For many the image of evolutionary processes brings to mind something on a macro scale. Perhaps that of the changing nature of protean life on earth writ large, depicted on a broad canvas such as in David Attenborough’s majestic documentaries over millions of years and across geological scales. But one can also reduce the phenomenon to a finer-grain on a concrete level, as in specific DNA molecules. Or, transform it into a more abstract rendering manipulable by algebra, such as trajectories of allele frequencies over generations. Both of these reductions emphasize the genetic aspect of natural history.
Obviously evolutionary processes are not just fundamentally the flux of genetic elements, but genes are crucial to the phenomena in a biological sense. It therefore stands to reason that if we look at patterns of variation within the genome we will be able to infer in some deep fashion the manner in which life on earth has evolved, and conclude something more general about the nature of biological evolution. These are not trivial affairs; it is not surprising that philosophy-of-biology is often caricatured as philosophy-of-evolution. One might dispute the characterization, but it can not be denied that some would contend that evolutionary processes in some way allow us to understand the nature of Being, rather than just how we came into being (Creationists depict evolution as a religion-like cult, which imparts the general flavor of some of the meta-science and philosophy which serves as intellectual subtext).
There is the fact of evolution. And then there is the long-standing debate of how it proceeds. The former is a settled question with little intellectual juice left. The latter is the focus of evolutionary genetics, and evolutionary biology more broadly. The debate is an old one, and goes as far back as the 19th century, where you had arch-selectionists such as Alfred Russel Wallace (see A Reason For Everything) square off against pretty much the whole of the scholarly world (e.g., Thomas Henry Huxely, “Darwin’s Bulldog,” was less than convinced of the power of natural selection as the driving force of evolutionary change). This old disagreement planted the seeds for much more vociferous disputations in the wake of the fusion of evolutionary biology and genetics in the early 20th century. They range from the Wright-Fisher controversies of the early years of evolutionary genetics, to the neutralist vs. selectionist debate of the 1970s (which left bad feelings in some cases). A cartoon-view of the implication of the debates in regards to the power of selection as opposed to stochastic contingency can be found in the works of Stephen Jay Gould (see The Structure of Evolutionary Theory) and Richard Dawkins (see The Ancestor’s Tale): does evolution result in an infinitely creative assortment due to chance events, or does it drive toward a finite set of idealized forms which populate the possible parameter space?*
The genetics and history of Tibet are fascinating to many. To be honest the primary reason here is elevation. The Tibetan plateau has served as a fortress for populations who have adapted biologically and culturally to the extreme conditions. Naturally this means that there has been a fair amount of population genetics on Tibetans, as hypoxia is a side effect of high altitude living which dramatically impacts fitness. I have discussed papers on this topic before. And I will probably talk more about it in the future, considering rumblings at ASHG 2012.
But to understand the character of the effect of natural selection on a population it is often very important to keep in mind the phylogenetic context. By this, I mean that evolutionary processes occur over history, and those historical events shape the course of subsequent of phenomena. Concretely, to understand how the Tibetans came to be adapted to high altitudes one must understand who they are related to, and what their long term history is. There is a paper in Molecular Biology and Evolution which attempts to do just that, Genetic evidence of Paleolithic colonization and Neolithic expansion of modern humans on the Tibetan Plateau:
The Pith: Natural selection comes in different flavors in its genetic constituents. Some of those constituents are more elusive than others. That makes “reading the label” a non-trivial activity.
As you may know when you look at patterns of variation in the genome of a given organism you can make various inferences from the nature of these patterns. But the power of those inferences is conditional on the details of the real demographic and evolutionary histories, as well as the assumptions made about the models one which is testing. When delving into the domain of population genomics some of the concepts and models may seem abstruse, but the reality is that such details are the stuff of which evolution is built. A new paper in PLoS Genetics may seem excessively esoteric and theoretical, but it speaks to very important processes which shape the evolutionary trajectory of a given population. The paper is titled Distinguishing between Selective Sweeps from Standing Variation and from a De Novo Mutation. Here’s the author summary:
Considerable effort has been devoted to detecting genes that are under natural selection, and hundreds of such genes have been identified in previous studies. Here, we present a method for extending these studies by inferring parameters, such as selection coefficients and the time when a selected variant arose. Of particular interest is the question whether the selective pressure was already present when the selected variant was first introduced into a population. In this case, the variant would be selected right after it originated in the population, a process we call selection from a de novo mutation. We contrast this with selection from standing variation, where the selected variant predates the selective pressure. We present a method to distinguish these two scenarios, test its accuracy, and apply it to seven human genes. We find three genes, ADH1B, EDAR, and LCT, that were presumably selected from a de novo mutation and two other genes, ASPM and PSCA, which we infer to be under selection from standing variation.
The dynamic which they refer to seems to be a reframing of the conundrum of detecting hard sweeps vs. soft sweeps. In the former you case have a new mutation, so its frequency is ~1/(2N). It is quickly subject to natural selection (though stochastic processes dominate at low frequencies, so probability of extinction is high), and adaptation drives the allele to fixation (or nearly to fixation). In the latter scenario you have a great deal of extant genetic variation, present in numerous different allelic variants. A novel selection pressure reshapes the frequency landscape, but you can not ascribe the genetic shift to only one allele. It is no surprise that the former is easier to model and detect than the latter. Much of the evolutionary genomics of the 2000s focused on hard sweeps from de novo mutations because they were low hanging fruit. The methods had reasonable power to detect them (as well as many false positives!). But of late many are suspecting that hard sweeps are not the full story, and that much of evolutionary genetic process may be characterized by a combination of hard sweeps, soft sweeps (from standing variation), various forms of negative selection, not to mention the plethora of possibilities which abound in the domain of balancing selection.
Many of the details of the paper may seem overly technical and opaque (and to be fair, I will say here that the figures are somewhat difficult to decrypt, though the subject is not one that lends itself to general clarity), but the major finding is straightforward, and illustrated in figure 4 (I’ve added labels):
I have blogged about the genetics of altitude adaptation before. There seem to be three populations in the world which have been subject to very strong natural selection, resulting in physiological differences, in response to the human tendency toward hypoxia. Two of them are relatively well known, the Tibetans and the indigenous people of the Andes. But the highlanders of Ethiopia have been less well studied, nor have they received as much attention. But the capital of Ethiopia, Addis Ababa, is nearly 8,000 feet above sea level!
Another interesting aspect to this phenomenon is that it looks like the three populations respond to adaptive pressures differently. Their physiological response varies. And the more recent work in genomics implies that though there are similarities between the Asian and American populations, there are also differences. This illustrates the evolutionary principle of convergence, where different populations approach the same phenotypic optimum, though by somewhat different means. To my knowledge there has not been as much investigation of the African example. Until now. A new provisional paper in Genome Biology is out, Genetic adaptation to high altitude in the Ethiopian highlands:
In reading The cultural niche: Why social learning is essential for human adaptation in PNAS I couldn’t help but think back to a conversation I had with a few old friends in Evanston in 2003. They were graduate students in mathematics at Northwestern, and at one point one of them expressed some serious frustration at the fact that so many of the science and business students in his introductory calculus courses simply wanted to “learn” a disparate set of techniques, rather than understand calculus. The reality of course is that the vast majority of people who ever encounter calculus aim to learn it for reasons of utility, not so that they can grok the fundamental theorem of calculus. With the proliferation of tools such as Mathematica and powerful portable calculators fewer and fewer people are getting their hands dirty with calculus in an analytic sense, and more often see it as simply a “requirement” which they have to pass.
Calculus, and mathematics generally, is a clean and crisp human invention. In the late 17th century Isaac Newton and Gottfried Leibniz originated calculus as we understand it. Later thinkers extended their work. But for the vast majority of humans who have ever learned calculus it is simply a “black box” set of techniques which work rather magically. They did not contribute anything new to the body of knowledge which they drew upon. Mathematics is part of our cultural patrimony, we implicitly stand upon the shoulders of giants without apology. Such is to be human.
In the image to the left you see three human males. You can generate three pairings of these individuals. When comparing these pairs which would you presume are more closely related than the other pairs? Now let me give you some more information. The rightmost image is of the president of Tanzania. The middle image is of the president of Taiwan (Republic of China). And finally, the leftmost image is of the prime minister of Papua New Guinea. With this information you should now know with certainty that the prime minister of Papua New Guinea and the president of Taiwan are much more closely related than either are to the president of Tanzania. But some of you may not have guessed that initially. Why? I suspect that physical inspection may have misled you. One of the most salient visible human characteristics is of the complexion of our largest organ, the skin. Its prominence naturally leads many to mistakenly infer relationships where they do not exist.
This was certainly an issue when European explorers encountered the peoples of Melanesia. An older term for Melanesians is “Oceanic Negro,” and some sources suggest that the Spaniards who named the island New Guinea did so with an eye to the old Guinea on the coast of West Africa. To the left is an unrooted tree which illustrates the relationships between Papuans, Bantu from Kenya, and Han Chinese. Since the font is small I’ve underlined the focal populations in red. Africans are always the “outgroup” to any two non-African populations. This is a robust pattern whenever you look at averaged total genome phylogenies. In other words, when you don’t privilege particular genes in a phylogeny humanity can be divided into African and non-African branches.
Last week I reviewed ideas about the effect of “exogenous shocks” to an ecosystem of creatures, and how it might reshape their evolutionary trajectory. These sorts of issues are well known in their generality. They have implications from the broadest macroscale systematics to microevolutionary process. The shocks point to changes over time which have a general effect, but what about exogenous parameters which shift spatially and regularly? I’m talking latitudes here. The further you get from the equator the more the climate varies over the season, and the lower the mean temperature, and, the less the aggregate radiation the biosphere catches. Allen’s rule and Bergmann’s rule are two observational trends which biologists have long observed in relation to many organisms. The equatorial variants are slimmer in their physique, while the polar ones are stockier. Additionally, there tends to be an increase in mean mass as one moves away from the equator.
But these rules are just general observations. What process underlies these observations? The likely culprit would be natural selection of course. But the specific manner in which this process shakes out, on both the organismic and genetic level, still needs to be elucidated in further detail. A new paper in PLoS Genetics attempts to do this more rigorously and deeply than has been done before for one particular world wide mammalian species, H. sapiens sapiens. We have spanned the latitudes and longitudes, and so we’re a perfect test case for an exploration of the broader microevolutionary forces which shape variation.
The paper is Adaptations to Climate-Mediated Selective Pressures in Humans. Its technical guts can be intimidating, but its initial questions and final answers are less daunting. So let’s jump straight to the last paragraph of the discussion:
President William Howard Taft
It is the best of times, it is the worse of times. On the one hand the medical consequences of human genomics have been underwhelming. This is important because this is the ultimate reason that much of the basic research is funded. And yet we’ve learned so much. The genetic architecture of skin color has been elucidated, and we’ve seen a clarification of patterns of natural selection in the human genome. The finding last spring of Neandertal admixture in modern human populations is perhaps the most awesome pure science finding of late, coming close to resolving a decades old debate in anthropology. This doesn’t cure cancer, but it does connect the dots about the human past, and that’s not trivial. We are species haunted by our memories, so we might as well get them right!
But all hope is not lost. Research continues. And one area which general surveys of genomic variation have usually shown to be targets of natural selection, and, also have clear and immediate biomedical relevance, is that of metabolism. How we eat, and how we process and integrate the food we eat, is of obvious fitness relevance in the evolutionary and medical senses. It turns out that there is even variation in our saliva which is probably due to natural selection. The combination of diversity in human cuisine and susceptibility to the diseases of modern life indicate possibilities as to the relationship between past selection pressures and contemporary patterns of genetic variation. Of course one has to tread softly in this area, there are the inevitable confounds of environment, as well the unfortunate probability of any given locus being of small effect size in its influence on any given trait.
A new paper in Genome Research reports a SNP which seems to have been subject to natural selection in Eurasians within the last 10,000 years. This variant is located within an exon on a gene, GIP, which produces peptides critical in the regulation of various metabolic pathways, in particular insulin response. A possible biomedical relevance to risk susceptibility is then explored subsequent to the evolutionary genomic preliminaries. Adaptive selection of an incretin gene in Eurasian populations:
When I was in college I would sometimes have late night conversations with the guys in my dorm, and the discussion would random-walk in very strange directions. During one of these quasi-salons a friend whose parents were from Korea expressed some surprise and disgust at the idea of wet earwax. It turns out he had not been aware of the fact that the majority of the people in the world have wet, sticky, earwax. I’d stumbled onto that datum in the course of my reading, and had to explain to most of the discussants that East Asians generally have dry earwax, while convincing my Korean American friend that wet earwax was not something that was totally abnormal. Earwax isn’t something we explore in polite conversation, so it makes sense that most people would be ignorant of the fact that there was inter-population variation on this phenotype.
But it doesn’t end there. Over the past five years the genetics of earwax has come back into the spotlight, because of its variation and what it can tell us about the history and evolution of humans since the Out of Africa event. Not only that, it seems the variation in earwax has some other phenotypic correlates. The SNPs in and around ABCC11 are a set where East Asians in particular show signs of being different from other world populations. The variants which are nearly fixed in East Asia around this locus are nearly disjoint in frequency with those in Africa. Here are the frequencies of the alleles of rs17822931 on ABCC11 from ALFRED:
Last month in Nature Reviews Genetics there was a paper, Measuring selection in contemporary human populations, which reviewed data from various surveys in an attempt to adduce the current trajectory of human evolution. The review didn’t find anything revolutionary, but it was interesting to see where we’re at. If you read this weblog you probably accept a priori that it’s highly unlikely that evolution “has stopped” because infant mortality has declined sharply across developed, and developing, nations. Evolution understood as change in gene frequencies will continue because there will be sample variance in the proportions of given alleles from generation to generation. But more interestingly adaptive evolution driven by change in mean values of heritable phenotypes through natural selection will also continue, assuming:
1) There is variance in reproductive fitness
2) That that variance is correlated with a phenotype
3) That those phenotypes are at all heritable. In other words, phenotypic variation tracks genotypic variation
Obviously there is variance in reproductive fitness. Additionally, most people have the intuition that particular traits are correlated with fecundity, whether it be social-cultural identities, or personality characteristics. The main issue is probably #3. It is a robust finding for example that in developed societies the religious tend to have more children than the irreligious. If there is an innate predisposition to religiosity, and there is some research which suggests modest heritability, then all things being equal the population would presumably be shifting toward greater innate predisposition toward religion as time passes. I do believe religiosity is heritable to some extent. More precisely I think there are particular psychological traits which make supernatural claims more plausible for some than others, and, those traits themselves are partially determined by biology. But obviously even if we think that religious inclination is partially heritable in a biological sense, it is also heritable in the familial sense of values passed from one generation to the next, and in a broader cultural context of norms imposed from on high. In other words, when it comes to these sorts of phenotypic analyses we shouldn’t get too carried away with clean genetic logics. In Shall the Religious Inherit the Earth? Eric Kaufmann notes that it is in the most secular nations that the fertility gap between the religious and irreligious is greatest, and therefore selection for religiosity would be strongest in nations such as Sweden, not Saudi Arabia. But as a practical matter biologically driven shifts in trait value in this case pales in comparison to the effect of strong cultural norms for religiosity.
Below are two of the topline tables which show the traits which are currently subject to natural selection. A + sign indicates that there is natural selection for higher values of the trait, and a – sign the inverse. An s indicates stabilizing selection, which tells you that median values have higher fitnesses than the extremes. The number of stars is proportional to statistical significance.
Evolution means many things to many people. On the one hand some scholars focus on time scales of “billions and billions,” and can ruminate upon the radical variation in body plans across the tree of life. Others put the spotlight on the change in gene frequencies on the scale of years, of Ph.D. programs. While one group must glean insight from the fossil remains of trilobites and ammonites, others toils away in dimly lit laboratories breeding nematodes and fruit flies, generations upon generations. More recently a new domain of study has been focusing specifically on the arc of animal development as a window onto the process of evolution. And so forth. Evolution has long been dissected by an army of many specialized parts.
And yet the core truth which binds science is that nature is one. No matter the disciplinary lens which we put on at any given moment we’re plumbing the same depths on some fundamental level. But what are the abstract structures of those depths? Can we project a tentative map of the fundamentals before we go exploring through observation and experiment? That’s the role of theoreticians. Charles Darwin, R. A. Fisher, and Sewall Wright. Evolution is a phenomenon which is on a deep level an abstraction, though through objectification we speak of it as if it was as concrete as the frills of the Triceratops. As an abstraction it is open to mathematical formalization. Models of evolution may purport to tell us how change over time occurs in specific instances, but the ultimate aim is to capture the maximum level of generality possible.
Last spring two very thorough papers came out which surveyed the genetic landscape of the Jewish people (my posts, Genetics & the Jews it’s still complicated, Genetics & the Jews). The novelty of the results was due to the fact that the research groups actually looked across the very diverse populations of the Diaspora, from Morocco, Eastern Europe, Ethiopia, to Iran. They constructed a broader framework in which we can understand how these populations came to be, and how they relate to each other. Additionally, they allow us to have more perspective as to the generalizability of medical genetics findings in the area of “Jewish diseases,” which for various reasons usually are actually findings for Ashkenazi Jews (the overwhelming majority of Jews outside of Israel, but only about half of Israeli Jews).
Just as the two aforementioned papers were deep explorations of the genetic history of the Jewish people, and allowed for a systematic understanding of their current relationships, a new paper in PNAS takes a slightly different tack. First, it zooms in on Ashkenazi Jews. The Jews whose ancestors are from the broad swath of Central Europe, and later expanded into Poland-Lithuania and Russia. The descendants of Litvaks, Galicians, and the assimilated Jewish minorities such as the Germans Jews. Second, though constrained to a narrower population set, the researchers put more of an emphasis on the evolutionary parameter of natural selection. Like any population Jews have been impacted by drift, selection, migration (and its variant admixture), and mutation. Teasing apart these disparate parameters may aid in understanding the origin of Jewish diseases.
The paper is open access, so you don’t have to take my interpretation as the last word. Signatures of founder effects, admixture, and selection in the Ashkenazi Jewish population:
One of the major issues which has loomed at the heart of biology since The Origin of Species is why species exist, as well as how species come about. Why isn’t there a perfect replicator which performs all the conversion of energy and matter into biomass on this planet? If there is a God the tree of life almost seems to be a testament to his riotous aesthetic sense, with numerous branches which lead to convergences, and a inordinate fascination with variants on the basic morph of beetles. From the outside the outcomes of evolutionary biology look a patent mess, a sprawling expanse of experiments and misfires.
A similar issue has vexed biologists in relation to sex. Why is it that the vast majority of complex organisms take upon themselves the costs of sex? The existence of a non-offspring bearing form within a species reduces the potential natural increase by a factor of two before the game has even begun. Not only that, but the existence of two sexes who must seek each other out expends crucial energy in a Malthusian world (selfing hermaphrodites obviously don’t have this problem, but for highly complex organisms they aren’t so common). Why bother? (I mean in an ultimate, not proximate, sense)
It seems likely that part of the answer to both these questions on the grande scale is that the perfect is the enemy of long term survival. Sexual reproduction confers upon a lineage a genetic variability which may reduce fitness by shifting populations away from the adaptive peak in the short term, but the fitness landscape itself is a constant bubbling flux, and perfectly engineered asexual lineages may all too often fall off the cliff of what was once their mountain top. The only inevitability seems to be that the times change. Similarly, the natural history of life on earth tells us that all greatness comes to an end, and extinction is the lot of life. The universe is an unpredictable place and the mighty invariably fall, as the branches of life’s tree are always pruned by the gardeners red in tooth and claw.
But it is one thing to describe reality in broad verbal brushes. How about a more rigorous empirical and theoretical understanding of how organisms and the genetic material through which they gain immortality play out in the universe? A new paper which uses plant models explores the costs and benefits of admixture between lineages, and how those two dynamics operate in a heterogeneous and homogeneous world. Population admixture, biological invasions and the balance between local adaptation and inbreeding depression:
How we perceive nature and describe its shape are a matter of values and preferences. Nature does not take notice of our distinctions; they exist only as instruments which aid in our comprehension. I’ve brought this up in relation to issues such as categorization of recessive vs. dominant traits. The offspring of people of Sub-Saharan African and non-African ancestry where the non-African parent has straight or wavy hair tend to have very curly hair. Therefore, one may say that the tightly curled hair form is dominant to straight or wavy hair. But, it is also the case that there is some modification in relation to the African parent in the offspring, so the dominance is not complete. When examining the morphology of the follicle, which determines the extent of the hair’s curl, the offspring may in fact exhibit some differences from both parents. In other words our perception of the outcomes of inheritance are contingent to some extent on our categorization of the traits as well as our specific focus along the developmental pathway.
Or consider the division between “traits” and “diseases.” The quotations are necessary. Lactose intolerance is probably one of the best cases to illustrate the gnarly normative obstructions which warp our perceptions. As a point of fact lactose intolerance is the ancestral human state, and numerically predominant. It is the “wild type.” Lactose tolerance is a relatively recent adaptation, found among a variety of West Eurasian and African populations. A more politically correct term, lactase persistence, probably better encapsulates the evolutionary history of the trait, which has shifted from the class of disease to that of genetic trait when we evaluate the bigger picture (obviously diseases are simply “bad” traits”).
I said yesterday I would say a bit more about the new paper on rapid recent high altitude adaptation among the Tibetans when I’d read the paper. Well, I’ve read it now. Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude:
Residents of the Tibetan Plateau show heritable adaptations to extreme altitude. We sequenced 50 exomes of ethnic Tibetans, encompassing coding sequences of 92% of human genes, with an average coverage of 18x per individual. Genes showing population-specific allele frequency changes, which represent strong candidates for altitude adaptation, were identified. The strongest signal of natural selection came from endothelial Per-Arnt-Sim (PAS) domain protein 1 (EPAS1), a transcription factor involved in response to hypoxia. One single-nucleotide polymorphism (SNP) at EPAS1 shows a 78% frequency difference between Tibetan and Han samples, representing the fastest allele frequency change observed at any human gene to date. This SNP’s association with erythrocyte abundance supports the role of EPAS1 in adaptation to hypoxia. Thus, a population genomic survey has revealed a functionally important locus in genetic adaptation to high altitude.
The exome is just the protein-coding part of the genome; so they’re focusing ostensibly on functionally relevant single nucleotide polymorphisms (SNPs). About a month and a half ago a similar paper on Tibetan high altitude adaptations was published in Science (I posted on that too), but their methodology was somewhat different. That group was looking at a set of genes, candidates, which they’d assume might have been under selection and so have functional significance in explaining Tibetan vs. non-Tibetan phenotypes at high altitudes. This second paper takes a more bottom up approach, scanning the genome of Tibetans and Han Chinese, and trying to spotlight regions which exhibit a great deal of between population variance, far greater than one might presume from the total genome genetic distances.
As to that last point…the timing of this has been causing a major problem with archaeologists. The supplements lays out the details a bit more than the press reports, so below is figure 2:
You probably are aware that different populations have different tolerances for high altitudes. Himalayan sherpas aren’t useful just because they have skills derived from their culture, they’re actually rather well adapted to high altitudes because of their biology. Additionally, different groups seem to have adapted to higher altitudes independently, exhibiting convergent evolution. But in terms of physiological function they aren’t all created equal, at least in relation to the solutions which they’ve come to to make functioning at high altitudes bearable. In particular, it seems that the adaptations of the peoples of Tibet are superior than those of the peoples of the Andes. Superior in that the Andean solution is more brute force than the Tibetan one, producing greater side effects, such as lower birth weight in infants (and so higher mortality and lower fitness).
The Andean region today is dominated by indigenous people, and Spanish is not the lingua franca of the highlands as it is everyone in in the former colonial domains of Spain in the New World. This is largely a function of biology; as in the lowlands of South America the Andean peoples were decimated by disease upon first contact (plague was spreading across the Inca Empire when Pizzaro arrived with his soldiers). But unlike the lowland societies the Andeans had nature on their side: people of mixed or European ancestry are less well adapted to high altitudes and women without tolerance of the environment still have higher miscarriage rates.