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john hawks weblog

paleoanthropology, genetics and evolution

Photo Credit: Rainy day at Amud Cave, Israel. John Hawks CC-BY-NC-ND


The North Carolina School of Science and Mathematics (NCSSM) is a science-focused high school. They have put on Flickr a large series of Creative Commons (CC-BY-SA-NC) licensed photos of their cast collection, including skulls of many hominins. I find it awesome to see a public high school taking this initiative, and I really appreciate the work behind this. Here’s a photo of the old Hadar A. afarensis reconstruction from their collection.

Cast of A. afarensis reconstruction, from NCSSM

Their photos are also available at their school’s webpage, including the ability to render them as 3-D rotations.


The museum and research center at Sangiran, Indonesia is capped by a large copper conical roof. The surrounding countryside is the source of Early and Middle Pleistocene fossils of many vertebrates, including Homo. It is intensively farmed with many small plots, rice, teak plantations and other crops.

Sangiran Museum from a distance

Link: Sustaining open access databases

Cameron Neylon considers some of the challenges in keeping open data access initiatives sustainable over the long term: “Squaring Circles: The economics and governance of scholarly infrastructures”. He examines some proposals for supporting scholarly “goods”, and emphasizes that they are usually initiated without much planning for what to do if support eventually is lost:

Second, we can look at stable long standing infrastructures (Crossref, Protein Data Bank, NCBI, arXiv, SSRN) and note that in most cases governance arrangements are an accident of history and were not explicitly planned. Crises of financial sustainability (or challenges of expansion) for these organisations are often coupled to or lead to a crisis in governance, and in some cases a breakdown of community trust. Changes are therefore often made to governance in response to a specific crisis.
Where there is governance planning it frequently adopts a “best practice” model which looks for successful examples to draw from. It is not often based on “worse case scenario” planning. We suggest that this is a problem. We can learn as much from failures of sustainability and their relationship to governance arrangements as from successes.

The Social Science Research Network is a potent example. Initiated as an open repository, it was recently taken over by Elsevier, which changed some policies and began to take down some user-contributed content. Many projects that are started by small groups of founders, or funded initially by grants from a single source, are risky over the long term because in some cases the only way to sustain them is to change their policies or accessibility.

I would observe that the open source software movement is a good source of examples for how to ensure that data will be sustained in the open in the event that funding to a project is lost, or a project is acquired by a private entity. Many open software projects have been acquired or developed by private entities, and when they want to change the license terms, the projects are often subject to forking, where the original project may change but a community maintains an open version. The key is that communities of people must coordinate action and be prepared to mount an equivalent project. Widespread public mirroring of source code by individuals and institutions is a major part of what makes this possible.

To me, this suggests that any open data initiatives should be working closely with universities to ensure that their data are mirrored in an open manner.

Large-scale academic and scientific projects sometimes generate so much data that a large number of redundant mirrors are impractical. But it is exactly these instances that we should focus attention upon and ensure that national or international funding bodies are involved in their maintenance.


Dennis Overbye in the New York Times covers this week’s news from the Large Hadron Collider at CERN, where hopes of “new physics” beyond the Higgs boson are not panning out: “The Particle That Wasn’t”.

The Higgs, one of the heaviest elementary particles known, weighs about 125 billion electron volts, in the units of mass and energy favored by particle physicists — about as much as an entire iodine atom. That, however, is way too light by a factor of trillions according to standard quantum calculations, physicists say, unless there is some new phenomenon, some new physics, exerting its influence on the universe and keeping the Higgs mass from zooming to cataclysmic scales. That would mean new particles.

Sabine Hossenfelder shares her perspective on this story of non-discovery, as a theoretical physicist: “The LHC ‘nightmare scenario’ has come true”.

That the LHC hasn’t seen evidence for new physics is to me a clear signal that we’ve been doing something wrong, that our experience from constructing the standard model is no longer a promising direction to continue. We’ve maneuvered ourselves into a dead end by relying on aesthetic guidance to decide which experiments are the most promising. I hope that this latest null result will send a clear message that you can’t trust the judgement of scientists whose future funding depends on their continued optimism.

My reaction was that a few billion dollars spent on human origins research would produce a much higher rate of discovery than the LHC.


This is a Daemonelix, burrow of the ancient beaver relative Palaeocastor. There is a nice exposure of Miocene deposits at Agate Fossil Beds National Monument. The surface of the bluffside displays dozens of natural casts of these ancient corkscrew burrows.

Daemonelix burrow at Agate Fossil Beds National Monument

This is SK 15, a lower jaw from Swartkrans, South Africa. Most scientists today attribute it to Homo erectus, but when Robert Broom and John Robinson found it, they named a new genus, Telanthropus capensis. This was the first solid demonstration that two different kinds of hominins were found at the same African fossil site. The very humanlike SK 15 contrasted with the “robust” australopithecines that make up most of the Swartkrans fossil collection.

SK 15 mandible in lateral view

However, the story is a bit more complicated. Some specialists long questioned whether SK 15 might be a small, presumably female, individual within a population where males had the form and size of the robust mandibles. That argument lost some force when later sites also demonstrated the coexistence of Homo and robust australopiths, but the variation of specimens attributed to Paranthropus robustus remains extremely extensive.

Meanwhile, a number of scientists more recently have referred SK 15 mandible to Homo habilis. Some have considered that it might represent a distinct species of Homo, more basal on the hominin phylogeny than H. habilis and H. erectus.

In other words, the taxonomic status of this specimen is really confused. To me, this is a great illustration of the problems of working with a single mandible, even though in this case the mandible is relatively complete. When you hear people talking with great confidence about the taxonomic identity of a partial mandible, SK 15 is a good case to keep in mind.


Last September, Aeon published a useful essay by science writer Jacob Mikanowski, touching on many of the ways that ancient DNA is changing the way we look at ancient population movements: “Origins: Paleogenetics is helping to solve the great mystery of prehistory: how did humans spread out over the earth?”

Mikanowski hits upon a big theme:

Before the Second World War, prehistory was seen as a series of invasions, with proto-Celts and Indo-Aryans swooping down on unsuspecting swaths of Europe and Asia like so many Vikings, while megalith builders wandered between continents in indecisive meanders. After the Second World War, this view was replaced by the processual school, which attributed cultural changes to internal adaptations. Ideas and technologies might travel, but people by and large stayed put. Today, however, migration is making a comeback.

If there is one overarching finding from these ancient DNA studies, it is that many prehistoric archaeological transitions really did involve the large-scale mass migration of groups of people.


Annalee Newitz describes a study in Science that examines a semi-legendary flood at the dawn of Chinese civilization, which turns out to have been a real event: “Incredible discovery reveals the truth behind an ancient Chinese legend”.

Purdue geoscientist Darryl Granger, who worked with the research team in China, described the flood at a press conference earlier this week. The flood waters, he said, "reached up to 38 meters above the modern river level." We know that because the scientists found distinctive sediments released by the flood in the Jishi Gorge and elsewhere downriver. Knowing the water levels helped the group figure out the volume of water, which, Dr. Granger said, "tells us that the flood was [traveling] about 300 to 50,000 cubic meters per second... It's among the largest known floods to have happened on Earth during the past 10,000 years."

These are more petroglyphs from Hawaii Volcanoes National Park, part of the Pu’u Loa group. During historic times, when a child was born, a small cupule would be engraved for the umbilical cord and covered with a stone. There are more than 20,000 of these in the grouping.

Petroglyphs umbilical dots from Hawaii Volcanoes National Park

Some words of advice from Steven Pinker about writing, in this interview with the Chronicle of Higher Education. I like the diagnosis:

First, academic writers start off with the wrong tacit goal. Rather than trying to show their readers something interesting in the world (what Francis-Noël Thomas and Mark Turner call "classic" style), their main goal is to prove that they are not naïve about how terribly difficult it is to assert anything about anything in their field (what they call "self-conscious," "ironic," or "postmodern" style). In that defensive stance, they clutter their prose with hedges, apologies, shudder quotes, narcissistic observations about their profession (as opposed to its subject matter), and metadiscourse (discourse about discourse).

We were in Hawaii last month and visited Hawaii Volcanoes National Park. The park has an area with exceptional petroglyphs from early Hawaiians, accessible by a short hike. Here is a group of human figures. These are carved into a lava flow that occurred sometime between A.D. 1250-1400, and people returned to this site for generations to cut new petroglyphs.

Human figure petroglyphs from Hawaii Volcanoes National Park

I really like this blog post reviewing the discovery of botulinum toxin by Rebecca Kreston: “The Bad Sausage & The Discovery of Botulism”.

Two years later, he published a second monograph chronicling the outcomes of 155 cases, speculating on the mechanism of what he would dub “the fat poison.” Kerner administered extracts of spoiled sausage mixed with honey to a menagerie of small captured animals – including flies, locusts, snails, birds, frogs, rabbits, and cats – finding identical presentations of “sausage poisoning” in fly and frog alike (2). He also made small incisions in the thighs of a rabbit and cat, daubing the exposed tissue with sausage extracts and found that the “fat poison” brought about a localized paralytic effect with complete recovery of the animals. Kerner also poisoned himself. Placing just a few scant drops of extract on his tongue, he noticed a “feeling of contraction and choking in the area of the larynx … some drops of the acid brought onto the tongue cause great drying out of the palate and the pharynx.”(2) The extract tasted sour, much like the spoiled sausages.

All of this unfolded in the 1820s.

Should we be surprised that Neandertals, Denisovans, and modern humans didn't form stable hybrid zones?

We’ve come a long way toward recognizing the complexity of modern human origins and dispersal. Ten years ago, I was one of a relative few who still maintained that mixture with Neandertals was important to our evolution. Over the last six years, the scale of Neandertal genetic introgression has been quantified by genetic comparisons from ancient DNA. We know that Neandertal ancestry contributed a small fraction of the genomes of living people in much of the world.

The amount of introgression varies across different parts of the genome. The Neandertal component is less in regions that are rich in genes. In some large blocks of the genome, nobody sampled today has any Neandertal DNA. This indicates that on the whole, Neandertal DNA didn’t work quite as well in recent populations. Modern human samples from the Upper Paleolithic of Europe had a higher fraction of Neandertal ancestry in gene-rich parts of the genome, indicating that this fraction was not excluded during the initial hybridization, but instead declined over time under natural selection. At the same time, some Neandertal-derived genes were adaptively useful in later populations and have increased in frequency far beyond the average amount of genetic introgression across the genome.

Neandertal in a suit

In 2006, before any nuclear DNA results from Neandertals were known, Greg Cochran and I published a paper, “Dynamics of Adaptive Introgression from Archaic to Modern Humans”, that examined the way that natural selection and hybridization would interact as Neandertal genes were absorbed into modern human populations. The paper included some simple population genetic modeling and drew upon a rich series of examples from non-human animal and plant species.

The early 2000s marked a time when genetic data increased the power of molecular ecology and biogeography. Geneticists moved toward larger-scale sampling of mtDNA in natural populations. More important, they started to develop the nuclear markers that are necessary to quantify and study hybridization across the genome. The first useful cases were those involving domesticated and model species, for which nuclear markers had already been studied for commercial purposes. But wild species were following. Already, it was clear that hybridization and introgression were widespread phenomena. Many natural and domesticated populations actually derive a small fraction of their DNA from a history of hybridization with distantly related populations, subspecies or species. Greg and I drew upon this literature and projected what this phenomenon would predict for modern humans and Neandertals.

The evidence has of course changed quite a lot since then. In some ways, we predicted the outcome of later research that followed the publication of the draft Neandertal genome in 2010. Of course we failed to foresee many of the more interesting findings, but I’m proud that we captured the central idea of how a small fraction of the genome might behave in the later human population. More important from the standpoint of biogeography and ecology, the evidence on non-human species has vastly increased. Phylogeographers have documented mixture and introgression in well-known domesticates and their close relatives, in cases of biological invasions, and in many other cases where natural populations did not undergo any recent biogeographic disruption. Whole-genome techniques have brought hybridization and introgression to the attention of evolutionary biologists in a way that was not true even ten years ago.

The cool thing about having massive genetic data is that we can imagine answering questions that wouldn’t have been possible for anyone to ask in the past. One of those was asked this spring in a commentary by Ajit Varki, “Why are there no persisting hybrids of humans with Denisovans, Neanderthals, or anyone else?”

The title is unfortunate, because of course the vast majority of people in the world, possibly all of them, are descendants of hybrids with Denisovans, Neandertals, or someone else. But the article is not about that aspect of hybridization and its later history. Instead, Varki considers that stable hybrid zones exist today among many other closely related species or subspecies, and he asks a very direct question: Why did modern humans not form stable hybrid zones with contemporary archaic human populations?

Current genomic and archaeological data indicate that BMHs arose in Africa ∼100,000–200,000 y ago and spread across the planet (including the rest of Africa), encountering other extant hominins like Neanderthals, Denisovans, archaic African hominins, and possibly other lineages from earlier diasporas of Homo erectus. Although genomic evidence indicates interbreeding, the number of functional genes incorporated is limited, resulting in a “leaky replacement” (3), without persistence of true hybrids. Thus, our single BMH (sub)species was the “winner” in every contact/replacement event, spanning tens of thousands of years. I cannot find any other example wherein a single (sub)species from one geographic origin completely replaced all extant cross-fertile (sub)species in every planetary location, with limited introgression of functional genetic material from replaced taxa, and leaving no hybrid species. Typically, one instead finds multiple cross-fertile (sub)species, with hybrid zones in between.

Actually, in our 2006 review, Greg and I pointed to some instances of “extinction by hybridization”, in which an invasive population is proliferating at the expense of a local endemic population but absorbing genes from that endemic in the process. One well-known case is mallard ducks in New Zealand, which have been absorbing genes from the native New Zealand brown ducks even as the brown ducks have declined in numbers. This is not a rare phenomenon in nature. The phrase “extinction by hybridization” brings 1450 results on Google Scholar. Our 2006 paper benefited substantially from the classic 1996 review by Rhymer and Simbeloff, but examples of the phenomenon have massively increased since then. Varki’s opinion piece neglects this area of genetic evidence, which is understandable considering its short length.

Varki is quite correct that there is an interesting contrast. Some closely related species and geographic variants within species seem to have formed stable hybrid zones. Others have failed to attain such spatial equilibria and one species or variant displaces the others. Humans during the Late Pleistocene were an extreme example of the latter case.

Hybrid zones are epiphenomena of the evolutionary forces of migration and selection. If a hybrid zone between two species or genetically differentiated subspecies persists over evolutionary time, it is because selection maintains it. The ecological circumstances of the resident population may disfavor the traits of hybrids, impeding gene flow deep into the resident population’s range. In such cases, a hybrid zone may be a demographic sink, absorbing migration from both source populations. Selection may also favor reinforcement, in which the members of a population favor mating with other members of their own population at the expense of hybrids. “Extinction by hybridization” occurs when selection is weak relative to gene flow from the invading population over the entire range occupied by the resident population.

We don’t see stable Neandertal and Denisovan hybrid zones in today’s world because when those populations existed, selection did not oppose modern human dispersal and gene flow into their geographic ranges. There’s nothing particularly curious about that in itself. What may seem puzzling is that the expansion of modern humans into these geographic ranges followed several hundred thousand years of existence of Neandertals and Denisovans in those parts of the world.

But it is possible to read too much into the apparent long persistence of the Neandertals and Denisovans. DNA tells us that the Neandertals were a highly structured population during the later part of their existence. Different regions of the Neandertal range contained inbred regional populations with a history of very low gene flow among them. These Neandertal populations were nearly as different from each other as the most different living human groups were in the 1400s. Mitochondrial DNA suggests that the later Neandertals in central and western Europe were not simple descendants of the earlier population of Neandertals there, they may instead have had much more ancestry from the eastern part of the Neandertal range. Neandertals did not persist in Europe so much as they were continually supplanted by other Neandertals. The entry of modern humans may simply have been one more step in a series of partial population replacements.

With this population dynamic unfolding, it would be impossible for a stable hybrid zone to persist for long.

However, that raises a contradiction that we should consider. Ancient DNA shows that human populations were much more strongly differentiated in the Pleistocene than in recent times. Ancient DNA makes it apparent that regional-scale population replacements may have been very common during Pleistocene human evolution. Ancient DNA also shows that Pleistocene human populations were strongly inbred, with little genetic variation compared to recent human populations. How can all three of these observations be true?

In widely-traveled medium-sized mammals like hominins, strong genetic divergence is unlikely to have resulted from strong geographic isolation alone, unless selection helped to maintain it. Strong selection fitting populations to local and regional ecology would explain how regional differences could persist, and yet would also generate demographic replacements when regional climatic, ecological, or cultural factors changed. If selection played a role in generating and maintaining the genetic divergence of these populations, then there probably were hybrid zones among human populations during some parts of the Pleistocene.

I’ll add one observation: Cultural adaptation can allow invasive human populations to attain parity in the face of other human populations with long genetic adaptations to particular ecologies. Many archaeologists have pondered the possible cultural factors underlying the invasion of modern humans. An interesting question is whether cultural differences may have made crucial differences to even earlier population replacements.

References

Hawks, J., & Cochran, G. (2006). Dynamics of adaptive introgression from archaic to modern humans. PaleoAnthropology, 2006, 101-115.

Rhymer, J. M., & Simberloff, D. (1996). Extinction by hybridization and introgression. Annual Review of Ecology and Systematics, 83-109.

Varki, A., 2016. Why are there no persisting hybrids of humans with Denisovans, Neanderthals, or anyone else?. Proceedings of the National Academy of Sciences, 113(17), E2354-E2354.

Bringing together climate and ancient DNA to look at a micro-instance of extinction

Ed Yong describes the results of a cool new study of mammoth extinction on Saint Paul Island, in the Bering Strait between Alaska and Russia: “The Lonely, Thirsty, Final Days of the Doomed Alaskan Mammoths”. The island was once a tiny part of the large Beringia landmass, and when sea levels rose 12,000 years ago, the mammoth population on the island was cut off from the mainland. Mammoths survived there until just under 6000 years ago, long after they became extinct on the mainland. Unlike some areas where the delayed arrival of humans could plausibly explain the later disappearance, in the case of St. Paul there seem to have been no humans until much later.

An interdisciplinary team of scientists looked at a range of climate indicators along with traces of mammoth presence. That included the fungal spores that are tracers of mammoth dung, a method that has already shown the decline of megafauna in North America (the program First Peoples relates Jacqueline Gill’s research on this).

Beth Shapiro, from the University of California, Santa Cruz, searched the samples for traces of mammoth DNA. Meanwhile, Yue Wang and John Williams from the University of Wisconsin, Madison, looked for spores from three fungi that grow in the dung of plant-eating animals. Large extinct beasts like mammoths produced a lot of dung, so scientists can track their disappearance by looking for sudden drops in the levels of these fungal spores.
To the team’s delight, the five lines of evidence—the mammoth remains, the DNA, and the three types of spores—all gave the same answer. They showed that mammoths survived on the island until 5,600 years ago, before finally going extinct. “We were really surprised that it all lined up well,” says Graham. “The nice thing about the cores is that they told us not just when the mammoths went extinct, but all this other information about climate. And that told us what caused the extinction.”

They arrive at the conclusion that salt water wedges coming up into the groundwater as sea levels rose probably drew down the fresh water supply on the island. Mammoths need a lot of water every day, and contributed to their own population decline by degrading the surface ponds, the island’s only water source.

What I like about the study is that the multiple sources of evidence all have a time depth, and the data cover a relatively large proportion of this small island. It’s a great case study of extinction. The reasons for apparent success in this study signal the great difficulty of drawing definitive conclusions for extinction across the vast area of continents, with their diversity of microclimates and habitats.

However, I hesitate on one point. I would not so quickly assume there was never a short or intermittent presence of humans on the island, and that humans may have been involved in the mammoth extinction.


Time magazine reveals that Neandertal genetics can confer a risk of method acting:

So why is Leto so weird? We learn that, based on the results of a genetic test, Leto can claim a rather different gene makeup than most of us. “I have a lot of Neanderthal in me,” he told Rolling Stone. “Maybe that’s why I’m so good at climbing.” Among other things.

That’s from a profile of actor Jared Leto, soon to be on screens as the Joker in Suicide Squad.