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john hawks weblog

paleoanthropology, genetics and evolution

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

A look at the glacial lakes of Siberia

Many readers in North America have heard of Glacial Lake Agassiz, Glacial Lake Missoula, Glacial Lake Bonneville, and many other large bodies of water in North America during the last Ice Age. Less well known are the large bodies of fresh water that once existed in northern Eurasia.

I was especially impressed to learn about the glacial lake that extended across parts of the West Siberian Plain, in the Ob and Yenesei drainages. Here’s an image showing the extent of this lake around 90,000 years ago:

Illustration showing location and extent of the glacial lake in West Siberia
Figure 2 from Mangerud et al. 2004. Original caption: "Reconstruction of ice-dammed lakes and rerouting of rivers during the Early Weichselian, about 90–80 ka. Ice margins are taken from Svendsen et al. (2004). In the hatched area the ice margin position is unknown, probably because it was overrun by the 60 ka ice advance. Stippled line on Taimyr shows a retreat phase damming a lake. Blue arrows show outlets. The arrow in the Barents Sea shows the longest modelled outburst route for Lake Komi, and the corresponding western ice margin. The shorter and more probable routes have the same starting point. See text for discussion. Sea level is lowered 50 m (Chappell et al., 1996) without considering any isostatic depression."

The glacial lakes on the northern tier of Eurasia changed markedly over time during the last glaciation, as the position of the ice sheet and eustatic sea level changed. According to Mangerud and coworkers (2004), the West Siberian glacial lake was near its maximum between 90,000 and 80,000 years ago, a bit lower by 50,000 years ago, and by the Last Glacial Maximum this lake had drained entirely.

During the LGM, lakes in the northern tier were more prominent in the White Sea embayment and further to the west. There were other glacial lakes in the mountainous regions to the southeast, some of which may have had massive outflows.

I thought the West Siberian glacial lake very interesting because of its sheer surface area. At its maximum extent, geologists think that it drained to the south into the Aral Sea basin (and ultimately into the Caspian and Black Seas). Neandertals were this far north in the European part of Russia, but it is not clear what extent of habitation they had at this latitude.

Still, I wonder whether this lake may have posed a substantial biogeographic barrier to their movement, or whether they sometimes saw its shores.

Yaks in Mongolia have more than 1 percent cattle DNA despite male hybrid sterility

Last year an interesting paper by Ivica Medugorac and coworkers presented data on introgression in domesticated yaks in Mongolia: “Whole-genome analysis of introgressive hybridization and characterization of the bovine legacy of Mongolian yaks”.

I have a long interest in the hybridization and introgression of genes among cattle and related species. It all started back in the 1980s when some family members were raising beefalo, a cattle breed that has a substantial fraction of bison ancestry. Hybrids of cattle, zebu, banteng, gaur, and bison featured in my 2006 paper on the feasibility introgression in Neandertals.

What’s interesting about yaks is that they have a good fraction of cattle genes despite hybrid male sterility.

Hybrid males are sterile, however, preventing the establishment of stable hybrid populations, but not a limited introgression after backcrossing several generations of female hybrids to male yaks. Here we inferred bovine haplotypes in the genomes of 76 Mongolian yaks using high-density SNP genotyping and whole-genome sequencing. These yaks inherited ∼1.3% of their genome from bovine ancestors after nearly continuous admixture over at least the last 1,500 years

A number of scientists have discussed whether some degree of reduced hybrid fertility is a possibility for Neandertals. The human X chromosome exhibits less introgression from Neandertals than the autosomes. Further, there are large “deserts” on the X chromosome with no evidence of Neandertal introgression in any living human samples.

However, in principle these features of X chromosome introgression may reflect selection over many generations rather than a great reduction in the fertility of male F1 hybrids.

The yak lineage diverged from the ancestors of cattle an estimated 4 million years ago, and male hybrid sterility is a common feature of sister species of mammals that have been separated for such a long time. Neandertals and modern humans have been separated for around 700,000 years.

An interesting historical story unfolds when thinking about female crossing and fitness within yaks. A relaxation of the intensity of breeding selection can in some instances increase the fraction of the genome that results from introgression:

Introgression was more intense during two periods (897–1121 CE and 1695–1828 CE), which coincide with the Medieval Climate Anomaly (900–1200 CE) and the Dzungar–Qing Wars (1687–1758 CE). These periods of intense introgression are most likely due to increased mortality of livestock during these difficult times that forced yak herders to breed all of the females available to restore their herds, including backcross-derived animals (Supplementary Note).

I am sure that many other species of domesticated animals have similarly interesting histories. The times that human populations had to struggle actually leave a mark in the genomes of the domesticated species.

Tracing the users of chimpanzee tools by their DNA fingerprints

A new paper by Fiona Stewart and coworkers does a bit of forensic DNA analysis on tools made and used by chimpanzees: “DNA recovery from wild chimpanzee tools”.

The authors collected termite fishing tools used by eastern chimpanzees in the Issa Valley, Tanzania. Over a span of two months, they kept track of thirty termite mounds, collecting any tools that the chimpanzees left there. They also collected fecal samples throughout the field site, identifying at least 67 individuals.

They collected 49 tools, and were able to get mitochondrial DNA haplotypes from 41 of them. They were able to get enough DNA to type microsatellites on 18 of the tools, which were made and used by 11 different chimpanzees in total.

Archaeologically, this ability to track an individual’s use of specific tools over that time is the equivalent of attempting to track the products of an individual stone knapper at a Palaeolithic human site [e.g., 45], but with the added detail and linkages provided by the genetic data. We anticipate that the routine and long-term application of our methods at a single site would reveal the links between social and genetic influences on tool selection and modification at a level that is currently unobtainable.

I think this work is really cool.

Obviously there is limited direct utility to getting DNA from tools at sites where behavioral ecologists track the chimpanzees and record their tool use.

But across broader areas of Africa, it would be really helpful to be able to examine tool use in areas where the chimpanzees have never been habituated or tracked by primatologists.

More interesting, chimpanzees usually learn how to make and use tools from their mothers. That means that the traditions of toolmaking may correspond to mitochondrial lineages over at least short time spans. If those traditions are mainly spread and maintained by females moving among groups, there may be long-lasting associations of mtDNA haplotypes that can be tracked over hundreds or even thousands of years.

That raises the potential of looking at different kinds of chimpanzee tool use on a multigenerational or even millennial time scale, without even having to habituate the chimpanzees.

Again, pretty cool!

Reference

Stewart FA, Piel AK, Luncz L, Osborn J, Li Y, Hahn BH, et al. (2018) DNA recovery from wild chimpanzee tools. PLoS ONE 13(1): e0189657. https://doi.org/10.1371/journal.pone.0189657

Link: History of The Population Bomb

Charles C. Mann has written a historical account of Paul Ehrlich’s The Population Bomb as a part of Smithsonian magazine’s retrospective on the year 1968: “The Book That Incited a Worldwide Fear of Overpopulation”.

I learned a number of things from the article that I hadn’t known about the book’s genesis (as a political tract) and Ehrlich’s march to prominence as a public intellectual (aided by Johnny Carson).

Mann also discusses the broader impact of the book in the movement toward population control worldwide:

Such statements contributed to a wave of population alarm then sweeping the world. The International Planned Parenthood Federation, the Population Council, the World Bank, the United Nations Population Fund, the Hugh Moore-backed Association for Voluntary Sterilization and other organizations promoted and funded programs to reduce fertility in poor places. “The results were horrific,” says Betsy Hartmann, author of Reproductive Rights and Wrongs, a classic 1987 exposé of the anti-population crusade. Some population-control programs pressured women to use only certain officially mandated contraceptives. In Egypt, Tunisia, Pakistan, South Korea and Taiwan, health workers’ salaries were, in a system that invited abuse, dictated by the number of IUDs they inserted into women. In the Philippines, birth-control pills were literally pitched out of helicopters hovering over remote villages. Millions of people were sterilized, often coercively, sometimes illegally, frequently in unsafe conditions, in Mexico, Bolivia, Peru, Indonesia and Bangladesh.

Mann has written a book that covers a part of the history of doomsaying in the early 20th century by William Vogt, and the technical optimism of Norman Borlaug. The book, The Wizard and the Prophet: Two Remarkable Scientists and Their Dueling Visions to Shape Tomorrow’s World, is released later this month.

I’m looking forward to it!

Are lab exercises worthless? If they try to reinforce concepts, maybe so.

An essay by Natasha Holmes and Carl Wieman in Physics Today recounts their experiences designing introductory physics labs: “Introductory physics labs: We can do better”.

I’m linking to this because of their counter-intuitive research finding: Introductory physics labs that reinforce lecture content don’t actually help any students learn physics concepts better.

As Holmes and Wieman describe, one good explanation is that lab exercises have been too distilled by instructors, leaving no room for independent thinking.

The only thinking the students said they did in structured and content-focused labs (the kind in our study of nine courses) was in analyzing data and checking whether it was feasible to finish the lab in time. Although the finding may seem surprising at first, if you break down the elements of a typical lab activity, you realize that all the decision making involved in doing experimental physics is done for the students in advance. The relevant equations and principles are laid out in the preamble; students are told what value they should get for a particular measurement or given the equation to predict that value; they are told what data to collect and how to collect them; and often they are even told which buttons to press on the equipment to produce the desired output.

Laboratory units can be irreplaceable for learning experimental methods, how to design experiments, how to increase the sensitivity and accuracy of measurements. But teaching those skills requires a basic change in design from most laboratories.

I’ve followed Wieman’s research for many years. He is a Nobel-prize-winning physicist who has turned much of his effort toward improving the teaching and learning of physics by undergraduate students. In my experience, many of his educational suggestions—for example, getting away from lectures and toward conversations and interaction—are common sense for teachers in the humanities and social sciences, but novel for teachers in the physical sciences.

Still, when it comes to this research on laboratory effectiveness, I pay close attention.

Exploded skull image
This isn't my laboratory, but we do have some exploded skulls like this one. Photo by Hannah Gibbs on Unsplash.

Laboratory experiences are very important to the way I teach my introductory biological anthropology courses. I have not designed them with the intention of reinforcing lecture components. This is because the laboratories enable hands-on experiences with bones and casts, which I think is the most effective way to teach these subjects. That means I cover evolution concepts in lecture, but not the specifics of bone anatomy.

The greatest overlap of material from both lecture and laboratory components happens with human evolution, where students are learning species and concepts related to their evolution in lecture, and studying casts in the laboratory. In recent semesters, laboratories are not having the effect I would like to see.

The challenges in my labs are very much like those described by Holmes and Wieman. There is always a time crunch, because laboratory sections are only an hour long. One way to enable students to think and design their own experiments is to set up inquiry-based assignments that extend over several weeks.

This has been one of our most successful and popular approaches. But the students still require a lot of instruction and guidance, and I think we can do even better.

The newfound respect for hybridization and introgression in mammals

An article in Quanta magazine in August by Jordana Cepelewicz is a very readable account of scientists’ newfound respect for hybridization and introgression in many lineages of mammals and insects: “Interspecies Hybrids Play a Vital Role in Evolution”.

I’m really proud to have been among the first to bring the term “introgression” into the conversation about human evolution. The evidence from hominins like Neandertals and Denisovans was part of the forefront of this new respect for hybridization, because of the investment in the Human Genome Project and development of ancient DNA in hominins first.

What has been happening over the last five years is a huge increase in genomic data from other mammalian families, where–surprise!–introgression is just as widespread as in hominins.

For example, Cepelewicz writes about new research on the phylogeny of the big cats and the evidence for introgression in jaguar evolutionary history:

Some of these adaptations, however, may not have originated in the jaguar lineage at all. Eizirik’s team found evidence of many crossings between the different Panthera species. In one case, two genes found in the jaguar pointed to a past hybridization with the lion, which would have occurred after their phylogenetic paths had forked. Both genes turned out to be involved in optic nerve formation; Eizirik speculated that the genes encoded an improvement in vision the jaguars needed or could exploit. For whatever reasons, natural selection favored the lion’s genes, which took the place of those the jaguar originally had for that trait.
Such hybridization illustrates why the Eizirik group’s delineation of the Panthera evolutionary tree is so noteworthy. “The bottom line is that this has all become more complex,” Eizirik said. “Species eventually do become separated, but it’s not as immediate as people would frequently say.” He added, “The genomes we studied reflected this mosaic of histories.”

The mosaic of histories is a nice way of expressing what in hominins we’ve been calling the “braided stream”. The fact is that different parts of our genomes have different histories. Some of our genes spent time in very different lineages of ancestral hominins.

Braided stream
A braided stream. Photo Credit: Sam Beebe, Ecotrust via Compfight cc

The same is true in elephants, in cats, in cattle, and dogs, and bears, and basically every familiar mammalian family with enough living members to compare genomes.

Related: “What is the ‘braided stream’ analogy for human evolution?”

Lida Ajer, early modern human remains in island Southeast Asia

In August of last year, Kira Westaway and colleagues published new dating results from Lida Ajer, Sumatra: “An early modern human presence in Sumatra 73,000–63,000 years ago”. The cave has a fossil-bearing breccia that was excavated by Eugene Dubois during the late 1880s.

Dubois lost interest in excavating Sumatran caves because he believed the fossils were too recent to document the “missing link” he sought. In 1948, D. A. Hooijer described some of the orangutan teeth from Dubois’ collection from Sumatra, along with two human teeth from Lida Ajer. He concluded that these two teeth, an upper central incisor and a likely second upper molar, were indistinguishable from modern human samples.

Westaway and colleagues were able to relocate the Lida Ajer cave by using Dubois’ notes, while they have been unable to find other caves that Dubois investigated.

Gilbert Price, one of the team members, has put a short video on YouTube giving some context of the team’s initial reinvestigation of the site.

It is great to be able to see the site’s surroundings and a bit of the fossil context in this way.

Hooijer had speculated that the fossil assemblage might have originated as a porcupine accumulation. The collection is nearly entirely teeth and some of them–including the two human teeth–bear evidence of porcupine gnawing. Westaway and coworkers agree with this assessment and further suggest that the fossil-bearing breccia may have flowed into its current location as a mass and later lithified.

The conclusion that the teeth are modern human rather than some archaic human form or Homo erectus is clear enough.

The Lida Ajer teeth are smaller than fossil orangutans and east and southeast Asian Homo erectus/archaic Homo sapiens (Extended Data Fig. 3). They show greater affinity to east Asian Late Pleistocene H. sapiens than to southeast Asian Late Pleistocene to mid Holocene H. sapiens (Supplementary Tables 3, 4). The relative enamel thickness of the incisor is most similar to mean values for modern humans, and exceeds the extant orangutan range (Extended Data Fig. 4 and Supplementary Table 5). Relative enamel thickness of the molar is intermediate between mean values of living humans and living and fossil orangutans. Discriminant function analysis of molar enamel–dentine junction morphology classifies it as H. sapiens (Extended Data Figs 4, 5, 6). Both teeth have a simple external morphology typical of H. sapiens. They lack traits that characterize east and southeast Asian H. erectus/archaic H. sapiens and Homo floresiensis. Furthermore, derived H. sapiens features are found in both teeth, such as incisor double shovelling (Supplementary Information). The combination of their small size and external and internal morphology demonstrates that they are anatomically modern Homo sapiens.

Westaway and coworkers have added substantially to Hooijer’s description by adding the microCT observations, including the enamel-dentin junction (EDJ) and data on enamel thickness. These teeth do not differ from the teeth of Late Pleistocene East Asian human samples, which include the very early teeth from Tam Pa Ling, Laos, and Liujiang, China, along with somewhat later Chinese, Vietnamese, and other archaeological sites.

Based on the authors’ model of site formation, they assume that the breccia deposit formed in a short period of time and does not sample fossils from across substantial geological time. They obtain estimates of geological age from the breccia in four ways: Uranium series dating of flowstones and other speleothem samples, uranium series dating of fossil teeth, ESR dating of the fossil teeth, and red thermoluminescence dating of quartz grains in the breccia.

All of these methods arrive at a similar picture. The U-series dates on the fossil teeth provide minimum ages, and these are all over 40,000 years ago, and most age estimates including ESR and red TL within the range from 80,000 to 60,000 years ago. The flowstones that bracket the top and bottom of the authors’ stratigraphic profile of the breccia are 71,000 +/- 7 and 203,000 +/- 17,000 years old. None of the U-series dates from within the breccia are nearly as old as the underlying flowstone.

As I read the paper and supplementary information, I kept looking for documentation to convince me that Dubois actually collected the two human teeth from within the breccia in the stratigraphic position shown by the authors. To me, the provenience of these two teeth is a critical question. I don’t have any specific reason to doubt that they come from within the breccia where they are reported, but with any site excavated so long ago, we do need to ask the question. The human teeth have no direct date, look like those of modern humans, while lacking the mineral staining seen on some of the faunal remains that they have pictured.

The cave has no evidence of stone tools or other artifacts. The authors discuss this in their supplementary text:

No evidence of archaeology was observed in the cave or surrounding region. Hooijer did “not consider the two teeth described above as evidence of human inhabitation in the prehistoric Sumatran caves”. Hooijer’s comments were made in reference to what he considered a non-occupation cave. No excavations have been conducted in the front of the cave, and whether or not prehistoric peoples used the cave remains to be demonstrated. Nevertheless, the assemblage reflects the fauna that were present on the landscape, humans included. Furthermore, we note the presence of human remains but an absence of archaeological evidence is a common feature in other Asian caves, such as Thum Wikin Nakin in Thailand, Punung in Java, and Fuyan in southern China.

It’s typical to hear that archaeological sites vastly outnumber sites with hominin remains. From that generalization, it might seem reasonable to suppose that archaeological sites document the dispersal of human populations with more fidelity than hominin bones and teeth.

But most time intervals are poorly represented by archaeological sites in most regions of the world. Southeast Asia and island Sundaland have a very sparse archaeological record, even though hominins were likely there in large numbers through most of the Pleistocene.

Archaeologists and anthropologists have expressed many ideas about that sparse record. Some of the area was forested during large spans of time, and many anthropologists have expressed the idea that hominins could not penetrate forested habitat effectively until the last 20,000 years.

Lida Ajer is the earliest hominin discovery in rainforest anywhere in the world [but see UPDATE below]. I don’t think that’s because hominins weren’t in these forests, I think it’s because these areas have not been explored with the intensity of lake edge sites and caves in arid and temperate habitats.

During the last fifteen years, there have been remarkable discoveries in island and mainland Southeast Asia, and I expect that to continue as people keep going.

UPDATE (2018-01-08): I have an e-mail from John de Vos informing me that I should investigate the Punung site on the island of Java.

Punung has a rainforest fauna dated to around the last interglacial (in other words, around 120,000 years ago) and a single human premolar, which is similar to modern humans in its measurements.

I’ll follow up with more information on Punung in a separate post.

The surprising connectedness of human genealogies over centuries

A new article by Adam Rutherford in Nautilus may be a good one for students in my genetics course this upcoming semester: “You’re Descended from Royalty and So Is Everybody Else”. The article is an excerpt of Rutherford’s book, A Brief History of Everyone Who Ever Lived: The Human Story Retold Through Our Genes.

Chang’s calculations get even weirder if you go back a few more centuries. A thousand years in the past, the numbers say something very clear, and a bit disorienting. One-fifth of people alive a millennium ago in Europe are the ancestors of no one alive today. Their lines of descent petered out at some point, when they or one of their progeny did not leave any of their own. Conversely, the remaining 80 percent are the ancestor of everyone living today. All lines of ancestry coalesce on every individual in the 10th century.

When you get up to around a trillion potential lines of genealogy, you have room for some surprisingly long-distance connections. Still, what people tend to ignore about this kind of logic is that incredibly tiny fractions of the genealogical tree are not different from zero when it comes to DNA ancestry.

The argument is based purely on number logic, and is not falsifiable by any empirical observations, short of impossibly complete genealogical knowledge.

In my opinion, we should be a bit more conservative (as Rutherford also reflects in this excerpt). But still, it’s very likely that common ancestors of all living humans have lived within the last 2000 years.

By the same logic, of course, every living human is a descendant of Neandertals. And every Neandertal that was an ancestor of the last Neandertal-modern hybrid was also an ancestor of all of us.

MOOCs after five years

Five years ago, I was just starting to prepare a massive open online course (MOOC). That course development would be an 18-month adventure for me.

Our team worked with the concept that technology can bring students who are learning outside the classroom even closer to the course content than students within the classroom. For a course in human evolution, that meant traveling to the field, bringing students to the sites where fossil hominins have been found. And it meant allowing real scientific experts to speak for themselves.

The course ran in the spring of 2014, with the title “Human Evolution: Past and Future”. People today can watch many of the course components on my YouTube channel, including some remarkable interviews and site visits.

I learned a lot while teaching the MOOC, which has helped me in many ways to develop other forms of public engagement. Many of the video presentations from my MOOC have been even more successful on YouTube than they were in the course with its 40,000 registered students.

Diane Lorillard and Eileen Kennedy, specialists in digital technologies and education, have a post in the Times Higher Education on massive open online courses (MOOCs) from today’s perspective: “Moocs can still bring higher education to those who really need it”.

Their post recognizes some of the ways that the MOOC scene has changed since 2012, and ends with a framework worth sharing:

Viable solutions to making online learning affordable and sustainable require an understanding of the true costs. What are the costs of a video to be shown over 10 runs of a course? What are the costs of facilitating a discussion for each of those 10 runs? How large can an online tutor group be? What combination of activities will produce the best experience for the learner?
More research on this activity-based costing approach will enable us to plan costs realistically in relation to the quality of the learning experience provided.
Online learning at scale has the potential to transform access to quality higher education. It also has the potential to transform what it means to teach in higher education. The question now is how can we make sure that this transformation is productive and sustainable for the future of higher education for all.

Initially, as universities began developing these courses in 2012, they were not driven by real sustainable motives. In the first couple of years, MOOCs were a way for premier universities to compete for status in a new area that was getting a lot of press.

What may have been less visible is that MOOCs were also a way for specialists in educational technology to test new platforms and methods of delivering teaching and interaction online.

My MOOC, for example, enabled the University of Wisconsin to train a large group of educational technology specialists in new technologies, at the same time that it gave more than 40,000 people the opportunity to learn about human evolution from the field.

Many people who were great fans of my MOOC ask, why don’t we do it again? I’ve been asked by other universities, also, to help develop MOOCs on similar subjects.

The truth is, doing a MOOC in anthropology well requires many people to invest time in those personal interactions, on the virtual forum, message boards, and giving personalized feedback on assignments. That kind of interaction may be less necessary in very technical fields, as very popular MOOCs in artificial intelligence and programming have demonstrated.

But to me, a course in anthropology is about the human interaction. That human interaction is labor-intensive. It’s hard to do at a large scale without sustainable funding.

Many institutions still see MOOCs as an inexpensive way to do education at a large scale. That’s not realistic in anthropology. A great MOOC may be relatively inexpensive for the scale, but it is not without substantial ongoing cost.

Still, MOOCs have a serious benefit: A huge population of people in Africa, South Asia, Southeast Asia, and rural areas of many other countries are underserved by local and regional educational institutions. MOOC-like courses can reach people where they live, on the devices that they use.

I dream of bringing those populations into the study of human evolution, where new discoveries are being made. Tomorrow’s generation of paleoanthropologists must represent the areas where tomorrow’s fossil discoveries will be made.

How can we empower people to be a part of this science? To me, that’s the big problem. My instinct is that we can build communities to make this kind of learning possible for people around the world.

Bonobo preferences: dominance over cooperation

An article in Current Biology by Christopher Krupenye and Brian Hare suggests that bonobos may have a social preference for individuals who wear their dominance on their sleeve: “Bonobos Prefer Individuals that Hinder Others over Those that Help”.

This has gotten a good amount of press attention this week, contrasting the bonobos with humans in terms of cooperativeness and prosociality. It’s an instance where the bonobos seem to be acting more like chimpanzees than the usual highly prosocial bonobo stereotype.

Michelle Rodrigues is a primatologist at the University of Illinois who has read the new study in detail and wrote a very helpful summary: “Human infants prefer helpers, but adult bonobos prefer hinderers”.

From the post:

So what do these results tell us? I think Krupenye and Hare have nicely demonstrated that adult bonobos in a sanctuary setting prefer "hinderers" or dominant individuals. However, these results don't hold for the younger bonobos (ages 4-9). And that's where the comparison to humans fall short. We can't compare human infants to adult bonobos, and then conclude that this is a species difference. I suspect that this may be an age difference in both species, though there also may be greater variation depending on culture, personality, socialization, etc.

It is a fascinating question to what extent apes may be enculturated by their exposure to a dominance hierarchy and the behavior of older individuals in their social groups. We know that humans are highly plastic in their development of social preferences. But we don’t know whether the complex landscape of social interactions may have “attractors” that may affect or reinforce cooperation versus competitiveness and dominance hierarchies.

Link: Expedition journal from Niah Caves

I was really pleased to see a post by Darren Curnoe recounting his team’s recent field season in Niah Caves in Borneo: “We Found Evidence of Early Humans in the Jungles of Borneo”.

Over a period of three weeks, we dug through what we believe to be around 20,000 years of human history. We uncovered several human bones, the remains of large mammals (probably deer and wild cattle) and marine oyster shells indicating a period of seafood meals. Stone tools and charred rocks were also unearthed.
It was exciting and a little bit daunting to be digging at Niah Caves, given its place in both the history of archaeology and more broadly of humankind.

Really great to see more teams keeping expedition journals, which are such powerful ways of communicating the real-life decisions and processes of archaeological science. Curnoe’s “Daily Dig Diary” on YouTube (indexed on his Facebook page) was an informative way to follow archaeological research as it happened.

Link: Implications of an 11,500-year-old genome from an infant skeleton from Alaska

A paper in Nature this week presents analysis of the ancient genome of an infant skeleton from Alaska, some 11,500 years old: “Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans”.

Jennifer Raff has done a very nice write-up for the Guardian of the implications of these new data for models of the initial habitation of the Americas: “What the ancient DNA discovery tells us about Native American ancestry”. Of particular interest is the way that this genome helps to resolve the approximate ages of population divergences as people entered Beringia and later the southern parts of the Americas.

She did not belong to either of the two major Native American genetic groups (Southern and Northern), but was equally related to both of them. One interpretation of this result is that her ancestors must have remained in Alaska after splitting from the ancestors of Native Americans sometime around 20,000 YBP. Her genome, provides new insight into the genetic diversity present in the ancestral Beringian population. One important component of that is that it gives us new estimates of the approximate dates of key events:
36,000 YBP: The ancestors of the ancient Beringians began to separate from East Asians, but gene flow between them continues until about 25,000 YBP
25-20,000 YBP: This population experienced gene flow with the ancient North Eurasian population (to which the Mal’ta boy belonged)
20,000 YBP: The ancestors of the Upward Sun River child diverged from the ancestors of other Native Americans.
17,000-14,600 YBP: The two major clades (genetic groups) of Native Americans differentiate from one another.
While this paper doesn’t yield any tremendous surprises, it does add new details to and confirms the predictions of a hypothesis for the initial peopling of the Americas that has been the focus of much research over the past few years.

I may have more to say about this later. It is of interest that this genome, like other Paleoamerican genomes so far, lacks the evidence of a slight fraction of South or Southeast Asian ancestry that some researchers have claimed to be present in some living populations from South America.

Neo one of the top 10 science images of 2017

Really honored to have one of my photos of Neo included as one of Cosmos magazine’s “Top 10 science images of 2017”.

Neo skull frontal view

It’s the frontal view of the Neo skull.

I’ve always thought that human evolutionary science has some compelling images, and we rarely see them in top science images lists, which often feature brightly colored micrographs. There’s something exotic about beautiful images that must be explained for people to see what they represent. With a fossil, the image portrays an object that speaks for itself in some ways.

This is a fun photo because I took it with old glass, a vintage 1970 Nikon manual lens that I use for many of my laboratory photos.

Link: A hookworm history in mining

I’ve been doing a bit of reading about hookworm infection for an essay, and I happened across a piece by Rebecca Kreston from Discover’s “Body Horrors” a few years ago: “Dark Pits of Disease: Mining’s History of Hookworm”.

I wasn’t really aware of the long association of hookworm and mining, later extended to tunnel-digging.

The extent of hookworm infection was properly assessed in the mid to late 1800s. The disease was recorded throughout the United States, Australia and and much of Europe (4). It was found in the gold and silver mines of Hungary, Sicily’s sulphur mines, and in the coal mines littering Germany, the Netherlands, Belgium and France (5). It was estimated that 20 to 90% of miners in Austria suffered from anemia in the late 1800s. More than half of the men slaving away in the goldmines in the California Gold Rush in the mid-nineteenth century were thought to carry hookworm, with some populations said to be infected at a rate as high as 80%. In 1916, when the California State Board of Health investigated the prevalence of hookworm among the 1400 miners based at the Grass Valley Gold Mining district in Sierra Nevada, all but two of the men were found to be harboring worms (1).

How many students in paleoanthropology can see casts of Australopithecus afarensis?

The other day I happened back upon an old post from 2005, the first full year of the blog: “NSF and data access”. The post recounts my perspective on the problems with data access back in the first decade of this century.

That post was written a couple of years after the famous “Glasnost” article in Science. That news article, by Ann Gibbons, reviewed some scientists’ perspectives on access to fossil evidence. That would prove to be an important article in documenting a phase of history.

But as I reflected at the time, the fact that scientists cannot examine recently-discovered fossils is a comparatively minor inconvenience.

The real problem is that twenty to thirty years after many fossils are uncovered, there is no cast availability, little public data access, few financial accommodations to make such access possible. Specialists like me often find ways around these barriers. But I do not think it would be overstating the problem to suggest that perhaps half the people teaching human evolution in four-year universities have never touched a cast of a Hadar fossil. I would be delighted to be proved wrong, but I don't think I am. Our field is educating students into a world in which A. afarensis is unknown in the laboratory and poorly represented in our textbooks. I'm not talking about new specimens, here, I'm talking about fossils that were found in the mid-1970's and monographed in 1982. Nor is this problem limited to early hominids. What proportion of people teaching about the modern human origins problem do you suppose have seen a cast of any "early modern" fossil other than Skhul 5?

I’ve said this quite a lot over the years. I still believe that Au. afarensis is not known in the laboratory for most instructors of biological anthropology at universities and colleges in the U.S. Indeed, I would say that a good fraction of instructors of specialty courses in paleoanthropology have not studied casts of Au. afarensis beyond LH 2 and LH 4 from Laetoli, Tanzania.

I was especially struck in 2012, when I organized the plenary session at the AAPA meetings, at which many anthropologists saw casts of fossil hominins that they had never seen before. The University of Oregon assisted by providing a second-generation cast of the Lucy skeleton. I was amazed at how many professional anthropologists clustered around the table with this cast skeleton. Many had seen a cast of Lucy mounted in a museum, but had never had the opportunity to handle parts of it, nearly forty years after its discovery.

My post from 2005 centered around the announcement of the new data access requirements for NSF grants in the physical anthropology program. I was hopeful, and reviewed several ways in which the official policy might make a difference.

But I did think that there was a real risk that the policy would give rise to extra paperwork for grant applicants without actually requiring any real changes in the way paleoanthropologists did things.

If the new policy is to be a success, then the proof of it cannot wait for ten to thirty years. It needs teeth. It needs two or three high-profile grants to be declined because of data access issues. And it needs those cases to be made public, so that everyone can have confidence in the openness of the process. This doesn't mean that the names of the applicants and their alleged sharing violations should be dragged through the press. It does mean that NSF should publish the number of grants (and their proposed funding amounts) declined for failings in the data access plan.

There has been positive progress. The data archive at Duke University, Morphosource, initially funded by NSF, has become an important data repository for surface scan data from some recent fossil hominin discoveries. None of those hominin fossil discoveries were themselves funded under NSF grants, but NSF funding did go toward recovery of a number of Turkana Basin hominin fossil specimens, for which photogrammetric models are available under the AfricanFossils.org initiative.

A cultural change is underway in data access and accessibility of 3-D models and casts of fossil hominin specimens. I am much more hopeful about the future of data access now than I was in 2005.

With fossils like those of Australopithecus afarensis, there are very specific heritage issues that pertain to the country of origin and limit scientists’ ability to share information about their fossils.

For example, researchers who work in Ethiopia have told me that only a single cast of any fossil specimen is allowed to be exported from the country by the discoverer. Obviously that requirement severely limits information exchange about such discoveries among professional anthropologists, much less the public. It also severely reduces the broader impact of fossil discoveries, unfortunately, because of the extreme difficulty of including them in comparative analysis.

I will be reflecting on these issues much more over the coming months. We are on the verge of some real changes in paleoanthropology’s profile in science and its impact on people’s awareness of science. A critical mass of anthropologists recognize the importance of working together on issues of access and data replicability.