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: How scientific societies are moving to combat sexual harassment

Cris Russell has a very strong piece in Scientific American covering the ways that some scientific societies are responding to combat sexual harassment and assault in scientific fields: “Confronting Sexual Harassment in Science”.

She focuses on quotes from Marcia McNutt, former editor of Science, now president of the U.S. National Academy of Sciences, and recent statements from the American Geophysical Union.

The AGU is also part of a new collaborative research project, funded by a $1.1-million, four-year grant from the National Science Foundation Foundation, that will update the teaching of research ethics by addressing sexual harassment as scientific misconduct. Led by University of Wisconsin–Madison researcher Erika Marín-Spiotta, the project will produce more effective training materials in Earth, space and environmental sciences that may serve as a model for other STEM fields. This includes development of tested bystander intervention workshops to help academic leaders respond to and prevent sexual harassment. There is limited data on the effectiveness of existing training programs and a sense that many were designed primarily to meet legal liability concerns.

I was really happy to read in Russell’s article that my own university, the University of Wisconsin-Madison, has a leadership role in the AGU effort to update teaching of research ethics. In my experience during the last several years, UW-Madison has been uniform in its message, from the Chancellor’s office through all levels of administration, that sexual harassment is unacceptable. The workplace training (required of all employees) on sexual harassment and assault is in my view very effective, and this year it is being supplemented by workshops to address implicit bias. In other words, I think my institution is very serious in its response to these issues.

But many of the problems in science are trans-institutional. Sexual harassment and assault often happen in settings removed from formal workplaces like universities and research institutes. Fieldwork is a special problem in anthropology and archaeology, with many practitioners adopting an attitude that “what happens in the field, stays in the field”. Professional conferences have also been locations where harassment and assault occur outside the bounds of their institutions. Professional associations can make a difference, by reinforcing professional standards of conduct among researchers outside of their own institutions.

Sexual misconduct graphic from Science story
Figure from Science magazine story on sexual misconduct in anthropology, illustrating some results of the Survey on Academic Fieldwork Experiences (2014).

The American Association of Physical Anthropologists responded strongly to this issue starting in 2015 and 2016, and I’m proud of the association for its strong stance. That response came in the wake of reported cases of sexual harassment at the professional conference of the AAPA. Another professional meeting, that of the European Society for the Study of Human Evolution, was the occasion of an alleged case of sexual assault in 2014.

Sexual harassment, assault, and other abuses during anthropological and archaeological fieldwork have driven talented people out of anthropology and archaeology for years. I have heard first-hand accounts of some of these abuses from colleagues, and I believe their personal stories. I have heard many more rumors of abuses second-hand or third-hand from many people—often with corroborating details that suggest that they are true. I have also seen directly the effects of misogyny and implicit bias by scientific referees, both as a coauthor of papers and as an academic editor.

I’m pleased that NSF is spending money to help develop better training in professional ethics and to study the effects of that training. It is important to the future of science that students and postdoctoral trainees be given the tools to defend themselves from professional misconduct of all kinds. It would be helpful for professional associations to develop ombudperson positions to help trainees find solutions when they are subjected to harassment and assault.

But I would further encourage NSF to investigate how it has awarded funds to abusers in the past.

We know from the 2014 SAFE study that harassment and assault have been very common in recent and existing field programs in archaeology and anthropology. Millions of dollars of funding have gone to researchers who maintain field projects that are widely rumored to be sites where abuses have happened for years. Researchers have used this support to intimidate and silence the targets of their abuse, and have evaded scrutiny from institutions because of the federal dollars they bring in (“Why do universities cover up high-profile harassment? Look for the money”). Meanwhile, the institutions who received 50% or more overhead on these NSF grants did not maintain minimal levels of professional standards by the site directors.

I hope that more of these stories will be made public so that the broader community of scientists can acknowledge this history and commit to stop covering up the unethical and immoral behavior by supposed leaders in the field.

Why is open science important in archaeology?

Are you curious about open science, but don’t really know what it means? The September issue of The SAA Archaeological Record includes an article that reviews “open science” approaches in archaeology: “Open Science in Archaeology”.

Marwick et al 2017 article header

This article was the brainchild of Ben Marwick, who has helped to organize the new Open Science Interest Group within the Society for American Archaeology. I’m proud to be able to support and participate in this group, and to have joined with 48 other professionals in this paper. I work at all levels within my scientific research to advance the principles that the article describes.

The paper begins with a short discussion of what “open science” actually means.

Often described as “open science,” these new norms include data stewardship instead of data ownership, transparency in the analysis process instead of secrecy, and public involvement instead of exclusion.

I approve strongly of this definition. Open science is nothing radically new, it reflects a recognition that responsible scientific approaches lie at one end of an axis, where the opposite end is really an antiscientific attitude of exclusion.

The new paper refers to open access (in publication), open data, and open methods. All these tend to increase transparency and replicability in the production of knowledge.

I would add a couple of aspects that the article doesn’t discuss in detail.

Archaeological sites are not merely data sources, they are physical places. Allowing colleagues and the public to see the sites and inspect work at sites is part of providing confidence and transparency in archaeologists as stewards of heritage. That access can be provided today with technology, as many projects (including our Rising Star project) are doing. Or access to sites can be provided in cooperation with national heritage authorities through responsible tourism and site visits.

Scientific projects are complex social undertakings that involve power and funding, and open collaboration may be just as important as open methods and open data in providing transparency of scientific processes.

Some people have the misconception that open approaches are less rigorous compared to approaches that involve long gestation of ideas in relative secrecy. Unfortunately, this misconception is still actively promoted by a few irresponsible scientists. Spreading such a misconception is much like the strategy of “fear, uncertainty, and doubt” that was once deployed by software companies in their battle for market share against open source software projects.

In my experience, open approaches are more rigorous than secretive ones. Open approaches rely strongly upon establishing transparent methods that emphasize replicability. When researchers follow through on a commitment to provide the data that underlie their analyses, they provide the means for independent researchers to check their results and conclusions. It’s a basic principle of scientific credibility: Conclusions that cannot be checked should not be believed.

The new paper is available and is a great resource. I know that academic articles about how to do academic work are not always exciting, but these articles are necessary to build the scholarly background for changing practices, especially in building support for responsible practices among institutions and grant agencies. I applaud the Society for American Archaeology for supporting this initiative.

There is no such thing as inertia—some people and institutions actively maintain processes that exclude colleagues and the public. Let’s subject those practices to examination and let institutions justify them if they are necessary. Meanwhile we must make the real costs of closed systems explicit, not hide them.

More: I’ve long been an advocate for open data practices, which I describe in my white paper, “Public interests in data from federally funded research”

Nature Genetics wants more context for citations, but doesn't notice that bad context comes from word limits

Nature Genetics has a remarkable editorial in the current issue that makes a point of criticizing citation practices by authors in “articles we have recently published”: “Neutral citation is poor scholarship”.

Neutral citation, for example, “this field exists (refs. 1–20),” may on the face of it seem to be a fair practice, giving evenhanded and minimal citation credit to a range of preexisting works as background to the current report. But it can also be malpractice, artificially inflating the metrics of irrelevant or trivially related works by including them in lists of relevant publications....

Those are tough words. The editors’ recommendation is to add more background that gives necessary context for cited works:

Best citation practice is to summarize the claim made in the cited work without distorting whether it was of cause, correlation or conjecture, much as you would for your own findings (Nat. Genet. 47, 305, 2015). The relevant reasons for citing pertinent publications should also be introduced early in the article rather than discussed as late afterthoughts. This best practice will often entail making statements that are strongly supported by prior publications in the background introducing your findings. We believe this is key to writing research papers with impact that can benefit from peer review, as it encourages explanation of the knowledge gap that motivates the research as well as clear explanation of the conceptual advances made by the main findings of the new research.

I’m strongly in favor of this approach. But take a look at the Instructions to Authors that lists the requirements for papers submitted to Nature Genetics:

Letters
The text is limited to 1500 words, excluding the introductory paragraph, online Methods, references and figure legends.
Articles
An Article is a substantial novel research study, with a complex story often involving several techniques or approaches. The main text (excluding abstract, online Methods, references and figure legends) is 2,000-4,000 words.

In a letter with only 30 references, giving appropriate context for each reference would take up 500 words – a third of the paper. For an article of 2000 words with 100 references, it would likewise take up 2/3 to half of the paper.

I agree that adding better context for citations would make better scientific papers. Adding more citations would in many cases improve papers. This is especially true in areas of science that lie on the boundaries of disciplines, where many readers will need more context to understand where citations fit together. But word limits and limits on citation number prevent authors from adding such context!

If Nature Genetics wants well-written and well-referenced papers, it is going to have to change its editorial practices to enable authors to spend the necessary words.

I especially like citation formats that enable authors to add context in the reference section—listing a short synopsis or reason why each citation is valuable. Books have that kind of facility in endnotes, so it’s a fairly widespread practice in scholarship. More scientific journals should enable greater context in references.

Reviewing the September excavation in the Rising Star cave system

In September, the team was underground in the Rising Star cave system, working at new excavations in the Lesedi Chamber and Dinaledi Chamber. I posted updates on the excavation goals and the progress at the end of the month on Medium, and I thought it would be helpful to provide links to those articles here.

A look at some photos of the live National Geographic Classroom events in the Rising Star cave system
A look at some photos of the live National Geographic Classroom events in the Rising Star cave system

In the first week, I reviewed the hypotheses that we set out to test: “Renewed excavations in the Rising Star cave”. Key among them is the formation of the fossil assemblage within the Dinaledi Chamber.

Many people have been curious whether some other entrance to this chamber may have existed in the past. So far, geological work in the chamber has found no other passage that might have allowed hominins or their bodies to get in. There’s a lot of evidence that the chamber must have been very inaccessible when the remains of H. naledi arrived — especially the clear difference in sediment composition between Dinaledi and other nearby chambers, and the lack of evidence for any other medium or large animal remains. It appears that the hominin remains must have entered the chamber in the same way we do today, down this Chute.
But nearly all of the hominin remains so far come from a tiny area of excavation, only 0.8 square meters, at the far end of the chamber more than 10 meters from the Chute.

Later, near the end of the excavation work, I reviewed some of the discoveries the team made: “What we’ve learned from the Rising Star cave system this month”. Perhaps the most interesting is a feature just beneath the base of the Chute:

This mass of bone has emerged just at the base of the Chute, the narrow entry channel into which the team enters the chamber. After weeks of careful excavation, the team can now see part of an articulated hand, ribs and a possible shoulder, even some teeth in what appears to be proper anatomical order.
This may be the partial skeleton of a single hominin individual. We do not know how much additional bone may yet remain just beneath the surface.

It will be some time before we know fully the results of the September excavation. We will need to consolidate the feature at the base of the Chute and extract it to the laboratory for further preparation. We will also need to get chemical and biological results back from samples taken inside both chambers. We have a lot of work ahead of us, and we’ll update as we can.

New project to scan vertebrate diversity across thousands of samples

Science reports on a new initiative to provide 3D scan data on thousands of vertebrates: New 3D scanning campaign will reveal 20,000 animals in stunning detail.

Then last year David Blackburn, a herpetologist at the Florida Museum of Natural History in Gainesville, saw Summers's #scanAllFish hashtag on Twitter and light-heartedly countered that he would "scan all frogs." Blackburn had just chatted with museum curators about starting a new digitization effort, so he also called Summers. They decided to up the ante and seek money to "scan it all." Now they have $2.5 million in National Science Foundation funding in hand, and on 1 September they will launch their project: oVert, for "Open Exploration of Vertebrate Diversity in 3D." Many scientists simply know it as the "scan-all-vertebrates" project.

The project, “oVert”, will deposit scans of museum specimens onto the MorphoSource site, so that people can download and use them. This is a tremendous win for open access science, and for the value of the MorphoSource repository.

Can you imagine the projects that will be fueled by this dataset? Amazing. It will become an essential morphological research tool–probably setting a new standard. And it will enable massive educational projects.

This is such an effective expenditure of money, and I wish that other NSF-funded projects would follow this model!

Arguing about species: Is it evidence, or ego?

For some people who follow human evolution news, recognizing “species” is really just about whether you’re a lumper or a splitter. Many people assume that the names of species are about ego, not evidence.

But nature presents us with real challenges, which still cause different scientists to approach the past with different assumptions. Let me give some examples.

Just today, I got notification of a new paper by Walter Neves and colleagues, in which they suggest that Australopithecus sediba and Homo naledi are actually South African representatives of Homo habilis. Some people might scoff at this—after all, the Dinaledi fossils are only 236,000–335,000 years old, while the latest-known H. habilis is around 1.6 million. But a young date for some fossils doesn’t bar them from from membership in a species with much older fossil representatives. Identity is tested with morphological evidence, not geological age.

Now, I disagree with the idea that H. naledi is the same species as H. habilis—Neves and colleagues have come to this taxonomic conclusion by neglecting all the morphological evidence showing H. naledi is different from H. habilis. But it’s not so easy to reject the idea that these species might be close relatives. As we pointed out earlier this year, H. naledi might even conceivably be a descendant of H. habilis or Au. sediba. On the other hand, Mana Dembo and colleagues showed last year that H. naledi seems to be closer to modern and archaic H. sapiens than to H. erectus (and much closer than H. habilis). These are stark differences of interpretation, from similar parts of the skeleton.

[see my article: “The plot to kill Homo habilis”]

At the other extreme, this week Jeffrey Schwartz is set to present results of his own examination of the Dinaledi Chamber sample. According to his abstract, all the teeth belong to one species, but some of the skulls represent another—two species in this assemblage, not just one. I haven’t seen the details of this analysis, but I’m pretty sure I disagree with this one, too.

I admit that it would be fatuous to say that ego plays no role in paleoanthropology. Scientists express provocative opinions that will draw attention from the press.

Still, the trouble with taxonomy isn’t just about new fossil discoveries like H. naledi or Au. sediba. We have seen similarly broad and vociferous diversity of opinions in the last few years about H. erectus, Au. deyiremeda, Au. anamensis, H. floresiensis, Denisovans, Neanderthals, H. heidelbergensis, Kenyanthropus platyops, and others. These are species new and old, and the same issues keep arising again and again.

Many people would say that taxonomic debates just reflect basic philosophy about variation—again, lumping versus splitting. But that’s really only one of the dimensions:

  1. How much variation should a species include? Broadly, all of us recognize that some species are polytypic (as humans are today), but small and fragmentary samples make it very hard to distinguish polytypy from distinct species. There are living polytypic species that include very extensive variation, and living sister species that barely differ from each other, making model selection difficult.

  2. What kind of data provide evidence of similarity or difference? Some researchers rely mainly on phenetic similarity measures, using geometric morphometrics, principal components or canonical variates approaches. Others examine discrete (or threshold) traits, counting shared derived traits as evidence of similarity and ignoring shared primitive traits. This group was once dominated by cladists, but in recent years Bayesian approaches have become more and more common.

  3. What temporal or geological information is sufficient to justify pooling fossil specimens into a single sample? Some scientists are willing to assume that fossils from the same 500,000-year period belong to a single population, even if they preserve different parts of the skeleton or minimally overlap. Others draw trees that separate every specimen into its own “operational taxonomic unit”. The concept of a paleodeme is based on lumping specimens by date and geography, an approach that has come more and more into question as the fossil record increases.

Anthropologists may get a bad rap from other biologists for arguing about taxonomy so much, but in reality many areas of taxonomy are undergoing seismic shifts following more widespread application of genetics and phylogeographic analyses.

For example, bovid systematists have been arguing for the last few years about whether to double the number of species they recognize—a debate about living species with abundant morphological samples and genetic data. Meanwhile, living and fossil elephants are on the verge of a complete revision of relationships, based on ancient DNA and the appreciation of deep diversity between forest and savanna African populations. Similar examples are unfolding across mammalian systematics.

Neandertal and Denisovan DNA has shown us that hominins also exchanged genes by introgression, occasionally but recurrently despite hundreds of thousands of years on their own trajectories. Genetic evidence of African “ghost lineages” means other long-lasting Pleistocene populations once existed.

H. naledi might potentially be one such lineage. I have no idea what the closest relative of H. naledi will prove to be. Whether it reproduced with human populations or not, it shows that many cherished human features may not have been uniquely derived evolutionary developments.

I can’t help but feel that we are standing at a special moment in the history of paleoanthropology. New data give us the opportunity to make progress on old areas of disagreement about species and phylogeny. We have to start by taking what we now know about the later Pleistocene, and seriously appling these lessons to earlier periods of human evolution. Our assumptions about the past really are changing.

Whatever we choose to call species won’t change their nature. But our assumptions determine the way we frame our future studies, including our attempts to find more fossil evidence. That makes it important to communicate clearly about what these ancient species mean, both with each other and with the public.

Is there a trade-off between publication impact and open approaches?

Two Dutch biomedical researchers discuss how they are trying to move their institution away from mere quantity of research and citations, and toward real clinical impact: “Do our measures of academic success hurt science?”. They begin their essay with a scenario that reminds me of human evolution research:

A Ph.D. student wants to submit his research to a journal that requires sharing the raw data for each paper with readers. His supervisors, however, hope to extract more articles from the dataset before making it public. The researcher is forced to postpone the publication of his findings, withholding potentially valuable knowledge from peers and clinicians and keeping useful data from other researchers.

I agree with much of what they say in this essay. But I think their opening scenario doesn’t really express a trade-off they are trying to illustrate between an artificial measure of “impact” and real impact.

What we keep finding in human evolution research is that sharing the data leads to higher impact. Papers are published faster, they are cited more widely, and they lead to career advancement for the authors.

It is true that some scientists try to keep datasets private so that other researchers cannot replicate their work. But that is counterproductive to their own research, not only to the field. Researchers who are publishing slowly, not distributing data in a way that can be inspected and used, are not achieving publications, citations, or “impact” even in the artificial, publication-oriented sense.

Using open approaches is not just the way to advance science and its impact on the public, it is also the way to advance careers. There is no trade-off here, not that I’ve experienced at least.

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.

Genomes of straight-tusked elephants

Earlier this month in eLife, Matthias Meyer and colleagues published a cool paper: “Palaeogenomes of Eurasian straight-tusked elephants challenge the current view of elephant evolution”.

The straight-tusked elephants lived in Europe and western Eurasia as far east as India during the Pleistocene. Most people are familiar with other extinct elephant relatives, such as mammoths or mastodons. The straight-tusked elephants were not mammoths, and they are assumed to be much more like living elephants because they seem to have entered more northerly parts of Europe mainly during interglacial times. Paleontologists have noted that the straight-tusked elephants share some morphological features with Asian elephants, as mammoths do also. For some paleontologists, these similarities are so compelling that they have classified Palaeoloxodon as part of the Asian elephant genus, Elephas.

Ancient DNA evidence is breaking open the study of how the extinct relatives of living elephants moved, interacted, and evolved. First mitochondrial, and more recently nuclear gene sequences have revealed different populations that lasted more than a million years, yet hybridized and mixed where they met.

During the last ten years, it has become clear that populations of elephants in the central African forest have a long history as an evolving lineage distinct from savanna elephants across most of Africa. Forest and savanna elephants have increasingly been recognized as two species, Loxodonta cyclotis in the forest, and L. africana across the rest of Africa. No fossils have been attributed to L. cyclotis, and the L. africana fossil record is quite sparse up until 20,000 years ago.

Before that time, Africa itself was rich in elephants attributed to Palaeoloxodon, especially P. recki, which many sources identify as Elephas recki. P. recki has been identified from fossils as early as 4 million years ago, and as late as 300,000 years ago. Other African species of Palaeoloxodon (again, often classified as Elephas) have been interpreted as part of a single P. recki lineage, including the earlier P. ekorensis and the later P. iolensis. P. iolensis survived until around 30,000 years ago. With so many species identified as Elephas or closely related to Elephas, and with mammoths sharing so many features with living Asian elephants, the basic idea has been the Asian elephant branch of the elephant phylogeny was once global, with mammoths spread across the northern tier of Eurasia and across the Americas, extinct P. antiquus in western Eurasia, extinct P. namascus further east in Asia, and extinct P. recki in Africa. Paleontologists have speculated that P. namascus may itself be the immediate ancestor of living Asian elephants, Elephas maximus. Living African elephants, Loxodonta, were the odd elephants out.

Meyer and colleagues obtained mitochondrial genomes from four individuals of P. antiquus, three of them from Neumark-Nord, Germany, and one from Weimar-Ehringsdorf, Germany. They find that the Neumark-Nord elephants probably date to the last interglacial, around 120,000 years ago, while the Weimar-Ehringsdorf elephant dates to the previous interglacial, around 230,000 years ago. This is a pretty small section of the overall geographic range covered by P. antiquus:

Palaeoloxodon sites across western Eurasia, from Meyer et al. 2017
Figure 1 from Meyer et al. 2017, original caption: "Palaeoloxodon antiquus, geographic range based on fossil finds (after Pushkina, 2007). White dots indicate the locations of Weimar-Ehringsdorf and Neumark-Nord."

What they found was that P. antiquus mitochondrial genomes are not related to Elephas at all; they’re related to forest elephants:

Surprisingly, P. antiquus did not cluster with E. maximus, as hypothesized from morphological analyses. Instead, it fell within the mito-genetic diversity of extant L. cyclotis, with very high statistical support (Figure 2). The four straight-tusked elephants did not cluster together within this mitochondrial clade, but formed two separate lineages that share a common ancestor with an extant L. cyclotis lineage 0.7–1.6 Ma (NN) and 1.5–3.0 Ma (WE) ago, respectively.

That’s not a small difference. Living Asian and African elephants came from a common ancestral population more than 6 million years ago, during the Late Miocene. They are about as different from each other genetically as humans and chimpanzees. The fossil story was just wrong–and it’s as big a difference as misidentifying a Neanderthal as a fossil chimpanzee.

Elephant phylogeny from Meyer et al. 2017
Elephant mtDNA and nuclear DNA phylogeny from Meyer et al. 2017. The Neumark-Nord (NN) and Weimar-Ehringsdorf (WE) straight-tusked elephants are indicated. The mtDNA tree has a time scale (bottom) but the nuclear DNA tree has no time scale associated with it.

All four of the P. antiquus mitochondrial lineages are on the same branch as living forest elephants, and in fact some forest elephants have mtDNA genomes that are closer to P. antiquus than to some other forest elephants. In other words, the mitochondrial genomes of P. antiquus fall within the variation of L. cyclotis. Within this variation, the mitochondrial lineage of the earlier Weimar-Ehringsdorf elephant is part of a different clade than the three Neumark-Nord elephants, so the P. antiquus mitochondrial genomes are not a monophyletic group.

Now, we might well expect the story with the nuclear genome would be different for elephants. We know that the story for Neandertals is different considering the mitochondrial and nuclear genomes: the Sima de los Huesos nuclear genome groups clearly with later Neandertals even though the mtDNA of later Neandertals is more similar to that of living humans.

There is another reason why elephant nuclear and mtDNA genomes might be discordant. In humans, mtDNA is markedly less diverse than most parts of the nuclear genome, and mtDNA types occur across wide geographic areas. Elephants are the opposite. Their mitochondrial DNA exhibits substantially greater variation among populations than the average for the nuclear genome, because female elephants very rarely transfer between groups. Most gene flow in elephants is male-mediated, and male elephants sometimes disperse over very long distances. These contrasting patterns of nuclear and mitochondrial diversity in elephants are consistent enough to provide a way to “triangulate” the region that ivory samples originated (Ishida et al. 2013).

Meyer and colleagues cannot assess yet whether the Weimar-Ehringsdorf elephant would yield a divergent nuclear genome, because they didn’t get nuclear evidence from it. But two of the Neumark-Nord P. antiquus specimens yielded nuclear genome data and they are a close sister group compared to all the forest elephants. That is, the African forest elephants were much broader in their mtDNA phylogeny, and tighter together in their nuclear genome, just as one would expect from the mass of evidence about them.

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

So, that’s an interesting data point about elephant evolution. A widespread extinct species of elephant, which on morphological grounds was interpreted as an Asian elephant relative, is actually related to forest elephants within Africa. Forest elephants today are a relative island species in central Africa, surrounded by savanna elephants. So from today’s standpoint, forest elephants look like a geographic and phylogenetic relict of a much more diverse lineage that once existed.

We already know that today’s situation did not exist earlier in the Pleistocene. In the past, many parts of Africa were inhabited not by today’s savanna elephants but instead by other extinct species, for much of the Early and Middle Pleistocene, P. recki. Savanna elephants are found in the fossil record as early as 500,000 years ago, but they are a relatively rare component of the elephant diversity in comparison to the extinct Palaeoloxodon species.

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.

Furthermore, the nuclear genome evidence presented by Meyer and colleagues does not establish whether the P. antiquus population may have exchanged genes with Asian elephants, thereby accounting for some of its anatomical resemblance to them. Hybridization has already been found to be widespread among the varieties of mammoths, and it continues to occur between savanna and forest elephants despite what appears to be a multi-million year separation. We might expect the same of other extinct elephant species.

When Eleftheria Palkopoulou presented on some of these data at a conference in 2016, she did talk about hybridization. Ewen Callaway reported on that conference presentation at the time: “Elephant history rewritten by ancient genomes”.

Palkopoulou and her colleagues also revealed the genomes of other animals, including four woolly mammoths (Mammuthus primigenius) and, for the first time, the whole-genome sequences of a Columbian mammoth (Mammuthus columbi) from North America and two North American mastodons (Mammut americanum). The researchers found evidence that many of the different elephant and mammoth species had interbred. Straight-tusked elephants mated with both Asian elephants and woolly mammoths. And African savannah and forest elephants, who are known to interbreed today — hybrids of the two species live in some parts of the Democratic Republic of Congo and elsewhere — also seem to have interbred in the distant past. Palkopoulou hopes to work out when these interbreeding episodes happened.

None of these scientific results concerning interbreeding and hybridization are in the new paper by Meyer and colleagues. So I expect we will see much more from these new genome sequences.


W. W. Howells, in the conclusion of the 1980 review, Homo erectus–Who, When and Where: A Survey”:

So we might be wise to be continually careful in writing about Homo erectus, making clear whether one is referring to a population or taxon with a workable definition (such as might embrace all the Chou-k'ou-tien and Javanese fossils), or to a grade taken broadly, or to a time zone (Campbell, 1972). The history of argument about the "Neanderthal phase" should show what the problems may be. As to subspecies of H. erectus, there [sic] are of course legitimate and what we should look for; we should expect their development and their survival over considerable periods. There is no reason to suppose that H. erectus as a species did not include all hominids for a long interval. But the bestowing of names, like having a child, carries responsibilities. To be too liberal with subspecific names, even awarding them to single specimens (e.g., H. e. leakeyi), rather than to recognizable populations, is both to injure their use and to confuse the search for real lineages.

I’m quoting Howells not to endorse this view but because he expresses clearly one opinion about the goals of naming species and subspecies.


A short piece “On the evolution of the science blogosphere” by the Andy Extance of the ScienceSeeker team has some interesting notes on current statistics in blogs.

A quote from late in the article:

It’s notable that despite this exorcism of sci-comm ghosts, the overall number of blogs aggregated by ScienceSeeker has fallen by less than 5%. Our new blogs are frequently soon featured in our weekly picks. Often, new additions are young scientists motivated by the issues of our times. They emphasise the powerful tools science has for illuminating the truth, and argue for national policies to adopt them.

As they point out, the lives of science bloggers change, and things become more or less active as they fit into other parts of life.

For myself, I’ve been very busy with the Homo naledi work and that has reduced the effort I can put into cleaning up my notes about the other parts of science for public consumption. Also, I have a book out, and that took some time to write and edit!

Should scientists refuse to review papers that do not make data available?

What should happen when scientists publish work that cannot be replicated?

That’s an important question that people are asking more and more. So often, the basic results of research are hidden inside of figures that display results but don’t allow other scientists to inspect them or combine them together with other work in their own research. So the results sit there, published but essentially useless for building anything new from them.

Early in 2016, Pete Etchells wrote in The Guardian about a modest proposal for peer review: Scientists should refuse to review papers that do not make their data and methods openly available: “How peer reviewers might hold the key to making science more transparent”.

On Wednesday, a new paper published in Royal Society Open Science argued for a new, grassroots approach to this problem, by putting the power back into the hands of scientists at the coalface of research, by changing the way that we think about the peer review process (full disclosure: both myself and fellow Head Quarters blogger Chris Chambers are co-authors on the paper). The Peer Reviewers’ Openness (PRO) Initiative is, at its core, a simple pledge: scientists who sign up to the initiative agree that, from January 1 2017, will not offer to comprehensively review, or recommend the publication of, any scientific research papers for which the data, materials and analysis code are not publicly available, or for which there is no clear reason as to why these things are not available. To date, over 200 scientists have signed the pledge.

The paper in Royal Society Open Science which came out last year was written by Richard Morey and colleagues; Etchells was one of the coauthors. The subsequent year has allowed some time to see results of this initiative. The opinion paper has been cited 37 times according to Google Scholar, which is a strong result for a paper a year out from publication. People are paying attention to the argument. The paper has been strongly cited within the field of psychology, where the “replication crisis” has resulted in many calls for more responsible publication of data and methods.

But on the other hand, the more than 200 scientists who had signed the pledge by early 2016 have increased now up to only 400 or so scientists, according to the Openness Initiative website. The call for direct action hasn’t had quite the level of participation that proponents of the initiative might have hoped.

I have been a very strong proponent of data access, particularly within the field of human evolution. Here are a few of my articles for background:

So why haven’t I signed the pledge?

I find in many of my conversations with paleoanthropologists that most of them just don’t understand what it means to provide data. When I raise the topic of data access, some of them assume that I am expecting scientists to distribute casts for free, or open the doors of fossil vaults to anybody on demand.

In other words, they view data accessibility as some kind of invasion of scientific privacy, or worse, an abrogation of national heritage.

I also see that the conversation about data access in human evolution is having two kinds of effects.

One of these effects is very positive. New papers are being published that include the data necessary for replication. What’s more, referees are demanding more data be included. I’m seeing this in the work on Homo naledi, I think it’s fair to say that my collaborators have done more than any other team in history to provide the data behind the analyses. We’ve included extensive data tables, full details for the multivariate analyses, and high-resolution surface models of the specimens. Even with all this, we are still challenging ourselves within the team to find new ways to do better, to provide more data in a more useful way. Meanwhile, peer referees are encouraging us to continue to raise the bar higher, providing more and more data—including data we have collected on fossils from other field sites.

The second effect is less encouraging. Some researchers who were failing to report basic measurements as recently as seven or eight years ago seem to have simply stopped publishing any new research on fossil material. This is surely not a coincidence. I think we’re finding that some researchers are having trouble bringing their field methods and analytical standards up to a level where they feel comfortable reporting the underlying data.

Genetics went through such a stage, way back in the 1990s. Every lab had its own distinctive protocols for validating basic sequence data or genotypes. The methods were finicky, and in a high-stakes funding environment, labs competed with each other on whether you could “trust” their data. I remember a conversation with a geneticist about one of his scientific rivals, and he said, “Sure, he has good ideas, but you can’t trust his A’s, C’s, G’s, and T’s.”

Opening up the doors and the records in genetics during the late 1990s and 2000s was not invasive, it helped to clear the air. Many genetics labs were working with outmoded processes that needed to be revised or fixed, and by adopting more open protocols, they were able to take advantage of the methodological advances made in other (often much bigger) labs. Meanwhile, sharing data openly before publication allowed people to leverage the common investment being made in sequencing across institutions.

Anthropologists participated in the debates that came from non-transparent methods in genetics. In the early 1990s, it was common to hear anthropologists say, “Sure, the geneticists say this today, but tomorrow the results will be different.” Consider the example of the original 1987 paper by Cann, Stoneking, and Wilson on “mitochondrial Eve”. The results from that paper were subjected to published challenges for the next eight years, including papers reanalyzing the original data by Alan Templeton in 1993 and Christopher Wills in 1995. It took those scientists a long time, with cooperation from the original researchers, to figure out what had originally been done in the analysis, and even longer to go through the subsequent process of review and publication of their reanalyses.

Today, things have changed. New results in genetics are more transparent, they have been seen by a broader range of scientists before publication, and there is often a robust conversation among different labs as a study is being conducted. Published studies may still have weaknesses, but these are more openly discussed than in the past and replication studies are carried out quickly, sometimes while the original research paper is still a preprint.

Paleoanthropology today is like genetics in the late 1990s. I say that as a very positive thing. We are moving as a field toward higher standards in data reporting and transparency. Data access is a process of continual improvement in record keeping, archiving, and communication. This is really the basic lesson of science from high schools onward—if you want to see where you might go wrong, where errors might creep into your analyses, you need to show your work.

What we must do is continue to insist that scientists use the data that have been published. Providing data is one thing, but the true value of providing data is when other scientists reuse it to make their own work better. We need data that we can trust, not data that cannot be replicated by anyone else. If our observations cannot meet that standard, we need to work on our methodology until they can.

Reference

Morey RD, Chambers CD, Etchells PJ, Harris CR, Hoekstra R, Lakens D, Lewandowsky S, Morey CC, Newman DP, Schönbrodt FD, Vanpaemel W, Wagenmakers E-J, Zwaan RA. 2016. The Peer Reviewers' Openness Initiative: incentivizing open research practices through peer review. Royal Society Open Science doi:10.1098/rsos.150547


This is a neat feature from NPR’s Science Friday giving resources for teachers who want to include the SciFri episode on Homo naledi as part of their classroom exercises: “Where does Homo naledi fit into our family tree?”.

It includes alignments with science standards for U.S. K-12 teachers.

Have students compare and contrast different hominid skulls using these drawings and timeline. Where does Homo naledi fit in? How does it compare to other hominid skulls? Using the diagrams and figures in this article about the Homo naledi discovery, relate your skull observations to how Homo naledi alters our view of the human evolutionary tree.

We’ve sure come a long way in a few years!

Homo naledi was chipping its teeth amazingly often

I’d like to point everyone to this new article that may give some insight into the diet or behavior of Homo naledi: “Behavioral inferences from the high levels of dental chipping in Homo naledi. Ian Towle from Liverpool John Moores University examined the H. naledi dental sample last year and, with his colleagues Joel Irish and Isabelle De Groote, he has shown something very interesting about Homo naledi in comparison to other primates: They chipped their teeth a lot.

Figure 1 from the paper tells the story:

Dental chipping frequency in H. naledi compared to other hominoid samples
Figure 1 from Towle et al. 2017, showing the dental chipping rates per tooth class in H. naledi and other samples

Compared to chimpanzees and gorillas, extinct hominins like Au. africanus and Paranthropus robustus crunched on things that chipped their teeth a lot more — for mandibular molars, 25% in Au. africanus, versus only 10% for gorillas. For maxillary molars, gorillas crunched a bit more, and P. robustus surprisingly little. So there seems to be a good bit of noise in the data. But H. naledi puts the apes and other hominins to shame, with 50% chipping in maxillary molars and premolars, 60% in mandibular molars, and 40% in mandibular premolars.

Whatever it was eating or doing with its postcanine teeth, H. naledi was chipping them a lot. And those chips are not microscopic things, they are obvious on visual inspection of the teeth:

Figure 2 from Towle et al showing dental chips
From Figure 2 of Towle et al., 2017, showing dental chips on H. naledi specimens.

In other words, these are macroscopic aspects of tooth wear. We have seen on the teeth of H. naledi that there is a very high wear differential between teeth, and they seem to really have distinctive patterns of wear. Towle and colleagues point out that it is not just anything that yields this kind of chipping, it is seen predominantly in populations that incorporate high amounts of grit into their normal diet. For example, baboons:

The extant primate samples may offer more useful comparisons for H. naledi. For example, in a microwear study by Nystrom et al. (2004), baboons in dry environments were reported to consume large amounts of grit. In the present, combined sample of hamadryas and olive baboons, we found similarities to H. naledi, with frequent small chips and a higher rate of chipping among posterior teeth relative to anterior teeth.

And humans that eat things that sometimes contain shell fragments:

A Late Woodland sample from Cape Cod in the U.S.A. has a pattern like H. naledi in terms of frequency and position (McManamon, Bradley, & Magennis, 1986). The overall frequency is 43% and molars are reported as the tooth type most prone to chipping, with interproximal surfaces most affected. Unfortunately, frequencies for tooth types and positions in that study are not reported. McManamon et al. (1986) suggest that the cause of this patterning was the incorporation of sand, gravel, and/or shell fragment contaminants into the food.

Towle and colleagues note also that the Taforalt sample from the Epipaleolithic of Morocco also has high rates of dental chipping, again thought to relate to the incorporation of shells and fruit stones into the diet. These are high quality food sources that have small, hard objects within them.

The fact that there are human samples with frequencies of chipping comparable to that in H. naledi makes this a bit less puzzling. I would suggest we are looking at dietary adaptability within a population that has a relatively high energy density in its foods. That idea is consistent with the fact that H. naledi has relatively small tooth sizes, despite having substantial chipping rates.

What will be interesting is to see what the microwear texture is like in H. naledi. The sampling for microwear has been done, and our team is now working on assessing it. Thus far, microwear studies have given counterintuitive results as applied to robust australopithecines like P. robustus and others like Au. africanus. “Nutcracker man” evidently wasn’t cracking nuts. That result is holding in this study according to chipping—when you look at the most robust dentitions here, in P. robustus, they have among the lowest rates of dental chipping.

Anyway, it is exciting to see these clues emerge. The picture from dental chipping is remarkably consistent across the H. naledi sample, and it is telling us something very interesting about the diet or other uses of the teeth in this species.

Features of the Grecian ape raise questions about early hominins

Today, Jochen Fuss and colleagues have published a new description of the morphology of a mandible of Graecopithecus freybergi, from Pyrgos Vassilissis Amalia, Greece: “Potential hominin affinities of Graecopithecus from the Late Miocene of Europe”. They carried out microCT imaging of the mandible and another fourth premolar attributed to Graecopithecus from Bulgaria.

Fuss and colleagues show that the fourth premolar root configuration has some similarities with Ardipithecus, Sahelanthropus and Australopithecus. On this basis, they argue that Graecopithecus should be accepted as a member of the human clade, a hominin, closer to humans than chimpanzees and bonobos.

They go further. These Graecopithecus specimens are both older than 7 million years, making them earlier than any known hominin in Africa. So Fuss and colleagues claim that the origin of the hominin clade may itself have been in Europe.

More fossils are needed but at this point it seems likely that the Eastern Mediterranean needs to be considered as just as likely a place of hominine diversification and hominin origins as tropical Africa.

Is it going too far to say that this fossil jaw is the earliest hominin?

Here’s what I think: Paleoanthropology must move past the point where a mandibular fragment is accepted as sufficient evidence.

As blog readers are my witnesses, if I ever describe an unassociated mandibular fragment, I will never claim it is the earliest hominin, the earliest Homo, or the earliest modern human. Again and again, discoveries of relatively complete skeletal evidence have shown that different hominin (and ape) lineages had mosaic morphological patterns across the skeleton. Parallelism and convergence among lineages have been widespread in our evolutionary tree, and no single feature or fragment can accurately indicate relationships.

What’s worse, when we look at the earliest hominins, very few scientists have actually examined the evidence. Ann Gibbons wrote in 2006 that only one scientist at that time had seen all the key fossils, and for all anyone knows that may still be the case – since one of the most important specimens remains unpublished fifteen years after its discovery. Most scientists have been mere spectators, forced to look at cartoon images of skull and pelvis reconstructions that have never to my knowledge been examined by any independent scientist.

I don’t want to take away from the value of the study of Graecopithecus here. It’s pretty cool that Fuss and colleagues were able to find some hidden morphological clues in these very fragmentary specimens. That mandible has only one good tooth in it!

Graecopithecus mandible from Fuss et al. 2017
Figure 1a and 1b from Fuss et al. 2017, showing Graecopithecus specimens. Original caption: a, Type mandible of G. freybergi from Pyrgos, Greece. b, RIM 438/387 –Left P4 of cf. Graecopithecus sp. from Azmaka, Bulgaria. From left to right: distal, mesial, lingual, buccal, occlusal and apical.

With very little to go on, they have done an admirable job of focusing on some interesting dental features that have been seen as important in the early evolution of hominins. I think the study is valuable and I do not question any of the morphological findings.

But consider the example of Ardipithecus. It has a partial skeleton with impressive cranial, dental, and postcranial morphology, and reasonable scientists still cannot decide if it is a hominin. If anyone actually thought we could trust the premolar roots, we wouldn’t be arguing over Ardi.

I think we should take seriously that Graecopithecus premolar root morphology may be yet another demonstration that supposed “hominin” characters actually evolved in other branches of apes during the Miocene. This feature is far from alone. Many other features that supposedly link Ardipithecus or Sahelanthropus with hominins are also found in other Miocene fossils. My colleagues and I documented some of these Miocene ape-like features in Sahelanthropus in 2006.

We need to look with a more critical eye at the fossil evidence for the earliest hominins. They really share very few features with later hominins like Australopithecus. I think we should consider that they might instead be part of a diversity of apes that are continuous across parts of Africa and Europe. Our real ancestry during this earliest phase of our evolution may still be undiscovered.

Reference

Fuss J, Spassov N, Begun DR, Böhme M (2017) Potential hominin affinities of Graecopithecus from the Late Miocene of Europe. PLoS ONE 12(5): e0177127. doi:10.1371/journal.pone.0177127

Wolpoff, M. H., Hawks, J., Senut, B., Pickford, M., & Ahern, J. (2006). An ape or the ape: is the Toumaï cranium TM 266 a hominid. PaleoAnthropology, 2006, 36-50.