Pressing reset

Although you don't tend to hear much about it, the Ordovician Period was a very peculiar time in Earth's history.

From beginning (485 million years ago) to the end (444 million years ago) it experienced two of the biggest global climatic swings the Earth has ever seen.  In the early Ordovician the climate was a sauna -- an intense greenhouse effect caused the highest temperatures the Paleozoic Era would see, and glacial ice all but vanished.  Life was abundant in the shallow seas.  One of the dominant groups were the conodonts:

[Image licensed under the Creative Commons Prehistorica, Panderodus unicostatus, CC BY-SA 4.0]

Those of you who know your fish might guess that conodonts like Panderodus were related to modern lampreys, and you're right.  But it took a really long time to figure that out.  Their soft bodies didn't fossilize well, so about all that we had were the cone-shaped teeth that gave them their name.  In fact, those teeth are the most common fossils in Ordovician sedimentary rocks, so we knew whatever grew them must have been abundant -- but it took a while to determine what kind of animal they came from.

So things were warm, humid, with tropical conditions virtually pole to pole.  Then... something happened.  We're still not entirely sure what.  Part of it was undoubtedly simple plate tectonics; the supercontinent of Gondwana was gradually moving toward the South Pole.  There's some evidence of a large meteorite strike, or possibly more than one.  But whatever the cause, by the end of the Ordovician, glaciers covered much of what is now Africa and South America, resulting in a drastic drop in sea level and a massive extinction that wiped out an estimated sixty percent of life on Earth.  

At this point, life was confined to the oceans. The first terrestrial plants and fungi wouldn't evolve until something like twenty million years after the beginning of the next period, the Silurian, and land animals only followed after that.  As the Ordovician progressed, and more and more ocean water became locked up in the form of glacial ice, much of what had been shallow, temperate seas dried up to form cold, barren deserts.  And that was all there was on land -- thousands of square kilometers of rock, sand, and ice, without a single living thing larger than bacteria to be found anywhere.

Then, the climate reversed again.  The seas flooded back in, and the warmer, sulfur-rich, oxygen-poor water upwelling from the bottom knocked out about twenty percent of the cold-adapted survivors.  By the time the period ended, the Earth had a seriously impoverished biosphere, with something like fifteen percent of the original biota making it through the double-whammy.

But what survived this pair of climate swings was to shape Earth's biological history forever.  Because it included primitive vertebrates with paired jaws -- the gnathostomes -- which became the ancestors of 99% of modern vertebrate animals, including ourselves.

The reason this comes up is some new research out of the Okinawa Institute of Science and Technology that analyzed thousands of fossils from species that made it through the Late Ordovician bottleneck -- and an equal number of those that didn't.  And they found two interesting patterns.  First, the survivors were mostly species that found their way into refugia -- small, isolated pockets of ecosystems with (slightly) more hospitable conditions that allowed them to squeak their way through the worst times.  Second, each of the major extinction pulses was followed by dramatic diversification, as the surviving populations expanded into niches vacated by the ones that weren't so fortunate.

"We pulled together two hundred years of late Ordovician and early Silurian paleontological research," said study lead author Wahei Hagiwara.  "By reconstructing the ecosystems within these refugia, we were able to measure changes in genus-level diversity over time.  Our analysis revealed a steady but striking rise in jawed vertebrate diversity following the extinction.  And the trend is clear -- the mass extinction pulses led directly to increased speciation after several millions of years."

As Ian Malcolm so accurately put it, "Life, uh, finds a way."

A couple of other things strike me about this research, though.

The first is how contingent our existence here is.  Evolutionary biologist Stephen Jay Gould wrote a provocative piece about "replaying the tape of life," coming to the conclusion if you were to start over from the beginning, so much of the path of evolution has rested on chance occurrences that the chances of it turning out exactly the same way is nearly zero.  In a situation like the Late Ordovician Mass Extinction, which assortment of species made it into the few hospitable refugia must have had as much to do with luck as with being well-adapted; had a different set of populations survived, life today almost certainly would look very different.

The second is the fact that both of the Ordovician climate swings were far slower than what we're currently doing to the environment.  Like, hundreds of times slower.  The second one, in fact -- the warm-up and subsequent melting of polar ice -- was almost certainly a very gradual rebound toward the greenhouse conditions that were to pertain by the mid-Silurian.  We're talking about something on the order of ten million years to go from cool to warm.

What we're doing now has taken only a couple of hundred.

What happened in the Late Ordovician should be a wake-up call for us.  Yet somehow, we arrogant humans think we're immune to the effects of our out-of-control fossil fuel burning.  We have a striking fossil record documenting the terrible effects of rapid climate change in prehistory; at the moment, mostly what we seem to be doing is saying, "Yeah, but it won't happen to us, 'cuz we're special."

So that's our cautionary tale for today.  The climate change deniers are fond of saying, "Earth's climate has changed many times before now," and almost never add, "... and when it did, enormous numbers of species went extinct."  And the difference, too, is that the natural fluctuations (such as those caused by plate movement, asteroid strikes, and changes in insolation) aren't something we could control even if we wanted to, but what we're doing now is entirely voluntary.

And until the people in charge realize that addressing climate change is in all of our best interest, I'm afraid our path forward is not likely to change.

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The advantage of simplicity

One of the most common misconceptions about evolution is that it is goal-oriented.

You hear it all the time.  Giraffes evolved longer necks so they could reach foliage higher up in tree branches -- as if some poor short-necked giraffes  were trundling about on the African savanna looking longingly up into the canopy and thinking, "Wow, that looks amazing," so their kids were born with longer necks.  It becomes even more insidious when you start talking about human evolution, because the way it's often presented is that waaaaaay back you had something like a jellyfish that evolved into something like a worm, and then into a primitive fish, into an amphibian, into a reptile, into a proto-mammal, into true mammals then primates then...

... us.  Sitting, of course, on the very top as befits the pinnacle of evolution, as if all along we're what the whole process had been aiming at.

This misses the boat in several very important ways.  One is that this linear view of evolution is simply wrong.  Evolution causes repeated branching; in fact, in our own lineage, many of the basic body plans we have today (flatworms, roundworms, jellyfish, annelids, mollusks, echinoderms, arthropods, and primitive vertebrates) all arose at around the same time, during what's called the Cambrian explosion.  During the intervening 540-million-odd years since that happened, some of the branches of the tree of life have changed a great deal more than others; but all living things on Earth have exactly the same length of evolutionary history.

A really critical way that the teleological model for evolution fails is that it misses completely how evolution actually works.  Natural selection isn't forward-looking at all; it operates by the environment selecting the forms that have the highest survival and reproductive potential now, irrespective of what the conditions might be a week from Tuesday.  It is very much the Law of Whatever Works, and what works today might not work at all if conditions change -- something we should pay attention to apropos of climate change.

A third problem is the perception that evolution always leads to higher complexity, strength, and intelligence.  None of these are true.  Consider that insects, especially beetles, are the most numerous and diverse animals on Earth by far -- both species-wise, and individual-for-individual, insects outnumber all other animals put together.  Sometimes simplicity has a higher survival advantage than complexity does, and -- to judge by the natural world, and even a significant fraction of the human part of it -- I'm not convinced that intelligence is always an advantage, either.

As a good example of the advantage of simplicity -- and the reason the topic comes up today -- consider the little plant species Balanophora fungosa.  It's found in warm, moist forests in Taiwan, Japan, and Okinawa, and on first glance it looks like a strange mushroom.  Balanophora is in the family Balanophoraceae, which comprises sixteen genera and is somewhat tentatively placed in order Santalales along with more familiar plants like sandalwood and mistletoe.  All the members of Balanophoraceae are obligate parasites, living off the roots of very specific species of trees.

Balanophora fungosa [Image credit: Petra Svetlikova]

Where it gets interesting is that Balanophora has done what superficially looks like evolution in reverse.  It's lost its ability to produce chlorophyll; it has no conventional root system.  Most of the plant kingdom have on the order of two hundred genes whose job it is to produce and operate plastids, the pigment-containing organelles that include chloroplasts; Balanophora has reduced that number to twenty.  Many species in Balanophoraceae produce seeds without fertilization, obviating the need for flowers.

What's curious is that these odd little plants have been around for a long time.  They branched off from the rest of the plant kingdom in the mid-Cretaceous period, something like a hundred million years ago, and have been quietly doing their thing ever since, gradually evolving to jettison structures (and even genes) they don't need along the way.  "Balanophora has lost much of what defines it as a plant, but retained enough to function as a parasite," said Petra Svetlikova, of the Okinawa Institute of Science and Technology, who led the study.  "It's a fascinating example of how something so strange can evolve from an ancestor that looked like a normal plant with leaves and a normal root system."

Because of its extreme specialization, both in terms of habitat and host species, Balanophora is threatened by habitat change.  "Most known habitats of Balanophora are protected in Okinawa, but the populations face extinction by logging and unauthorized collection," Svetlikova said.  "We hope to learn as much as we can about this fantastic, ancient plant before it's too late.  It serves as a reminder of how evolution continues to surprise us."

So there you have some cool research about an evolutionary holdout from a hundred-million-year-old split in the tree of life.  Here, simplicity, not complexity, seems to have been the key to its long survival.  One can only hope that this strange little plant hasn't lasted so long only to reach the end because of us.

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Scattered to the winds

One of the more puzzling aspects of evolutionary theory is the phenomenon of peripheral isolates.

This term refers to widely-separated populations of seemingly closely-related organisms.  One of the first times I ran into this phenomenon came to my attention because of my obsession with birdwatching.  There's a tropical family of birds called trogons, forest-dwelling fruit-eaters that are prized by birdwatchers for their brilliant colors.  There are trogons in three places in the world... Central and South America (27 species), central Africa (3 species), and southern Asia (11 species).

These are very far apart.  But take a look at three representatives from each group -- it doesn't take an ornithologist to see that they've got to be closely related:

The Elegant Trogon (Trogon elegans) of Central America [Image licensed under the Creative Commons dominic sherony, Elegant Trogon, CC BY-SA 2.0]

The Narina Trogon (Apaloderma narina) of central Africa [Image licensed under the Creative Commons Derek Keats from Johannesburg, South Africa, Narina Trogon, Apaloderma narina MALE at Lekgalameetse Provincial Reserve, Limpopo, South Africa (14654439002), CC BY 2.0]

The Red-headed Trogon (Harpactes erythrocephalus) of southeast Asia [Image licensed under the Creative Commons JJ Harrison (jjharrison89@facebook.com), Harpactes erythrocephalus - Khao Yai, CC BY-SA 3.0]

I know, I've gone on and on in previous posts about how misleading morphology/appearance can be in determining relationships, but you have to admit these are some pretty convincing similarities.

The question, of course, is how did this happen?  Where did the group originate, and how did members end up so widely separated?  To add to the puzzle, the fossil record for the group indicates that in the Eocene Epoch, fifty-ish million years ago, there were trogons in Europe -- fossils have been found in Denmark and Germany -- and the earliest fossil trogons from South America come from the Pleistocene Epoch, only two million years ago.

So are these the remnants of what was a much larger and more widespread group, whose northern members perhaps succumbed due to one of the ice ages?  Did they start in one of their homelands and move from there?

And if that's true, why are there no examples of trogons from all the places in between?

Another example of this is the order of mammals we belong to (Primata).  Primates pretty clearly originated in Africa and spread from there; the earliest clear primates were in the Paleocene Epoch, on the order of sixty million years ago, but the ancestor of all primates was probably at least twenty million years before that, preceding the Cretaceous Extinction by fourteen million years.  From their start in east Africa they seem to have spread both east and west, reaching southeast Asia around fifty million years ago.  Some of the earliest members to split were the lorises and tarsiers, along with the lemurs of Madagascar.

But the next group to diverge -- and the reason the whole topic of peripheral isolates came up -- are the "New World monkeys," the "platyrhines" of Central and South America.  It looks like this split happened during the Oligocene Epoch, around thirty million years ago... but how?

At that point, Africa was separated from South America by nine hundred miles of ocean -- narrower than the Atlantic is today, but still a formidable barrier.  But a paper in Science describes recently-discovered evidence from Peru of some fossilized primate teeth from right around the time the New World/Old World monkey split happened.

What this discovery suggests is staggering; all of the New World monkeys, from the spider monkey to the black howler monkey to the Amazonian pygmy marmoset, are descended from a single group that survived a crossing of the Atlantic, probably on a vegetation raft torn loose in a storm, only a little over thirty million years ago.

"This is a completely unique discovery," said Erik Seiffert, the study's lead author and Professor of Clinical Integrative Anatomical Sciences at Keck School of Medicine of the University of Southern California, in an interview with Science Daily.  "We're suggesting that this group might have made it over to South America right around what we call the Eocene-Oligocene Boundary, a time period between two geological epochs, when the Antarctic ice sheet started to build up and the sea level fell.  That might have played a role in making it a bit easier for these primates to actually get across the Atlantic Ocean."

So here we have a possible explanation for one of the long-standing puzzles of evolutionary biology.  Note that these puzzles aren't a weakness of the theory; saying "we still have some things left to explain" isn't the same as saying "the theory can't explain this."  There will always be pieces to add and odd bits of data to account for, but I have one hundred percent confidence that the evolutionary model is up to the task.

Now, I wish it could just come with an explanation for the trogons, because for some reason that really bothers me.

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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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