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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

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.

Legacy of a candidate gene and replication in genomics

During the 1990s and early 2000s, many human geneticists and other scientists (especially psychologists) tried to study the genetics of human traits by following a candidate gene approach. In this approach, researchers studying a phenotype identified a genetic polymorphism and tested it within a sample of individuals to see whether it correlated with their phenotype.

The criteria for identifying a polymorphism as a “candidate gene” varied from study to study. The single most widespread criterion was that the polymorphism had to be easy to genotype using early 1990s-era genetic approaches. Length polymorphisms and microsatellite (STR) loci were especially common as polymorphic markers. Later, when microarray approaches became cheaper and more reliable, many researchers continued to rely upon the length polymorphisms and STR markers because they were comparable with older literature. To do this, researchers worked to find which SNP haplotypes were linked to the length polymorphism, enabling them to impute length polymorphism alleles from SNPs.

Ideally, researchers hoped to identify genes with protein products that had a plausible biochemical connection to a trait. The idea was that biochemistry and cell biology could identify networks of genes that had a structural or regulatory role in generating a phenotype, and that systematic investigation of the variation in those specific genes would enable researchers to discover the genetic causes of variation in the phenotype.

One of the most famous of the “candidate gene” length polymorphisms for psychological and behavioral phenotypes is the 5-HTTLPR polymorphism. This is a length polymorphism that lies in or near the 5’ promoter region of the gene SLC6A4. Serotonin, also known in the biochemical literature as 5-HT, is transported into neurons by SLC6A4. The serotonin transporter protein became known as the 5-HT transporter, or 5-HTT.

Armin Heils and coworkers during the mid-1990s found a tandem repeat polymorphism in the promoter region of 5-HTT, which they found to be connected to gene expression activity: “Allelic Variation of Human Serotonin Transporter Gene Expression”. They named this polymorphism 5-HTTLPR, and hypothesized that it may be related to variation in behavior:

We have recently characterized the human and murine 5‐HTT genes and performed functional analyses of their 5′‐flanking regulatory regions. A tandemly repeated sequence associated with the transcriptional apparatus of the human 5‐HTT gene displays a complex secondary structure, represses promoter activity in nonserotonergic neuronal cells, and contains positive regulatory components. We now report a novel polymorphism of this repetitive element and provide evidence for allele‐dependent differential 5‐HTT promoter activity. Allelic variation in 5‐HTT‐related functions may play a role in the expression and modulation of complex traits and behavior.

This kind of assertion was very exciting to psychologists who were looking for ways that genetics might influence behavior. The 5-HTTLPR polymorphism was easily genotyped with mid-1990s-era approaches. It wasn’t cheap, but it was cutting edge science. A possible large-effect variant affecting behavior would fit well with behavioral psychology approaches that relied on samples of dozens of individuals. One lab after another began to test whether 5-HTTLPR was related to behavior.

Later, a similar polymorphism was discovered in the 5-HTT gene of rhesus macaques. The monkey polymorphism enabled experimenters to test how the gene might influence responses to maternal deprivation, alcohol exposure, and many other conditions.

All of this has been a long-winded way of introducing a recent blog post by Scott Alexander, who looked into the legacy of this research on the 5-HTTLPR polymorphism and psychological and behavioral phenotypes: “5-HTTLPR: A pointed review”.

To make a long story short, twenty years of research into this candidate gene appear to have been largely a waste of time and effort. Today, well-powered studies involving thousands of research subjects have shown that SLC6A4 makes little to no difference in clinical conditions or normal behavior.

Alexander reviews this result and emphasizes the depth of the problem in a way that I’ve seen few state so clearly:

First, what bothers me isn’t just that people said 5-HTTLPR mattered and it didn’t. It’s that we built whole imaginary edifices, whole castles in the air on top of this idea of 5-HTTLPR mattering. We “figured out” how 5-HTTLPR exerted its effects, what parts of the brain it was active in, what sorts of things it interacted with, how its effects were enhanced or suppressed by the effects of other imaginary depression genes. This isn’t just an explorer coming back from the Orient and claiming there are unicorns there. It’s the explorer describing the life cycle of unicorns, what unicorns eat, all the different subspecies of unicorn, which cuts of unicorn meat are tastiest, and a blow-by-blow account of a wrestling match between unicorns and Bigfoot.
This is why I start worrying when people talk about how maybe the replication crisis is overblown because sometimes experiments will go differently in different contexts. The problem isn’t just that sometimes an effect exists in a cold room but not in a hot room. The problem is more like “you can get an entire field with hundreds of studies analyzing the behavior of something that doesn’t exist”. There is no amount of context-sensitivity that can help this.

Today, there are geneticists who criticize the GWAS approach. GWAS identifies statistical associations between SNP alleles in a sample and phenotypes, but most of these associations have not led to better knowledge of the biochemical or developmental pathways by which genes affect phenotypes.

Indeed, the genetic variations that actually cause phenotypic variations are invisible to GWAS. The method’s reliance on the phenomenon of genetic linkage between common SNPs and causal variants means that findings from any one population may have little application to other populations that share a different history that gave rise to different linkage patterns.

Still, many geneticists who began their careers within the last fifteen years may not know the history of the 1990s and early 2000s-era human genetics. At that time, some geneticists strongly pushed the idea that gene discovery must be supported by clear biochemical evidence demonstrating the mechanism by which gene variants affect phenotypes.

In those days, I had many conversations with human geneticists who were endlessly frustrated that they couldn’t get their work published because it was based upon genome-wide analyses. Some reviewers insisted on biochemical work to support statistical evidence of gene-phenotype associations.

5-HTTLPR was strongly pushed by those who wanted this kind of biochemically-informed approach to genomics. The variant was almost the perfect candidate gene.

Chimpanzees learn to crack nuts faster than humans

Early this year, Christophe Boesch and coworkers released a paper describing their observations on how fast chimpanzees and humans learn to crack nuts. They collected data on human foragers from the Mbendjele group, and chimpanzees of the Taï forest, watching how children and juvenile chimpanzees learn from other individuals, the extent that older individuals “teach” by intentionally directing their behavior toward the learners, and measuring the rate at which individuals can get panda nuts out of their shells.

The method that each group uses to crack nuts is very similar.

Most people’s intuition probably would suggest that humans would learn how to crack nuts faster than chimpanzees. Boesch and coworkers found the opposite: Chimpanzees learn much faster than humans, and chimpanzees attain adult proficiency at much younger ages than humans do.

Figure showing nutcracking speed versus age in chimpanzees and human hunter-gatherers
Figure 1 from Boesch et al. 2019. Original caption: "Learning curves for the ‘number of nuts cracked per minute’ in Taï chimpanzees and Mbendjele foragers; (a) when considering absolute age (above) and (b) when considering relative age whereby 1.0 corresponds to the population-specific age of first reproduction. Indicated are the fitted model and its confidence intervals. For the plot age was binned (bin width: 0.1 year), and the number nuts cracked per minute was averaged per age bin. Symbol area represents the total observation time per age bin (0.1 to 15.8 hours)."

This is just an incredible figure. Taï chimpanzee adults and Mbendjele adults both end up with a similar pace of nutcracking – the humans average a bit higher but the variation among human and chimpanzee adults overlaps completely.

The paper includes a nice paragraph describing the acquisition of technical knowledge in humans from many small-scale societies. The overarching generalization is that human foragers and small-scale agriculturalists take many years to attain maximum performance in tasks that require some technical learning:

Recent studies about the acquisition of technical intelligence skills in humans revealed that apprentices may need many years of practice before reaching adult expertise. Despite social exposure to expert tool users’ performances and advice, apprentices only acquire the skills after many years of practice and with slow progress in performance. For example, stone knappers in Langda, New Guinea begin to acquire the technique as adults but appear to encounter difficulties in following the guidance and advice from skilled individuals, as for at least five years, they continue to produce much shorter adze heads employing different strategies than the ones demonstrated to them. A similar pattern has been observed in Khambhat, India, with the acquisition of another type of stone knapping technique, where apprentices pay no attention to some aspects of the technique used by experts, such that their final products are quite different from those of the latter. As a result, high quality beads are produced only after seven to ten years of practice. Similarly, long learning processes have also been documented for the hourly return rate in hunting and honey, palm heart, or tuber gathering among the Ache or the Hiwi, for the reported age of acquisition in different tasks ranging from food and craft production to music and story-telling among the Tsimane of South America, and for the production of knapping stones as tools for hideworking in Ethiopia.

The cross-cultural buildup of such data over the last 20 years has given rise to the idea that learning technical processes is so difficult that humans must be specially adapted to be able to learn this stuff. In such studies, the apparently very long period of skill acquisition is characteristic even of tasks like honey collection and digging tubers.

But the fact that chimpanzees learn to crack nuts much faster than humans causes Boesch and coworkers to suggest an alternative hypothesis. Humans are slower at learning how to do things because humans have a larger number of specialized technical tasks to learn how to do. They term this a “life history” hypothesis, because their proposition is that humans develop slower and need to attain full competency at adulthood, not as juveniles, and so humans have the luxury of taking longer at each individual task, possibly enabling them to learn a larger number of specialized tasks.

Both of these hypotheses take what seems like a bug and try to make it a feature. Humans in foraging societies take 20 years to achieve peak hunting returns. Why should this be, when lions manage to achieve peak returns in only 3 or 4 years? According to the “hard to learn” hypothesis, it is because human hunting is a lot harder to do than lion hunting, because humans are using a very technical set of abilities. According to the “life history” hypothesis, it is because humans have lots of other things on their plate, and their learning has to balance all these things against the timeline of development.

Obviously, the nutcracking example busts the “hard to learn” logic, because chimpanzees are using the same method as humans, and achieve peak performance much faster.

But the “life history” hypothesis doesn’t seem to describe the pattern for learned skills that humans start to perform as adolescents and fail to become fully proficient until age 35 or higher. I come back to the question of why it takes humans 20 years to achieve peak hunting success. The problem is similar in timeline to the “apprenticeship” examples of specialized tool manufacture mentioned above.

One answer might be that the “life history” hypothesis works for easier tasks, and the “hard to learn” hypothesis works for harder ones. Chimpanzees do not become craft specialists or tenured professors. Maybe these really are uniquely difficult, and that’s why it takes humans so long to become proficient at them (and many never become proficient).

I would offer an alternative possibility: Humans may take a long time to gain apparent efficiency of performance in such tasks because human social relationships hold back performance.

Some tasks are communal, meaning that all individuals in a group may benefit from one person’s effort, while no person can monopolize the fruits of her labor. As a result, individuals are disincentivized from maximal performance, as long as that performance has costs. For example, hunters in a hunting and gathering society vary greatly in their average success rate and return rate of meat. Studies of hunters in such societies have shown that adolescents have low return rates, which increase gradually up to age 35 or 40. Those returns later decline at older and older ages. This pattern has previously been explained as the delay caused by the time needed to learn complicated hunting skills. But such a hypothesis neglects the costs of hunting. Such costs include energetic costs from hunting effort, risk of injury or death while hunting, the opportunity costs of socializing or pursuing other activities, and the social obligations that are imposed upon good hunters, among others. In a food sharing group, a young hunter would be entirely rational to pursue a strategy of increasing learning effort only as older hunters decline in their abilities.

Likewise, an apprentice often would be best served not to attain too great a skill while still under the thumb of his master. If the apprentice can actually monopolize the benefits of his own labor, the situation would be different, but an apprentice’s independence depends on an intricate network of social relationships, not purely the quality of his work.

It is at the same time quite true that some human technical tasks are made vastly more complicated by cultural rules. For example, something as simple as a bead has many culturally determined characteristics, including length, diameter, smoothness, type of drill hole, material, and many others that increase the difficulty of an craftsman attaining the necessary precision.

My point is that watching how fast individuals in real societies attain maximal performance is a very bad measure of how fast they might be able to learn. Human motivation is social, not merely economic.

Pointing to a need for better data presentation

Knowable magazine, which is an outlet of the Annual Reviews series of journals, has a great current article by Betsy Mason on the need to improve how scientists present their data: “Why scientists need to be better at data visualization”.

The problem of meaningful data visualization is approaching critical proportions in the study of human population genomics. Common means of portraying variation among genomes simply typically be interpreted by anyone without deep experience in examining them.

Mason’s article doesn’t touch upon these more difficult types of visualization, but it provides some solid context on the bigger picture of misleading graphs and color schemes across the sciences. I endorse this point about tools: Scientists won’t spend time learning good visualization methods themselves, but they have to use tools.

One way to combat the power of precedent is by incorporating better design principles into the tools scientists use to plot their data (such as the software tools that have already switched from the rainbow default to more perceptually even palettes). Most scientists aren’t going to learn better visualization practices, O’Donoghue says, “but they’re going to use tools. And if those tools have better principles in them, then just by default they will [apply those].”
Scientific publishers could also help, he says. “I think the journals can play a role by setting standards.” Early-career scientists take their cues from more experienced colleagues and from published papers. Some journals, including PLoS Biology, ELife and Nature Biomedical Engineering have already responded to Weissgerber’s 2015 work on bar graphs. “In the time since the paper was published, a number of journals have changed their policies to ban or discourage the use of bar graphs for continuous data, particularly for small data sets,” she says.

Even in paleoanthropology, where beautiful physical objects like fossils and stone tools are an important part of our work, we could do much better than most current practice in finding ways to make information comprehensible to readers.

Working toward more ethical anatomical collections at the University of Cape Town

Victoria Gibbon of the University of Cape Town has written a piece for The Conversation recounting how UCT is addressing some historical wrongs in the development of its human anatomy collection: “Skeletons and closets: How one university reburied the dead”.

I returned to the University of Cape Town (UCT) and examined the Human Skeletal Repository records. Unfortunately, I found 11 individuals with known names or dates of deaths or which were known to the donor in life. The research suggested these remains should not be at the university.
Fast forward to 2018 after a lengthy process of figuring out a way forward. With the university’s Office of Inclusivity and Change we have embarked on the initial phase of the restitution project. Of the 11 unethically procured sets of remains, nine are from the town of Sutherland in the Northern Cape. We decided to start there.

This case has been in the news in South Africa during the last few weeks, and this essay is a good opportunity to see the case from the perspective of a biological anthropologist.

Anopheles mosquitoes disperse over long distances by wind

This is decidedly unsettling: “Windborne long-distance migration of malaria mosquitoes in the Sahel”.

Studies seeking to understand the paradoxical persistence of malaria in areas in which surface water is absent for 3–8 months of the year have suggested that some species of Anopheles mosquito use long-distance migration. Here we confirm this hypothesis through aerial sampling of mosquitoes at 40–290 m above ground level and provide—to our knowledge—the first evidence of windborne migration of African malaria vectors, and consequently of the pathogens that they transmit.

The work is by Diana Huestis and coworkers in Nature. The long-distance dispersal helps to address why it is so hard to eliminate malaria. It looks like females (80% of those dispersing this way) take on blood meals and then hitch a ride on the wind.

Are three-rooted molars evidence of Denisovan introgression in Asia?

During the 1980s and 1990s, the idea of multiregional evolution of modern humans was based upon the observation that today’s people living in various regions of the world share traits with archaic humans who lived in the same regions. Such traits provided evidence of regional continuity of ancestry.

This summer a brief report by Shara Bailey, Jean-Jacques Hublin, and Susan Antón suggested that three-rooted mandibular premolars in today’s Asian populations have actually been inherited from Denisovans: “Rare dental trait provides morphological evidence of archaic introgression in Asian fossil record”.

According to this idea, three-rooted mandibular molars are a regional continuity trait in Asia. Molars in the mandibular dentition usually have two roots, but a three-rooted form occurs in East Asian people fairly commonly.

It has long been thought that the prevalence of 3-rooted lower molars in Asia is a relatively late acquisition occurring well after the origin and dispersal of H. sapiens. However, the presence of a 3-rooted lower second molar in this 160,000-y-old fossil hominin suggests greater antiquity for the trait. Importantly, it also provides morphological evidence of a strong link between archaic and recent Asian H. sapiens populations. This link provides compelling evidence that modern Asian lineages acquired the 3-rooted lower molar via introgression from Denisovans.

Here is the illustration including the virtual model of the Xiahe M2.

Figure 1 from Bailey et al. 2019, showing the three-rooted alveoli for M1 and CT scan of three-rooted M2 from the Xiahe mandible
Figure 1 from Bailey et al., 2019. Original caption: The 3-rooted lower molar anomaly. Three-rooted lower first molar alveolar sockets showing distolingual position of accessory root and the 3-rooted lower first molar (lingual view); (Inset) 3-rooted lower second molar of Xiahe Denisovan individual (lingual view). Left and Middle images courtesy of Christine Lee (California State University, Los Angeles, CA). M, mesial; L, lingual; D, distal; B, buccal. Credit Bailey et al. CC-BY-NC-ND 4.0

I think that Bailey and coworkers here present an interesting hypothesis. This idea brings back to my mind some of the 1990s-era discussion about how scientists should recognize evidence of genetic admixture or introgression from morphological traits.

During the 1990s, several scientists were highly critical of others’ identification of “continuity features”. They noted that it was difficult to prove that any feature was a unique markers of descent from local archaic humans, because the fossil record is incomplete and biased. Some features that had been identified as continuity traits in Neandertals and later Europeans, they argued, might also have been present in earlier African populations but not yet sampled in the tiny fossil record of the Middle Pleistocene in Africa. Much discussion about regional continuity during the 1990s (and to some extent even earlier) focused upon whether “Neandertal” traits in later Europeans really were uniquely found in Neandertals, or whether they might have been in other populations at non-negligible frequencies.

Many advocates of an “out of Africa” model of evolution also suggested that apparent continuity traits might instead have resulted from parallelism or convergence in the newly-arrived modern humans. In their view, early modern humans might rapidly evolve to become similar to archaic humans in the same parts of the world, because of natural selection in the same local environments.

My own concern at the time was that continuity traits suffer an analytical bias that is hard to deal with. A strange trait that we see in a Neandertal is easy to notice when we see it in later European skeletal remains. But we don’t really know how likely such similarity may be without considering the total number of traits we didn’t notice.

This brings us back to sampling. In the period just before the apparent dispersal of modern humans from Africa, anthropologists have found many Neandertals and relatively few of anything else. If we accept that the Xiahe mandible is really a Denisovan (which maybe we should be more cautious about), that still brings the net number of Denisovan specimens with lower first molars to the grand total of one.

I always thought it was quite reasonable to start from the assumption that the data probably reflect a simple mixture model, and a Neandertal trait that was present at a lower frequency in Upper Paleolithic Europeans probably reflected some ancestry into that population from Neandertals.

I still think that’s reasonable, but my perspective has changed a bit. The main difference in my thinking today is that we know that the fractions of ancestry from many archaic groups are small—on the order of a few percent. I don’t think we can predict much about how such small levels of ancestry may affect morphology.

Europeans do have Neandertal ancestors—we now know that beyond any question. But East Asians today also have Neandertal ancestors. In fact, Neandertals contributed more genetic ancestry to East Asians than they did to Europeans. And Neandertals contributed more than ten times as much ancestry to East Asians as Denisovans contributed to East Asians.

Which morphological traits of East Asians today are markers of their Neandertal ancestry? That’s a question that presently has no answer. The answer might even be “none”. But it would be strange for East Asian people today to have no skeletal signs of Neandertal ancestry if European people (with less Neandertal ancestry) have some skeletal features that point that direction.

And it would be even more remarkable for many East Asians to have a dental trait that uniquely reflects their 0.002 fraction of Denisovan ancestry and have none that reflect their 0.02 fraction of Neandertal ancestry.

Maybe it’s really true. If so, we should probably guess that natural selection has acted on three-rooted mandibular molars differently from other traits, favoring its persistence in later populations.

I think it’s good to be alert for morphological connections between living and archaic groups. I don’t assume that they will reflect the frequency of contribution of genes from archaic groups. If the frequency of a trait diverges a great deal from the small fraction of genetic ancestry, it may be a sign of interesting evolutionary dynamics.

Quote: Darwin on the tree of life

Charles Darwin, in On the Origin of Species, introduced the idea that the relationships between organisms form a tree.

Darwin was not the first to propose that species resulted from evolution, but earlier ideas like Lamarck’s envisaged evolution as a transformation along a chain of species.

Darwin, near the end of Chapter 4 of Origin, discussed his idea about the relationships of organisms as part of a tree. This passage is not as quoted as the famous “tangled bank” passage, but it has similar power:

The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth. The green and budding twigs may represent existing species; and those produced during each former year may represent the long succession of extinct species. At each period of growth all the growing twigs have tried to branch out on all sides, and to overtop and kill the surrounding twigs and branches, in the same manner as species and groups of species have tried to overmaster other species in the great battle for life. The limbs divided into great branches, and these into lesser and lesser branches, were themselves once, when the tree was small, budding twigs; and this connexion of the former and present buds by ramifying branches may well represent the classification of all extinct and living species in groups subordinate to groups. Of the many twigs which flourished when the tree was a mere bush, only two or three, now grown into great branches, yet survive and bear all the other branches; so with the species which lived during long-past geological periods, very few now have living and modified descendants. From the first growth of the tree, many a limb and branch has decayed and dropped off; and these lost branches of various sizes may represent those whole orders, families, and genera which have now no living representatives, and which are known to us only from having been found in a fossil state. As we here and there see a thin straggling branch springing from a fork low down in a tree, and which by some chance has been favoured and is still alive on its summit, so we occasionally see an animal like the Ornithorhynchus or Lepidosiren, which in some small degree connects by its affinities two large branches of life, and which has apparently been saved from fatal competition by having inhabited a protected station. As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications.

Milk proteins in Neolithic dental calculus

A new research paper by Sophy Charlton and coworkers looks at calculus on human teeth from several Neolithic-era sites in England, finding that many of the individuals have trace evidence of milk consumption: “New insights into Neolithic milk consumption through proteomic analysis of dental calculus”.

There has long been debate over the origins of dairy consumption within European populations. Whilst it was previously assumed that lactase persistence (LP) was under positive selection following the advent of agriculture, recent genetic studies of prehistoric human remains have revealed LP may have only emerged in Europe in the last 4000 years. These findings stand in contrast to organic residue analysis of Neolithic pottery indicating the utilisation of dairy products, and zooarchaeological mortality profiles consistent with dairying herds at Neolithic sites. The recent discovery of the milk protein β-lactoglobulin (BLG) within human dental calculus presents a new method via which to explore dairy product consumption in the archaeological past. Here, we apply shotgun proteomic analysis to dental calculus samples from three British Neolithic sites, revealing the earliest identification of BLG in human dental calculus to date. The presence of BLG peptides in individuals who are unlikely to possess LP provides new insight into dairying in the British Neolithic, suggesting the potential processing of milk by Neolithic populations to reduce the lactose content of dairy products.
Additionally, organic residue analysis of pottery from Hambledon Hill has indicated the presence of both porcine and ruminant fats, and ruminant adipose and dairy fats (Copley et al. 2003, 2005a, b, 2008). The presence of dairy fats in > 25% of potsherds analysed has been suggested to indicate that ‘dairying was a very important element of animal husbandry at Hambledon Hill’ (Copley et al. 2008, p. 535).

It’s nice to have confirmation that milk trace residues in pottery co-occur with milk trace residues in human dental calculus. More and more sites where these data show a pattern will help us to understand the big picture – both by helping us to interpret sites where preservation is not as good, and by looking at smaller-scale shifts in diet.

It is no surprise that people in Britain started relying upon animal milk before lactase persistence was common in northern European populations. That’s how natural selection works. The environment changes, creating different survival and fertility conditions. Only then can genes that are adaptive in the new environment proliferate due to selection in the population.

Can methylation of DNA in ancient bones really predict the morphology of Denisovans?

Last week, Cell published a new paper by David Gokhman and coworkers that tries to infer the skeletal form of Denisovans from signatures of methylation in the Denisovan genome data. The paper is here: “Reconstructing Denisovan Anatomy Using DNA Methylation Maps”.

I’m a skeptic about the paper. The authors follow an approach that has not been shown to predict the morphology of any living humans or any other species.

The study tries to justify its method by looking at Neanderthal methylation and saying that the methylation pattern can accurately predict Neanderthal bone shapes. This may look convincing on the surface. But it’s actually not. This is a case where “researcher degrees of freedom” are very high.

I am working on a comment to submit to Cell about the study, focusing on some technical issues. I hope that the editors will be interested in publishing a critical exchange on the approach.

In the meantime, I want to point readers to a related study by another group of researchers that has been mostly ignored in the press coverage on this new paper.

Genevieve Housman and coworkers released a preprint earlier this year on biorXiv that looked at methylation patterns in several primate species (chimpanzees, macaques, vervet monkeys, baboons, and marmosets) to see if methylation could predict skeletal morphology within species or between species.

The preprint is here: “Intra- and Inter-Specific Investigations of Skeletal DNA Methylation and Femur Morphology in Primates”.

Housman and coworkers carried out a careful study that includes several analyses that are not in the new Cell paper by Gokhman and colleagues. Housman and coworkers measured DNA methylation in bone cells taken from the femur of each primate individual, and they actually took caliper measurements on the femur of each individual. This means that in every case they compared like with like. That’s different from what Gokhman and colleagues could do with ancient DNA, where the samples are coming from different parts of the skeleton from a mixture of different cell types.

Housman and coworkers found some methylation differences that seemed to associate with morphology in their samples. But these were small effects that they could not separate from other possible influences (genetic and environmental differences). I would add that the small sample sizes in the study (only 4 chimpanzees, for example) make it possible that the observed effects might be spurious effects of small samples.

When they looked between species, Housman and colleagues found differences in methylation, similar to Gokhman and coworkers in this new study. Some of those differences in methylation are near genes that matter to skeletal form. Gokhman and coworkers found the same thing for Denisovans and Neanderthals. But in the living primates, the methylation differences actually did not correlate well to the phylogenetic relationships of the primate species. While Housman and coworkers suggest that the methylation differences between species might make some difference to the evolution of their traits, they did not try to predict what those differences were. That’s very reasonable considering the lack of clear signatures within species and the small proportion of the genome included in these regions with different methylation.

What I think: Studying methylation differences is a promising avenue of research, but we are a long way from understanding how differences in methylation may relate to differences in the skeleton. It is important to match like with like – in the Housman study, the methylation of femur bone cells was used to study femur form.

It’s not outlandish to think that the pattern of methylation across promoters in the genome might give a clue about morphology. But there are huge gaps in our knowledge. And there are things we know about methylation in bone that this study doesn’t seem to represent. Those make me skeptical that this study is doing much more than presenting an interesting hypothesis.

I’ve seen a number of geneticists quoted in news stories, saying that now paleoanthropologists will have to test what methylation has told us about Denisovan morphology. That’s only partly correct. A test with paleontology cannot be valid until comparative evidence supports the proposed mechanism connecting differential methylation to morphology—remember, based here upon indirect functional inference for only 2.2 genes per trait.

But if we’re looking for a paleontological test, the Xiahe mandible may already provide one. Gokhman and coworkers predict that the Denisovan dental arch should be longer than modern humans and also longer than Neandertals. The Xiahe mandible, with its complete M3 agenesis, does not have a long dental arch.