Written in the genes

Two years ago, I wrote about a mysterious plunge in global average temperature that occurred 12,800 years ago.  It's nicknamed the "Younger Dryas event," after the tundra wildflower Dryas octopetala, which showed a population explosion over the following millennium (as judged by pollen in ice core samples).  This plant only flourishes when the winters are extremely cold, and the pollen spike, along with various other lines of evidence, supports a rapid drop in temperature averaging around six degrees Celsius worldwide.

[Image licensed under the Creative Commons xulescu_g, Dryas octopetala (41907904865), CC BY-SA 2.0]

The obvious question, of course, is what could cause such a rapid and catastrophic drop in temperature.  There are three reasonably plausible answers that have been suggested: 

1. an impact by a comet or meteorite causing an ejection of ash into the atmosphere, blocking sunlight
2. the collapse of an ice dam across what is now the St. Lawrence Seaway -- the temperature had been warming prior to the event -- allowing the emptying of an enormous freshwater lake into the North Atlantic, shutting off the thermohaline circulation and propelling the Northern Hemisphere back into an ice age
3. a nearby supernova in the constellation Vela frying the ozone layer, causing a collapse of ecosystems worldwide and an atmospheric chain reaction resulting in a global drop in temperature

The discussion amongst the scientists is ongoing, but the weight of evidence seems to favor the impact hypothesis.  (The link I posted above has more details, if you're curious.)

What's more certain is that the Younger Dryas event had a massive effect.  A number of large mammal groups -- including mastodons, North American camels, dire wolves, and gomphotheres (a bizarre-looking elephant relative) -- all went extinct shortly after the event itself, whatever it was, occurred.  Humans very nearly bit the dust, too; two of the dominant cultures of the time, the Natufian culture of the Middle East and the Clovis culture of North America, both collapsed right around the same time.

It's the latter that brings the topic up, because of some fascinating new research that came out last week, led by Paula Paz Sepúlveda of the Universidad Nacional de La Plata (Argentina), which looks at the effects this wild climate reversal had on the human genome.

What the researchers did was look at the makeup of the Q Y-DNA haplogroup.  You probably already know that two bits of our genome, the Y chromosome and the mitochondrial DNA, are frequently used for analyzing ethnic group affiliations because they don't recombine each generation -- they're passed down intact through (respectively) the paternal and maternal line.  So your mtDNA is the same as your mother's mother's mother's (etc.), and if you're male, your Y DNA is the same as your father's father's father's (etc.).  This means that the only differences in either one are due to mutations, making them invaluable as a measure of the degree of relatedness of different ethnic groups, not to mention providing a way to track patterns of human migration.

The Q haplogroup is ubiquitous in indigenous people of North and South America, so it was a good place to start looking for clues that the climate shift might have written into the human genome.  And they found them; coincident with the Younger Dryas event there was a marked drop in genetic diversity in the Q haplogroup.  It looks like the climate calamity caused a bottleneck -- a severe reduction in population, resulting in a loss of entire genetic lineages:

The YD impact hypothesis states that fragments of a large disintegrating asteroid/comet hit North America, South America, Europe, and Western Asia at 12,800 cal BP.  Multiple airbursts/impacts produced the YD boundary layer (YDB, Younger Dryas boundary), depositing peak concentrations of a wide variety of impact markers.  The proposed impact event caused major changes in continental drainage patterns, ocean circulation, in temperature and precipitation, large-scale biomass burning, abrupt climate change, abrupt anomalous distribution of plants and animals, extinction of megafauna, as well as, cultural changes and human population decline.  The diversity of the set of markers related to the cosmic impact is found mainly in the Northern hemisphere, including Venezuela, but they have also been recorded in the Southern hemisphere, in Chilean Patagonia, and Antarctica.

It's fascinating to think of our own genomes, and (of course) the genomes of other species, as being a kind of proxy record for climate; that not only gradual fluctuations, but sudden and unexpected events like impacts and volcanic eruptions, can leave their marks on our DNA.  It brings home once again how interlocked everything is.  Our old perception of humans as being some kind of independent entity, separate from everything else on Earth, is profoundly wrong.  We were molded into what we are today by the same forces that created the entire biosphere, and we can't separate ourselves from those forces any more than we could disconnect from our own heartbeats.  As Chief Seattle famously put it, "Man did not weave the web of life, he is merely a strand in it.  Whatever he does to the web, he does to himself."

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The Spanish replacement

It's strange to think about, but there is a point in human history at which you can divide all of the inhabitants into two categories: those who left no living descendants at all, and those who are the ancestors of every single person alive today.

Anthropologists differ as to when that date is, but it's probably more recently than most of us would guess.  It certainly happened after the Toba bottleneck, a point about 74,000 years ago when there was a massive eruption of the Toba volcano (in the Indonesian archipelago) and a worldwide climate impact that may have reduced the entire population of ancestral humans to fewer than 7,000 total.  (Nota bene: scientists are still debating how big the bottleneck was, and whether it was the volcano that actually caused it; but I'm referring to the event by its most common nickname even so.)

What's cool is that with our current ability to do genetic analysis, we can narrow in on the answers to these sorts of questions.  Just last week, some research was published in Cell giving us an interesting lens into settlement patterns in Spain -- and that only 4,500 years ago, an influx of people from Eastern Europe and Russia resulted in the replacement of nearly all of the Y-chromosomal DNA that had been there for the previous forty thousand years.

This doesn't mean that the previous inhabitants left no descendants (although that could be true) -- all we can infer with certainty is that the men who had lived there prior to the invasion left very few patrilineal descendants.  As Y-chromosomal DNA is passed only father-to-son, any male descendants a man has through his daughters would share none of his Y-DNA.  (The same is true, but with the opposite genders, about mitochondrial DNA, which is only passed through the maternal line.)

In "Survival of Late Pleistocene Hunter-Gatherer Ancestry in the Iberian Peninsula," by Vanessa Villalba-Mouco, Marieke S. van de Loosdrecht. Cosimo Posth, Pilar Utrilla, Johannes Krause, and Wolfgang Haak, of the Max Planck Institute for the Science of Human History working with the University of Zaragoza, the authors write:

The Iberian Peninsula in southwestern Europe represents an important test case for the study of human population movements during prehistoric periods.  During the Last Glacial Maximum (LGM), the peninsula formed a periglacial refugium for hunter-gatherers (HGs) and thus served as a potential source for the re-peopling of northern latitudes...  Western and central Europe were dominated by ancestry associated with the ∼14,000-year-old individual from Villabruna, Italy, which had largely replaced earlier genetic ancestry, represented by 19,000–15,000-year-old individuals associated with the Magdalenian culture.  However, little is known about the genetic diversity in southern European refugia, the presence of distinct genetic clusters, and correspondence with geography.  Here, we report new genome-wide data from 11 HGs and Neolithic individuals that highlight the late survival of Paleolithic ancestry in Iberia, reported previously in Magdalenian-associated individuals.  We show that all Iberian HGs, including the oldest, a ∼19,000-year-old individual from El Mirón in Spain, carry dual ancestry from both Villabruna and the Magdalenian-related individuals.  Thus, our results suggest an early connection between two potential refugia, resulting in a genetic ancestry that survived in later Iberian HGs.  Our new genomic data from Iberian Early and Middle Neolithic individuals show that the dual Iberian HG genomic legacy pertains in the peninsula, suggesting that expanding farmers mixed with local HGs.

A different study, also published last week in the journal Science, added another piece to the puzzle.  "The Genomic History of the Iberian Peninsula Over the Past 8000 Years," by a team of scientists far too lengthy to list working at over a dozen research institutions, examined the DNA of 271 individuals and came to some fascinating conclusions about the settlement of Spain:

We assembled genome-wide data from 271 ancient Iberians, of whom 176 are from the largely unsampled period after 2000 BCE, thereby providing a high-resolution time transect of the Iberian Peninsula.  We document high genetic substructure between northwestern and southeastern hunter-gatherers before the spread of farming.  We reveal sporadic contacts between Iberia and North Africa by ~2500 BCE and, by ~2000 BCE, the replacement of 40% of Iberia’s ancestry and nearly 100% of its Y-chromosomes by people with Steppe ancestry...  Additionally, we document how, beginning at least in the Roman period, the ancestry of the peninsula was transformed by gene flow from North Africa and the eastern Mediterranean.

This influx pushed the Iberian farmers, who before had occupied the entire peninsula, into the mountainous northeastern parts of Spain -- and they are, apparently, the ancestors of today's Basque people, who are not only genetically distinct but who speak a language thought to be unrelated to any other existing language.  "The Basque country is a really difficult place to conquer; there are quotes from French rulers in medieval times saying that this is a nasty place to get in an army," said population geneticist Mattias Jakobsson of Uppsala University in Sweden, who was not part of either of the present studies.

Iñigo Olalde, a postdoc in the lab of population geneticist David Reich at Harvard Medical School in Boston, who is himself Basque, and who participated in the second study, agrees.  "The present-day Basques look like Iron Age people from Iberia," Olalde said.

What I find most fascinating about this is how we can use genetic analysis as a lens into a time period from which we have no written records at all, and make inferences about the movements of people who before had been entirely a mystery.  There's a lot we still don't know, of course, including how this genetic replacement took place.  "It would be a mistake to jump to the conclusion that Iberian men were killed or forcibly displaced," Olalde said, "as the archaeological record gives no clear evidence of a burst of violence in this period."

This opens up the potential for using this technique to study other time periods that are historical enigmas -- like the European "Dark Ages," between the Fall of Rome and consolidation of the Holy Roman Empire with the crowning of Charlemagne in 800 C.E.  Amazing that genetics, which tells us about who we are here and now, can also be seen as a history of where we came from -- a continuous record of information back to our earliest ancestors.

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This week's Skeptophilia book recommendation is a look at one of the most peculiar historical mysteries known: the unsolved puzzle of Kaspar Hauser.

In 1828, a sixteen-year-old boy walked into a military station in the city of Ansbach, Germany.  He was largely unable to communicate, but had a piece of paper that said he was being sent to join the cavalry -- and that if that wasn't possible, whoever was in charge should simply have him hanged.

The boy called himself Kaspar Hauser, and he was housed above the jail.  After months of coaxing and training, he became able to speak enough to tell a peculiar story.  He'd been kept captive, he said, in a small room where he was never allowed to see another human being.  He was fed by a man who sometimes talked to him through a slot in the door.  Sometimes, he said, the water he was given tasted bitter, and he would sleep soundly -- and wake up to find his hair and nails cut.

But locals began to question the story when it was found that Hauser was a pathological liar, and not to be trusted with anything.  No one was ever able to corroborate his story, and his death from a stab wound in 1833 in Ansbach was equally enigmatic -- he was found clutching a note that said he'd been killed so he couldn't identify his captor, who signed his name "M. L. O."  But from the angle of the wound, and the handwriting on the note, it seemed likely that both were the work of Hauser himself.

The mystery endures, and in the book Lost Prince: The Unsolved Mystery of Kaspar Hauser, author Jeffrey Moussaieff Masson looks at the various guesses that people have made to explain the boy's origins and bizarre death.  It makes for a fascinating read -- even if truthfully, we may never be certain of the actual explanation.

[If you purchase the book from Amazon using the image/link below, part of the proceeds goes to supporting Skeptophilia!]

Insect rebound

I vividly recall my first visit to the American Museum of Natural History in Washington, DC, perhaps fifteen years ago.  Having a fascination for evolutionary biology and paleontology, I was thrilled to take a walk down the hallway with exhibits of each biological taxon, in phylogenetic order -- put simply, all the groups of living things in the order they come on the family tree of life.

So I'm walking up the hall, and things are progressing the way I'd expect -- bacteria to protozoans to plants to primitive animals, and within Kingdom Animalia, jellyfish to flatworms to roundworms to more complex invertebrates, and then on to fish, amphibians, reptiles, birds, and mammals.

But that wasn't the end of the hall.  The usual approach to the "Great Tree of Life" -- with, of course, mammals at the top of the heap and humans at the top of the mammals, as befits the pinnacle of evolution -- wasn't applied here.  If you progress past mammals, you're into Phylum Arthropoda, those animals with jointed legs and an exoskeleton, which include arachnids, crustaceans, centipedes, millipedes, and the most successful creatures on Earth...

... insects.

Being that it's the end of summer in upstate New York, I can verify that insects are highly successful life forms, given that there are millions of mosquitoes in my back yard alone, every single one of which divebombs my wife whenever she goes outside.  Something about Carol just attracts biting insects.  In fact, she claims that I bring her along to tropical destinations just to draw the mosquitoes away from me.

Which is not true.  Honestly.

In all seriousness, there is incredible diversity amongst insects, and many taxonomists believe that the number of insect species outnumbers all other kinds of animals put together.  Just beetles by themselves -- Order Coleoptera -- represents over 400,000 species, or about 25% of the total animal biodiversity on Earth.

This is the origin of the famous story about biologist J. B. S. Haldane, who was not only a vocal proponent of evolution but was an outspoken atheist.  Haldane frequently had hecklers show up at his talks, and one such asked him at the end, "So, Professor Haldane, what has your study of biology told you about the nature of God?"

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

Metallic Shield Bug (Scutiphora pedicellata) from Australia [Image licensed under the Creative Commons Benjamint444, Metallic shield bug444, CC BY-SA 3.0]

It's curious that such a diverse and ubiquitous group still has a great many questions unresolved about its origins.  It's known that the big jump in insect diversity came after the Permian-Triassic Extinction of 252 million years ago, the "Great Dying" that wiped out (by some estimates) 95% of life on Earth.  There's a common pattern that a sudden burst of species formation always follows a mass extinction, but in this case, because of a poor fossil record following the event, it's been hard to connect later biodiversity to speciation amongst the survivors.

We just got a huge boost in what we know about insect evolution because of the discovery of a fossil deposit in China dating from 237 million years ago, or only ("only!") fifteen million years after the extinction itself.  The site had eight hundred fossils representing 28 different insect families that had survived the bottleneck, including the ancestors of modern beetles, flies, and cockroaches.

The study, done jointly by Zheng Daran and Wang Bo of the State Key Laboratory of Paleobiology and Stratigraphy in Nanjing, China and Chang Su-Chin of the University of Hong Kong, is only a preliminary analysis of the fossils at the site, and has already helped to connect the dots between pre-Permian-Triassic insects and more modern ones.  As Elizabeth Pennisi, senior correspondent for Science magazine, writes:

The sites underscore that this burst of evolution took place much earlier than researchers had thought, particularly for water-loving insects.  Among the remains are fossil dragonflies, caddisflies, water boatmen, and aquatic beetles.  Until now, paleontologists had thought such aquatic insects didn’t diversify until 130 million years ago.  These insects—which include both predators and plant eaters—helped make freshwater communities more complex and more productive... moving them toward the ecosystems we see today.

It's always fascinating when we add something to our knowledge of past life, and even more impressive when it's about one of the most diverse groups that has ever existed.  Seeing how life rebounded after the Permian-Triassic Extinction should also give us hope -- that even after a cataclysm, the survivors can still come back and rebuild Earth's biodiversity.

Or, as Ian Malcolm put it in Jurassic Park, "Life finds a way."

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This week's Skeptophilia book recommendation is part hard science, part the very human pursuit of truth.  In The Particle at the End of the Universe, physicist Sean Carroll writes about the studies and theoretical work that led to the discovery of the Higgs boson -- the particle Leon Lederman nicknamed "the God Particle" (which he later had cause to regret, causing him to quip that he should have named it "the goddamned particle").  The discovery required the teamwork of dozens of the best minds on Earth, and was finally vindicated when six years ago, a particle of exactly the characteristics Peter Higgs had described almost fifty years earlier was identified from data produced by the Large Hadron Collider.

Carroll's book is a wonderful look at how science is done, and how we have developed the ability to peer into the deepest secrets of the universe.

[If you purchase the book from Amazon using the image/link below, part of the proceeds goes to supporting Skeptophilia!]

Science shorts

After the last three days' depressing posts, I thought it was once again time to retreat to my happy place, which is: cool new scientific research.  So, for your reading entertainment, here are some early-summer shorts.

[Image licensed under the Creative Commons marcore! from Hong Kong, China, Board shorts 4, CC BY 2.0]

No, not those kind of shorts.  The scientific variety.

First, we have some research that appeared last week in the Journal of Applied Research in Memory and Cognition, done by Julia Soares and Benjamin Storm of the University of California.  In their paper, entitled, "Forget in a Flash: A Further Investigation of the Photo-Taking Impairment Effect," what Soares and Storm found that for reasons still unknown, taking a photo of something impairs your ability to remember it -- even if you know that you won't have access to the photo later.

The authors write:

A photo-taking-impairment effect has been observed such that participants are less likely to remember objects they photograph than objects they only observe.  According to the offloading hypothesis, taking photos allows people to offload organic memory onto the camera's prosthetic memory, which they can rely upon to “remember” for them.  We tested this hypothesis by manipulating whether participants perceived photo-taking as capable of serving as a form of offloading.  In [our] experiments, participants exhibited a significant photo-taking-impairment effect even though they did not expect to have access to the photos.  In fact, the effect was just as large as when participants believed they would have access to the photos.  These results suggest that offloading may not be the sole, or even primary, mechanism for the photo-taking-impairment effect.

The authors were interviewed by Alex Fradera for the Research Digest of the British Psychological Society, and there's a possible explanation for the phenomenon, although it's still speculative.  Fradera writes:

Soares and Storm have a speculative second interpretation.  They suggest that the effort involved in taking a photo – getting the framing right, ensuring the lens is in focus – leads to the sense that you’ve done a good job of encoding the object itself, even though you have been focusing more on peripheral features.  So you’re not mentally slacking-off because you think the camera has it covered – but because you think you already have.  It may be relevant that people who take photographs at events report afterwards feeling more immersed in the experience, which would tally more with this explanation than the disengagement-due-to-fiddling idea.  In any case this is further evidence that those of us who approach exciting life events through the lenses of our electronic devices may be distancing ourselves from fuller participation.

From the Department of Geophysics at the University of Texas comes a study of the most famous (although not, by a long shot, the largest) mass extinction event -- the Cretaceous-Tertiary Extinction of 65 million years ago, which took out the dinosaurs, with the exception of the ancestors of today's birds.  The accepted explanation of the event is a collision by a massive meteorite near what is now the Yucatán Peninsula, forming the Chicxulub Crater.

A long-unanswered question about mass extinctions such as this one is how fast life rebounded.  The problem is that the difference between a thousand, ten thousand, and a hundred thousand years in the geological record isn't that great, so the error rate for any estimates were bound to be high.  But now, geophysicists Chris Lowery, Gail Christeson, Sean Gulick, and Cornelia Rasmussen, working with Timothy Bralower, a micropaleontologist at Pennsylvania State University, have found evidence that narrows that window down -- and surprisingly, shows that life recovered pretty quickly.

The key was finding a sediment core that contained 76 centimeters of brown limestone that came from the years immediately following the impact.  It contained debris from the event, including crystals of "shocked quartz" (quartz crystals showing signs of sudden, extreme temperatures and pressures).  And what the researchers found was that a little as a few thousand years, the ecosystem was beginning to rebound.

"You can see layering in this core, while in others, they’re generally mixed, meaning that the record of fossils and materials is all churned up, and you can’t resolve tiny time intervals," Bralower said.  "We have a fossil record here where we’re able to resolve daily, weekly, monthly, yearly changes."

Speaking of catastrophes, a fascinating piece of research from Stanford University anthropologists Tian Chen Zeng, Alan Aw, and Marcus Feldman gives us a possible explanation for a peculiar calamity that the human race experienced only seven thousand years ago.  By analyzing the genetic diversity among human Y-chromosomal DNA (inherited only father-to-son) and comparing it to the diversity in mitochondrial DNA (inherited only mother-to-child), they found something decidedly odd; the data suggested a serious genetic bottleneck -- but one that affected only males.

The difference was huge.  Zeng et al. showed that the disparity would only make sense if there was a point about seven thousand years ago when there was one male with surviving descendants for every seventeen females.

Feldman writes, in a press release to EurekAlert!:

After the onset of farming and herding around 12,000 years ago, societies grew increasingly organized around extended kinship groups, many of them patrilineal clans - a cultural fact with potentially significant biological consequences. The key is how clan members are related to each other.  While women may have married into a clan, men in such clans are all related through male ancestors and therefore tend to have the same Y chromosomes.  From the point of view of those chromosomes at least, it's almost as if everyone in a clan has the same father. 

That only applies within one clan, however, and there could still be considerable variation between clans.  To explain why even between-clan variation might have declined during the bottleneck, the researchers hypothesized that wars, if they repeatedly wiped out entire clans over time, would also wipe out a good many male lineages and their unique Y chromosomes in the process.

So as weird as it sounds, if you go back a few thousand years, we all have far fewer unique male ancestors than unique female ancestors.


Last, I would be remiss if I didn't make at least a brief mention of research that appeared in the Journal of Clinical Endocrinology and Metabolism last week.  Authored by Audrey J. Gaskins, Rajeshwari Sundaram, Germaine M. Buck Louis, and Jorge E. Chavarro, the paper was entitled "Seafood Intake, Sexual Activity, and Time to Pregnancy," and amongst its conclusion was that the quantity of seafood eaten correlates positively with the number of times per month people have sex.

The researchers speculate that the reason may be the higher quantity of long-chain omega-3 fatty acids, common in seafood, has an effect on the reproductive hormones, increasing sex drive.  It does, however, make me wonder how anyone thought of correlating these, but my puzzlement is probably indicative of why I never went into research.

In any case, I thought it was interesting.  And makes me glad I brought leftover scampi for lunch.  Hope springs eternal, you know?

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This week's recommended book is one that blew me away when I first read it, upon the urging of a student.  By groundbreaking neuroscientist David Eagleman, Incognito is a brilliant and often astonishing analysis of how our brains work.  In clear, lucid prose, Eagleman probes the innermost workings of our nervous systems -- and you'll learn not only how sophisticated it is, but how easy it can be to fool.