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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

The importance of kindness in scientific work

Nature has a “Career Feature” by Kendall Powell recounting a recent scientific meeting in New Zealand meant to promote the idea of kindness in scientific work: “Should we steer clear of the winner-takes-all approach?”

While working on another topic, I was just thinking of how much more valuable kind researchers are. I believe that promoting kind behavior and rewarding cooperation are essential in training the next generation of scientists. In paleoanthropology, we have to break a cycle of bad behavior that existed in the aging population of senior scientists.

One thing that interested me in the linked article is that some researchers recognize the explicit connection between kindness in science and effectiveness within in communities where we work.

This is from James Ataria, a Maori researcher:

Kindness is quite an evocative term, but I see it come through when researchers experience how their work is changing a community. Likewise, from the community’s perspective, being at the decision-making table and co-generating research is empowering, and is a form of kindness. We’ve got these concerns, you’ve got expertise: how can we pair them together? Collaboration with communities can both create conditions for kind science and produce good scientific outcomes.

There is a place in scientific work for healthy, good-spirited competition. Science today is a team sport, and teams work together well when the players have a team spirit. And we need to be making the communities where we work part of the team.

Congress looking to investigate why so much federal grant money has gone to serial sexual harassers and abusers

Two years ago this month, I asked, “Why do universities cover up high-profile harassment? Look for the money”.

Now the U.S. Congress seems to be asking the same question: “Congress Is Demanding Answers About Why Federal Grants Are Given To Harassers In Science”.

The letter asks NIH, NSF, USDA, DOE, and NASA to report: how many cases of sexual harassment or assault have actually been investigated at their agencies; what they do when they receive complaints about a grantee; and whether they require grantees to inform them of allegations of sexual harassment or gender discrimination.

This appears to be a bipartisan request from the House Committee on Science, Space, and Technology. In the field of anthropology, we know enough from the Survey of Academic Fieldwork Experiences study to know that millions of federal dollars have been directed toward field research programs where sexual harassment and assault, bullying, and hazing have been frighteningly routine.

As I wrote last year:

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.

More details about these abuses need to be brought to light.

Are these moustached monkeys a species unto themselves?

I ran across a news article from the BBC by Paul Rincon, about a proposed taxonomic revision to patas monkeys in northeastern Africa: “Moustached monkey is separate species”.

Scientists took a fresh look at the distribution and physical appearance of patas monkeys in Ethiopia, confirming there were two species rather than one.
It was originally described as a separate species in 1862, but was later folded in - incorrectly - with other patas monkeys to form a single species.

This is not “a new species being discovered” as some might expect from a news story. It’s one researcher, Spartaco Gippoliti, who has written a paper presenting some history of the taxonomy of patas monkeys. He suggests that a species name (Erythrocebus poliophaeus), first given in 1862 but later discarded, now be revived to apply to a geographic population of patas monkeys in Ethiopia. The paper is in the journal Primate Conservation and is available online: “On the Taxonomy of Erythrocebus with a Re-evaluation of Erythrocebus poliophaeus (Reichenbach, 1862) from the Blue Nile Region of Sudan and Ethiopia”.

In the paper, Gippoliti refers directly to the possible importance of this species to broader issues of conservation in Ethiopia:

Monkeys of the genus Erythrocebus are potential flagships for important African ecosystems, and may well be at greater risk than is generally believed.

Recognizing more monkey species would cause greater awareness of the threat to regional populations. Patas monkeys are not listed as threatened, but the populations in Ethiopia are at much greater risk than patas monkeys in other parts of Africa.

But is it scientifically valid to name species for conservation reasons?

I don’t want to criticize this specific proposal about patas monkeys. I agree with Gippoliti that scientists need to know a lot more about them, and this is an urgent conservation concern. They should be conserved where they are at risk.

What surprised me when I followed up the original research paper, is just how little evidence it presents about the variation in patas monkeys and how this population compares to other patas monkey populations.

Truth is, I’ve become accustomed to seeing genetic evidence about population divergences. Most recent papers that claim evidence to support a novel distinction at the species level between primate populations include some evidence about genetic variation within and between populations. Genetic evidence is valuable because it can demonstrate that populations have been evolving along separate trajectories with little gene flow between them for a long time.

That’s not to say that genetic data is always sufficient to establish that a species is valid. Even large genetic differences may not be enough demonstrate that speciation has taken place between two populations. Two populations may exchange genes rarely, yet often enough to prevent the evolution of reduced hybrid fertility or viability.

The paper does discuss coat and skin coloration as evidence for a distinction. But it doesn’t present evidence about the variation of these traits in either population, nor does it present other morphological data about their variation. Mainly, the paper presents a case that scientists don’t know enough about the patas monkey variation.

Considering the geographic separation and distinctive external appearance, I have no hesitation in considering poliophaeus to be a distinct species. Its closest taxon in appearance seems to be baumstarki, for which species’ status is also warranted. The recognition of these patas monkeys as species, highlights the need for field surveys to assess their geographic range and conservation status in both Ethiopia and Sudan.

To me, this is a very sharp example of the old debate between splitters and lumpers as applied to conservation.

Gippoliti discusses the history of the naming of these monkeys, and suggests that prior workers who lumped the monkey populations may have been overly influenced toward lumping them together, by variation and developmental changes to the skin color and coat changes. For him, the geographic separation and differences in appearance are enough to justify a separate species designation.

My philosophical inclination is toward lumping groups together, and recognizing geographic variation below the level of species. Occasional gene flow between genetically differentiated groups has been important to the evolution of ancient humans and other primates. Since long-range gene flow can make such a difference to adaptation within species, and since it has happened so often, I’m inclined to be conservative in naming such groups. Ideally, I’d like have some evidence of reduced fertility before recognizing them as different species.

Yet biologists have come to accept more and more that hybridization and introgression between populations are common in mammal evolution, even when hybrids have reduced fertility. Speciation is much less of a barrier to adaptive gene flow than biologists once assumed.

For those of us who care about the mechanism of adaptation and the particular history of adaptation in hominins, that makes species names much less important than they once seemed. Morphological traits don’t predict evolutionary potential in the way many anthropologists used to think.

For scientists who are deeply engaged in conservation biology, species names make a lot more difference.

Still, with genetics, we’ve become accustomed to having actual data on diversity, rather than the often-subjective assessments of taxonomists. Hopefully some further genetic information from patas monkeys will help to clarify the variation in these populations.

UPDATE (2018-01-19): Reflecting on this, I realized what is bothering me about this instance. We should have many more short papers discussing the history of taxonomies and their problems matching current data on species’ natural distributions. That’s helpful to advancing new data collection and research. I learned a lot about patas monkeys from this paper I didn’t know.

But those kinds of papers, lacking any new empirical data, should not be trumpeted in the press as “discoveries”.

Scientific discussion about species is valuable, and recognizing underappreciated diversity can advance conservation goals. But when a data-free paper is reported in the press as a “discovery of a new primate species”, it damages the credibility of conservation efforts. Such publicity makes it appear that scientific judgments about species are merely arbitrary, motivated by politics and not data.

Linking out to a book review on sociogenomics

The journal Nature has a review of the new book, Social by Nature: The Promise and Peril of Sociogenomics, by Catherine Bliss. The review is written by Nathaniel Comfort: “Nature still battles nurture in the haunting world of social genomics”.

After reading the review I plan to read the book and bring some of this topic into my genetics course this semester.

Comfort’s review presents Bliss’ book as a critical survey of work in social genomics. I can’t assess from Comfort’s review whether the book is really accurate about the genomics research that it describes, and that’s my main interest.

That’s because a historian of science writing about a sociologist uses a hecka lot of jargon.

For instance, the “genomic gaze”:

What the historian Andrew Hogan has called the “genomic gaze” isn’t the fault of individual bad-guy researchers: it’s structural. Bliss is careful to acknowledge the good, even noble intentions of many of the scientists she spoke to (as a sociologist, she keeps the names of her ‘informants’ confidential). But she finds that the funding and publicity mechanisms integral to biology drive it towards genes-first explanations. The stakes are high: finding an SNP associated with a risk increase from 0.01% to 0.03% (a threefold rise) for a disease such as breast cancer could make a career. “While researchers do not intend to lift the focus off of the environment,” Bliss writes, “they are forced to recast social phenomena as ‘evolutionary phenotypes’ so that they can make scientific claims” that sound relevant to biomedical funders.

It seems like sociologists always disappoint me when they talk about the motivations of geneticists. “Finding a SNP” is hardly likely to “make a career” these days.

To be sure, like other areas of science, genetics has a publication bias toward positive findings. But during the last fifteen years genomics has raised the standard of evidence necessary to publish positive associations. A good discussion of this subject would describe the candidate gene approach, still heavily used in some areas of behavior genetics. The candidate gene approach has been strongly criticized within genomics, as genome-wide association studies demand vastly larger sample sizes and result in stronger evidence of association.

This is relevant because today many of the most interesting findings in human behavior genetics are coming from large GWAS-scale samples of tens or hundreds of thousands of research subjects.

The paragraph I’ve selected from Comfort’s review uses as its example a fictitious example chosen to illustrate a very small effect size (“a risk increase from 0.01% to 0.03%”). But “breast cancer” is a pretty poor fit to this fiction. The lifetime incidence of breast cancer in women in the U.S. today is more than 12 percent, three orders of magnitude higher!

Numbers matter. A risk of 0.02% is two cases in every ten thousand people. A study of a candidate gene with 80% power to find a significant difference between 0.01% and 0.03% would have more than 60,000 cases and controls. Geneticists who study rare disorders that actually have such low incidences make extensive use of pedigree data to find genetic regions of interest. Finding a genetic influence so small out of a genome-wide association study is not statistically credible.

In other words, if it seems ridiculous to focus on such a small difference, that’s because the contrived example is nonsensical.

Comfort’s general point has some truth to it. Human genomics has led to the discovery of many genetic variations that have small effects on traits. The “one gene one trait” model, such a wide misconception among the public, is wrong. Meanwhile, the best summaries of genetic associations today still leave a large fraction of heritable variation unexplained.

But those issues have been advanced by professional geneticists, not sociologists. During the last year, one of the most important theoretical questions in quantitative genomics has been whether such small effect size mutations actually matter to anything. They may simply be evolutionary noise. And still, the variation in many human traits is the sum of hundreds of such small genetic effects. Those genetic effects make people different from each other. Some of them seem to have been targets of natural selection in the last couple of generations.

I’ll be reading Bliss’ book carefully to see how she describes the results of behavior genomics. Also I’m curious to see how she describes the origin of the term, “sociogenomics”. It’s not one I’d ever heard before seeing this review.

UPDATE (2018-01-17): As I was writing this, I saw a tweetstream by Jeremy Freese, a social scientist who is quoted in the book. He notes numerous apparent errors of fact in the text, from misspelled names and incorrect dates, to paraphrases of quotes that differ from their sources.

I have no further information but it is a point of concern.

When genomic ancestry tests lead to confusion

An article in Gizmodo by Kristen Brown asks an uncomfortable question about today’s proliferating genomic ancestry industry: “How DNA Testing Botched My Family’s Heritage, and Probably Yours, Too”.

Her family thought their ancestry was mostly Syrian, and they were surprised to get a very different assortment of results from different genome tests for ancestry. That’s not unusual, it happens a lot.

Brown accentuates the explanation that the tests seem to work better for people with predominantly European ancestry because the comparative samples are much larger and pose a limited set of problems compared to other regions.

In my opinion, that’s really not true; it’s just that the issues appear on a different scale. People who derive their ancestry from different parts of Europe are often given results that don’t correspond to their genealogical history.

The article does a good job of discussing the way that people’s expectations of these tests doesn’t match what the scientists are trying to provide.

A big problem is that many of us have a basic misunderstanding of what exactly we’re reading when Ancestry or 23andMe or National Geographic sends us colorful infographics about how British or Irish or Scandinavian we are. It’s not that the science is bad. It’s that it’s inherently imperfect, an estimation based on how much our DNA matches up with people in other places around the world, in a world where people have been mixing and matching and getting it on since the beginning of human history.

But right now the science really is bad.

To me, the great promise of personal genomics is that people can advance the science by engaging with their place in this history. Naturally people are most interested in their own places in the human genealogical web. Anyone can be forgiven if they see this genealogical web as a tree of populations with names like French, German, Italian, or Hausa, Bengal, or Syrian.

So a person’s place in the history seems like it should be some combination of these names, like a pedigree.

It’s very easy for genetics to deliver a combination of names. Trouble is, a single combination of genes may map pretty closely to several different combinations of population names.

Geneticists study samples of human genomes from many different parts of the world as a basis for these ancestry assessments. Those samples of human genomes are simply too small in most regions of the world and most ethnic groups. As much as we know, we are still learning about how today’s groups have originated, and today’s nation-states have come together from ethnic groups in many different ways.

Samples are of adequate size in much of Europe, but still, humans across hundreds of years have not behaved in ways that make it easy to reliably apportion ancestry into geographic bins.

In other words, our knowledge of recent human genetic history is a work in progress. Any one individual’s place in recent history is contingent on the whole story. We know some parts better than others, but even the well-traveled parts of human genetic history have hidden chapters.

Populations did sort of behave like a tree during much of human prehistory–but a tree with millions of interconnections between branches. Anthropologists and geneticists are trying to reconstruct that tree with greater accuracy. They are also using ancient DNA to rediscover branches that are missing from conventional histories.

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

Even though individuals belonged to populations, the genealogies of individuals do not reduce well to a tree of populations. Populations are loosely defined by swarms of individuals with similar genealogies for a few hundred years. Any one individual’s genealogy may diverge quickly from the mainstream of the swarm.

I’d like to promote a broader view of genealogy, one that celebrates the differences between individuals and the populations that some of their ancestors identified with. That has more genetic reality than the alternative, in which people are defined into hardened populations.

See also: “The surprising connectedness of human genealogies over centuries”

Link: Gendered academic space in political science

Macartan Humphreys, of Columbia University, has written a short essay on “Gender discrimination in political science and the problem of poor allies”. It begins with a personal story, then moves into broader issues in his field of political science.

Looking back I think I found it easy to explain things away because at bottom I thought of myself as someone who does not discriminate and so there must be reasonable explanations for things that others might see as discrimination.
With quite a bit of distance though I can see problems with my self explanations.

These are important issues to be conscious of.

Link: On the importance of altruism in starting academic careers

Jenny Martin has recounted a personal story about her first highly cited paper, which followed an altruistic decision from her postdoctoral supervisor, and includes a nice tribute to the late Ben Barres: “selfless in seattle”

Actually, this post has nothing to do with Seattle. I just liked the title. The theme, eventually, is science leadership through altruism. But to get there, first I need to relate a story that has been on my mind the past week or two.

It’s a good story, and a good lesson about the sources of discoveries.

Testing the sex of ancient individuals from their enamel proteins

A recent paper by Nicolas Stewart and colleagues presents a way to determine the sex of ancient individuals by examining the composition of their tooth enamel: “Sex determination of human remains from peptides in tooth enamel”.

Amelogenin is a protein component of tooth enamel. Humans have two different genes for amelogenin, AMELX on the X chromosome, and AMELY on the Y chromosome. The protein products of these genes have slightly different amino acid sequences. Enamel from males, who have both X and Y chromosomes, has a mix of the two proteins, while females have only the AMELX product.

Stewart and coworkers etch the ancient enamel with an acid, freeing protein fragments, or peptides. They use a mass spectrometer to detect the signatures of the Y chromosome and X chromosome specific peptide variations.

The ability to determine the sex of infant and juvenile remains completely revolutionizes studies of growth, child care, epidemiology, and demography in the past. For the first time, it will allow osteologists to examine sex-specific cultural treatment and differentiate between the health of boys and girls, as well as sex-specific growth trajectories and past developmental milestones, such as age of puberty and subsequent repercussions for fertility. Sites with poor preservation are common in archaeological contexts, and at such sites teeth generally survive better than bone, and thus sex can be established for adults as well as juvenile skeletons in the absence of key skeletal identifiers. In addition, the dimorphic peptide sequence is identical in apes (Fig. S1) and so should be present in all hominins.

This is potentially very important for a number of questions that cannot be answered from archaeological sites without direct evidence of sex. The sex of young children in particular is almost impossible to establish reliably from skeletal indicators. In some recent contexts, sex can be inferred from grave goods or from inscriptions. But for most ancient people–including Neandertals and other Paleolithic populations–the sex of young children is unknown.

Amelogenin has previously been used as a forensic sex determination test in humans and in other mammal species. In humans, this test fails to identify males a small fraction of the time because the Y chromosome sometimes has large deletions that include the Y amelogenin (AMELY) gene. That implies that a small fraction of misidentification (biased toward misidentifying males as females) should result from this test applied to ancient samples.

It’s not known whether this difference between males and females has any functional consequences for enamel. Some researchers have been interested in whether the presence of an additional amelogenin variant in males might influence caries. In some populations, females are more likely to have caries than males. The AMELY protein makes up only around 10 percent of the total amelogenin in a tooth, as the Y chromosome version of the gene is not expressed as highly as the X version, but the presence of an alternative form of the protein might make some difference. However, it is very hard to test whether sex-specific life history traits, such as diet differences during development, pregnancy, or other environmental factors, might instead lead to a difference in caries risk.

At any rate, caries incidence was very, very low during most of our evolutionary history compared to the past 20,000 years (and is low in nearly all other mammals). The amelogenin in both sexes did its job pretty well for most of our existence.

Reference

Stewart, N. A., Gerlach, R. F., Gowland, R. L., Gron, K. J., & Montgomery, J. (2017). Sex determination of human remains from peptides in tooth enamel. Proceedings of the National Academy of Sciences, 114(52), 13649-13654.

Link: Article on changing perspectives on Neandertals

A couple of years ago I pointed to a news article about archaeological work at Descubierta Cave, Spain: “Link: Neandertal burial ritual with antler hearths”. Last year Juan-Luis Arsuaga and coworkers presented on the work at the European Society for Human Evolution conference.

It sounds like a very interesting case because of the overall context – human remains, with nearby small hearths, horn cores and antlers of numerous animals.

Sandra Ackerman has written an article for American Scientist that reports on the conference talk, as well as other recent work on Neandertals: “Neanderthals Reenvisioned”.

How to explain such a bizarre assemblage? In a presentation at the conference, Arsuaga laid out his research team’s reasoning: “This association could have been produced by chance, but we consider this improbable, given the preponderance of horns; also, the presence of fire points to an anthropogenic origin.” He continued, “Could it have been subsistence? There is no evidence of human consumption.” As another possibility, it might perhaps have been functional—but we know Neanderthals didn´t use organic substances such as horn, antler, or bone as raw material for implements or ornaments. Moreover, there’s no evidence, such as partly worked bones or a concentration of bone fragments, to indicate that this was a site of industry. To the researchers who discovered them, these carefully arranged horns and skulls looked almost like modern-day hunting trophies. Indeed, at 40,000 to 45,000 years old, Descubierta Cave may contain “possibly the strongest evidence yet for symbolic behavior in Neanderthals,” Arsuaga concludes—although, he says, alternative explanations are welcome.

I’ll be looking forward to hearing more about these discoveries.

Is this better evidence for symbolic culture than the long record of ornaments made and worn by Neandertals? How we answer that question depends on the fine details of defining “symbolic culture”.

A site described as Descubierta has been described has tremendous potential information about cultural ritual. An ornament carries similar information about repeated visual communication. These are different things, and they may inform about different cultural abilities. They certainly inform us about different cultural functions.

I don’t want to minimize the other aspects of the American Scientist article, including the great shout-out to the work of Zenobia Jacobs on dating some of these sites with luminescence methods.

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?”