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220px-Pointes_de_chatelperron A new paper in PNAS, Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne, weighs in the question of whether the Châtelperronian culture were Neandertals, with an answer in the affirmative in this case:

The displacement of Neandertals by anatomically modern humans (AMHs) 50,000–40,000 y ago in Europe has considerable biological and behavioral implications. The Châtelperronian at the Grotte du Renne (France) takes a central role in models explaining the transition, but the association of hominin fossils at this site with the Châtelperronian is debated. Here we identify additional hominin specimens at the site through proteomic zooarchaeology by mass spectrometry screening and obtain molecular (ancient DNA, ancient proteins) and chronometric data to demonstrate that these represent Neandertals that date to the Châtelperronian. The identification of an amino acid sequence specific to a clade within the genus Homo demonstrates the potential of palaeoproteomic analysis in the study of hominin taxonomy in the Late Pleistocene and warrants further exploration.

The details about stratigraphy are beyond me. But the protein and mtDNA evidence is pretty conclusive in my opinion that there are Neandertal individuals in this assemblage. Therefore, assuming their stratigraphy is correct, what you see in the Châtelperronian may be a cultural influence upon Neandertals by anatomically modern humans who were pushing into Europe at this time.

51r8Ph-vcaL._SY344_BO1,204,203,200_ But cultural influence may not be the only dynamic at work. In The 10,000 Year Explosion: How Civilization Accelerated Human Evolution Greg Cochran hypothesized that Châtelperronian culture may have been a vector for Neandertal genes coming into modern human populations. And now we know that this isn’t always one directional. That is, just as modern humans absorbed genes from “archaic” populations, so archaic groups absorbed ancestry from modern populations (or at least humans closer to the main stem of modern humanity).

51dw0Uce+XL._SX330_BO1,204,203,200_ In The Third Chimpanzee Jared Diamond posited that the Châtelperronian Neandertals were analogous to native peoples in the New World such as the Cherokee, who adopted many aspects of European settler culture in their attempt to resist cultural absorption and marginalization. But one dynamic we need to remember about these tribes is that they also had a lot of European ancestry, in part because of the rapidly unbalanced population sizes. It seems entirely likely, as some have posited, that the last “Neandertal” populations were also substantially admixed. Therefore, it is not entirely surprising that they would also tend to exhibit cultural features more commonly found among modern humans.

My prediction is that when whole genomes of Châtelperronian Neandertals are available it is highly likely that they often show evidence of modern human ancestry.

Note: Diamond’s The Third Chimpanzee is in my opinion a very underrated work. It is a bit dated today, but I still think it is quite worth reading.

 
• Category: Science • Tags: Evolution, Genomics, Human Evolution 
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41Y1PqrWh5L._SX392_BO1,204,203,200_ One of the interesting things about genetics, and population genetics even more specifically, is how the theory and analysis outran the biophysical mechanism of the phenomenon. By this, I mean that the Mendelian laws inferred from transmission of physical characteristics predate any understanding about how genes were embedded within chromosomes, let alone the structural nature of DNA.

Population genetics, which fused the quantitative evolutionary thinking of the biometrical school with Mendelism, arguably outran the data by decades. Until the molecular evolution revolution of the 1960s controversies such as the role of selection and drift in shaping variation were rhetoric rich and data poor. Though the allozyme era was clarifying, I do think people who were shaped by that era get a bit fixated on being a particular camp. In contrast, with the genomics revolution many researchers seem to be more willing to let the data speak, because the data is so copious. A model that is relevant in one part of the tree of life may not be as predictive in another portion of it.

The rise of data makes old questions live again. With that, I present a paper in PNAS where the first author is Jonathan Wakely, a pioneer of coalescent theory, Effects of the population pedigree on genetic signatures of historical demographic events:

Genetic variation among loci in the genomes of diploid biparental organisms is the result of mutation and genetic transmission through the genealogy, or population pedigree, of the species. We explore the consequences of this for patterns of variation at unlinked loci for two kinds of demographic events: the occurrence of a very large family or a strong selective sweep that occurred in the recent past. The results indicate that only rather extreme versions of such events can be expected to structure population pedigrees in such a way that unlinked loci will show deviations from the standard predictions of population genetics, which average over population pedigrees. The results also suggest that large samples of individuals and loci increase the chance of picking up signatures of these events, and that very large families may have a unique signature in terms of sample distributions of mutant alleles.

The paper is open access, so read the whole thing. The major math is tucked away in the extended material. Many of the formalisms in the text are those you’d regularly encounter in population genetics. The issue they’re addressing here is the fact that real populations exhibit pedigree structure, and even unlinked loci, which we treat as independent evolutionary histories, share a pedigree history.

If you read the text though it is notable how robust standard population genetic inferences are to the fact that in a literal sense they’re based on false assumptions. Massive demographic expansion (e.g., Genghis Khan haplotype) and unrealistic selection coefficients don’t seem to disturb the lineages enough so that the assumption of independent assortment starts to become misleading.

This shouldn’t be entirely surprising. I would argue that genomics has not really revolutionized evolution or population biology. The big frameworks are vindicated because nature is one, and the glimmers of reality you see in sparse data nevertheless sample from a comprehensible underlying distribution. As we get more data we’re getting more clarity, but the overall picture is not shocking or surprising.

Citation: John Wakeley, Léandra King, and Peter R. Wilton, Effects of the population pedigree on genetic signatures of historical demographic events

 
• Category: Science • Tags: Evolution, Genetics 
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shape-ancient-thought-comparative-studies-in-greek-indian-thomas-mcevilley-hardcover-cover-art Reading The Shape of Ancient Thought. Not a light read, but worthwhile so far. I’m not a big fan of metaphysics in general, but the empirical patterns are interesting. Surprised at the likely Mesopotamian influence on both India and Greece, though in hindsight it makes sense. More to say on this later….

Some people are asking me about this Jeff Jacoby column, Sex is etched in our DNA, but race is all in our heads. Actually, everything is in our heads. Everything is socially constructed. It just so happens that some social constructions (e.g., gender binary) robustly map onto patterns in reality, while others (e.g., gender is purely a function preference) do not. The idea that “our racial and ethnic identities are purely subjective” seems to be pretty false if you think of it as a prediction you can use. Someone of my physical appearance could plausibly “pass” as a range of ethnic groups across the 10/40 Window, but no one is likely to accept that I’m ancestrally Chinese, Swedish, or Dinka.

Rakhigarhi ancient DNA paper probably a while away.

A suggestion for debaters. Basically, debate science in your own specialization and don’t claim broad knowledge you lack.

34% of my readers supported Donald Trump in the survey last month. Over 50% had graduate degrees. A bit lower than the average proportion for readers of this weblog, but not that much.

Poll: Utah would vote for a Democrat for president over Trump. I don’t accept this poll. I think Trump will get nominated, and he will win Utah. But, this poll, and results from Idaho, suggest that Mormons have a particular antipathy toward Donald Trump. Reiterates that though Southern Evangelicals and Mormons are allies in the political realm, there are deep cultural differences between the two groups.

Global median income has doubled in the last 13 years.

Article on why Bangladesh does so much peacekeeping. My cousin is in Bangui right now, so on my mind.

Stannis died in the show. How about the books? I guess we’ll know in the 2020s….

Statisticians issue warning over misuse of P values. R. A. Fisher warned about this.

Causes of molecular convergence and parallelism in protein evolution.

 
• Category: Science • Tags: Evolution, Genetics 
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neaScience just published another paper on archaic admixture, Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals. It’s open access, so you should read it. And really, you should read the supplements. The paper is fine enough, but the space limitations are a real bummer here.

But what I want to talk about is Carl Zimmer’s write-up in The New York Times, Ancestors of Modern Humans Interbred With Extinct Hominins, Study Finds. It’s good, I have no quibbles with Carl’s journalism. I am just perplexed at the title (which he’s not responsible for). Why would you say “hominins” instead of humans? Because that’s what these distant lineages, which contributed some ancestry to our own, were, by any reasonable definition.

I have not given much thought to animal experimentation, though I am not comfortable personally with research on apes (I did read The Great Ape Project). I would definitely oppose research on sister hominin lineages if they were to be discovered alive in some obscure and isolated location, because they are human, even if they are different. There is some ambiguity in the science journalism right now as to what is or isn’t a human from what I can tell by the constant semantic fluidity. Often you finesse the issue by stating “modern human.” I think that’s fine. But we need to seriously think about collapsing the semantic distinction between these diverse lineages when it comes to their human status. Humanity as a characteristic is an ancestral trait of the hominin lineage, not a derived one.

 
• Category: Science • Tags: Evolution 
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The top four are the areas of biology which are my stomping ground….

 
• Category: Science • Tags: Evolution 
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Screenshot - 10262015 - 05:22:41 PM Iain Matheison, first author of Eight thousand years of natural selection in Europe, has a short note up at his website, Selection on height in Europe. He concludes:

More generally, it seems strange that height is the only trait for which a robust signal of polygenic selection has been observed. It’s hard to imagine that traits like diabetes risk and lipid levels were not also under selection in this period. I think it’s mostly down to lack of power in the predictors for other traits. Possibly larger GWAS and better predictors will reveal more. Finally, most of the work in this area has focussed on Europe, since that’s where the large cohorts are. But similar dynamics must also have happened in the rest of the world and it’s only by looking at other populations that we’ll be able to understand more generally the process of human adaptation.

North Chinese are also taller than South Chinese. And there are many quantitative traits in humans. We’re living in a golden age of phylogenomic analysis of humans in particular, but at some point in the near future the lens will begin to turn back onto classical population genetic questions of the parameters which shape the nature of variation. The initial wave of enthusiasm for selection scans ~2005 seems to have abated somewhat, but I think it’s only a slight pause, as polygenic selection and “soft sweeps” come onto the radar of genomicists….

 
• Category: Science • Tags: Evolution, Genomics 
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speciationJerry Coyne, an eminent evolutionary geneticist and all around public intellectual, is retiring, and has posted a bittersweet and hopeful farewell letter to his conventional scientific career. For the general public Coyne is probably more famous as a New Atheist, though Coyne is actually a vocal atheist of long standing. His most recent book was on that topic, Faith Versus Fact: Why Science and Religion Are Incompatible. I’m an atheist, but on the balance I demur form many of his positions in regards to religion and science. More precisely, I am quite willing to defend atheism and dismiss religion, but on philosophical or meta-scientific grounds, not scientific grounds as such.

When it comes to science on the whole I tend to agree with Coyne more often than not. In particular, his attitude toward the dynamics driving evolutionary process. In regards to the science, this section jumped out at me:

What I’m proudest of, I suppose, is the book I wrote with my ex-student Allen Orr, Speciation, published in 2004. It took each of us six years to write, was widely acclaimed and, more important, was influential. I still see that book as my true legacy, for it not only summed up where the field had gone, but also highlighted its important but unsolved questions, serving as a guide for future research.

As readers know I read Speciation in 2005, and it has really influenced my perspective on the broader topic. It’s an ambitious book even if the focus is on the process of speciation, rather like Structure of Evolutionary Theory in spirit, though far more economical in terms of prose and clearer in execution. I don’t know if Speciation is out of date or not, as I don’t study speciation, but I’d recommend it to anyone who wants to understand how an evolutionary geneticist might view the process and concept.

 
• Category: Science • Tags: Evolution 
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51fQMbh-NnL._SY344_BO1,204,203,200_ A few months ago the anthropologist Pat Shipman published a book, The Invaders: How Humans and Their Dogs Drove Neanderthals to Extinction. I’ve read Shipman before, and because of my interest in domestication it’s been on my radar, but I haven’t gotten around to purchasing it. The major reason is that as I understand it the title is somewhat misleading, in that there’s a lot less in the text on human-dog cooperation than one might think. Which is reasonable, it’s a speculative hypothesis at best.

Perhaps the biggest problem is that there’s no strong evidence that dogs were domesticated or distinct as early as ~35 thousand years ago, when modern humans replaced Neandertals in Europe. This comes up in a very highly rated comment on Amazon in fact. The best genetic work, Genome Sequencing Highlights the Dynamic Early History of Dogs, implies a date of ~15,000 years before the present, at the earliest.

But now it looks like it’s time to update our priors on this. Shipman’s speculative theory, still unlikely in opinion, is no longer extremely unlikely. The reason is ancient DNA. Ancient Wolf Genome Reveals an Early Divergence of Domestic Dog Ancestors and Admixture into High-Latitude Breeds:

The origin of domestic dogs is poorly understood…with suggested evidence of dog-like features in fossils that predate the Last Glacial Maximum…conflicting with genetic estimates of a more recent divergence between dogs and worldwide wolf populations…Here, we present a draft genome sequence from a 35,000-year-old wolf from the Taimyr Peninsula in northern Siberia. We find that this individual belonged to a population that diverged from the common ancestor of present-day wolves and dogs very close in time to the appearance of the domestic dog lineage. We use the directly dated ancient wolf genome to recalibrate the molecular timescale of wolves and dogs and find that the mutation rate is substantially slower than assumed by most previous studies, suggesting that the ancestors of dogs were separated from present-day wolves before the Last Glacial Maximum. We also find evidence of introgression from the archaic Taimyr wolf lineage into present-day dog breeds from northeast Siberia and Greenland, contributing between 1.4% and 27.3% of their ancestry. This demonstrates that the ancestry of present-day dogs is derived from multiple regional wolf populations.

gr2_lrg As you can see from the figure to the left the Taymyr sample diverges at about the same time as the common ancestor of wolves and modern dogs. In other words, you have a polytomy. Not only that, but there has been introgression from the Taymyr lineage into particular northern dog populations.

Genetics and genomics are big deals. But at this point I have to point out that archaeologists have really been here the whole time. Archaeologists reported that the Amerindians brought dogs with them over through Berengia. Historians know that the indigenous people had dogs. Yet in 2010 geneticists published, in Nature, Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication, who put the focus on the Middle East and the Neolithic revolution. There was basically no way this really made sense. Then you had a 2011 paper in PLOS ONE, A 33,000-Year-Old Incipient Dog from the Altai Mountains of Siberia: Evidence of the Earliest Domestication Disrupted by the Last Glacial Maximum. Even the authors themselves assumed that this was a “false dawn.” That this dog-like canid probably did not give rise to later dog lineages. But if the results above are correct, then in fact this 33,000 year old individual may actually be part of the extant proto-dog population.

Let’s let this sink in: if the results above hold, then the arrival of modern humans to northern Eurasia may have been coincident with the emergence of a distinct dog lineage. The term “man’s best friend” takes on a whole new meaning. The relationship between man and dog may be nearly as ancient as modern humans as we understand them, that is, populations capable of copious and protean symbolic cultural production which explode out in the archaeological record over the past ~40.000 years. In addition, I also believe we now need to totally reconceptualize how we view the relationship of wolves and dogs. Rather than an ancestral and derived set of populations, whose “species” status is only semantic convenience, they are actually sister clades. The results in this paper confirm other findings that the wolves of North America and Eurasia seem to share a post Last Glacial Maximum origin. Wolves as we understand them today may have emerged simultaneously with dogs, both descending from the melange of canid lineages which flourished during the Pleistocene. There’s a reason that feral dogs, such as dingos, do not “revert” to wolves. The ancestor may not have even been a wolf!

Additionally, the authors also note that the features of the dog which are hallmarks of domestication may themselves be derived within the dog lineage. That is, the separation of the ancestors of dogs and wolves predates the Last Glacial Maximum, ~20,000 years ago. But the evolution of dogs so that they exhibit particular derived traits may have occurred far later in time. In fact, I would hold that perhaps the true story is one of co-evolution between dogs and humans.

The ultimate moral of this true story to me is that many Pleistocene mega-fauna with wide ranges in Eurasia were subject to similar evolutionary dynamics. Extinction of distinct local lineages was the rule, not the exception. Recolonization from populations which dodged extinction was also inevitable. The phylogenetic tree was pruned repeatedly, but tempered somewhat in the ferocity of clipping by admixture and introgression, as branches fused together.

 
• Category: Science • Tags: Evolution, Human Genetics, Science 
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Citation:,/b> Tree of life reveals clock-like speciation and diversification

Citation: Tree of life reveals clock-like speciation and diversification

speciation Perhaps Charles Darwin was wrong about how species originated? This shouldn’t be so surprising. If you read The Origin of Species you’ll be struck by how much Darwin got wrong, and, how much he got right. As a fully grown adult with some knowledge of evolution re-reading Darwin in the original confirmed for me what a genius he was. The man was writing over 150 years ago in a pre-genetic era. Not only did he not have molecular phylogenetics, but he didn’t even have a proper theory of inheritance! It’s a miracle Charles Darwin got so much right. It’s no sin that he missed the mark even on the big questions.

simonconway05_16 With that I have to admit it’s awkward when people ask me about big picture evolutionary questions (as opposed to, for example, the rate of new mutations in humans), as unfortunately I’m not very well versed in macroevolution. Much of what I know about speciation in particular I know from Jerry Coyne and H. Allen Orr’s mid-2000s book Speciation. It’s true that both are population geneticists by training, so that might give me a biased view, so I’ve also read Stephen Jay Gould’s books (e.g, The Structure of Evolutionary Theory). But with Gould it’s hard to tell when he’s transmitting consensus, and when’s presenting his own heterodox views, unless you engage in very close reading. Simon Conway Morris wrote The Crucible of Creation specifically to rebut what he felt were Gould’s misrepresentation of his research in Wonderful Life (by the way, I feel that Gould’s literary style is best suited to essay format; in books he’s interminable).

A new open access paper in MBE, Tree of Life Reveals Clock-Like Speciation and Diversification, concludes that speciation is a clocklike and neutral process. As you can see from the figure above it looks as if ~2 million years is some major peak when it comes to the point at which lineages which are species converge in terms of their last ancestral populations. First, it seems clear that they’re using the biological species concept. Second, their mechanism is totally unoriginal. Rather than positive selection due to exogenous natural pressures (think Darwin’s finches, though he himself gave a lot of thought to sexual selection as the driver of speciation) the authors indicate that neutral mutational differences between diverged populations eventually lead to genetic incompabilities. This was an idea that was part of the neo-Darwinian Synthesis, so we’re talking about modulating weights, not overturning of the established order. This is an active area of research in population genetics today, see Emergent speciation by multiple Dobzhansky-Muller incompatibilities. It’s not crazy on the face of it as a hypothesis.

But it’s a whole different thing to generalize about the tree of life. Quanta Magazine has a collection of responses from researchers in the field, A Surprise for Evolution in Giant Tree of Life: Researchers build the world’s largest evolutionary tree and conclude that species arise because of chance mutations — not natural selection. I think the title is misleading for the general audience, as this isn’t a novel thesis at all, but the piece itself is more evenhanded. As noted within phylogenetics is a highly statistical enterprise. Leibniz’s famous injunction “let us calculate” is a bit more complicated when you have biased data to put into your inference generation machine. Obviously the authors couldn’t sample extinct lineages, as noted by some in the Quanta piece. They try to account for this, but the devil is in the details. Overall a ~2 million year figure invariant across arthropods and vertebrates strikes me as strange, and likely a statistical artifact if I had to put money on it (or perhaps low effective population size lineages exhibit more build up of neutral alleles producing genetic incompabilities, while large Ne groups are more impacted by positive diversifying selection, when it comes to speciation?).

Time will tell. This is not the final answer, and my passing acquaintance with this field suggests that a “first look” often does not hold up because people are missing part of this very big picture. The whole tree of life is a big thing to tackle when it comes to generalization. But, I am optimistic that this generation shall not pass before we have enough sequence across the tips of the tree and computational power to analyze it to come to more robust conclusions.

Citation: S. Blair Hedges, Julie Marin, Michael Suleski, Madeline Paymer, and Sudhir Kumar, Tree of Life Reveals Clock-Like Speciation and Diversification, Mol Biol Evol (2015) 32 (4): 835-845 first published online March 3, 2015 doi:10.1093/molbev/msv037

Addendum: I should note also that natural selection itself is somewhat stochastic over short enough time intervals. Don’t know if that would produce neutrality in speciation over the long term.

 
• Category: Science • Tags: Evolution 
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The_Journey_of_Man_-_A_Genetic_Odyssey Being part of a patrilineage is a big deal today. Ask anyone who is a Cohen, or claims to be a Sayyid, or a descendant of Confucious. Old school cultural anthropologists would assume that these patrilineages are “fictive,” that they exist to bind together disparate elite lineages as a social force. To some extent this is likely true. But not entirely. The complex genetic story of the Cohens highlights that kinship may not always be fictive. In the case of the Sayyids I assume that a lot of this is fictive. When it comes to people in South Asia with the surname Khan there isn’t even a pretense that we descend in any way from a Genghiside lineage. Rather, Khan has gone from being a surname to an honorific.

In my post Patriarchy Came with Cain and Abel I connected a social phenomenon with the drastic crash in Y chromosomal effective population in the mid-Holocene, as reported in the new paper in Genome Research, A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Unfortunately some of the press related to paper seems rather misleading. For example, “8,000 Years Ago, Only One Man Had Children for Every 17 Women” (here’s another take). Aside from the fact that the effective population crash only is true for a subset of lineages, like Greg Cochran I’m skeptical of the image of a winner-take-all reproductive mating market. Specifically, I don’t think there was a given generation where only ~5% of men in a given population had offspring, while the others did not. Rather, I assume that cumulative reproductive skew probably had the impact of socially privileging men from particular patrilineages, so that Y chromosomal haplotypes “swept” through the population over the course of many generations.

k10181 My basic idea dovetails with Greg Clark’s in The Son Also Rises. Clark’s economic historical data sets suggests that over the long term elite lineages are surprisingly insulated from decay in status. Though there is a great deal of inter-generational churn, over the long haul there is a strong trend line of elite lineages remaining elite, and non-elite ones remaining non-elite. This may be due to cultural or genetic forces; Clark is ultimately agnostic on that. But, it suggests that social status is highly heritable. Was it always so? I suspect that these sorts of dynamics only date to the Holocene, with the rise of complex societies, and social status being connected to accumulation of material objects and power which can be passed from father to son. Additionally, with complex societies there emerged group level competitive games which were winner-take-all, as patrilineages faced off against each other with the ultimate outcome being final victory or defeat.

Ultimate this is very different from the image we have of a literal “harem society” that might emerge in small scale societies with such reproductive skew. Rather, it’s a more subtle and gradual rich-get-richer dynamic, where status and privilege compound over the generations in a genetic sense.

Addendum: Both Greg Cochran and the Genome Research paper point out that effective population does not seem to have crashed concomitantly on the autosome, as you’d expect. One minor point I’d add is that admixture can inflate population size inferences, since it elevates diversity. Most of the Holocene populations seem to have been subject to admixture, so autosomal effective population may have been artificially inflated.

 
• Category: Science • Tags: Evolution, Y Chromosome 
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250px-Paonroue Evolutionary biology predates genetics. This is well known. One of the major problems with Charles Darwin’s original theory is that its lack of a plausible mechanism of inheritance meant that it was difficult for him to conceive of how heritable variation could be maintained over the generations. A “blending” model, where the offspring are a synthesis of the trait values of the parent, is intuitively appealing, but also implies that all the variation is going to be “mixed away” very quickly. In contrast, a Mendelian genetic framework, where traits are encoded by discrete and particulate units of inheritance, “genes,” illustrates simply how variation can be maintained despite mixing between lineages in sexual organisms. In short, each generation is simply a reconfiguration of the discrete elements of variation of the previous generation (see: Mendel’s laws).

255217 Eventually R. A. Fisher fused what had been rival traditions, the Darwinian/biometrical and Mendelian genetical, into a single framework in his The Correlation between Relatives on the Supposition of Mendelian Inheritance. This was further extended in The Genetical Theory of Natural Selection, and elaborated in more detail by the broader coterie of population geneticists in the early to middle decades of the 20th century, culminating in the Neo-Darwinian Synthesis.

The fusion of genetics with evolutionary biology allowed for a deeper investigation of the dynamics of evolutionary process. This is because of the fact that genes are concrete and definable units of evolutionary bookkeeping (the reason that economics is the most prominent of the social sciences also is grounded in the existence of transparent currencies which mediate exchanges). Though there are models of evolutionary processes which do not rely explicitly on genes, when possible genetic models are optimal. The broader population genetic worldview conceives of evolution as change in allele frequencies over time, and as such made evolution measurable in a very concrete sense via genetic analysis. The emergence of molecular methodologies in the 1960s, and genomics in the 2000s, has resulted in progressively more power to understand how evolutionary change affects the distribution of genetic variation amongst organisms. With genome-wide analyses now available researchers can ascertain the power of selection (positive, negative, background, and balancing) within natural populations.

But one area of evolutionary biology that has been relatively untouched by the genomics revolution is that of the study of sexual selection. This is a major gap, because sexual selection is an intuitively appealing idea which often serves as a deus ex machina when you have no other explanation on hand. So it was of great interest to me to see this review paper, The locus of sexual selection: moving sexual selection studies into the post-genomics era, in the Journal of Evolutionary Biology. There are several major issues with genomics and sexual selection which are highlighted in this review. First, it seems that many sexually dimorphic traits which are being driven by sexual selection vary due to differences in gene expression across the sexes, possibly due to modifications on regulatory elements or alternative splicing. Simple sequence level analyses then may not be good at capturing these sorts of dynamics. Second, sexual selection can leave different signatures because in some cases there are antagonistic pressures between the two sexes. Additionally, sexual selection is often frequency dependent, rather than a simple positive sweep toward fixation (as noted in the paper, a simple sweep would result in exhaustion of variation, meaning sexual selection is a very ephemeral phenomenon). Finally, there is extensive discussion of the utilization of GWAS to discover loci associated with mating fitness. Much of this work has already been done in Drosophila.

Which brings me to the point that from reading this review I have a hard time believing that sexual selection is a strong force for humans for most of history. The reason being that our reproductive skew is just not that notable in comparison to the experimental models cited within the paper. But it seems to me that a better understanding of the relationship between sequence level and regulatory variations in humans could get at this question indirectly, since there are still live debates as to the long term nature of human mating patterns. Presumably if sexual selection was copious then there’d be more extant regulatory variation, perhaps maintained by balancing selection.

Citation: Wilkinson, Gerald S., et al. “The locus of sexual selection: moving sexual selection studies into the post‐genomics era.” Journal of Evolutionary Biology (2015).

 
• Category: Science • Tags: Evolution, Genomics, Sexual Selection 
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51fULuoOGAL._SY344_BO1,204,203,200_ In the comments below I mention offhand that though on the order of half the genetic ancestry of Latin Americans is European, many salient aspects of their culture are overwhelmingly European (e.g., language, religion, and dress etc.), despite being inflected by Amerindian influences. This is not surprising. Analogies between cultural and biological evolutionary process are useful because one can leverage similarities in terms of formal modeling, but, one can also realize that there are large differences in the dynamics. In particular, cultural evolutionary process exhibit a great deal of horizontal transmission and age cohort effects, and biases in vertical inheritance. Though biological evolution via Mendelian genetics is not a blending process on the fine grain, in the aggregate one inherits half their genetic material from each parent to produce a blended genome. Not only that, but via the law of segregation one exhibits an equal probability of inheritance of one’s parents’ paternal or maternal genetic copies (meiotic drive being an exception to this).

41eQOJU5FBL._SY344_BO1,204,203,200_ On the population wide scale this enforced symmetry between parental contribution has consequences. Between two diverging populations with common ancestry one only needs one migrant between the two per generation to prevent drift apart. The logic is rather straightforward. Large populations require less migration because of reduced genetic drift. Small populations exhibit more drift, but one individual is a much larger proportion of the population, dampening the divergence. This is why between group inter-demic selection (“group selection”) is treated with some skepticism by many biologists; for selection to operate one needs heritable variation partitioned between the groups. That variation is unlikely to accrue between neighboring populations, and it is strange to imagine “competition at a distance” with no interaction (as between inter-continental scale population differences).

The difference with cultural group differences can be traced to the nature of parental inheritance. An individual whose parents speak different languages does not usually speak a language which is a hybrid between the two, which would be the case if a biological analogy with complex traits were appropriate. Rather, they may speak both of their parents’ languages, or even a single one. If the latter, often it is the case that the individual conforms to the dominant culture of their peer group within the population in which they were raised. In this way populations can develop very strong between group differences, which partition groups nearly perfectly due to a high between population differences in trait and marginal within population differences.

As a concrete example in a pre-state society one can imagine endemic warfare between two valleys in Papua resulting in the exchange of women due to raiding and kidnapping producing relatively little genetic distance across them. But the cultural distance could easily be maintained if the children of foreign women careful to adhere to the cultural norms of their paternal heritage, so as to minimize the perception that they are any less “real” members of the group into which they were born. Probably the most famous example of trivial non-functional between group differences that serve to signal in such a manner is the origin of the term shibboleth.

 
• Category: Science • Tags: Evolution 
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41f91FCrhhL Very often I get a question of the form “what book should I read to understand evolution?” This is a somewhat awkward issue for me. Unlike with population genetics the only textbook I’ve read to understanding evolution is Doug Futuyma’s originally titled Evolution. Of course The Origin of Species is an easy suggestion. But beyond that I’m not quite sure. I know some people think that Stephen Jay Gould’s The Structure of Evolutionary Theory is an important work, but I’m of the camp that it is really just a somewhat prolix reduction of only Gould’s very idiosyncratic thoughts. A major problem with this whole question is that “evolution” encompasses many distinct fields, from natural history all the way to population genetics (the old Neo-Darwinian Synthesis has been modified and appended by new fields such as evolutionary ecology). I know my way around pop gen, but really am at a loss (unfortunately) as to the scientific literature in natural history and macroevolutionary processes.download Though I do think Mark Ridley’s reader, Evolution, is quite good (I don’t know about the textbook of the same name by Ridley because I haven’t read it). Ernst Mayr’s What Evolution Is is more like a very soft primer for those with weak science backgrounds, rather than a nuts & bolts treatment. Richard Dawkins’ scientific works have the same problem as Gould’s, they give a very personal perspective of evolutionary theory (though I like them quite a bit more because Dawkins is less an outlier than Gould was).

Reader comments/suggestions welcome here. For genetics though I can make an informed comment. If you want keep it manageable, then it’s John Maynard Smith’s dense but compact textbook. If you are ambitious, Charlesworth & Charlesworth. Also, I know it’s a bit “old” now, but Joe Felsenstein’s Inferring Phylogenies is great (this another case where the author has his own particular perspective, but he’s a very eminent scientist respected by all, so that’s OK).

 
• Category: Science • Tags: Evolution 
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Citation: Misof, Bernhard, et al. “Phylogenomics resolves the timing and pattern of insect evolution.” Science 346.6210 (2014): 763-767.

There’s another paper in Science which I don’t have much intelligent to say about, but which I want to point to because it seems really cool, Phylogenomics resolves the timing and pattern of insect evolution. Earlier work in phylogenetics tended to use a few characters or genetic markers. As noted in the abstract they used nearly 1,500 protein coding genes to construct this phylogeny. Some of my friends who know particular organisms have objected to specific branching patterns near the tips, but what I’d like to emphasize is how ancient insect lineages seem to be. Our own mammalian branch of the tree of life really only diversified over the last ~100 million years or so. Most of the big groups of insects had already started to coalesce by 300 million years ago! As far as land animals goes, insects are incredibly diverse and ancient. Near the end of the paper they state: “The almost linear increase in interordinal insect diversity suggests that the process of diversification of extant insects may not have been severely affected by the Permian and Cretaceous biodiversity crises.” There will always be insects….

 
• Category: Science • Tags: Evolution 
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6a00d8341bf68b53ef010534c22ae7970c-800wi It seems that rather regularly there is a debate within evolutionary biology, or at least in public about evolutionary biology, where something new and bright and shiny is going to revolutionize the field. In general this does not pan out. I would argue there hasn’t been a true revolution in evolutionary biology since Mendelian genetics and classical Darwinism were fused in the 1920s and 1930s during the period when population genetics as a field was developed, and the famous “synthesis” developed out of the interaction of the geneticists with other domains of evolutionary relevance. This does not mean that there have not been pretenders to the throne. Richard Goldschmidt put forward his “hopeful monsters,” neutralism reared its head in the 1970s, and evo-devo was all the rage in the 2000s. Developments that bore scientific fruit, such as neutralism, were integrated seamlessly into evolutionary biology, while those that did not, such as Goldschmidt’s saltationism fell by the wayside. This is how normal science works.

bc_structure_evolutionary_theory_cover But every now and then you have a self-declared tribune of the plebs declaring that the revolution is nigh. For decades the late Stephen Jay Gould played this role to the hilt, decrying “ultra-Darwinism,” and frankly misrepresenting the state of evolutionary theory to the masses from his perch as a great popularizer. More recently you have had more muted and conventional revisionists, such as Sean Carroll, who promote a variant of evo-devo that acclimates rather well to the climes of conventional evolutionary biology.

Nature now has a piece out which seems to herald the launching of another salvo in this forever war, Does evolutionary theory need a rethink? It’s written in the form of opposing dialogues. I’m very much in the camp of those believe that there’s no reason to overturn old terms and expectations. Evolutionary biology is advancing slowly but surely into new territory. There’s no problem to solve. The one major issue where I might have to make a stand is that it focusing on genetics is critical to understanding evolution, and dethroning inheritance from the center of the story would eviscerate the major thread driving the plot. The fact that evolutionary biologists have the conceptual and concrete gene as a discrete unit of information and inheritance which they can inspect is the critical fact which distinguishes them from fields which employ similar formalisms but have never made comparable advances (such as economics).

 
• Category: Science • Tags: Evolution 
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Brawand, David, et al. "The genomic substrate for adaptive radiation in African cichlid fish." Nature (2014).

Brawand, David, et al. “The genomic substrate for adaptive radiation in African cichlid fish.” Nature (2014).

A new paper on cichlid evolutionary genetics in Nature is pretty interesting. It’s open access, so everyone can read it, The genomic substrate for adaptive radiation in African cichlid fish:

Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.

Reading a paper like this makes it very clear to me why organismic information is very critical in trying to understand evolutionary processes. R. A. Fisher was a great scientist, but his attempt to create very general rules for evolutionary processes as outlined in The Genetical Theory of Natural Selection seems quixotic in hindsight. As a professor of mine once said “biology is the science of exceptions.” This is probably one reason that the old 19th century vogue for creating “laws” went into decline; laws are useful only when the exceptions to them are very few. The diversity and specificity of evolutionary biological processes is why I think arguments in the form of dichotomies are in vain. For example, “selectionists vs. neutralists” or those who argue for the primacy of contingency in evolutionary outcomes, or those who favor convergence toward deterministic outcomes. It strikes me that the answer to all these questions must be predicated by the phrase “it depends….”

electr10The story of African cichlids is relatively well known. You have a huge range of phenotypic outcomes which seem to be the result of relatively recent diversification. Not only that, but cichlids look cool. The question though is what can this tell us about evolution? The paper does a lot of genomic slicing and dicing of a few select lineages. Before we knew about genes the nature of transmission in evolution was something of a black-box. With DNA that changed, and now with genomics we can look at how various features differ across lineages and over time. For example copy number variation, coding regions, regulatory elements, and characters more abstruse to those outside of genomics, such as LINEs. Sequencing a bunch of cichlids gets you a publication in Nature, but that’s not the point of it all. The point is what does it tell you about evolution, at least in this case?

Basically it seems that cichlid radiation has occurred due to selection on the natural genetic variation across many loci that already existed in the ancestral lineage. It was easy enough to type, but in some ways this reality is a bit difficult, in that classical models of selection were often predicated on new mutations emerging in the genetic substrate, and rapid sweeps to fixation from the original mutant form. A human illustration of this is lactase persistence, which seems to be due to a change in gene regulation via a new mutation that arose ~5,000 years ago, and quick swept to near fixation across many diverse human lineages. This sort of phenomenon is like striking a hammer at the genome; it leaves a big mark which is easy to detect. In contrast to hard selection, soft selection on standing variation operates across many loci, and rather than a novel genotype in a singular sense produces a change in underlying allele frequencies. In some ways this is more classical Darwinian, but it also generates more work and is not as elegant as a simple model of a hard sweep from a new mutation. But that’s just how it is. At least in the cichlid lineage.

41SWwcvSm6L._SX258_BO1,204,203,200_ Actually, I suspect that’s how it is in many complex organisms. For a human illustration, see The Genetics of Human Adaptation: Hard Sweeps, Soft Sweeps, and Polygenic Adaptation. I’m betting that it’s also the norm among our many domestic animals. For example rabbits. A few years ago at a conference Claire Wade reported that the focus on traits and genes with disjoint distributions across dog breeds had obscured the reality that much of the variation in this lineage is still shared, and there is probably a lot of soft selection on polygenic traits going on.

So the near future is in quantitative traits, and natural selection reshaping the variation which is already present in lineages. Perhaps people should start re-reading Genetics and Analysis of Quantitative Traits. And as a weird side effect, if I was interested in such things I bet that the emphasis on selection from standing variation probably supports philosophical monism. All is one. Or something.

 
• Category: Science • Tags: Evolution 
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"Domestic fox"

“Domestic fox”

The latest issue of Genetics has an interesting hypothesis paper, The “Domestication Syndrome” in Mammals: A Unified Explanation Based on Neural Crest Cell Behavior and Genetics. It sounds grand, but if you read the details it makes a lot of sense that changing the developmental pathway of neural crest cells has perturbed a great many traits. The target of selection in this case is “tameness,” the exact parameters of which they elucidate in the text. But there are numerous other phenotypic side effects which are hallmarks of domestication. Basically these are likely the outcome of the genetic correlation, as a given genetic alteration can have multiple downstream consequences. The paper is open access, so I invite you to read it yourself and make up your own mind.

For me the most interesting point is the argument that across mammals (and perhaps other vertebrates!) the disruption of development is due singularly to changes in neural crest cells, but on the genetic level the evolutionary process is polygenic and diverse. In other words the developmental pathway will exhibit similarities, ergo, similar correlated side effect traits. But the genetic architecture of the change across species may vary, because there are many genes which are effected by the phenotypic target of selection. Another way to state this is that there is no gene for domestication in the lineages under consideration, but rather many genes which have significant, but not overwhelming, effect. Of course there’s polygenic, and then there’s polygenic. One of the common side effects of domestication is depigmentation of the pelage of mammals, but this is one case where the number of genes effecting the trait is relatively low, on the order of ten genes account for more than half the variation. In contrast you have polygenic traits like height where you’re lucky to find one locus which can explain one percent of the variation. If domestication is like the latter then the role of standing variation in the evolutionary story is going to be large, nearly total. In contrast if pigmentation is representative than classical selection on new mutations of large effect unique to particular lineages may still be important. Not to be lame, but the answer is probably going to be in the middle, on average.

Second, there are broader questions about contingency, the genetic architecture of salient traits, and selection as a driver for adaptation, which come to mind after reading this paper. It seems hard to deny that if you constrain the phylogenetic space enough then there are many instances where evolutionary forces will basically result in broadly similar phenotypic and genetic outcomes. Though there are some differences in traits and genetic variations, there is a great deal of overlap across mammalian taxa which have been targeted by artificial selection. Though the authors don’t address this directly it, seems clear that many of the phenomena which revolve around domestication also apply to humans. If they do, and if “domestication” occurs through gradual selection upon standing variation, then the search for the gene which makes us uniquely human (e.g., “the language gene”) may be futile. Rather than a gene, our humanity may have emerged out of gradual change as the underlying frequency of alleles is shifted. This is not a sexy answer which will result in genomic fame for a researcher who discovers the gene-which-makes-us-human. Finally, there is the issue where we bracket artificial selection and domestication as if they are unique processes which derive from human agency. My own position is that though for semantic purposes we may speak of ‘artificial selection’,’ sexual selection’, and ‘natural selection,’ there’s really no fundamental difference at the root for these phenomena. Selection is selection, and the rest is commentary. To me that implies that attempting to understanding domestication may actually allow us to understand evolution more broadly (and Charles Darwin would agree with that point I suspect).

 
• Category: Science • Tags: Evolution 
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Graph of hominin encephalization by Luke Jostins

Graph of hominin encephalization by Luke Jostins

After my post, Functions oh So Random, which comments on old arguments about contingency in evolutionary biology, a reader pointed me to an excellent feature in Nautilus, If the World Began Again, Would Life as We Know It Exist? It explores the question in greater depth, and reviews many of the contemporary players. The primary representative for the idea that evolutionary processes will tend to converge upon a finite set of specific adaptive peaks is still Simon Conway Morris, who seems to argue that experimental evolutionary results which indicate the likelihood of contingency just haven’t gone on long enough (I wonder, how many generations, Dr. Conway Morris?). It strikes me that Conway Morris is unlikely to ever be satisfied unless we discover life on another planet, which has the potential to falsify his model. But his comments probably did push me more toward the power of contingency, in particular:

Conway Morris believes that, over time, natural selection leads organisms to evolve a limited number of adaptations to the finite number of ecological niches on Earth. This causes unrelated organisms to gradually converge on similar body designs. “Organisms have to configure themselves to the realities of the physical, chemical, and also biological world,” he says. In Conway Morris’s view, these constraints make it all but inevitable that if the tape of life were replayed, evolution would eventually reproduce organisms similar to what we have today. If humans’ ape ancestors had not evolved big brains and the intelligence that goes with them, he believes that another branch of animals, such as dolphins or crows, might have, and filled the niche that we now occupy. Gould disagreed.

The idea that physics implies particular body plans strikes me as plausible. Here there seem to be limits to contingency. But the assertion that intelligence is in some way a niche is a jump too far for me, at least to an extent. More on that later. First, let’s note that it seems highly unlikely that organisms adapt to a niche which exists in a Platonic sense as a fixed idea in the firmament. Organisms evolve in the context of each other, adapting not only to the physical world, but inter and intra specific pressures. Ergo, the idea that sex persists among complex organisms despite its cost because of co-evolutionary pressures of infection by pathogens.* But when it comes to intelligent life forms we can extend the complexity further, because arguably one of the primary adaptive feedbacks of these organisms is going to be their own cultural production. In other words, one would have to also argue that cultural production itself exhibits some level of inevitable convergence upon a fitness peak.

But I don’t want to get carried away. Obviously there are some cultural forms which are not adaptive. Shaker obligate celibacy comes to mind. But the range of possibilities for cultural expression is still complex. And going back in time I think it is important to suggest that even if contingency rules over the macroscale, it may not be as powerful over a shorter timescale. A few years ago Luke Jostins produced the above figure to show that distinct hominin lineages, which we believe were genetically isolated by and large, nevertheless were all increasing in cranial capacity over the Pleistocene. We do not know why, but the chart suggests that there are some powerful common forces which can overcome phylogenetic divergence.

41wehNqV33L._SY300_ Ultimately though the argument about contingency is fascinating, it strikes me that it is not entirely scientific in its deepest level. It reminds me of an argument I encountered in Cultural Evolution: How Darwinian Theory Can Explain Human Culture and Synthesize the Social Sciences. Recounting the emergence of the neo-Darwinian synthesis in the 1930s and 1940s the author suggests that it took so long partly because geneticists and naturalists were focusing on different evolutionary scales (micro vs. macro) and utilizing unintelligible languages. Because of the discrete Mendelian nature of inheritance geneticists were skeptical of Darwinian gradualism in evolutionary process and phenotypic characteristics. While naturalists had difficulty conceiving of how isolated mutations could result in the panoply of diversity they saw around them. The conflict was resolved with the development of a formal language which could translate the two scales, population genetic theory. Population genetics illuminated quite elegantly how numerous genes of discrete effect could combine to produce quantitative traits and gradual evolutionary change, and, how low rates of mutation might nevertheless allow for rapid change on a geological scale through selection pressures. Without a formal language the two groups had to rely on intuition and kept talking past each other.

We’re at a similar juncture when it comes to nearly meta-scientific questions such as contingency. We can’t even know who is right until we know the right questions to ask. At that point the write up will be in Nature Reviews Genetics, rather that long popular science books or features.

* Obviously the physical world itself can be changed by biology. Oxygen producing bacteria totally reshaped the biosphere.

 
• Category: Science • Tags: Contingency, Evolution 
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adaptivelandscape150 years after Charles Darwin’s The Origin of Species there are many open questions in evolutionary biology. For example I have been wavering between the possibility that on the molecular genomic scale evolutionary process is predominantly neutral and stochastic, and a new possibility that selection is pervasive (a new possibility that is actually old). The nice aspect of this area of study today is that empirical data can be brought to bear upon ancient arguments. Previously the dialogues were fruitless in terms of actually resolving opposing viewpoints, as interlocutors dug into their presuppositions, and the same theoretical paradigms flew through data free debates.

One area where this was clear was in relation to the of whether evolutionary process is deterministic or stochastic on the most general level. More prosaically, is evolution an experiment which one can broadly reproduce genetic and functional outcomes over and over? Stephen Jay Gould was the most famous proponent of the position that evolution is not a reproducible experiment. Rather, it is a contingent historical process. You can’t rewind the clock and expect the result to resemble what came before. In contrast Richard Dawkins has tended to defend the stance that there are broad inevitabilities as evolution explores the adaptive space of possibilities (see The Ancestor’s Tale for his detailed position). Over the past few years Joe Thornton’s lab has been looking at this issue by examining the evolutionary genetic trajectory of steroid receptors. This may seem abstruse, but obviously these are functionally significant, and, they’ve been able to utilize ingenious biophysical methods to “rerun” evolution. The general conclusion seems to be that steroid receptors as we understand them are subject to path dependence in a fashion where the outcome is sensitive to unlikely sequences of mutations.

The group now has a paper in Nature, Historical contingency and its biophysical basis in glucocorticoid receptor evolution (ungated). Let me jump straight to the conclusion:

If evolutionary history could be replayed from the ancestral starting point, the same kind of permissive substitutions would be unlikely to occur. The transition to GR’s present form and function would probably be inaccessible, and different outcomes would almost certainly ensue. Cortisol-specific signalling might evolve by a different mechanism in the GR, or by an entirely different protein, or not at all; in each case, GR—or the vertebrate endocrine system more generally—would be substantially different. Because GR is the only ancestral protein for which alternative evolutionary trajectories to historically derived functions have been explored, the generality of our findings is unknown. The specific biophysical constraints, and in turn the degree and nature of contingency, that shape the evolution of other proteins are likely to depend on the particular architecture of each protein and the unique historical mechanisms by which its functions evolved.

170px-Type_C_OrcasThe issue about generality is important. Read the whole paper and you’ll be struck by the level of experimental detail that went into making the inferences they arrive at. There’s a reason that these papers get into glamour journals. But is this just a story about a particular class of proteins, or the story of evolution writ large? When molecular evolutionary neutralism became ascendant in the 1980s some responded that though stochasticity might dominate on the sequence level of A, C, G, and T, there was no such randomness when it came to morphology. The power of this argument seems most evident when it comes to the body plans of some metazoans which are clearly dictated by the laws of physics. Marine mammals have evolved toward a morphology which has clear parallels with that of species of the fish lineage which occupy the same niche. Similarly, the elephantine legs of ancient sauropods were no coincidence. As land animals become large their massive bulk becomes unwieldy for more gracile body plans, and there is a tendency toward stout builds, as the cross-section of bone and muscle attempts to race up to the massively increased volume and mass.

The same tension seems to be at play in these sorts of results, which focus on the contingencies of a specific piece of biological machinery. Is there only one way to construct a particular a component due to biophysical constraints? Perhaps. But what does this tell us about the construction of the whole organism, which is the stitching together of innumerable biomolecular parts? In science fiction is not peculiar to imagine worlds where gross morphology is broadly recognizable, but none of the organisms are edible to humans because of divergences in biochemistry. Ultimately as implied in the paper above other groups have to reproduce this sort of work on other families of proteins to see how ubiquitous contingency really is.

 
• Category: Science • Tags: Contingency, Evolution 
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Citation: Benson RBJ, Campione NE, Carrano MT, Mannion PD, Sullivan C, et al. (2014) Rates of Dinosaur Body Mass Evolution Indicate 170 Million Years of Sustained Ecological Innovation on the Avian Stem Lineage. PLoS Biol 12(5): e1001853. doi:10.1371/journal.pbio.1001853

Citation: Benson RBJ, Campione NE, Carrano MT, Mannion PD, Sullivan C, et al. (2014) Rates of Dinosaur Body Mass Evolution Indicate 170 Million Years of Sustained Ecological Innovation on the Avian Stem Lineage. PLoS Biol 12(5): e1001853. doi:10.1371/journal.pbio.1001853

Most of the time I’m focusing on population genetic time scales when I think of evolutionary change. That is, allele frequency shifts within a species level lineage, or narrower. Since this is amenable to experimental analysis obviously there are advantages. But sometimes I really wonder if I’m doing a disservice to myself not paying more attention to examinations of evolutionary change on the scale of tens of millions of years and across whole clades which might have thousands of species. A new paper in PLoS BIOLOGY, Rates of Dinosaur Body Mass Evolution Indicate 170 Million Years of Sustained Ecological Innovation on the Avian Stem Lineage
is very interesting. Here’s the author summary:

Animals display huge morphological and ecological diversity. One possible explanation of how this diversity evolved is the “niche filling” model of adaptive radiation—under which evolutionary rates are highest early in the evolution of a group, as lineages diversify to fill disparate ecological niches. We studied patterns of body size evolution in dinosaurs and birds to test this model, and to explore the links between modern day diversity and major extinct radiations. We found rapid evolutionary rates in early dinosaur evolution, beginning more than 200 million years ago, as dinosaur body sizes diversified rapidly to fill new ecological niches, including herbivory. High rates were maintained only on the evolutionary line leading to birds, which continued to produce new ecological diversity not seen in other dinosaurs. Small body size might have been key to maintaining evolutionary potential (evolvability) in birds, which broke the lower body size limit of about 1 kg seen in other dinosaurs. Our results suggest that the maintenance of evolvability in only some lineages explains the unbalanced distribution of morphological and ecological diversity seen among groups of animals, both extinct and extant. Important living groups such as birds might therefore result from sustained, rapid evolutionary rates over timescales of hundreds of millions of years.

As this paper is predicated on nifty statistical analysis one has to be careful at taking the results at face value. Subsequent reanalysis might yield a different conclusion. But it is certainly an intriguing possibility that clade-level selection of some sort might be operating. I’m still very skeptical of what to even think about this, or how to conceptualize the dynamic. But that’s often a good thing.

 
• Category: Science • Tags: Dinosaurs, Evolution, Macroevolution 
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Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at http://www.razib.com"