Jaw dropping

One consistent misapprehension a lot of people have about evolution is that the process of natural selection always leads toward organisms becoming stronger, smarter, faster, and more complex.

As my evolutionary biology professor put it, this is incorrect because at its core, "evolution is the law of whatever works."  The most successful, widespread, diverse, and numerous animals on Earth are, by far, insects -- they're not necessarily any of the aforementioned things (especially smart), they are just exceedingly good at reproducing fast and filling available niches.  Whatever traits happen to be selected for by the environment at the time result in the direction evolution takes.  And this can change if the environment changes -- as has been observed in a number of fossil lineages where the average body size increased for a while, then reversed course and decreased.

Evolution is not goal-oriented.  The idea that it's heading in a particular pre-determined direction is a holdover from the old Aristotelian idea of the scala naturae, where there's a ladder of increasing complexity and intelligence, with humans, of course, occupying the top rung.  (At least until the concept was adopted by medieval Christian scholars; at that point humans got knocked down a couple of pegs, with the higher rungs taken up by angels and, at the top, God.)  But you still hear people -- even scientific, rational types -- talk about "primitive" and "advanced" species, and ones being "highly-evolved" (or not), when the truth is that all modern life forms, from bacteria to birch trees to baboons, have exactly the same length of evolutionary history, going back to LUCA (the "last universal common ancestor") something like four billion years ago.

It's just that in those four billion years, some of them have changed a great deal more than others have.

Given that even people who are quite knowledgeable often still have that bias floating around, it can come as a significant shock to find out that there are some anatomically simple animals that are actually quite recently evolved -- and close to other species we consider "advanced."  Two of the most striking examples are echinoderms (such as starfish and sea urchins, which undergo a peculiar decentralization during development, losing most of their sophisticated organs up to and including the central nervous system) and tunicates (sometimes referred to as "sea squirts," which superficially look like filter-feeding sponges but are actually some of the closest invertebrate relatives to vertebrates).  In both cases, the larvae give away their actual placement in the family tree of life, as does their DNA; both of these groups represent fairly recent developments, as these things go.

Another example, and the reason this topic comes up, is Class Agnatha, which includes lampreys and hagfish, and sometimes are called "jawless fish."  (The term "fish" actually has no evolutionary relevance; it lumps together very distantly-related groups, excluding others that are far closer cousins.  Lungfish and coelacanths, for example, are more closely related to amphibians -- and thus to us -- than they are to your standard-issue fish.)

European river lamprey (Lampetra fluviatilis) [Image licensed under the Creative Commons Tiit Hunt, Jõesilmud2, CC BY-SA 3.0]

In any case, lampreys and hagfish are distinguished on the gross anatomical level by lacking lower jaws, and -- by the typical way of thinking about this -- must be some kind of "primitive" holdover from before paired jaws were developed by the rest of us vertebrates.  It's true they branched off early, and are only distantly related to other vertebrates, but some research that came out last week in Nature Ecology & Evolution suggests that their lineage lost their lower jaws, not that our direct ancestors somehow gained them along the way.

The research looked at the genetic control over jaw development, and found that the pattern was strikingly similar between vertebrates with jaws and those without -- but that those without had switched off a gene called pou5 that guides cells in the neural crest, a cluster of cells in the head of the embryo that specialize to produce a number of different structures.  Lampreys and hagfish have the gene, they just don't express it in the embryonic tissue that in other vertebrates leads to the mandible -- suggesting strongly that they evolved from ancestors that had it and expressed it.

"While most of the genes controlling pluripotency are expressed in the lamprey neural crest, the expression of one of these key genes -- pou5 -- was lost from these cells," said Joshua York of Northwestern University, lead author of the paper.  "Amazingly, even though pou5 isn't expressed in a lamprey's neural crest, it could promote neural crest formation when we expressed it in frogs, suggesting this gene is part of an ancient pluripotency network that was present in our earliest vertebrate ancestors."

So this once again confounds our tendency to fit things into a scala naturae-like pattern.  Evolution can happen not only from gaining features, but from losing them.  In the case of lampreys and hagfish, a pretty important structure -- without which, nevertheless, they appear to do just fine.

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The family tree of dogs

We've had both our dogs DNA tested -- purely for our own entertainment, not because we have any concern about "pure breeding" -- and both of them gave us results that were quite a shock.

First, there's Guinness, whom the rescue agency told us was a black lab/akita mix.  You can see why:

Turns out he is neither -- he's American Staffordshire terrier, husky, chow, and Dalmatian.

Then there's Rosie, who we thought sure would turn out to be fox terrier/beagle:

Once again, not even close.  She came out to be a mix of about ten different breeds in which Australian cattle dog predominates.  Not a trace of hound, which is surprising not only because of her facial features, but her temperament.  We've had hounds several times before, and they are sweet and loving... and stubborn, headstrong, and selectively deaf, all of which describe Rosie perfectly.

I'm not sure that it's reasonable to expect a fifty-dollar mail-order dog DNA test to be all that reliable, mind you.  In Guinness's case, though, there are features that do make sense -- the ebullient disposition and square face of the AmStaff, and the curly tail and thick, silky undercoat of his husky/chow ancestry.  Whatever its accuracy, though, it's fascinating that any signal of ancestry at all shows up in a simple saliva test.

Especially given that just about every dog breed in existence traces back to wild dog populations in only a few thousand years.  That's an extremely short time to have any evolutionary divergence take place.  But genetic testing has become sophisticated enough that we can now retrace the steps in dog evolution -- creating a family tree of dog relationships encompassing 321 different dog breeds (including several sorts of wild dogs).

A team of geneticists led by Jeff Kidd of the University of Michigan, Jennifer R. S. Meadows of Uppsala University, and Elaine A. Ostrander of the NIH National Human Genome Research Institute did a detailed study of two thousand different DNA samples containing over forty-eight million analyzable sequences.  They identified three million SNPs -- single nucleotide polymorphisms, or "snips" -- that were characteristic of certain breeds. 

"We did an analysis to see how similar the dogs were to each other," Kidd said.  "It ended up that we could divide them into around twenty-five major groups that pretty much match up with what people would have expected based on breed origin, the dogs' type, size and coloration."

Interestingly, wild dogs and "village dogs" -- dogs that are somewhere between domesticated and feral, something you find in a lot of towns in developing countries -- have significantly more genetic diversity than domestic breeds do.  This, of course, contributes to their vigor (and, conversely, is why many "pure" dog breeds are susceptible to particular health problems).  It's also why it's so easy to identify behavioral characteristics of particular breeds, like the cheerfulness of golden retrievers, the intelligence and independent nature of huskies, and the nervousness of chihuahuas.

And the fact that if you want to partake in an exercise in frustration, try to housebreak a cocker spaniel.

If you take the time to read the original paper -- highly recommended, because it's amazingly cool -- you'll get to see the final "family tree" of dog breeds and see who's related to whom.

Now y'all'll have to excuse me, because Guinness wants to go outside and play.  I wonder what gene controls the trait of Wanting To Retrieve Tennis Balls For Hours.  Because whatever it is, I think Guinness has like fifty copies of it.

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In vino veritas

One of the best explanations of how modern evolutionary genomics is done is in the fourth chapter of Richard Dawkins's fantastic The Ancestor's Tale.  The book starts with humans (although he makes the point that he could have started with any other species on Earth), and tracks backwards in time to each of the points where the human lineage intersects with other lineages.  So it starts out with chapters about our nearest relatives -- bonobos and chimps -- and gradually progresses to more and more distantly-related groups, until by the last chapter we've united our lineage with every other life form on the planet.

In chapter four ("Gibbons"), he describes something of the methodology of how this is done, using as an analogy how linguists have traced the "ancestry" (so to speak) of the surviving copies of Chaucer's The Canterbury Tales, each of which have slight variations from the others.  The question he asks is how we could tell what the original version looked like; put another way, which of those variations represent alterations, and which were present in the first edition.

The whole thing is incredibly well done, in the lucid style for which Dawkins has rightly become famous, and I won't steal his thunder by trying to recap it here (in fact, you should simply read the book, which is wonderful from beginning to end).  But a highly oversimplified capsule explanation is that the method relies on the law of parsimony -- that the model which requires the fewest ad hoc assumptions is the most likely to be correct.  When comparing pieces of DNA from groups of related species, the differences come from mutations; but if two species have different base pairs at a particular position, which was the original and which the mutated version -- or are both mutations from a third, different, base pair at that position?

The process takes the sequences and puts together various possible "family trees" for the DNA; the law of parsimony states that the likeliest one is the arrangement that requires the fewest de novo mutations.  To take a deliberately facile example, suppose that within a group of twelve related species, in a particular stretch of DNA, eleven of them have an A/T pair at the third position, and the twelfth has a C/G pair.  Which is more likely -- that the A/T was the base pair in the ancestral species and species #12 had a mutation to C/G, or that C/G was the base pair in the ancestral species and species #1-11 all independently had mutations to A/T?

Clearly the former is (hugely) more likely.  Most situations, of course, aren't that clear-cut, and there are complications I won't go into here, but that's the general idea.  Using software -- none of this is done by hand any more -- the most parsimonious arrangement is identified, and in the absence of any evidence to the contrary, is assumed to be the lineage of the species in question.

This is pretty much how all cladistics is done.  Except in cases where we don't have DNA evidence -- such as with prehistoric animals known only from fossils -- evolutionary biologists don't rely much on structure any longer.  As Dawkins himself put it, "Even if we were to erase every fossil from the Earth, the evidence for evolution from genetics alone would be overwhelming."

The reason this comes up is a wonderful study that came out this week in Science that uses these same techniques to put together the ancestry of all the modern varieties of grapes.  A huge team at the Karlsruher Institut für Technologie and the Chinese Yunnan Agricultural University analyzed the genomes of 3,500 different grapevines, including both wild and cultivated varieties, and was able to track their ancestry back to the southern Caucasus in around 11,000 B.C.E. (meaning that grapes seem to have been cultivated before wheat was).  From there, the vine rootstocks were carried both ways along the Silk Road, spreading all the way from China to western Europe in the process.

[Image licensed under the Creative Commons Ian L, Malbec grapes, CC BY 2.0]

There are a lot of things about this study that are fascinating.  First, of course, is that we can use the current assortment of wild and cultivated grape vines to reconstruct a family tree that goes back thirteen thousand years -- and come up with a good guess about where the common ancestor of all of them lived.  Second, though, is the more general astonishment at how sophisticated our ability to analyze genomes has become.  Modern genomic analysis has allowed us to create family trees of all living things that boggle the mind -- like this one:

[Image licensed under the Creative Commons Laura A. Hug et al., A Novel Representation Of The Tree Of Life, CC BY 4.0]

These sorts of analyses have overturned a lot of our preconceived notions about our place in the world.  It upset a good many people, for some reason, when it was found we have a 98.7% overlap in our DNA with our nearest relatives (bonobos) -- that remaining 1.3% accounts for the entire genetic difference between yourself and a bonobo.  People were so used to believing there was a qualitative biological difference between humans and everything other living thing that to find out we're so closely related to apes was a significant shock.  (It still hasn't sunk in for some people; you'll still hear the phrase "human and animal" used, as if we weren't ourselves animals.)

Anyhow, an elegant piece of research on the ancestry of grapes is what got all this started, and after all of my circumlocution you probably feel like you need a glass of wine.  Enjoy -- in vino veritas, as the Romans put it, even if they may not have known as much about where their vino originated as we do.

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The evolution of Little Red Riding Hood

Every once in a while, I'll run across a piece of scientific research that is so creative and clever that it just warms my heart, and I felt this way yesterday when I stumbled onto a link to the article in PLoS ONE called "The Phylogeny of Little Red Riding Hood," by Jamshid Tehrani of the University of Bristol.

The reason I was delighted by Tehrani's paper is that it combines two subjects I love -- evolutionary biology and mythology and folklore.  The gist of what Tehrani did is to use a technique most commonly used to assemble species into "star diagrams" -- cladistic bootstrap analysis -- to analyze worldwide versions of the "Little Red Riding Hood" story to see to what degree a version in (for example) Senegal was related to one in Germany.

Cladistic bootstrap analysis generates something called a "star diagram" -- not, generally, a pedigree or family tree, because we don't know the exact identity of the common ancestor to all of the members of the tree, all we can tell is how closely related current individuals are.  Think, for example, of what it would look like if you assembled the living members of your family group this way -- you'd see clusters of close relatives linked together (you, your siblings, and your first cousins, for example) -- and further away would be other clusters, made up of more distant relatives grouped with their near family members.

So Tehrani did this with the "Little Red Riding Hood" story, by looking at the similarities and differences, from subtle to major, between the way the tale is told in different locations.  Apparently there are versions of it all over the world -- not only the Grimm Brothers Fairy Tales variety (the one I know the best), but from Africa, the Middle East, India, China, Korea, and Japan.  Oral transmission of stories is much like biological evolution; there are mutations (people change the story by misremembering it, dropping some pieces, embellishment, and so on) and there is selection (the best versions, told by the best storytellers, are more likely to be passed on).  And thus, the whole thing unfolds like an evolutionary lineage.

In Tehrani's analysis, he found three big branches -- the African branch (where the story is usually called "The Wolf and the Kids"), the East Asian branch ("Tiger Grandmother"), and the European/Middle Eastern Branch ("Little Red Riding Hood," "Catterinella," and "The Story of Grandmother").  (For the main differences in the different branches, which are fascinating but too long to be quoted here in full, check out the link to Tehrani's paper.)

Put all together, Tehrani came up with the following cladogram:

WK = "The Wolf and the Kids," TG = "Tiger Grandmother," "Catt" = "Catterinella," GM = "The Story of Grandmother," and RH = "Little Red Riding Hood;" the others are less common variations that Tehrani was able to place on his star diagram.

The whole thing just makes me very, very happy, and leaves me smiling with my big, sharp, wolflike teeth.

Pure research has been criticized by some as being pointless, and this is a stance that I absolutely abhor.  There is a completely practical reason to support, fund, and otherwise encourage pure research -- and that is, we have no idea yet what application some technique or discovery might have in the future.  A great deal of highly useful, human-centered science has been uncovered by scientists playing around in their labs with no other immediate goal than to study some small bit of the universe.  Further, the mere application of raw creativity to a problem -- using the tools of cladistics, say, to analyze a folk tale -- can act as an impetus to other minds, elsewhere, encouraging them to approach the problems we face in novel ways.

But I think it's more than that.  The fundamental truth here is that human mind needs to be exercised.  The "what good is it?" attitude is not only anti-science, it is anti-intellectual.  It devalues inquiry, curiosity, and creativity.  It asks the question "how does this benefit humanity?" in such a way as to imply that the sheer joy of comprehending deeply the world around us is not a benefit in and of itself.

It may be that Tehrani's jewel of a paper will have no lasting impact on humanity as a whole.  I'm perfectly okay with that, and I suspect Tehrani would be, as well.  We need to make our brains buckle down to the "important stuff," yes; but we also need to let them out to play sometimes, a lesson that the men and women currently overseeing our educational system need to learn.  In a quote that seems unusually apt, considering the subject of Tehrani's research, Albert Einstein said: "I am enough of an artist to draw freely upon my imagination.  Imagination is more important than knowledge.  Knowledge is limited.  Imagination encircles the world." 

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I was an undergraduate when the original Cosmos, with Carl Sagan, was launched, and being a physics major and an astronomy buff, I was absolutely transfixed.  Me and my co-nerd buddies looked forward to the new episode each week and eagerly discussed it the following day between classes.  And one of the most famous lines from the show -- ask any Sagan devotee -- is, "If you want to make an apple pie from scratch, first you must invent the universe."

Sagan used this quip as a launching point into discussing the makeup of the universe on the atomic level, and where those atoms had come from -- some primordial, all the way to the Big Bang (hydrogen and helium), and the rest formed in the interiors of stars.  (Giving rise to two of his other famous quotes: "We are made of star-stuff," and "We are a way for the universe to know itself.")

Since Sagan's tragic death in 1996 at the age of 62 from a rare blood cancer, astrophysics has continued to extend what we know about where everything comes from.  And now, experimental physicist Harry Cliff has put together that knowledge in a package accessible to the non-scientist, and titled it How to Make an Apple Pie from Scratch: In Search of the Recipe for our Universe, From the Origin of Atoms to the Big Bang.  It's a brilliant exposition of our latest understanding of the stuff that makes up apple pies, you, me, the planet, and the stars.  If you want to know where the atoms that form the universe originated, or just want to have your mind blown, this is the book for you.

[Note: if you purchase this book using the image/link below, part of the proceeds goes to support Skeptophilia!]

Bird trees

I'm a birdwatcher, which in my specific case kind of crosses the line into a mild mental illness.  I've traveled all over the world to see new birds, which is kind of cool, but it's also led me to do stuff like standing calf-deep in the snow, in far-below-freezing temperatures and gale-force winds, to see a rare species of duck that happened to end up for some reason in nearby Cayuga Lake in midwinter.  From the standpoint of seeing a bird species I'd never seen before, it was a great day.

It was a somewhat less-than-great day with respect to frostbite, hypothermia, and people in passing (heated) cars rolling down their windows to yell "What the hell is wrong with you?"

The reason this all comes up because of how excited I am about a recent release of new information by the Bird 10,000 Genomes Project, which has as its fairly lofty goal the sequencing of the genomes for all ten-thousand-plus species of birds currently living on the Earth.

The cool thing about genetic information to determine relationships is that it's much more accurate than relying on such obvious characteristics as external appearance or behavior.  Through genetic analysis, the B10K Genomes Project, as it's affectionately known, has found the following surprises:

• Flamingos are fairly closely related to grebes, a family of small diving water birds, and both as a group are more closely related to pigeons than to any other species of aquatic bird.
• Likewise, the bizarre flightless dodos, now extinct but once common on two remote islands in the Indian Ocean, are most closely related to pigeons.
• The three main groups of birds that regularly prey on mammals -- hawks and eagles, owls, and falcons -- aren't closely related at all, and their similarities seem to have developed through convergent evolution.
• Despite superficial similarities in appearance and behavior, vultures in North and South America are only very distantly related to vultures in Africa and Europe.
• Hummingbirds, swifts, and nightjars (such as the more-often-seen-than-heard whippoorwill) are all on the same branch of the bird family tree.  A different branch includes such disparate groups as loons, pelicans, albatrosses... and penguins.
• Emus, ostriches, and kiwis -- flightless species that are on the same basic branch, a group called ratites -- all descend from a common ancestor that could fly, and apparently evolved flightlessness independently.

Here's a circular representation of what we know so far, with illustrations of a few selected species:

Clockwise from the top: golden eagle, thick-billed murre, ruddy turnstone, white-bellied storm petrel, western bronze ground dove, squirrel cuckoo, Anna’s hummingbird, marbled wood quail, little spotted kiwi, redwing blackbird, akiapolaau, black sunbird, wall creeper, Cape rockjumper, chestnut wattle-eye, chowchilla, Amazonian royal flycatcher, rosy-faced lovebird and keel-billed toucan.  [Image courtesy of S. Feng et al./Nature, 2020; Illustrations by Jon Fjeldså]

So the study is pretty cool, expanding greatly what we know about the feathered dinosaurs we see flitting about every day.  As the B10K Genome Project site puts it:

The B10K project will allow the completion of a genomic level tree of life of the entire living avian class, decode the link between genetic variation and phenotypic variation, uncover the correlation of genetic evolutionary and biogeographical and biodiversity patterns across a wide-range of species, evaluate the impact of various ecological factors and human influence on species evolution, and unveil the demographic history of an entire class of organisms...  We envision this project will have significant scientific and public impact that will change our understanding of avian biology and evolution, which in turn will affect our understanding of other organisms and open doors to new areas of research.

I'm really looking forward to seeing what else they uncover.  It might not explain my obsession with trying to see every bird there is -- something a friend of mine calls "Pokémon for Adults" -- but it certainly will give me something new to think about when I'm shivering in the snow looking for rare ducks.

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This week's Skeptophilia book-of-the-week is one that has raised a controversy in the scientific world: Ancient Bones: Unearthing the Astonishing New Story of How We Became Human, by Madeleine Böhme, Rüdiger Braun, and Florian Breier.

It tells the story of a stupendous discovery -- twelve-million-year-old hominin fossils, of a new species christened Danuvius guggenmosi.  The astonishing thing about these fossils is where they were found.  Not in Africa, where previous models had confined all early hominins, but in Germany.

The discovery of Danuvius complicated our own ancestry, and raised a deep and difficult-to-answer question; when and how did we become human?  It's clear that the answer isn't as simple as we thought when the first hominin fossils were uncovered in Olduvai Gorge, and it was believed that if you took all of our millennia of migrations all over the globe and ran them backwards, they all converged on the East African Rift Valley.  That neat solution has come into serious question, and the truth seems to be that like most evolutionary lineages, hominins included multiple branches that moved around, interbred for a while, then went their separate ways, either to thrive or to die out.  The real story is considerably more complicated and fascinating than we'd thought at first, and Danuvius has added another layer to that complexity, bringing up as many questions as it answers.

Ancient Bones is a fascinating read for anyone interested in anthropology, paleontology, or evolutionary biology.  It is sure to be the basis of scientific discussion for the foreseeable future, and to spur more searches for our relatives -- including in places where we didn't think they'd gone.

[Note: if you purchase this book using the image/link below, part of the proceeds goes to support Skeptophilia!]

Reptilian splits

One of my favorite lectures in my AP Biology class was about how there's no such thing as a reptile.

If you took your last biology class before about 1995, you probably learned about Class Reptilia, containing turtles, lizards, snakes, crocodiles, alligators, and a few other assorted groups.  The class was defined by having dry, scaly skin, internal fertilization, "amniote" eggs with shells, and hearts that had incomplete septa (the wall down the center that separates the oxygenated left side from the deoxygenated right side).

Well, the last one wasn't 100% true, and that should have been a clue to what was going on.  Crocodiles and alligators have four-chambered hearts, and are also partial endotherms -- they show some capacity for internally regulating their own body temperatures, just as birds and mammals do.

It was genetic testing that finally settled who was related to whom, and that was when a lot of us got a shock (not so much the evolutionary biologists, who kind of expected this was how it was gonna work out).  The word "reptile" has no real taxonomic significance, because it lumps together groups that really aren't very closely related, and excludes others that are closer.  Here's how this branch of Kingdom Animalia evolved:

As you can see from the diagram, the problem was birds.  Crocodiles are more closely related to birds than they are to lizards (despite superficial appearance); and if you throw dinosaurs into the mix, it becomes even clearer, because birds are dinosaurs.

Think about that the next time you feed the chickadees.

So if you throw all the reptiles together, by the rules of cladistic taxonomy, you'd have to include birds, and nobody much wanted to call birds reptiles.  So the entire Class Reptilia was broken up, now as three different classes: Lepidosauria (lizards, snakes, and the oddball tuatara of New Zealand), Testudines (turtles), and Crocodilia (obviously crocodiles et al.).  Birds have their own class (Aves).

But what this brings up is how such different-looking animals as turtles and snakes evolved from a common ancestor.  The differences between the different groups of reptiles is pretty dramatic.  The explanation has usually been that it was adaptive radiation, a phenomenon that deserves some explanation.

Adaptive radiation is when a group undergoes rapid diversification to fill many available niches.  The classic example is Darwin's finches, a group of birds on the Galapagos Islands, which descend from a common ancestral group that split up to occupy different niches because of bill size and strength (which determines what they can eat).  That's a pretty drastic oversimplification, but it captures the essence: many available niches, and a population with sufficient genetic diversity to split up and specialize into those niches.

Because of the "many available niches" part, adaptive radiation is most common under two scenarios: a population colonizing a previously-uninhabited territory (as with Darwin's finches), and remnant populations left after a major extinction.  This was what was thought to have powered the split-up of the reptiles -- the "Great Dying," the Permian-Triassic extinction of 252 million years ago that by some estimates wiped out 95% of life on Earth.

Nota bene: there is fairly good evidence that the trigger for the Permian-Triassic extinction was hypercapnia -- a sudden increase in atmospheric carbon dioxide.  This led to drastic warming of the atmosphere and ocean acidification.  The cause -- according to a paper that just came out two weeks ago in the journal Geology -- was massive burning of coal.  Sound familiar?  In this case the cause was natural; it's thought to have been triggered by massive volcanism.  But the end result was the same as what we're doing now by runaway use of fossil fuels.  I'd like to think this would be a cautionary note, but the world's leaders seem to specialize in ignoring science unless it can directly make them money and/or keep them in power, so I'm not holding my breath.

But back to the reptiles.  The study that triggered this post, which came out this week in Nature Communications, points out the flaw in the argument that the adaptive radiation of reptiles was due to the Permian-Triassic extinction.  According to recent analysis, the split up was already well underway before the extinction started.  And the extinction itself was sudden, at least in geological terms; from start to catastrophic finish, the whole event took about a hundred thousand years.  In geological strata, this length of time is a very, very narrow band.

Plus, the different groups of reptiles individually show drastically different rates of specialization. "Our findings suggest that the origin of the major reptile groups, both living and extinct, was marked by very fast rates of anatomical change, but that high rates of evolution do not necessarily align with taxonomic diversification," said study lead author Tiago Simões of Harvard University, in an interview in Phys.Org.  "Our results also show that the origin of snakes is characterized by the fastest rates of anatomical change in the history of reptile evolution -- but that this does not coincide with increases in taxonomic diversity [as predicted by adaptive radiations] or high rates of molecular evolution."

The end result of the study is that the cause of the adaptive radiation is unknown.  It probably was pushed along by the mass extinction -- the species that survived the hypercapnia and the resulting environmental devastation were set up to have a whole empty world to colonize.  But what was driving the split-up of the group prior to the extinction itself?

Unknown, but the current study shows that clearly the adaptive radiation had already started.

I love puzzles like this.  In science, there are almost always more questions than answers, and every answer brings up new questions.  But another feature of science is the conviction that there is an answer even if we don't currently know what it is.  And chances are, further study will elucidate what exactly was going on -- and what led to the fragmentation of a group that now, over 250 million years later, comprises some of the best-known and most familiar critters who have ever walked (or flown across) the Earth.

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This week's Skeptophilia book recommendation of the week is for anyone who likes quick, incisive takes on scientific topics: When Einstein Walked with Gödel: Excursions to the Edge of Thought by the talented science writer Jim Holt.

When Einstein Walked with Gödel is a series of essays that explores some of the deepest and most perplexing topics humanity has ever investigated -- the nature of time, the implications of relativity, string theory, and quantum mechanics, the perception of beauty in mathematics, and the ultimate fate of the universe.  Holt's lucid style brings these difficult ideas to the layperson without blunting their scientific rigor, and you'll come away with a perspective on the bizarre and mind-boggling farthest reaches of science.  Along the way you'll meet some of the key players in this ongoing effort -- the brilliant, eccentric, and fascinating scientists themselves.

It's a wonderful read, and anyone who is an aficionado of the sciences shouldn't miss it.

[Note: if you purchase this book using the image/link below, part of the proceeds goes to support Skeptophilia!]

All in the family

Over my nearly thirty years of teaching AP Biology, one of the topics that changed the most was taxonomy.

This might come as a surprise, given the changes in fields such as genetics, but honestly the two are closely related.  When I started my career, classification of species was done primarily by morphology (shape and structure), and the identification of which characteristics of an organism were plesiomorphies (structures inherited from, and therefore shared with, the ancestral species) and which were apomorphies (structures that were innovations unique to a single branch of the family tree).

One of many difficulties with this approach is that useful innovations can evolve more than once, and therefore aren't necessarily indicative of common ancestry.  This process, called convergent or parallel evolution, can generate some amazingly similar results, the most striking of which is the flying squirrel (a rodent) and the sugar glider (a marsupial), which look nearly identical at a quick glance (even a longer one, honestly).  To be fair, the fact that the two are not very closely related would be evident on any kind of moderately careful analysis, where giveaways like tooth structure and the presence of a pouch in the female sugar gliders would be enough to show they weren't on the same branch of the mammalian family tree.

Southern flying squirrel (top) [Image is in the Public Domain] and sugar glider (bottom) [Image licensed under the Creative Commons Joseph C Boone, Sugar Glider JCB, CC BY-SA 4.0]

But sometimes it's more difficult than that, and more than once taxonomists have created arrangements of the descent of groups of species only to find out that further study shows the original placement to be wrong.  As one of many examples, take the two groups of large-eyed nocturnal primates from southern and southeastern Asia, the lorises and tarsiers.  Based on habits and range, it's understandable that they were lumped together as "prosimians" on the same branch of the primate tree, but recent study has found the lorises are closely related to lemurs, and tarsiers are closer to monkeys and apes -- despite the superficial similarity.

Slow loris [Image licensed under the Creative Commons David Haring / Duke Lemur Center, Sublingua of a slow loris 001, CC BY-SA 3.0]

 

Tarsier [Image licensed under the Creative Commons yeowatzup, Tarsier Sanctuary, Corella, Bohol (2052878890), CC BY 2.0]

These revisions, and the sometimes surprising revelations they provide, have largely come from a change in how taxonomy is done.  Nearly all classification is now based upon genetics, not structure (although certainly structure plays a role in who we might initially hypothesize is related to whom).  But when it comes down to a fight between morphology and genetics, genetics always wins.  And this has forced us to change how we look at biological family trees -- especially when genetic evidence is obtained where it was previously absent.

This all comes up because of a discovery of intact DNA in a fossil of a primate much closer to us than the tarsiers and lorises -- a species from our own genus called Homo antecessor.  The species name suggests it was one of our direct ancestors, which is a little alarming because there's good evidence it was cannibalistic -- bones of the species found in Spain showed clear evidence of butchering for meat.

Now, however, the recovery of DNA from a tooth of an H. antecessor fossil -- at 800,000 years of age, the oldest DNA ever recovered from a hominid fossil -- has shown that it probably wasn't our ancestor after all, but a "sister clade," one that left no descendants.  (Bigfoot and the Yeti notwithstanding.)  The study was the subject of a paper in Nature last week, authored by a team led by Frido Welker of the University of Copenhagen, and required yet another reconfiguring of our own family tree.  The authors write:

The phylogenetic relationships between hominins of the Early Pleistocene epoch in Eurasia, such as Homo antecessor, and hominins that appear later in the fossil record during the Middle Pleistocene epoch, such as Homo sapiens, are highly debated.  For the oldest remains, the molecular study of these relationships is hindered by the degradation of ancient DNA.  However, recent research has demonstrated that the analysis of ancient proteins can address this challenge.  Here we present the dental enamel proteomes of H. antecessor from Atapuerca (Spain) and Homo erectus from Dmanisi (Georgia), two key fossil assemblages that have a central role in models of Pleistocene hominin morphology, dispersal and divergence.  We provide evidence that H. antecessor is a close sister lineage to subsequent Middle and Late Pleistocene hominins, including modern humans, Neanderthals and Denisovans.  This placement implies that the modern-like face of H. antecessor—that is, similar to that of modern humans—may have a considerably deep ancestry in the genus Homo, and that the cranial morphology of Neanderthals represents a derived form.

I find that last bit the most interesting, because it turns on its head our usual sense of being the Pinnacles of Evolution, clearly the most highly evolved (whatever the hell that actually means) species on the planet, definitely more advanced in all respects than those brute Neanderthals.  What this study suggests is that the flatter face of the Neanderthals is actually the apomorphy -- the more recently-evolved, "derived" characteristic -- and our narrower, more protruding faces are a plesiomorphy, inherited from our older ancestors.

This kind of stuff is why I'm endlessly interested in evolutionary biology -- as we find more data and develop new techniques, we refine our models, and in some cases have to overturn previously accepted conventional wisdom.  But that's what science is about, isn't it?  Basing your model on the best evidence you've got, and revising it if you get new and conflicting evidence.

 Just as well in this case.  One less cannibal in the family tree.  Not that there aren't probably others, but my genealogy already contains some sketchy enough characters.  No need to add more.

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This week's Skeptophilia book recommendation of the week is brand new -- only published three weeks ago.  Neil Shubin, who became famous for his wonderful book on human evolution Your Inner Fish, has a fantastic new book out -- Some Assembly Required: Decoding Four Billion Years of Life, from Ancient Fossils to DNA.

Shubin's lucid prose makes for fascinating reading, as he takes you down the four-billion-year path from the first simple cells to the biodiversity of the modern Earth, wrapping in not only what we've discovered from the fossil record but the most recent innovations in DNA analysis that demonstrate our common ancestry with every other life form on the planet.  It's a wonderful survey of our current state of knowledge of evolutionary science, and will engage both scientist and layperson alike.  Get Shubin's latest -- and fasten your seatbelts for a wild ride through time.

The family tree

One of the things I find endlessly fascinating about evolution is that we can use information we have in the present to infer what happened in the (very) distant past.

And I'm not even talking about fossils, here, as interesting as they are.  As Richard Dawkins points out, even if the entire fossil record ceased to exist, the evidence for evolution would still be overwhelming.  What I'm thinking about is the use of DNA to determine relationships between current species, and from that theorize about when their most recent common ancestor lived, and even what it might have looked like.

This comes up because of a recent paper in Nature that analyzed the genomes of over a thousand different species of plants and algae to construct the most detailed and accurate cladogram (which you can think of as a family tree) of the entire kingdom that has ever been created.  There are an estimated 500,000 species of plants currently in existence, so while this is still using a partial data set, it's pretty damned impressive.

"Some species began to emerge and evolve several hundreds of millions of years ago," said plant physiologist Professor Marcel Quint from the Institute of Agricultural and Nutritional Sciences at Martin Luther University Halle-Wittenberg, in an interview with Science Daily.  "However, today we have the tools to look back and see what happened at that time...   Some of these gene families have duplicated over the course of millions of years.  This process might have been a catalyst for the evolution of plants.  Having significantly more genetic material might unleash new capacities and completely new characteristics."

The results, as you might expect, provided a few surprises.  "We used to think that the greatest genetic expansion had occurred during the transition to flowering plants," said Martin Porsch, also from MLU-Halle-Wittenberg.  "After all, this group contains the majority of existing plant species today.  However, the new data reveal that the genetic foundations for this expansion in biodiversity had been laid much earlier.  The transition from aquatic to terrestrial plants was the starting point for all further genetic developments.  This development was the greatest challenge for plants, and so they needed more genetic innovations than ever before."

"We found an enormous increase in genetic diversity at the time of this transition, after that it reached a plateau," added Ivo Grosse, bioinformatician at MLU-Halle-Wittenberg, who co-authored the paper.  "From this time on, almost all of the genetic material was available to drive evolutionary progress and generate the biodiversity we see today."

So without further ado, here's their cladogram:

It confirmed something that I found fascinating when I first heard about it, back in the early 2000s -- that the division of flowering plants into "monocots" and "dicots" -- familiar to every high school biology student -- needed to be revisited, because "dicot" isn't a monophyletic clade -- all descended from a single ancestor that includes no other descendants.  It was found that the peculiar New Zealand species Amborella was technically a dicot (networked leaf veins, flower parts in fours or fives, two seed leaves) but was far more distantly related to other dicots than monocots (such as grasses, lilies, palms, and so on) were.

Amborella trichopoda [Image licensed under the Creative Commons Scott Zona from USA (original upload author), Amborella trichopoda (3065968016) fragment, CC BY 2.0]

When it was later found that the same was true of water lilies, it clued the geneticists in that there was something seriously amiss with our understanding of the family tree of plants.

So the new cladogram supports the older research, putting Amborella, water lilies, lotuses, and star anise as outgroups within the entire phylum of flowering plants; a self-contained clade with all the monocots next; and the rest of the dicots scattered along the remainder of the tree.

I know I'm a science nerd, and a little over-enthusiastic about genetics sometimes, but I think this research is amazingly cool.  The idea that we could look at a plant's DNA, here in 2019, and infer its relationship with other species from which it branched off hundreds of millions of years ago, is boggling.  It makes me wonder what other surprises are out there in the DNA of the nine-million-odd species of life on Earth -- and also realize that when it comes to understanding the other denizens with which we share the planet, we've only barely begun.

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This week's Skeptophilia book of the week is brand new; Brian Clegg's wonderful Dark Matter and Dark Energy: The Hidden 95% of the Universe.  In this book, Clegg outlines "the biggest puzzle science has ever faced" -- the evidence for the substances that provide the majority of the gravitational force holding the nearby universe together, while simultaneously making the universe as a whole fly apart -- and which has (thus far) completely resisted all attempts to ascertain its nature.

Clegg also gives us some of the cutting-edge explanations physicists are now proposing, and the experiments that are being done to test them.  The science is sure to change quickly -- every week we seem to hear about new data providing information on the dark 95% of what's around us -- but if you want the most recently-crafted lens on the subject, this is it.

[Note: if you purchase this book from the image/link below, part of the proceeds goes to support Skeptophilia!]

Going to the dogs

I am the proud owner of two dogs, both rescues, who are at this point basically members of the family whose contributions to the household consist of barking at the UPS guy, sleeping most of the day, getting hair all over everything, and making sure that we get our money's worth out of the carpet steamer we bought five years ago.

First, there's Lena the Wonder-Hound:

And her comical sidekick, Grendel:

Both of them are sweet and affectionate and spoiled absolutely rotten.  Lena's ancestry is pretty clear -- she's 100% hound, probably mostly Blue-tick Coonhound, Redbone, and Beagle -- but Grendel's a bit of a mystery.  Besides his square face and coloration, other significant features are: (1) a curly tail; (2) a thick undercoat; and (3) a tendency to snore.  This last has made us wonder if he has some Pug or Bulldog in his background somewhere, but that's only speculation.

This all comes up because of a recent delightful study in one of my favorite fields, cladistics.  The idea of cladistics is to create a tree of descent for groups of species based on most recent common ancestry, as discerned from overlap in DNA sequences.  And a group of researchers -- Heidi G. Parker, Dayna L. Dreger, Maud Rimbault, Brian W. Davis, Alexandra B. Mullen, Gretchen Carpintero-Ramirez, and Elaine A. Ostrander of the Comparative Genomics Branch of the National Human Genome Research Institute -- have done this for 161 breeds of dog.

The authors write:

The cladogram of 161 breeds presented here represents the most diverse dataset of domestic dog breeds analyzed to date, displaying 23 well-supported clades of breeds representing breed types that existed before the advent of breed clubs and registries.  While the addition of more rare or niche breeds will produce a denser tree, the results here address many unanswered questions regarding the origins of breeds.  We show that many traits such as herding, coursing, and intimidating size, which are associated with specific canine occupations, have likely been developed more than once in different geographical locales during the history of modern dog.  These data also show that extensive haplotype sharing across clades is a likely indicator of recent admixture that took place in the time since the advent of breed registries, thus leading to the creation of most of the modern breeds.  However, the primary breed types were developed well before this time, indicating selection and segregation of dog populations in the absence of formal breed recognition.  Breed prototypes have been forming through selective pressures since ancient times depending on the job they were most required to perform.  A second round of hybridization and selection has been applied within the last 200 years to create the many unique combinations of traits that modern breeds display.  By combining genetic distance relationships with patterns of haplotype sharing, we can now elucidate the complex makeup of modern dogs breeds and guide the search for genetic variants important to canine breed development, morphology, behavior, and disease.

Which is pretty cool.  What I found most interesting about the cladogram (which you can see for yourself if you go to the link provided above) is that breeds that are often clustered together, and known by the same common name -- such as "terrier" -- aren't necessarily closely related.  This shouldn't be a surprise, of course; all you have to do is look at the relationships between birds called "buntings" or "sparrows" or "tanagers" to realize that common names tell you diddly-squat about actual genetic distance.  But it was still surprising to find that (for example) Bull Terriers and Staffordshire Terriers are more closely related to Bulldogs and Mastiffs than they are to (for example) Scottish Terriers; that Corgis are actually related to Greyhounds; and that Schnauzers, Pugs, Pomeranians, and Schipperkes are all on the same clade.  The outgroup (most distantly related branch) of the entire clade is the peculiar Basenji, a Central African breed with a strange, yodel-like bark, a curly tail, and pointed ears, whose image has been recorded almost unchanged all the way back to the time of the ancient Egyptians.

Anyhow, it's an elegant bit of research, and sure to be of interest to any other dog owners in the studio audience.  Me, I'm wondering where Grendel fits into the cladogram.  Considering his peculiar set of traits, he might have a branch all his own, and give the Basenji a run for its money as the oddest breed out there.

The evolution of the anti-evolutionists

Sometimes I see a piece of scientific research that is so brilliant, so elegant, all I can do is sit back in awestruck appreciation.

Such was my reaction to Nicholas J. Matzke's paper in Science this week entitled, "The Evolution of Antievolution Policies after Kitzmiller v. Dover."  And if you're wondering... yes, he did what it sounds like.

He used the techniques of evolutionary biology to show how anti-evolution policy has undergone descent with modification.

I read the paper with a delighted, and somewhat bemused, grin, blown away not only by how well it worked, but how incredibly clever the idea was.  What Matzke did was to analyze the text of all of the dozens of bills proposed since 2004 that try to shoehorn religious belief into the public school science classroom, and generate a phylogenetic tree for them -- in essence, a diagram summarizing how they are related to each other, and how they have changed.

In other words, a cladistic tree of evolutionary descent.

"Creationism is getting stealthier in the wake of legal defeats, but techniques from the study of evolution reveal how creationist legislation is evolving," Matzke said in an interview.  "It is one thing to say that two bills have some resemblances, and another thing to say that bill X was copied from bill Y with greater than 90 percent probability.  I do think this research strengthens the case that all of these bills are of a piece—they are all ‘stealth creationism,’ and they all have either clear fundamentalist motivations, or are close copies of bills with such motivations."

"They are not terribly intelligently designed," Matzke added.  "Some of the bills don’t make sense, they’ve been copied from another state and changed without thought."

He linked the bills to each other by doing statistical analysis of patterns in the text, much as evolutionary biologists use patterns in the DNA of related organisms, and arranged them into a cladistic tree using the "principle of maximum parsimony," which (simply put) is the arrangement that requires you to make the least ad hoc assumptions.

So without further ado, here is Matzke's tree linking 65 different, but related, pieces of legislation:

In particular, he was able to show where the documents incorporated language from a 2006 anti-evolution proposal in Ouachita Parish, Louisiana, and how subsequent generations had pieces of it remaining, often -- dare I say -- mutated, but still recognizable.

"Successful policies have a tendency to spread," Matzke said. "Every year, some states propose these policies, and often they are only barely defeated.  And obviously, sometimes they pass, so hopefully this article will help raise awareness of the dangers of the ongoing situation."

So when there are iterations that are better fit to the environment, in the sense that they went further in the court systems before being defeated or (hard though this is to fathom) were actually approved, the anti-evolutionists passed those versions around to other states, while less-successful models were outcompeted and become extinct.

There's a name for that process, isn't there?  Give me a moment, I'm sure it'll come to me.

Okay, it's not that I think this paper will make much difference amongst the creationists and supporters of intelligent design.  They don't spend much time reading Science, I wouldn't suppose.  But even so, this is a coup -- using the techniques of cladistic analysis to illustrate the relationships between bills designed to force public school students to learn that cladistic analysis doesn't work.

I can't help but think that Darwin would be proud.