Cat tales

Humans have been keeping pets for a very long time.

A lot of it now is companionship, and I have to admit that despite Guinness having to play fetch-the-tennis-ball for several hours a day so he runs off enough energy that he won't get fidgety and eat the sofa, he's kind of entertaining to have around.  The thought is that dogs probably began the human/canine relationship as fierce and loyal guardians of home and hearth, and from there moved into closer emotional links, ultimately giving rise to phenomena like pugs wearing knitted sweaters with matching stocking caps.

Cats, on the other hand, aren't much good at home security, and at first were most likely kept around as mousers.  It must be said, however, that all of the cats I've owned were kind of non-starters as mousers.  They mostly specialized at sitting around looking bored, only moving when the block of sunshine they were occupying had the nerve to go somewhere else.  In my experience, they were more like dubiously-useful home décor items that pooped in a box in the laundry room.

Still, the human/feline association goes back a long way as well.  Back in 2017 a study at the Jacques Monod Institute in Paris used mitochondrial DNA from both ancient cat skeletons and modern cats to show that people were bringing cats with them when they migrated as long ago as 4,500 B.C.E.  The researchers used the frequency of the "blotched tabby" allele -- a gene that causes cats to have swirls of color in their coats instead of parallel stripes -- followed human migration patterns throughout the Middle East and Europe, making cat genetics a useful tool in determining where their human owners traveled.

[Image licensed under the Creative Commons Helgi Halldórsson from Reykjavík, Iceland, Cute cat (1698598876), CC BY-SA 2.0]

This wasn't the first study to connect cat genetics with human migration.  All the way back in 1977, an article in Scientific American by Neil Todd showed that the polydactyly gene -- which gives cats six toes per foot -- jumped from colonial New England to Nova Scotia and New Brunswick after the British lost the Revolutionary War.  A lot of Loyalists went to Canada and apparently brought their six-toed cats with them, creating pockets of high frequency of that allele in areas where the Loyalists ended up.

In 2005 a study appeared in the Journal of Heredity that created a family tree for 32 different cat populations, focusing particularly on cats in Arkansas and Tennessee, and found that the genetics of domestic cats was consistent with the genetics of whoever settled the area -- that places predominantly settled by people of Scottish descent, for example, still today have cats that are more closely related to their Scottish cousins than to cats in France or Switzerland.  It's kind of fascinating to think that our kitties here in the United States have their own migration patterns, from the Middle East to Europe to America, and that the routes they took are the same ones followed by their human owners.

The reason all this comes up is a study that showed up this week in Nature Scientific Reports called "The Earliest Domestic Cat on the Silk Road," by a team led by A. F. Haruda of the University of Exeter.  In it we find that pet cats -- not just practical semi-feral barn cats -- were being kept by Kazakh pastoralists a thousand years ago.

The authors write:

We present the earliest evidence for domestic cat (Felis catus L., 1758) from Kazakhstan, found as a well preserved skeleton with extensive osteological pathologies dating to 775–940 cal CE from the early medieval city of Dzhankent, Kazakhstan.  This urban settlement was located on the intersection of the northern Silk Road route which linked the cities of Khorezm in the south to the trading settlements in the Volga region to the north and was known in the tenth century CE as the capital of the nomad Oghuz.  The presence of this domestic cat, presented here as an osteobiography using a combination of zooarchaeological, genetic, and isotopic data, provides proxy evidence for a fundamental shift in the nature of human-animal relationships within a previously pastoral region.  This illustrates the broader social, cultural, and economic changes occurring within the context of rapid urbanisation during the early medieval period along the Silk Road.

The study looked at an amazingly complete cat skeleton that was buried beside a trade route.  What was remarkable was that the cat had apparently had a rough life -- it had several broken bones -- but those bones had healed, meaning it had been cared for post-injury.  Isotopic analysis of its bones showed that it had a very high protein diet, suggesting it was fed by humans rather than foraging on its own.  Toward the end of its life, it lost most of its teeth, so the fact that its diet remained good throughout is a pretty good indicator that someone was caring for it as a prized pet.

We often associate reverence for cats with the ancient Egyptians, but it's clear they weren't the only ones who held our feline friends in high regard.  We've been fond of our companion animals for a very long time, and wherever we go, they do.

Which I think is pretty sweet.  Even if they're only useful as décor.

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This week's Skeptophilia book of the week is for anyone fascinated with astronomy and the possibility of extraterrestrial life: The Sirens of Mars: Searching for Life on Another World, by Sarah Stewart Johnson.

Johnson is a planetary scientist at Georgetown University, and is also a hell of a writer.  In this book, she describes her personal path to becoming a respected scientist, and the broader search for life on Mars -- starting with simulations in the most hostile environments on Earth, such as the dry valleys of central Antarctica and the salt flats of Australia, and eventually leading to analysis of data from the Mars rovers, looking for any trace of living things past or present.

It's a beautifully-told story, and the whole endeavor is tremendously exciting.  If, like me, you look up at the night sky with awe, and wonder if there's anyone up there looking back your way, then Johnson's book should be on your reading list.

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

Paleo-walkabout

The classic account of the origins of Native Americans is that during the last Ice Age, the seas were lower, and what is now the floor of the Bering Sea was a broad, flat valley.  This allowed people to cross from Siberia into Alaska, and when the weather warmed and the seas rose, this cut off the "land bridge" and left the migrants North Americans for good.

Some cool new research out of the University of Copenhagen has shown that this story is a vast oversimplification, and that what actually happened is considerably more complex than a one-way hike from west to east.

In a paper in Nature called "The Population History of Northeastern Siberia Since the Pleistocene," by lead author Martin Sikora and no less than 53 co-authors, we find out that there wasn't just a single wave of migrants, and there was considerable back-and-forth, even after the seas flooded in and cut Alaska off from Siberia.  Sikora's team analyzed the DNA extracted from teeth from 34 different burials, from Finland all the way across to northeastern Siberia, and compared this to genetic material from Native American populations in northwestern North America.

What Sikora found is that there were several surges of migration across the "Bering Land Bridge," starting over thirty thousand years ago.  Each new wave of travelers mixed and mated with the preceding group of settlers -- and then some of them went back the other direction, settling in northeastern Siberia (where many of their descendants still live).  The authors write:

Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood.  Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago.  We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of ‘Ancient North Siberians’ who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to ‘Ancient Palaeo-Siberians’ who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name ‘Neo-Siberians’, and from whom many contemporary Siberians are descended.  Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas.

This study adds to some earlier work, published late last year, that found that the movement of those migrants once they got to North America was equally complex, going in (at least) three waves as they colonized the continent southward and eastward, with the second wave carrying people all the way to Tierra del Fuego.  This blows a neat hole into the idea that "Native American" is some kind of monolithic race of people all of whom are closely related -- which anyone who knows about the very disparate groups of Native American languages would find completely unbelievable anyhow.

[Image licensed under the Creative Commons 맛좋은망고, Langs N.Amer, CC BY-SA 4.0]

So as usual, reality turns out to be both more complicated and more interesting than the accounts you usually hear.  The walkabout taken by the ancestors of the indigenous inhabitants of the Americas was like most patterns of human movement; messy, unpredictable, with new groups mixing with old and the blended groups backcrossing and mixing with the ones who were left behind.  But this is what makes population genetics fascinating, isn't it?  It gives us a lens through which to view our own origins, and causes us to question the definition of terms like "race" that a lot of us think we understand -- but which, on analysis, turn out not to mean anything even vaguely scientific.

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Aptly enough, considering Monday's post about deciphering scripts, this week's Skeptophilia book recommendation is Steven Pinker's brilliant The Stuff of Thought.  Here, experimental psychologist Pinker looks at what our use of language tells us about our behavior and neural wiring -- what, in fact, our choice of words has to do with human nature as a whole.

Along the way, he throws out some fascinating examples -- my favorite of which is his section on the syntax of swearing.  I have to admit, the question, "Just what does the 'fuck' in 'fuck you' actually mean?" is something I've never thought about before, although it probably should have given that I'm guilty of using the f-word a lot more than is generally considered acceptable.

So if you're interested in language, the human mind, or both, this is a must-read.  Although I'll warn you -- if you're like me, it'll leave you thinking, "Why did I just say that?" several times a day.

Language injection

Two of my biggest interests are genetics and linguistics, so when there's a study that combines the two, it makes my little heart go thumpety-thump.

I found out about a recent one yesterday from a friend and long-time reader of Skeptophilia, and it is a pretty cool intersection between the two fields.  The paper on the research, called "The Arrival of Siberian Ancestry Connecting the Eastern Baltic to Uralic Speakers Further East," was authored by a team led by Lehti Saag of the Department of Evolutionary Biology at the University of Tartu (Estonia), and found that an input of migrants from Siberia into northeastern Europe coincided with the diversification of the Finnic languages (Finnish, Estonian, and Hungarian).  This supports the relationship between the Finnic languages and the Yukaghir languages -- a small family of languages spoken in eastern Siberia.

[Image licensed under the Creative Commons ExRat, Finnic languages, CC BY-SA 4.0]

The team came to this conclusion after analyzing the DNA from 33 skeletons dated from 1200 B.C.E. to 1600 C.E., which allowed them to see how the genetics changed due to the infusion of migrants.

What's interesting is when this happened -- the first millennium B.C.E., which is a lot later than I would have expected (not that my opinion means much; my area of linguistic research in graduate school focused on Scandinavian and northern Germanic languages).  The newcomers from Siberia intermarried with the pre-existing western European populations, resulting in today's Finns, Estonians, and Hungarians:

Our findings are consistent with [Bronze-Age Estonia] receiving gene flow from regions with strong Western hunter-gatherer (WHG) affinities and [Iron-Age Estonia] from populations related to modern Siberians.  The latter inference is in accordance with Y chromosome (chrY) distributions in present day populations of the Eastern Baltic, as well as patterns of autosomal variation in the majority of the westernmost Uralic speakers.  This ancestry reached the coasts of the Baltic Sea no later than the mid-first millennium BC; i.e., in the same time window as the diversification of west Uralic (Finnic) languages.  Furthermore, phenotypic traits often associated with modern Northern Europeans, like light eyes, hair, and skin, as well as lactose tolerance, can be traced back to the Bronze Age in the Eastern Baltic.

"Since the transition from Bronze to Iron Age coincides with the diversification and arrival time of Finnic languages in the Eastern Baltic proposed by linguists, it is plausible that the people who brought Siberian ancestry to the region also brought Uralic languages with them," Saag said, in an interview with Science Daily.  "Studying ancient DNA makes it possible to pinpoint the moment in time when the genetic components that we see in modern populations reached the area since, instead of predicting past events based on modern genomes, we are analyzing the DNA of individuals who actually lived in a particular time in the past."

When they merged with the indigenous population, it injected this Siberian DNA signature into a population that already had its own distinct characteristics.  "The Bronze Age individuals from the Eastern Baltic show an increase in hunter-gatherer ancestry compared to Late Neolithic people and also in the frequency of light eyes, hair, and skin and lactose tolerance," said Kristiina Tambets, also of the University of Tartu.  "We see these characteristics continuing amongst present-day northern Europeans."

The coolest thing about this is that a study of DNA extracted from skeletons can shed light on how languages have changed.  I'd love to see this done elsewhere -- especially in places where there are linguistic isolates, which are languages that seem to be unrelated to any other extant languages.  (Examples are Ainu, Basque, Korean, Etruscan, and Vedda.)  These intersections in research have resulted in some fascinating answers to previously unsolved questions -- and show us again that understanding the past is the window to understanding the present.

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I grew up going once a summer with my dad to southern New Mexico and southern Arizona, with the goal of... finding rocks.  It's an odd hobby for a kid to have, but I'd been fascinated by rocks and minerals since I was very young, and it was helped along by the fact that my dad did beautiful lapidary work.  So while he was poking around looking for turquoise and agates and gem-quality jade, I was using my little rock hammer to hack out chunks of sandstone and feldspar and quartzite and wondering how, why, and when they'd gotten there.

Turns out that part of the country has some seriously complicated geology, and I didn't really appreciate just how complicated until I read John McPhee's four-part series called Annals of the Former World.  Composed of Basin and Range, In Suspect Terrain, Rising from the Plains, and Assembling California, it describes a cross-country trip McPhee took on Interstate 80, accompanied along the way with various geologists, with whom he stops at every roadcut and outcrop along the way.  As usual with McPhee's books they concentrate on the personalities of the people he's with as much as the science.  But you'll come away with a good appreciation for Deep Time -- and how drastically our continent has changed during the past billion years.

[Note:  If you order this book using the image/link below, part of the proceeds will go to support Skeptophilia!]

Escapees from Siberia

As you might expect from someone who is passionately interested in both genealogy and evolutionary genetics, when there's a study that combines both, it's a source of great joy to me.

This week, Nature published a study on the evolutionary history of humans in northern Europe, specifically the Finns.  Entitled, "Ancient Fennoscandian Genomes Reveal Origin and Spread of Siberian Ancestry in Europe," it was authored by no less than seventeen researchers (including Svante Pääbo, a Swedish biologist who is widely credited as founding the entire science of paleogenetics) from the Max Planck Institute, the University of Helsinki, the Russian Academy of Sciences, the Vavilov Institute for General Genetics, and the University of Turku.

Quite a collaborative effort.

It's been known for a while that Europe was populated in three broad waves of settlement.  First, there were hunter-gatherers who came in as early as 40,000 years ago, and proceeded not only to hunt and gather but to have lots of hot caveperson-on-caveperson sex with the pre-existing Neanderthals, whose genetic traces can be discerned in their descendants unto this very day.  Then, there was an agricultural society that came into Europe from what is now Turkey starting around 8,000 years ago.  Finally, some nomadic groups -- believed to be the ancestors of both the Scythians and the Celts -- swept across Europe around 4,500 years ago.

Anyone with European ancestry has all three.  Despite the genetic distinctness of different ethnic groups -- without which 23 & Me genetic analysis wouldn't work at all -- there's been enough time, mixture, and cross-breeding between the groups that no one has ancestry purely from one population or another.

Which, as an aside, is one of the many reasons that the whole "racial purity" crowd is so ridiculous.  We're all mixtures, however uniform you think your ethnic heritage is.  Besides, racial purity wouldn't a good thing even if it were possible; that's called inbreeding, and causes a high rate of homozygosity (put simply, you're likely to inherit the same alleles from both your mother and father).  This causes lethal recessives to rear their ugly heads; heterozygous individuals are protected from these because the presence of the recessive allele is masked by the other, dominant (working) copy.  It's why genetic disorders can be localized to different groups; cystic fibrosis in northern Europeans, Huntington's disease in people whose ancestry comes from eastern England, sickle-cell anemia from sub-Saharan Africa, Tay-Sachs disease in Ashkenazic Jews, and so on.

So mixed-ethnic relationships are more likely to produce genetically healthy children.  Take that, neo-Nazis.

Map of ethnic groups in Europe, ca. 1899 [Image is in the Public Domain]

In any case, the current paper looks at the subset of Europeans who have a fourth ancestral population -- people in northeastern Europe, including Finns, the Saami, Russians, the Chuvash, Estonians, and Hungarians.  And they found that the origin of this additional group of ancestors is all the way from Siberia!

The authors write:

[T]he genetic makeup of northern Europe was shaped by migrations from Siberia that began at least 3500 years ago.  This Siberian ancestry was subsequently admixed into many modern populations in the region, particularly into populations speaking Uralic languages today.  Additionally... [the] ancestors of modern Saami inhabited a larger territory during the Iron Age.

The coolest part is that this lines up brilliantly with what we know about languages spoken in the area:

The Finno-Ugric branch of the Uralic language family, to which both Saami and Finnish languages belong, has diverged from other Uralic languages no earlier than 4000–5000 years ago, when Finland was already inhabited by speakers of a language today unknown.  Linguistic evidence shows that Saami languages were spoken in Finland prior to the arrival of the early Finnish language and have dominated the whole of the Finnish region before 1000 CE.  Particularly, southern Ostrobothnia, where Levänluhta is located, has been suggested through place names to harbour a southern Saami dialect until the late first millennium, when early Finnish took over as the dominant language.  Historical sources note Lapps living in the parishes of central Finland still in the 1500s.  It is, however, unclear whether all of them spoke Saami, or if some of them were Finns who had changed their subsistence strategy from agriculture to hunting and fishing.  There are also documents of intermarriage, although many of the indigenous people retreated to the north...  Ancestors of present-day Finnish speakers possibly migrated from northern Estonia, to which Finns still remain linguistically close, and displaced but also admixed with the local population of Finland, the likely ancestors of today’s Saami speakers.

Which I think is pretty damn cool.  The idea that we can use the genetics and linguistics of people today, and use it to infer migratory patterns back 40,000 years, is nothing short of stunning.

Unfortunately, however, I have zero ancestry in Finland or any of the other areas the researchers were studying.  According to 23 & Me, my presumed French, Scottish, Dutch, German, and English ancestry was shown to be... French, Scottish, Dutch, German, and English.  No surprise admixtures of genetic information from some infidelity by my great-great-grandmother with a guy from Japan, or anything.

On the other hand, I did have 284 markers associated with Neanderthal ancestry.  Probably explaining why I like my steaks medium-rare and run around more or less naked when the weather's warm.  Which I suppose makes up for my lack of unexpected ethnic heritage.

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Ever wonder why we evolved to have muscles that can only pull, not push?  How about why the proportions of an animals' legs change as you look at progressively larger and larger species -- why, in other words, insects can get by with skinny little legs, while elephants need the equivalent of Grecian marble columns?  Why there are dozens of different takes on locomotion in the animal world, but no animal has ever evolved wheels?

If so, you need to read Steven Vogel's brilliant book Cats' Paws and Catapults.  Vogel is a bioengineer -- he looks at the mechanical engineering of animals, analyzing how things move, support their weight, and resist such catastrophes as cracking, buckling, crumbling, or breaking.  It's a delightful read, only skirting some of the more technical details (almost no math needed to understand his main points), and will give you a new perspective on the various solutions that natural selection has happened upon in the 4-billion-odd years life's been around on planet Earth.

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