New York Magazine has a rundown of the attitudes of some of the G.O.P. candidates for the nomination in regards to evolution. Remember, this is an issue which is split down the middle in the American populace, but elites have a strong skew toward accepting evolution. This is probably why despite a majority Creationist primary electorate in 2008 the majority of Republican candidates still agreed with the evolutionary position. In 2012 it looks like the Creationism or semi-Creationist contingent is going to get larger.
In the General Social Survey they asked in the late 2000s whether respondents accepted that “humans developed from animals.” The response was dichotomous. Here are some results for various population groups:
“Is Evolution Predictable?” asks a piece in Science. Here’s the first paragraph:
If one could rewind the history of life, would the same species appear with the same sets of traits? Many biologists have argued that evolution depends on too many chance events to be repeatable. But a new study investigating evolution in three groups of microscopic worms, including the strain that survived the 2003 Columbia space shuttle crash, indicates otherwise. When raised in a lab under crowded conditions, all three underwent the same shift in their development by losing basically the same gene. The work suggests that, to some degree, evolution is predictable.
The “some degree” part is the catch. I’m a big fan of general ideas, but the more I learn about evolution the more suspicious I become of broad truths. A given dynamic often has some degree of validity, but extending it too far leads to error or confusion in innumerable specific cases. Evolution may be the most robust and powerful theory for deductive inference in biology, but even here rationalism has its limits. For example, before the rise of molecular methods in exploring polymorphism the debates as to the nature of genetic variation in natural populations tended to focus on outcomes based on adaptive pressures. One school followed R. A. Fisher and argued that polymorphism was strongly constrained by negative selection, with periodic bouts of genetic diversity at a given locus as a positively selected allele was in transience between ~0% and ~100%. Sewall Wright on the other hand suggested that balancing selection (e.g., frequency dependence, heterozygote advantage, environmental heterogeneity) would maintain polymorphism within a population. The logic in both cases was clear, crisp, and plausible. But it turned out that in a deep way the argument was in the “not even wrong category.” Neutral theory and its heirs pointed out, correctly it seems, that at the molecular level most variation was driven by non-adaptive forces such as random genetic drift. Though some thinkers had conceptualized the model in its broad outlines prior to the empirical results, it was the latter which crystallized the need for a robust model and marginalized the older debate centered around adaptation and natural selection. But even here neutrality is not a model to explain it all. There are cases where adaptation and natural selection are relevant. In some instances you see classical dynamics with transients generated by positive selection sweeping through populations, and in other cases balancing dynamics may be operative. The overall point is that we must always be careful about bald assertions of the form “the latest research overturns….” in this area. Evolution is such a sprawling and cosmopolitan intellectual empire. Nature is subtle and richly textured, and our conceptual frameworks map onto the shape of reality only coarsely.
As for the paper itself, it’s nice and elegant. Patrick Phillips, who knows a thing or two about evolution and elegans is quoted in Science as saying that “”It’s an amazing study….” The letter to Nature is Parallel evolution of domesticated Caenorhabditis species targets pheromone receptor genes. Here’s the abstract:
In lieu of lots of text, above is a stylized representation of the routes which Neo-Africans took ~50 thousand years ago from their point of departure to parts unknown. The two colors represent two models. The red lines show two major streams issuing out of Africa, a northern route which pushed into the heart of Central Asia, and a southern oceanic one, which pushed all the way into Australia. The second differs, with eastern and western branches of non-African humanity. The models really start to break down within the last ~10,000 years. For example, by either model India has seen an admixture even between the two branches in the Holocene. Additionally, there may have been “false dawns” and admixtures.
In the early 2000s I accept the probable likelihood of the first model. But today I am more leaning toward the second. What’s your stance, and why? I’ll give my rationale below….
I just read a very strange article in the journal Evolution, Sex reduces genetic variation. In it the authors argue that contrary to conventional wisdom and evolutionary orthodoxy the rationale for the prevalence of sex amongst eukaryotic organisms is not maintenance of genetic variation, but rather a constraint upon genetic variation! This is a very peculiar view, and as someone not immersed in the literature on sex totally surprising to me.
The standard model is simple: sex allows organisms to swap genetic material and generate new combinations. This is at a particular premium for large, complex, and slow-breeding lineages, as is the norm amongst eukaryotes. In contrast, bacteria and their ilk have huge population sizes to draw from, and are quite literally protean in their ability to shift strategies to climb whatever adaptive landscape nature throws at them. Carl has a nice review of a paper in Science which reported just this finding in keeping with expectation. Increase the pathogen pressure, and eukaryotes which exchange genes marginalize those which do not because they can dodge the punches that their evolutionary adversaries throw in their direction.
The Pith: The rarer the genetic variant, the more likely that variant is to be specific to a distinct population. Including information about the distribution of these genetic variants missed in current techniques can increase greatly the precision of statistical inferences.
A few days ago I mentioned in passing an article in The New York Times which reported on results from a paper which illustrated how starkly differentiated populations might be on rare alleles. By this, I mean that some genetic variants are present at very low frequencies. It turns out that many of these are low frequency variants private to particular populations, in contrast to higher frequency variants which span varied human populations. The explanation presented by one of the authors of the referenced paper was that higher frequency variants presumably date back to a time before human populations had become geographically diversified across the world. Shared variants at higher frequencies then are shadows of shared past history. In contrast, rare variants are a reflection of more recent events, narrowing the circle of those effected.
I have now read the paper in question, Demographic history and rare allele sharing among human populations. From what I can gather The New York Times article was really an elaboration upon some of the issues which were highlighted in the discussion. The “meat” of the paper in terms of methods and results is actually rather technical and deeply embedded in the language of mathematical statistics. For example:
After further consideration, I have decided that I shall spare you my own clumsy exposition in plain English as to the details of site frequency spectrum calculations. There are after all enough points of interest in the paper at which I can throw my verbal talents more effectively. First, the abstract:
There’s a write-up in The New York Times on a new paper to come out in PNAS soon on the relationship of disease variants to human demographic history over the past few hundred thousand years. I’ll probably review the paper when it comes out, but since it is the holidays & all here in the states it might be delayed a bit more than typical. Roots of Disease Found to Vary by Continent is the article. Here’s the most important bit:
The Stanford study also sheds light on major aspects of human population history, like the time at which the first modern humans emigrated from Africa. Archaeologists believe it was about 50,000 years ago, since no modern human remains older than this have yet been found outside of Africa, but geneticists have long favored much earlier dates. Dr. Gravel and Dr. Bustamante now calculate that 51,000 years ago, give or take several thousand years, is the date best supported by genetic data, bringing the geneticists’ date into alignment with the archaeologists’ favored time for the exit from Africa.
The common variations in the human genome were mostly present in the ancestral human population in Africa and have been inherited by all the descendant populations around the world. The rare variants occurred more recently.
“Most of the common variants hark back to pre-Out of Africa,” Dr. Bustamante said. “Most of the rare variants come after the Neolithic revolution.” This is the event that marked the beginning of agriculture about 10,000 years ago and led to significant increases in the size of human populations.
On the first part, I’ll have to wait on the paper. I’ve kind of become more and more skeptical at taking these estimates at face value. Though the point about the lack of archaeological finds is a major alternative confirmation of the result though which should make us amenable to its plausibility. When it comes to rare variants being different across populations, the logic of this should be pretty obvious. Imagine for example if natural selection results in the rise to higher frequency of a range of rare variants from novel mutations which happen to be favored in the Neolithic environment. This is going to differentiate groups as far as the Neolithic events occurred to different populations, since they’ll draw from a different random set of mutations. One can make the same sort of case for demographic events such as population bottlenecks, which could reshape the pattern of population substructure in a historically contingent manner and groups are subject to fission over time.
Is there any substantive difference between natural, sexual, and artificial selection? Or is it just semantic sugar, useful for humans in our own cognitive bookkeeping? I lean toward the latter proposition. To some extent I would think that this is an irrelevant issue, selection is selection, but I have encountered folks who seem surprised at analogies between “artificial” and “natural” selection quite regularly. Of course Charles Darwin famously elided the distinctions across the two categories in his original works in the 19th century (this was later a subject of controversy, insofar as Darwin’s conflation of the properties of artificial and natural selection may have misled him in terms of the weight of factors shaping evolution in the wild).
These are the questions which bubble to the fore of my mind when I encounter reports such as Elizabeth Pennisi’s in Science, On the Trail of Brain Domestication Genes:
Researchers have proposed that bonobos evolved domesticated behavior to encourage group living. By isolating a group of 40 putative brain domestication genes in the prefrontal cortex and comparing their expression in humans versus chimps and bonobos, researchers found that the activity of that gene group in bonobos was clearly “domesticated” compared with chimps, they reported at the Biology of Genomes meeting.
The full piece is gated, so here’s the relevant section in the details:
As late as the 1980s it is reputed that prominent Saudi clerics were making the case for geocentrism. Of course presumably most Saudis are not geocentrists, but their religious establishment is so calcified that medieval science still retains some hold upon their imaginations. That’s why I’m very, very, curious about the possibility which is emerging that a critical period of human evolution occurred in the Arabian peninsula. Maju points me to a paper in Quaternary Science Reviews which reports on the discovery of a site in north-central Saudi Arabia, the heartland of the House of Saud, which suggests human occupation ~75,000 years B.P. Middle Paleolithic occupation on a Marine Isotope Stage 5 lakeshore in the Nefud Desert, Saudi Arabia:
Major hydrological variations associated with glacial and interglacial climates in North Africa and the Levant have been related to Middle Paleolithic occupations and dispersals, but suitable archaeological sites to explore such relationships are rare on the Arabian Peninsula. Here we report the discovery of Middle Paleolithic assemblages in the Nefud Desert of northern Arabia associated with stratified deposits dated to 75,000 years ago. The site is located in close proximity to a substantial relict lake and indicates that Middle Paleolithic hominins penetrated deeply into the Arabian Peninsula to inhabit landscapes vegetated by grasses and some trees. Our discovery supports the hypothesis of range expansion by Middle Paleolithic populations into Arabia during the final humid phase of Marine Isotope Stage 5, when environmental conditions were still favorable.
The material describing the site is basically Greek to me, so I had to “hum” my way through. Let’s jump to the final paragraph:
Going by the numbers rice is the real staff of life. Rice is the staple for ~50% of humans alive today. So the science of rice is of major pragmatic importance of all humans (even if a major disease which impacts rice doesn’t result in mass starvation, it will probably generate a price spike for all other staples due to Asian demand). One major issue which I’ve kept track of over the years has been the origin of rice agriculture: was it a parallel multi-hearth origination or a single-hearth event? We know that there were at least two instantiations of agricultural civilization in the world without any cultural diffusion: in the New World and the Old. More likely there were at least several independent hearths in the old world which utilized local wild crops. Wheat and barely in the west, millet and rice in the east, etc. But there is also a model that rice agriculture had two independent origins, in India and China, which gave rise to the indica and japonica strains from the welter of wild rice lineages. Some genetics has supported the model of two hearths by reporting a deep time depth to the last common ancestor of these strains, on the order of ~100,000 years. The implication from phylogenetics is that there were two adaptations of local lines, which later converged in morph due to parallel selection pressures.
The interest in this issue has application to our understanding of human history. Peter Bellwood in First Farmers argues that what L. L. Cavalli-Sforza termed the “great human diasporas” have their roots ultimately in distinctive domestication events. Bellwood goes on to suggest that the contemporary genetic and linguistic patterns of variation we see around us are the products of rapid population growth of these ancient agricultural nuclei (the genome blogger Digonenes works within this framework). The implication then would be that two domestications of rice would imply two population pulses. A single domestication would imply one pulse. Therefore there is a connection here between historical human population genetics and agricultural history & genetics. This stands to reason in that our own species is so parasitic on domestic crops.
In the wake of yesterday’s review of a paper on heritable variance in trait preferences realized in romantic partners I couldn’t help but be intrigued by this new study out of PLoS ONE, Evolutionary History of Hunter-Gatherer Marriage Practices. It’s actually a pretty thin piece of work in all honesty from what I can tell. They wanted to query ancestral ranges of marriage patterns by mapping the cultural variation in customs onto a phylogenetic tree. To generate that tree they took mtDNA sequences, which to me seems kind of old school. Using the cultural patterns present in living hunter-gatherer groups they presumed they could infer the ancestral state.
So combining these two sources of data they generated this:
Last summer I made a thoughtless and silly error in relation to a model of human population history when asked by a reader the question: “which population is most distantly related to Africans?” I contended that all non-African populations are equally distant. This is obviously wrong on the face of it if you look at any genetic distance measures. West Eurasians, even those without recent Sub-Saharan African admixture (e.g., North Europeans) are closer than East Eurasians, who are often closer than Oceanians and Amerindians. One explanation I offered is that these latter groups were subject to greater genetic drift through a series of population bottlenecks. In this framework the number of generations until the last common ancestor with Sub-Saharan Africans for all groups outside of Africa should be about the same, but due to evolutionary factors such as more extreme genetic drift or different selective pressures some non-African groups had diverged more from Africans than others in terms of their genetic state. In other words, the most genetically divergent groups in relation to Africans did not diverge any earlier, but simply diverged more rapidly.
Dienekes Pontikos disagreed with such a simple explanation. He argued that admixture or gene flow between Africans and non-African groups since the last common ancestor could explain the differences. I am now of the opinion that Dienekes may have been right. My own confidence in the “serial bottleneck” hypothesis as the primary explanation for the nature of relationships of the phylogenetic tree of human populations is shaky at best. Why my errors of inference?
There were two major issues at work in my misjudgments of the arc of the past and the topology of the present. In the latter instance I saw plenty of phylogenetic trees which illustrated clearly the variation in genetic distance from Africans for various non-African groups. Why didn’t I internalize those visual representations? It was I think the power of the “Out of Africa” (OoA) with replacement paradigm. Even by the summer of 2010 I had come to reject it in its strong form, due to the evidence of admixture with Neanderthals, and rumors of other events which were born out to be true with the publishing of the Denisovan results. But to a first approximation the clean and simple OoA was still looming so large in my mind that I made the incorrect inference, whereby all non-Africans are viewed simply as a branch of Africans without any particular differentiation in relation to their ancestral population. Secondarily, I also was still impacted by the idea that most of the genetic variation you see in the world around us has its roots tens of thousands of years ago. By this, I mean that the phylogeographic patterns of 25,000 years in the past would map on well to the phylogeographic patterns of the present. This assumption is what drove a lot of phylogeography in the early aughts, because the chain of causation could be reversed, and inferences about the past were made from patterns of the present. My own confidence in this model had already been perturbed when I made my errors, but it still held some sort of sway in my head implicitly I believe. It is one thing to move on from old models explicitly, but another thing to remove the furniture from your cognitive basement and attic.
I have moved further from my preconceptions between then and now. It took a while to sink in, but I’m getting there. A cognitive “paradigm shift” if you will. In particular I am more open to the idea of substantive back migration to Africa, as well as secondary migrations out of Africa. A new paper in Genome Research is out which adds some interesting details to this bigger discussion, and seems to weigh in further against my tentative hypothesis that serial bottlenecks and genetic drift can explain variation in distance to Africans of various non-African groups. Human population dispersal “Out of Africa” estimated from linkage disequilibrium and allele frequencies of SNPs:
Yesterday I alluded to the Court Jester hypothesis of evolutionary change, which is often contrasted with the Red Queen hypothesis. The main embarrassment for me as a person who fancies himself a fan of evolutionary process is that I hadn’t ever heard of the Court Jester Hypothesis before yesterday. Therefore I went back to the paper which outlined many of the basic ideas of the model in 2001, Distinguishing the effects of the Red queen and Court Jester on Miocene mammal evolution in the northern Rocky Mountains. To be fair, the hypothesis itself is a tightening of a range of ideas which were long in the air. I did know, for example, about the Turnover-pulse hypothesis. These are all a set of models which emphasize the abiotic selective pressures on life forms, as opposed to the biotic ones. An abiotic pressure would be something like the Younger Dryas cold snap. A biotic pressure might be an exotic invasive species spreading through the landscape.
In my own mind selection is selection, so I didn’t distinguish them too stridently. In fact, most people seem to have abiotic pressures in mind when they conceive of natural selection, so I generally prefer to emphasize the competition and cooperation between and within species. Additionally, it seems that biotic models are more formally tractable and elegantly constructed (I know much of climate change is cyclical, but I assume that “catastrophe” exhibits a poisson distribution?). I generally lack the “thick” knowledge to really make sense of a lot of detailed natural historical treatments, so I probably avoided them because I didn’t think I’d get much out of them. In hindsight, this seems foolish and shortsighted. Rather like economists focusing on equilibrium states because of their ease of modeling when periodic exogenous shocks are a major variable within our real lives.
Foraminifera, Wikimedia Commons
The Pith: The tree if life is nourished by agon, but pruned by the gods. More literally, both interactions between living organisms and the changes in the environment impact the pulsing of speciation and extinction.
No one can be a true “Renaissance Man” today. One has to pick & choose the set of focuses to which one must turn one’s labor to. Life is finite and subject to trade offs. My interest in evolutionary science as a child was triggered by a fascination with paleontology. In particular the megafauna of the Mesozoic and the Cenozoic, dinosaurs and other assorted reptilian lineages as well as the hosts of extinct and exotic mammals which are no more. Obviously I don’t put much time into those older interests at this point, and I’m as much of a civilian when I read Laelaps as you are. More generally when it comes to evolution I focus on the scale of microevolution rather than macroevolution. Evolutionary genetics and the like, rather than paleontology. This is in part because I lean toward a scale independence in evolutionary process, so that the critical issue for me has been to understand the fundamental lowest level dynamics at work. I’m a reductionist.
I am not quite as confident about the ability to extrapolate so easily from evolutionary genetic phenomena upwards in scale as I was in the years past. But let’s set that aside for a moment, and take a stroll through macroevolution. When I speak of natural selection I often emphasize that much of this occurs through competition within a species. I do so because I believe that the ubiquity of this process is often not properly weighted by the public, where there is a focus on competition between species or the influence of exogenous environmental selective pressures. The intra- and inter- species competition dynamic can be bracketed into the unit of selection debate, as opposed to the exogenous shocks of climate and geology. The former are biotic and the latter are abiotic variables which shape the diversity and topology of the tree of life.
A new paper in Science attempts to quantify the effect of these two classes of variables on the evolutionary arc of a particular marine organism over the Cenozoic, roughly the last 65 million years since the extinction of the dinosaurs. Interplay Between Changing Climate and Species’ Ecology Drives Macroevolutionary Dynamics:
The Pith: In this post I review a paper which covers the evolutionary dimension of human childbirth. Specifically, the traits and tendencies peculiar to our species, the genes which may underpin those traits and tendencies, and how that may relate to broader public health considerations.
Human babies are special. Unlike the offspring of organisms such as lizards or snakes human babies are exceedingly helpless, and exhibit an incredible amount of neoteny in relation to adults. This is true to some extent for all mammals, but obviously there’s still a difference between a newborn foal and a newborn human. One presumes that the closest analogs to human babies are those of our closest relatives, the “Great Apes.” And certainly the young of chimpanzees exhibit the same element of “cuteness” which is appealing to human adults. Still there is a difference of degree here. As a childophobic friend observed human infants resemble “larvae.” The ultimate and proximate reason for this relative underdevelopment of human newborns is usually attributed to our huge brains, which run up against the limiting factor of the pelvic opening of women. If a human baby developed for much longer through extended gestation then the mortality rates of their mothers during childbirth would rise. Therefore natural selection operated in the direction it could: shortening gestation times. You might say that in some ways then the human newborn is an extra-uterine fetus.
A new paper in PLoS Genetics attempts to fix upon which specific genomic regions might be responsible for this accelerated human gestational clock. An Evolutionary Genomic Approach to Identify Genes Involved in Human Birth Timing:
Diversity is a major question in evolutionary biology. In particular, why is there so much diversity, so that the tree of life manifests a multitude of morphs? Might there not be some supreme replicator which emerges from the maelstrom to conquer all before it? This is actually the scenario which unfolds in much of science fiction, with monomorphic grey goo eating everything in its path (a more aesthetically differentiated variant of the super-species emerges in Brian W. Aldiss’ Helliconia Winter). As it is, life on earth does not seem to be converging upon an optimum phenotype for all individuals. In contrast, it seems to be going in the opposite direction broadly speaking (thinking on billion year scales), with the shift from the monotony of communal cyanobacteria to the riotous diversity of tropical forest biomes and coral reefs.
There are many ways you might be able to explain this diversity. Temporal and spatial heterogeneity produces perpetually shifting selection pressures, resulting in transient morphs one after the other. Negative frequency dependent selection, whereby the fitness of a phenotype runs up against its own success. This dynamic is one of the drivers of the Red Queen Hypothesis; the evolutionary arms race in some cases witnessing the resurrection of old techniques against which defenses are no longer recalled. Then there is the possibility that the lack of natural selection as an efficacious evolutionary force could allow for the diversification of phenotypes through random drift. Finally, it may simply be that the gusher of mutation is powerful enough that novelty overwhelms selection and drift’s attempt to pare it back.
A new paper in Nature offers up another possibility. It does so by examining the fact that biological diversity remains operative even within a homogenized chemostat. A chemostat in this context refers to a controlled environment where inputs and outputs are balanced to maintain constant equilibrium conditions for a bacterialculture. Therefore, an unbeatable strategy should emerge in this medium perfectly tailored to the environmental constants, resulting in a homogeneous biota to match. Empirically this is not what occurs. So some explanation is warranted.
At The Intersection Sheril Kirshenbaum posts some rather stark data from Gallup and a Canadian outfit on the differences in attitudes toward evolution between Americans and Canadians. Those Tories are different! The answers seem very similar to those on offer for the General Social Survey’s “CREATION” question. I thought I’d compare Canadians to various American demographics. The question was asked in 2004 of over 1,400 Americans. I find it somewhat ironic in that I think there has been some question as to the Prime Minister of Canada, Stephen Harper, and his attitude toward evolution. Harper is a member of the Evangelical Protestant Christian and Missionary Alliance (and apparently has appointed known Creationists to various government positions, something controversial or notable in Canada). In contrast, Barack Hussein Obama is famously more grounded in evolution than angels.
There’s a rather perplexing paper out in PNAS which I stumbled upon today, An evolutionary process that assembles phenotypes through space rather than through time. Perplexing because I wonder if it is almost so obvious as to be boring, in the trivial but true category, or if it points to a rather deep dimensions of evolutionary process which we’ve ignored. The authors themselves offer up that they’re attempting to reintroduce a concept which has long been in the literature, and, they admit that there isn’t much empirical data to test the importance of the dynamic which they’re outlining. For example, after discussing the consequences which might be entailed by the widespread significance of the phenomenon which they’re describe, they note, “We do not have enough data to test this proposition.”
Here’s their abstract:
In classical evolutionary theory, traits evolve because they facilitate organismal survival and/or reproduction. We discuss a different type of evolutionary mechanism that relies upon differential dispersal. Traits that enhance rates of dispersal inevitably accumulate at expanding range edges, and assortative mating between fast-dispersing individuals at the invasion front results in an evolutionary increase in dispersal rates in successive generations. This cumulative process (which we dub “spatial sorting”) generates novel phenotypes that are adept at rapid dispersal, irrespective of how the underlying genes affect an organism’s survival or its reproductive success. Although the concept is not original with us, its revolutionary implications for evolutionary theory have been overlooked. A range of biological phenomena (e.g., acceleration of invasion fronts, insular flightlessness, preadaptation) may have evolved via spatial sorting as well as (or rather than) by natural selection, and this evolutionary mechanism warrants further study.
The Pith: I review a recent paper which argues for a southern African origin of modern humanity. I argue that the statistical inference shouldn’t be trusted as the final word. This paper reinforces previously known facts, but does not add much that both novel and robust.
I have now read the paper which I expressed a touch of skepticism toward yesterday. Do note, I did not dispute the validity of their results. They seem eminently plausible. I was simply skeptical that we could, with any level of robustness, claim that anatomically modern humans arose in southern vs. eastern, or western, Africa. If I had to bet, my rank order would be southern ~ eastern > western. But my confidence in my assessment is very low.
First things first. You should read the whole paper, since someone paid for it to be open access. Second, much props to whoever decided to put their original SNP data online. I’ve already pulled it down, and sent off emails to Zack, David, and Dienekes. There are some northern African populations which allow us to expand beyond the Mozabites, though unfortunately there are only 55,000 SNPs in that case (I haven’t merged the data, so I don’t know how much will remain after combining with HapMap or HGDP data set).