Big apple

On August 14, 2003, my wife and I were returning from a trip to Hawaii.  It was a lovely vacation, but the return home was, to put it mildly, fraught with mishaps.  The most spectacular one occurred as we were descending into LaGuardia Airport in New York City.  It was late afternoon and I was watching the lights of the city zooming along below us, when, all of a sudden...

... the entire skyline went dark.

I nudged Carol and asked her to confirm that I was, in fact, seeing what I thought I was seeing.  The pilot landed the plane, but the jet bridges weren't working so we deplaned via a rolling ladder.  The entire airport was dark except for a few lights that were kept on by a generator.  Remember that this is a little less than two years after 9/11, so our immediate (and terrifying) thought was that it was a terrorist attack, but it turned out we'd gotten caught up in the Great Northeastern Blackout, which knocked out the electricity to a huge chunk of the northeastern United States and eastern Canada, and which apparently had been triggered by a software bug.

The upshot was we got stuck in the airport overnight with a bunch of other people who were also trying to get back to the Ithaca area, and one of these was a very nice woman who worked for the Apple Genomics Project at Cornell Orchards.  That evening she and I had a real Nerd-O-Rama about the ins and outs of plant genetics, which was a very peculiar way to make the best of a bad situation.

She and her team had a fascinating job -- going all over Europe, the Caucasus, Anatolia, and Central Asia looking for apple germ line -- basically, anything that can be used to reproduce an entire tree (seeds and cuttings being two of the most obvious examples).  They hired translators to accompany them, who asked locals to point out the best apple trees for various uses -- cooking, cider, making wine or vinegar, drying/preserving, or eating fresh -- and they took samples of germ line (along with copious notes) to bring home to the Orchards for growing and hybridizing.  Besides just looking for good fruit quality, they were also interested in finding strains that are resistant to pests and diseases.

The most diversity they discovered was in Kazakhstan and Uzbekistan, which is where apples originate.  ("American as apple pie" is about as inaccurate as you can get; apples not only aren't native to the United States, they were brought into North America in the mid-1600s by a Frenchman, Pierre Martin -- who settled in Nova Scotia.)  And some research out of the Max Planck Institute for the Science of Human History that appeared last week in Frontiers in Plant Science found that the spread of apples from their homeland, thousands of miles across Europe, was due to two factors; megafauna and the Silk Road.

[Image licensed under the Creative Commons Sandstein, Civni-Rubens apple, CC BY 3.0]

The modern apple is the result of hybridization between at least four wild species, followed by centuries of backcrossing and artificial selection.  Let apples cross-pollinate and plant the seeds, and you'll end up with something like a wild crabapple.  Originally, the bright fruits of apples were eaten by large herbivores like horses and wild cattle, and the seeds dispersed long distances, but with the disappearance of the huge herds that used to exist in central Asia, apple seeds were poorly dispersed.  (Apples aren't the only plants that got into trouble when their seed-disperser disappeared, something about which I wrote in more detail a couple of years ago.)  Fortunately for apples, though, their many uses were noted by humans, and when people moved -- especially along the Silk Road -- they took apple germ line with them, just as my Cornell researcher friend did a thousand years later.

The author, Robert Nicholas Spengler, writes:

Large fruits in Rosaceae [the family apples belong to] evolved as a seed-dispersal adaptation recruiting megafaunal mammals of the late Miocene.  Genetic studies illustrate that the increase in fruit size and changes in morphology during evolution in the wild resulted from hybridization events and were selected for by large seed dispersers.  Humans over the past three millennia have fixed larger-fruiting hybrids through grafting and cloning.  Ultimately, the process of evolution under human cultivation parallels the natural evolution of larger fruits in the clade as an adaptive strategy, which resulted in mutualism with large mammalian seed dispersers (disperser recruitment).

Current archaeobotanical evidence seems to suggest that apple domestication took place over a period of less than 100 generations, much less for the earliest morphological changes.  It seems feasible that rapid domestication through hybridization occurred in as little as one or a few generations, and most of the modern diversity in landraces is probably a recent phenomenon, through directed breeding.  Not only do protracted models of domestication fall short when discussing apples, the concept of a “center” of domestication is misleading. Genetic studies illustrate that wild apple populations across Europe and West Asia collectively contributed to the modern domesticated apple in a hybrid complex of species distributed across a continent and a half.

So that's something to think about next time you bite into a crisp apple -- you're enjoying a fruit that has roots reaching back millions of years, the current shape, color, and taste of which were created by megafaunal seed dispersers and the travel of human populations down the Silk Road.

Oh, and we eventually did get back home.  Carol and I, our geneticist friend, and four other people finally decided to hire a limousine when it became obvious that (1) the power, and therefore the airport, was going to be out of commission for a long time, and (2) there wasn't a rental car to be had anywhere in the New York City area.  We figured that splitting the cost of a limousine all the way to Ithaca seven ways wasn't going to be much more than each of us separately hiring a rental car anyhow.  All was going well until the limousine overheated and died in the middle of nowhere in the Poconos, leaving us stranded by the side of the highway with all our luggage.

By then, even my new friend and I didn't feel much like talking about genetics.

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Pink, pink, gold

When I was in Ecuador in 2019, I was blown away by its natural beauty.  The cloud forests of the mid-altitude Andes are, far and away, the most beautiful place I've ever been, and I've been lucky enough to see a lot of beautiful places.  Combine that with the lovely climate and the friendliness of the people, and it puts the highlands of Ecuador on the very short list of places I'd happily move to permanently.

What brought me there were the birds.  It's a tiny country, but is home to 1,656 species of birds -- about one-sixth of the ten-thousand-odd species found worldwide.  Most strikingly, it has 132 different species of hummingbirds.  Where I live, in upstate New York, we have only one -- the Ruby-throated Hummingbird (Archilochus colubris) -- but there, they have an incredible diversity within that one group.  Because each species is dependent on particular flowers for their food source, some of them have extremely restricted ranges, often narrow bands of terrain at exactly the right climate and altitude to support the growth of that specific plant.  You go a few hundred meters up or downhill, and you've moved out of the range where that species lives -- and into the range of an entirely different one.

The most striking thing about the hummingbirds is their iridescence.  My favorite one, and in the top five coolest birds I've ever seen, is the Violet-tailed Sylph (Aglaiocercus coelestis):

[Image licensed under the Creative Commons Andy Morffew from Itchen Abbas, Hampshire, UK, Violet-tailed Sylph (33882323008), CC BY 2.0]

What's most fascinating about birds like this one is that the feathers' stunning colors aren't only due to pigments.  A pigment is a chemical that appears colored to our eyes because its molecular structure allows it to absorb some frequencies of light and reflect others; the chlorophyll in plants, for example, looks green because it preferentially absorbs light in the red and blue-violet regions of the spectrum, and reflects the green light back to our eyes.  Hummingbirds have some true pigments, but a lot of their most striking colors are produced by interference -- on close analysis, you find that the fibers of the feathers are actually transparent, but when light strikes them they act a bit like a prism, breaking up white light into its constituent colors.  Because of the spacing of the fibers, some of those wavelengths interfere destructively (the wavelengths cancel each other out) and some interfere constructively (they superpose and are reinforced).  The spacing of the fibers determines what color the feathers appear to be.  This is why if you look at the electric blue/purple tail of the Violet-tailed Sylph from the side, it looks jet black -- your eyes are at the wrong angle to see the refracted and reflected light.  Look at it face-on, and suddenly the iridescent colors shine out.

So the overall color of the bird comes from an interplay between whatever true pigments it has in its feathers, and the kind of interference you get from the spacing of the transparent fibers.  This is why when you recombine these features through hybridization, you can get interesting and unexpected results -- as some scientists from Chicago's Field Museum found out recently.

Working in Peru's Cordillera Azul National Park, on the eastern slopes of the Andes, ornithologist John Bates discovered what he'd thought was a new species in the genus Heliodoxa, one with a glittering gold throat.  He was in for a shock, though, when the team found out through genetic analysis that it was a hybrid of two different Heliodoxa species -- H. branickii and H. gularis -- both of which have bright pink throats.

"It's a little like cooking: if you mix salt and water, you kind of know what you're gonna get, but mixing two complex recipes together might give more unpredictable results," said Chad Eliason, who co-authored the study.  "This hybrid is a mix of two complex recipes for a feather from its two parent species...  There's more than one way to make magenta with iridescence.  The parent species each have their own way of making magenta, which is, I think, why you can have this nonlinear or surprising outcome when you mix together those two recipes for producing a feather color."

The gold-throated bird apparently isn't a one-off, as more in-depth study found that it didn't have an even split of genes from H. branickii and H. gularis.  It seems like one of its ancestors was a true half-and-half hybrid, but that hybrid bird then "back-crossed" to H. branickii at least once, leaving it with more H. branickii genes.  All of which once again calls into question our standard model of species being little cubbyholes with impermeable walls.  The textbook definition of species -- "a morphologically-distinct population which can interbreed and produce fertile offspring" -- is unquestionably the most flimsy definition in all of biology, and admits of hundreds of exceptions (either morphologically-identical individuals which cannot interbreed, or morphologically-distinct ones that hybridize easily, like the Heliodoxa hummingbirds just discovered in Peru).

In any case, the discovery of this hybrid is fascinating.  You have to wonder how many more of them there are out there.  The fact that its discovery ties together the physics of light, genetics, and evolution is kind of amazing.  Just further emphasizes that if you're interested in science, you will never, ever be bored.

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Grandpa the pig

It bears mention that having a Ph.D. (or other advanced credentials) is no guarantee against being a complete wingnut.  This topic comes up because of a website link sent to me by a regular reader of Skeptophilia that was authored by Eugene McCarthy, Ph.D. in genetics, and author of Handbook of Avian Hybrids of the World.

It starts off reasonably enough; McCarthy describes the fact that, contrary to our perception of species as being little watertight compartments, hybridization (and thus gene flow between species) is rather common.  Not all hybrids are sterile, like the familiar example of the mule; a lot of them are back-fertile to either parental species (an example is the "Brewster's Warbler," which was once thought to be a separate species and is now known to be a hybrid between the Golden-winged and Blue-winged Warblers).

So McCarthy asks an interesting question: are humans a hybrid?  The answer, apparently, is yes; recent studies have shown that most human populations show the genetic signature of three ancestral populations -- modern humans, Neanderthals, and Denisovans.  (Biologists disagree, however, as to whether these three represent different species -- a distinction that, in reality, probably doesn't mean very much.  The concept of species is one of the hardest-to-pin-down terms in all of biological science.)

But, unfortunately, it isn't this intermixing between three proto-hominins that McCarthy is talking about.  He thinks we're a much more interesting hybrid than that.  He gives his evidence first: humans have low fertility, and males produce a great many abnormal sperm (kind of a surprise given our reproductive success -- you have to wonder, if this is true, how there can be seven billion of us).

What?  You want more evidence than that?  Sorry, that's it.  Guys produce lots of abnormal sperm, and allegedly we have low fertility.  So we're hybrids.  That's enough, right?

Of course right.  So now, if we're hybrids, we have to figure out which two species gave rise to humans.  One of them, McCarthy says, was clearly something like a chimp.  But he states, in all apparent seriousness, "Many characteristics that clearly distinguish humans from chimps have been noted by various authorities over the years."  Can't argue with that.  But then he goes right off the edge of the cliff:

One fact, however, suggests the need for an open mind: as it turns out, many features that distinguish humans from chimpanzees also distinguish them from all other primates. Features found in human beings, but not in other primates, cannot be accounted for by hybridization of a primate with some other primate. If hybridization is to explain such features, the cross will have to be between a chimpanzee and a nonprimate — an unusual, distant cross to create an unusual creature.

If this sets alarm bells off, good -- because this would require a fertile hybrid being produced from a mating of animals not just from two different genera, or two different families, but two different orders.  Entirely possible, McCarthy says, despite the fact that there is not a single example -- not one -- of an interordinal hybrid known from nature.  Anywhere.  That includes animals, plants, fungi, and so on.

Nevertheless, that doesn't stop McCarthy:

Looking at a subset of the listed traits [unique features of humans are listed in the sidebar on page two of his website; there are too many to list here], however, it's clear that the other parent in this hypothetical cross that produced the first human would be an intelligent animal with a protrusive, cartilaginous nose, a thick layer of subcutaneous fat, short digits, and a naked skin. It would be terrestrial, not arboreal, and adaptable to a wide range of foods and environments. 

So, let's not dillydally any more; if a chimp is one of our parental species, what's the other?

What is this other animal that has all these traits? The answer is Sus scrofa, the ordinary pig. What are we to think of this fact? If we conclude that pigs did in fact cross with apes to produce the human race, then an avalanche of old ideas must crash to the earth. But, of course, the usual response to any new perspective is "That can't be right, because I don't already believe it." This is the very response that many people had when Darwin first proposed that humans might be descended from apes, an idea that was perceived as ridiculous, or even as subversive and dangerous. And yet, today this exact viewpoint is widely entertained. Its wide acceptance can be attributed primarily to the established fact that humans hold many traits in common with primates. That's what made it convincing... Let us take it as our hypothesis, then, that humans are the product of ancient hybridization between pig and chimpanzee.

So, basically, the logic is, "people laughed at Darwin, and he turned out to be right, so if people laugh at me, I must be right?"

But I don't want to be accused of jumping to conclusions ("That can't be right, because I don't already believe it"), so I took what I think is a critical look at the list of allegedly unique features of humans -- ones that, in McCarthy's view, must have come from our other, non-primate parental species.  And most of them have to do with quantities and sizes -- "sparse" hair, "large amounts" of elastic fiber in the skin, "richly" vascularized dermis, "narrow" eye opening, "heavy" eyelashes, and so on.  Traits involving quantities and sizes are highly responsive to selective pressures, the idea being once you have genes for the production of a feature, it is relatively straightforward to evolve to produce more or less of it.

Of the features he claims are found only in humans and pigs, it appears that in several cases, he is simply wrong.  Take multipyramidal kidneys -- he is correct that only humans have this feature amongst primates, but it is hardly unique in the mammalian world.  Besides humans and pigs, elephants have multipyramidal kidneys, as do bears, rhinoceroses, bison, and "nearly all marine mammals," according to a paper by M. F. Williams (available here).  Williams' contention is that multipyramidal kidneys evolved in animals that lived in coastal or marine environments in order to deal with high levels of salt -- and that each of these lineages evolved it independently, as it represents a unique feature on separate, distantly related branches of the phylogenetic tree (evolutionary biologists call these features "apomorphies").

Then, of course, he has some things on the list of allegedly unique human characteristics that are simply weird.  "Particular about place of defecation?"  (Has he ever owned a cat?)  "Snuggling?"  "Extended male copulation time?"  "Good swimmer?"

I'm sorry, Dr. McCarthy, but I'm calling bullshit on this.

Now, please understand; it's not like I have any particular problem with our having a checkered ancestry.  I'm an evolutionary biologist by training, for cryin' in the sink, I know we're animals.  But the idea that Homo sapiens arose when a chimp had sex with a pig... that stretches credulity too far.

Even if you do have a Ph.D.