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paleoanthropology, genetics and evolution

Photo Credit: Contemporary human skull compared to the Kabwe cranium. John Hawks CC-BY-NC 2.0

Quote: Eileen Whitehead Erlanson defining taxonomic inflation

I was reading today to find the origin of the term “taxonomic inflation”. This is a common idea today from people who criticize an overzealous attention to defining species. The term “taxonomic inflation” is especially used by detractors of the phylogenetic species concept, on the logic that this species concept results in naming species from insufficient data.

In a discussion of species concepts, I wanted to provide this perspective and cite its origin, and I found that nobody who today uses the term ever cites its origin.

I found the earliest use of the term in a 1934 paper by the botanist Eileen Whitehead Erlanson. She uses it in a discussion of the problems of recognizing varieties below the species level:

The taxonomist must find some way of describing all the multitude of natural forms, and in Rosa the problem of how to treat the units smaller than a species is perplexing. GREGOR (23) pointed out that if a varietal name is appended to every specimen which differs in some minor point from the general description of the group, then "every genotype and every clonal modification of an individual would ultimately deserve varietal or sometimes specific rank." To name all the possible combinations of minor characteristics leads to such a state of taxonomic inflation that the categories below the genus lose all practical value. Nor can the morphological criteria alone be accepted as supplying a completely reliable system of classification (23), for morphologically similar forms may differ markedly physiologically, as has been found in R. acicglaris, R. woodsii Lindl., and R. arkansana Porter. Probably the most promising method for dealing with the smaller units is that of distinguishing minor variations by numbers or letters, which makes it possible to express dif- ferent character combinations clearly and succinctly without degrading scientific nomenclature. This has been advocated by VAVILOV (42), HALL and CLEMENTS (26), CLAUSEN (7), and HALL (25). It was recommended for the varieties of rose species by MATTHEWS (31) and is a method that I also would endorse.

The paper is “Experimental Data for a Revision of the North American Wild Roses” in the Botanical Gazette, which later became the International Journal of Plant Sciences.

The next person to use the term “taxonomic inflation” was the paleontologist William K. Gregory in a 1936 paper, On the Meaning and Limits of Irreversibility of Evolution”. I mention this because it is the only other early use of the term, but Gregory used it in a very different way that is not similar to the present usage of the term. Gregory was concerned that paleontologists were overzealous in their application of the idea that specializations cannot be reversed in evolution, and that this caused them to accept a much higher antiquity for some species lineages than they would if they could accept that specialized characters sometimes reverse to an ancestral state. Hence, the number of evolutionary lineages is “inflated” by the assumption that they must have separated before any specialized traits evolved.

The use of the term, taxonomic inflation, really took off in the 1960s after the president of the Linnaean Society of London, one T. M. Harris, devoted a speech to “The Inflation of Taxonomy”. This was a wholesale critique of oversplitting at every level of taxonomy, and was clearly influential upon later authors. However, as a speech, Harris seems to have felt no need to cite earlier authors. Nor did many later authors cite Harris’ work.

It seems that “taxonomic inflation” was an idea that many wanted to use, and few sought for the term’s source. I’m going to credit Erlanson.

Quote: Colin Groves on primate species

In 2001, the Australian zoologist Colin Groves published an essay in the journal Evolutionary Anthropology giving his perspective on classification in primates: “Why Taxonomic Stability Is a Bad Idea, or Why Are There So Few Species of Primates (Or Are There?)”. The essay is historically interesting. Groves was known as one of the premier taxonomic splitters in the study of mammals.

The first edition of the Smithsonian's Mammal Species of the World listed 181 species of the order Primates. The second edition had 233 species. The new “Bible,” Groves’ Primate Taxonomy, (2001) has 356. What is going on? And have we reached maximum yet?

Today there are more than 500 named species and subspecies of primates. Groves remained one of the scientists most connected to increasing the recognition of species until the end of his life in 2017.

New York Times looks at the hidden cost of amber paleontology

This week, scientists announced a study of one of the most significant Cretaceous fossil discoveries within a chunk of amber from Myanmar, the tiny skull of a dinosaur or dinosaur-like reptile. Lucas Joel in the New York Times looks at the human and environmental toll of the amber-mining:

A report published last year in Science Magazine detailed how the amber is mined in a state where Myanmar’s military has long fought another ethnic minority, the Kachin, and how amber gets smuggled into China, where it can fetch high prices, potentially fueling that conflict.
These concerns are leading more scientists, especially in Western countries, to shun the use of this amber in paleontological research.
“Ever since the Rohingya crisis, I’ve boycotted the purchase of Burmese amber, and have urged amber colleagues to do the same,” said David Grimaldi, a paleontologist and the curator of amber specimens at the American Museum of Natural History in New York.

Fossil discoveries in amber are often very exciting, but the most high-profile discoveries are a tiny fraction of a much larger amber industry. Finding a tiny dinosaur head and promoting it across the world fuels more interest in amber, and gives a slightly higher market value to every piece of amber with a fossil insect in it.

It’s not easy to know what a paleontologist should do. It’s not too unusual that many paleontologists decline to work on fossil material from Myanmar amber. What’s interesting is the number of paleontologists in the article who have declined to comment on discoveries from amber.

How much have baboons and geladas hybridized during their evolution?

A recent paper from Jerilyn Walker and coworkers in the journal BMC Mobile DNA reports that today’s baboons and geladas may have mixed in their history more than previously suspected: Alu insertion polymorphisms shared by Papio baboons and Theropithecus gelada reveal an intertwined common ancestry”.

The paper considers Alu insertions unique to the various species of Papio and T. gelada, finding that many are shared polymorphically across these, and that P. kindae shares more with geladas than do any of the other species of baboons. On the whole, the authors consider their results as evidence of hybridization from geladas within the history of baboons.

Some observations of extant baboons and geladas suggest that even after 4 mya of separate evolution, the possibility of gene flow between them is not completely excluded by an intrinsic barrier. A suspected hybrid individual has been observed in a natural gelada-olive baboon overlap zone [63]. In a zoo environment, completely viable first-generation hamadryas baboon x gelada hybrids of both sexes are reliably reported. While the hybrid males are suspected to be infertile, female hybrids have produced viable offspring by backcrossing to Papio hamadryas [64]. Especially during the earlier phases of their long period of co-existence, Papio x Theropithecus matings (including with T. oswaldi) may have allowed ongoing, low-frequency genetic exchange. Our Alu insertion polymorphism data support this hypothesis.

Measured in years, geladas have not quite diverged as much from baboons as humans have from chimpanzees, but getting close to that. Measured in generations instead of years, the divergence between geladas and baboons is within the margin of error of the human-chimpanzee-bonobo divergence.

The evidence from Alu insertions is limited compared to a SNP comparison. That restricts what the researchers can say about the timing and extent of mixture. It’s possible that much of the mixing happened early in baboon and gelada evolutionary history. However, the different pattern in kinda baboons raises the possibility that mixture might have happened after the diversification of today’s baboon species began in the Pleistocene.

I expect that we’ll see whole-genome SNP comparisons soon.

Mixture may not have involved T. gelada itself, which is limited to highland Ethiopia. Today’s geladas have many extinct relatives, including T. oswaldi and T. brumpti. There’s a lot to learn about the evolution of these cercopithecoid primates, which existed across much of the known hominin range during the Early and early Middle Pleistocene.

Walker, J.A., Jordan, V.E., Storer, J.M. et al. Alu insertion polymorphisms shared by Papio baboons and Theropithecus gelada reveal an intertwined common ancestry. Mobile DNA 10, 46 (2019). https://doi.org/10.1186/s13100-019-0187-y

Quote: Broom on fossils as ancestors

In the last few years, a surprising number of paleoanthropologists have published papers claiming that various fossil species could not be ancestors of others because the fossils that represent them have the wrong geological age. Usually, the claim has been that a fossil is “too recent” to be an ancestor of living people, or Homo more generally.

The last fifteen years of fossil discovery have shown just now much we still do not know about the diversity of fossil hominins. So I think that purely statistical research on the duration of various species is not very illuminating. We’re not in a position to test how long most hominin species existed, or what their geographic extent may have been.

Still, it’s a topic that seems to return again and again.

I think that I’ve noted before that Robert Broom wrote thoughtfully on exactly this topic. Lee Berger and I reference Broom’s thoughts in our book, Almost Human.

When Raymond Dart published his initial work on the Taung specimen, Broom was the one who had the most insight about the possible age of the hominin skull. Finding Pleistocene baboons in the Taung fossil assemblage, Broom initially considered that the Taung skull itself might be fairly recent in geological age. As time went on, both Broom and Dart appreciated that the Taung hominin specimen and much of the fossil deposit were likely earlier, Pliocene in age.

But from the first publication of the Taung specimen, some critics maintained that a recent geological age must mean that it could not be connected to human origins. In their view, the age was prima facie evidence that the Taung specimen was an extinct ape, not a human relative.

As I was reading some background research today, I found a very clear exposition by Broom in a Scientific American article from 1929: “What the World Owes to South Africa.” The article is a retrospective by Broom of important paleontological findings from South Africa, not only the Taung specimen but a broad array of findings from Permian and Mesozoic times also.

In his discussion of human origins specifically, Broom addresses the relevance of the geological age of the Taung specimen.

Certain anthropologists have maintained that Australopithecus could not have been a human ancestor because it lived at a time after mankind had probably appeared on the earth. Manifestly, as the specimen died when five or six years old, it could not have been the ancestor of any one, but there is no objection to considering this little specimen as a representative of a race which may have survived hundreds of thousands of years; and that one member of the same tribe, perhaps in early Pliocene times, may have been the ancestor of mankind.

It is a cardinal mistake to think that a fossil is literally the genealogical ancestor of some living animals. Fossils are dead creatures and their individual reproductive fates are unknown. All fossils are related by a tree to living forms, however, and that relationship allows us to test hypotheses about the evolution of living forms. Whether an ancient population or species is a literal ancestor of some living animals is potentially testable, but only if the duration of the species and its boundaries are very well documented.

We know that Neandertals, as a population, include many literal ancestors of today’s humans. That does not mean that any particular fossil Neandertals were among those genealogical ancestors. Many of them belonged to local populations that became extinct, even if most regional populations of Neandertals in the long run contributed some genes to the modern human population.

Do we know that highly diverse hominins like Paranthropus could not have been ancestors of living people? Over the past ten years, it has become abundantly clear that hybridization and introgression were widespread among Pleistocene hominins. Genealogical ancestors trace every genealogical line, and the idea that Homo was hermetically sealed from co-existing closely related lineages is hard to imagine. I expect that P. boisei was a human ancestor, if genealogical ancestry and introgression are how we characterize ancestry.

Many anthropologists may admit that such minority ancestors might be interesting but still maintain that hybridization is not the central issue. They are interested in the predominant ancestry of living people, and that the ancestor of living humans must be a unique species at any one moment in time. They assume a model in which species disappear immediately at the moment that they give rise to a daughter species. In such a model, if a fossil representative of a species is, say, 2.0 million years old, then the species cannot be the ancestor of another species represented by a fossil that existed, say, 2.4 million years ago.

Quote: Dart on Piltdown and ape relationships

I was flipping through a 1929 paper by Raymond Dart, “A note on the Taungs skull”, in the South African Journal of Science. In this, Dart gives a scientific overview of some of his thinking about human origins in light of his discovery. Most of this, in retrospect, was wrong, and in fact I was looking through this to cite some of Dart’s assumptions about climbing and terrestriality in Australopithecus which have turned out to be erroneous.

In the process, I was struck by one paragraph. It gives a very tight overview of why Dart assumed that the human lineage must have become separate from apes at a very early date, much earlier than the diversification of today’s great apes.

Now it is a very important matter that man, especially a primitive man (like Piltdown man) has many features in which he is related, not only to the gorilla and chimpanzee on the one hand, hut also to the orang on the other. We know from this that the human stock was derived from the ape stock at a remote period, that is, before the chimpanzee and orang had left the main stem, in other words, while the capacity for giving rise to chimpanzoid and orangoid features were both inherent in the common human-ape stock. When we find man is a mixture and has characters linking him to two such widely divergent apes as the chimpanzee and orang, we say that man arose from a generalised, and not a specialised ape stock. We know that man's true ape ancestor must be still more generalised, still more of a mixture than the most primitive of men known, that this ancestor will be still more of a mixture, as it were, between the chimpanzee and the orang. (I do not refer particularly to the gorilla because it is more specialised and more different anatomically from man than the chimpanzee, and, therefore, further removed from the human stock, and also because the chimpanzee is sufficiently representative of the specialisations which we find in its near cousin, the gorilla.) Man's ape ancestor must, therefore, be an ape intermediate in character between the divergent chimpanzee and orang, but must be sufficiently advanced in its features towards those qualitative anatomical characters which are strictly human to justify the expectation that it would, with further evolutionary development, give origin to the earliest known types of human being such as Pithecanthropus, the ape-man of Java, and Eoanthropus, the Dawn-man of England.

This, in light of a century of evidence, was also wrong. But Dart’s reason for being wrong here is his reliance upon the Piltdown evidence. One might say he was wrong for reasons that seemed eminently logical.

Piltdown had orangutan-like features because its jaw was an orangutan jaw.

Humans and fossil hominins, we know today, are closer to chimpanzees and gorillas than any of them are to orangutans. Yet anthropologists from the mid-nineteenth century onward tended to accept that the living great apes form a natural group, and that the human lineage diverged from this group at a very early period, as early as the Eocene.

Clearly the general anatomical distinctiveness of humans from the living great apes contributed the most to this perception of a deep split between them. Most anthropologists accepted this scenario long before the Piltdown hoax was perpetrated, and many continued to accept it long after the hoax was revealed.

Still, this little detail shows how a singular fossil can reinforce scientists’ thinking. A testament from the past that confirms their predispositions is likely to carry much weight in their description of evolution, even if the fossil did not contribute to the way they formed their hypotheses. It is valuable to be especially critical of findings that align with one’s own views.

A look at a 'total genomic information' world

Razib Khan has an essay out in National Review drawing attention to some current trends in genomic technology and some of their implications: “Dime-store genomics”.

The 2010s was the decade when “consumer genomics” became a term that reflected something in reality. The 2020s have the potential to be the decade when genomics becomes so ordinary and ubiquitous as to be unworthy of mention or note. We will be entering the “total genomic information” world.

Standing at the intersection of many streets, the view down some of them is obvious. Yes, many people have genealogical surprises in store, and there will be no ducking the subject. Old crime scene evidence will take on new meaning.

Still, the alleys and side-streets have more action, and may be less apparent. We live in a world where we are tracked everywhere, every click, and our phones are listening. The resulting data have no use to most of us, but they are already shaping our perceptual worlds because of the immense money to be made on the tiny margins of our attention.

Hardly any of the information in our genomes is actionable to us as individuals. The genetic basis of most traits is distributed across hundreds and hundreds of genes, each with a miniscule effect. Prediction of traits on an individual basis is so imprecise that simply looking at family members does a better job for most traits.

The question is what money is to be made on the tiny margins of genomic information across millions of people.

Quote: No 'anatomically modern' elephants

In the field of human evolution, every so often a scientist will note the absurdity of talking about “anatomically modern humans”. Biologists don’t talk about other kinds of animals as “anatomically modern”. The words carry a connotation of end-directed evolutionary progress that is not compatible with the way that genetic change works in populations.

The first person I know to have emphasized this point was Phillip Tobias. Tobias contributed a chapter to the volume edited by Sydney Brenner and Kazuro Hanihara in 1995, Origin And Past Of Modern Humans As Viewed From DNA, in which he challenged the term “anatomically modern humans”. Tobias in this chapter more or less espoused the view of Wolpoff (1986), citing him directly in this passage:

First, it is important to stress that some recent and modern human beings do not have smooth brows. Prominent among the exceptions are the heavily-browed crania of Aboriginal Australians. Similar cranial forms are encountered among some recent peoples of India, Sri-Lanka [sic] and Indonesia (Wajak). Also exceptional are a number of protohistoric South African crania (e.g., Bayville, Cape Flats, Canteen Koppie, Ladybrand, Mistkraal and Zuurberg), whose brow ridges were so prominent as to lead Drennan (1937) and Wells (1952) to dub them (unacceptably) "australoid" or "proto-australoid" respectively. Attempts to arrive at a morphological definition of the so-called "anatomically modern man" (Day and Stringer 1982, Stringer and Andrews 1988) failed in that the formulations excluded these modern humans of Australia, Asia, and Africa. Clearly one does not need a smooth brow to be a modern human being. As Kennedy (1992) has pointed out, there is as yet no consensus on what the autapomorphies of modern humans are, while Kidder et al. (1992: 175) conclude, from a multivariate study of crania, that the formulating of a definition of modern Homo sapiens "is not yet possible even for European and Near Eastern samples". Yet many investigators have continued to use this term, "anatomically modern humans", as though it could be applied to all living and recent human beings, that is, to all members of the living subspecies H. sapiens sapiens. This author pleads guilty to using the term unthinkingly not long ago (Tobias 1992). If the term cannot be defined it should be discarded (Wolpoff 1986). Instead of speaking of "anatomically modern human beings", we should speak of "modern" or "recent" humans, using a temporal not a morphological descriptor (Tobias 1993a). After all, we are not in the habit of speaking of "anatomically modern elephants" or "anatomically modern hippopotami"!

The term “modern humans” really did originate in the late 19th century at a time when biologists and anthropologists took seriously the idea of end-directed evolutionary process.

Today’s evidence makes it clear that the genetic ancestry of living people comes mainly from African populations that had come to be separated by 300,000 years ago, with smaller components from Neandertals, Denisovans, and other populations that existed much earlier, separating from each other before 600,000 years ago.

The earliest fossils that anthropologists have described as “modern” in their anatomical features represent individuals that lived later, the earliest now being the Apidima 1 posterior cranial specimen from around 210,000 years ago. There remains much debate about what combination of anatomical features to recognize as “modern”. Specimens like Apidima 1, the maxilla from Misliya Cave, Israel, and the Zhiren Cave mandible from China show that “modern” morphological patterns existed in Eurasia much earlier than anthropologists imagined only 10 years ago. These specimens may be “anatomically modern” but possibly have little to do with the ancestry of today’s people. Two of them have been found at times and places where they were clearly succeeded by Neandertals. That complex biogeographic patterning – with a large possible contribution of African-derived populations to Neandertals in West Asia and Europe – is the opposite of an end-directed progression toward living people.

Paleoanthropologists need to come to grips with these patterns and come up with better terminology to describe the anatomical and genetic similarities between groups.

Looking at layoffs from consumer genomics firms

CNBC has an article by Christina Farr looking at the recent layoffs at consumer genomics firms 23andMe and Ancestry.com: “Consumer DNA testing is a bust: Here’s how companies like Ancestry and 23andMe can survive”.

Both companies have cited a slump in new customers as the reason for laying off large numbers of employees. The business analysts cited in the article suggest that the press surrounding the capture of the Golden State Killer and increasing concerns about genetic privacy are important to the decline:

Privacy concerns are at the forefront, Barry believes. Consumers have seen a slew of reports in the past few years about how companies are using their personal data for targeted advertising, without their knowledge, and might be feeling particularly sensitive about their health information.
23andMe CEO Anne Wojcicki has previously referred to these concerns as the “Facebook effect.” In her view, consumers are increasingly freaked out about stories they’re reading in the press about privacy, mostly about Facebook and other technology companies, and are reacting by feeling anxious about getting DNA tests.

The CNBC article suggests that both companies might pivot away from genealogy and toward medical and health-related information might help. I’m skeptical that such a move would provide much additional impetus for a broader number of people to pursue genotyping.

Florisbad: How old is the 'early Homo sapiens' skull?

This week, Lee Berger and I posted a new preprint in which we investigate the context of the Florisbad fossil hominin specimens. Our preprint is on the open AfricArXiv site for free download: “Revisiting the age of the Florisbad hominin material”.

In 1996, Rainer Grün and coworkers used electron spin resonance (ESR) and other methods to estimate the geological age of a hominin tooth from the site, finding it to be 259,000 ± 35,000 years old. The most significant hominin fossil from the site is a fragmentary skull with parts of the forehead, face, and parietals. The combination of archaic and modern aspects of this skull led researchers to think that it may be a transitional form that preceded the first modern humans.

A transitional pre-modern human form in southern Africa 259,000 years ago was exactly what researchers expected to find in 1996. In 2020, that same finding looks more and more problematic. Today we know that Homo naledi lived around 400 km from Florisbad at around the same time. The Florisbad date seems to show that a large-brained human population existed in the same geographic region as H. naledi. Did these two very different hominin populations coexist?

Neo skull reconstruction compared to Florisbad and Jebel Irhoud 1, in oblique view
"Neo" skull of Homo naledi (left) compared to Florisbad calvaria (center) and Jebel Irhoud 1 (right)

We thought it was time to revisit the 1996 Florisbad age result to see how solid it looks from today’s perspective. What we found is that there are several reasons to doubt that the fossil is really 259,000 years old. The history of the Florisbad spring site and its excavations reveals many problems that the 1996 work mostly did not consider.

I have to say I am constantly struck by today’s ability to look into the history through contemporary papers and documents. To estimate the geological age of any fossil hominin specimen, we must understand the original context. In the case of Florisbad, very little of that context was recorded to a standard that would enable today’s geochronologists to be confident about the original placement of the hominin fossils.

What was recorded about the site gives serious pause to any attempt to work out the age of the hominin specimens. Methane emerging from the springs periodically erupted, mixing sediments through parts of the site where the skull and tooth were found, questioning their association and placement within the site. The original excavations reported that the hominin skull fragments came from a peat layer, but the radiation in this peat was never measured by geochronologists. That’s an important omission, because as we found, today’s geochronologists recognize peat as a seriously impressive natural concentrator of uranium.

I don’t think we’ll ever know the age of the Florisbad hominin material. It’s tragic that so much of the African hominin fossils that are now attributed to the Middle Pleistocene was unearthed at a time when detailed spatial and stratigraphic context were not often recorded. It is a mistake to think there is any “silver bullet” approach that can provide the ages of such fossils.

Stopping the misuse of DNA samples from African research participants

In my course on anthropological genetics last semester, I spent a week on the ethical challenges with appropriate consent by research participants for the re-use of their DNA samples and data.

A case that made headlines that very week was the alleged misappropriation by the Wellcome Sanger Institute of DNA samples taken from South African research participants. The story revolved around the commercial use of data in development of a gene chip that used genetic markers that vary in Africans. South African participants had signed consent forms that expressly excluded commercial uses. In my course I was able to cover the extreme difficulty of separating commercial from noncommercial uses of DNA data, and the tangled connections of research institutes focusing on population history, those focusing on medical applications, and commercial enterprises that sell products to those laboratories.

Now, a great commentary by Keymanthri Moodley of Stellenbosch University adds some broader perspective to this story from a South African perspective: “Africa’s genetic material is still being misused”.

She reviews work that her team undertook several years ago looking at the reasons why people volunteer for genetic studies, and their expectations about the research.

Most participants were supportive of research. But many expressed concerns about export of their blood samples and data out of South Africa.
For their part, researchers viewed the biosamples as donations. But participants believed they had ownership rights and were keen on benefit sharing. Almost half of the participants were not in favour of broad consent delegated to a research ethics committee. Their preference was to be contacted again for consent in the future.
The legitimacy of using broad consent models for genomic research and biobanking occupies a contested space among bioethicists and researchers globally. Broad consent allows researchers to use biosamples and data indefinitely for future research.

There is much more in the article, including some recommendations for reform in the South African setting. She focuses on the need for real engagement with research participants, with “co-creation of knowledge production and benefit sharing”, as well as tiered consent as described in a recent paper by Victoria Nembaware and collaborators (including Moodley’s lab): “A framework for tiered informed consent for health genomic research in Africa”.

These recommendations should be examined closely by researchers in other contexts.

Border Cave rhizomes from the early Middle Stone Age

I’m pretty excited about today’s paper revealing new evidence of cooked rhizomes from Border Cave in South Africa. The paper is in Science, by Lyn Wadley and coworkers: “Cooked starchy rhizomes in Africa 170 thousand years ago”.

It’s not that the results are unexpected. The underground storage organs of various plant species are rich sources of calories and nutrients, especially in seasonally dry environments. Many of them are fibrous, defended by toxins, or otherwise hard to digest, and cooking helps to make them more palatable and enables hominins to get more nutrition from them. Finding, collecting, and sharing tubers, rhizomes, and bulbs is important to many hunting and gathering peoples around the world. The idea that cooking these may have been important o many species of extinct hominins is not novel thinking; it has been suggested by many scientists of whom Richard Wrangham has been the most vocal in recent years.

What has me fascinated is the quality of the plant remains from Border Cave. One of the greatest challenges of the archaeological record is the rapid decay and breakdown of plant remains. Almost certainly, hominins used perishable materials like wood, leaves, and grasses vastly more than they used stone. Perishable animal parts like leather, sinew, and feathers would also have been part of their technologies. The diet of most ancient hunter-gatherers probably consisted of a majority of plants and invertebrates without hard parts, like insects. Yet animals with bones and shells make up most of the archaeological traces of ancient diets.

Technology in recent years has begun to even the score. Change has come from microscopic detective work, such as the ancient starch grains and opal phytoliths preserved in dental calculus. Phytoliths have also become important to identifying the use of plants within archaeological sites. For example, many archaeological sites preserve the ash from ancient fires, and phytoliths preserved within the ash have enabled archaeologists to identify the species of trees that hominins foraged for firewood.

But then there are the exceptional archaeological sites that preserve ancient plant remains more directly. Many of those are charred, such as the pistachios and other plant seeds from Gesher Benot Ya’aqov in Israel, roughly 800,000 years old.

In Border Cave, recent archaeology has already shown some exceptional organic preservation. Lucinda Backwell and coworkers reported in 2012 on digging sticks, beeswax, and a stick with traces of poison from approximately 24,000 years ago. The team has also reported on grasses and other plants used as bedding material in the cave in layers going back to nearly 40,000 years.

I also want to point out that botanical remains, including rhizomes, are known from many other sites. In southern Africa, that includes Ngalue in Mozambique, where seeds from sorghum have been preserved from more than 100,000 years ago, and Klasies River Mouth in South Africa, where some kind of underground parts of a plant come from approximately 120,000 years ago.

The charred rhizomes from Border Cave extend this evidence further back, as far as 170,000 years ago, and that’s a very interesting time period. Modern humans may not have even been present in southern Africa at this time, and if they were, they were probably not alone.

Charred evidence of rhizomes from Border Cave, from Wadley et al. 2020
Charred remains of rhizomes from Border Cave. Figure S2 from Wadley et al. 2020.

As I’ve been reading about this new paper, there seems to be an assumption going around that these rhizomes were burned by modern humans. The paper mostly avoids saying anything about which hominin species may have left these rhizomes at Border Cave. Only in two places does the paper mention Homo sapiens, both in the context of saying that a better understanding of this site may inform us about the capabilities of H. sapiens.

I don’t assume this.

The artifacts in the Member 4 and 5 deposits at Border Cave include large Levallois blades and points similar to those attributed to the “Pietersburg” industry elsewhere in South Africa. Backwell and colleagues reviewed the Border Cave archaeology in 2017 and discuss this industry at some length: “New Excavations at Border Cave, KwaZulu-Natal, South Africa”. Pietersburg assemblages have been more commonly identified at sites in the interior rather than the coast and all predate 100,000 years ago.

The most abundant species in the interior during the early Middle Stone Age was Homo naledi. Now, we cannot say for sure that H. naledi still existed 170,000 years ago. Fossil remains never tell us when a species became extinct; they only tell us the last time they were preserved. With a tiny fossil record of H. sapiens or any archaic humans, our fossil sample is not enough to say which species existed where, or if multiple species of hominins coexisted.

At Border Cave, the time period represented by these members appears to stretch between 100,000 and 160,000 years ago. There is no reason to assume that the archaeology in the cave was homogeneous across this entire time, and that hypothesis should be tested. Lumping a series of discrete, small episodes within a cave site may hide important variations in behavior.

I would not be the least surprised if Homo naledi were consuming the calorie and nutrient-rich parts of plants underground. That would help to explain the high degree of dental chipping we have found on the remains, as well as their small teeth. It would take digging sticks and fire. If H. erectus was using these plant resources, as many anthropologists have suggested, then surely H. naledi was as well.

That doesn’t mean that some of the Border Cave early MSA was not made by humans—whether archaic or modern. Maybe they were there. But we need to re-examine these exceptional sites with all the knowledge we have from multiple disciplines.

We are entering a fascinating time in archaeology. If we imagine that we are only finding behavioral evidence of “modern humans” or Homo sapiens, I think in another decade we may look back on that idea and laugh.

Nuclear insertions of mitochondrial DNA from Denisovans

A paper last week by Robert Bücking and coworkers trawled through the recently-sequenced Indonesian Genome Diversity Project dataset looking for snippets of mitochondrial DNA (mtDNA) that have been inserted into the nuclear genome. These snippets, called “NUMTs”, arise every so often as a result of DNA transfer from the mitochondrion into the chromosomes.

No, I don’t think you pronounce this “numpty”. These insertions are a cool indication of ancient population diversity, because they sometimes preserve ancient mtDNA variation that has become extinct.

The paper, “Archaic mitochondrial DNA inserts in modern day nuclear genomes”, is in BMC Genomics.

NUMTs occur in many kinds of organisms. They are not typically functional, making them one of the many components of junk DNA. In the nuclear genome, they evolve very much like other noncoding sequences, which means they are often subject to mutations including insertions and deletions. But once in the nuclear genome, the rate of change by mutations is quite a bit slower than in the mitochondrial genome, which means the NUMTs can act almost like a “fossil record” of ancient mitochondrial variation.

From the background section of the paper:

In the human reference genome, a total of 755 NUMTs have been identified [7]. In addition to these NUMTs, many more polymorphic NUMTs have been detected in various human populations around the world [8] and the analysis of additional populations is expected to reveal many more polymorphic NUMTs.

Most of the 755 in the draft reference genome are fixed in human populations, but a small fraction are polymorphic. This polymorphic/fixed ratio is a reflection of the high rate of genetic drift throughout most of human evolution, up until the expansion of modern human populations. The citation [8] above is to a 2014 paper by Gargi Dayama and coworkers, “The genomic landscape of polymorphic human nuclear mitochondrial insertions”, which surveyed the 1000 Genomes Project samples for polymorphic NUMTs, finding an additional 141, which suggested that more would eventually be found by sampling more populations.

Nuclear insertions of mitochondrial DNA are tricky to find. They can represent any part of the roughly 16,000 base pairs of the mtDNA, and many of them are less than 300 base pairs. Short-read sequencing methods tend to align reads of NUMTs with the mtDNA, so it takes some close study of the flanking sequences to confirm that these are present in the nuclear genome. NUMTs that are longer than the short reads of the sequencing platform could not be fully examined in this paper; instead they considered only around 1000 base pairs from each end.

Here are the conclusions of the new paper:

We modified an existing method to detect NUMTs in next-generation sequence data, and applied the method to whole genome sequences from Indonesians and Papuans, in order to detect NUMTs arising from archaic human mtDNA. In high coverage genomes, an average of 16 NUMTs per individual is detectable. Most of these NUMTs seem to be population specific, indicating their insertion in recent human history. This finding further supports previous findings of an ongoing transfer of mtDNA to the nucleus in humans and suggests that the analysis of additional populations would lead to the discovery of many more NUMTs. A Denisovan NUMT could be identified in 16 samples from Indonesia and Oceania. Analyses of the flanking region of this NUMT reveals that it is part of a Denisovan haplotype. This suggests that the insertion of the NUMT most likely happened in a Denisovan individual and then introgressed into modern humans within nuclear DNA. Our pipeline can be applied to newly sequenced genomes in the future, which could reveal additional archaic NUMT insertions and new insights into the nature of interbreeding events.

The paper caught my attention because of the discovery of a Denisovan-origin NUMT. The analysis suggests that the NUMT was originally part of the mtDNA of a Denisovan individual and that it was incorporated into the nuclear genome in an ancient Denisovan sometime before their mixture with modern humans. This insertion is designated as NUMT 3_1384 in the paper.

NUMT 3_1384 is present in 15 samples from eastern Indonesia and New Guinea (Additional file 1: Table S1). A sequence of 251 bp was generated, which is identical to two Denisovan mtDNAs. It forms a clade with Denisovans and Sima de los Huesos, distinct from all other humans (Fig. 3e) and falls outside of all modern human and Neanderthal variation (Fig. 4c). The alignment contains 13 variable positions within hominins (Additional file 3). For five of these positions, Denisovans and the NUMT share an allele which differs from all modern humans. This suggests that it originated from Denisovan mtDNA rather than from mtDNA of a modern human or an ancestor of Denisovans and modern humans (Additional file 1: Figure S3).

It’s not very long at 251 bp. Across that sequence, the NUMT is identical to two ancient Denisovan mtDNA seqeunces and one nucleotide different from the other two. The closest Neandertal differs by four nucleotides, the closest modern human mtDNA by five. It’s interesting that the mtDNA that now exists as a NUMT in Indonesian individuals is so close to the Siberian ancient genomes—in other words, that it does not seem to reflect much clade diversity within the Denisovan population—since other evidence from across the nuclear genome suggests this population was very diverse. But that’s not too meaningful over this short part of the mtDNA genome.

I’m interested in the broader picture of NUMT variation. Here, one aspect is that Denisovan-origin NUMTs are not the only components of archaic variation. More ancient parts of the modern human mtDNA tree and deeper ancestral populations are also represented among these NUMTs. The paper identified three polymorphic NUMTs that appear to be outgroups to the present-day variation of human mtDNA but closer to modern than Neandertal or Denisovan mtDNA sequences. These insertions into the human nuclear genome are fossils of ancient African mtDNA variation. They may represent the diversity of ancestral African groups that contributed to the modern human gene pool but did not survive within our bottlenecked mtDNA variation. Or they may represent archaic populations of Africa that, like Denisovans, contributed only a small fraction of the genetic variation found today. Unfortunately, these NUMTs are short and don’t give a great deal of information that would enable possible identification of the time when they entered the nuclear genome.

There is a lot of promise for this approach to highlight additional mtDNA variation from past populations. This paper did not look at NUMT sequences that originated from within the known modern mtDNA tree, but those may have a lot of information about the connections between the mtDNA tree and nuclear genomes in past populations. After all, any mismatch between a NUMT found in a population and its present mtDNA variation suggests ancient population contacts and partial replacement of maternal genealogical lines.

Fake spiders and paleontological forgery

A paper by paleontologist Paul Selden in Paleoentomology describes an interesting case of paleontological forgery: “The supposed giant spider Mongolarachne chaoyangensis, from the Cretaceous Yixian Formation of China, is a crayfish”. I found the story from a news piece by Michelle Star, who gives a layperson’s background to the case: “A Fossil Spider Discovery Just Turned Out to Be a Crayfish With Some Legs Painted On”.

"These things are dug up by local farmers mostly, and they see what money they can get for them," Selden explained.
"They obviously picked up this thing and thought, 'Well, you know, it looks a bit like a spider.' And so, they thought they'd paint on some legs - but it's done rather skilfully. So, at first glance, or from a distance, it looks pretty good.
"It's not until you get down to the microscope and look in detail that you realise there are clearly things wrong with it. And, of course, the people who described it are perfectly good palaeontologists - they're just not experts on spiders."

The article discusses how such forgeries are becoming increasingly common as a part of the fossil trade to private collectors.

How weird would long-distance Acheulean obsidian transport be?

In 1987, J. Desmond Clark published a review of Acheulean archaeological occurrences in two Ethiopian field areas: “Transitions: Homo erectus and the Acheulian: the Ethiopian sites of Gadeb and the Middle Awash”. I was reading this article today and was interested to run across this paragraph describing obsidian transport at a very early date:

Especially interesting also is the presence of four handaxes made from obsidian, a stone found nowhere on the South-East Plateau but with the nearest sources in the Ethiopian section of the Rift Valley, ca. 100 km to the west. This implies some form of population movement or exchange between the plateau and the rift between 1.4 and 0.7 million years B.P. Since, as yet, no earlier cultural material has been found there, it was during this time, on the Gadeb evidence, that the first occupation by hominids of the Ethiopian high plateaux took place.

I’ve been looking closely at this 1987 paper because of its title reference to Homo erectus. There are no hominin fossils from these Gadeb localities. Clark thought the various local occurrences of archaeology on the Gadeb Plateau dated between 1.4 million and 700,000 years ago, based on geological work by Williams and coworkers (1979). In the years since, no further investigations have examined these dates.

People who have been following me for a while know that I am not willing to accept accept old dates without critical examination. I am also unwilling to accept associations of hominin populations and archaeological assemblages without strong evidence. There were multiple species of hominins in Africa during the Early and Middle Pleistocene, and without some strong evidence of association, we cannot say which species was responsible for particular stone tool assemblages.

On that account I have more to write. Here I want to examine the way that standards of evidence have changed over time in stone age archaeology.

Long-distance obsidian transport was not the only claim made of the Gadeb sites that would later attract attention. Ignacio de la Torre (2011) revisited the Gadeb Acheulean assemblages to evaluate whether some of the claims could be confirmed: “The Early Stone Age lithic assemblages of Gadeb (Ethiopia) and the Developed Oldowan/early Acheulean in East Africa.” He included a list:

The Gadeb record has contributed to a variety of paleoanthro- pological discussions. For example, Clark and Kurashina (1979a) emphasized the importance of Gadeb as the earliest evidence of human occupation in high altitudes, a point also highlighted by Roche et al. (1988). The presence of some obsidian handaxes, considered to be imported from a source 100 km away (Clark and Kurashina, 1979a), has also been mentioned as early evidence of long distance transfer of raw materials (e.g., Féblot-Augustins, 1990). Documentation of burned rocks in Gadeb 8E (Barbetti et al., 1980) has been repeatedly claimed as possible early evidence for the use of fire (Gowlett et al., 1981; James, 1989; Bellomo, 1993). Likewise, the partial skeleton of a hippopotamus in Gadeb 8F was interpreted as an early case of a butchery site (Clark and Kurashina, 1979a; Clark, 1987), and referred to as such by other authors (Isaac, 1984; McBrearty, 2001). Finally, Gadeb is also known for the purported inter-stratification of Developed Oldowan and Acheulean sites throughout the sequence (Clark and Kurashina, 1979a), a claim that has been widely discussed in recent years (Stiles, 1980; Isaac, 1981; Binford, 1985; Potts, 1991; Bar-Yosef and Goren-Inbar, 1993; Schick and Toth, 1994; Kyara, 1999; de la Torre, 2008).

I added the emphases there just to reflect the importance of the site to many different topics related to Early Pleistocene hominin behavior.

Looking closely at these 1970s and 1980s era publications, it is remarkable how little documentary detail they provide. Archaeologists for forty years were citing—are still citing—all these claims from Gadeb. The early fire, the hippo butchery, the interstratification of Developed Oldowan and Acheulean, and the raw material transport have all come in to reviews of the evidence and debates about the behavior of Early Pleistocene hominins. Yet, as de la Torre reflected, the basic details were not widely available for examination.

Despite regular referencing to Gadeb in recent literature on the East African Early Stone Age, no revision of the lithic assemblages has been carried out since the original studies by Clark and Kurashina in the 1970s. In fact, the only systematic account of the Gadeb assemblages (Kurashina, 1978) was never published, and no other detailed reports of the lithics were made available.

So much in Paleolithic archaeology of the 1960s and 1970s was accepted on the authority of the researcher, especially those working in Africa. Journal articles allowed the illustration of only a tiny handful of artefacts from any assemblage, and authors tended to select illustrations that confirmed their assessment of typology.

For example, the 1979 Nature article describing the Gadeb assemblages has only two illustrations of artifacts, this one representing two distinct sites:

Figure 4 from Clark and Kurashina 1979, illustrating the tools from Gadeb 8E and 8F

The tool indicated by number 2 in this figure was the only artifact illustrated in the article from the “hippo butchery” site of Gadeb 8F. That’s only one out of 385 artifacts, of which 18.4%, or 71, were reported to be “shaped tools”. The hippo remains were not illustrated; de la Torre (2011:774) discussed these hippo remains (citing Kurashima 1978) noting that the “partial skeleton” consisted only of three tusks, one rib, and a left scapula.

What do I make of this?

Although many have cited the observation of long-distance obsidian transport at Gadeb, few examined the claim critically. An exception is Nick Blegen, who in 2017 described a later instance of obsidian transport at Baringo, Kenya. The Baringo study is a nice example of geoarchaeology, in which the chemical composition of rocks provides evidence of where they came from on the landscape. “The earliest long-distance obsidian transport: Evidence from the ~200 ka Middle Stone Age Sibilo School Road Site, Baringo, Kenya”.

Blegen explained that the source of the obsidian in the Gadeb handaxes had not been confirmed by chemical evidence:

Obsidian artifacts are rare at Acheulean sites in the Early and Middle Pleistocene of eastern Africa. When present, obsidian comprises a tiny proportion (<0.1%) of the overall lithic artifact composition (Ambrose, 2012). Four obsidian handaxes from Gadeb, Ethiopia are asserted to derive from as far away as 100 km (Clark, 1987; Féblot-Augustins, 1990), but these are not geochemically confirmed and many sources in this region remain to be documented (see Ambrose, 2012). Geochemically confirmed examples of Acheulean obsidian transport include Melka Kunture in the Ethiopian rift, where obsidian comes from 7 km away (Negash et al., 2006), and Kariandusi, Kilombe and Katabuya in the central Kenyan Rift (Merrick et al., 1994). None of the obsidian from these central Kenyan Rift sites demonstrates transport distance >15--30 km. The obsidian at all the Acheulean sites listed above was probably not acquired farther away than the sources of other, coarser grained, raw materials such as lavas (Merrick and Brown, 1984; Merrick et al., 1994). The only geochemically confirmed exception is a single obsidian artifact found in the excavations of the Acheulean site Isenya on the Athi-Kapiti Plain, Kenya, sourced to Kedong ~60 km away (Merrick et al., 1994). The Middle Pleistocene MSA sites of Gademotta are situated at the source of the Worja obsidian, and this seems to be the raw material used for most (>94%) of their lithic raw materials (Sahle et al., 2014).

From that point of view, Clark’s 1987 claim cannot be substantiated. Without a comprehensive attempt to find all obsidian sources, there may be a closer source of which Clark was unaware. But the unknown possibility of a closer obsidian source doesn’t falsify Clark’s claim of long-distance transport. The possibility is an alternative explanation that should be tested. Yet this points to an important way that standards of evidence have changed since the mid-1980s. Today, claims about the possible transport of stone by ancient hominins must rely upon data about the geochemistry of rocks across a broad region. Such data now often make it possible to positively identify obsidian sources. If a geoarchaeologist wants to say something negative about identification (“no closer source than 100 km”), that statement should be accompanied by some good sampling of rocks across that 100 km region to rule out a closer source.

But it’s also possible to go too far toward uncritical rejection of evidence. Some archaeologists have considered long-distance obsidian transport to be a “marker of behavioral modernity”. They have identified long-distance transport with trade, social organization, and logistical planning—all things that sound very advanced and complicated. From this point of view, if a species that wasn’t a modern human actually moved a few obsidian flakes across the Gadeb Plateau, it looks like an inconsistency. This bias makes the claim look extraordinary.

And we know what extraordinary claims require.

In my opinion, archaeology needs new ways to talk about rare observations. Obsidian is a rare raw material in most archaeological sites. It stands out.

In recent times, stone knappers have highly valued obsidian and traded for it over long distances. It is tempting to look at long-distance transport as evidence of such trading networks. But 100 km is only two or three days’ travel. Finding a rare handful of cases in the Middle Stone Age of obsidian transport over such a distance does not establish the ubiquity of trading networks, any more than finding a single instance much earlier in time requires a trading network. Rare behaviors happen. They may enlighten us about the capabilities or broader behavior patterns of past people, or they may just tell us about singular events or circumstances.

It is reasonable to seek additional evidence to make claims about rare behavior in the past more reliable and replicable. Sometimes when archaeologists first notice a rare observation and start seeking out additional cases, they find them un unexpected abundance.

This was what happened after Marco Peresani and coworkers reported in 2011 on the Neanderthal harvesting of feathers from birds at Fumane Cave: “Late Neandertals and the intentional removal of feathers as evidenced from bird bone taphonomy at Fumane Cave 44 ky B.P., Italy”. Other archaeologists examined collections from Neandertal sites, some excavated more than a hundred years before, and found more and more evidence of the same behavior. That has been a beautiful example of how new discoveries prompt scientists to re-examine old evidence for signs they might have missed.