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Category: Evolution
Dog and man: a 30,000 year friendship
Cite: Wang, Guo-dong, et al. “The genomics of selection in dogs and the parallel evolution between dogs and humans.” Nature Communications 4 (2013): 1860.
To the left is a figure which illustrates the phylogenetic inferences from a new paper in Nature Communications, The genomics of selection in dogs and the parallel evolution between dogs and humans (see Carl Zimmer’s coverage in The New York Times). Why is this paper important? The first thing that jumped out at me is that because they’re using whole genomes (~10X coverage) of a selection of dogs and wolves the results aren’t as subject to the bias of using “chips” of polymorphisms discovered in dogs on wolves (see: Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication). The second aspect is that the coalescence of the dog vs. wolf lineage is pushed further back in time than earlier genetic work, by a factor of three. A standard model for the origin of dogs is that they arose in the Middle East ~10,000-15,000 years ago , possibly as part of the broad shift of lifestyles which culminated in the Neolithic Revolution.
This model is now in serious question. Though there have always been claims of fossils of older domestic canids (adduced as such in terms of morphology) than the ones discovered in the Middle East ~15,000 years ago, this year there has been publication of ancient mtDNA results from ~30,000 years before the present which imply the separation of putative domestic and wolf lineages at least to that date. Over the past few years I have wondered about the specific nature of the emergence of both modern humans and modern dogs, and their co-evolutionary trajectory, over the Pleistocene and into the Holocene, in light of these results.
Human mutation unveiled
Credit: Campbell, Catarina D., and Evan E. Eichler. “Properties and rates of germline mutations in humans.” Trends in Genetics (2013).
What a great age we live in. Until recently critical parameters in population genetics such as mutation rates had to be inferred and assumed, even though they served as bases for much more complex inferences. Now with humans (and humans are only the beginning!) much of what was inferred is being assessed in a more direct fashion. Caterina Campbell and Even Eichler have a review in Trends in Genetics which surveys the field as it stands now, Properties and rates of germline mutations in humans. Notice that there’s a rough convergence using pedigree analysis of a mutation rate in the low 10-8 range. Additionally, it does seem that a disproportionate number of novel mutations come through the paternal lineage via sperm. This should increase our moderate worry about older fathers (something reiterated in the piece, with caveats). Finally, the authors suggest these results are a floor for the mutational rate, in part due to the long term conflict with the inferred ‘evolutionary rates,’ which are higher. This matters because to infer the last common ancestors between lineages the value of the mutation rate is obviously critical.
Turtles all the way down!
Nature Genetics (2013) doi:10.1038/ng.2615
No time to comment extensively, but check out The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan (open access). The paper and the ScienceDaily press release allude to some phylogenetic confusion as to the relationship of turtles to other reptilian lineages, but my own superficial knowledge of this area left me rather unsurprised by this tree. What am I missing? Though reading the Wikipedia entry it seems that spotty marker coverage has produced a lot of controversy. What’s more striking to me is that so many terrestrial vertebrate lineage seem to have emerged over a relatively short period of time. Though presumably this may simply be an artifact of the reality that most lineages go extinct so we’re only left with relatively deep branching patterns. Someone who knows fossils can chime in.
Does one need math for a career in science?
E. O. Wilson has a op-ed in WSJ which I find quite interesting, Great Scientist ≠ Good at Math:
For many young people who aspire to be scientists, the great bugbear is mathematics. Without advanced math, how can you do serious work in the sciences? Well, I have a professional secret to share: Many of the most successful scientists in the world today are mathematically no more than semiliterate.
…
This imbalance is especially the case in biology, where factors in a real-life phenomenon are often misunderstood or never noticed in the first place. The annals of theoretical biology are clogged with mathematical models that either can be safely ignored or, when tested, fail. Possibly no more than 10% have any lasting value. Only those linked solidly to knowledge of real living systems have much chance of being used.
Wilson has been on this for a bit now, to the bewilderment of some of the scientists I follow on Twitter (granted, the people I follow tend to be quantitative genomics types whose backgrounds may have been in math, physics, or statistics). Two immediate things come to mind reading this. First, a disproportionate number of the famous and successful scientists alive today are old, like E. O. Wilson. Just because you could get by with a certain level of mathematical fluency as an enfant terrible in the 1970s does not mean that that will cut it in the 2010s. Great scientists who are mathematically weak often have collaborators, post-docs, and graduate students, who do their bidding. It might be a different matter if you aren’t one of the Great Ones of the earth. From what I can tell scientists who are doing the hiring who don’t have mathematical skills prefer candidates who do have mathematical skills.
William D. Hamilton: science without artifice
In Nature Oren Harman has a review up of Nature’s Oracle: The Life and Work of W. D. Hamilton. It seems as if he gives it a B. Not enough science? Too much biography? For those who want more science and depth, Hamilton’s collected papers are where you should start: Narrow Roads of Gene Land: Evolution of Social Behaviour, Narrow Roads of Gene Land: Evolution of Sex, and Narrow Roads of Gene Land: Last Words. These books consist of an alternating series of (auto)biographical sketches and scientific papers. Unfortunately Hamilton died before much work went into the last volume, so we don’t get to hear him in his own voice. This is a shame, because the first two volumes place much of the science in fascinating, if not necessary, social context. The equivalent chapters for the last volume were written by colleagues and collaborators, but the outcome is not surprisingly more pedestrian. The second volume in particular is worth picking up because it is basically unedited Hamilton (his untimely death meant that the normal back and forth which would have slimmed down the verbosity and softened the candor was simply not possible).
The “placental explosions”
Spinger et al. doi: 10.1073/pnas.0334222100
By this time I’m sure you’ve encountered articles about the reconstructed last common ancestor of all placental mammals. Greg Mayer at Why Evolution is True has an excellent review of the implications, along with a link to a moderately skeptical piece by Anne Yoder in Science. Yoder’s piece is titled Fossils vs. Clocks, while the original paper is The Placental Mammal Ancestor and the Post–K-Pg Radiation of Placentals. The results clearly support the “Explosive Model” in the figure to the left for the origination of placentals. That might prompt the thought: “isn’t this what we knew all along?”
The standard story for the last generation in the popular imagination is that a massive asteroid impact was the direct cause of the extinction of all dinosaurs (and of course a host of other groups) except the lineage which we now term birds. And yet it turns out that there is actually some debate about this, though at least in some form it seems likely that the impact is going to be important (see this Brian Switek piece for exploration of this issue, and the general opinion of the scientific literature as of now). The second aspect to focus on is timing. Contrary to the intuition of many, over the past 20 years molecular phylogenetics has inferred a very definite (on the order of tens of millions of years) pre-K-T boundary coalescence for the common ancestors of the disinct mammalian lineages. A plausible explanation for this is that these lineages diversified through allopatry, as the Mesozoic supercontinent fragmented. Morphological diversification of these mammalian lineages also may have occurred after the K-T event.
Nature’s Oracle finally has a publication date
The W. D. Hamilton biography, Nature’s Oracle finally has a publication date. Amazon says March 1st, and other places say April 1st (For the USA). I don’t care much either way, I pre-ordered. Now it would be nice if more academic books were available in Kindl format though. I’m not anticipating the “physical pleasure” of have it shipped to me when I could just get it emailed to me on the day of its release.
The feathery Neandertal
Birds of a Feather: Neanderthal Exploitation of Raptors and Corvids:
The hypothesis that Neanderthals exploited birds for the use of their feathers or claws as personal ornaments in symbolic behaviour is revolutionary as it assigns unprecedented cognitive abilities to these hominins. This inference, however, is based on modest faunal samples and thus may not represent a regular or systematic behaviour. Here we address this issue by looking for evidence of such behaviour across a large temporal and geographical framework. Our analyses try to answer four main questions: 1) does a Neanderthal to raptor-corvid connection exist at a large scale, thus avoiding associations that might be regarded as local in space or time?; 2) did Middle (associated with Neanderthals) and Upper Palaeolithic (associated with modern humans) sites contain a greater range of these species than Late Pleistocene paleontological sites?; 3) is there a taphonomic association between Neanderthals and corvids-raptors at Middle Palaeolithic sites on Gibraltar, specifically Gorham’s, Vanguard and Ibex Caves? and; 4) was the extraction of wing feathers a local phenomenon exclusive to the Neanderthals at these sites or was it a geographically wider phenomenon?. We compiled a database of 1699 Pleistocene Palearctic sites based on fossil bird sites. We also compiled a taphonomical database from the Middle Palaeolithic assemblages of Gibraltar. We establish a clear, previously unknown and widespread, association between Neanderthals, raptors and corvids. We show that the association involved the direct intervention of Neanderthals on the bones of these birds, which we interpret as evidence of extraction of large flight feathers. The large number of bones, the variety of species processed and the different temporal periods when the behaviour is observed, indicate that this was a systematic, geographically and temporally broad, activity that the Neanderthals undertook. Our results, providing clear evidence that Neanderthal cognitive capacities were comparable to those of Modern Humans, constitute a major advance in the study of human evolution.
Not to be too skeptical, but has anyone done an analysis of a possible change in the nature of publications about the cognitive capacities of Neandertals since it was established that there is a high likelihood of admixture between that lineage and ours (i.e., that that lineage is to some extent ours)? This is where I have to point to Luke Jostins’ loess curve illustrating the increase in cranial capacity of hominins over the past few million years. As Luke notes “brain size increases gradually in all lineages.”
This isn’t to deny that there seem some qualitative differences between the descendants of anatomically modern humans and other hominins. Neandertals, Denisovans, etc., never made it to the New World or Oceania. But there are differences, and there are differences. One model which was rather popular, and which I tacitly accepted, is that modern humans, the “descendants of Eve,” are sui generis. Somehow, somewhere, ~50-100,000 years ago a lineage of geniuses came upon the scene and swept all others away. I don’t accept this proposition anymore. Rather, it may be that 1-2 million years ago the hominin lineages took some irreversible step, and all the parallel and reticulate branches were hurtling toward a new evolutionary equilibrium.
What the substrate tells
One of the weird things about genetics is that it encompasses both the abstract and the concrete. The formal and physical. You can talk to a geneticist who is mostly interested in details of molecular mechanisms, and is steeped in structural biology. For these people genes are specific and material things. In contrast there are other geneticists who focus more on genes as units of analysis. In this case genes are semantic labels for the mediators within an intersection of phenomena. Recall that genetics predates the knowledge of its concrete substrate by 50 years! By the 1920s Mendelian genetics had been fused with evolutionary biology to create a systematic framework in which we could understand the patterns of inheritance across the generations. In the 1950s the DNA revolution was upon us, but as W. D. Hamilton recalls this had only a minimal impact on the evolutionary genetic thinkers of the era. With the Lewontin and Hubby allozyme paper in the mid-1960s this sort of benign disciplinary evasion was no longer possible; the field of molecular evolution came into its own.*
Today with genomics these human-imposed artificialities are fading away. Consider the concept of genetic recombination. Originally an abstraction in a formal Mendelian system, today it is of great interest to molecular biologists who are curious as to its exact mechanism and purpose, and genomicists who are interested in the constraints upon the phenomenon due to its physical parameters (e.g., recombination hotspots). If we were to discover alien beings I assume that there would be some sort of genetics in an abstract sense. But would they package their genes in chromosomes? Would their complex organisms tend toward dioecy? I wouldn’t be surprised if the genetics of alien species have their own particular kinks subject to the contingent nature of the physical scaffolding of the process.
An ontology of genetic diversity
Implicit in the title The Origin Of Species is the question: why the plural? In other words, why isn’t there a singular apex species which dominates this planet? One can imagine an abstract system where natural selection slowly but gradually sifts through variation and designs a best-of-all-replicators. And yet on the contrary it seems that our planet has exhibited an overall tendency of going from lower to higher diversity. The age of stromatolites may be the last epoch when we had the best-of-all-replicators.
Evolution: its ideological self-refutation
Recently I stumbled upon the fact that Honey Boo Boo‘s sister had a child at age 18. The grandmother, Honey Boo Boo’s mother, is 33 years old. Younger than I am! Then I see headlines in trashy British tabloids of the form: The three men who have fathered 78 children with 46 different women… and they’re not paying child support to any of them. Here I am, in the fullness of man-childhood, a new father, groping to understand evolutionary process in all its glory, and here are they who live evolution! There are those around us who don’t blink at maximizing their fitness in the modern world. Here’s some data from the GSS:
Why aren't we all tall?
There’s a fair amount of social science and anecdata that tall males are more reproductively fit. More precisely, males one to two standard deviations above the norm in height seem to be at the “sweet spot” as an idealized partner (e.g., leading males). And, short men often have fewer children. Short women will pair up with tall men. Tall women will generally not pair up with shorter men. The question then has to be asked: why isn’t natural selection producing a situation where we’re all tall?
As it is, height is a highly heritable trait where there’s a lot of genetic variation present in the population. One hypothesis might be that short(er) people are simply individuals with a higher mutational load. In other words, there’s going to be variation in the load of deleterious alleles from person to person, and one’s value on quantitative traits (intelligence, height) is a reflection of one’s genetic fitness. There are problems with this model, starting with the fact that one you need to tease apart inter-population variation. Also, within families there doesn’t seem to be a correlation between height and intelligence, which you would expect to see if quantitative traits are reflections of variation in mutational load.
So naturally you have to move the possibility of balancing selection. I have suggested in the past that inter-population differences in height may be a function of expected levels of nutritional stress. Short people are smaller, and need to eat less. The same dynamic could produce variation in height within populations as well. But a new paper outlines what I think I think is the most elegant solution (though elegant does not mean right!), Intralocus sexual conflict over human height:
Selection of and in groups
Eric Michael Johnson has an excellent round-up of and commentary upon recent debates about “group selection” (also, a decent primer on the basics). If there is one major issue I might take with the narrative outlined, it is the idea that E. O. Wilson has made a recent about-face in regards to group selection, going from a skeptic to a believer. In Defenders of the Truth: The Sociobiology Debate Ullica Segerstrale pointed out that this was obviously not the case even in Wilson’s grand book Sociobiology. If you don’t accept this, David Sloan Wilson seems to implicitly confirm Segerstrale’s position in his semi-autobiographical book Evolution for Everyone. Finally, I’ve heard it from acquaintances at Harvard that it was an open secret that E. O. Wilson was skeptical of the “Hamiltonian orthodoxy” ascendant in evolutionary biology and ecology. The controversy over the notorious paper, The evolution of eusociality, was years in the making. From what I gather many of Wilson’s colleagues at Harvard were skeptical that he comprehended the depths of the mathematics which he promoted to support his more intuitive empirically informed skepticism of the power of inclusive fitness. It isn’t an unheard of sin for an eminent empiricist to go shopping for a theoretician to add some luster to his logic, but it does frame the reason that some of Wilson’s colleagues seem so irritable about the whole affair.
Why the kids don't know no algebra
A few days ago I stumbled upon a really interesting post. And I’m wondering if my readers are at all familiar with the phenomenon outlined here (it was a total surprise to me), The myth of “they weren’t ever taught….”:
Stage One: I will describe this stage for algebra I teachers, but plug in reading, geometry, writing, science, any subject you choose, with the relevant details. This stage begins when teachers realize that easily half the class adds the numerators and denominators when adding fractions, doesn’t see the difference between 3-5 and 5-3, counts on fingers to add 8 and 6, and looks blank when asked what 7 times 3 is.
Ah, they think. The kids weren’t ever taught fractions and basic math facts! What the hell are these other teachers doing, then, taking a salary for showing the kids movies and playing Math Bingo? Insanity on the public penny. But hey, helping these kids, teaching them properly, is the reason they became teachers in the first place. So they push their schedule back, what, two weeks? Three? And go through fraction operations, reciprocals, negative numbers, the meaning of subtraction, a few properties of equality, and just wallow in the glories of basic arithmetic. Some use manipulatives, others use drills and games to increase engagement, but whatever the method, they’re basking in the glow of knowledge that they are Closing the Gap, that their kids are finally getting the attention that privileged suburban students get by virtue of their summer enrichment and more expensive teachers.
At first, it seems to work. The kids beam and say, “You explain it so much better than my last teacher did!” and the quizzes seem to show real progress. Phew! Now it’s possible to get on to teaching algebra, rather than the material the kids just hadn’t been taught.
But then, a few weeks later, the kids go back to ignoring the difference between 3-5 and 5-3. Furthermore, despite hours of explanation and practice, half the class seems to do no better than toss a coin to make the call on positive or negative slopes. Many students who demonstrated mastery of distributing multiplication over addition are now making a complete hash of the process in multi-step equations. And many students are still counting on their fingers.
Born to conform
There is a new paper in Nature, Social networks and cooperation in hunter-gatherers, which is very interesting. As Joe Henrich observes in his view piece the panel of figure 2 (see left) is probably the most important section.
The study focuses on the Hadza, a hunter-gatherer population of Tanzania. Their language seems to be an isolate, though there have been suggestions of a connection to Khoisan. Additionally the genetic evidences tells us that like the Bushmen and Pygmies the Hadza do descend from populations which are basal to other human lineages, and were likely resident in their homeland before the arrival of farmers. And it is critical to also note that the Hadza are probably uninterrupted hunter-gatherers in terms of the history of their lifestyle, as agriculture likely arrived in Tanzania on the order of two thousand years ago, and their genetic distinctiveness indicates a separation from groups like Bantus far deeper in time. When it comes to Paleolithic model populations the Hadza are relatively “uncontaminated.”
The milkmen
Dienekes and Maju have both commented on a new paper which looked at the likelihood of lactase persistence in Neolithic remains from Spain, but I thought I would comment on it as well. The paper is: Low prevalence of lactase persistence in Neolithic South-West Europe. The location is on the fringes of the modern Basque country, while the time frame is ~3000 BC. Table 3 shows the major result:
Lactase persistence is a dominant trait. That means any individual with at least one copy of the T allele is persistent. As Maju noted a peculiarity here is that the genotypes are not in Hardy-Weinberg Equilibrium. Specifically, there are an excess of homozygotes. Using the SJAPL location as a potentially random mating scenario you should expect ~7 T/C genotypes, not 2. Interestingly the persistent individual in the Longar location also a homozygote.
James F. Crow, 1916-2012
Sad news. John Hawks passes along that James F. Crow has died. Further mention from the National Center For Science Education. A little over 5 years ago I sent Crow an email with only minimal expectation of response, asking about an interview. He responded in less than 24 hours! I think it says a lot about the man that he would respond to sincere questions out of the blue from basically a nobody. Here is his Wikipedia entry. And remember that Genetics has commissioned a series of retrospective essays in Crow’s honor.
The Genetical Theory of Natural Selection
I flog R. A. Fisher’s The Genetical Theory of Natural Selection a fair amount on this site. You don’t need to understand everything in the book, nor do you have to agree with everything in it, but it is a great point of departure toward understanding evolutionary genetics. I’ve noted that you can get it free in PDF format. But if you want to browse it online in a easier format, here you go:
Out of Africa to Out of Arabia
Dienekes and Greg Cochran have been talking about this possibility for a few years. But a combination of archaeological finds and the current unsettled nature of the human evolutionary genomics literature means that “Out of Arabia” is a real possibility (not laugh-out-loud crazy and weird). So I took the liberty of cooking up a new design for the RichardDawkins.net website. Science is about updating our prior assumptions, so it shouldn’t be too much of an issue. What I wonder: how would the population of the Kingdom of Saudi Arabia feel about replacing Ethiopia and Kenya in human evolution documentaries? Addendum: To be clear, this isn’t to say I accept “Out of Arabia” for the origin of most modern humans, including within Africa. Rather, I think it’s not a crazy idea anymore, especially in light of the weird results which imply that West Africans may be genetically closer to non-Africans than to Pygmies and San (and it would make more sense of older uniparental results which imply back-migration from Eurasia into Africa).
The last word on dog genesis is not nigh!
In my post below Rob commented:
Surely the genetic evidence is pointing towards a single domestication event (see http://news.sciencemag.org/sciencenow/2011/11/new-data-fuels-dogfight-over-the.html?ref=hp)
My general response is not to accept the latest press release about the genetic origin of dogs. I keep track of the literature and it’s rather fluid. For example, I woke up this morning, and this is what showed up in my RSS, Modern dogs are more Asian fusions than Euro pups, study finds:
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Razib’s Pinboard
- Alice E. Kober, 43 - Lost to History No More - NYTimes.com
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- Egg freezing: Why the procedure is worse than PMS but better than the dentist.
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- Life as One of the Most-Persecuted Ethnic Groups on the Planet - Jeffrey Stern - The Atlantic
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- About That Dissertation | National Review Online
- Study: Kids Are Prejudiced Against Fat People by Age 4 - Lindsay Abrams - The Atlantic
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- Investigative Genetics | Abstract | Clinal distribution of human genomic diversity across the Netherlands despite archaeological evidence for genetic discontinuities in Dutch population history
- Archaeological genetics: It's not all as old as it at first seems
- Trends in Genetics - Properties and rates of germline mutations in humans
- www.culturalcognition.net - Cultural Cognition Blog - Annual "new study" finds 97% of climate scientists believe in man-made climate change; public consensus sure to follow once news gets out
- Will Google Glass finally make doing this gauche? - Quartz
