Genes, lost and found

There's a famous anecdote about British biologist J. B. S. Haldane.  Haldane was a brilliant geneticist and evolutionary biology but was also notorious for being an outspoken atheist -- something that during his lifetime (1892-1964) was seriously frowned upon.  The result was that religious types frequently showed up at his talks, whether or not the topic was religion, simply to heckle him.

At one such presentation, there was a question-and-answer period at the end, and a woman stood up and asked, "Professor Haldane, I was wondering -- what have your studies of biology told you about the nature of God?"

Without missing a beat, Haldane said, "All I can say, ma'am, is that he must have an inordinate fondness for beetles."

There's some justification for the statement.  Beetles, insects of the order Coleoptera, are the most diverse order in Kingdom Animalia, with over four hundred thousand different species known.  (This accounts for twenty-five percent of known animal species, in a single order of insects.)  The common ancestor of all modern species of beetles was the subject of an extensive genetic study in 2018 by Zhang et al., which found that the first beetles lived in the early Permian Period, on the order of three hundred million years ago.  They survived the catastrophic bottleneck at the end of the Permian and went on to diversify more than any other animal group.

One striking-looking family in Coleoptera is Buprestidae, better known as "jewel beetles" because of their metallic, iridescent colors.  Most of them are wood-borers; a good many dig into dying or dead branches, but a few (like the notorious emerald ash borer, currently ripping its way through forests in the northern United States and Canada) are significant agricultural pests.

A few of them have colors that barely look real:

An Australian jewel beetle, Temognatha alternata [Image licensed under the Creative Commons John Hill at the English-language Wikipedia]

What's curious about this particular color pattern is that beetles apparently had a gene loss some time around the last common ancestor three hundred million years ago that knocked out the ability of the entire group to see in the blue region of the spectrum.  This kind of thing happens all the time; every species studied has pseudogenes, genetic relics left behind as non-functional copies of once-working genes that suffered mutations either to the promoter or coding regions.  However, it's odd that animals would have colors they themselves can't see, given that bright coloration is very often a signal to potential mates.

That's not the only reason for bright coloration, of course; there is also aposematic coloration (also known as warning coloration), in which flashy pigmentation is a signal that an animal is toxic or otherwise dangerous.  There, of course, it's not important to be seen by other members of your own species; all that counts is that you're visible to potential predators.  But jewel beetles aren't toxic, so their bright colors don't appear to be aposematic.

The puzzle was solved in a paper in Molecular Biology and Evolution that came out last week, in which a genetic study of jewel beetles found that unlike other beetles, they can see in the blue region of the spectrum -- and in fact, have unusually good vision in the orange and ultraviolet regions, too.  What appears to have happened is that a gene coding for a UV-sensitive protein in the eye was duplicated a couple of times (another common genetic phenomenon), and those additional copies of the gene were then free to accrue mutations and take off down their own separate evolutionary paths.  One of them gained mutations that altered the peak sensitivity of the protein into the blue region of the spectrum; the other gave their hosts the ability to see light in the orange region.

The result is that jewel beetles became tetrachromats; their eyes have acuity peaks in four different regions of the spectrum.  (Other than a few people --who themselves have an unusual mutation -- humans are trichromats, with peaks in the red, green, and blue regions.) 

What this shows is that lost genes can be recreated.  The gene loss that took out beetles' blue-light sensitivity was replaced by a duplication and subsequent mutation of a pre-existing gene.  It highlights the fundamental misunderstanding inherent in the creationists' mantra that "mutations can't create new information;" if that's not exactly what this is, there's something seriously amiss with their definition of the word "information."  (Of course, I'm sure any creationists in the studio audience -- not that there are likely to be many left -- would vehemently disagree with this.  But since willfully misunderstanding scientific research is kind of their raison d'être, that should come as no surprise to anyone.)

Anyhow, the jewel beetle study is a beautiful and elegant piece of research.  It showcases the deep link between genetics and evolution, and reminds me of the quote from Ukrainian-American biologist Theodosius Dobzhansky, which seems a fitting place to end: "Nothing in biology makes sense except in light of evolution."

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Butterfly effect

Most of you probably know the basic story you were taught in high school biology; DNA has information-containing chunks called genes, which sit in specific places in packages called chromosomes.  Each of those genes is the instruction set for building a specific protein, and the instructions are read by creating an intermediary copy (called mRNA) of the specific gene in question, which then is transported to a structure in the cell called the ribosome, where the sequence is read and used to assemble the protein from smaller bits called amino acids.  The protein thus created -- it could be an enzyme, a structural protein, an energy carrier, a pigment, or any of dozens of other types -- goes on to do its specific job in the organism.

This pattern -- gene (DNA) to mRNA to protein -- was thought to be more or less the whole story by the people who unraveled the pattern, James Watson and Francis Crick, so in their typical self-congratulatory fashion they called it the "Central Dogma of Molecular Genetics."  (And if you know anything about their history, you'll understand why I'm calling it "typical.")  So it was a considerable shock when researchers found out that there was DNA in the genome of every species studied that didn't work this way.

It was a considerably bigger shock when it was found that the amount of DNA that did work this way was around one percent.

You read that right; between ninety-eight and ninety-nine percent of your genome is non-coding DNA.  It does not encode the instructions for building proteins.  Watson and Crick's "Central Dogma" only applies directly to less than two percent of an organism's DNA.  When this was discovered in the 1960s and 1970s, researchers (speaking of arrogance...) called it "junk DNA," following the apparent line of reasoning, "If we don't know what it does right now, it must be useless."

The whole "junk DNA" moniker never made sense to me, especially with the discovery of short tandem repeats, chunks of DNA between two and ten base pairs long that repeat over and over again (the average number of repeats is twenty-five).  Short tandem repeats are common in eukaryotic DNA, and their function is unknown.  That they do have a function -- and are not, in fact, "junk" -- is strongly supported by the fact that they're evolutionarily conserved.  Mutations happen, and if there really was no function at all for STRs, over time the pattern would get lost as mutations altered one base pair after another.  The fact that the pattern has been maintained argues that they have an important function of some kind, and mutations knock that function out and are heavily selected against.

We just don't know what it is yet.

The reason all this comes up is the discovery by a team right here in my neck of the woods, at Cornell University, that at least some of the patterns in butterfly wings are controlled by "genetic switches" in their non-coding DNA.  The team, led by Anyi Mazo-Vargas, looked at forty-six regions of non-coding DNA, and found out that a significant number of them, when disabled (a technique called gene knockout), cause huge changes in the butterfly's wing pattern.  Take, for example, the brightly-colored Heliconius butterflies:

[Image licensed under the Creative Commons Heliconius mimicry, CC BY 2.5]

Knock out a DNA sequence called WntA, and the stripes disappear; disable Optix, and the wings come out jet black.

Other than the obvious deduction -- that these non-coding sequences are acting as switches determining deposition of pigments and arrangements of the cells that generate iridescence -- not much is known about how these sequences work.  "We see that there's a very conserved group of switches that are working in different positions and are activated and driving the gene," Mazo-Vargas said.  

"We have progressively come to understand that most evolution occurs because of mutations in these non-coding regions," added Robert Reed, who co-authored the paper.  "What I hope is that this paper will be a case study that shows how people can use this combination of ATAC-seq and CRISPR [two techniques used in gene modification and knockout] to begin to interrogate these interesting regions in their own study systems, whether they work on birds or flies or worms."

So once again, as we look more closely at things, we find intricacies we never dreamed of.  What I love about research like this is that a seemingly small discovery -- that small stretches of non-coding DNA control macroscopic traits like coloration -- could have an impact on our understanding of how genetics works in general.

Truly -- a "butterfly effect."

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Jurassic rainbow

Regular readers of Skeptophilia might recall that about a year ago, paleontologists announced the discovery of a bird fossil from northeastern China that had a long, pennant-like tail -- and that from the extraordinary state of preservation, they were able to determine that the outer tail feathers had been gray, and the inner ones jet black.

Determining feather, hair, and skin color of prehistoric animals is remarkably tricky; the pigments in those structures break down rapidly when the animal's body decomposes, and the structures themselves are fragile and rarely fossilize.  The result is that when artists do reconstructions of what these animals may have looked like, they base those features on analogies to modern animals.  This is why in old books on dinosaurs, they were always pictured as having greenish or brownish scaly skin, like the lizards they were thought to resemble, even though dinosaurs are way more closely related to modern birds than they are to modern lizards.  (To be fair, even the paleontologists didn't know that until fairly recently, so the artists were doing their best with what was known at the time.)

But it does mean that if we were to get in the TARDIS and go back to the Mesozoic Era, we'd be in for a lot of surprises about what the wildlife looked like back then.  Take, for example, the late Jurassic Period fossil found by a farmer in China that contained the nearly-complete skeleton of a birdlike dinosaur.  Here's the fossil itself:

What's remarkable about this fossil is that the feathers were so well-preserved that paleontologists were able to get a close look at the melanocytes -- the pigment-containing cells -- and from the arrangement and layering of those cells, they determined that the dinosaur's head feathers were arrayed like a rainbow, similar to modern hummingbirds, sunbirds, and trogons.

So here's the current reconstruction of what this species looked like:

[Reconstruction by artist Velizar Simeonovski, of The Field Museum]

Kind of different from the drab-colored overgrown iguanas from Land of the Lost, isn't it?

The species, christened Caihong juji from the Mandarin words meaning "big rainbow crest," adds another ornate member to the late Jurassic and early Cretaceous fauna of what is now northern China.  And keep in mind that we only know about the ones that left behind good fossils -- probably less than one percent of the total species around at the time.  As wonderful as it is, our knowledge of the biodiversity of prehistory is analogous to a future zoologist trying to reconstruct our modern ecosystems from the remains of a sparrow, a cat, a raccoon, a deer, a grass snake, and a handful of leaves from random plants.

I think my comment about being "in for a lot of surprises" if we went back then is a significant understatement.

Even so, this is a pretty amazing achievement.  Astonishing that we can figure out what Caihong juji looked like from some impressions in a rock.  And it gives us a fresh look at a long-lost world -- but one that was undoubtedly as rainbow-hued and iridescent as our own.

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The origins of Old Yeller

Since the last few days (hell, the last few years) of news has been filled with one horrible thing after another, today I'm retreating into my happy place, namely: the cool scientific discovery of the week.

And puppies.  Lots o' puppies.

I don't know if it's ever occurred to the dog lovers in the studio audience how unusual dog coat coloration is.  I can't think of another animal species that has such striking variability -- from the jet black of black labs to the solid bronze of golden retrievers to the spots of Dalmatians to the particolored patches of collies, there is huge variation in fur color across the species.

One additional one that is especially curious is called agouti coloration -- when the base of the hair is yellow and the tip is black.  This is frequently seen in German shepherds, and was also the coat pattern in my beloved rescue dog Grendel:

If you're wondering, Grendel was not spoiled.  At all.

As you can see, Grendel also looked a bit like someone created a Frankendog by stitching together parts of about six different breeds.  He didn't have any other German-shepherd-like characteristics, but he definitely seemed to have pilfered his fur from one while it wasn't looking.

Well, a new piece of research that appeared in Nature Ecology and Evolution this week indicates that five very common coat color patterns in dogs come from the activity of a single gene.  Where and when this gene activates (and creates a gene product called the agouti signaling protein) determines the deposition of two pigments -- eumelanin (which is black) and pheomelanin (which is yellow).  The amount and placement of these two pigments creates five different color patterns, as shown below:

[Image from Bannasch et al.}

One of these alleles, dominant yellow, is apparently of ancient origins; the researchers determined that it was present in an extinct canid species that branched off from wolves over two million years ago.

I'm a little curious about another dog coat feature, the white blaze, something my current non-spoiled dog Guinness has:

He also has white toes, which may or may not be related:

As you can see from the image from Bannasch et al., some of the dogs expressing each pattern have white blazes and some don't, so whatever genetic mechanism controls it must be independent of the agouti gene.

But if you have a dog with some yellow or agouti coloration, you now know that your pooch descends from a branch of the canine family tree that is two million years old.  As far as Guinness goes, I flatly refuse to believe he descends from wolves.  His level of fierceness is somewhere between "cream puff" and "cupcake."  He is basically a seventy-pound lap dog. 

In any case, that's the latest from the field of canine genetics and evolution.  Me, I wonder where another important dog feature comes from, and that's the cute head tilt.  There's no doubt that it's a significant selective advantage:

Guinness:  Play ball? 

Me:  Dude.  It's raining outside. 

Guinness:  Please play ball? 

Me:  Don't you want to wait?  I really don't want to go stand out in the... 

Guinness: *adorable head tilt* 

Me:  Dammit.

Speaking of which, I need to go get my dogs their breakfast because they're staring at me.  You'd think if they really are descended from wolves, they could go hunt down a squirrel or something, but I guess the decision to take advantage of sofas was made at the same time as they figured out it was easier to wait for someone to place a bowl full of dog food in front of them than to wear themselves out chasing some scrawny squirrel.

You gotta wonder who has trained whom, here.

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

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

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

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