Tag Archives: Helen Briggs

Ancient Chewing Gum Yields DNA!

This winter researchers from Europe report a fascinating find from a salvage archeology site in Denmark, a piece of birch pitch that was chewed by a woman approximately 5,700 years ago.  The interesting thing is that the tarry pitch evidently preserved the traces of tissue and microbes from her mouth, sufficiently well that the DNA could be sequenced [2].   Wow!

Piece of 5,700-year-old birch pitch from Syltholm, southern Denmark. Image Credit: Theis Jensen (From [1])

“In the process of chewing, the DNA becomes trapped in the pitch where it is preserved due to the aseptic and hydrophobic properties of the pitch which both inhibits microbial and chemical decay.” ([2], p. 7)

My first question was, how did they recover the DNA?

As far as I can tell, the saliva and whatnot were just folded into the tar, which sealed over and preserved it.  Carefully dissolving samples of tar release the trapped DNA.


This sample provides an amazing window into the person who chewed the tar.  She was female, and probably beautifully brown skinned. Age unknown.  Statistics suggest she was related to populations from central Europe, though she lived in Denmark at a time when Neolithic farmers were taking over.

The samples also include DNA from many microbes, mostly the normal contents of her mouth.   There are suggestions of gum disease and possible pneumonia.  My impression is that the outstanding thing is that it is very similar to contemporary humans.  I don’t know much about this biome, but I have to assume that this sample would be of interest to the study of the evolution of these symbiotic microbes over the last 5,000 years.

There were also traces of DNA from ducks and hazelnuts, which the researchers attribute to a recent meal. She probably wasn’t lactase tolerant, suggesting that her people were not dairy herders.  Her genome is related to hunter gatherer groups, indicating that groups from the south were still present in Scandinavia as the development of farming began.

“The genomic information preserved in chewed pieces of birch pitch offers a snapshot of people’s lives, providing information on genetic ancestry, phenotype, health status, and even subsistence. In addition, the microbial DNA provides information on the com-position of our ancestral oral microbiome and the evolution of specific oral microbes and important human pathogens.” ([2], p. 7)

Very interesting.

  1. Helen Briggs, DNA from Stone Age woman obtained 6,000 years on, in BBC News – Science & Environment. 2019. https://www.bbc.com/news/science-environment-50809586
  2. Theis Z. T. Jensen, Jonas Niemann, Katrine Højholt Iversen, Anna K. Fotakis, Shyam Gopalakrishnan, Åshild J. Vågene, Mikkel Winther Pedersen, Mikkel-Holger S. Sinding, Martin R. Ellegaard, Morten E. Allentoft, Liam T. Lanigan, Alberto J. Taurozzi, Sofie Holtsmark Nielsen, Michael W. Dee, Martin N. Mortensen, Mads C. Christensen, Søren A. Sørensen, Matthew J. Collins, M. Thomas P. Gilbert, Martin Sikora, Simon Rasmussen, and Hannes Schroeder, A 5700 year-old human genome and oral microbiome from chewed birch pitch. Nature Communications, 10 (1):5520, 2019/12/17 2019. https://doi.org/10.1038/s41467-019-13549-9
  3. Knvul Sheikh, What a 5,700-Year-Old Wad of Chewed Gum Reveals About Ancient People and Their Bacteria, in New York Times. 2019: New York. p. 2. https://www.nytimes.com/2019/12/17/science/ancient-gum-dna.html

DNA from Stone Age woman obtained 6000 years on,

What a 5700-Year-Old Wad of Chewed Gum Reveals About Ancient People and Their Bacteria

Neolithic Baby Bottles

Neanderthal kids ran all over the place.

This fall researchers from Europe report new evidence that spouted ceramic vessels made in Europe about 7,000 years ago were used to feed infants [2].  These vessels have been found in many locations, and sometimes have zoomorphic shapes.  They have been interpreted as having been used by people to suck liquid from the stem, presumably, animal product in some cases (milk? blood? soup?)

The new research examined some of these vessels and found chemical residues that indicate the presence of animal milk.  The researchers suggest that these vessels were used to feed babies or young children.  They note that several graves have been documented containing a young child with a stemmed vessel closely associated.

If so, this suggests that the milk of domestic animals was an important foodstuff for these people.  They also argue that changes to weaning by augmenting children’s diets with animal milk may have contributed to the population growth observed at that time [3].  On the other hand, they point out that different animal milks have different nutritional and health implications, and unpasteurized milk risks infection and disease.

This is certainly an interesting and suggestive combination of evidence (child burials, evidence of milk consumption, use of domestic ruminants).  Of course, it is possible that these vessels were used by people of all ages, or by only some infants some of the time (e.g., when mother’s milk was not available).

In any case, it is certainly an indication that Neolithic people were every bit as concerned and inventive about child rearing as we are.  How far back does this idea go? I note that there are lots of ways to do this kind of feeding with milk (or any kind of slurry), including a tube of hide or fiber that would not be likely to be well preserved. So, the idea could have been around for a long time before people made ceramic vessels to do it.

Did Neaderthals bottle feed, too?

We also can speculate on possible evolution of the human digestive system in parallel with animal husbandry.  If some Neolithic people fed young children milk of domestic animals, there would have been selective advantage for those children who could tolerate and thrive on these animals, and dire disadvantage for others.  If so, then observations of, say, genetic tolerance for cows milk might reflect, at least in part, the results of long past cultural practices about feeding children.

  1. Helen Briggs, Prehistoric babies fed animal milk in bottles, in BBC News – Science & Environment 2019. https://www.bbc.com/news/science-environment-49813039
  2. J. Dunne, K. Rebay-Salisbury, R. B. Salisbury, A. Frisch, C. Walton-Doyle, and R. P. Evershed, Milk of ruminants in ceramic baby bottles from prehistoric child graves. Nature, 2019/09/25 2019. https://doi.org/10.1038/s41586-019-1572-x
  3. Siân E. Halcrow, Early Europeans bottle-fed babies with animal milk, in Nature – News and Views. 2019. https://www.nature.com/articles/d41586-019-02805-z

Homo sapiens v. Cave Bears

It has long been apparent that the arrival of humans in the Western Hemisphere coincided with the decline and extinction of the megafauna.  Similarly, humans wiped out the megafauna (and sometimes all the fauna) on many islands, including the unique megafauna of New Zeeland.  This pattern seems to extend back to the earliest ancestors of humans— we are descendants of the most dominant hunter of the last 100,000 years.

To be fair, climate and other non-anthropogenic factors contributed to population changes as well.  But the arrival of humans is consistently followed by the decline in populations of large animals, whatever other stresses might exist.

In this light, a study published this summer that shows evidence that Pleistocene humans wiped out Cave Bears is far from surprising [2].  It would have surprised me to find otherwise.

Now, the case of the vanishing Cave Bears is not simple.  They lived pretty much all across Europe, though primarily in caves (i.e., a limited habitat).  They appear to have been vegetarian, though they were big fierce enough to be arned hard to kill.

They disappeared about the time of the Last Glacial Maximum, i.e., at a time when cold conditions would have decimated plant life that Cave Bears depended on.  This was also the time when modern humans spread in the area.  For that matter, there is evidence that they slowly declined for thousands of years before their disappearance.  So what happened to the CBs?

A team of European researchers analyzed mitochondrial DNA extracted from the bones of 59 cave bears from locations in Europe, which was augmented by 64 previously collected samples. In addition, the research sequenced whole genomes. This is the largest and most complete sample yet collected, and included individuals from across much of the geographical range and 20,000 years.

From this relatively detailed dataset, the researchers found evidence of migration patterns of different populations of CBs over the time period, probably reflecting the geographical displacement of habitats.

The dataset shows that Cave Bear populations were quite stable, even across several cycles of glaciation and thawing.  The authors note that this hardiness is consistent with the observation that “cave bears were well adapted to severe climate as indicated by their appearance beyond the Arctic Circle” ([2], p. 6)

This finer grained temporal data shows that the decline was rapid, and started 20,000 years after the beginning of the Last Glacial Maximum.  This decline started during a time when Homo neaderthalis was common, but accelerated at the time of the expansion of Homo sapiens.

“Although the initial decline in population size started shortly before 50 ka BP during the end of the Mousterian associated with Neanderthals, the more drastic downturn of the European cave bear took place at around 35 to 40 ka BP at the onset of the Aurignacian and the expansion of anatomically modern humans in Europe “ ([2], p.7)

The study confirms a strong “homing” tendency, suggesting that Cave Bears lived their lives in their birth cave. This means that there would have been a fierce competition with humans for these caves, even if the humans weren’t preying on the bears for food (which they probably did).  The competition would have become acute during glacial maxima, when plant food was scarce and small populations—of both bears and humans—took refuge in caves.

There is always reason to be cautious about drawing complicated inferences from mitochondrial DNA, especially from just over 100 individuals scattered over tens of thousands of kilometers and years.  But the results here align with other information about the behavior of Cave Bears, not to mention what is know about Homo sapiens.

In short, there is pretty clear evidence that humans wiped out the Cave Bears, which fits the pattern seen with many species around the world.

  1. Helen Briggs, Extinction: Humans played big role in demise of the cave bear, in BBC News – Science & Environment. 2019. https://www.bbc.com/news/science-environment-49345392
  2. Joscha Gretzinger, Martyna Molak, Ella Reiter, Saskia Pfrengle, Christian Urban, Judith Neukamm, Michel Blant, Nicholas J. Conard, Christophe Cupillard, Vesna Dimitrijević, Dorothée G. Drucker, Emilia Hofman-Kamińska, Rafał Kowalczyk, Maciej T. Krajcarz, Magdalena Krajcarz, Susanne C. Münzel, Marco Peresani, Matteo Romandini, Isaac Rufí, Joaquim Soler, Gabriele Terlato, Johannes Krause, Hervé Bocherens, and Verena J. Schuenemann, Large-scale mitogenomic analysis of the phylogeography of the Late Pleistocene cave bear. Scientific Reports, 9 (1):10700, 2019/08/15 2019. https://doi.org/10.1038/s41598-019-47073-z


New global survey of viruses in oceans

The oceans are full of life (and energy and chemistry).  It stands to reason that the oceans are full of viruses, too, but we have little knowledge of what’s there.

This spring an international team reports on a global survey of virus genomes (viromes) in all the oceans, including the Arctic.  The Tara Oceans expeditions identify nearly 500,000 viral populations (each population has billions of individuals per cubic meter), which is more than ten times as many groups as known before [2].

Do tiny viruses matter?  You bet.  For one thing, they kill/eat bacteria, a lot of bacteria, and so release carbon and other nutrients—a lot of carbon and nutrients.  They also horizontally transfer genes– 10^28 per day!—with significant impacts on evolution.

The survey sampled viruses around the globe at depths down to 4000m, and, for the first time, sampled the Arctic Ocean.  Viral DNA from the samples was identified (from previous studies and heuristics), and sequenced.  With so many new groups identified, obviously most are outside previously known groups.  As in many surveys like this, we know there are a lot of viruses, and a lot of diversity, even though we don’t know much about most individual groups.

Now viruses are important, but they are at the edge of “life”, and challenge the concepts of species and genome.  For that matter, there are many interesting viruses that rely on RNA instead of DNA.  So the result reported in the study have to be interpreted with caution.

The paper discusses microdiversity versus macrodiversity and other technical issues that I really don’t grok.  So I have to be especially cautious in my own interpretations.

The study found five distinct geographic / ecological zones.  The viral ecology seems correlated with microbial ecology, but not with other nutrient or resources that seem to define microbiological ecological zones.  This seems logical, assuming that viruses are primarily  interacting with bacteria.  However, not much is understood about adaptation to these different zones.

“This suggests that we have a lot to learn about the function of genes that most likely drive niche-differentiation across the ecological zones.” ([2], p. 6)

The Arctic Ocean showed high macrodiversity, i.e., a lot of different virus groups. This was a maybe a surprise, given the temperature sensitivity of viral-microbe interactions.  I.e., it seems too cold for viruses to thrive, but they do—at least for now. The fate of these virus populations raises yet more questions about the long term implications quickly warming Arctic seas.

One thing this study does not address, but that I’m sure will be of great interest, is the relationship between the virus populations of the ocean, land, and air.  The oceans are connected to the air and land, so their micro populations are surely connected, possibly in very interesting ways.

  1. Helen Briggs, Hundreds of thousands of viruses in oceans, in BBC News – Science & Environment. 2019. https://www.bbc.com/news/science-environment-48066332
  2. Ann C. Gregory, Ahmed A. Zayed, Nádia Conceição-Neto, Ben Temperton, Ben Bolduc, Adriana Alberti, Mathieu Ardyna, Ksenia Arkhipova, Margaux Carmichael, Corinne Cruaud, Céline Dimier, Guillermo Domínguez-Huerta, Joannie Ferland, Stefanie Kandels, Yunxiao Liu, Claudie Marec, Stéphane Pesant, Marc Picheral, Sergey Pisarev, Julie Poulain, Jean-Éric Tremblay, Dean Vik, Silvia G. Acinas, Marcel Babin, Peer Bork, Emmanuel Boss, Chris Bowler, Guy Cochrane, Colomban de Vargas, Michael Follows, Gabriel Gorsky, Nigel Grimsley, Lionel Guidi, Pascal Hingamp, Daniele Iudicone, Olivier Jaillon, Stefanie Kandels-Lewis, Lee Karp-Boss, Eric Karsenti, Fabrice Not, Hiroyuki Ogata, Stéphane Pesant, Nicole Poulton, Jeroen Raes, Christian Sardet, Sabrina Speich, Lars Stemmann, Matthew B. Sullivan, Shinichi Sunagawa, Patrick Wincker, Marcel Babin, Chris Bowler, Alexander I. Culley, Colomban de Vargas, Bas E. Dutilh, Daniele Iudicone, Lee Karp-Boss, Simon Roux, Shinichi Sunagawa, Patrick Wincker, and Matthew B. Sullivan, Marine DNA Viral Macro- and Microdiversity from Pole to Pole. Cell, https://doi.org/10.1016/j.cell.2019.03.040



Ancestors of Kangaroos Could Hop

Kangaroos are wonderfully weird animals, hopping swiftly across flat country with an unmistakable gait (not to mention counterbalancing tail).

So how did this locomotion evolve?

This winner researchers from Sweden (!) report on fossils from 20 million years ago that they identify as ancestors of contemporary kangaroos [2].  These animals are similar to ancient “giant tree rats”, which is a great name for a band, but also seems to be the ancestry of kangaroos.

The new study examined the skeletons indicate that these animals were arborial, climbing and living in trees.  However, modelling the skeletons suggests that they were capable of hopping and other familiar kangaroo locomotion (including “pentapedal”, i.e., tail-ful walking(.

“We, therefore, prefer to interpret our results as indicative of comparable gait versatility in ancient fossil macropodoids, which potentially employed higher-speed bipedal hopping and/or quadrupedal bounding, in conjunction with pentapedal progression or asynchronous walking at slower speeds.” ([2], pp. 8-9)

From the limited fossil record, it isn’t clear how these animals lived and moved, or what evolutionary pressures may have influenced their anatomy and behavior.  The current study is based on statistics, but the samples are small and pretty iffy, so the results must be taken with a bit of care.

However, if these findings hold up, it seems that the basic ability to hop was present a very long time ago.  And if so, then contemporary kangaroos would have evolved to be extreme exemplars of these traits, adapting to the progressively drier climate of the last few million years.

This hypothesis reduces the mystery of how such an amazing adaptation could develop so rapidly.  Of course, it makes the earlier history more complicated.  However long legged hopping might have first appeared, it seems that some to these “giant tree rats” adapted to living in trees for a long time, yet retained the ability to hop on the ground.  How did these animals really live?

One notable point about this research is that the team refrained from assigning the specimens to a specific taxon.  As in most paleontology, the evidence is sparse—very sparse—so taxonomic assignments are quite iffy. But people seem prone to rush to give things a name, often coining new taxonomic labels, which are then overthrown by later research.

The Swedish researchers recognize that the fossils they studied are similar to some poorly described species, but there simply isn’t enough data to say how the sparse finds might be related to each other.  So they “deferred a formal classification”, referring to the specimens by their catalog numbers.  Good for them!

“we have deferred a formal classification herein because these remains cannot yet be distinguished from those of the closely related Propleopinae (extinct ‘giant rat-kangaroos’) […], whose postcranial osteology is virtually unknown” ([2], p. 10)

  1. Helen Briggs, When did the kangaroo hop? Scientists have the answer, in BBC News – Science & Environment. 2019. https://www.bbc.com/news/science-environment-47130734
  2. Wendy Den Boer, E. Campione Nicolás, and P. Kear Benjamin, Climbing adaptations, locomotory disparity and ecological convergence in ancient stem ‘kangaroos’. Royal Society Open Science, 6 (2):181617, https://doi.org/10.1098/rsos.181617

PS.  More great ideas for band names:

Giant Hopping Tree Rats
Kangaroo Ancestors
Prehistoric kangaroos
(Pretty much anything with “kangaroo” in it!)



Pterosaur Fur!

…and feathers?

One of the great controversies about dinosaurs is just what was their skin like?  It is clear that many dinosaurs had feathers, not least because contemporary birds are dinosaurs and they are, well, absolutely covered with feathers.

And there were clearly non-avian dinosaurs that were extremely birdlke, and had feathers.  But what about terrestrial dinosaurs and related animals?  Did they have “feathers”? “Fur”?

To a certain extent, we are misled by the animals we know today. Birds’ feathers have a rather distinct structure, clearly descended and diversified from ancient ancestors.  Other animals have varieties “hair”, which has a different structure, and likewise has an evolutionary history.

But even today, there are animals that are covered with “fluff” or “bristles” or other things.  These variations may look the same and have analogous functions, but they can be identified genetically as evolved from either “hair” or “feathers”.

And, the truth be told, hair and feathers (and horns and claws and scales) are similar; basically variations of ‘ways that skin can grow a covering’.  So “hair” versus “feathers” may be an important dichotomy now, but there is no reason why it should always be that way.  There are different ways to get to the same evolutionary result.

I shouldn’t be surprised that the dinosaurs and cohorts probably worked out different ‘ways that skin can grow a covering’.

This month, and international team reports some new finds of pterosaurs with well-preserved skin [2].  These fossils were uncovered in the wonderfully rich beds in North East China.  The remains include the well-preserved  membrane of wings as well as what may be traces of what was covering the outside, including melanosomes indicating dark coloring.

The evidence suggests that the animal was covered with ‘filaments’, which would have looked ‘fuzzy’, and probably brown.

What pterosaurs might have looked like. Credit: Yuan Zhang/Nature Ecology & Evolution (From [1])
Actually, the study identifies four types of these filaments, some of which seem to be hairlike and some that might be featherlike.  So, hey, pterosaurs could be both hairy and feathery.  The study speculates on functional roles for the different styles of filaments. “insulation, tactile sensing, streamlining and colouration”. ([2], p. 28 )

The main reason why people are fussing about whether these are feathers or not is the question of the evolutionary history of feathers, i.e., the genetic mechanisms that underlie contemporary birds’ feathers [1].

Pterosaurs are very distantly related to birds, so if they share the same genes for developing feathers then those genes must date back a long, long time.  Much longer than previously suspected. (Alternatively, it is possible that feathers developed independently.)

This means feathers were not a bird innovation, not even a dinosaur innovation, but evolved first in a much more distant ancestor.” (Steve Brusatte quoted in [1])

This argument is hard to settle, because we are trying to infer genetic mechanisms from phenotypes, and sparse evidence of the phenotypes at that.  We’re also dealing with pretty long time periods, which leaves plenty of opportunity for ‘evolutionary stuff’ to happen.  (How’s that for a scientific term)

We know a bit about the genetic mechanisms that seem to control the development of skin, coloration, fur, feathers, scales, and so on in contemporary animals. We assume that these mechanisms evolved over time, and so precursors existed in ancient ancestors.  However, there is a lot we can only guess.  For instance, there could be variations on current pathways that do similar things, but have died out.  For another, there is a possibility of lateral genetic transfer, that would obscure the actual “age” of the genetic complexes.

For myself, I’m not as concerned with trying to infer how old “feather” or “fur” might be, especially considering the iffy nature of inferring from comparisons of phenotypes–and very poorly represented phenotypes for the ancient species.

It is clear that dinosaurs and pterosaurs were probably covered with something like fur and/or feathers for the same functional reasons as contemporary animals are.  They may not have been genetically or developmentally identical, but they probably looked a lot like contemporary animals.

I understand that a fuzzy, mouse brown pterosaur isn’t nearly as scary as the leathery, mummylike monsters of the movies.  But I’m pretty sure they were just as deadly to their prey.

The land that time forgot, photo from the film (From Wikicommons)

  1. Helen Briggs, Pterosaurs: Fur flies over feathery fossils, in BBC News – Science & Environment. 2018. https://www.bbc.com/news/science-environment-46572782
  2. Zixiao Yang, Baoyu Jiang, Maria E. McNamara, Stuart L. Kearns, Michael Pittman, Thomas G. Kaye, Patrick J. Orr, Xing Xu, and Michael J. Benton, Pterosaur integumentary structures with complex feather-like branching. Nature Ecology & Evolution, 3 (1):24-30, 2019/01/01 2019. https://doi.org/10.1038/s41559-018-0728-7


PS. A Good Name for a Band:

Pterosaur Fur!
Pterosaur Pfur!

New Pesticides No Better For Bees?

Over the past decade, concern has risen about the decline in pollinators, including bees.  Like every other species, including H. sap., bees are subject to many environmental stresses, including loss of habitat, invasive species, and climate change.

In addition, pollinators are especially susceptible to unintended effects of agricultural chemicals, because bees live on plants, so anything happening to plants is happening to bees, too.

There is substantial evidence that many common pesticides are harmful to bees, though the effects may be complicated.  Some pesticides have been banned in the EU, specifically to protect pollinators.

Obviously, there is good reason to develop alternative pest controls that are safer for helpful species.

This summer, British researchers report investigations of a replacement for neonicotinoids, sulfoximine [2].  In particular, the study looked at long term effects low levels of exposure, which are typical for unintended exposure, and which, in the case of neonicotinoids, have been shown to be associated with colony declines.

The study suggests that low level exposures the new chemicals early in life are associated with lower reproductive success in bumblebees. Like the neonicotinoids, they are not immediately fatal to bees, but unintentional exposure to trace amounts seems to be bad.

This is a red flag, because even careful use of the chemicals in agriculture are likely to leave residuals that bees will encounter. Indeed, this is exactly the problem with neonicotinoids that we are trying to replace.

The research is notable because this type of chronic, low level exposure is generally not examined during usual assessment of chemicals. Unfortunately, these side effects are usually discovered after deployment, when natural populations are damaged.  The researchers describe the work as “preemptive”—testing before wide deployment.

Assuming the findings of this study are confirmed, the new compounds seem to be just as harmful for pollinators as the products they are intended to replace. This will certainly create a challenge for regulators, who must weigh the limited (but believable*) evidence against the need for pesticides.

* When I say “believable”, I making a sort of Bayesian inference here.  Given the experience with neonicotinoids, the Bayesian “priors” certainly have a reasonable probability that the replacement that is used the same way could have similar chronic effects.  Thus, even a single study tends to push the expectations pretty far.

Of course, regulations are not based on Bayesian inference, though they often have “priors” set by policy.

  1. Helen Briggs, New pesticides ‘may have risks for bees’, in BBC News – Science & Environment. 2018. https://www.bbc.co.uk/news/science-environment-45185261
  2. Harry Siviter, Mark J. F. Brown, and Ellouise Leadbeater, Sulfoxaflor exposure reduces bumblebee reproductive success. Nature, 2018/08/15 2018. https://doi.org/10.1038/s41586-018-0430-6