Header image

john hawks weblog

paleoanthropology, genetics and evolution

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

The dawn of bread

Archaeologists working at Shubayqa 1, a site in northeastern Jordan, found tiny fragments of an ancient unleavened bread as they were excavating a hearth. The site was made by people of the Natufian culture, 14,400 years ago. The paper describing the discovery, by Amaia Arranz-Otaegui and coworkers, documents the use of a mixed unleavened dough to make bread more than 4000 years before the introduction of agriculture in this region of the world.

The paper includes a photo of the fireplace and structure where the team found the oldest of the charred bread remains. It is one of the most beautiful site photos I’ve ever seen in an archaeological paper:

Image of the fireplace from Shubayqa 1 from Arranz-Otaegui and coworkers
Figure 2 from Arranz-Otaegui et al. 2018. Original caption: "The site of Shubayqa 1 showing Structure 1 and one of the fireplaces (the oldest one) where the bread-like remains were discovered."

Many of the bread fragments showed evidence of grain from various species. But five of them were a mixture that included tubers from a plant known as the club rush.

Ethnobotanical and experimental evidence indicates club-rush tubers are best consumed as gruel or flour to make bread, instead of boiling or steaming (18, 19). Pure club-rush tuber bread is brittle, crumbly, and flaky, but the addition of bread wheat (Triticum aestivum) flour (i.e., gluten) allows for the production of elastic dough that can be pressed onto the walls of a tandir-type oven structure and be baked (18). Evidence for cereal and club-rush tuber preparations have been identified at late Neolithic sites in Turkey (2) and The Netherlands (20). The finds from Shubayqa 1 suggest a considerably earlier date for their dietary use.

It’s a fascinating discovery that adds perspective to the systematic use of various wild plants and food preparation in these semi-nomadic people.

Link: New stratigraphy chart

The International Commission on Stratigraphy has released the 2018 version of Earth’s stratigraphic intervals, illustrated with a very helpful chart:

2018 stratigraphic chart from the International Commission on Stratigraphy

The original, in PDF format, is easily blown up to look at the dates for each interval.

Link: DNA conspiracy theories

In a post this week on the Anthropology News site of the American Anthropological Association, the sociologist Joan Donovan describes her work on DNA identity and self-described white nationalists: “Written in Blood”.

As social scientists, we wanted to know more about how white people, particularly white nationalists, interpret DNA ancestry tests to justify racial purity. It was an important question for us because we were also witnessing the early growth of a white nationalist movement, rebranded as “the Alt-Right” in 2015. Fast forward to December 2017 and the satirical website Cracked.com reported that an anonymous employee from a DNA ancestry company said that they were purposefully messing with some customers’ data in order to anger racists. How and why does a conspiracy theory like this emerge and spread?

This piece is worth reading as a contribution to the conversation on DNA and race.

I have a slightly different perspective than Donovan on this issue.

Cracked.com is in fact a satire site, and many “conspiracies” today get started as satire. But I don’t think there’s anything ridiculous about the idea of DNA genealogy companies “tipping the scales” on ancestry results. For one thing, during just the last few months, we’ve seen a number of stories in which DNA genealogy testing companies gave “Native American” ancestry to samples that (without the companies’ knowledge) had been taken from dogs.

Here’s a story describing one of these cases: “Another DNA Testing Company Reportedly Gets Fooled by Dog DNA”.

Such cases point to the real problem that some companies doing business in this area are not maintaining best practices, to say the least. Without commenting on these particular cases, consumers should make themselves aware that some DNA ancestry tests may be unscrupulous or fraudulent. Indeed, even companies recognized as legitimate businesses may have been reporting results to customers that diverge substantially from the best scientific knowledge about human genetics.

And it is well-known that even the most responsible companies base their reports of “geographic ancestry” upon samples that are very large in Europe but tiny in Africa and the Americas.

All this makes it hard even for experts to tell genuine from fraudulent results in this area, without having access to the algorithms and DNA results. For the public, such “ancestry” tests are simply a black box.

With this “Wild West” atmosphere, it is hardly a stretch to think that a company might report DNA results more skewed to political or commercial interests than to reality.

Link: A new field season of the Deep Roots project at Victoria Falls

Larry Barham of the University of Liverpool and international collaborators have a field project in Zambia examining the “Deep Roots of Human Behavior”, investigating the beginning of compound tools and the transition to the Middle Stone Age. Last year the project disseminated its fieldwork by a very successful blog.

Earlier this month, the first post of the new field season details some of their research aims as they try to understand the MSA of the Victoria Falls area.

Much of the 2017 season was spent looking for sites recorded by Desmond Clark in the 1940s and earlier. We have his maps but those were the days before GPS and there just wasn’t enough detail to re-locate most of the key sites. By way of a recap, we’re looking for sites that preserve stone artefacts from a time period roughly 600,000 to 200,000 years ago. Over this period our species, Homo sapiens, evolved, but there were at least two other human ancestors in the region that we know of, Homo naledi and Homo heidelbergensis. So we can’t be sure who made the tools we’re finding and it’s the tools we’re interested in, because they document a basic change in the way humans thought about technology.

I think it’s great that they are explicitly including multiple species as possible makers of MSA artifacts. If there were biogeographic boundaries among hominin species in Africa during the last half million years, the Zambezi basin is a key area to understand.

Ejecta rays point to the problem with 'ideal' models

The PNAS Journal Club points to an interesting research study on craters: “Journal Club: Researchers may’ve finally solved mystery of crater ray formation”.

The problem is that craters on celestial objects like the Moon are surrounded by distinct rays of ejecta, but those didn’t form in experiments at high velocity.

Full moon showing ejecta rays around craters
Photo: Renden Yoder

Why did the model fail to generate the real-world phenomenon of ejecta rays? Because the model conditions were too ideal:

The team tried to vary every parameter they could imagine—changing the grains’ diameters, mixing grains of different sizes, increasing the speed of the balls—but the eventual solution came about by accident. One day, Chakraborty’s fatigued postdoc, Tapan Sabuwala, failed to follow normal protocols and smooth down the surface of their sandbox before dropping in their impactor. After the drop, voilà—a beautiful crater and its rays appeared.
The jagged landscape, which schoolroom students naturally produced when they haphazardly dumped out their bags of flour, seemed to be the key to creating crater rays. The team followed-up with 135 more experiments in which they pressed a repeating hexagonal honeycomb pattern into their granular surface and found that they could consistently make rays. Moreover, the number of crater rays depended on only two factors—the size of the impactor and the spacing of the hexagonal bumps.

There is a strong rationale to use simple models in physics. You want the conditions to be easily described with mathematics, and easily replicable by other scientists, so you specify exactly the ideal conditions for the model.

But the kids were using an even simpler model, in the sense that anybody can make a pile of flour and throw stuff at it. What is ideal is not necessarily simple. In this case, the real-world physics of planets and asteroids is more similar to the real-world physics of particles than the ideal physics of surfaces and ballistics.

As I read this story, I thought about genetics. We use a lot of “simple” ideal models in human genetics. The hypothetical reconstructions of populations like the “Basal Eurasians” are based upon ideal panmictic populations with mathematically ideal genetic exchanges. The quantification of Neanderthal genetic contributions to humans has likewise been based upon ideal population models and discrete mixture events.

These ideal populations may be easy to model with math, but they bear little resemblance to the spatial heterogeneity of living human populations or the irregular temporal distribution of mixture and contact.

What would a more realistic model look like? For human populations, it would have heterogeneity—not populations as single points, but populations with a spatial extent, varying degrees of mixture as they came into contact, and biased growth.

Would the outputs of such a model look more like the real world? It’s not easy to say. Possibly there is no real difference, and the more complex models come with a greater danger of overfitting because they add so many parameters.

But not all parameters are created equal. My biggest concern about simplistic population models is that they fit data better when new point populations and sources of mixture are added. What if some of those “ghost populations” are really not necessary, if we examine a more complex, more realistic model?

Today’s most surprising findings about human prehistory are pretty strongly model-dependent, and few population geneticists are examining the effect of model selection on these conclusions.

Reinforcing the antiquity of hominins in China

In Nature yesterday, Zhaoyu Zhu and collaborators published a paper describing the paleomag chronology of Shangchen, a site in Lantian county, China. The oldest layers bearing stone artifacts at this site appear to be approximately 2.1 million years old, making these stone tools the oldest yet documented within China.

I was really interested in seeing this new archaeological study published. China is taking on a much more important role in human evolution research. The science of human evolution has advanced markedly within China during the last 20 years, just as it has in many other parts of the world. I had the great privilege of visiting the Institute for Vertebrate Paleontology and Paleoanthropology in Beijing earlier this year, and I’ll be sharing more from that trip soon.

The Shangchen site shows two things clearly.

First, it confirms that there were hominins making stone tools in this part of China by 2.1 million years ago. That’s not the earliest date ever found in China — another cave site called Longgupo has stone tools that archaeologists think are 2.2 million years old or older. But other archaeologists have questioned the very early dates from Longgupo, so this new Shangchen chronology helps to put the early evidence on a more secure footing.

Second, the Shangchen site is not merely one ancient discovery but a long series of archaeological layers. With seventeen archaeological layers across the period from roughly 1.4 million to 2.1 million years ago, Shangchen presents a more impressive record of habitation of the Chinese Loess Plateau than any other part of Eurasia.

Loess stratigraphy showing position of artifacts from Zhu et al. 2018
Figure 3 from Zhu et al. (2018), showing the loess and paleosol stratigraphy at Shangchen. The position of artifact-bearing layers in the deposit is shown at left, while the global paleomag chronology is at far right. There is an impressive correlation between the paleomag signatures at the site and the global paleomag chronology.

Still, seventeen artifact-bearing layers in 700,000 years leaves a lot of room for significant changes and hiatuses. At some times, the climate in this region was very arid, the deserts of western and northern China became larger, and huge amounts of dust blew from those deserts and dropped onto this central part of China. At those times, there are some archaeological layers but not too many. Other times, the climate was moist, less dust blew from the deserts, and stable layers of soils formed on the surface at Shangchen. Those ancient paleosols are richer and denser in stone tool assemblages.

So this site seems to show evidence of a long habitation of China by human relatives, but whether it was the same hominin species or population across all that time is not clear. Whoever was living there, they were responding to the local climate in the way they behaved in this region.

Large areas of central and western China are covered in loess from the early Miocene period—as early as 22 million years ago—on up to recent times. During relatively arid periods, desert expanded in western and northern China and Mongolia, generating large amounts of windblown dust. Some of this dust settled in western and central China, creating layers of loess. Today, a thick succession of loess deposits occur in the Chinese Loess Plateau. The sediment is composed of fine particles that were carried by the wind. During wetter periods, the loess deposition greatly slowed, and stable soils formed on the ground surface, so today’s stratigraphy is an alternating series of loess layers and paleosols.

Water easily erodes these layers, so gullies and streams create deep cuts across the stratigraphy. Of course, hominins didn’t enter China as early as the Miocene, as far as we know. Archaeologists have focused on the Pleistocene stratigraphy of the Loess Plateau, surveying these layers where stone tools contrast markedly with the fine-grained loess. A huge region of China is covered by these ancient windblown sediments, and there have been many, many important archaeological discoveries, from Upper Paleolithic all the way back to the dawn of hominin occupation of China.

The paleomagnetic chronology presented in this paper is only one aspect of a much larger program of dating loess events across the Pleistocene. The systematic approach to identifying these dry time periods with large loess deposits is really important, because it is allowing scientists to tie together ancient landscapes and evaluate tools and fossils from many different sites.

For example, the same approach gave rise to the redating of the Gongwangling fossil material by the same research group in 2015. (They argued that the fossil is around 1.65 million years old, far more ancient than thought previously.) This program of chronology across sites has been underway for several years, and I think it is going to lead to many more important discoveries.

I’ll be writing a bit more in the next few days about what scientists know about the earliest movements of hominins out of Africa. All the headlines I’ve seen in the last day are wrong.

Every story I’ve seen has accentuated that Shangchen is 300,000 years older than Dmanisi, which the stories claim was previously the oldest evidence of human habitation of Eurasia. This is wrong.

Now, Dmanisi is very important, but it’s simply not accurate that it’s the oldest evidence outside Africa. There are older sites. Even within China, Longgupo has an earlier published chronology, and Longgudong is estimated to be as old as the oldest Shangchen layer. In India, there are sites with earlier published evidence, one as old as 2.6 million years.

That doesn’t mean scientists should blindly accept every “earliest” date for every archaeological occurrence. Any find that demands that we revise our models for human evolution should be supported by multiple lines of evidence. So when only one or two methods point to the geological age, I want to see more. Early sites often have only a few observations suggesting a minimum age, and history shows that those “earliest” dates are often revised. Even for the new Shangchen chronology, where the paleomagnetic chronology is impressive, we should seek more cross-validation.

Still, even with my mistrust of geological age estimates, I have to say that the evidence points against the old idea that the first out-of-Africa dispersal was by stone tool-making Homo erectus within the last 2 million years.

We now have five or six sites earlier than Dmanisi, and Dmanisi itself is the first occurrence of “H. erectus” anywhere in the world. With the Gongwangling cranium and the earliest Sangiran material older than 1.5 million years, H. erectus has a better record and greater diversity in Eurasia than in Africa in the same time period.

At least, what we’ve been calling H. erectus. If there was a single, early colonization of Eurasia by hominins, it must have been much earlier than the first occurrence of H. erectus. I would suggest instead that there were many movements and dispersals from Africa and back into Africa, starting much earlier than 2 million years ago and extending up to the most recent. We already know this is true of the Middle and Late Pleistocene—it is not a single dispersal and stasis, there were many partial replacements with interaction of earlier people and new migrants.

The old H. erectus single migration model just can’t account for the data of early sites in Eurasia, it doesn’t deal well with the morphology of the Dmanisi and early African H. erectus fossil material, and it doesn’t add any explanatory power.

There’s a big story brewing here.

References

Zhu Z, Dennell R, Huang W, Wu Y, Qiu S, Yang S, Rao Z, Hou Y, Xie J, Han J, Ouyang T. 2018. Hominin occupation of the Chinese Loess Plateau since about 2.1 million years ago. Nature (online). doi:10.1038/s41586-018-0299-4

Zhu, Z. Y., Dennell, R., Huang, W. W., Wu, Y., Rao, Z. G., Qiu, S. F., ... & Zhou, H. Y. (2015). New dating of the Homo erectus cranium from Lantian (Gongwangling), China. Journal of Human Evolution, 78, 144-157. doi:10.1016/j.jhevol.2014.10.001

A pre-Clovis tradition from the Gault site, Texas

The Gault site, on Buttermilk Creek near Austin, Texas, is one of the most significant early American archaeological sites. The whole site covers an enormous area, with excavations that have been carried out formally and informally for more than a hundred years. Scientific investigation of the site in recent decades has focused upon a number of distinct excavation areas.

This week, Science Advances published a new paper by Thomas Williams and coworkers describing their work in Area 15 of the Gault site. Their paper documents a rich, previously unknown culture that existed more than 16,000 years ago.

They call this early tradition the “Gault Assemblage”.

Gault assemblage artifacts from Williams et al. (2018)
Gault Assemblage artifacts from Williams et al. (2018). Original caption: "Gault Assemblage artifacts (A to D, F, and L) Bifaces. (E) Blade core. (G) Quartz projectile point. (H and I) Projectile points. (K) Projectile point tip. (M, V, and W) Blade. (N) Unifacial tool. (O and T) Gravers. (P) Discoidal biface. (Q) End scraper. (R to U) Modified flake tools. (X and Y) Lanceolate projectile points. Descriptions are given in the Supplementary Materials."

A number of sites in North America preserve artifacts proposed to be earlier than the spread of the Clovis tradition, around 13,500 to 11,500 years ago. The Gault site is very interesting because it presents a pre-Clovis archaeological tradition in stratified context beneath Clovis archaeological material. The new paper provides an optically-stimulated luminescence (OSL) chronology for the entire archaeological sequence at the site. The team obtained age estimates for four samples from the Gault Assemblage layers, which all lie between 16.7 and 21.7 thousand years ago. They also dated four samples from the overlying Clovis layers, all between 11.9 and 13.2 thousand years ago.

Stratigraphy and OSL chronology of the Gault area 15 site, from Williams et al. (2018).
Figure S4 from Williams et al. (2018). Original caption: "Relationship between the stratigraphy and cultural components in Area 15. Stratigraphic unit numbers are shown in the stratigraphic interpretation and the cultural horizons are highlighted in gray."

There is not a sterile layer between Clovis and Gault Assemblage, but the flake count in that interval is quite low, and the Clovis itself is low-representation compared to the much earlier Gault Assemblage layers. It would seem hard to explain away this assemblage as a product of artifact migration downward from Clovis or later layers.

That is relevant because several years ago, a team of scientists criticized the interpretation of another pre-Clovis assemblage stratified beneath Clovis material. This site, also on Buttermilk Creek, is called the the Debra L. Friedkin site, with the pre-Clovis material first published by Michael Waters and colleagues in 2011 in Science. In Waters’ and colleagues’ (2011) description, a pre-Clovis artifact assemblage between 15.5 and 13.2 thousand years ago is stratigraphically below Clovis at the site, and differs from the Clovis assemblage in many ways. Waters and coworkers called this the “Buttermilk Creek Complex”. They suggested that this was evidence for a tradition earlier and different from Clovis.

Juliet Morrow and colleagues (2012) objected to this interpretation. They offered the alternative interpretation that (a) the apparently early age of this assemblage might be the result of downward migration of isolated artifacts from higher, Clovis layers, and (b) even if the site itself is chronologically early, it may simply be an early variant of the Clovis tradition.

Jennings and Waters (2014) responded with a statistical comparison of Buttermilk Creek Complex with Clovis, concluding that they are different and distinguishable on technical grounds, although the Buttermilk Creek might have been antecedent to the Clovis. And Driese et al. (2013) undertook a close analysis of the sediments, concluding that layers were not mixed, and downward vertical displacement of material could not have been substantial.

I review this mainly to show that a number of archaeologists found the earlier claim of a stratified pre-Clovis-to-Clovis context to be controversial, and it gave rise to both a published critique and subsequent research. I imagine that similar criticism may emerge of this current research study.

In the new paper on the Gault site, Williams and colleagues do not provide a comparison between the Gault Assemblage and the Buttermilk Creek Complex. Considering that the Gault Assemblage may be 2000 years or more earlier than the pre-Clovis material from the Debra L. Friedkin site, they may not be comparable. But this seems like an obvious comparison that I’d like to see.

As an aside, for those who want to know more about work at the Gault site, earlier this year, SAPIENS ran a book excerpt by Craig Childs about the site. This gives some nice context for the excavations: “In the Land of the Mammoth Eaters”.

References

Williams TJ, Collins MB, Rodrigues K, Rink WJ, Velchoff N, Keen-Zebert A, Gilmer A, Frederick CD, Ayala SJ, Prewitt ER. 2018. Evidence of an early projectile point technology in North America at the Gault Site, Texas, USA. Science Advances 4: eaar5954. doi:10.1126/sciadv.aar5954

Waters MR, Forman SL, Jennings TA, Nordt LC, Driese SG, Feinberg JM, Keene JL, Halligan J, Lindquist A, Pierson J, Hallmark CT, Collins MB, Wiederhold JE. 2011. The Buttermilk Creek Complex and the Origins of Clovis at the Debra L. Friedkin Site, Texas. Science 331: 1599-1603. doi:10.1126/science.1201855

Morrow JE, Fiedel SJ, Johnson DL, Kornfeld M, Rutledge M, Wood WR. 2012. Pre-Clovis in Texas? A critical assessment of the “Buttermilk Creek Complex”. Journal of Archaeological Science. 39:3677-3682. doi:10.1016/j.jas.2012.05.018

Jennings TA, Waters MR. 2014. Pre-Clovis lithic technology at the Debra L. Friedkin site, Texas: Comparisons to Clovis through site-level behavior, technological trait-list, and cladistic analyses. American Antiquity. 79(1):25-44. doi:10.7183/0002-7316.79.1.25

Driese SG, Nordt LC, Waters MR, Keene JL. 2013. Analysis of site formation history and potential disturbance of stratigraphic context in vertisols at the Debra L. Friedkin archaeological site in central Texas, USA. Geoarchaeology. 28:221-248. doi:10.1002/gea.21441

Looking at Luzon hominins, from the perspective of 1985

In light of this week’s paper by Ingicco and colleagues showing evidence of 700,000-year-old human activity from Kalinga, on Luzon, I’ve been doing a little reading.

I found an interesting article by Lawrence Heaney, published in the 1985 volume of Modern Quaternary Research in Southeast Asia. The title is: “Zoogeographic evidence for Middle and Late Pleistocene landbridges to the Philippine Islands”. In case you wonder about the title, the article shows that there were no land bridges to the Philippines, although there were several ancient land bridges connecting various islands within the Philippines.

The part worth quoting at length has to do with speculations that Homo erectus may have reached the Philippines.

Comments on Homo erectus and land bridges
Given the strong evidence against land bridges from Asia to the Philippines, what does this tell us about the probability of finding Homo erectus in the Philippines?
First, it must be recognized that this analysis has been general; it has not dealt with any specific species, and does not prove that a single species cannot behave in a different fashion from most or all others. The fact that a single species of monkey, Macaca fascicularis, is now recognized to occur in much of Southeast Asia including nearly all of the Philippines, could be taken as evidence that it is possible, however unlikely, that Homo erectus had a similar distribution.
However, it must also be recognized that if Homo erectus did occur on Luzon, for example, they arrived there by crossing over several sea channels that were over 10 km wide, and could have been over 25 km wide. It is possible to imagine a small population of monkeys floating accidentally out to sea on a mass of trees and branches and being rafted to an island 25 km away; it is far, far more difficult to imagine a similar thing happening to a group of proto-humans. Thus, I suggest that if Homo erectus did occur on Luzon, they arrived by deliberate construction of rafts and dispersal across sea channels.

The chapter goes on to consider whether any evidence about Homo erectus on Java suggested that they might have crossed water to islands. This discussion is a bit outmoded from today’s perspective: Although it has long been known that Java was connected to the Asian mainland during the Late Pleistocene, it was not always so evident that all of Java had such connections during the Early Pleistocene, since the island has coalesced as a result of Pliocene and Early Pleistocene uplift and volcanism. So some authors had suggested that the earliest evidence of Homo erectus on Java might have occurred before Trinil was part of the Asian landmass, for example.

More relevant today is that we now know that hominins occupied Flores, Sulawesi, and now Luzon, all prior to 100,000 years ago. Flores and Luzon were peopled during the early Middle Pleistocene.

What’s more, the Flores hominins may represent a hominin group that diverged earlier than the last common ancestor of Homo erectus and archaic and modern humans. This is not a question of Homo erectus dispersing to islands, it may be a question of a branch of hominins that–except for H. floresiensis–is presently unknown.

Link: Are physicists barking up the wrong tree?

Sabine Hossenfelder has a book coming out next month, Lost in Math: How Beauty Leads Physics Astray. She pursues the question of why physicists today follow research paths toward “beautiful” or “natural” theories, and critically examines past theories, noting that successful ones were rarely viewed as “beautiful” at the time they were proposed.

The implication is that today’s efforts to develop new theories may be barking up the wrong tree.

She has done an interview with Edge.org on her work: “Looking in the Wrong Places”, which is both thoughtful and provocative:

The problems that I see in my own community worry me a lot. Not so much because I’m so terribly worried about quantum gravity. On a certain level, even though it’s my personal interest, I realize that for most of the people on the planet making progress in quantum gravity is not that terribly important. It worries me because I have to question how well science itself is working.
The problems that I was speaking about in my own community—that people work on certain topics just because the money is there, because it’s something that is popular and that their colleagues appreciate—are problems that almost certainly exist in most scientific communities. My extrapolation from my own field would tell me that I should be very skeptical about whatever comes out of the scientific community. And that’s not good. Clearly that’s not good.

I’m looking forward to this book.

Link: Following fieldwork in Malawi

Emory University has done a nice story about Jessica Thompson’s archaeological fieldwork in Malawi: “Bonding over bones, stones and beads”.

Thompson's fieldwork in Malawi has uncovered hunter-gatherer remains that yielded DNA ranging in age from about 2,500 to 6,100 years old. And her work is ongoing at a site where a skeleton recovered in 1950 was recently dated to 8,100 years ago and also yielded DNA.
The samples are by far the oldest-known human DNA from Africa, preserved by the cool, arid ecosystem of the highlands of northern Malawi.

University press sites often do a really nice job telling stories that give the day-to-day context of fieldwork. This is a great example, seeing the joy of students making discoveries and hearing the way that Thompson is planning her upcoming field season.

A new perspective on Homo floresiensis from one of the discoverers

In the South China Morning Post, a great story featuring Indonesian archaeologist Emanuel “Wahyu” Saptomo: “Indonesian archaeologist recalls Flores ‘hobbit’ fossil find 15 years on, and what it meant for him and Indonesian archaeology”.

Saptomo’s comments provide a good account of how the American and European media have marginalized scientists from developing countries.

According to Wahyu, although Indonesia has led the research into Homo floresiensis, it has not been easy for the nation to gain global recognition for these efforts. Credit for the discovery often goes to Australia-based scientists, which Wahyu believes stems from how it has been reported.
Most of the journalists following the hobbit story work for “big companies”, he says, and cater to audiences that expect such significant discoveries to be made by Westerners.

I think the media environment has actually become much worse in the last 14 years since the Homo floresiensis story broke. Today most stories are written by freelancers and not staff journalists at big companies. Many freelancers are incredibly talented reporters, but few of them have the breadth of international contacts that help them to report a story like this in depth. Few will penetrate into research teams to find diverse voices beyond the first or corresponding authors of a study.

As a result, we see lots and lots of stories about the same new paper, all quoting the same few experts.

Scientists and teams of scientists can do much to make reporting more accurate and representative. They can make sure that any press release includes quotes from diverse scientists with different roles in the research. They can make sure that contact information is available for a breadth of researchers, especially those representing institutions in the country where research is undertaken.

It’s not just about providing information passively; teams can reach out. Scientists can do “inreach” with other experts in advance of a news release, so that external voices are armed with information leading to more team members, not just the “lead” scientist on a project. And scientists and institutions can do targeted outreach with trusted journalists to make sure they know the full story and can represent team members from countries where the research is done.

In today’s environment, scientists can do much to recognize key collaborators and broaden the narrative behind their science.

Chimpanzees don't necessarily live where biologists thought they did

Distribution maps of wild species are inaccurate for lots of reasons. When it comes to distribution maps of wild primates in tropical Africa, one of the biggest reasons why they’re inaccurate is that many of the areas have not been surveyed for wild primate populations by biologists in modern times.

This point helps to explain a paper from last year by Thierry Aebischer and coworkers (2017) describing evidence for chimpanzee geographic distribution in the Central African Republic.

Here we report the presence of a viable population of Eastern chimpanzees (Pan troglodytes schweinfurthii) in the eastern part of the Central African Republic (CAR). Their location at the northern limit of the chimpanzee distribution and their heterogeneous habitat in the forest-savanna ecotone make them an ecologically relevant population for the long term survival of the species (Plumptre et al., 2010). Surprisingly, the population appears confined to habitats east of the Chinko River as no evidence for chimpanzees was found west of that river despite considerable survey effort. This geographic distribution is in contrast to recent distribution models that predicted much more favorable environmental conditions west of the Chinko River and classified most parts of Eastern CAR and the entire eastern part of CNR as unsuitable (Junker et al., 2012; Plumptre et al., 2010). At least 25000 km2 (27%) (IUCN SSC A.P.E.S. database, Drexel University and Jane Goodall Institute, 2016), or 57290 km2 (62%) (Plumptre et al., 2010) of the supposed chimpanzee distribution in Eastern CAR as estimated by the International Union for the Conservation of Nature (IUCN) and the Wildlife Conservation Society (WCS), respectively, is most likely not or no longer occupied by chimpanzees. Our study thus showcases some limitations of relying solely on remote sensing data to predict distributions of endangered species in regions for which limited or no training data is available, and therefore illustrates the necessity of extensive field surveys to accurately assess population density in remote and scientifically underrepresented areas. This is especially relevant for species like chimpanzees that may adapt their lifestyle to diverse environmental conditions but are heavily affected by anthropogenic disturbances.

Over the years, there have been a number of scientists who have tried to work out the ancient geographic ranges of Neandertals and other hominins, based upon predictions about their ecological habitat preferences.

How do scientists determine which habitats the Neandertals preferred? First, they map known Neandertal sites. They consider what we know about those sites and their local ecologies. Of course, there is a huge bias in that hominin-bearing sites have been subject to much greater intensity of excavation and investigation. From each site comes some ideas about local ecology at the time Neandertals (or other hominins) lived there—mostly based on the faunal list.

Across many sites, this gives a picture of the habitat preferences or tolerances of Neandertals (or any other hominin population). Apply this to a climate model, and you can predict where you should have been able to find Neandertals at any point in the past.

The problem with this approach is epitomized by the chimpanzee survey. Chimps are absent many of the areas in the eastern Central African Republic that were predicted to be good chimpanzee habitat. Meanwhile, chimpanzees are living densely in some areas that were predicted not to have large chimpanzee populations.

It’s doubtful that we can do much better than this for any ancient hominin population. The quantity of data on ancient sites is highest for Neandertals, and lower for every other hominin.

Where they actually lived was likely episodic and fluctuated over time. The places where we find them are a footprint of thousands of years of low-intensity activity, not necessarily a guide to what they preferred or could tolerate.

Link: Sharing research highlights using video

Adrian Smith is a biologist and researcher on ants, who has written an account of his newfound skills for sharing his research highlights on video: “YouTube your science”.

He tells the story of sitting with his mom in a video studio, an experience which helped him realize how much his science was removed from the language that ordinary non-scientists can understand.

First-person accounts of science were not a part of my life when I was younger. I am a first-generation university graduate with no immediate or extended family members who are involved in scientific careers. As a child, I’d never known a working scientist. When I was filming that video with my mum, I realized that I was presenting myself as a professional scientist to a family member who also had never had a personal connection to science before me. Making videos and using press releases to distribute them has helped me to introduce myself and my colleagues to the world as scientists. I now view the impact of my research not just in relation to the metrics around my journal articles, but also in terms of how well I can make my work available to those outside my profession.

This is such an important moment in the history of science, and we need many more scientists to heighten the engagement of the public in our work.

Link: What about the coauthor?

Anna Reser writes about a troubling instance of “Hiding in Plain Sight”.

I saw a woman being erased from the history of science in real time.

The origin of the Africa-into-Neandertal mtDNA introgression hypothesis

I was reading through some papers for a post on neutral evolution versus selection in human diversification. That’s a topic I’ve written about several times, and one of my papers (written with Jim Ahern and Sang-Hee Lee) in particular focused on the relatively great morphological differences between human populations compared to some other primates.

The following passage, near the end of the paper, comes directly after a discussion of morphological distances (which is why genetics are “on the other hand” here).

On the other hand, the genetic similarities across the geographic range of hominoid species can indicate a history of gene flow (Gagneux et al., 2001). Genetic evidence for recent gene flow includes great similarities among some genes, amid a background of strong genetic differentiation among subspecies. From ancient DNA evidence, it would appear that the Neandertal-human difference is smaller than that among subspecies of either chimpanzees or gorillas (Krings et al., 1999; Hawks and Wolpoff, 2001), despite the relatively greater morphological difference. It is currently premature to claim that the known pattern of ancient mtDNA diversity is evidence of gene flow between the ancestors of Neandertals and the ancestors of living people, and indeed such a finding does not preclude the hypothesis that Neandertals speciated after this shared ancestor. But certainly the critical morphological evidence to address whether Neandertals were a distinct species is the pattern of change in both populations over time (Hawks and Wolpoff, 2001). The hypothesis that Neandertals and modern humans were conspecific predicts that they shared a common evolutionary trajectory, regardless of the degree of morphological difference between them. Future multivariate work may pursue the extent to which different characters may provide comple- mentary evidence of such shared trajectories among ancient human populations.

I’ve bolded the part that struck me as I was re-reading the paper today. Look at that, we predicted that the mtDNA of Neanderthals came from modern humans as an introgression!

What drove us to this provocative (and in our words, “premature”) hypothesis?

We were writing in this paper about how to interpret what seemed like large morphological differences between modern humans and Neanderthals. Modern humans and Neanderthals are morphologically more different from each other than different subspecies of chimpanzees, for example. We pointed out that it is puzzling that two “species” that look morphologically different still have mtDNA sequence divergence that (at the time) was estimated to be less than 500,000 years. That was a lot less than the estimated mtDNA divergence of chimpanzee subspecies.

At that time, what we knew about Neanderthal DNA came exclusively from Svante Pääbo’s research group. They had found that the mtDNA sequences of Neanderthals share sequence motifs that they never found in any mtDNA sequences of living humans. In particular, a paper by David Serre and coworkers from Pääbo’s lab had shown that 24 Neanderthal and 40 early modern humans in Europe had complete lack of haplotype sharing. This reinforced the finding that a Neanderthal mtDNA clade had once existed, an outgroup to all the mtDNA clades found in living people, and that no surviving descendants of the Neanderthal mtDNA clade had yet been found. Laurent Excoffier and Mathias Currat (2004) had also emphasized the lack of modern humans who share the Neanderthal mtDNA haplotype, especially unexpected in a growing population of modern humans.

That view carried a lot of weight before the initial sequencing of a part of the Vindija 33.16 genome in 2006, which for the first time raised the substantial likelihood of introgression from Neanderthals. And of course the last eight years have completely transformed matters. We now know that (1) modern people have Neanderthal ancestors, (2) the Neanderthal component of ancestry is higher in East Asia than elsewhere, (3), modern populations almost everywhere in the world experienced massive genetic turnovers during the last 30,000 years, meaning that the immediate post-Neanderthal populations of Europe have little to do with today’s Europeans.

At any rate, Krings and coworkers (1997) first recovered Neandertal mtDNA from the Feldhofer 1 skeleton, finding that it had a type never yet found in any living people. They estimated that this mtDNA haplotype had diverged from the mtDNA clade leading to modern humans around 465,000 years ago. That time of divergence appeared to put an upper limit on the time that modern humans and Neandertals parted ways.

That limit was surprisingly young, much shorter than the divergence times at which other primate sister species have become intersterile. In particular, as we pointed out in 2005, the time was very young compared to the mtDNA divergence times of today’s chimpanzee subspecies.

One possibility to consider for Neandertals and modern humans is that mtDNA had introgressed from one to the other, despite the fact that Neandertals and modern humans were more morphologically different than chimpanzee subspecies.

This has turned out to be almost certainly true. Yet the morphological difference between Neandertals and modern humans is still anomalously large compared to that between chimpanzee subspecies—or, more probably, the chimpanzee morphological differences are anomalously small compared to their great genetic diversification. The good evidence for recurrent introgression among Neandertals, modern humans, and Denisovans (and among chimpanzee subspecies) makes none of this much of a surprise today.

But the reason for the mtDNA introgression from ancestral African to Neandertal populations is unknown. Was there some adaptive value to the African mtDNA that caused it to succeed in later Neandertals? Did the original Neandertal mtDNA variation suffer from the high genetic load that other Neandertal genes later did? Was this all just chance?

At the moment, we have no easy way to tell.

References

Ahern, J. C., Hawks, J. D., & Lee, S. H. (2005). Neandertal taxonomy reconsidered… again: a response to Harvati et al. (2004). Journal of human evolution, 48(6), 647-652.

Currat, M., & Excoffier, L. (2004). Modern humans did not admix with Neanderthals during their range expansion into Europe. PLoS biology, 2(12), e421.

Serre, D., Langaney, A., Chech, M., Teschler-Nicola, M., Paunovic, M., Mennecier, P., ... & Pääbo, S. (2004). No evidence of Neandertal mtDNA contribution to early modern humans. PLoS biology, 2(3), e57.