Header image

john hawks weblog

paleoanthropology, genetics and evolution

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

Link: A plea to think about the ethics of sampling ancient bodies

Chip Colwell writes in The Conversation about the questionable ethics involved in some ancient DNA sampling: “Rights of the dead and the living clash when scientists extract DNA from human remains”.

As an archaeologist, I share in the excitement around how technology and techniques to study DNA are leaping ahead. As never before, the mysteries of our bodies and histories are finding exciting answers – from the revelation that humans interbred with Neanderthals, to how Britain was populated, to the enigma of a decapitated Egyptian mummy.
But, I have also closely studied the history of collecting human remains for science. I am gravely concerned that the current “bone rush” to make new genetic discoveries has set off an ethical crisis.

The link on the term “bone rush” points to “a short piece in Technology Review that attributes the phrase “bone rush” to me. I didn’t take the phrase from anybody else, and I think we’ve entered a scary atmosphere from the point of view of ethics of ancient DNA.

I haven’t written here yet about the case of the “Ata” body. The body was allegedly removed illegally from Chile and made the subject of a documentary film production. Tissue samples were removed and the body’s genome was sampled by geneticists from Stanford and the University of California–San Francisco. Colwell mentions the case in this essay, and there is more to say on this case.

In just the last few weeks, the egregious “Ata” case has been reported, NPR has carried out a DNA-free chemical sampling of a classroom skeleton, the FBI helped identify an Egyptian mummy using ancient DNA methods, ancient DNA was applied to an early Medieval case of head-binding, and the New York Times has reported that David Reich is sampling thousands of ancient bones, systematically removing the inner ears of ancient skulls. And those stories are just a small sampling of ancient DNA science news in the last few weeks.

My profession is the study of dead skeletons. Even for me, the current landscape of ancient DNA is bewildering. I think we should do as much as possible to bring the stories of ancient people to light. But every piece of evidence we have from past populations is precious, and every one can benefit from the engagement of a broader community, including possible descendant communities, local and national governments, and other stakeholders.

My concern is that scientists are rushing to bring out results, using today’s limited technology, without broadening the base of support for the science. Scientists may individually be working within the ethical framework they understand, but I believe we could do much better work.

Quote: Looking back at Clovis-first

This is a nice paragraph from Waters and Stafford (2013) on the Clovis-first paradigm for initial habitation of the Americas:

At least three major anomalies cannot be explained or no longer ignored by the Clovis-First paradigm. First, at 13,000 cal yr BP both North and South America were occupied by humans. In North America there is the Clovis complex, with its distinctive technologies and tools. In South America the sites of this age are characterized by generalized toolkits with many ake tools and some bifaces, but no diagnostic artifact type. Thus, at the time of Clovis in North America, you have sites of the same age and with different stone-tool technologies and assemblages in South America. Second, there are several credible sites dating before the time of Clovis. These sites have biface, blade, bladelet, and osseous technologies that date at least to 15,000 cal yr BP. These sites are found in both North and South America in well-dated and secure geologic contexts. Third, the current genetic evidence suggests an older-than-Clovis colonization of the Americas between 16,000 and 15,000 cal yr BP. It is now time to create a new model for the peopling of the Americas and explore new questions about the first inhabitants of the Americas.

I’m noting this, not because it’s news, but I ran across it in the course of lecture preparation. The book chapter (in Paleoamerican Odyssey) is mostly a review of the radiocarbon chronology for Clovis and pre-Clovis sites in the Americas.

After this book chapter was published, the flood of paleogenomic studies on early American skeletal remains began. Among those studies were results that suggested an initial habitation of the Americas in a single major wave preceding 15,000 years ago, as well as the results pointing to the contribution of a “ghost population” to some South American native peoples. Also after this book chapter have been several new archaeological discoveries, including evidence of human activity at Monte Verde as early as the Last Glacial Maximum.

When I lectured about this subject in my MOOC in 2014, the wave of archaeological information that clearly rejects a Clovis-first hypothesis was still fairly fresh, and some archaeologists were still hold-outs. Now there may be hold-outs, but the picture has been thoroughly transformed. Clovis culture now seems a mere afterthought to the main events in the initial habitation of the Americas.

This chapter provides a nice summary and has some good thinking in it about archaeological paradigms as applied to the Clovis phenomenon. What I also notice is that among its 33 citations in Google Scholar, not a single one is from any of the paleogenomic studies on early American specimens that came after this paper was published.

Archaeologists and paleogenomics specialists are embedded within different modes of publication and recognition of scholarship, as I noted earlier this week. “Should archaeologists really fear and loathe geneticists?”

It’s not that the two fields don’t cite each other; it’s that the citations are shallow, targeting just a few kinds of academic outputs. Some people have reacted to my earlier post by saying that the field of ancient DNA will eventually merge with archaeology, as their subjects of study become more and more entwined. I doubt it.

What I think is more likely is that the specialized studies of genetics will have their day and then fade, and a broader, more holistic kind of scientist—probably trained in archaeology or anthropology—will synthesize the genetic results.


Waters, M. R., & Stafford, T. W. (2013). The first Americans: A review of the evidence for the Late Pleistocene peopling of the Americas. Paleoamerican Odyssey, 541-560.

Is Facebook killing science news?

I’ve observed that the coverage of genetics and evolution in mainstream media has become worse over the last several years. It seems that social media, especially Facebook, may be contributing very negatively to that trend. In The Daily Beast, a report by Tanya Basu looking at patterns of social media sharing of science news: “Study: We F**king Love Lousy Science on Facebook”.

The headline is a bit unfair, I think, because the popular page “I F**king Love Science” actually carries a lot of science news stories. Its reporting and selection of stories to promote may not be ideal, but it would be hard to categorically say it is different from mainstream sources like The Daily Beast, Newsweek, or LiveScience for accuracy and scope.

The real problem is our Facebook friends. Now that Facebook promotes friends and family posts, whatever science you see is pretty much what they like and share. And it’s crap.

The problem is, it’s crap even when it comes from “top scientific thinkers and pop-culture icons”…

Second, you might think that getting access from top scientific thinkers and pop-culture icons might help drive serious science coverage and conversation. Indeed, astrophysicists like Tyson, Michio Kaku, and the late Stephen Hawking are the leading pages followed by Facebook users. But little of their content is original, and in fact, much of it is either generated from other sources or might not have anything to do with specific scientific discoveries at all.
That trend is made worse by groups like Smart Is the New Sexy, whose links were found to be “far afield from science topics.” That, in fact, illustrates a huge problem with Facebook “science” posts: For many of them with health or nutrition bents, advertising and promotions can sometimes form a dominant majority of content.


Look, few of us who write about science on blogs and social media are getting paid for this kind of work. That means that a lot of people who are writing about on blogs and social media are using their writing as a hustle to get paid for other things.

For some of us, we get paid for the occasional article, or even a whole blog, written for a mainstream outlet. That kind of work is frustrating to me, because not everybody can read what I write for many mainstream outlets, so I don’t do as much of that kind of writing as I could. But it’s respectable and often worthwhile, because mainstream outlets continue to have substantial readership that benefits from accurate science writing.

So where are the social media sources of science news getting their funding? Big personalities make it through simply being famous – lectures, tours, paid TV appearances, book sales. A good social media strategy for this kind of celebrity is just to spread things that their followers will share and spread.

Science media disseminating their work via your friend and family network have very low-paid writers or aggregators. They rely on clickbait, click-through lists, and using (or stealing) science images and video content without their context. Non-media groups that are “science-adjacent” on social media are selling things or supporting a sales network: supplements, treatments, etc. Meanwhile, there are the “true believers” who share contrarian science theories, or stories about mainstream scientists being wrong.

What can anyone do about this?

Help to bring attention to science writing that is accurate and not sensationalist. Stop and think for a moment before you share science news, to make sure that it actually is science and not a sales pitch or clickbait. Help to create high-quality science resources such as photos and videos, that are curated by real scientists and not click farms. Build something.

If you’re a scientist, stop allowing your institution or funder to issue press releases that you haven’t personally vetted. Let your voice be heard when a science media outlet gets your field of research wrong.

If you do nothing else, if you are a scientist, you need to develop some self-awareness of when you are acting like a crank. You have professional colleagues who have devoted years of effort and training to engage the public effectively in their work. Try talking with them.

Should archaeologists really fear and loathe geneticists?

Ancient DNA is following its Moore’s Law-like progression toward greater and greater sample sizes from past populations. Until this year, it may not have seemed apparent that every archaeological site will have ancient DNA techniques applied to it before long.

Ewen Callaway in Nature has a long feature article focusing on the tension between archaeologists and ancient DNA specialists as they try to understand the past with their different approaches: “Divided by DNA: The uneasy relationship between archaeology and ancient genomics”.

The article has a number of recent examples, mainly big studies of ancient DNA that were published in Nature with results pointing to major population replacements or migrations that had been unexpected by archaeologists. It is well worth reading in its entirety if you haven’t been following the field of ancient DNA super-closely.

Genetic information from ancient populations has settled some 100-year-old (or even 150-year-old) debates in archaeology. For example, we now know that the Indo-European languages did not spread into Europe and India along with the Neolithic revolution and introduction of farming from Anatolia. Instead those languages spread later, from an early Bronze Age origin on the steppe. We now know that the introduction of Bell Beaker pottery across much of Europe was in some places a result of people changing their material culture to adopt the new pottery style, and in other places (including England) the result of new people invading and almost completely replacing the resident farmers. We know now that the Inuit peoples of the Arctic are the latest wave of migration, largely replacing earlier Dorset culture peoples which contributed little to later populations. Those insights would not be possible without DNA evidence, and they demand that archaeologists and anthropologists rethink some of the ways they conceive of ancient population contacts and culture changes.

This is wonderful. Knowing who made past artifacts and how they are related to other people is transformative. All manner of woolly-headed archaeological ideas can now be thrown straight out the window. What’s not to like?

Some geneticists (and this article) compare the new ancient DNA approaches to the advent of radiocarbon dating. Knowing accurately when ancient people made sites and artifacts did indeed transform archaeology. Not always for the better, of course. The patina of white coat science sometimes enables scientists to push wrong ideas beyond the data’s real power.

But some archaeologists are dissatisfied with the course of these events.

I found a section near the middle of the article to express some of the main conflicts from the point of view of archaeologists.

“While I have no doubt they are basically right, it is the complexity of the past that is not reflected,” Heyd wrote, before issuing a call to arms. “Instead of letting geneticists determine the agenda and set the message, we should teach them about complexity in past human actions.”
Ann Horsburgh, a molecular anthropologist and prehistorian at Southern Methodist University in Dallas, Texas, attributes such tensions to communication problems. Archaeology and genetics say distinct things about the past, but often use similar terms, such as the name of a material culture. “It’s C. P. Snow all over again,” she says, referring to the influential ‘Two Cultures’ lectures by the British scientist lamenting the deep intellectual divide between the sciences and the humanities. Horsburgh complains that genetic results are too often given precedence over inferences about the past from archaeology and anthropology, and that such “molecular chauvinism” prevents meaningful engagement. “It’s as though genetic data, because they’re generated by people in lab coats, have some sort of unalloyed truth about the Universe.”
Horsburgh, who is seeing her own field of African prehistory start to feel the tremors of ancient genomics, says that archaeologists frustrated at having their work misinterpreted should wield their power over archaeological remains to demand more equitable partnerships with geneticists. “Collaboration doesn’t mean I send you an e-mail saying ‘hey, you’ve got some really cool bones. I’ll get you a Nature paper.’ That’s not a collaboration,” she says.

What’s going on here?

The two disciplines have different modes of work, publication, and citation. Much of the great archaeology on periods within the past 10,000 years is published in book form. The Horse, the Wheel, and Language by David Anthony has probably been the most influential presentation of the anti-Colin Renfrew view that Indo-European languages spread from the Pontic Steppe during the early Bronze Age. It runs 568 pages in paperback form, took years to write and publish, and brings together evidence from archaeology, linguistics, and genetics from much of Europe and West Asia. While the book is scholarly, it should also be recognized that it is a semi-popular presentation, much more accessible than the book-length archaeological reports that contain much of the primary literature. It is also the work of a single author who has synthesized results from three very different fields of study.

Meanwhile, the 2015 paper by Wolfgang Haak and colleagues that described ancient DNA evidence for this idea runs seven text pages in Nature and had 44 references. This may seem short or insubstantial, but this one paper took collectively years of effort from 39 authors, it reported 69 new ancient genomes, and included 141 pages of supplementary text.

These two works illustrate a massive change in the mode of scientific work in prehistory. Where archaeological research 30 years ago required the efforts of dozens or hundreds of people, most of these were not even recognized as authors of the research. Instead, nearly all the credit went to the scientist “at the top”. What other archaeologists most valued were theories that attempted to synthesize years of data.

The standard in genetics is different. What other geneticists value is the ability to lead and mobilize effective empirical research programmes that generate highly-cited peer-reviewed research papers. They often recognize trainees, postdocs, or tenure-track scientists as first authors of research papers, and this does nothing to detract from the role of team leaders.

The “two cultures” comment in the passage above is pretty appropriate to this situation. And as has been the case in the 1950s, the side perceived as “science” is winning and the more “humanities” side losing a struggle for hearts, minds, and funding.

Some cool bone tools from an ancient Chinese site

Today’s reminder that stone tools are not all that matter in human behavior: “Discovery of circa 115,000-year-old bone retouchers at Lingjing, Henan, China”.

Luc Doyon and colleagues document several pieces of bone that were used in the process of removing fine, small flakes from the edges of stone artifacts, called “retouchers”:

In this paper, we describe bone retouchers recovered at the Lingjing site (Xuchang, Henan, China) in a level dated to circa 125–105 ka BP. These artefacts represent the first evidence from Eastern Asia for the use of bone as raw material to modify stone tools. This discovery has implications for the ongoing debate on the nature of Late Pleistocene cultural adaptations in China. The lithic technology that characterizes most Chinese assemblages attributed to this period is interpreted either as reflecting a peculiar facies of the Middle Palaeolithic [34,35] or the persistence of essentially Lower Palaeolithic cultural traditions [36–39]. The Lingjing bone retouchers and the behavioural consistencies their analysis highlights show that in spite of the apparent simplicity of lithic reduction sequences identified at the site [40], Lingjing hominins integrated in their behavioural repertoire the use of bone fragments to shape stone tools. These results corroborate the view that early Late Pleistocene cultural adaptations from China must be understood as reflecting original cultural trajectories whose degree of complexity cannot be evaluated solely through the study of lithic assemblages.

Here’s a photo of one of the retouchers, made on an antler of an extinct deer:

Antler retoucher from Lingjing
Figure 8 from Doyon and coworkers (2018). Original caption: Retoucher 9L0151 from Lingjing. White bracket indicates the area where impact scars are present. Scale = 1 cm.

So-called “soft hammer” percussion uses bone or other non-stone materials to remove flakes from stone cores in a more controlled way. The use of bone and antler retouchers is widely known for Mousterian sites in Europe and western Eurasia. They are also known for MSA sites in Africa. It’s fair to describe these kinds of artifacts as a regular part of “Middle Paleolithic-MSA” technical modes of making sharp edges.

There has been some debate in the past about whether an equivalent mode of stone tool manufacture is present in China or other parts of East Asia. I think it’s fair to say that some archaeologists have had a very crystallized view of what technical abilities should be found together within assemblages, so that if you see one type of artifact, you should be able to predict the presence of many others. The Chinese archaeological record tends to disappoint such strict expectations.

There was once an idea that hominins had to be especially clever and sophisticated to use bone in their toolkits. Like most early assumptions based on limited evidence from European sites, this one didn’t stand the test of time. We have bone artifacts from some very early toolkits, and a range of different specialized uses of bone in Neandertal and other archaic human-associated sites.

But it is still interesting to see close study of bone artifacts from new parts of the world and different times. This particular case helps us to see the logical connections between the process of making stone tools and the infrastructure needed to keep those tools useful. They also remind us that some of the most important elements of ancient technology were not stone, and are not things that we see very often in the archaeological record.

Link: National Geographic looks at its history on race

NPR reports on National Geographic’s new issue devoted to the topic of race, and the way that the organization has examined its own history: “‘National Geographic’ Reckons With Its Past: ‘For Decades, Our Coverage Was Racist’”

I found it interesting to hear about one reporter’s look through the photo archives—the story is not only what was chosen to represent in the magazine over the years, but all the photos that were not chosen because they didn’t fit the editorial mold. As someone who has spent a lot of time working in South Africa, this passage stands out to me, looking back at a 1962 article on the country:

"There are no voices of black South Africans," Mason told Goldberg. "That absence is as important as what is in there. The only black people are doing exotic dances ... servants or workers. It's bizarre, actually, to consider what the editors, writers, and photographers had to consciously not see."

Of course the magazine grew to be enormously successful by knowing and catering to its subscriber base. Anthropologists also catered to their audience, an academic audience who reveled in strange practices and imagined exotic places.

Link: Archaeomagnetism in Iron Age contexts in southern Africa

Michael Greshko in National Geographic has written a neat story about the hunt for southern hemisphere records of Earth’s magnetic field: “What Ancient African Huts Reveal About Earth’s Magnetic Flips”.

To study the last few millennia—younger than ancient rocks, but older than direct scientific monitoring—scientists can measure magnetic orientations in certain archaeological artifacts. But this record is heavily biased toward the north. More than 90 percent of the data about the last 2,000 years of Earth’s magnetic field come from above the Equator.
To track the South Atlantic Anomaly, researchers are searching for more sites in the Southern Hemisphere. In 2015, scientists announced a fascinating new data source: burned huts in the Limpopo River Valley, an area that falls within modern-day Botswana, South Africa, and Zimbabwe.

Iron Age peoples of southern Africa burned their structures periodically, with fires hot enough to preserve the floors as durable clay. It’s remarkable that literally the floors beneath the feet of ancient people are connected to the dynamics deep within the Earth, and our protection from the stars.

Link: Why are captive gorillas getting heart disease?

The Atlantic has a wonderful long-read story by Krista Langlois looking into the heart health of captive male gorillas in the U.S.: “Something Mysterious Is Killing Captive Gorillas”.

Like many captive male gorillas, Mokolo suffers from heart disease—specifically, fibrosing cardiomyopathy, a condition that turns red, healthy heart muscle into bands of white scar tissue too rigid to pump blood. Although heart disease is nearly absent in wild populations, it’s the leading killer of captive male gorillas around the world. Roughly 70 percent of adult male gorillas in North America have heart disease, and often die prematurely as a result. Other great apes, such as orangutans and chimpanzees, suffer at similar rates.
For more than a decade, zookeepers, veterinarians, epidemiologists and others have struggled to figure out why heart disease is so prevalent among captive apes, and how to prevent the animals from developing it. Now they may be closing in on answer—one that lies not in the 20-ounce time bombs housed in gorillas’ chests, but in the microscopic bacteria that flourish in their guts.

The article covers the history of health and diet in zoo gorillas, talks about the ways that zoos have changed over the years, and focuses in on some of the science of diet in primates.

It’s such a good account of these issues that I’ve assigned the article to my 300 students.

Link: Finding identity in an historical photograph

Following on my last post about massive genealogy research, the Globe and Mail has an interesting story about how genealogical and census information allowed researchers to uncover the probable identity of a young girl pictured in a famous 1913 Toronto photograph: “A little girl in Toronto lost to history – and now found”.

The life of Dorothy Cooperman suddenly comes into focus on the genealogy site Ancestry. A user related to the Coopermans through an in-law has sketched the key moments in Dorothy's life, from her birth in Kiev (then part of the Russian Empire) to her marriage, the births of her children and her death in 1979 in Oak Park, Mich., a suburb of Detroit.

The faces that look out of old photos and paintings are people of the past. All of them are connected to the living, although those connections have often been lost. A large fraction of people in past generations have no living descendants. Others have them, but no full accounting of them exists.

It is part of my profession to recover what science can of the histories of unknown ancient peoples. The individual histories of recent people are no less interesting, and in many cases are unknown.

Link: Interview with Yaniv Erlich and massive human genealogy

The Atlantic has a nice interview with Yaniv Erlich, the geneticist who this week revealed the largest scientific analysis of a single human genealogical tree, including some 13 million people: “The ‘Genome Hacker’ Who Mapped a 13-Million-Person Family Tree”.

The interview is by reporter Sarah Zhang, and she focuses on the effective collaboration of private and university interests in this kind of research.

Zhang: Your study is published now, but it seems like this is a beginning rather than an end. I’d imagine what you’re really interested in is overlaying genetic data on top of the family tree.
Erlich: Exactly. At MyHeritage, we started to offer DNA tests to users in November 2016. Since then we’ve collected 1.2 million DNA profiles of users.
Zhang: And why make the jump to MyHeritage? Are there things you can do at a company you couldn’t do in academia?
Erlich: I think this is a model for the future. There are certain things that you can only do in academia. There are certain things you can only do in companies. If you want to move in scientific endeavors, collaborating with companies is a very fruitful direction.

The research involving the genealogical data has documented the genealogical effects of some interesting social changes over the last two hundred years. But once genetics starts to be added into the tree, people are going to find a lot of discordance, a lot of natural selection, and possibly a good amount of segregation distortion.

It will be interesting to shine a light into odd corners of inheritance. I’m not sure people are anticipating what discoveries will be made using their own genealogical research.

Ancient footprints emerge from the coast of South Africa

According to the Canadian Broadcasting Corporation, the hominin footprints discovered in South Africa and published last week were discovered by some dedicated avocational paleontologists: “Ancient human footprints discovered by B.C. family on vacation in South Africa”.

A B.C. family's hobby of hunting for fossils has led to the discovery of a rare set of ancient human footprints on the south coast of South Africa.
The existence of the tracks, estimated to be approximately 90,000 years old, was revealed in an article published in the open-access journal Scientific Reports, maintained by the editors of the UK publication Nature.
The lead author of the report is Charles Helm, a former family physician in Tumbler Ridge, B.C., who is originally from South Africa.

This is such a great story, a case study in how discoveries are made. Some new scientific discoveries come from exploring where nobody else has been before. But most discoveries emerge from someone looking in a well-trodden area with new eyes. They may see something that no one else has noticed before.

These footprints are actually embedded within the walls and ceiling of a cave. What is today a cave actually formed within a dune sand breccia. The erosion naturally happened along ancient natural surfaces, leaving the impressions preserved within layers that had originally filled in the footprints, stratigraphically above them.

Imagine, studying footprints on the ceiling of a cave!

Footprints in figure 4a of Helm et al 2018
Footprints illustrated in figure 4a of Helm et al. (2018)

The research paper is in Scientific Reports, which is open access: “A New Pleistocene Hominin Tracksite from the Cape South Coast, South Africa”. The paper makes it clear that this was no chance discovery. These hominin footprints were just the most interesting results of a systematic survey of coastal sites for trackway evidence.

The hominin tracks reported here were discovered as part of a ground survey by the senior author along a 275 km stretch of coastline from Witsand in the west to Robberg in the east, undertaken between 2007 and 2016 (Fig. 1). Over 100 Late Pleistocene vertebrate tracksites were identified in coastal aeolianites, and in 2016 natural cast tracks on the ceiling of a ten-metre long cave (Fig. 2) were identified as human in origin. In 2017 further hominin tracks were identified in this cave on a lower layer. The focus of this paper is to describe these tracks and to briefly place them in their sedimentary and palaeoecological context.

The larger footprints are 23 cm long, and there are shorter ones that are around 17 cm long. The paper suggests that all these footprints likely belong to modern humans. That is by no means impossible, but I note that all these footprints are within the size range that I would expect for Homo naledi as well.

It may take some time for archaeologists to change their outdated assumption that the entire African Pleistocene record documents a linear succession of modern human ancestors. With every discovery, we need to be critical about documenting context and associations.

New excavations starting at Rising Star, an article pointing to some ways to follow the expedition

Newsweek is running a great story by Meghan Bartels about our renewed excavations in the Rising Star cave over the next month, and the strategies the team is following for sharing its underground progress: “Explore the cave where mysterious human ancestor Homo naledi was discovered in live broadcasts from South Africa”. She corresponded with Lee Berger and he shared some of the motivations for integrating live outreach directly into the excavation protocols:

For Berger, that broadcast is not just about sharing cool findings, it's about making science as a whole more accessible to non-scientists. "I believe we must pull all aspects of science from the “black box” where it typically resides," Berger wrote in an email to Newsweek. He is particularly dismayed by the secrecy often surrounding subject areas like human origins, with only a limited few gaining access to information around discoveries. As he sees it, "these fossils and this science is about our shared human heritage."

The team had some tremendous successes engaging schools and the public from our expedition in September of last year, and I’m really excited about some of the ways we’ll be building on those activities over the next month.

He plans to livestream regularly to the public and to classrooms, including both conversations and footage of the actual excavation work. Other outreach projects associated with the dig include an account tweeting and streaming video updates in Sesotho and Setswana, two local African languages. The team is also using 3D cameras to film the site and wants to explore virtual reality technology as well.

That account is from team member Mathebela Tsikoane, and I encourage anyone to follow him on Twitter, where he tweets in English as well as other languages.

Building participation and engagement in African languages is so important to the project, as is engaging with technologies that work with phones, which are the primary internet tool across Africa.

I’m following along with the expedition right now, until I join the team in South Africa in a couple of weeks. They’ve already found some new fossil material of Homo naledi in an unexpected part of the cave chamber.

Link: Kate Clancy testimony from congressional hearing on sexual harassment

Yesterday, the U.S. Congress conducted a hearing on the topic of sexual harassment in science. Anthropologist Kate Clancy provided testimony at the hearing, and she has now shared her spoken remarks on her blog: “Transcript of my oral testimony from February 27th Congressional hearing on sexual misconduct in the sciences”.

Everyone should read her full remarks. I will quote a section that resonates with me:

We say that asking a nasty question at a colloquium is how we push people to be better scientists. We say when we see an all-male research team that it must just be that the best scientists for the job were all men....
Too often I’ve heard that harassment and bad behavior are the price we must pay for star scientists. But are they really doing star science? When I’m writing my papers or analyzing my data on sexual harassment in the sciences, I’m thinking of the victims and the science we’ve lost. We lost their ideas, we lost their perspectives. We scientists do this work because we want to give the best of ourselves to the advancement of science. Women keep trying to give us their best, and we blow ash in their faces and push them down mountains.

The last sentence is a reference to alleged behavior by Antarctic researcher David Marchant.

Wired magazine also has coverage of the congressional hearing: “Congress takes on sexual harassment in the sciences”.

STAT news has a very good interview with Clancy from the lead-up to the hearing: “Sexual harassment pervades science. This scientist is talking to Congress about how to change that”. One of the most powerful points she makes is that employers, including universities, select online training programs which they know are ineffective, because Title IX requires training but does not rely upon data about effectiveness.

Sexual harassment training itself is a great example. There are so many papers that show that the type of sexual harassment training that most universities offer, which is often online with really extreme examples, can backfire. That they reinforce gendered beliefs, that they develop resentment, that they increase the risk of retaliation. At best, what they do is increase the knowledge base of the people taking them so they know what the worst types of sexual harassment are. But it doesn’t ever seem to change the climate.

My perception is that the climate is changing. Many researchers have committed to be inclusive when they build scientific projects, and use their leadership to create healthy workplaces and field situations.

How can scientific conferences make more of a difference in the cities where they meet?

I’d like to draw attention to this effort from the American Association for the Advancement of Science to make an impact on local schools where they have their annual meeting: “AAAS Classroom Science Days”.

For over 25 years, AAAS has produced a day of science in conjunction with the AAAS Annual Meeting, working with the local community—--including informal educators, teachers and scientists—--to leave strengthened connections to communities that don’t get needed exposure to science or scientists. At the 2017 meeting in Boston, we talked with groups of scientists from different universities in the Boston area who want to initiate, expand, or improve programs that help scientists engage with K-12 students and teachers. They believe that AAAS can be a hub for these various groups to network, find resources, recruit scientists and connect with teachers. We organized 20 scientists (undergraduate, graduate students, postdocs, professors and researchers in industry) to visit 20 schools and give short talks about their educational and career paths. Scientists, teachers and students all agreed that the talks were a success! Some scientist teacher pairs made plans for future events including lab tours and more talks.

I think this is important.

Consider that every scientist who visits those meetings spends an average of $1500+ on airfare, hotel, meeting registration, meals. A scientific conference is a multimillion dollar investment in a city. It would be great to see that multimillion dollar presence pay off in real public and educational engagement, beyond what would happen otherwise.

What’s unfortunate is that AAAS has built its effort upon entirely local scientists, postdocs, and students. Last year, it had 20 volunteers, this year only 30. That’s a very tiny impact.

Still, AAAS is an exception. Other scientific societies I’m involved with do vastly less. Maybe they organize a teacher workshop, or give a single public lecture.

We should be aiming much higher. Why don’t we see real public forums involving our major scientists associated with conferences? Why don’t we see many more school visits and events, across a broader geographic area than the immediate city? Why don’t we see television programming associated with the conferences?

I hope that scientific societies will think about how they can better leverage the exceptional opportunities that these conferences create for engagement on a local and regional scale.

Hybrid origins of the straight-tusked elephants

Elephants are one of the most important comparisons for human origins. Like humans, they’re long-lived animals that have complex social behavior, they require extensive home ranges and sometimes migrate over long distances.

What genetics has discovered about their evolution and diversification over the last few years provides some fascinating parallels to human evolution in the Pleistocene. Mammoths are their own fascinating story—I wrote about them several years ago, and again in 2016, and the story continues to develop.

But in the last year, the other ancient elephants have been at the forefront of new discoveries. In particular, the “straight-tusked elephant”, Palaeoloxodon antiquus, has yielded two ancient genomes that have disrupted what paleontologists thought they knew about Pleistocene evolution.

Straight-tusked elephant skull and reconstruction from Torralba, Spain
Straight-tusked elephant skull and reconstruction from Torralba, Spain. Photo: José-Manuel Benito via Wikipedia

Last summer I wrote about sequencing work on the ancient straight-tusked elephant: “Genomes of straight-tusked elephants”.

At that time, Matthias Meyer and colleagues had demonstrated that the genomes of two individuals of Palaeoloxodon antiquus from Germany were closer to African forest elephants (Loxodonta cyclotis) than savanna elephants (Loxodonta africana).

That was newsworthy. Paleontologists had mostly thought that Palaeoloxodon was related to the Asian elephant and mammoth clade. It turns out that it’s one of the African elephants. The result also emphasized the deep phylogenetic separation of the savanna and forest elephants in Africa. Those two living African elephant populations, once assumed to be part of a single species, are substantially different genetically from each other, perhaps as much as mammoths and Asian elephants were.

It also raised new questions about the relationships of the extinct African lineage, Palaeoloxodon recki. Once widely known as Elephas recki, this was the major component of the elephant fauna in the Pleistocene African fossil record. Today’s savanna elephants, L. africana, are virtually unknown through much of the African Pleistocene. Nobody really knows where the living lineage may have been hiding, nor does anybody know why P. recki might have become extinct.

Palaeoloxodon antiquus tooth, by Khruner (Wikimedia)
P. antiquus tooth. Photo credit: Khruner, CC-BY.

In my post last June, I hinted that there might be more to the story. Ewen Callaway had reported on a conference presentation by Eleftheria Palkopoulou that discussed evidence for hybridization among these ancient elephants: “Elephant history rewritten by ancient genomes”.

Now, Palkopoulou’s analysis has been published in PNAS: “A comprehensive genomic history of extinct and living elephants”. The title is a bit overblown in my opinion, because I have many questions that the new paper doesn’t answer. But the paper does add two important details to Meyer’s results from last year.

First, Palkopoulou and colleagues show that the straight-tusked elephant genome from Neumark-Nord, some 120,000 years old, is not a simple branch of the elephant phylogeny. This individual’s ancestry derives mostly from a branch that stemmed from the common ancestors of savanna and forest elephants. But it also has substantial ancestry from woolly mammoths. And up to a third of its genome came from a population genetically similar to today’s forest elephants from Sierra Leone, in West Africa.

A third of the genome is pretty high to be interpreted as a “ghost population”. The straight-tusked elephant population of Europe in the early Late Pleistocene was apparently a mixture of two source populations, one with a long independent evolutionary history, and one with continuing strong genetic connections to African forest elephants.

This strong African forest connection was not with every population of forest elephants. The Sierra Leone L. cyclotis individual in the study bears strong similarity to the ancient straight-tusked elephant, but the Central African Republic-sampled L. cyclotis genome does not.

Second, Palkoupoulou and coworkers used a combination of analyses to jointly examine the effective population sizes of elephant species and genetic divergence times between them. There are lots of details in this analysis, with so many lineages sampled, and I wouldn’t trust many of these details too far until more individuals are added to the African elephant and Palaeoloxodon samples.

Still, these analyses reinforce what the evidence for introgression shows. The two sampled forest elephants demonstrate a long divergence, with an estimated divergence time between 463,000 and 609,000 years ago for the populations that these two sampled individuals represent.

These two populations of forest elephants from different parts of Africa are around as different from each other as Neandertals and Denisovans were.

Clearly, we are not going to understand the evolution of the forest elephants, or their connection with straight-tusked elephants, until geneticists sample a lot more of them. Two genomes from each are not enough.

Another detail of the new analysis bears upon the long-time absence of the savanna elephant from the Pleistocene African fossil record:

The two savanna elephants had lower Ne relative to forest elephants for hundreds of thousands of years (Fig. 4D), potentially reflecting ecological competition from the African elephant Palaeoloxodon recki (including Palaeoloxodon iolensis) that dominated the African savannas until the Late Pleistocene (2, 19), or the high levels of male–male competition documented in this species.

That’s a possibility. I find it fascinating that the savanna elephant lineage is very ancient indeed, separated from forest elephants for the last 2 million years. The identity of the P. recki population remains obscure, and the great difference between today’s forest elephant samples suggests that a better sample of elephant DNA from across Africa may yield additional genetically differentiated lineages. It’s even conceivable that some lineage of forest elephant might turn out to be a close relative of P. recki or P. iolensis.

Or then again, maybe P. recki will turn out to be a true ghost, not closely related to P. antiquus at all. As I wrote last year:

Of course, without ancient DNA evidence, it’s not certain that these other extinct Palaeoloxodon species are closely related to the forest elephants and P. antiquus.

I just want to reiterate this sentiment. Discovering that P. antiquus isn’t what paleontologists once thought does not give me confidence that paleontologists really know where P. recki or P. namascus belong. For that matter, I have no confidence that P. recki within Africa is really a single lineage. Until recently, most biologists considered L. africana and L. cyclotis to be a single lineage.

I can’t wait to see results from a bigger sample of ancient elephants. The story of the straight-tusked elephants is likely much broader than two German skeletal samples. There are many challenges to ancient DNA study in temperate and low-latitude situations, but if there’s any species with plenty of tissue to sample, it should be elephants.