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john hawks weblog

paleoanthropology, genetics and evolution

Photo Credit: Dental chipping in Homo naledi. Ian Towle and colleagues

Darwin Day in St. Louis

Next Saturday, February 9, I will be in St. Louis speaking at the Darwin Day event at Washington University: “Institute for School Partnership: 2019 Darwin Day Celebration”.

DATE: Saturday, February 9, 2019
TIME: Registration & continental breakfast 8 am. Program 8:25 am to 1:00 pm
LOCATION: Room 202, Life Sciences Building, Washington University Danforth Campus

If you’re in the St. Louis area and interested in evolution, it should be a great event. I’ll be talking about “New discoveries and insights into our African origins”.

Family Tree DNA database now available to FBI investigators

Salvador Hernandez reports for Buzzfeed that Family Tree DNA has now opened its database of genetic information from more than a million users to the FBI: “One Of The Biggest At-Home DNA Testing Companies Is Working With The FBI”.

In December 2018, the company changed its terms of service to allow law enforcement to use the database to identify suspects of “a violent crime” such as homicide or sexual assault, and to identify the remains of a victim.
In a statement, Bennett Greenspan, the president and founder of Gene-by-Gene, Family Tree's parent company, said the firm would not be violating its terms of privacy to its customers, despite the FBI's access.
"We came to the conclusion that if law enforcement created accounts, with the same level of access to the database as the standard FamilyTreeDNA user, they would not be violating user privacy and confidentiality," Greenspan said.

That’s a devious interpretation of the terms of service. Since anyone can upload data to the service, it is probably already true that people have uploaded genome data that doesn’t belong to them. It might therefore have been trivial for the FBI to work within the Family Tree DNA service even without any formal permission from the company.

Then again, here’s a shot from the company’s current website:

Family Tree DNA privacy promise

Hmmm….

How worried about this should anyone be?

When it comes to it, the science is clear that once a critical number of people have voluntarily shared their genome data, essentially every individual will have a third cousin or closer relative in the database. Crimes today are being solved not because criminals themselves have uploaded their data, but because their distant relatives have done so.

With more than a million individuals, the Family Tree DNA database kickstarts that process. It’s a larger dataset than the public ones that law enforcement agencies used last year to catch the Golden State Killer and others.

Family Tree DNA is not, however, unique or essential to the process. I don’t think there’s much question that a million people in the U.S. would voluntarily provide their genomes to a law enforcement database if it were marketed to them. “Help us catch the killers!” It really wouldn’t take much more than that, and the government could have its own version. Or the present freely available upload sites would just have to grow larger, which they already are on track to do.

Such databases have different blind spots, since genealogy buffs contribute their DNA for different reasons than the genome neighborhood watch. But we are inevitably within a couple of years of law enforcement being able to track down a third cousin of any genetic sample they collect.

In light of this inevitability, it would be wise for the FBI and government to think carefully about how they want citizens to participate in the process. The Family Tree DNA process today requires issuing a warrant to obtain information about distant relatives of a suspect DNA sample.

I think it is unwise to create a situation where courts are issuing such warrants to distant relatives solely because of partial DNA matches. It’s entirely avoidable by relying upon people who actually volunteer to help authorities search for criminal matches.

None of these tactical issues adjust the underlying reality: We are very near the point when every individual will be identifiable through DNA matches, even if that individual has not contributed his or her own DNA samples to any database.

NSF grants track language used in abstracts

Hmm… this is interesting from David Markowitz: “Text analysis of thousands of grant abstracts shows that writing style matters”.

Two other results were telling about the NSF data. First, using fewer common words was associated with receiving more award funding, which is inconsistent with the NSF’s call and commitment to plain writing.
Second, the amount of award funding was related to the writing style of the grant. Prior evidence suggests that we can infer social and psychological traits about people, such as intelligence, from small “junk” words called function words. High rates of articles and prepositions, for example, indicate complex thinking, while high rates of storytelling words such as pronouns indicate simpler thinking.
NSF grant abstracts with a simpler style – that is, grant abstracts that were written as a story with many pronouns – tend to receive more money. A personal touch may simplify the science and can make it relatable.

Correlation is not causation, standard exceptions apply, your mileage may vary.

Genomes and the complicated history of baboons

Today, Science Advances has released a paper by Jeffrey Rogers and coworkers on the genome diversity of six species of baboons: “The comparative genomics and complex population history of Papio baboons”.

This paper represents a significant advance in scientific knowledge of the history and evolution of baboons across Africa. The genus Papio arose around the same time as our own genus, Homo, and the diversity of baboons across Africa today reflects a history of divergence and mixture during the last million years.

Our team pointed to an earlier stage of knowledge of baboon population history in our 2017 paper, Homo naledi and Pleistocene hominin evolution in subequatorial Africa”. Our interest has been the geographic distribution of Homo species in Africa, in light of the occurrence of H. naledi in the later Middle Pleistocene.

Anthropologists have recognized baboons as a very relevant comparison to hominins for more than a hundred years, and in particular the work of Clifford Jolly has focused upon baboon population differences as useful models for the adaptive differences that may have separated ancient hominins. I wrote about Jolly’s perspectives on hybrid zones and introgression in baboons back in 2005: “Look to the baboons; there will you your insights find!”

Baboons of course are not alone as relevant comparisons to hominins. Carnivores and ungulates both show some similar biogeographic patterns to baboons, at least based upon mitochondrial DNA variation. But the whole-genome analysis of these species within Africa is only beginning. So getting a clear whole-genome picture of baboon population history is one of the first views of species that lived in the same habitats as ancient humans.

First, a quick introduction to baboon species. There are six of them:

  1. Papio papio in extreme west Africa,
  2. Papio anubis across most of the Sahel to Sudan and Ethiopia, and from there south into the Lake Tanganyika area,
  3. Papio hamadryas in Eritrea, the Afar region, and across the Red Sea in the Arabian Peninsula,
  4. Papio cynocephalus on the eastern coast of Africa from Somalia to Mozambique,
  5. Papio kindae from Angola to Zambia, and
  6. Papio ursinus in southern Africa.
Map showing geographic distribution of six species of baboons in Africa from Rogers et al. 2019

Rogers and coworkers looked at the genomes of a total of 17 baboons, which represented “2 to 4 individuals” from each of the 6 species. This was not a sample chosen to probe geographic diversity within each species. Only two individuals (both from the Aberdare region of Kenya) were chosen to examine historically recent hybridization and introgression. So it is a very restricted picture of variation, and that is important to keep in mind when trying to make sense of the phylogenetic inferences in the paper.

The study provides a composite tree giving a topology for the relationships of the six species as well as approximate times when they diversified:

Baboon composite phylogeny from Rogers et al. 2019

The main features of this picture include:

  1. A primary split between northern (P. hamadryas, P. anubis and P. papio) and southern (P. cynocephalus and P. ursinus) lineages around 1.4 million years ago.
  2. A subsequent hybridization of a northern and southern branch to form P. kindae. Neither of these branches is closely aligned with any of the other five extant lineages.
  3. A ghost lineage from the base of the genus contributing around 10% of the ancestry of P. papio.
  4. The speciation of today’s species date to between around 400,000 and 800,000 years ago, with the exception of the hybrid origin of P. kindae which was within the last 100,000 years.

These events were sketched out using f-statistics and the CoalHMM software, both of which have been used for hominins as well as chimpanzees and gorillas, so this tree is very comparable to the tree presented for chimpanzees and bonobos by de Manuel and coworkers (2016), for example.

Additional analyses in the paper look at phylogeny using different methods, including Bayesian and parsimony phylogenetic analyses. These give rise to various results that are mostly unreconcilable, and it’s not obvious to me that they add anything to the paper, since none of them are capable of handling the degree of mixture that the f-statistics infer for P. kindae.

The big limitation of the study is the lack of geographic coverage of variation within each species. The small sample size should give rise to more tree-like phylogenetic results than a broader sample. The same is true of ancient hominin genomes: We have only a handful of ancient genomes, and the results are very treelike. But the introgression from Neanderthals and Denisovans in living people samples a broader number of populations from these groups and is not so simply treelike as the high-coverage ancient genomes themselves.

So I think we still have a way to go to really understand the importance of hybridization in the ancestry of today’s baboons.

A hint of upcoming results comes from the two Kenya individuals of P. anubis examined in the study. Both individuals reflect historically recent introgression from P. cynocephalus. The passage describing this is very interesting:

Our results also shed new light on the historical dynamics of hybridization between P. anubis (a northern clade species) and P. cynocephalus (a southern clade species), which has previously been reported in southern Kenya near Amboseli National Park (17). Behavioral observations and microsatellite-based analyses support recent introgression from P. anubis into P. cynocephalus since the 1980s (25, 26). Our analysis of genome-wide haplotype block sharing indicates that a P. anubis individual from the Aberdare region of Kenya, more than 200 km north of Amboseli, is also admixed with P. cynocephalus, carrying ~546 Mb of nuclear DNA derived from P. cynocephalus (fig. S7). If we assume that this resulted from a single admixture event, then it is estimated to have occurred about 21 generations (~220 years) ago. However, other more complex explanations are also possible. The second individual from the P. anubis Aberdare population also carries P. cynocephalus haplotypes, but these shared genomic segments are fewer and shorter and likely result from more ancient introgression. Consistent with other studies (27), our findings suggest that there have been multiple episodes of gene flow involving these two species over a considerable time span and that the effects of past hybridization extend far beyond the current hybrid zone. This complexity may well be representative of the complexity of other known baboon hybrid zones (10, 12, 15, 18, 19, 28).

The heterogeneity between two individuals in the same population with respect to recent introgression is really striking. These two genomes emphasize that the movement of individuals and spread of genes between two hybridizing species are more of a turbulent interface than a smooth cline. We have a hint of this turbulent interface in the Oase genome results from Romania, an individual with a high and recent degree of Neanderthal ancestry.

The taxonomy of baboons seems to be relatively stable now. Twenty years ago, there was substantial debate about how many species should be recognized across Africa. At that time much less was known about the reproductive fitness of hybrids. Jolly (2001) emphasized the “indiscriminate” hybridization of different populations of baboons in captivity :

In captivity, all allotaxa appear to hybridize indiscriminately (Jolly, unpublished data), and there is no evidence for hybrid breakdown, behavioral incompatibility, or intrinsic sterility. Similarly, there is no evidence that Papio, baboon allotaxa ever avoid interbreeding when they meet in the wild, though many boundary areas have yet to be investigated. The fact that documented baboon hybrid zones are narrow, in spite of the lack of obvious, intrinsic barriers to gene-flow, strongly suggests that they are the result of secondary contact following range oscillations (Barton and Hewitt, 1985; Hewitt, 2001; Harrison, 1993).

The current story is very different from Jolly’s (2001) account. As discussed by Rogers and coworkers, scientists have observed a number of indications that hybridization among species of baboons is not fitness neutral.

Another topic of broad interest is the origin of reproductive isolation among incipient species (1). One expectation for the genus Papio is that, given the timing of the radiation and the degree of morphological and behavioral differentiation among species, incipient barriers to gene flow may be evident between some pairs of species. Studies of the present-day hybrid zone between northern clade P. anubis and southern clade P. cynocephalus find no readily apparent barriers to reproduction between these species (17, 26). However, studies of captive P. anubis × P. cynocephalus hybrids document significantly elevated frequencies of craniodental anomalies in hybrids, especially hybrid males, indicating some degree of genetic incompatibility (39). Field studies of the hybrid zone between P. ursinus and P. kindae describe a deficit of hybrid individuals carrying Y chromosomes from P. ursinus and mtDNA from P. kindae compared to the converse (18). This suggests that when hybridization began between these two forms, some type of barrier (premating or postmating) reduced the frequency or fertility of matings by male P. ursinus with female P. kindae, while the converse mating type was more successful (18). Last, P. anubis and P. hamadryas differ substantially in their social organization and social structure (11, 28, 40). Among anubis baboons, both males and females are polygamous. Hamadryas societies are multi-level, with “harem”-like, one-male breeding units (OMUs) as basal social entities. In these OMUs, the single adult male defends exclusive access to one or more adult females. Other differences in sex-specific dispersal and social relationships are also observed (11). Despite the dramatic differences in social systems, these species hybridize in the wild (28). Hybrid males can achieve substantial reproductive success, at least in groups consisting mainly of hybrids (19). There is no clear evidence for a barrier to gene flow between the species, although the geographic distribution of phenotypically recognizable hybrids is narrow.

The various regional populations of chimpanzees (Pan troglodytes) are classified as subspecies, and they originated across roughly the same time span as these species of baboons. Chimpanzee regional populations do not exhibit the same variation in mating system, coat coloration, and morphology as baboons. So there is a good phylogenetic species concept (PSC) argument for baboons being different species that is not there for chimpanzees. Meanwhile, the observations noted by Rogers and colleagues are evidence that the baboon species should be recognized under the biological species concept (BSC). Chimpanzees and bonobos are different species under both BSC and PSC criteria, but neither concept suggests that the various subspecies of chimpanzees should be recognized as species instead.

The divergence among Neanderthals, Denisovans, and African ancestors of modern humans also took place across approximately the same time period, around 600,000–700,000 years. With both chimpanzees and Neanderthals, there is evidence for occasional introgression of genes among the ancient populations.

Aside from recent hybridization and the possible “ghost lineage” contributing to P. papio, the baboon picture of ancient gene flow is not clear from the results presented by Rogers and colleagues. The mismatches among Bayesian and parsimony phylogenetic results, and the different results obtained by looking at Alu insertion data, all suggest that incomplete lineage sorting or ancient reticulations may have been very important to the baboon pattern of variation.

To summarize, this paper provides important new data about the divergence of baboon species. Much more data would be valuable, especially samples that would tell us more about the geographic variation within baboon species and the long-term record of hybridization and introgression at the boundaries of these species.

Link: Wired on the legacy of Jim Watson

A fascinating read in Wired by C. Brandon Ogbunu: “James Watson and the insidiousness of scientific racism”.

That one person separates me, an African-American computational biologist, from James Watson—Nobel Laureate and mouthpiece of racist opinions—presents a quandary. For years, I have reveled in the powers of DNA, yet one of the people most associated with its discovery has made abhorrent comments about my race. The dilemma raises several questions: How does it feel to be a black scientist who owes much to James Watson in general, and in my case, is linked to his specific pedigree? Is it much ado about nothing, or might the black scientist occupy a special place in modern conversations about scientific racism?

I like the final thought experiment.

Link: How accurate are age-at-death estimates for older adults?

IEEE Spectrum covers a new research study looking at the accuracy of a method for determining the age-at-death of skeletal remains: “Errors Found in Forensic Software Meant to Assess Age-of-Death of Skeletal Remains”.

Research conducted by biological forensic scientists at North Carolina State University and the University of South Florida has uncovered “serious problems” in a recently released forensic software application available online called DXAGE that is supposed to predict the age-at-death of skeletal remains based on bone mineral density.
The study, published in the Journal of Forensic Sciences, reported that the software’s predicted ages could be off by 14.25 years on average when DXAGE-generated results were compared against known samples. The system’s accuracy was particularly poor for the remains of elderly individuals.

Since the software does nothing more than apply a set of algorithms to observations taken on bone, its results can be no better or worse than the variability of age-related changes in bone. That variability is really big! Biological anthropologists recognize that we cannot accurately estimate the age of older individuals, errors of 15-20 years on age estimates are very common.

So my reaction to this story is, “How did a method for age-at-death estimation that made claims of greater accuracy get started in the first place?”

It is just misleading to think that software gives better accuracy than an expert armed with the same statistics. It’s the white coat phenomenon. Unfortunately, the misperception of “computer precision” has huge influence on juries.

Bone mineral density changes are an interesting consequence of aging, and they have been the topic of some debate as applied to the ages of Neanderthals and other prehistoric people. When we look at ancient populations, there are the possibility of nutritional differences, lifestyle differences, and genetic differences that may have influenced both the peak bone density and the pattern of age-related bone loss.

All these are reasons why we cannot be very definitive about the age-at-death of most older adults in the fossil record. Once they have progressed to a point far enough beyond third molar eruption that tooth wear is not an accurate indicator of age, there are few biological indicators that would not also vary across populations for many reasons.

'Stand Up Science' in Madison Tuesday, January 29

On Tuesday evening, January 29, I’ll be taking part in a show at Comedy on State here in Madison, with comedian Shane Mauss: “Stand-up comedians + scientists = Stand Up Science”.

Award-winning stand-up comedian and science podcast host Shane Mauss presents Stand Up Science!
Learn and laugh as local scientists, comedians and other special guests join Shane to bring you an unforgettable 2 hour show that is equal parts ahas and hahas
Stand-up comedy and science have a lot in common. They both reveal truth, change our perceptions, and challenge the status quo. So why are they so underappreciated? Admittedly, comedy sometimes underestimates the intelligence of their audience, catering to the lowest common denominator. And science has the stigma of being overly complicated, unrelatable or boring. Until now.

Should be a fun evening, and if you’re in Madison, you should check it out!

Will biological anthropologists start publishing in American Anthropologist again?

Adam Van Arsdale and Mary Shenk put out a call in American Anthropologist for more biological anthropologists to submit their work to American Anthropologist: “Biological and Evolutionary Perspectives in American Anthropologist: An Editorial Provocation”.

As sections of AAA, the Biological Anthropology section and the Evolutionary Anthropology section have seen declining membership over the past decade, collectively representing fewer than six hundred active members. This decline can be seen within the pages of American Anthropologist as well. Ironically, the past two biological anthropology year‐in‐review pieces published in the journal (Gokcumen 2018; Nelson 2017) cite a total of just three articles published in American Anthropologist, two of which are themselves reflections of the kind of mixture of introspection and identity crisis that have come to dominate many of the conversations around biological anthropology's place within anthropology since the time of Boas: a copy of Alan Goodman's AAA presidential address, “Bringing Culture into Human Biology and Biology Back into Anthropology” (2013), and Wiley and Cullin's “What Do Anthropologists Mean When They Use the Term Biocultural?” (2016).

During the 1990s, American Anthropologist published some of the most important papers on modern human origins. I’m proud of my 2003 article in the journal that reviewed this history, which was an important contribution to my early career record. It was especially neat to have this article included in the “virtual issue” last fall, “Genetics, Biology, and Race: Understanding Human Difference”.

With that kind of innovative publishing, the journal has a chance of recovering some of the attention of biological anthropologists. It’s a pity that the American Anthropological Association has not taken the chance to move this journal to an open access policy, but I can’t see it being very long before that change happens.

Link: The academic battles of ancient DNA

This week the talk of archaeology and human genetics is a long feature article in the New York Times Magazine about the academic struggles of ancient DNA: “Is Ancient DNA Research Revealing New Truths — or Falling Into Old Traps?”

Of course the answer to the title question is, “Both”. Ancient DNA evidence has generated enormous advances in our understanding of past human societies, and the relationships of present-day peoples.

The author of the article, Gideon Lewis-Kraus, gives the broad context of the science for readers who haven’t been following advances closely. He also focuses on a recent series of papers looking at the population genetics and ancestry of people in Vanuatu. So there is the intersection of studying the ancestral bones of people who are not represented in industrialized DNA labs, the rivalry between competing labs who are publishing on other archaeological samples addressing the same “big questions” about the peopling of the Pacific, and the complex interactions between archaeologists and geneticists in their attempts to understand the past.

It is a long article with much complexity.

I want to quote a passage from the middle, which helps to explain why David Reich has become such a focus of attention and controversy in this field. It is the avowed establishment of a “factory” approach:

So in 2013, Reich, along with a veteran of Paabo’s lab and a longtime mathematician collaborator, retooled his shop at Harvard Medical School as one of the country’s first dedicated ancient-DNA labs. The idea, he writes in his book, “was to make ancient DNA industrial — to build an American-style genomics factory” that would liberate such fields as archaeology, history and anthropology from hitherto insoluble debates.
He was more successful than even he anticipated. By the end of 2010, only five ancient genomes had been sequenced in total, but in 2014, 38 were done in one year. Soon the number will be close to 2,000. Reich’s lab alone is responsible for at least half of the published output, which doesn’t include some 5,500 more bones in the process of being analyzed and 3,000 more in storage. “Ancient DNA and the genome revolution,” he declares in his book’s introductory overture, “can now answer a previously unresolvable question about the deep past: the question of what happened.

I have many thoughts about the current state of this field. I think it has gone too far in destroying bone samples that are irreplaceable, and it has done so in a way that is unsustaintable in scientific terms.

Using the language of industrial processes is appropriate. In ten years, the factory will be outmoded, the resource depleted, and scientists who remain genuinely interested in broadening participation in understanding ancient people will be picking up the pieces. Maybe there will be a new factory.

It will take me some time to write up those thoughts in a more concrete way.

In the meantime, the one thing that disturbs me the most about this article, which I have pointed out on Twitter, is the sheer number of scientists who were willing to give insight on this field, but who requested to remain anonymous.

There thus reigns, in the world of ancient DNA, an atmosphere of intense suspicion, anxiety and paranoia, among archaeologists and geneticists alike. In dozens of interviews with practitioners of both disciplines, almost everyone requested anonymity for fear of professional reprisal. Many archaeologists described a “smash and grab” culture in which hopeful co-authors source their bones by any means necessary. Among teams at work on any given excavation, it takes only a single colleague to deliver a bone to one of the industrial giants for the entire group to lose control of their findings. Museums, too, are being swept up by the perverse incentives: One of the geneticists told me stories about having brokered an agreement to sample a particular collection, only to arrive and discover that someone else showed up the previous day to claim the same bones under a false pretense. The weaker the institutions of the country, the harder it is for local researchers to have a fighting chance. Scientists in Turkey and Mexico told me that museum curators routinely had to explain that they had promised their native bone collections elsewhere. As one ancient-DNA researcher in Turkey put it to me, “Certain geneticists see the rest of world as the 19th-century colonialists saw Africa — as raw-material opportunities and nothing else.”

I want to be clear. This passage describes my experience of this field. I also personally know dozens of archaeologists and geneticists working with ancient DNA who share this experience.

How capable were early hominins of crossing water?

Last summer I published a piece on Medium about the possible ancient existence of hominins on Luzon: “This is where scientists may find the next hobbits”.

For people who may not be familiar with this story yet, a study in Nature last year by Ingicco and colleagues (http://dx.doi.org/10.1038/s41586-018-0072-8) reports on the butchered remains of an ancient rhinoceros from a place called Kalinga, on the island of Luzon. The bones have cutmarks and at least one percussion mark, and were found with some stone flakes, and one hammerstone. The remains are around 700,000 years old.

A reader asked me to dig back into the behavior issue:

I have a question for Prof Hawks. Given the recent discovery of hominin presence in the Philippines, do you think that paleoanthropologists have been underestimating the extent of behaviour possible by archaic humans as far as possibly Homo erectus?

The islands of Indonesia had very different geographic connections in the past. Java, Borneo, and Sumatra are large islands that were connected to the Asian mainland during periods when the sea level was 120 meters lower than today. That’s why they had (and still have) animals like rhinoceros, tigers, and orangutans that were also common in Southeast Asia.

Philippines ancient sea level map
Philippines and neighboring areas. Present land areas are shown in green, also shown is the 120-meter depth line marking ancient land areas during the last glaciation.

Java, at least, also had Homo erectus populations starting as early as 1.5 million years ago, and lasting up to a half million years ago. We do not have evidence of any other hominins on Java at this time or earlier, but there is some good evidence now that the Homo floresiensis population may be a descendant of an earlier branch than even H. erectus. So maybe we’re talking about a hominin with an even more distant relationship to humans today.

The Philippines were never connected to the Asian mainland. The animal species there must all have crossed water at some point to get there. This was definitely possible for many non-human species, and the Philippines had both extinct forms like rhinoceroses and stegodonts, and surviving forms like tarsiers. All of them must at some point in the past have made one or more water crossings to get to these islands. The tarsiers have been there for more than 30 million years, so we’re not looking at one pulse of events leading to today’s species, at all – ancient humans and modern humans were both part of a much longer story.

This seems like a parallel case to the island of Flores, where hominins were living and making stone tools by a million years ago. Some of those Flores hominins survived, and we find their remains as Homo floresiensis, with one fragment of jaw 800,000 years old, and more skeletal remains in the period leading up to 65,000 years ago from Liang Bua cave.

Many archaeologists doubt that any hominins 700,000 years ago, or a million years ago, or even Neandertals 100,000 years ago, had the cultural and cognitive ability to make boats. They think it is more likely that some “lucky” individuals were caught up in a tsunami, and washed across the sea from Java or Borneo to these islands.

To support this idea, they point to the 2004 tsunami that affected Aceh, Sumatra, and washed many people far out to sea. Some of them survived for many days before being rescued:

https://www.telegraph.co.uk/news/worldnews/asia/indonesia/11309717/Boxing-Day-tsunami-I-survived-nine-days-alone-in-the-Indian-Ocean.html

Nothing about that idea is impossible. Maybe some ancient hominins were lucky survivors. But the idea gives early hominins very little credit for knowledge of their environment.

Some scientists start from the notion that we cannot assume “complex” behavior without extraordinary evidence. But what is “complex”? Is it hard to imagine that a medium-sized mammal species, which relies on foraging across 100 square kilometers or more for high-energy foods, would be aware of islands that are in sight?

Personally, I have a different opinion. I think we have to recognize a continuum of abilities. Extraordinary ideas and abilities probably existed in most ancient populations. Today, in our very large population with huge economic and social incentives for innovation and discovery, those abilities can change the world. But in the past, in low-density populations living on the edge of survival, most innovations could never have become sustained, long-term traditions that leave an abundance of archaeological evidence.

Nonetheless, they changed the world for an individual, or a group.

When it comes to colonizing a new island, it is the exceptional that matters. In fact, if crossings were regular, island populations could never evolve to be very different from nearby mainland populations. It is the very fact that crossing is rare that allows island adaptations to emerge after the population is established.

But it is also the group that matters. A single individual cannot found a new population.

When you look at these places in island Southeast Asia with early hominin activity, ancient sea levels were much lower and all these islands are one or two small hops across narrow straits. Palawan is an island between Borneo and the Philippines, and today these water crossings are hundreds of kilometers, but in the past they may have been as narrow as ten kilometers.

That’s not very far to imagine hominin individuals making crossings, if they were already playing with very basic ways of crossing rivers and using near-beach water resources.

How much did Y chromosome haplogroups shape our current picture of early modern humans?

Earlier this month I published a piece on Medium about our changing picture of modern human origins in Africa: “Three big insights into our African origins”. There really have been amazing changes during the last few years, and those comments–directed at geneticists–raise many questions about the way forward.

Last year, after the announcement of redating of hominin material from Jebel Irhoud, Morocco, I had a reader question that is very relevant to this topic:

Is the recent redating of "anatomically modern humans" and the reclassification of North African Archaics (like Jebel Irhoud) in part a response to the finding of the introgressed A00 haplogroup?

This is a great question. It’s hard to say exactly what goes into the background of people’s thinking. The data that tell us something about “early modern” humans has just changed enormously in the last five years.

The A00 haplogroup was described by Fernando Mendez and colleagues back in 2013 (https://doi.org/10.1016/j.ajhg.2013.02.002). It is a Y chromosome branch that seems to diverge from the rest of the modern human Y chromosome tree between 240,000 and 580,000 years ago. It’s found today in some Mbo men from present-day Cameroon, and some African-American men.

That’s very early compared to the rest of the Y chromosome tree. It is not very early compared to the autosomal genome, which shows that African populations started to become genetically differentiated around 300,000 years ago or so.

There’s a suspicion that this haplogroup may have entered recent human populations by interbreeding with a more ancient, diverged branch of archaic humans. It’s possible. The story of African “archaic” humans today is intricate, because we have just enough data to raise questions and not enough data to answer those questions.

For example, the Iwo Eleru skull fragment, from Nigeria, is a specimen that we now recognize is less than 16,000 years old, but is archaic-looking in some details of its anatomy (https://doi.org/10.1371/journal.pone.0024024). Maybe this is a late-surviving pre-modern human population in West Africa that contributed to today’s people in some degree.

There is evidence for “ghost population” contributions to West African people, and central African hunter-gatherers. All of this evidence comes from statistical examination of genomes of living people, and different research groups have come to different conclusions – some point to multiple admixtures, from very ancient, diverged groups that may have been as different as today’s people from Neanderthals, but all within Africa.

Others point to a possible “pre-modern” population, an outgroup to all of today’s modern people but maybe only 400,000 or 500,000 years diverged, that contributed a much bigger fraction of West African genetic ancestry today. I think there’s a good chance that the Jebel Irhoud hominins belonged to such a “pre-modern ghost” population. The anatomy of these crania is not what I think the common ancestor of all of today’s African populations probably looked like. But that’s a guess.

It’s going to be a while before these studies start to converge on a single picture, because they’ve been using different samples and different methodologies.

Honestly, I think the Y chromosome haplotypes are not coming into people’s thinking. The reason for this is that most people now recognize that the uniparental lineages, the mtDNA and Y chromosome, are not very helpful once you get back into the initial stages of diversification of today’s African populations.

The A00 haplogroup does not seem to mark that early diversification, because it isn’t present in Khoesan as far as we know. And if our mtDNA mutational timeline is correct, the autosomal differentiation of Africans started long before the mtDNA “Eve” lived.

Personally, I think these uniparental systems are probably reflecting natural selection on various haplogroups, and the introgression dynamics are driven by their fitness in different environments and genetic backgrounds.

Link: 'Africa' in the desert? Stop it now

This is going around from people who think it’s hipster and cool and ought to know better: “Africa by Toto to play ‘for all eternity’ in Namib desert - video”.

'I … wanted to pay the song the ultimate homage and physically exhibit 'Africa' in Africa,' Siedentopf told NPR. 'The Namibian desert — which is, with 55 million years, the oldest desert in the world — seemed to be the perfect spot for this.'

I like Toto’s “Africa”, but this is graffiti on the Mona Lisa. I hope somebody finds this thing and eliminates it with extreme prejudice.

Link: Field Museum Native American collection

This is an important article in Chicago magazine, “An Artist Addresses the Field Museum’s Problematic Native American Hall”. The article is a review of a new art installation happening at the Field, by artist Chris Pappan and it includes many nice images with the story of the exhibit.

For me, the most significant part is near the beginning of the article, looking at the way that the Field is planning how to exhibit its collections moving forward into the next century:

The case labeled “Indians of the Chicago Region,” for instance, makes no mention that the greater metropolitan area now has the nation’s third largest Native American urban population. This restricted view can be traced back to the museum’s beginning. Native American objects acquired for the 1893 World’s Columbian Exposition by anthropologist Franz Boas — who believed he was salvaging remains of disappearing cultures — were part of its founding collections.
After six decades of this static display, the tribal nations connected to these objects will finally have a voice in their presentation, emphasizing their place in living culture. In October, the museum announced a three-year renovation of the hall. When it reopens in 2021, it will not just represent a new direction for the Field Museum but will reconsider what natural history museum ethnographic galleries can, and should, be in the 21st century. The challenge is in recognizing the colonialism in their roots while involving indigenous voices that have long been left out.

It is valuable and critically important to include the diversity of cultural experiences in museums. But the creation of these exhibits and collections in the past was based upon incorrect views, often racist and Eurocentric. I cannot even express how many exhibits I have seen that were created during the 1960s to the 1980s, that describe cultures as if they stopped in time when the objects were collected.

The Field has a remarkable collection, and I am glad they are moving to find new ways to tell the stories, including the voices of descendant populations.


Notable paper: Zanolli, C., Pan, L., Dumoncel, J., Kullmer, O., Kundrat, M., Liu, W., … & Tuniz, C. (2018). Inner tooth morphology of Homo erectus from Zhoukoudian. New evidence from an old collection housed at Uppsala University, Sweden. Journal of human evolution, 116, 1-13. doi:10.1016/j.jhevol.2017.11.002

Synopsis: Zanolli and coworkers studied a small sample of teeth in Uppsala that had been taken to Sweden by Otto Zdansky in the 1920s. Being held in Sweden, these teeth escaped the loss of the rest of the Zhoukoudian fossils during the Second World War. Zanolli’s team carried out CT scanning of the fossils and studied their enamel-dentine junction (EDJ). This part of the internal structure of the tooth reflects the initial stages of development of the tooth crown, and can preserve evidence of anatomy even as the occlusal surface of the tooth develops wear.

Interesting because: The results suggest that Chinese H. erectus may have been taking a different evolutionary pathway from H. erectus in Indonesia. Zanolli and coworkers emphasize that an Indonesian H. erectus sample from later in the Middle Pleistocene, from Ngandong, has “simplified” EDJ morphology compared to earlier Indonesian samples. Zhoukoudian teeth have a more similar form to earlier Indonesian teeth than to Ngandong teeth, even though the Ngandong teeth are more similar in age. That difference might just be teeth, although the cranial and mandibular morphology also shows some consistent differences between Zhoukoudian and Ngandong, as evident since Franz Weidenreich studied the samples. This may be a sign of deep population divergences and history within the sample long known as Asian H. erectus.

Evolutionary connections: As pointed out in this paper, Yousuke Kaifu and colleagues (2015) examined the EDJ morphology of Homo floresiensis teeth, and concluded that they reflected a very simplified form compared to H. erectus. That seems to be a similarity with later H. erectus specimens from Java like Ngandong. That’s interesting in light of the observations by Debbie Argue and coworkers (2017) and Mana Dembo and colleagues (2016) that H. floresiensis seems to be deeply rooted in the phylogeny of Homo and not closely related to Indonesian H. erectus.

Link: A historic mystery about blue specks on teeth

A new article in The Atlantic by Sarah Zhang looks at some fascinating detective work on ancient teeth by Christina Warriner and Anita Radini: “Why a Medieval Woman Had Lapis Lazuli Hidden in Her Teeth”.

The study of microscopic and chemical remains that are embedded in ancient dental calculus has become very important to understanding prehistoric diets, health, and lifestyles. What a lot of readers might be less aware of is the way that they can inform about much more recent, historic populations.

If pigments can be preserved in tartar—the gunky yellow stuff on teeth that dental plaque hardens into—that means that fibers, metals, and other dyes could be, too. “This is genuinely a big deal,” says Mark Clarke, a technical art historian at Nova University Lisbon who was not involved in the new study. You could imagine identifying metalworkers, carpenters, and other artisans from the particles embedded in tartar, Clarke says. “It’s opening up a new avenue in archaeology.”