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paleoanthropology, genetics and evolution

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

'Where my house is, those trees were once growing'

The New York Times reports on a revival of the agricultural variety: “Finding Lost Apples and Reviving a Beloved Cider”.

Mr. Rosen, the former chief executive of a Manhattan advertising agency that promoted Svedka vodka and Mike’s Hard Lemonade, wants to reintroduce Newark cider, an 18th- and 19th-century alcoholic drink once famously compared to Champagne.
Newark cider was both a point of pride and big business for the region — requested by name, reportedly lauded by George Washington and produced by dozens of Newark-area cideries with acres of orchards. The secret wasn’t a recipe, but the blending of a quartet of superior apples born in the region: Campfield, Poveshon, Granniwinkle and Harrison, the most celebrated of the four.

I’m always inspired by these discoveries of lost varietals, which give us the potential of tasting the foods and drinks of the past, while recovering variation that might be useful or valuable again.

Richard Lee tells a story about the nuclear arms race

Richard Lee is best known to followers of anthropology as one of the co-organizers of the “Man the Hunter” conference in 1966. His fieldwork with the Dobe !Kung helped dispel some old anthropological myths about hunting and gathering peoples, and served as a nucleus for ideas about the evolution of human sociality.

He has written an article in this year’s Annual Review of Anthropology that examines both uses and misuses of hunter-gatherer ethnography in theory-building about human nature: “Hunter-Gatherers and Human Evolution: New Light on Old Debates.”

In the introduction to the article, he recounts a story involving his “Man the Hunter” co-editor, the late Irven DeVore:

Senator William Fulbright of Arkansas, a brilliant US legislator in the 1960s and the founder of the scholarship program that bears his name, was just one public figure struggling to come to grips with the import of Lorenz’s theses. I vividly remember the late Irven DeVore coming into my office at Harvard University. “I just got off the phone with Senator William Fulbright calling from Washington,” Devore said. “He asked me ‘Professor DeVore, if Konrad Lorenz is right, how are we ever to negotiate a nuclear arms reduction treaty with the Soviet Union?’”
DeVore reassured Fulbright that Lorenz’s views were far from universally accepted among anthropologists, that violence in human history was a variable not a constant, and that its causes and expressions were far more complex than could be explained simply by pure animal instinct.
DeVore’s disclaimers appeared to calm Senator Fulbright’s nerves, and in fact the United States and the Union of Soviet Socialist Republics (USSR) went on to successfully negotiate a series of nuclear arms reduction treaties over the years. Nevertheless, the question of violence in human history continued to animate the debate within anthropology, fueled by Robert Ardrey’s “killer ape” hypothesis in his books African Genesis (Ardrey 1961) and The Territorial Imperative (Ardrey 1966). Interest was sustained by Napoleon Chagnon’s (1968) influential ethnography of the “fierce” Yanomamo and more recently by the writings of Wrangham & Peterson (1996), such as Demonic Males: Apes and the Origins of Human Violence. I have labeled this persistent thread within anthropology and related disciplines as the “Bellicose School” (Lee 2014).

I am spending some time reading this review and taking notes, and it bears close reading. Lee’s theme is that many people who use “hunter-gatherers” as a category are actually lumping things that are quite different from each other. If you want to use ethnographic studies of today’s people to say anything about prehistoric people, you need to understand that any living group may be like ancient people in some ways, and very different from ancient people in other ways. Lumping across the entire category of “hunter-gatherers” doesn’t work if some of those living hunter-gatherers have economies, subsistence patterns, and social organization that is unlike anything that archaeology tells us about prehistoric groups.

Here’s a teaser from a box that discusses the work of Steven Pinker:

Despite the apparent magnitude of the Ju/’hoan/!Kung homicide rate, these still represent only 1.0–1.6% of overall deaths, compared to the 8–58% figure referenced in Pinker’s TED Talk.

I’ll hopefully be able to write a bit more about this as I read.

Reference

Lee, Richard B. 2018. Hunter-Gatherers and Human Evolution: New Light on Old Debates. Annual Review of Anthropology 47 (online early) doi:10.1146/annurev-anthro-102116-041448

The fattest bear

I enjoyed the Washington Post account of the “annual fattest bear contest” in Katmai National Park: “America’s fattest bear has now been crowned”.

The science nugget that drives the outreach here is that grizzlies in Alaska lose a third of their body mass over their hibernation in the winter. They have to put on fat during the summer and early fall to survive, and the result is one of the largest cycles of annual weight gain and loss. The outcome is impressive (with photos at the article).

They were probably too busy on the small Brooks River, an upstream bottleneck for hundreds of thousands of the 62 million salmon that passed through Alaska’s Bristol Bay this year, LaValle said. There, the bears easily snatch the fish, then promptly massacre them for the fattiest parts — the skin, fat and brain — before nonchalantly discarding the flesh for which we humans might pay upward of $30 a pound.
LaValle compares this surgical approach to not filling up on bread at a restaurant — the fat is the good stuff, and there’s plenty more where it came from.

Lots to think about for students who are learning about optimal foraging.

Micro-museums, cabinets of curiosities

On the subject of natural history museums changing for the future, this update from the Simons Foundation is fascinating: “Science Sandbox: The changing face of science museums”.

MICRO, a nonprofit founded in 2016 by computational ecologist Amanda Schochet and media producer Charles Philipp, works with designers, artists and scientists to pack knowledge into cabinets of curiosity about the size of a vending machine. MICRO increases exposure to science learning by partnering with venues such as the Brooklyn Public Library, Ronald McDonald House and Rockefeller Center to install these tiny museums. The first museum in their ‘fleet,’ the Smallest Mollusk Museum, can go almost anywhere, from hospital waiting rooms to community centers and malls, reaching people where they already are.

This is such a cool idea. It’s like a tiny bookmobile for mollusc science.

I’m going to start planning a tiny cabinet that might work in public outreach for human origins. I think this has a lot of promise.

Some thoughts on museums, new species descriptions, and collections

What is the value of museum collections? One way of looking at this value is to watch people who newly describe species based upon specimens from collections taken long in the past. Today’s broader knowledge of biological diversity has created opportunities for scientists to recognize and describe specimens that don’t fit within recognized species.

Natural history museums are in a difficult place right now. Their budgets are tight and rely heavily upon their work in public education and engagement. The research side of these museums is having more and more trouble retaining talent in a landscape where universities and research institutes are better-funded. The age of genomics has brought new scientific interest to many collections, but the highest-profile results often benefiting highly-funded external researchers who snap up the low-hanging fruit.

Jake Buehler in Gizmodo tells the story of a new description of a parasitic plant species in Japan, and draws broader implications for the value of museum collections: “Mysterious New Plant Discovered in Museum Collection Is Probably Already Extinct”

This propensity to show up briefly only to vanish without a trace is likely a consequence of fairy lanterns’ strange life-cycle. Since they don’t need to photosynthesise, they can lay dormant underground for years, only sending miniscule flowers to the surface when they’re in a reproductive mood.
The discovery of the new fairy lantern highlights the crucial role museum collections play in our understanding of Earth’s biodiversity. Wurdack noted that in the in the Smithsonian’s U.S. National Herbarium alone, “we have hundreds of new species awaiting scientific description and further research.”

I don’t have a quarrel with this idea. There is a value to scientific description and understanding, as a way to alert people to the loss of biodiversity and the need to protect habitats.

But collection is also by its nature an act of destruction. Could this little fairy lantern have been the last of its kind? I’m interested that genetics was not a part of this story, although more and more it will be. We need to step up our means of noninvasive documentation of all kinds, from incidental genomic sampling to photo and photogrammetric documentation.

Future biological museums will mostly be data repositories. Natural history museums were established as repositories for physical collections. But the science in the future will rely upon vastly more data than physical specimens. We are not preparing museum supporters well for the coming era.

Another reaction: It’s indisputably true that museums possess many undescribed species within their collections. Important paleontological specimens keep emerging from the massive, incompletely-prepared collections from the nineteenth and early twentieth centuries.

That’s not a reason to praise these collections. All the undescribed specimens in these collections are the result of what today we would consider to have been near-indiscriminate destruction of sites.

In fortunate cases, the original collector recorded some contextual information, which is still associated with those specimens in the collections. Contextual information is often better for zoological and botanical specimens, mainly because living creatures were collected as complete bodies, skins, leaves, or skeletons, and the essential context is the collection location and time. The situation for paleontological and archaeological specimens is much worse, because excavation practices often did not result in any accurate idea of stratigraphic context. In many cases of both types, contextual information has been lost over time.

Sure, it’s a good thing that museums have stored these collections, often bringing them up to modern standards of curation that make such scientific description possible. Clever people can find some details of context even if original data are absent or poor. This scientific value is why we must maintain old physical collections and keep them as an intrinsic part of biology.

At the same time we must also redirect our scientific collections to integrate new models of data acquisition.

Obviously, a plot of forest that is about to be made into a parking lot is not the place to fret about leaving plant specimens in the field. My knowledge and concerns are more tuned toward paleontological cases, and as a paleoanthropologist I’m fortunate to work at sites that are either protected or have a strong potential to become protected because of their heritage value.

But that position gives us a broader responsibility. Paleoanthropologists should be at the leading edge of developing new and better ways of data collection, and finding ways to integrate those new approaches with old collections.

Thalamus in the spotlight

Knowable magazine, which covers research published in Annual Reviews journals, has a nice interview by writer Emily Underwod of Michael Halassa, an expert on the functional neuroscience of the thalamus: “A long-overlooked brain region may be key to complex thought”.

In the interview, Halassa emphasizes that the thalamus has often been assumed to function basically as a relay station between the senses and the cortex, based mainly on visual processing as a model for the rest:

What’s so interesting about primate vision and visual cognition is that when we interact with the world, we’re not just interacting with pixel intensities, we’re building internal representations of objects. That’s why you can categorize any cup you see, even if you've never actually seen that particular cup before, and it looks different from other cups. Neurons that can specifically recognize male or female faces, or respond only to a photo of Jennifer Aniston — all that exciting stuff happens in the cortex, which is part of the reason that the thalamus has been sort of shoved to the side.
But there are many other areas of the thalamus besides the LGN and other sensory areas that interact with the cortex, including areas involved in motor control and cognition. Now we are studying those too.

If you did purely imagine the thalamus as a relay station, that would not mean it was unlikely to be important to cognition. In the real-world telecommunications network, relays have to work fast and flawlessly. But to evolution, noise in a relay system is potentially a source of adaptive variation. A small change to the relay, like a slightly greater or lesser degree of crosstalk to one or another region, might often be a negative, but once in a great while might have an effect on cognition that enhanced survival or reproductive fitness. Even if the relay functions are strongly conserved among species, getting these connections slightly wrong would occasionally be useful in one or another lineage.

Humans, with a rapidly evolving brain and vastly larger cortex, might be just the lineage in which “wrong” connections might have a positive effect once in a while.

Nobel Wikipedia lapse points to the holes in science journalism

This story from Marina Koren in The Atlantic about new Nobel laureate Donna Strickland has an important message: “One Wikipedia Page Is a Metaphor for the Nobel Prize’s Record With Women”.

Unlike her fellow winners, Strickland did not have a Wikipedia page at the time of the announcement. A Wikipedia user tried to set up a page in May, but it was denied by a moderator with the message: “This submission’s references do not show that the subject qualifies for a Wikipedia article.” Strickland, it was determined, had not received enough dedicated coverage elsewhere on the internet to warrant a page.

As a science writer friend pointed out, this is a hole in science journalism. Here we have Nobel-Prize-winning work, and before the Prize was awarded this week, there were not enough stories to justify a page.

The vast majority of wonderful and important work in science will never win a Nobel. Far more good science, I’m sure, than there are writers who write about science. To have a Nobel-winning area that hasn’t been covered in depth by science writers since the 1980s is far from an unthinkable circumstance.

But clearly in this case the science press has had different priorities from physicists who judge the long-term significance of research. That means the public isn’t seeing the spectrum of highly-significant work. How many pages have been printed, and internet virtual ink spilled, on string theorists and untestable ideas? In the meantime, how much of the real empirical record of physics has gone unheralded by any journalists at all?

This is equally true in most fields of science, probably all of them. There are amazing, rich discoveries in human evolution that I think are really cool that don’t get the attention they should. I do what I can to bring attention to many of them, and I’ll keep on trying to do so.

Looking at linguistic echoes of extinct species

Priscilla Wehi and coworkers have a neat article in The Conversation describing a recent research paper that looked at traditional sayings in Māori, to try to understand whether they contain a trace of how the Māori ancestors interacted with bird species that the first encountered when reaching New Zealand: “Dead as the moa: oral traditions show that early Māori recognised extinction”.

It takes all kinds to study the past. Our team includes a conservation biologist, a linguist, a bioinformaticist and experts in Māori culture. Together, we delved into the wealth of ecological knowledge embedded in Māori oral traditions. We unpicked language cues, historical events and cultural contexts to understand habitats, animals, landscapes and the relationships between them.
Many whakataukī (pithy sayings like English proverbs) reveal intimate observations about nature. The link between flowering times and animal activity expose seasonal cycles. Whakataukī note the abundance of food resources.
Of those that refer to birds, a disproportionate number talk about moa. What they looked like. How they trampled through the forest with their heads in the air. How best to eat them.

This really is a fascinating concept, that the way that ancient people interacted with different species may be recorded in subtle ways by oral traditions. For those people who are curious about the stories of “ancients” in various parts of the world, this is the kind of linguistic research that might open a crack into unrecognized histories.

Remembering King Leopold's human zoo

National Public Radio (U.S.) has a story about one of the evils of Belgian colonization of the Congo: King Leopold brought hundreds of Congolese to Belgium to live in a mock African village for public display: “Where ‘Human Zoos’ Once Stood, A Belgian Museum Now Faces Its Colonial Past”.

The site near Tervuren is now part of the current grounds of the Royal Museum for Central Africa. As the story details, it wasn’t a one-off:

Fifty years later, Belgium built another mock African village at the 1958 Brussels world's fair. The Congolese who traveled to Belgium for the exposition thought it would be a cultural exchange, says Zana Etambala, a historian at the Royal Museum for Central Africa.
Instead, they found themselves standing behind a bamboo fence, on live display for Europeans, some of whom made monkey noises to get their attention.
"They were throwing bananas and peanuts to [the Congolese]," says Etambala, who grew up in Belgium and Congo. "And the Congolese protested against that. They wanted to be respected and not seen as animals in a zoo."

The Royal Museum today is undergoing a renovation that will bring some of the horrific stories of colonial abuses into the public displays.

The postmortem grandchild

What???

The British couple’s only child, a son, had died suddenly in a motorcycle accident, at the young age of 26. Somehow, the son’s body wasn’t recovered for two full days.
But after the discovery of the body, his parents apparently jumped into action quickly; they had their son’s sperm extracted from his body. Once extracted, the parents began the process of trying to use the sperm to bring into the world their own grandchild. Oh boy.

With a donor egg and a surrogate, the couple now has a three-year-old biological grandchild. The linked article goes into the legal aspects, including the problem that this was all impossible in the U.K., where the couple lives, and so they brought their grandchild into the world in the U.S.

Engaging scientists from indigenous communities in genomic data

This is an important news article by Lizzie Wade in Science, covering the Summer Internship for Indigenous Peoples in Genomics: “To overcome decades of mistrust, a workshop aims to train Indigenous researchers to be their own genome experts”.

The internship is a program that provides training and information about genomic research for scientists who are members of indigenous groups around the world. The idea is to bridge the mistrust that has emerged from past interactions, where scientists took samples from communities without sharing anything back.

The article gives some background on the anthropological geneticist Ripan Malhi, who has helped to organize the program. I wanted to share this paragraph describing one of his early career experiences that epitomizes why such an effort is important.

[In Malhi's early career] he kicked off his effort with a lecture at a reservation in Northern California. It was the first time he had spoken with a Native American community, despite years of studying their genetics. Expecting to gather dozens of DNA samples, "I brought a bunch of cheek swabs with me," he recalls. But at the end of his talk on DNA variation and the importance of filling in sampling gaps, the room fell uncomfortably silent. "Then one person stood up and said, ‘Why should we trust you?’" Malhi remembers. "That's a formative memory. I had not learned about anthropologists going to communities, taking samples, and just leaving."
He got no samples that day.

As Kim TallBear, quoted in the article, puts it: “If you’re going to work with Indigenous communities collaboratively on genetics, you have to be willing to make lifelong relations”.

The point is, you cannot engage people as research subjects and then just disappear. The approach of scientists in the past to indigenous groups has been fundamentally exploitative: Scientists went to communities and got samples, then did analyses, published papers, and built careers, but provided no opportunity for research subjects to shape the research, and gave nothing of value back to the people who volunteered their time and genetic information.

Changing that bad history means making real collaborations in which the research subjects have agency and influence on the study design and research questions. I would add something not reflected in this article: Descendant communities should equally have the ability to influence the shape of research on DNA from ancient remains.

This is an article that has many observations and stories worth reading, and I plan to distribute it to my classes. I highly recommend it.

Upcoming lecture: Michigan State University

For readers and friends in the Lansing area, I’ll be giving a lecture at Michigan State University on Thursday, October 4.. The talk is in the International Center room 115, at 2:15 pm.

Here’s a promo:

Hybrids and Ghosts: How ancient DNA and new fossils are changing the science of human origins.

John Hawks is delivering a lecture on Ancient DNA & Human Origins. The rapidly changing field of ancient DNA has settled into a kind of normal science, as several teams of researchers have coalesced around a set of approaches to discover the genetic relationships among ancient peoples.

I’ll be talking about Neandertals, Denisovans, and various signatures of other ancestral human populations, as well as the increasingly complex fossil record.

A better track of contamination in ancient DNA

A new paper from Anja Furtwängler and coworkers finds that the usual way of estimating contamination fraction in ancient DNA samples may fall short: “Ratio of mitochondrial to nuclear DNA affects contamination estimates in ancient DNA analysis”.

The upshot is summarized in the abstract:

We therefore analyzed ancient DNA from 317 samples of different skeletal elements from multiple sites, spanning a temporal range from 7,000 BP to 386 AD. We found that the mitochondrial to nuclear DNA (mt/nc) ratio negatively correlates with an increase in endogenous DNA content and strongly influenced mitochondrial and nuclear contamination estimates in males. The ratio of mt to nc contamination estimates remained stable for overall mt/nc ratios below 200, as found particularly often in petrous bones but less in other skeletal elements and became more variable above that ratio.

DNA from living or recently dead people can enter ancient samples at many different stages of recovery, conservation, and curation of remains. Some laboratory methods preferentially amplify modern DNA, which is a problem for researchers who want to reduce the cost of sequencing runs. So the cost-effectiveness of ancient DNA research depends upon finding ways to increase the fraction of endogenous DNA in sequencing runs.

Reducing costs is the main reason why ancient DNA labs have thrown so much effort into obtaining petrous bones. It is not a matter of better preservation so much as a matter of higher endogenous DNA content, which makes sequencing with today’s approaches relatively cheaper. The finding in this paper that petrosal samples have a more stable relation of mitochondrial and nuclear contamination rates will probably be cited as another point in favor of the predictability of petrosal versus other sampling approaches.

Brexit fears affecting U.K. archaeologists

I have no political position on the impending departure of Britain from the European Union. Nevertheless, I wanted to point to this article in The Guardian that discusses the way that “Brexit” is affecting archaeologists and museums in the U.K.: “Archaeologists and curators leaving UK over Brexit fears”.

Kate Geary, from the Chartered Institute for Archaeologists, said EU nationals made up to 60% of workers on some projects. She said the obligation to carry out such work may be scrapped due to staff shortages, which would be “detrimental to the country’s heritage”.

A number of early career archaeologists on Twitter have added their voices, saying that they are planning to leave Britain, or have already left, to maintain their access to European Research Council funding. Hiring for academic posts in the U.K. over the past 20 years has brought many European nationals into positions in U.K. universities, and the future of many of these scientists is uncertain.

ZooMS finds more Denisovans

A nice news article in Nature about the “zooarchaeology by mass spectrometry”, or ZooMS work being done at Denisova Cave by Katerina Douka and coworkers: “Denisovan hybrid cave yields four more hominin bones”.

This approach uses the slight variations in amino acid sequence of the collagen protein to identify the mammal species represented by a small sample of bone. Within many archaeological sites, the average bone fragment is an unidentifiable piece of bone shaft that even the most skilled anatomist is unlikely to identify to species. That means the “faunal collection” of the average Paleolithic archaeological site may contain hominin pieces that cannot be identified.

Excavation at Denisova Cave, credit John Hawks CC-BY-NC-ND
Excavation at Denisova Cave, credit John Hawks CC-BY-NC-ND

The ZooMS technique allows a basic identification of a bone specimen to biological family or in some cases species. It relies upon differences in the amino acid sequence of the collagen protein in different animals.

Archaeologists can use this information on bone fragments to add resolution about prey species exploited at a site. Being able to quantify bovid, cervid, or equid from fragments might help show which species hyenas were bringing into a site, and which the hominins were hunting. But the most newsworthy use of the method has been to find hominin fragments, which then can be moved into a queue for ancient DNA sampling.

ZooMS was how Samantha Brown and coworkers identified the Denisova 11 specimen, whose DNA sequence was reported earlier this year. The Vindija 33.16 specimen originally targeted for sequencing by Pääbo’s research group was not found using collagen chemistry, but it had a similar history: a barely-identifiable bone fragment, it was assigned to the faunal collection and later identified by an anthropologist as hominin.

This week’s story, reporting on a conference presentation by Brown at the European Society for Human Evolution, is that the Denisova ZooMS sampling has uncovered an additional four hominin fragments. The work goes on, systematically going through thousands of bone fragments:

Meanwhile, Douka, Brown and a handful of volunteers will continue to sift through thousands more bone fragments.
So far, they have found 1 hominin bone for about every 1,000 animal ones in this cache. At this rate, they could find as many as 400 more hominin specimens.

If you could open up any museum drawer and find one previously-unidentified hominin bone in every 1000 bone fragments, it would be a massive advance by any measure. If you could identify such bone fragments at every archaeological site, the resulting sample would provide an unparalleled record of hominin populations in the past–not to mention, we’d find a few ghosts in the process.

Most fossil settings are dominated by fragments, and most bone fragments within mixed assemblages are not identifiable to species. An advance like ZooMS should remind everyone of just how much useful biological information has been lost from sites excavated in historic times when archaeologists simply did not collect unidentifiable bone fragments. The backdirt of old archaeological sites is full of bone fragments and stone artifacts that were “not good enough” to bother cataloging and collecting. In a few cases, recent archaeologists have returned to those backfill deposits, finding bone fragments–even refitting them to broken specimens that made it into museums. Without such extraordinary luck, those massive backdirt piles remain contextless, drifting flotsam of bad archaeology. ZooMS can’t fix that problem now; the context is already gone.

Digging sites responsibly means recording and preserving context for the future. Archaeology is inevitably an act of destruction and it is not possible to retain every microscopic detail or chemical trace, especially since what makes those traces meaningful is their position and situation within a site. Recording every site at a microscopic level is not possible with today’s approaches.

Tomorrow’s approaches will be better. Testing every bone fragment has just come into the realm of possibility, but remains incredibly time and resource-intensive. It can yield huge dividends at a site like Denisova where the information can catalyze ancient DNA recovery. This kind of large-scale chemical testing may not presently justify the cost for most archaeological sites, but it will be cheaper in the future–or may help to justify a reduced intensity of digging and a higher intensity of sampling at some sites.

Recognizing how technology brings the potential for better information recovery, archaeologists must sample sites deliberately, with an eye toward what is possible today with time-intensive methods, and what must remain for the science of future generations.

The ZooMS method, as exciting as it is, relies upon collagen preserved in bone fragments, and so archaeologists can apply it only to sites where collagen is preserved, which are mostly within the past 100,000 years or so. Will we ever have a method that will allow paleontologists to make use of the fragments of bone within older sedimentary contexts? I think we will.

Related:

“A visit to La Grotte de Cotencher”

“Identifying the species used to make bone arrowheads”