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john hawks weblog

paleoanthropology, genetics and evolution

Photo Credit: Pre-Clovis Gault Assemblage artifacts. Thomas Williams et al. (2018) CC-BY-NC

The so-called Toba bottleneck didn't happen

Chad Yost and colleagues have a long and detailed article in the current Journal of Human Evolution about why the Toba volcanic eruption 74,000 years ago did not drive ancient humans near extinction.

I want to quote the last two paragraphs of this paper, which give a crystal clear discussion, with references, of why there is no evidence for a massive Toba effect on human populations.

4.7. A falsified Toba catastrophe hypothesis
Since the publication of Ambrose (1998), the Toba supereruption and its proposed 6-year-long volcanic winter continues to be cited repeatedly, particularly in introductory paragraphs, as the natural catastrophe that brought humanity to the brink of extinction (human populations reduced to 10,000 individuals). Recent studies have clearly shown that volcanic winter conditions never occurred in East Africa after the eruption (Lane et al., 2013a ; Jackson et al., 2015), and we have shown that there was a very limited vegetation perturbation in the Southern Rift Valley of East Africa after the eruption. Further, we demonstrated the overestimation of SO2 injections in Toba supereruption climate model simulations by one or two orders of magnitude. This overestimation includes the early models of Rampino and Self (1992) that helped to build the volcanic winter model proposed in Ambrose (1998). The hypothesis that Toba triggered the 1000-year GS-20 cold period is also unlikely to be correct given that rapid cooling in the NH actually started a few hundred years before the Toba eruption, not to mention the fact that modeling by Robock et al. (2009) using a 900× Pinatubo SO2 injection failed to initiate NH glaciation.
Numerous genetic analyses have not detected a bottleneck that coincides with the Toba eruption. In fact, if the source population for the OOA expansion suffered a severe bottleneck, there should be a poorer linear fit to the decline of heterozygosity with distance from Africa (Henn et al., 2012). With the advancement of whole genome sequencing, the once elusive 100–50 ka Late Pleistocene human genetic bottleneck is now converging on ∼50 ka (Lippold et al., 2014; Karmin et al., 2015 ; Malaspinas et al., 2016) and is being attributed to an OOA founder effect bottleneck (Mallick et al., 2016) instead of a population reduction bottleneck. Studies focusing on reconstructing population histories are identifying a possible population reducing bottleneck between ∼150 and ∼130 ka (Li and Durbin, 2011 ; Kidd et al., 2012), which coincides with the penultimate ice ace during MIS 6. However, the peak in Ne at ∼150 ka could have also arisen from increased genetic diversity due to population structure involving separation and admixture (Li and Durbin, 2011), which is reasonable to expect during a cooler and drier MIS 6 climate in Africa. The hypothesis that human populations were reduced to 10,000 individuals after the Toba eruption is currently unsupported, as AMH populations were always relatively low, started to decline around 150 ka, and continued to decrease until ∼30 ka (see Discussion above). As paleoenvironmental, archaeological, and genetic research continues to accumulate, it is becoming increasingly hard to find evidence in favor of the Toba catastrophe hypothesis.

There is no question that the Toba eruption was a massive geological event. Investigating this event in earth systems research has always been a valuable idea.

But it has been a massive distraction for archaeologists.

The Toba bottleneck idea came from the initial observation that there might be a coincidence between population expansion times and the Toba eruption, made 20 years ago. But many geneticists (including me) quickly pointed out that the dates of population expansion have little connection to the dates of population contraction, and that effective population size might be orders of magnitude smaller than the actual human population. Even in 20-year-old mitochondrial DNA data, it was clear that a single short bottleneck post-Toba could not account for the pattern of variation found in African populations.

Meanwhile, human populations in the coldest climate zones, like the Neandertals of Europe, never seemed to show any obvious signs of population reduction at the time of the Toba event. Later, it became clear that the archaeological record much closer to Toba, in India and later Sumatra itself, showed no signs of a major interruption caused by the volcano. It also became clear that the aerosols that cool global climate, like sulfur dioxide, did not scale with the volume of rock ejected by the Toba eruption.

Yet this idea remains surprisingly entrenched in the minds of the public and of documentary filmmakers. I’m surprised there hasn’t been a Toba feature movie. Worse, it seems to dominate an unusual degree of attention in the minds of paleoclimatologists, and in their grant applications.

This is such an example of the failure to communicate effectively between geneticists, geologists, and paleoclimatologists about the limits of their data. The “coincidence” of these events from genetics and geology was only a small overlap between enormous confidence limits.

The idea was still worth investigating, sure, but on the other side of the balance were several negative indicators that were ignored or minimized at the time. If the Toba eruption had massively shocked global climate, that should have been evident in ice core data available in the 1990s, yet there was no such pattern. At the time, researchers dismissed this contradictory observation, suggesting that the Toba eruption might have initiated a longer-term cold cycle that was apparent in the ice cores (now known to have started before the eruption). And while the lack of any effect of the eruption on Neanderthals was fairly clear, the archaeological data were also dismissed as too sparse to disprove some population discontinuity. After all, proponents of the idea reasoned, even if Neanderthals seemed to be going strong for 30,000 years after the Toba eruption, a massive volcanic winter still might have softened them up a little.

Here’s the thing: It’s very hard to disprove the idea that the Toba eruption had some effect on ancient humans. As a massive event, it probably was not unnoticed by ancient humans who lived at the time of the eruption, 74,000 years ago. Many of those ancient people may have suffered from some adverse effects of the eruption, both locally and around the world. Many people around the world suffered adverse effects from the Mt. Pinatubo eruption in 1991, and we know from observations and climate modeling that those effects are not always noticeable even to the people who experience them!

But that doesn’t justify what has become a widespread public belief that Late Pleistocene humans were an endangered species, driven near extinction by a volcano. It is a myth that we now know is false.

We now have an opportunity to explain to people how many scientists got this wrong, how paleoclimate science and genetics have both progressed, and how massively the archaeological record has grown.

We also have the opportunity to exhibit some appropriate skepticism at other hypotheses about strong climate forcing in human prehistory. We need a better understanding of how ancient humans may actually have responded to local and regional changes in environments.

Link: Sci-Hub profiled

Verge has a long article on Sci-Hub, focusing on its founder, Alexandra Elbakyan: “Science’s Pirate Queen”.

If you have not heard of Sci-Hub, it is a major search engine and repository allowing people around the world to download scientific research articles for free, without paying publishers. Some describe it as piracy, others as a necessary workaround to provide access to people who cannot afford to spend $30 to read an article.

Sci-Hub provided press, academics, activists, and even publishers with an excuse to talk about who owns academic research online. But that conversation — at least in English — took place largely without Elbakyan, the person who started Sci-Hub in the first place. Headlines reduced her to a female Aaron Swartz, ignoring the significant differences between the two. Now, even though Elbakyan stands at the center of an argument about how copyright is enforced on the internet, most people have no idea who she is.

The story is fascinating, involving Russian politics that are obscure to the rest of the world, and emphasizing the recent legal efforts by the American Chemical Society to shut down the Sci-Hub repository.

Link: Robots in retail

MIT Technology Review has an interview with an exec from a company making robots for Walmart: “Walmart’s new robots are loved by staff—and ignored by customers”.

Erin: How have employees responded to the robots? Have you received any pushback because of the “robots are taking my job” idea?
Martin: When we first deployed a robot in a store, the associates were the people that understood it first. This boring, repetitive task of scanning the shelves—we have yet to meet someone who has liked to do that. Employees instantly become the advocates for the robot.
One way they do that is by giving it a name—the robots all have Walmart name badges on. The employees have competitions to see what the right name is for each robot. They also advocate for the robot to the general public. It’s the store staff saying, “It’s helping me.” We see them now defending the robot.

My department used to have a course on the books called “Robotics: Human Dimensions”, which was had been 1970s-era course that looked at the social changes from robotics in manufacturing. For some time, I thought it would be fun to revive the class to make it actually about robotics and the integration of robots into human societies.

Now I see that the two are blending together.

Link: China CRISPR-ing away

Gizmodo: “China Has Already Gene-Edited 86 People With CRISPR”.

In China’s 2015 CRISPR trial, the WSJ reports, 36 patients with cancers of the kidney, lung, liver and throat had cells removed from their bodies, altered with CRISPR, and then infused back into their bodies to fight the cancer. Other Chinese trials have sought to use CRISPR to treat HIV, esophaegeal cancer, and leukemia. A trial slated for this year in China will enroll 16 patients. Meanwhile, the first human CRISPR trial in the U.S., at University of Pennsylvania, will enroll just 18 people, and is designed primarily to test whether CRISPR is safe.

In an unrelated related story, Donald Trump’s State of the Union Address is notable for his mention of “Right to Try” legislation. From Ike Swetlitz at STAT: “In State of the Union, Trump endorses ‘right to try’ for terminally ill patients”

“We also believe that patients with terminal conditions should have access to experimental treatments that could potentially save their lives,” Trump said in his speech. “People who are terminally ill should not have to go from country to country to seek a cure — I want to give them a chance right here at home. It is time for the Congress to give these wonderful Americans the ‘right to try.’”

I expect that gene editing experiments are not far off in the U.S.

Link: Science blogs back!

Nature this week has a nice feature article on blogging in science, by Eryn Brown and Chris Woolston: “Why science blogging still matters”.

This marks my fifteenth year of blogging, and so I obviously think it’s worthwhile. I think the process of blogging is a lot like science itself – there are many ways to accomplish something, there are many more very smart people than there are obvious opportunities, and to be a real success, you have to find ways to do things that other people wouldn’t think of.

Of course, sometimes that just means persevering!

The survey uncovered some telling attitudes towards blogs and other forms of science outreach. Nearly two-thirds of respondents said that a lack of time was a ‘great obstacle’ to any sort of science communication.
But almost 70% agreed that communicating science can help to advance a researcher’s career, and nearly 90% said that it could help to recruit more bright minds to science.

I don’t think that blogs are especially good for reaching new audiences who do not already care about science. Blogs can be very good for helping already-interested people keep in the loop about new developments in a specialized area.

What I’ve noticed over the last few years is that a lot of professionals are now writing brief comments on new scientific work on Facebook, and linking to news articles, etc. And that has really yielded a “dumbing down” of commentary. Mainstream reporting on human evolution has actually gotten a lot worse in the last few years.

I’ve been happy to see a number of researchers in the last year or so publishing “blog posts” about their research findings on The Conversation. That’s a nice outlet enabling researchers to share their ideas directly, and gives a much better context for research findings than most media articles. What I’m a bit dismayed by is that these posts do not get shared very often on Facebook and other social media.

A trip to Israel, presenting about 'Time'

I’ll be in Israel this week to present a lecture for a symposium of the Israel Academy of Sciences and Humanities. The theme of the symposium is, “Time”, and I’ll be reflecting the deep time of human origins and evolution.

I’m excited about this presentation. Over the last two years, our field has seen an array of new discoveries that have changed the way we think about the origins of living people from mostly African ancestors. To me, right now, the most critical area where we know the story was complex, and badly need new data and models to understand that complexity, is around 250,000 to 350,000 years ago.

It was then that our modern human ancestors in Africa began to differentiate from an initially small population into branches that still exist in different regions of Africa today. It is now clear that many other hominin populations existed at the same time, including Homo naledi and some archaic forms of humans in Africa, Neandertals, Denisovans, and possibly other archaic humans in Eurasia, Homo floresiensis in Flores (and maybe others). In Africa, in Europe, and in Asia, some ancient populations experimented with, and ultimately adopted, new stone tool forms.

The big questions of human evolution all now cause us to focus upon this time interval for answers. How did culture influence our evolutionary pathway? How did ancestral hominins become modern humans? How did these hominin populations fit into their environment in ways that enabled them to survive and coexist?

I don’t have answers to these questions, but I now think that this critical time period is where we must look. I’ll be reflecting the big questions and the data that lead us to examine this time in my lecture.

Link: 'Myths of Human Genetics'

As the semester is getting rolling, and I am teaching Mendelian genetics in two courses this week, I want to link again to the invaluable “Myths of Human Genetics” website, from John McDonald at the University of Delaware.

McDonald has collated a series of human traits that have been used, at one time or another, to teach Mendelian inheritance in humans. None of them are Mendelian traits in reality, and many of them are demonstrably non-genetic in their etiology.

Some traits, such as tongue rolling, were originally described as fitting a simple genetic model, but later research revealed them to be more complicated. Other traits were shown from the very beginning to not fit the simple genetic model, but somehow textbook authors decided to ignore this. A quick search in the standard reference on human genetics, Online Mendelian Inheritance in Man (OMIM), makes it clear that most of these traits do not fit the simple genetic model. It is an embarrassment to the field of biology education that textbooks and lab manuals continue to perpetuate these myths.

Tongue rolling, hitchhiker’s thumb, asparagus urine – they’re all there, along with many references and citations to studies that show what scientists actually know about their inheritance.

I’m introducing students to a few more anthroposcopic traits than usual this semester, and it’s interesting what they come in already “knowing” about the inheritance of various traits. Thanks, High School Biology!

Link: The beauty of invasive species

Proceedings of the National Academy of Sciences is running an article by Carolyn Beans that profiles the work of Ellie Irons: “Science and Culture: Painting with invasive pigments”. Irons is a painter who has chosen to feature the pigment products of invasive plants in her work.

About one quarter of the weeds in Irons’ color palette are native to the northeastern United States. The rest are introduced, often highly invasive plants—some of which the city is actively working to eradicate from forested areas. Such efforts are undertaken for good reason; invasive species spread can devastate an ecosystem.
But Irons believes urban ecosystems are different. After all, many native plants couldn’t survive the harsh conditions. Where native plants fail, hardy weedy plants, she reasons, can step up to provide a wealth of ecosystem services—from stabilizing soil and reducing nutrient and stormwater runoff to cooling the air and providing food and habitat for animals.
Two Meadows, by Ellie Irons. Featured by Ecological Society of America
"Two Meadows Paintings", by Ellie Irons. Featured by the Ecological Society of America on Flickr. An installation of her work was exhibited at the ESA annual meeting in 2017. </figure> There are no "pure" ecosystems in the world, all have changed over time. But the pace of human change has posed unique challenges to some species and opportunities to others. It is for us to learn and recognize the workings of the world around us, to understand how we may best survive in the future.

What explains mtDNA introgression among archaic human populations?

In case anyone still wonders how variation in mitochondria might have been important to Neandertals and other archaic humans:

A bizarre find: Tiny powerhouses in your cells run at 122 degrees
The researchers grew human kidney cells and skin cells in petri dishes, which they kept at 38 degrees Celsius. Into these cells the scientists inserted a new type of fluorescent dye, which brightens as it cools. When the mitochondria became active, the fluorescence dimmed. This indicated that the temperature within the mitochondria rose between seven and 12 degrees Celsius, or an average of 10 degrees, as reported in the journal PLOS Biology on Thursday.

Previous researchers have suspected that human variation in mtDNA might relate to the tradeoff of heat production and ATP efficiency in mitochondria, with advantages for some mtDNA haplogroups in cold-adapted human populations. Circumstantial evidence for this hypothesis has been known for more than a decade, and I wrote about it back in 2005: “Mitochondrial DNA adaptations in living human populations”.

Even if important differences in mitochondrial function exist between human populations, mitochondrial DNA may not be the cause. Most of the genes that influence mitochondrial function are encoded in the nuclear genome, not the mtDNA. Yet some of the genes on the mtDNA do influence mtDNA function in ways that may have been selected in humans. Also, the mtDNA is the only part of the eukaryotic genetic complement that must function inside the mitochondrion itself, exposing it to a distinctive intracellular environment with its own possible effects on transcription.

The story of mtDNA in archaic humans has become more and more intricate. The earliest-known members of the Neandertal lineage, from Sima de los Huesos, Spain, have an ancient haplogroup that has not been found in later Neandertals or modern humans. This clade has been identified in Denisovans, although the variants in the Denisovan individuals known so far are fairly distant from the chronologically earlier Sima de los Huesos individuals.

Meanwhile, later Neandertals share a mtDNA clade that connects them more closely to the common mtDNA ancestor of modern humans, including all living African and non-African people. The origin of this clade is not known. It may have originated in Africa and have been exchanged into Neandertals by introgression some 250,000 years ago or more. Alternatively, it may have originated elsewhere and introgressed into both African and Neandertal populations. The extensive introgression of this mtDNA variant, in the absence of strong evidence of nuclear genome introgression at the same time, suggests that natural selection may have driven the mtDNA introgression.

No living people have been found with a mtDNA haplotype within the variation found within either the Neandertals or the Denisovans. Instead, everyone living today belongs to a subclade that originated within the last 300,000 years.

It is not currently clear whether this mitochondrial Eve lived before the populations that gave rise to all modern humans began to differentiate from each other. That differentiation began before 300,000 years ago, according to recent studies of African genetic variation from the nuclear genome. That’s earlier than most estimates of the date of the common mtDNA ancestor.

Within Africans today is much more mtDNA clade diversity than outside Africa. Throughout the pre-Columbian populations of most of the world, all people have mtDNA sequences that belong to two narrow branches of the mtDNA tree, which seem to have originated in the last 100,000 years. It is within these low-variation branches that a few functional variants have been found that might differentiate cold-climate populations from others. The adaptive story that has been examined so far for mtDNA does not relate to the much greater mtDNA variation that still exists within sub-Saharan African peoples.

I’ve been interested in mtDNA selection for a long time, and wrote about it in a 2006 paper: “Selection on mitochondrial DNA and the Neanderthal problem”.

There is a lot left to learn, which will no doubt leave today’s knowledge looking pretty inadequate. But what seems like mtDNA total replacement within Neandertals was a pretty striking event, and deserves more consideration as a possible case of adaptive evolution.

Is it meaningful if geneticists find that marriage can be influenced by genes?

The power of gene-trait association studies has increased markedly over the last few years. Samples of hundreds of thousands of individuals with genotype and phenotype data are coming online.

This statistical power has opened the door to discovering genes that have very small but significant effects on traits. In the process, a good fraction of what was once called “missing heritability” has actually turned up. Rare genes of medium effect, and common genes of incredibly tiny effect both matter to some extent.

Geneticists have started to ask a simple question: If most genes that affect a trait have incredibly tiny effects, are we discovering anything biologically interesting?

For many years, human geneticists have argued for larger and larger studies of gene-trait associations based upon the idea that genes will highlight biological networks. Any one gene might have a small effect, but finding many genes will allow geneticists to understand the inner workings of biology.

For some traits, that has proven not to be the case. Hundreds of genes, each with very small effects, don’t fit into any coherent biological network. In some sense, these genetic associations reflect all the different aspects of physiology that can influence human growth, metabolism, and behavior.

Behavioral traits seem to fit into this model, which has been dubbed the omnigenic model, in a recent paper Evan Boyle, Yang Li, and Jonathan Pritchard. Today it’s commonplace to see studies finding genetic associations for traits that are most salient in social psychology, identifying a few genes of fairly small effect for traits like “educational attainment”, or “age at birth of first offspring”.

Eric Turkheimer writes in the Genetics and Human Agency Project blog: “Why marital status is heritable.

It is only in the weakest (softest!) possible sense that you can refer to these genes as “genes for” the phenotype, or as “causal variants” for a phenotype, because they don’t actually have anything to do with the phenotype, with divorce, per se. The are cellular level body size effects, or appearance effects, or impulsivity, or alcohol or ginger hair effects, and even listing them like that probably makes their effects much more discrete and concrete than they actually are. If I had to guess most of the genetic action is at the cellular level, so causally distant from how you feel after a fight with your spouse that there is no point in even talking about it.
Heritability in and of itself has no particular relevance to questions about whether things like intelligence or divorce are biological as opposed to social constructions. Social constructions are heritable.

The main idea of Turkheimer’s post is that heritability by itself does not tell us that biology (as opposed to social phenomena) is relevant to explaining a trait. That is, correlation is not causation, and a genetic explanation for a trait that involves tiny influences of hundreds of genes is not a meaningful explanation.

And yet, I’m not very satisfied by this example.

Turkheimer has chosen the example of marriage status precisely because we are meant to assume that any important causal explanations must be totally psychological and social. Surely it is absurd to suggest that genes have any causally important role in such a social institution.

In some sense Turkheimer appears obviously correct. “Marriage status” in the United States or Europe in the early 21st century is an absurdly specific phenotype. It didn’t exist in our evolutionary past, and our genes could not possibly have adapted to it. Right?

But widen the frame a bit. Long-term pair bonding is exactly the kind of thing that mattered to natural selection during human evolution.

Look at another trait that is a major component of fitness: “age at birth of first offspring”. Some individuals have children very early in their adult lives, and others only have children much later. The proximate causes of these behavioral outcomes are unquestionably social and psychological. Yet age at first birth is heritable in populations today, and a number of genes found to explain small fractions of the additive component of variation in large samples of people. The trait is also quite strongly selected within the human populations where it has been examined. On average, women who have given birth to their first child earlier in their lives also have more children over their life spans.

How can this be? It would seem like trait that is so strongly correlated with lifetime reproductive success should have very little additive genetic variance in a population that has been at equilibrium with its environment for a long time.

Humans, of course, have not been anywhere near equilibrium recently. Our environment, both cultural and physical, has changed radically during the last 50,000 years, and continues to change rapidly even now. “Marriage” is a social institution that means something different today than it did 50 years ago. Marriage has different participation rates by age in today’s United States than in many other countries, and different rates in comparison to the recent past. Sure, it is reputed as one of the most stable institutions in human societies, but its psychological and social dimensions nonetheless can change rapidly.

In that sense, heritability of marriage status as a trait does have at least one salient biological explanation. Some genetic factors might correlate with marriage status in today’s populations precisely because the genetic differences that exist today are those that persisted in past social and physical environments, which were in some ways different from today’s environment.

There’s nothing trivial about noting that today’s social environments are markedly different from the past, and that by itself is a biological fact that influences gene-trait associations.

Link: Looking at the Misliya Cave maxilla

Bruce Bower last week had a nice article about the new Misliya Cave dating in Science News: “An ancient jaw pushes humans’ African departure back in time”.

The story in a nutshell is that a demi-maxilla from Misliya has been placed between 177,000 and 194,000 years ago. The teeth lack any close similarity with Neandertal teeth and are modern in size, and the morphology of the bone doesn’t resemble European Neandertals. That makes it indistinguishable from the cranial material from Qafzeh and Skhul, which are only between 90,000 and 110,000 years old. Up to double their age, the Misliya maxilla could be the earliest modern human outside Africa.

But I’m not so sure:

Hawks isn’t so sure the jaw belongs to H. sapiens. Interbreeding between H. sapiens, Neandertals and perhaps other Homo species in the Middle East could have produced a hybrid Misliya population characterized by humanlike jaws connected to bulkier, Neandertal-style bodies, Hawks says.
Or a Homo species closely related to H. sapiens — but not known from any previous fossils — may have traveled to Misliya Cave, he speculates. “This new discovery from Misliya Cave raises more questions than answers,” Hawks says.

I’m writing more on the implications of this discovery in the context of other recent work. There is a major change underway in how we understand “out of Africa”. I don’t think the traditional framing of “out of Africa” is very effective anymore, as leaving Africa is a tiny event, repeated many times over the last several hundred thousand years.

In the context of other discoveries, I think that “modern human” has lost much of the meaning it may once have had.

The big questions concern what was happening inside Africa, where many genetically diverse populations existed and interacted. How many ancestral populations gave rise to the growing population of modern humans after 100,000 years ago? How many African-derived people were involved in mixture with Neandertals 250,000 years ago, or 120,000 years ago? Did African-derived humans make it to China, or to Java, before 100,000 years ago?

Those are open questions, with some evidence pointing toward faster, more widespread dispersal, more mixture, and repeated genetic replacements.

Link: Searching for knotweed and other early North American domesticates

Annalee Newitz has written an article about Natalie Mueller’s search for the ancient food crops of North America: “Hunting for the ancient lost farms of North America”.

Over 2,000 years ago in North America, indigenous people domesticated plants that are now part of our everyday diets, such as squashes and sunflowers. But they also bred crops that have since returned to the wild. These include erect knotweed (not to be confused with its invasive cousin, Asian knotweed), goosefoot, little barley, marsh elder, and maygrass. We haven’t simply lost a few plant strains: an entire cuisine with its own kinds of flavors and baked goods has simply disappeared.

The article focuses upon the case of erect knotweed, but the others are worth comment also. The biological experimentation of ancient people was impressive, and in North America, the spread of maize farming reduced or eliminated many early domesticates.

The archaeology of plants has become more and more important to our understanding of ancient peoples—before, during, and after the adoption of agriculture. It will be amazing to see whether these aborted domesticates have any genetic signs of the ancient human manipulation.

What I think is so neat about these plants is that they trace the complexity of information exchanges across a network of societies over more than a thousand years:

She had assumed, based on previous studies, that knotweed was domesticated in Illinois, possibly about 1,200 years ago. But then she spoke with a Kentucky museum curator who told her about a mysterious grave from the 2,000-year-old Hopewell culture, found stuffed with seeds.
Examining the seeds, Mueller identified them as domesticated erect knotweed. This find makes the plant’s domestication roughly a millennium older than previously thought. But given that these fruits probably came after generations of breeding by farmers, it hints at a much older date.

It will be astounding to have greater knowledge of these kinds of exchanges in both the Americas and in Eurasia and Africa.

Link: The underrated takin

This is a fun article on an underappreciated mammal: “Meet the Takin: The Largest Mammal You’ve Never Heard Of”.

The takin is adapted to its mountainous environment in Asia. While its range includes many countries – including parts of India, Bhutan and Myanmar – most naturalists and hard-core mammal watchers encounter the species in China. Strangely enough, there it shares its range with one of the most beloved and well-known of large mammals, the giant panda. In fact, one of the first documented instances of a giant panda eating meat is trail camera footage of one of the fuzzy critters noshing on a takin carcass.

The fossil record of takin in China goes back to the Pliocene, with a number of fossil representatives in the Pleistocene of central China.

Sexual harassment as research misconduct

Scientific American has issued an editorial bringing attention to the new policy by the American Geophysical Union that redefines scientific research misconduct to include sexual harassment and other sexual misconduct in scientific research: “Science Suffers from Harassment”.

A number of scientific societies have recently issued statements condemning sexual harassment and assault, along with guidelines for ethical behavior among their members. The AGU’s approach is stronger and more direct. It argues that harassment is as egregious as the big scientific sins of data fabrication, falsification and plagiarism. Members found guilty of sexual harassment may thus be banned from presenting at conferences or publishing their research in AGU-run scientific journals, among other consequences that would limit their participation in the field.

Some more perspective on this can be found in a recent post in which I link to the AGU in a broader story: “Link: How scientific societies are moving to combat sexual harassment”.

It seems to me that this kind of redefinition puts much more pressure on coauthors and research collaborators of those who have carried out sexual harassment and assault.

When scientists are found to have been plagiarists, or fabricated data, there are very few circumstances in which they are rehabilitated as valuable coauthors and collaborators to other scientists. In the past, when instances of sexual misconduct have been treated internally and quietly by institutions, those individuals have continued in collaborations and coauthorship, and have continued to present and publish research without any connection between the two.

The AGU has forged a connection, and that has to change the way people operate in collaborations. This will have far-reaching effects.

Why do bamboo lemurs have such a diversity of gut microbes?

North Carolina State University has put out a news article about some recent work by Erin McKenney, who is studying the gut microbiome of lemurs: “Can You Guess Which Species Has the Most Gut Microbes?”.

The article has some statistics I’d never seen before about microbial community diversity in these lemurs:

[B]ecause McKenney studies lemurs, she hadn’t really looked at the gut diversity data for unrelated species. So when she shared the bamboo lemur’s diversity numbers with her mentor, NC State applied ecology professor Rob Dunn, she was surprised to learn that bamboo lemurs are superlative: They are home to more types of gut microbes than any other animal in the world (that we know of).
Specifically, McKenney has identified an average of 13,816 different “operational taxonomic units” (OTUs) – or types of microbes – in captive bamboo lemurs.

That’s more than any other animal yet examined, and roughly 14 times more diversity than in humans—even human hunter-gatherers like the Hadza, whose microbiomes are more diverse than agricultural populations.

Bamboo lemur
Golden bamboo lemur. Photo by Brian Gratwicke via Flickr. CC-BY 2.0

Bamboo lemurs have an interesting diet, which includes an ability to tolerate a level of cyanide that would be extremely harmful for most other mammals, so that dietary ecology might be related to their microbial diversity. That’s a “just-so” explanation, and who knows what diet has to do with it?

I just think this is a really interesting question. What difference does it make to have a diverse microbiome? Why would some species vary so much from each other, even within an order (like Primates)? Is this just a series of historical accidents leading to great diversity in some creatures? Or is their evolutionary history shaped by creating microbial niches inside themselves?