA. The theory thus suggests that present day modern humans are not exclusively derived from early modern Africans, but have a significant genetic inheritance from non-African archaics as well.

In this paper, we explore this proposed scenario through simulations of a modified version of the numerical model of Eswaran (2002). We use the model to compute population statistics of the emergent modern populations for two cases simulating (a) the spread of modern humans from a regional source across a one-dimensional world through the replacement of archaic types, and (b) the analogous spread of a modern human type defined by an advantageous combination of some C unlinked genes. We show that while the replacement case reproduces some of the gross features of the genetic data, the model replicates its subtler details only in the assimilation case—thereby arguing that significant assimilation from non-African archaics accompanied the modern human transition. Our model is the simplest implementation of the idea of a coadapted gene complex, a phenotype, and the consequences for the neutral genome of a selective phenotype sweep.

…

Discussion
How pervasive was assimilation?

The question immediately arises as to how widespread was archaic assimilation in the human genome. Even a rough estimate suggests that assimilation was surprisingly high—surprising because the debate until now has been whether there was any assimilation at all. The simulations conducted here have shown that significant TD-values are strongly correlated with low assimilation, and conversely, that loci with high assimilation usually yield non-significant (but often negative) TD-values.

The Tajima D statistic is ideally suited for detecting assimilation from archaic populations. Given the long history of humans living outside of Africa, there would have been significant geographical structure (which increases TD) in the global human population at the time of the wave initiation, ca. 100,000 years ago. Thus, any assimilation from non-African archaic humans would inevitably increase TD, reducing the possibility of a significant signal of expansion. Therefore, TD is less likely to show expansions than other statistics if assimilation occurs. [See Yu et al. (2002) for a possible case in point.]

We can make a stronger assertion based on a comparison of nuclear loci with mtDNA. The deep differences between Neandertal and modern mtDNA, a
nd the extremely low variability and geographical structure in modern mtDNA leaves little doubt that archaic mtDNA was largely, if not completely, replaced. The empirical TD for mtDNA in non-African populations is −2.28 (Ingman et al., 2000). While such a low TD-value is not obtained in the simulations of 10,000 individuals that we described above, it is well within the range of TD-values obtained for simulated world populations of 30,000 or 50,000.

Recovery from the wavefront bottlenecks in these larger simulated populations leads to stronger signals of expansions, i.e., more negative values of TD, even while the effective populations indicated by the mean pairwise differences remain below 10,000 at the simulated present day (as the pairwise differences have not fully recovered their equilibrium values after the wave). These latter simulations are, we believe, closer to the putative modern human diffusion wave, as they deliver highly negative TD-values in the range empirically seen in mtDNA. However, the TD-values for the replacement cases in these larger simulated populations nearly always fall within the 90% significance range (TD ≤ −1.5). This suggests that any loci with empirical TD-values that are less than 90% significant are likely to have been affected by assimilation. For example, the “geography-based” sample of 437 loci presented by Ptak and Prezeworski (2002) shows fewer than 25% of the values are below −1.55, implying, by the above argument, that around 75% of the loci had significant assimilation. These are astoundingly high figures.

Other data, too, suggest pervasive assimilation. Scans of 624 STR loci by Storz et al. (2004) revealed that 13 of these had significantly reduced variability by their very strict criterion, which the authors attributed to selection, but which we think signals “replacement” loci. Even among the 13 loci, reduced variation occurred either in Europe or Asia, but rarely in both—which seems peculiar if selection were involved, but is entirely likely if random fixation of certain alleles carried by the wavefront independently occurred in the separate Asian and European waves. Only one of the 13 apparent sweeps was seen in Africa, where the diffusion wave model predicts some sub-Saharan populations would not have been subjected to the wave. Therefore, we believe the STR pattern better fits the diffusion wave hypothesis than the selectionist one. By looser criteria, approximately 25% of their loci showed this pattern of reduced variability outside of Africa—in either Europe or Asia, but not both. While Storz et al. (2004) proposed that the patterns are due to selection, it is important to note that they studied STRs with no known functional significance.

The immediate objection to the possibility of such pervasive assimilation in the nuclear genome may come from physical anthropologists. If such a degree of assimilation occurred during the modern human transition, they may ask, why did the modern human morphology remain essentially the same across the world, rather than showing physical signs of admixture with archaics from Asia and Europe? One possible answer to this question has already been given by Eswaran (2002), who argued that the modern morphology itself may have given the coadapted modern advantage—possibly due to reduced childbirth mortality—that propagated modernity. Thus, the modern morphology, and the alleles that “coded” for it, could be fixed in all modern populations even while the rest of the human genome carried a considerable number of assimilated archaic human alleles. Other aspects of modern human morphology could also have been selectively advantageous, but it is not immediately apparent what they could have been. Some correlated aspect of energy requirement and usage might be involved.
Assimilation at functional loci

With the exception of the C loci associated with modernity, the simulations presented here consider only neutral loci. Thus, the interpretation of the contrasting signals of expansions may be thought to hold only for such loci. To take an extreme view: is it possible that assimilation from archaics affected only neutral parts of the genome, while the functional parts were entirely derived from early modern Africans?

The evidence weighs heavily against this possibility. Many, even most, functional loci globally surveyed (e.g., β-globin, MC1R, PDHA1, Dys44, Y-chromosome, etc.) show deep structure both geographically and temporally, with coalescence times for non-African variation extending to much earlier time periods than the first emergence of modern humans in Africa. This strongly suggests that archaic assimilation affected these loci. The TD values, too, are usually non-significant and even positive, not even remotely suggesting population expansions. Moreover, in functional loci, an expansion would cause strongly negative TD-values in a random mating population, except in cases where deep phylogenetic structure was preserved by balancing selection before the expansion. Two of us (HCH, ARR) proposed balancing selection as an explanation for the lack of signals of expansions at functional loci (Harpending and Rogers, 2000), but such loci do not show some other signs of such selection (Wall and Przeworski, 2000). On the other hand, assimilation from archaic humans is a sufficient explanation for the missing signs of expansions, especially since loci with local selective advantage are more likely to be assimilated (Eswaran, 2002), and loci under balancing selection are also more likely to be assimilated.
Conclusions

The simulations presented here suggest resolutions for a number of crucial puzzles in the genetic data on modern human origins.

A diffusion wave of a complex genotype can explain why mismatch distributions of high-mutation-rate loci (such as mtDNA) show late Pleistocene expansions, while those of lower-mutation-rate SNPs show a contraction (Marth et al., 2003). It also explains why the more rapidly responsive site frequency spectra of SNPs show a bottleneck-and-expansion history (Marth et al., 2004). These explanations follow directly as consequences of a low assimilation-rate diffusion wave of moderns spreading out of Africa.

The same mechanism also explains why the expansions in Europe and Asia followed so late after the expansions in Africa (Harpending et al., 1993, Reich et al., 2001 and Gabriel et al., 2002), while certain populations in sub-Saharan Africa show no signs of expansions (Excoffier and Schneider, 1999). The model suggests that these populations are directly descended from the first modern populations in the “core region,” which would not be swept by the wave (Eswaran, 2002). But perhaps the most interesting explanations offered by the model concerns why—even among non-Africans—certain other loci do not show the characteristic bottleneck-and-expansion pattern and why, while most show mildly negative Tajima D values, there is so much variation in these values. These empirical findings directly suggest that assimilation from archaic human populations accompanied the modern human transition across the world. The bottleneck at the wavefront, while greatly restricting the genetic diversity in the non-African (and north African) modern populations, randomly allowed—at least at neutral loci—either African polymorphisms to spread worldwide, or else allowed non-African polymorphisms to be assimilated and spread along with the wavefront. In the first case, we see strong signals of expansions, as in mtDNA; in the second case, we see less clear-cut signals of expansions, often accompanied by signs of deep population subdivision, significant numbers of unique non-African polymorphisms, and great time depths in non-African populations. The latter signs have been found in numerous nuclear loci studied in the last few years. We conjecture that as much as 80% of the nuclear genome is significantly affected by assimilation from archaic humans (i.e., 80% of loci may have some archaic admixture, not that the human genome is 80% archaic).

While each locus has its own history, the above reasoning suggests that African-dominated loci would all roughly tell the same story, while the others would each have its own—for assimilation would have varied in time and place in each case. Thus in the late 1990s, after a decade when most geneticists became convinced of the strict replacement recent African origin model, there was confusion when many nuclear loci—each in its own way—contradicted the patterns first seen in mtDNA. Yet, the following of that particular model remained strong, as there was no other theory that could explain the contrasting patterns. Now there is such a theory, and it tells us that while modern humans first emerged in Africa, living human populations carry within them a substantial genetic inheritance that had its origins in non-African archaics.

Posted by razib at 03:26 PM