A new paper, The Dawn of Human Matrilineal Diversity, is out in AJHG. I read too much John Hawks to really be all that excited about mtDNA based studies, and this paper is Mitochondrial Eve to the n^th power. But...I do think it is indicative of a trend which suggests a rollback from the most extreme Out of Africa scenarios; i.e., that one band somewhere in Eastern Africa arose ~100,000 years ago and expanded demographically so that they were the exclusive ancestors of all human beings.¹ The introgression story is one angle; but the likelihood of preexistent population substructure within Africa itself is another. If you don't read the paper (which is Open Access), just check out Figure 1 and the map. Breathless description of the study over at ScienceDaily of course....

Related: Kambiz comments in more detail.

1 - Some of this was more about public perception than reality; just like the one mtDNA ancestor was conflated with one female ancestor (the same trick of course applied to the NRY).

Labels: Evolution

One of the "debates" currently occupying evolutionary biology is whether evolution occurs primarily via changes in protein-coding sequence or via changes in gene regulation (apparently it's become so heated that battles between the two camps are now fought through t-shirts).

As understanding of the genetics of adaptation advances, this debate will likely fade away--a priori, it's easy to make the case for either, and well-studied individual examples are showing that, as one might expect, evolution isn't particularly dogmatic about the sources of variation it works with.

It's these case studies that are most interesting--take, for example, a recent study on the adaptation of Arabidopsis halleri to the heavy-metal-polluted soils it now occupies. This is quite a nice example of evolution via gene regulation--the authors map the ability to tolerate heavy metals to a particular candidate gene, then identify both a change in copy number as well as changes in the promoter region of the gene that lead to high levels of expression. To complete the story, they then pop this highly expressing version of the gene back into A. thaliana (the model organism) and show they're able to recreate the crucial aspects of the adaptation in that species.

Labels: Evolution, Genetics

As you probably know at my other weblog I've been going through Stephen Jay Gould's The Structure of Evolutionary Theory chapter by chapter. I just finished the first part of the work, which is a history of science as opposed to a discussion of contemporary science. I've blogged chapter 1, 2, 3, 4, 5, 6 and 7 so far. If you're interested in the topics covered by Gould so far I recommend Peter J. Bowler and Will Provine. Bowler is a lot more concise about 19th century evolutionary theory, in part because that's his academic specialty. Provine offers a Sewall Wright-centric perspective, but that's a good starting point to get a sense of the arc of 20th century evolutionary biology.

Labels: Evolution

Just noticed that Nature's Oracle: A Life of W. D. Hamilton is finally out. I haven't read it yet, but will have soon once my copy arrives. If you don't know who W. D. Hamilton is, you know his work. Hamilton's early theoretical papers on the evolution of sociality (e.g., kin selection) were the root of many of the ideas presented by Richard Dawkins in The Selfish Gene, while his later ideas about the origins of sex figured in the background of Matt Ridley's The Red Queen. If you wish to familiarize yourself more directly with Hamilton's science and life, I highly recommend his collections of papers with commentary, Narrow Roads of Gene Land, Volume 1: Evolution of Social Behaviour, Narrow Roads of Gene Land, Volume 2: Evolution of Sex and Narrow Roads of Gene Land, Volume 3: Last Words (you will sometimes find cheap copies on Ebay or in used book stores). The author of Nature's Oracle, Ullica Segerstrale, is a sociologist of science (with a background in chemistry) who wrote Defenders of the Truth: The Sociobiology Debate. Hamilton is second only to E. O. Wilson in Segerstrale's narrative, so it is no surprise that she would choose to focus on him now. In the end I suppose the greatest tribute to a scientist is to remember their intellectual contributions and integrate them so thoroughly into contemporary thought that they become background assumptions; but as humans we are interested in personal narrative, and I look forward to exploring the more human (and eccentric) aspects of W. D. Hamilton's character. Though it does nothing to further understanding of science as such, it seems fitting to remember the man.

Related: Richard Dawkins' euology for Hamilton.

Update: I lied! Turns out that the pub date on the Amazon page is wrong and it won't come out until mid-March. Don't blog 'till you "checkout."

Labels: Evolution

Evidence for declines in human population densities during the early Upper Paleolithic in western Europe:

In western Europe, the Middle to Upper Paleolithic (M/UP) transition, dated between ~35,000 and ~40,000 radiocarbon years, corresponded to a period of major human biological and cultural changes...New faunal data from the high-resolution record of Saint-Cesaire, France, indicate an episode of significant climatic deterioration during the early Upper Paleolithic (EUP), which also was associated with a reduction in mammalian species diversity. High correlations between ethnographic data and mammalian species diversity suggest that this shift decreased human population densities. Reliance on reindeer (Rangifer tarandus), a highly fluctuating resource, would also have promoted declines in human population densities. In this context, the possibility that a modern human expansion occurred in this region seems low. Instead, it is suggested that population bottlenecks, genetic drift, and gene flow prevailed over human population replacement as mechanisms of evolution in humans during the EUP.

I bolded words which I thought emphasized the provisional and tenuous nature of the contingent sequences of inferences being made in this paper. A summary in National Geographic where the first author is quoted is less equivocal:

Morin argues that Neandertal populations thinned out gradually as Europe's environment became harsher, with some groups going extinct.

But climate stresses may have wrought evolutionary adaptations in surviving Neandertals, leading them to develop characteristics like those of modern humans, Morin added.

"Neandertals adapted to this harsher climate by expanding their social networks, a process that allowed the diffusion of 'modern traits' into the Neandertal gene pool," he said.

Some modern humans may have migrated to Europe during this period, Morin added, "but I don't think it happened to the large scale implied by many scholars."

Such an influx probably didn't occur until about 10,000 years ago, with the spread of agriculture from the Middle East, he said.

I don't know much paleontology. Like history this is a field where theory can only take you so far, and you have a comparative advantage if you can cogitateoff an empirical distribution data that you've already internalized via years of close study. But because it is a historical science you also have to place your hypothesis is a bigger context, and the conditional and probabilistic nature of evolutionary processes makes a broader framework essential. Remember the Etruscan story? Archaeologists confronted with extremely strong genetic data (from multiple angles) simply shrugged and expressed ignorant skepticism, as opposed to changing their priors and shifting their paradigm.

When a palaeoanthroplogist makes assertions in a field where I'm not very clear about the details I pay attention to the things they say which I can evaluate. Concluding that 'modern' humans (or, specifically, the descendants of Africans of ~50,000 years B.P.) only arrived during the Neolithic seems to shed an unfavorable light on a scholar's credibility; genetic data suggests that Middle Eastern (Anatolian) Neolithic lineages (e.g., haplogroup J2) are extant across Europe on the order of ~25% penetration (peer reviewed range of 20-50%). In terms of the structure of scientific theories its seems that the researcher above is making an inference based upon their own data and model, which is disputable, and dismissing a far stronger body of work which contradicts said inference (or perhaps the author is ignorant of that body of work?).

There's also the large network of causal factors. In After the Ice Steven Mithen recounts how computer simulations show that the dynamic of a joint impact of both environmental stress (e.g., climate change) and modern human predation is the best explanation for the pattern of megafaunal extinctions we see around the world in the past few thousand years. Specific data points such as the extinction of Cuban ground sloths are highly persuasive to me. Evolutionary pressures are often interspecific, intraspecific and environmental; there is no need to assume the operation of one excludes the operation of another. And yet in natural history there is this constant tendency to present "silver bullet" models with one primary causal factor. Just because a condition is necessary does not mean that it is sufficient. I have no doubt that the correlations are highly striking, but the sequence of events need to be assessed in light of the full data set we have in terms of time and space. "Cold snaps" and extinctions are not sui generis, but rather are recurrent features of the history of our planet. Neandertals persisted for hundreds of thousands of years across at least half of Eurasia; during this period there were no doubt great fluctuations in temperature and ecological conditions. And yet they, and most other "archaic" types, disappeared in the space of several tens of thousands of years as "modern" morphologies spread across the world, while at the same time geneticists do conclude that the predominant (if not exclusive) element of our ancestry derives from the African continent within the last 100,000 years. Should we ditch this model because of a set of analyses of faunal remains? I'm skeptical, largely because I don't see the data above as falsifying the orthodoxy. Rather, it is compatible with a range of hypotheses.

As I tried to make clear in my post about cultural anthropology science that isn't physical or mathematical is hard. It's messy. There are lots of interlocking factors, statistical variation and historical contingency. I don't think that means it is impossible, but it does mean that it requires care, humility and an attention to detail. The logical structure of math is perfect, in theory you need to know only patches to infer enormous expanses. An ecologist I knew once joked about the shock that a physicist who was moon-lighting in a biostatistics class in graduate school experienced in terms of the noise that they had to confront in every experiment and analysis. In the historical and human sciences knowing a patch and generalizing from that locality seems to be a waste of time, and only justifies the critiques of extreme subjectivists. Rather, the structure of knowledge is by its nature a big picture with a riot of small details, and those details make no sense unless you familiarize yourself with the whole.

Note: The last sentence of the abstract, "it is suggested that population bottlenecks, genetic drift, and gene flow prevailed over human population replacement as mechanisms of evolution in humans during the EUP" is problematic for me...I kind of smell the tendency to use genetic drift as a deux ex machina here. Just like Judith Rich Harris pointing out the use of "interaction effects" as a get out of jail card in much of behavior genetics in No Two Alike.

Related: At Anthropology.net.

Labels: Evolution

A Human Ancestor for the Apes?

Labels: Evolution

A few recent evolution/genetics-related posts worth reading:

1. Jonathan Eisen on the fascinating story of the metabolic symbiosis going on in the cells of the glassy-winged sharpshooter.

2. Evolgen on the evolution of sexually antagonistic genes.

3. Popgen Ramblings on the genetics of the sex ratio.

Labels: Evolution, Genetics

Economists Oded Galor of Brown and Omer Moav of Hebrew U. argue in a new paper that the Agricultural Revolution created longer lifespans. A simple version of their model goes like this:

Agriculture-->Disease-->Somatic Investment in stronger bodies-->Longer lifespans once things settle down.

This result hoists Jared Diamond on his own petard: If the Agricultural Revolution really did make life worse (as he frequently argues), then the forces of evolution would have noticed that fact and reacted in some way. Galor and Moav argue that evolution would respond by building stronger bodies in high-disease environments, and the result would be longer lifespans once those dangers of disease recede in the modern world.

More importantly, Galor and Moav argue that we're still living through the Agricultural Revolution: Groups that went agricultural early on went thorough bigger genetic changes. That means that early agriculture should cause longer lifespans.

An interesting theory, but what's the evidence? They use Putterman's new estimates of the year that countries went agricultural, control for a lot of the usual suspects, and find this:

[C]ontrolling for geographical and continental characteristics of each country, as well as income, education and health expenditure per capita, every 1000 years of earlier Neolithic transition contributes to life expectancy 1.6-1.9 years.

A couple of facts about the agricultural transition: The differences across countries are big, according to Putterman:

The average country went agricultural about 4500 years ago (mean and median within a couple of hundred years).

Standard deviation: 2400 years.

10th percentile: 1500 years ago (mostly sub-Saharan countries, plus some New World countries)

90th percentile: 8000 years ago (Eastern and Southern European countries--the Middle East was earlier).

So the cross-country differences appear big enough to be evolutionarily important a priori.

But back to Galor and Moav's big result: Almost 2 years of life for a thousand years of agriculture: Maybe that number will become a new stylized fact in the economics-and-evolution literature. It'll be interesting to see if this result comes up in political debates over health care reform.....

Labels: Economics, Evolution

Matt finds some unexpected data regarding MHC polymorphism & mating systems. That's the great thing about science: confusing or unexpected results can be a good thing! Science is in part about 3 1/2 yard runs which push the ball forward and extend the drive. But sometimes science is also about leaving the stadium and starting a new game. I have a friend who just stumbled onto results which might decide a central debate within his field, against the "side" he was on! But he's happy about it, it might make his career, and he was probably wrong so it is all for the good.

Labels: Evolution

Couldn't find a thread on this yet: Actor/Politico/Author Ben Stein has apparently become a "You can't handle the truth"er. He appears in a documentary on the persecution of the intelligent design movement *yawn* but here's his key claim:

...[Stein] said in a telephone interview that he accepted the producers' invitation to participate in the film not because he disavows the theory of evolution - he said there was a "very high likelihood" that Darwin was on to something - but because he does not accept that evolution alone can explain life on earth.

He said he also believed the theory of evolution leads to racism and ultimately genocide, an idea common among creationist thinkers. If it were up to him, he said, the film would be called "From Darwin to Hitler."

So it's not that he doesn't believe in evolution, it's (partially) that he doesn't trust the masses with the knowledge. There, he could be onto something.....

Related: I'm in the middle of reading Watson's very entertaining Avoid Boring [Other] People, and he notes that at his 1946 U Chicago commencement, the university president said the only hope of avoiding disasters like WWII was to believe in the "brotherhood of man," a belief that was supposedly impossible without a parallel belief in the "fatherhood of God." Watson has a lot of great things to say about religion so far--no surprises, but still fun.

He also has a lot of good academic career advice in handy numbered lists at the end of each chapter (e.g., "Have friends close to those who rule," "Channel rage through intermediaries," "Extend yourself intellectually through courses that initially frighten you," etc.,).

Labels: Bueller, Evolution, Intelligent Design, Watson

Actually I don't know, but there's some evidence that extinct Neandertals were red heads!

Labels: Evolution

Some readers may recall something of a discussion on these pages between myself and Larry Moran regarding the relative importance of natural selection and drift in phenotypic evolution. My refrain was "it's an empirical question", so I'll point to two recent reviews that touch on the growing body of data that can be used to address the question.

The first is titled, conveniently enough, "Which evolutionary processes influence natural genetic variation for phenotypic traits?". The authors, of course, can't really answer the question, but they point to a number of studies examining specific traits and how natural selection has influenced their evolution. The picture is from a striking example of adaptive variation in coat color in mice. Another example that particularly caught my eye was that of variation in flower color in Linanthus. Those of you familiar with classic population genetics will recall that Linanthus was one of Sewall Wright's preferred examples of neutral phenotypic variation driven by isolation [pdf]. He was, as it turns out, probably wrong. Molecular data has the power to answer a lot of these questions, or at least allow them to be posed in a more testable manner.

The second review focuses on the species that is becoming/has become the modern "model organism" for studies of selection-- humans. It's a very thorough summary of the recent scans for selection in the human genome, and anyone looking to get up to speed on the topic should read it. Selection in pervasive in the genome, and perhaps the only way to understand how it acts is through statistical analysis of genome sequence. The authors make this explicit, with an interesting nod to the oft-cited Lewontin and Gould spandrels paper. There are those who argue that functional evidence is essential for defining a region of the genome as being under selection, however, the deductive logic between selection and phenotype only goes in one direction-- that is, a region identified as being under selection using statistical methods is necessarily functional (with a certain false positive rate), but, as a modern fan of the spandrels paper might write, evidence of function does not necessarily imply selection.

Human evolution has become something of a trendy topic, but as is often the case, it's trendy for a reason-- there is extensive data on genotype, phenotype, and environment coming available on our species, and this will allow us to tackle some of the longest standing debates in evolutionary biology. They are, after all, empirical questions.

Labels: Evolution, Genetics, Population genetics

Ecological consequences of early Late Pleistocene megadroughts in tropical Africa:

Extremely arid conditions in tropical Africa occurred in several discrete episodes between 135 and 90 ka...Fossil and sedimentological data show that Lake Malawi itself, currently 706 m deep, was reduced to an ~125 m deep saline, alkaline, well mixed lake. This episode of aridity was far more extreme than any experienced in the Afrotropics during the Last Glacial Maximum (~35-15 ka). Aridity diminished after 95 ka, lake levels rose erratically, and salinity/alkalinity declined, reaching near-modern conditions after 60 ka. This record of lake levels and changing limnological conditions provides a framework for interpreting the evolution of the Lake Malawi fish and invertebrate species flocks. Moreover, this record, coupled with other regional records of early Late Pleistocene aridity, places new constraints on models of Afrotropical biogeographic refugia and early modern human population expansion into and out of tropical Africa.

Labels: Evolution

The genetic architecture of normal variation in human pigmentation: an evolutionary perspective and model:

It has long been noted that the vast majority of the genetic diversity found in the human species is distributed within geographic populations...Only 5-15% is observed between groups, reflecting our recent origin less than 200,000 years ago. In contrast and intriguingly, an estimated 88% of the total variation in skin color is found among geographic groups...The discordance is probably the consequence of intense selective pressure in the past on important attributes of the skin, the organ that most immediately and extensively interfaces with our environments.

In terms of heuristics which allow us to filter and bias our perception of new data we look to the distribution of facts and processes which we know of prior. For example if I see that a trait is normally distributed and highly heritable I'm assuming that it hasn't been subject to a long period of strong direction selection, because that tends to eliminate the standing genetic variation necessary for these sorts of phenotypes. So you see two large geographic populations which are fixed for alternative alleles. Selection? Bottlenecks? Hitchhiking?

Labels: Evolution

Here is an "interesting" paper, Changes in Sperm Quality and Numbers in Response to Experimental Manipulation of Male Social Status and Female Attractiveness:

Here we show in the fowl Gallus gallus, where social status determines copulation success, that dominant males produce more sperm than subordinates but that the quality of dominant males' sperm decreases over successive copulations, whereas that of subordinates remains constant. Experimentally manipulating male social status confirmed that ejaculate quality (the number and quality of sperm produced) was a response to the social environment rather than the result of intrinsic differences between dominant and subordinate males. We further show that dominant males responded to variation in female sexual ornamentation, which signals reproductive quality, by adjusting the number and quality of sperm they transferred, whereas subordinate males did not: they transferred ejaculates of similar quality to females with different ornament sizes. These results indicate that trade-offs between traits influencing reproductive success before and after copulation, combined with variation in social dynamics and female quality, may favor the evolution of phenotypically plastic alternative reproductive strategies.

Related: Sperm competition.

Labels: Evolution

I don't know if we should believe Svante Paabo anymore, but his lab has some new findings re: Neandertal mtDNA:

Neanderthals in central Asia and Siberia Nature advance online publication 30 September 2007. doi:10.1038/nature06193

Authors: Johannes Krause, Ludovic Orlando, David Serre, Bence Viola, Kay Prufer, Michael P. Richards, Jean-Jacques Hublin, Catherine Hanni, Anatoly P. Derevianko & Svante Paabo

Morphological traits typical of Neanderthals began to appear in European hominids at least 400,000 years ago and about 150,000 years ago in western Asia. After their initial appearance, such traits increased in frequency and the extent to which they are expressed until they disappeared shortly after 30,000 years ago. However, because most fossil hominid remains are fragmentary, it can be difficult or impossible to determine unambiguously whether a fossil is of Neanderthal origin. This limits the ability to determine when and where Neanderthals lived. To determine how far to the east Neanderthals ranged, we determined mitochondrial DNA (mtDNA) sequences from hominid remains found in Uzbekistan and in the Altai region of southern Siberia. Here we show that the DNA sequences from these fossils fall within the European Neanderthal mtDNA variation. Thus, the geographic range of Neanderthals is likely to have extended at least 2,000 km further to the east than commonly assumed.

Labels: Evolution

John Hawks has put up an inaugural post in a series on natural selection. His background as an English major shows (in a good way). It is interesting to note that John alludes to the Malthusian background of natural selection, since Greg Clark's work presupposes exactly this dynamic up until the 19th century for our species (Clark notes we were subject to the same dynamics as any other animal, though I would add that more or less we still are).

Labels: Evolution

I had what I seemed to me like an interesting thought when I read this, and I wanted to explore it further. But I have been very busy these days, and I just don't have the spare cycles, so I'm just going to throw it out there. My biggest question is: "What am I missing?" R. A. Fisher didn't think that epistasis was an important evolutionary force. I can't believe he would miss this, so the only alternative is that he considered it...

From the link:

Finally, that we failed to find a significant grandfather effect in our monogamous society in which we restricted our data to those men who married only once in their lifetimes (and hence could only gain fitness by grandfathering after the menopause of their wife) strongly suggests that the evolution of prolonged life in men cannot be explained by the selective benefits of grandfathering.

My thought, as I expressed in the comments of that post, was that average fitness is not particularly meaningful, since a relatively small number of males at the top of the social pyramid probably had a disproportionate evolutionary impact - what really counts is the grandfather effect among them. I can easily imagine a scenario where grandfathers decrease fertility of ordinary families (another mouth to feed...), but increase it among the rich. The long-term fitness impact of grandfathers could well be positive, even though the average impact is negative, since the rich have the biggest long-term evolutionary impact.

I can tell this same story on the gene level. Imagine a population which is 99% "aabb" and 1% "aabB", each of which have equal fitness. Now, imagine that there's a mutation "A" that reduces fitness by 10% in "bb" individuals, but raises fitness by 10% in "bB" individuals. Let's say by chance we get a "aAbB" individual before the "A" allele dies out. That "aAbB" individual will have the same fitness as a normal "aabb" individual, since its offspring will be 25% "aabb" (average fitness), 25% "aAbb" (10% lowered fitness), 25% "aAbB" (10% higher fitness), and 25% "aabB" (average fitness). Nevertheless, over time, the "A" allele will increase and eventually fix (together with the "B" allele). (Those of you who want to quibble about the percentages can adjust them accordingly.)

Now that seems like an interesting result to me! We talk a lot about average fitness here, but if I am not mistaken, average fitness can tell a story that's very different from what's really going on. Increasing the fitness of winners seems to count a lot more than decreasing the fitness of losers - and in evolution it's the winner's story that will eventually be told.

Labels: epistasis, Evolution, Genetic

As many of our readers are aware, humans and chimpanzees are rather different, and have diverged considerably since we last shared a common ancestor a few million years ago. An interesting question in evolutionary biology is: what the hell happened? What makes us so different? Comparing the consensus genome sequences of humans and chimps shows millions and millions of base pairs that have changed; which of those are functionally relevant?

One of the hypotheses that has been "rediscovered" in the last few years is that the important changes should be involved in gene regulation, rather than protein sequence itself (this is of course from the classic King and Wilson paper). A new paper takes a look at putative regulatory regions at a number of genes, and concludes that, yes, some of them have been under positive selection since the divergence of humans and chimps. Further, they run a quick and dirty analysis on the functions of the genes whose regulation appear to be under positive selection, and see some enrichment in neural and nutrition-related categories. From this, they conclude, "the present survey...suggests that human cognitive, behavioral and dietary adaptations have arisen primarily through changes in cis-regulatory sequences." Meh.

That could, of course, be true. But frankly, the input of this paper didn't really change the weight I put on that possibility at all (that is, I'd estimate the Bayes factor of this paper at about zero). Here's why:

1. I'm starting to become somewhat ill-at-ease with tests for selection that are based on estimating evolutionary substitution rates (in this paper, they compare rates at promoters with those in introns). What exactly do tests like these detect? Ultimately, this is a population genetics question-- how many new positively selected alleles have to arise and become fixed for this test to be significant? And why would you expect that many are necessary for phenotypic change (as opposed to, say, one really well-placed substitution)? For example, a recent paper showed that three regulatory substitutions completely accounted for a major morphological difference between two Drosophila species. Is that enough for a significant result in a test like this? If not, what kind of functional biases are being introduced into the results?

2. I'm always ill-at-ease with results based on enrichment in gene ontology categories. In this case, the most significant result is in "protein folding", which is neither a neural nor nutrition-related category. The next ones: 0.01 p-values for "other neuronal activity" and "neurogenesis", and a 0.02 p-value for "neuronal activities". The categories are non-disjoint (presumably "neuronal activities" and "other neuronal activity" share many of the same genes, for example), so are the enrichment results due to a few genes that fall in every neural-related category? And how can one conclude, based on this evidence, that "human cognitive, behavioral and dietary adaptations have arisen primarily through changes in cis-regulatory sequences" ? Given what we're working with, that's still pretty much speculation.

So yes, changes in regulatory sequences seem to be important in driving the divergence of humans from chimps (though not necessarily to the exclusion of other changes). But the precise changes, and the traits they involve, are certainly still up in the air.

Labels: Evolution, Genetics

Evolution by Doug Futuyma & and Evolution by Mark Ridley are probably two the most common intro texts used by instructors. Well, there's an enormous new textbook out creatively titled Evolution. Here is the important bit from the website:

Evolution, to be published on June 27, 2007, is designed to serve as the primary text for undergraduate courses in evolution. It differs from currently available alternatives in containing more molecular biology than is traditionally the case. But this is not at the expense of traditional evolutionary theory. Indeed, a glance at the Table of Contents and the authors' interests reveals the range of material covered in this book. The authors are world-renowned in population genetics, bacterial genomics, paleontology, human genetics, and developmental biology. The integration of molecular biology and evolutionary biology reflects the current direction of much research among evolutionary scientists. Click here to read more.

The book is being published by Cold Spring Harbor Press.

Labels: Evolution