The skull in the cave

"If humans came from monkeys, why are there still monkeys?"

If there is one phrase that makes me want to throw a chair across the room, it's that one.  (Oh, that and, "The Big Bang means that nothing exploded and became everything.")  Despite the fact that a quick read of any of a number of reputable sites about evolution would make it clear that the question is ridiculous, I still see it asked in such a way that the person evidently thinks they've scored some serious points in the debate.  My usual response is, "My ancestors came from France.  Why are there still French people?"  But the equivalence of the two seems to go so far over their heads that it doesn't even ruffle their hair.

Of course, not all the blame lies with the creationists and their ilk.  How many times have you seen, in otherwise accurate sources, human evolution depicted with an illustration like this?

It sure as hell looks like each successive form completely replaced the one before it, so laypeople are perhaps to be excused for coming away with the impression that this is always the way evolution works.  In fact, cladogenesis (branching evolution) is far and away the more common pattern, where species split over and over again, with different branches evolving at different rates or in different directions, and some of them becoming extinct.

If you're curious, this is the current best model we have for the evolution of hominins:

The cladogenesis of the hominin lineage; the vertical axis is time in millions of years before present  [Image licensed under the Creative Commons Dbachmann, Hominini lineage, CC BY-SA 4.0]

The problem also lies with the word species, which is far and away the mushiest definition in all of biological science.  As my evolutionary biology professor put it, "The only reason we came up with the idea of species as being these little impermeable containers is that we have no near relatives."  In fact, we now know that many morphologically distinct populations, such as the Neanderthals and Denisovans, freely interbred with "modern" Homo sapiens.  Most people of European descent have Neanderthal markers in their DNA; when I had my DNA sequenced a few years ago, I was pleased to find out I was above average in that regard, which is undoubtedly why I like my steaks medium-rare and generally run around half-naked when the weather is warm.  Likewise, many people of East Asian, Indigenous Australian, Native American, and Polynesian ancestry have Denisovan ancestry, evidence that those hard-and-fast "containers" aren't so water-tight after all.

The reason all this comes up is because of a new study of the "Petralona Skull," a hominin skull found covered in dripstone (calcium carbonate) in a cave near Thessaloniki, Greece.  The skull has been successfully dated to somewhere between 277,000 and 539,000 years ago -- the uncertainty is because of estimates in the rate of formation of the calcite layers.

The Petralona Skull  [Image licensed under the Creative Commons Nadina / CC BY-SA 3.0]

Even with the uncertainty, this range puts it outside of the realm of possibility that it's a modern human skull.  Morphologically, it seems considerably more primitive than typical Neanderthal skulls, too.  So it appears that there was a distinct population of hominins living in southern Europe and coexisting with early Neanderthals -- one about which paleontologists know next to nothing.

Petralona Cave, where the skull was discovered [Image licensed under the Creative Commons Carlstaffanholmer / CC BY-SA 3.0]

So our family tree turns out to be even more complicated than we'd realized -- and there might well be an additional branch, not in Africa (where most of the diversification in hominins occurred) but in Europe.  

You have to wonder what life was like back then.  This would have been during the Hoxnian (Mindel-Riss) Interglacial, a period of warm, wet conditions, when much of Europe was covered with dense forests.  Fauna would have included at least five species of mammoths and other elephant relatives, the woolly rhinoceros, the cave lion, cave lynx, cave bear, "Irish elk" (which, as the quip goes, was neither), and the "hypercarnivorous" giant dog Xenocyon.  

Among many others.

So as usual, the mischaracterization of science by anti-science types misses the reality by a mile, and worse, misses how incredibly cool that reality is.  The more we find out about our own species's past, the richer it becomes.

I guess if someone wants to dismiss it all with a sneering "why are there still monkeys?", that's up to them.  But me, I'd rather keep learning.  And for that, I'm listening to what the scientists themselves have to say.

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Who benefits?

One of the most curious features of evolutionary biology is the cui bono principle.

Cui bono? is Latin for "who benefits?" and is an idea that found its first expression in courts of law.  If a crime is committed, look for who benefitted from it.  In evolutionary biology, it's adjuring the researcher to look for an evolutionary explanation for seemingly odd, even self-harming behavior.  Somebody, the principle claims, must benefit from it.

A while back, I did a post on one of the strangest and most complex examples of cui bono; the pathogen Toxoplasma gondii, a protist that primarily infects humans, cats, rats, and mice.  In each, it triggers changes in behavior, but different ones.  It turns rats and mice fearless, and in fact, makes them attracted to the smell of cat urine.  Infected cats are more gregarious and needing of physical contact (either with other cats or with humans).  Humans are more likely to be neurotic and anxious, impelling them to seek comfort from others... including, of course, their pets.  Each of these behaviors increases the likelihood of the pathogen jumping to another host.

That this behavioral engineering is successful can be gauged by the fact that by some estimates three billion people are Toxoplasma-positive.  Yes, that's "billion" with a "b."  As in, one third of the human population.  I can pretty much guarantee that if you've ever owned a cat, you are Toxoplasma-positive.

What effects that has had on the collective behavior of humanity, I'll leave you to ponder.

I just ran into another cool example of cui bono a couple of days ago -- well, cool if you're not a tomato grower.  This is another one for which the answer to "who benefits?" turns out to be a pathogen, this time a virus called tomato yellow leaf curl virus, which has the obvious effect on infected plants.

Uninfected (top) and infected (bottom) tomato plants [Image credit: Zhe Yan et al., MDPI]

The researchers, led by Peng Liang of the Chinese Academy of Agricultural Sciences, noticed a strange pattern; there's a pest of tomato plants (and many other crops) called the silverwing whitefly (Bemisia tabaci) that shows a distinct preference for tomato plants depending on who is infected with what.  If the whitefly is uninfected with the virus, it's preferentially attracted to infected tomato plants; if the whitefly is already infected, it shows a preference for uninfected plants.

So cui bono?  The virus, of course.  Infected whiteflies pass the virus along to uninfected plants, and uninfected whiteflies pick the virus up from infected plants.  Clever.  Insidious, but damn clever.

Liang et al. found that the virus accomplishes this by meddling with a chemical signal from tomato plants called β-myrcene.  The virus actually up-regulates the β-myrcene gene -- essentially, turning the volume up to eleven on β-myrcene's production -- which attracts uninfected whiteflies.  Once the virus gets into the whiteflies, it dials down the sensitivity of the whiteflies' β-myrcene receptors, making them less attracted to it.  

No need to be lured in by the infected plants if you're already infected yourself.

So like with Toxoplasma, we have here a microscopic pathogen that is manipulating the behavior of more than one host species.  It's fascinating but creepy.  You have to wonder what other features of our behavior are being steered by pathogens we might not even be aware of.  Recent studies have found that between five and eight percent of our DNA is composed of endogenous retroviruses -- scraps of DNA left behind by viruses in the genomes of our forebears, and which are suspected to have a role in multiple sclerosis and some forms of schizophrenia.

Who knows what else they might be doing?

If you find this whole topic a little shudder-inducing, you're not alone.  Science is like that sometimes.  If there's one thing I've learned, it's that the universe is under no compulsion to make me feel comfortable.  If you agree, sorry I put you through reading this.  Go cuddle with your kitty.

I'm sure that'll make you feel better.

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The most alien-looking place on Earth

George Wynn Brereton Huntingford was a British anthropologist, linguist, and historian, who traveled widely and was famed for his perceptive observations of societies and cultures.  And if you had to guess which of the many places he traveled during his 77 year life he labeled "the most alien-looking place on Earth," what would you come up with?

His vote was for the island of Socotra, a 132-by-42 kilometer island which lies at at the mouth of the Gulf of Aden.  To the north is the Arabian Sea; to the southwest, the Guardafui Channel separates it from the Horn of Africa.  It's nearer to Africa than to the Arabian Peninsula (232 versus 380 kilometers), but is controlled by the government of Yemen, as much as Yemen's political disaster is currently controlling anything.

Most of Socotra is desert to semi-desert:

[Image licensed under the Creative Commons Rod Waddington from Kergunyah, Australia, Socotra Island (11007223546), CC BY-SA 2.0]

Although it does get more rainfall than either Yemen and Oman (to the north) or Somalia (to the east), so it has a great deal more vegetation than its neighbors:

[Image licensed under the Creative Commons Rod Waddington from Kergunyah, Australia, Wadi, Socotra Island (14495206039), CC BY-SA 2.0]

The main reason for Socotra's uniqueness -- and why evolutionary biologist Lisa Banfield called it "the Galapagos of the Indian Ocean" -- isn't the climate; it's the fact that geologically, it's part of Africa.  During the Miocene Period, about twenty million years ago, Africa and the Arabian Peninsula were joined, but a rift formed that split the two, opening up the Gulf of Aden.  Socotra is a chunk of the Somali Plate that was torn loose and got separated from the rest of the land mass that now forms the easternmost part of Africa.  (Interestingly, the rifting has continued, joining up with a fault system that runs up north through the Red Sea and south into the East African Rift Zone, which one day will tear away a much huger chunk of Africa -- all the way down to Mozambique.)

The issue is that since Socotra's separation from Africa around twenty million years ago, it's been largely isolated, so evolution has veered the community off into its own direction..  This has led to a high degree of endemism -- the fraction of species found nowhere else on Earth.  11% of its bird species, 37% of its plants, 90% of its reptiles, and 95% of its mollusk species are endemic.  One of the most iconic plants is the "dragon's blood tree" (Dracaena cinnabari), which looks like it was invented by Dr. Seuss:

[Image licensed under the Creative Commons Alex38, Dragonblood tree in Socotra 2, CC BY 4.0]

Then, there's the cucumber tree (Dendrosicyos socotranus), which -- as the name would suggest -- is the only species in the cucumber family (Cucurbitaceae) that grows into a tree.  As far as I've heard, though, the fruit isn't edible, which is a good thing, because it'd be a hell of a climb to harvest one for your dinner salad:

[Image licensed under the Creative Commons Gerry & Bonni, Cucumber tree (6407165121), CC BY 2.0]

Like many places with unique and isolated ecosystems, Socotra's oddball assemblage of biota are endangered, from introduced species like cats and rats, from land use by the island's sixty-thousand-odd inhabitants, and from climate change.  The ongoing Yemeni civil war isn't helping, either; the government's priority is certainly not protecting peculiar-looking trees, and the ecotourists whose revenue might help the situation are mostly staying away for their own safety.

In any case, that's one anthropologist's vote for "the most alien-looking place on Earth" -- an island that's geologically African, politically and culturally Arabian, and biologically like nowhere else.  It's a place I'd love to visit one day if the situation calms down.  Adding some bird species to my life list that are found only on one speck of land in the Arabian Sea would be amazing.

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The broken branch

When I first became interested in paleontology, I think what came as the biggest surprise was how many lineages had become completely extinct.

I knew about the dinosaurs, of course; everyone knew about the dinosaurs.  But I remember one of my books on prehistoric animals showing a family tree of mammals, and branching off way near the bottom was a line marked multituberculates, that suddenly just... ended.  What on earth were those?

Turns out they're a group of small, superficially rodent-like mammals with strange knobbly teeth, that thrived for 130 million years -- coexisting with the dinosaurs for much of it -- before suddenly and inexplicably vanishing during the Miocene Epoch.  But they were hardly the only broken branch on the tree.  There were also the massive, hulking brontotheres, including the famously slingshot-horned Brontops, that lived during the Paleocene and Eocene, dying out around 34 million years ago.  And around the same time there were the mesonychids, scary-ass carnivorous mammals that looked like a cross between a bear and a wolf but were actually more closely related to horses.

All three groups gone forever, leaving no descendants.

Far from being the common picture of a slow, gradual progression, from something like a worm to a fish to an amphibian to a reptile to a primitive mammal to primates to *trumpet fanfare* Homo sapiens, sitting of course on top of the evolutionary tree as befits the Pinnacle of Creation, the family tree of life is more like an unruly and tangled shrub with thousands of splits and bifurcations -- and just as many snapped-off branches.  Whole groups of organisms have turned into dead ends; I wrote a couple of years ago about the bizarre Ediacaran Assemblage, a group of Precambrian species that are so different than the familiar life forms we see around us today that paleontologists have been unable to determine where exactly they fit in the overall taxonomic scheme, or if perhaps they, too, left no descendants.

But they are hardly the only species that are, as the researchers put it, "of uncertain affinities."  In fact, the whole topic comes up because of a paper by Corentin Loron of the University of Edinburgh et al., that looked at a peculiar life form that was one of the first really huge terrestrial organisms, an eight-meter-tall... um... something called Prototaxites.

From their cell wall structure, they pretty clearly weren't plants.  The hypothesis was that Prototaxites was some kind of enormous fungus; a mushroom the size of a small tree, more or less.  But now... well, here's what Loron et al. found:

Prototaxites was the first giant organism to live on the terrestrial surface, reaching sizes of 8 metres in the Early Devonian.  However, its taxonomic assignment has been debated for over 165 years.  Tentative assignments to groups of multicellular algae or land plants have been repeatedly ruled out based on anatomy and chemistry, resulting in two major alternatives: Prototaxites was either a fungus or a now entirely extinct lineage.  Recent studies have converged on a fungal affinity...  Here we test this by contrasting the anatomy and molecular composition of Prototaxites with contemporary fungi from the 407-million-year-old Rhynie chert.  We report that Prototaxites taiti was the largest organism in the Rhynie ecosystem and its anatomy was fundamentally distinct from all known extant or extinct fungi.  Furthermore, our molecular composition analysis indicates that cell walls of P. taiti include aliphatic, aromatic, and phenolic components most similar to fossilisation products of lignin, but no fossilisation products characteristic of chitin or chitosan, which are diagnostic of all groups of extant and extinct fungi, including those preserved in the Rhynie chert.  We therefore conclude that Prototaxites was not a fungus, and instead propose it is best assigned to a now entirely extinct terrestrial lineage.

After reading this, my brain (being basically like the neural equivalent of a giant, out-of-control pinball game) immediately bounced from there to thinking about the "Abominable Mi-Go" from the Lovecraft mythos, which were giant race of creatures that lived in Antarctica when it was warm and habitable hundreds of millions of years ago, and were "fungoid, more vegetable than animal, but truly allied to neither."  Of course, in Lovecraft's universe, the Mi-Go also had wings and kidnapped people and stored their consciousness in what amounted to big metal test tubes, and I don't think Loron et al. think Prototaxites could do all that.

In any case, the current study is fascinating from a couple of standpoints.  First, that the world in the early Devonian would have looked drastically different than it does today -- no trees, and in fact barely any plants larger than club mosses and (very) early ferns.  And second, that there were these towering things sticking up in the landscape, like giant accusing fingers, bearing only a distant (and as-yet uncertain) connection to any other living organism.

Recent advances in paleontology have shown that the nineteenth-century conception of the Great Chain of Being was missing out on some of the most interesting parts -- organisms so different from today's nine-million-odd species that we can't even figure out quite where to pigeonhole them.  And as we uncover more fossil evidence, we're sure to find others, and add further branches to the snarled and twisted family tree of life on Earth.

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Taking flight

One of the many things I find fascinating about the evolutionary model is how different lineages can happen on the same "solution" to the problems of surviving and reproducing, leading to similarities cropping up that don't result from common ancestry.  This is a phenomenon called convergent evolution, and explains why the North American flying squirrel and Australian sugar glider look a lot alike, even though they are only distantly related.  (The flying squirrel is a rodent, and the sugar glider a marsupial more closely related to kangaroos.)

I put the word "solution" in quotes and use it with caution, because this makes it sound like evolution is forward-looking, which it is not.  As Richard Dawkins explains brilliantly in his book The Blind Watchmaker, to trigger evolution, all you have to have is an imperfect replicator (in this case, DNA) and a selecting agent.  To phrase it more like Darwin would have put it: variation coupled with differences in survival rate.

I recall how surprised I was to learn that the eye has actually evolved multiple times.  Starting with light-sensitive spots, such as you still find today in many microorganisms, variations on different lineages came up with a variety of different "solutions" -- the pinhole-camera eye of a chambered nautilus, the cup-shaped eye of a flatworm, the compound eye of a fly, and our own eye with a transparent lens like that of a refracting telescope.  All these adaptations work just fine for the animal that has them.  (Eye formation in a number of species is controlled by the paired-box 6 [PAX6] gene, without which eyes won't form at all.  It's such a critical gene that it is conserved across thousands of species -- in fact, your PAX6 gene and a mouse's are identical, base-pair-for-base-pair.)

The reason this subject comes up is because of some research published in the journal Current Biology that showed another trait -- flight -- not only evolved separately in groups like insects and birds, but even in the dinosaurian ancestors of today's birds, it evolved more than once.

A team led by paleontologist Rui Pei of the Chinese Academy of Sciences analyzed bone and feather structure of various dinosaur groups to see if they flew, glided, or were using their feathers for a different purpose (such as keeping warm).  To their surprise, it was found that multiple lineages were capable of flying, or nearly so.  The authors write:

We [used] an ancestral state reconstruction analysis calculating maximum and minimum estimates of two proxies of powered flight potential—wing loading and specific lift.  These results confirm powered flight potential in early birds but its rarity among the ancestors of the closest avialan relatives (select unenlagiine and microraptorine dromaeosaurids).  For the first time, we find a broad range of these ancestors neared the wing loading and specific lift thresholds indicative of powered flight potential.  This suggests there was greater experimentation with wing-assisted locomotion before theropod flight evolved than previously appreciated.  This study adds invaluable support for multiple origins of powered flight potential in theropods (≥3 times), which we now know was from ancestors already nearing associated thresholds, and provides a framework for its further study.

Here are their results, in graphical form:

As you can see, actual birds -- labeled "Later-diverging avialans" near the bottom of the tree -- were far from the only ones to have flight capability.  Rahonavis, Microraptor, and several of the anchiornithines were probably fliers, and only the last mentioned is on the same clade as today's birds.

Flying is pretty useful, so it's no wonder that when feathers evolved from scales -- probably, as I mentioned earlier, in the context of warmth and insulation -- it was only a small step remaining toward lengthening those feathers to the point that their owners could catch a breeze and glide.  After that, the same kind of refinement took over that happened with the eye, and eventually, you have true flight.

So that's yet another cool bit of research about prehistory.  Wouldn't you like to know what those prehistoric fliers looked like?  I'd love to see them.  From a distance, because a lot of them were predators.  For example, Microraptor is Greek for "tiny hunter," and were a little like miniature velociraptors with wings.

If you wanted an image to haunt your dreams.

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Little cat man

It's amazing how many attempts it took for primates to successfully colonize North America.

There's only one primate species currently in the continent.  Us.  Other mammalian groups -- carnivores, rodents, ungulates, insectivores, bats, and so on -- have done fine here, flourishing and diversifying and lasting for tens of millions of years.

Primates haven't been so successful.

The first primates -- well, proto-primates -- in North America were the plesiadapiformes, which first appear in the fossil record in the early Paleocene Epoch, right after the Chicxulub Impact pretty well wiped out all the big animal species (most notably, the non-avian dinosaurs).  To modern eyes, they would have looked a bit like squirrels:

[Image licensed under the Creative Commons Nobu Tamura (http://spinops.blogspot.com), Plesiadapis NT, CC BY-SA 3.0]

Despite the superficially squirrelly appearance, their skulls, and especially their teeth, show clear affinities with primates, not with rodents.

These guys were widespread, living throughout North America, Europe, and Asia.  All of those continents were still connected at this point -- what had been Pangaea had broken into a northern continent (Laurasia) and a southern continent (Gondwanaland, made up of what are now South America, Australia, and Antarctica).  But things were changing, as they are wont to do.  The Central Atlantic Magmatic Province had kicked into high gear, rifting Laurasia and splitting what would become North America from the rest of the continent, opening up the North Atlantic Ocean.  At that point, the primate species (and everyone else) in North America were pretty well stuck there.

And they lasted a while.  But at the end of the Eocene Epoch, around 34 million years ago, the North American continent got significantly cooler and drier.  This drove all the warmth-loving native primates to extinction.

[Nota bene: South American monkeys come from a different lineage.  Recall that at this point, North and South America were pretty far apart, and there was a lot of ocean in between.  South America was a great deal closer to Africa, though -- and was colonized by primates from Africa, probably by monkeys and other species clinging to rafts of plant roots and brush torn loose during storms.  They seem to have made this amazing journey in several pulses, starting about thirty million years ago.  In any case -- the genetic and structural evidence is clear that South American monkeys are related to primates from Africa, not the extinct groups in North America.]

In any case, North America was primateless for about four million years.  Then, suddenly, a primate appeared in what is now Nebraska.  This species, named Ekgmowechashala (the name is Sioux for "little cat man"), weighed about three kilograms, and looked a bit like a lemur.  But where the hell did it come from?

The whole topic came up in the first place because of new research into this odd creature, which appeared in the Journal of Human Evolution last week.  A thorough analysis of Ekgmowechashala fossils dating from around thirty million years ago found that they most closely resemble primate species in China and eastern Siberia.  Apparently, the ancestors of Ekgmowechashala did what the ancestors of the Native Americans would do, millions of years later.  They took advantage of the fact that the cooler conditions locked up more sea water in the form of ice, lowering sea levels.  Among other things, this turned what is now the Bering Sea into a broad valley with rolling hills (nicknamed Beringia), allowing them to cross into North America.

"The 'Lazarus effect' in paleontology is when we find evidence in the fossil record of animals apparently going extinct -- only to reappear after a long hiatus, seemingly out of nowhere," said Chris Beard, of the University of Kansas, who was senior author of the paper.  "This is the grand pattern of evolution that we see in the fossil record of North American primates. The first primates came to North America about 56 million years ago at the beginning of the Eocene, and they flourished on this continent for more than 20 million years.  But they went extinct when climate became cooler and drier near the Eocene-Oligocene boundary, about 34 million years ago.  Several million years later Ekgmowechashala shows up like a drifting gunslinger in a Western movie, only to be a flash in the pan as far as the long trajectory of evolution is concerned.  After Ekgmowechashala is gone for more than 25 million years, Clovis people come to North America, marking the third chapter of primates on this continent. Like Ekgmowechashala, humans in North America are a prime example of the Lazarus effect."

So the "little cat man" didn't last very long -- the continual cooling of the climate, peaking with the repeated continental glaciations of the "Ice Ages," was more than primates could cope with.  But as Beard points out, that didn't stop our own species from doing the very same thing, eventually colonizing all of North America, and more inhospitable places yet.

But it's odd to think that thirty million years ago, there was something very like a lemur living near what is now Omaha.

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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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The beat goes on

I am blessed with a good innate sense of rhythm.

I've always felt rhythms in my body; I never had to struggle to keep the beat while playing music.  One of my band members nicknamed me "The Metronome," and quipped that if one of us missed a note, it might well be me -- but if someone screwed up the rhythm, it was definitely not me.

I've often wondered about the origin of this.  I've listened to music ever since I can remember, but I dropped out of band in sixth grade, was not allowed to take music lessons however much I begged my parents, and didn't participate in anything in the way of formal music training until I was in my mid-twenties.  The result is that I'm largely self-taught -- with all of the good and bad that kind of background brings.

I've always loved music with odd rhythms.  There's a reason two of my favorite classical composers are Igor Stravinsky and Dmitri Shostakovich.  Then, I discovered Balkan music when I was in my teens, and even before I knew cognitively what was going on, was magnetically attracted to the strange, asymmetrical beat patterns.

For example, what do you make of this tune?

If you know any Slavic languages, the name of it will give you a clue -- Dvajspetorka.  There are twenty-five beats (!) per measure; the name comes from the Macedonian word for "twenty-five" (dvaeset i pet).  But if you're wondering how the hell you count that, you'll no doubt be relieved to find that you don't count up to twenty-five and then start back at one.  Most of these Balkan tunes are dances (or derived from them), and they're all broken down into slow steps (that get a count of three beats) and fast steps (that get a count of two beats).  This one is slow-fast-fast, slow-fast-fast, fast-fast-slow-fast-fast.  When I've taught Balkan music workshops, I've found it helps to speak the rhythm, using the word "apple" for the fast, two-beat steps and "cinnamon" for the slow, three-beat ones.

So the rhythm of Dvajspetorka would be cinnamon-apple-apple, cinnamon-apple-apple, apple-apple-cinnamon-apple-apple.

Which, if you count it up, adds to an entire apple pie with twenty-five beats per measure.

What got me thinking about all of this is a couple of papers I ran into yesterday, one from PLOS-One Biology called, "The Nature and Perception of Fluctuations in Human Musical Rhythms," by Holger Henning et al., and the other from Psychonomic Bulletin and Review called, "Sensorimotor Synchronization: A Review of Recent Research" by Bruno Repp and Yi-Huang Su.  And what I learned from these is as fascinating as it is puzzling.  Among the takeaways:

• Humans tend not to like perfectly steady rhythms.  When musical recordings are made using a computer-synchronized beat, they're judged as "emotionless" and "devoid of depth."  So small, deliberate fluctuations in the tempo are part of what give music its poignancy.
• Throwing in random fluctuations doesn't work.  Test subjects caught on to that immediately, saying the alterations in tempo sounded like mistakes.  There's something about the fluid, organic sound of actual human musicians making minor shifts in rhythm that are what create emotional resonance in the listener.
• That said, really good musicians have extraordinarily accurate abilities to keep a steady beat when they want to.  Told to hold a rhythm as rock-solid as they can, professional percussionists deviated from the pulse of the music by an average of only a few milliseconds per beat.
• fMRI studies have shown that there is a specific part of the brain -- the basal ganglia-thalamo-cortical circuitry in the cerebellum -- that fires like crazy when people try to match a rhythm.  So the rhythmic ability in humans is hardwired.  In fact, research suggests that are are other animals that have this ability as well -- other primates, rats, and some birds all show various levels of rhythmic awareness.
• As far as why this apparently innate ability to keep a musical rhythm exists, evolutionary biologists admit that their current answer is "damned if we know."

It seems like an odd thing to evolve, doesn't it?  The obvious guess is that it might have something to do with communication, but there's no human language (or non-human animal communication we know of) that is sensitive to rhythm to an accuracy of a few milliseconds.  If I say "I'm leaving for work now" to my wife, and say it with various rhythms and speeds, the meaning doesn't change (although for certain speed and rhythm combinations, she might well give me a perplexed look).

So how such an incredibly precise ability evolved is still a considerable mystery.

Anyhow, that's our curious bit of science for the day.  How humans keep the beat.  And if you'd like to end with another challenge, what time signature do you think this is in?  Have fun!

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The nibblers

I'm always on the lookout for fascinating, provocative topics for Skeptophilia, but even so, it's seldom that I read a scientific paper with my jaw hanging open.  But that was the reaction I had to a paper from a couple of months ago in Nature that I just stumbled across yesterday.

First, a bit of background.

Based on the same kind of genetic evidence I described in yesterday's post, biologists have divided all living things into three domains: Eukarya, Bacteria, and Archaea.  Eukarya contains eukaryotes -- organisms with true nuclei and complex systems of organelles -- and are broken down into four kingdoms: protists, plants, fungi, and animals.  Bacteria contains, well, bacteria; all the familiar groups of single-celled organisms that lack nuclei and most of the other membrane-bound organelles.  Archaea are superficially bacteria-like; they're mostly known from environments most other living things would consider hostile, like extremely salty water, anaerobic mud, and acidic hot springs.  In fact, they used to be called archaebacteria (and lumped together with Bacteria into "Kingdom Monera") until it was discovered in 1977 by Carl Woese that Archaea are more genetically similar to eukaryotes like ourselves than they are to ordinary bacteria, and forced a complete revision of how taxonomy is done.

So things have stood since 1977: three domains (Bacteria, Archaea, and Eukarya), and within Eukarya four kingdoms (Protista, Plantae, Fungi, and Animalia).

But now a team led by Denis Tikhonenkov, of the Russian Academy of Scientists, has published a paper called "Microbial Predators Form a New Supergroup of Eukaryotes" that looks like it's going to force another overhaul of the tree of life.

Rather than trying to summarize, I'm going to quote directly from the Tikhonenkov et al. paper so you get the full impact:

Molecular phylogenetics of microbial eukaryotes has reshaped the tree of life by establishing broad taxonomic divisions, termed supergroups, that supersede the traditional kingdoms of animals, fungi and plants, and encompass a much greater breadth of eukaryotic diversity.  The vast majority of newly discovered species fall into a small number of known supergroups.  Recently, however, a handful of species with no clear relationship to other supergroups have been described, raising questions about the nature and degree of undiscovered diversity, and exposing the limitations of strictly molecular-based exploration.  Here we report ten previously undescribed strains of microbial predators isolated through culture that collectively form a diverse new supergroup of eukaryotes, termed Provora.  The Provora supergroup is genetically, morphologically and behaviourally distinct from other eukaryotes, and comprises two divergent clades of predators—Nebulidia and Nibbleridia—that are superficially similar to each other, but differ fundamentally in ultrastructure, behaviour and gene content.  These predators are globally distributed in marine and freshwater environments, but are numerically rare and have consequently been overlooked by molecular-diversity surveys. In the age of high-throughput analyses, investigation of eukaryotic diversity through culture remains indispensable for the discovery of rare but ecologically and evolutionarily important eukaryotes.

The members of Provora are distinguished not only genetically but by their behavior; to my eye they look a bit like a basketball with tentacles, using weird little tooth-like structures to nibble their way forward as they creep along.  (Thus "nibblerid," which is their actual name, despite the fact that it sounds like a comical monster species from Doctor Who.)  The first one discovered (in 2017), the euphoniously-named Ancoracysta twista, is a predator on tropical coral, and was found in (of all places) a home aquarium.  Since then, they've been found all over the place, although they're not common anywhere; the only place they've never been seen is on land.  But just about every aquatic environment, fresh or marine, has provorans of some kind.

An electron micrograph of a provoran [Image from Tikhonenkov et al.]

The provorans appear to be closely related to no other eukaryote, and Tikhonenkov et al. are proposing that they warrant placement in their own supergroup (usually known as a "kingdom").  But it raises questions of how many more outlier supergroups there are.  A 2022 analysis by Sijia Liu et al. estimated the number of microbial species on Earth at somewhere around three million, of which only twenty percent have been classified.  It's easy to overlook them, given that they're microscopic -- but that means there could be dozens of other branches of the tree of life out there about which we know nothing. 

It's amazing how much more sophisticated our understanding of evolutionary descent has become.  When I was a kid (back in medieval times), we learned in science class that there were three divisions; animals, plants, and microbes.  (I even had a Golden Guide called Non-Flowering Plants -- which included mushrooms.)  Then it was found that fungi and animals were more closely related than fungi and plants, and that microbes with nuclei and organelles (like amoebas) were vastly different from those without (like bacteria).  There it stood till Woese came along in 1977 and told us that the bacteria weren't a single group, either.

And now we've got another new branch to add to the tree.  The nibblers.  Further illustrating that we don't have to look into outer space to find new and astonishing things to study; there is a ton we don't know about what's right here on Earth.

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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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