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Jónsson, Hákon, et al. "Speciation with gene flow in equids despite extensive chromosomal plasticity." Proceedings of the National Academy of Sciences 111.52 (2014): 18655-18660.

Jónsson, Hákon, et al. “Speciation with gene flow in equids despite extensive chromosomal plasticity.” Proceedings of the National Academy of Sciences 111.52 (2014): 18655-18660.

Last week I expressed my qualms about allopatric speciation the biological species concept. I didn’t quite say it that way, but that’s really what I was getting at. When talking about the phylogenetic relationship of populations the level of species is just another systematic layer. Arguably its the only one that’s “natural” or “fundamental.” And that is because of the role of the biological species concept. Basically, that refers to the fact that two species are labeled as such when they can’t exchange genes through hybridization. As I have noted before this is very much an instrumental standard, and not an iron law. For whatever reason the new vogue among paleoanthropologists seems to be to label Neandertals a separate species (e.g., H. neanderthalensis). That doesn’t bother me, but, please do remember that there’s now a rather overwhelming amount of circumstantial evidence that ~2% of the ancestry of most modern humans, H. sapiens, derives from this population. Because of the deficiency of Neandertal ancestry in the X chromosome, a common indicator of hybrid breakdown, we can infer that the ~500,000 year old separation between the African root stock of sapiens and neanderthalensis, was not without consequences. The biological species concept is useful, but not as an iron law. Rather, it is a reference point at one end of the distribution of the viscosity of gene flow between two populations.

And this is one area where whole genome sequences seem to be resulting in changes in perceptions. A paper in PNAS emphasizes this for equids, primarily donkeys and zebras, Speciation with gene flow in equids despite extensive chromosomal plasticity.

Horses, asses, and zebras belong to a single genus, Equus, which emerged 4.0-4.5 Mya. Although the equine fossil record represents a textbook example of evolution, the succession of events that gave rise to the diversity of species existing today remains unclear. Here we present six genomes from each living species of asses and zebras. This completes the set of genomes available for all extant species in the genus, which was hitherto represented only by the horse and the domestic donkey. In addition, we used a museum specimen to characterize the genome of the quagga zebra, which was driven to extinction in the early 1900s. We scan the genomes for lineage-specific adaptations and identify 48 genes that have evolved under positive selection and are involved in olfaction, immune response, development, locomotion, and behavior. Our extensive genome dataset reveals a highly dynamic demographic history with synchronous expansions and collapses on different continents during the last 400 ky after major climatic events. We show that the earliest speciation occurred with gene flow in Northern America, and that the ancestor of present-day asses and zebras dispersed into the Old World 2.1-3.4 Mya. Strikingly, we also find evidence for gene flow involving three contemporary equine species despite chromosomal numbers varying from 16 pairs to 31 pairs. These findings challenge the claim that the accumulation of chromosomal rearrangements drive complete reproductive isolation, and promote equids as a fundamental model for understanding the interplay between chromosomal structure, gene flow, and, ultimately, speciation.

There’s a lot in this paper which I will elide. For example, like most large species during the Pleistocene it seems that we need to start rethinking the importance of meta-population dynamics. But interestingly the evidence of gene flow across lineages reinforces the result that chromosome number differences are no barrier to hybridization. This should be obvious in some ways with equids, Przewalski’s horse has a different number than the domestic horse! I wouldn’t be surprised if this pattern of gene flow, especially near the root of the emergence of a lineage which we define as a “species”, is not uncommon with mobile genuses which span the world island.

And going back to hominins and hominoids, the title is a reference to a 2006 paper, Genetic evidence for complex speciation of humans and chimpanzees. The argument in that paper was that there was evidence of hybridization events after the initial divergence. This is highly disputed, and I haven’t followed the literature closely. But after all that we’ve found out about hybridization between distant lineages within Homo since 2006 should we surprised that this would occur within Africa in the incipient Pan and Homo lineages?

Last month Aeon Magazine asked: Genes that leap from one species to another are more common than we thought. Does this shake up the tree of life? Perhaps. But it shouldn’t. The universe is far more wondrous than can be imagined in our small philosophy.

• Category: Science • Tags: Speciation 
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Carrion Crow

Carrion Crow

Haeckel's "tree of life"

Haeckel’s “tree of life”

Being the way we are we humans attempt to comprehend the world in a manner which is intuitively graspable. Obviously some ideas are derived from environmental inputs. If you learn a little math and start talking about a multi-dimensional universe beyond the three spatial ones which we can grasp, then obviously you’re seeing the power of higher order abstraction detached from lived experience. But science is usually not so rarefied in relation to our lived reality. Our intuitions about the world often interface with our broader theories, many of which clearly shape scientific models, even if in the end these models extend far beyond the limits of our Gestalt cognition. How we grasp the whole of the universe has an effect on how we break nature apart at its joints.

The evolutionary ideas which were ascendant in the Victorian age, crowned by Charles Darwin’s theory of the origin of species via natural selection, illustrate both of these realities. On the one hand evolutionary ideas are as old as the Greeks, and likely older in that the Ionians made formal and abstract many folk theories which were likely floating about in the world of antiquity. But there were those then, and now, who had difficulty comprehending the evolutionary nature of speciation, and the morphological change which results in phyletic gradualism (e.g., for Creationists “macroevolution” is always the problem). The likely psychological root of skepticism of speciation is that humans seem to have innate ideas as to the nature of kinds and categories. Plato’s speculations about eternal forms leverage deep intuitions that we have about the world around us which can be discerned even in infants that there are essences, an order and plan. What evolutionary biologists term “population thinking” is not natural, and continuity is often rendered in a discrete fashion when it comes to everyday terminology. A concept such as species has the dual benefit of both being intuitive and aligning with our natural prejudices about the world, and also being useful in the everyday practice of science. But the fact is species are not a real phenomenon, such as the acceleration of a ball in space, but a useful shorthand which brackets a range of concepts.

speciation My attitude toward the term “species” is strongly informed by the instrumental views which are interleaved throughout H. Allen Orr and Jerry Coyne’s book from the mid-aughts, Speciation. That is not to say that the book is perfect, at least from the perspective of some plant biologists. But that’s why I emphasize an instrumental view of species, what might be a useful classification for a plant biologist may not be a useful one for a zoologist, let alone a bacterial geneticist. Species as a concept only exists to delineate and clarify our thinking unless you have a religious model which presupposes ideal kinds brought about by the hand of a designer. Scientific taxonomy is only a rough and approximate mapping of the reality of natural history and evolutionary genetics, which it purports to collapse informatively. And with all the problems with the species concept, recall that it is the “most real” of taxonomic categories which we use (e.g., the biological species concept is moderately coherent).

Naturally this does not mean that there are no differences between the populations we term species, simply that we shouldn’t lose sight of the fact that the way we describe nature is often shorthand which obscures as well as illuminates. The debate about species concepts can be informative and interesting, but it has its limits. I do not hold to the position that there is “one definition to rule them all.” Which brings me to a new paper in Science on crows, The genomic landscape underlying phenotypic integrity in the face of gene flow in crows:

The importance, extent, and mode of interspecific gene flow for the evolution of species has long been debated. Characterization of genomic differentiation in a classic example of hybridization between all-black carrion crows and gray-coated hooded crows identified genome-wide introgression extending far beyond the morphological hybrid zone. Gene expression divergence was concentrated in pigmentation genes expressed in gray versus black feather follicles. Only a small number of narrow genomic islands exhibited resistance to gene flow. One prominent genomic region (<2 megabases) harbored 81 of all 82 fixed differences (of 8.4 million single-nucleotide polymorphisms in total) linking genes involved in pigmentation and in visual perception—a genomic signal reflecting color-mediated prezygotic isolation. Thus, localized genomic selection can cause marked heterogeneity in introgression landscapes while maintaining phenotypic divergence.

Citation: Poelstra, J. W., et al. "The genomic landscape underlying phenotypic integrity in the face of gene flow in crows." Science 344.6190 (2014): 1410-1414.

Citation: Poelstra, J. W., et al. “The genomic landscape underlying phenotypic integrity in the face of gene flow in crows.” Science 344.6190 (2014): 1410-1414.

You may wonder how a paper on the population genomics of crows relates to the broader philosophical issues I was alluding to earlier. Simple, as science advances it sheds light on the true and fine-grained shape of the world around us, rather than our coarse preconceptions. We look through the glass darkly to infer our innate ideas. Modern taxonomy has its origins in Carl Linnaeus’ system, and the status of carrion vs. hooded crow in terms of whether they are species or subspecies has a history which goes back at least to this period. This paper in Science seems to have “solved” the issue in substance, if not style. By substance I mean that the authors have extracted enough genetic information that all the blank spots in our discussion are filled in to my satisfaction. On the whole genome level one can’t differentiate the two crow species/subspecies as clear and distinct entities. German carrion crows are genetically closer to Polish hooded crows in terms of total genome content. But, when it comes to a few specific regions of the genome which affect diagnostic physical characteristics, the pigment of pelage, as well as variation in behaviour, the two groups in fact are quite distinct. To obtain these sorts of results the science had to be top notch. Or at least 2014, not 1814. They sequenced a male hooded crow to greater that 100x coverage to generate a reference sequence, which is very high. Then they sequenced a 60 carrion and hooded crows to greater than 10x coverage, which is reasonable for population genomic work, especially if you can align it to the reference.

Citation: Poelstra, J. W., et al. "The genomic landscape underlying phenotypic integrity in the face of gene flow in crows." Science 344.6190 (2014): 1410-1414.

Citation: Poelstra, J. W., et al. “The genomic landscape underlying phenotypic integrity in the face of gene flow in crows.” Science 344.6190 (2014): 1410-1414.

The basic major result is illustrated in the figure to the right. What you see is that overall the genetic divergence between German carrion crows and Spanish carrion crows, the latter being the putative source population, is rather large comparatively (Spanish vs. Germany vs. Swedish vs. Polish). In contrast there is minimal genetic divergence between German carrion crows and Polish hooded crows, as one might predict by geographic. But, there are exceptional regions of the genome, as is clear when you look at the emphasized spikes in F ST. In other words, continuous gene flow has homogenized between population differences, as you’d except from basic theory (across two demes N >= 1 sufficient to prevent divergence), but selection pressures along very salient traits have resulted in a shaper distinction along a few genomic regions. The interesting point here is though that this isn’t due to any ecological distinction. For example, when it comes to pigmentation some human populations (e.g., Africans and Melanesians) resemble each other despite huge whole genome differences (Melanesians are just another branch of “Out of Africa” humanity). But one can posit a clear ecological rational for why this might be. Not so for carrion and hooded crows. Intuitively it seems obvious that Germany shares more ecologically with Poland than it does with Spain. So what’s going on? The authors provide a likely answer: “A key feature that distinguishes the crow system is the apparent lack of ecological selection on the maintenance of separate phenotypes. Instead, the data presented here are consistent with the idea that assortative mating and sexual selection can exclusively cause phenotypic and genotypic differentiation.” Instead of a speciation gene, these may be “speciation genomic regions” (yes, it has less of a ring to it, I admit).

So where does this leave us in terms of species concept? Well, your mileage may vary. In the accompanying commentary by Peter de Knijff there is some bashing the bar code of life idea of systematically identifying species differences using DNA. I don’t think there’s a problem with the bar code of life as long as one understands that one shouldn’t confuse the measure with what one is measuring. The concept species is not like the speed of light, it is freighted with assumptions, and means different things to different people. If one understands that ahead of time then a consistent language or measuring stick can still be highly useful, if not ultimately informative in a deep ontological sense (i.e., atoms/quarks are fundamental to material objects in a way that species are not in regards to variation among living organisms).

This specific result is also not entirely surprising, though it is nice to see it worked out in a specific case. The connection between physical appearance and species distinctions is an old and intuitive one, despite the importance of genealogical concepts when it comes to our intuitive essentialism. And this applies to taxonomic levels which are lower, as far back as Charles Darwin sexual selection was posited as the reason for racial differences in appearance for humans (Jared Diamond promoted this view in The Third Chimpanzee). Back in 2003 Henry Harpending brought to my mind the idea that human differences in phenotypes can persist across populations despite overall genomic similarities. To me this reinforces that genomics has come not to bring peace to old truths, but a sword of empirical reality to old preconceptions. Rather than dithering as to the “best” term to describe genetic variation and evolutionary process, we can actually go about describing it in close to its entirety, and let the chips fall where they may. Compute and quantify. The rest is commentary.

• Category: Science • Tags: Genomics, Population Genetics, Speciation 
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A monkey frog

The Pith: The Amazon Rainforest has a lot of species because it’s been around for a very long time.

I really don’t know much about ecology, alas. So my understanding of evolution framed in its proper ecological context is a touch on the coarse side. When I say I don’t know much about ecology, I mean that I lack a thick network of descriptive detail. So that means that I have some rather simple models in my head, which upon closer inspection turn out to be false in many specific instances. That’s what you get for relying on theory. Today I ran into a paper which presented me with some mildly surprising results.

The question: why is the Amazon Rainforest characterized by such a diversity of species? If you’d asked me that question 1 hour ago I would have said that it was a matter of physics. That is, the physical parameters of a high but consistent rainfall and temperature regime. This means the basic energetic inputs into the biome is high, and its consistency allows the organisms to plan their life schedule efficiently, maximizing the inputs. All that naturally produces a lot of diversification in the “climax” ecosystem. To some extent I would acknowledge this was pretty much a “Just-So,” but I’d have thought it was a good shot, and probably representative of the internal logic of many people. But no, a new paper in Ecology Letters seems to imply that that the answer we must look to is history and not physics. From the perspective of someone who is rooted in are reductionist conception of evolutionary biology this isn’t the answer I was “rooting” for, but if it is, it is. What’s their logic?

First, the abstract, Phylogenetic origins of local-scale diversity patterns and the causes of Amazonian megadiversity:

What explains the striking variation in local species richness across the globe and the remarkable diversity of rainforest sites in Amazonia? Here, we apply a novel phylogenetic approach to these questions, using treefrogs (Hylidae) as a model system. Hylids show dramatic variation in local richness globally and incredible local diversity in Amazonia. We find that variation in local richness is not explained primarily by climatic factors, rates of diversification (speciation and extinction) nor morphological variation. Instead, local richness patterns are explained predominantly by the timing of colonization of each region, an d Amazonian megadiversity is linked to the long-term sympatry of multiple clades in that region. Our results also suggest intriguing interactions between clade diversification, trait evolution and the accumulation of local richness. Specifically, sympatry between clades seems to slow diversification and trait evolution, but prevents neither the accumulation of local richness over time nor the co-occurrence of similar species

Thankfully species richness is pretty easy to understand. It’s a count of the number of species in a given area. In this case they limited their count to a specific clade, the tree frogs. This clade seems to have a common ancestor ~60-80 million years before the present from which it descends.

Below is a phylogenetic tree (scaled to time on the horizontal) representing the relationships of contemporary tree frog species, as well as a distribution of the species across the world:

Visual inspection tells you immediately that Amazonia is overloaded with tree frog species. But to get at the question of what explains the variation in species richness the authors used standard statistical techniques relating predictors such as temperature and precipitation values to the outcome, species richness. The authors did find a relationship between precipitation and temperature and species richness. But once they controlled for phylogeny in their regression, that is, take into account history, the relationship went away. In other words the correlations may have been an artifact of the fact that the Amazon is warm and wet and rich with species. Controlling for the phylogeny of the clade, which is a record of contingent history, the expected picture relating physical parameters to diversification changes. The two panels above and to the left show the relationships between species richness (y-axis) and first colonization event. The left panel is pegged from the first colonization of any tree frog lineage, while the second sums up distinct colonization events by different clades (so the x-axis has a larger magnitude). The r-squared, the proportion of the variance of y explained by variance in x, is nearly 0.50 in the left and 0.70 in the right. That’s pretty good.

There’s some interesting material in the paper sympatry vs. allopatry in regards to the tree frogs. Basically, how they vary in size and diversity as a function of whether they co-occur in the same ecosystem or whether they’re physically separated (so allopatric speciation is when two lineages are separated while sympatric is when they are geographically overlapping but diverge anyhow, perhaps through occupation of differing niches).

But that’s not my primary concern or interest. How generalizable are these results form tree frogs? I don’t know this literature well. Surely someone has done a phylogenetic least squares with a lot of different clades and checked for this? If the results here are generalizable then the diversity of the Amazon ecosystem is in large part a function of its longer term stability and persistence. I have posited that at the “end of history” natural selection will have shaped an exceeding simply and energetically optimized biosphere, dominated by a few species. But in Amazon is a case in the opposite direction, as clade diversification increases as a function of the time of ecosystem integrity. Is this monotonic? In other words, is there going to be a time when a rare evolutionary event may given rise to a species which sweeps away all the accumulated variation?

Those are questions for the future I suppose.

Citation: Wiens JJ, Pyron RA, & Moen DS (2011). Phylogenetic origins of local-scale diversity patterns and the causes of Amazonian megadiversity. Ecology letters PMID: 21535341

Image credit: Colin Burnett

• Category: Science • Tags: Diversity, Ecology, Environment, Speciation 
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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:

Ecological change provokes speciation and extinction, but our knowledge of the interplay among the biotic and abiotic drivers of macroevolution remains limited. Using the unparalleled fossil record of Cenozoic macroperforate planktonic foraminifera, we demonstrate that macroevolutionary dynamics depend on the interaction between species’ ecology and the changing climate. This interplay drives diversification but differs between speciation probability and extinction risk: Speciation was more strongly shaped by diversity dependence than by climate change, whereas the reverse was true for extinction. Crucially, no single ecology was optimal in all environments, and species with distinct ecologies had significantly different probabilities of speciation and extinction. The ensuing macroevolutionary dynamics depend fundamentally on the ecological structure of species’ assemblages.

The foraminifera went from 2 species early in the Cenozoic to over 30. Additionally, as noted in the paper they’re well sampled across the whole time period. It is a cliché that paleontology suffers from a deficit of thick data sets, but this seems far less the case with marine organisms which are numerous and mineralize copiously, such as the foraminifera. Ecology here seems to be defined both by position in the water column as well as morphology of the species. Presumably this intersection defines specific niches inhabited by the species of this lineage.

Figure 2 and 3 illustrate the primary results of this paper:

The scatter plots in figure 2 are pretty striking. Using one parameter there’s almost no prediction of clade growth. Remember that R-squared simply tells how how much of the variance of axis y can be explained by axis x. But, when you include the interaction between two variables, the R-squared starts to become significant. And when you have three variables, it isn’t too shabby at ~0.66. That means the interaction between clade diversity, climate, and ecology, can explain 2/3 of the variance in clade growth.

Diversity just measures inter-specific competition and interaction. A diversity focused model would predict that clades rapidly expand to fill available niches when it is low, and that one attains a steady state equilibrium when species richness has increased. Climate is rather self-evident. Finally, as I note above, ecology seems to be a compound of characteristics and indicates the positioning of a population in relation to others and their environment. In this paper the authors refer to the Red Queen’s Hypothesis, as well as the “Court Jester Model.” Honestly I don’t really know specifically what the latter is aside from what is mentioned in the paper. That certainly highlights my ignorance. But from what I can tell the Red Queen Hypothesis of evolutionary arms races correspond to biotic pressures, while the Court Jester Model denotes the climatic shocks and shifts which are outside of the closed system of species’ interactions.

So figure 2 shows that both forces are critical in determining the specific state of species’ richness. But the third figure illustrates that they have somewhat different roles. “E” is ecology and “C” climate, while “D” is diversity. You see that diversity (or lack of more accurately) correlates with speciation, while ecology & climate are more relevant for prediction of of extinction. The former is due to the “early burst” of adaptive radiation which occur in a low diversity state. Why is the diversity low? Probably because of a massive extinction event due to an exogenous shock. So the two classes of variables do influence each other, insofar as biotic dynamism surges in the wake of an abiotic perturbation.

Much of the above is common sense, and we understand it non-quantitatively. Of course both exogenous and endogenous dynamics are at work in shaping the specific nature of the tree of life. By exogenous, I’m referring to climatic shifts, comets, geologic activity, etc. By endogenous I’m referring to the cycles of interactions which might be triggered by a sequence of co-evolutionary arms races. Many readers of this weblog with some biological background will be familiar with chaotic phenomena bubbling out of purely endogenous parameters. In theory a cycle of extinctions and clade radiations could be due to endogenous processes. But the above data suggest that at least for life on earth, that is not so. Perhaps in a low energy universe trillions of years in the future, in a universe with few surprises, we’ll see purely closed ecosystems at work. But not right now. A surprise is always in the cards!

Citation: Ezard TH, Aze T, Pearson PN, & Purvis A (2011). Interplay between changing climate and species’ ecology drives macroevolutionary dynamics. Science (New York, N.Y.), 332 (6027), 349-51 PMID: 21493859

• Category: Science • Tags: Ecology, Evolution, Extinction, Speciation 
Razib Khan
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