Tag: paleontology

Paleogenetics

We recently put together a DNA sequence for the earliest mammal genome, 75 ma old. The cool thing is that you can get a lot of information about ancestral genomes just by crunching probabilities — even if you don’t have any fossils, or mosquitos-trapped-in-amber, or time machines, or whatever.

2008-11-20: Scientists are also reactivating a disabled virus in human DNA after millions of years. Welcome to Paleovirology. And crappy michael crichton novels, probably. And you can take it further to Paleo‐metagenomics:

Surviving fragments of genetic material preserved in sediments allow metagenomics researchers to see the full diversity of past life — even microbes.

2014-02-14: The largest unwritten story is ~200 ka of prehistory. We’ll write the major outlines of it in the next 100 years.

Genetic data identified over 100 events occurring over the past 4 ka: the Mongol empire, Arab slave trade, Bantu expansion, European colonialism, as well as unrecorded events, revealing admixture to be an almost universal force shaping human populations

2014-03-27: Amazing overview from the guy who sequenced neanderthals and denovisans, including recent research into FOXP2, the language gene.

2015-06-16: (long) overview of the state of genetics in prehistory

By the middle years of the 2000s researchers had gone back to a focus on recombining autosomal markers. But now they had a whole human genome to compare it to, as well as SNP-chips which quickly yielded large troves of data with little effort. In 2008 a paper was published which took the origin HGDP data set collected by Cavalli-Sforza and his colleagues, and utilized the new technologies to make deeper inferences. First, instead of 100s of markers you had 650k SNPs. Second, the emergence of powerful new analytic and computational resources allowed for the complemention of tree-based and PCA visualizations of genetic relationship with model-based understandings of genetic variation and population structure. By “model-based,” I mean that the algorithm posits particular parameters (e.g., “3 ancestral populations”) and operates upon the data (e.g., “650k SNPs in 1000 individuals”) , to generate results which are the best representation of the fit of the data to the model. This different from PCA, which has fewer assumptions, and represents genetic variation geometrically (each axis represents an independent dimension of variation within the data). Model-based clustering is very clear and aesthetically appealing. It gives precise results. But, the model itself is not necessarily right.

2015-09-15: A perspective

Ancient genomics is a powerful tool for the study of prehistory, but it is still in its infancy. The first true population studies using ancient nuclear DNA – with samples numbering in the 10s instead of single digits – are only 1 month old. For the moment, we have just 2 ancient genomes from the Americas. For other parts of the world, such as Africa, South and East Asia, we have 1 or 0. With so few data points available, the world of prehistory seen through the lens of ancient DNA is like a landscape sporadically illuminated by lighting. Plenty of surprises are left in store. The situation right now is a bit like that of archaeology just after the invention of Carbon-14 dating. A revolution is on its way, but we don’t yet know what it will bring.

2016-05-10: There have been multiple population replacements in Europe

~50 ka ago humans leave Africa, and mix with a number of Neanderthals. ~40 ka ago, they arrive in Europe. ~35-40 ka ago the first modern Europeans are replaced by another population. This second population is culturally similar to the first, and contributes some (though small proportionally) ancestry to modern Europeans. It is replaced by another population, which does not contribute much to modern Europeans (Gravettians), though populations related to it do. It is replaced by a population related to the first Europeans with descendants (Magdalenians, who are descended in part from Aurignacians, and do not share much drift with Gravettians). Then, the Magdalenians are replaced by Villabruna populations, the very late Paleolithic populations at the tail end of the Ice Age. The Villabruna have mixture from both the Near East, and to a lesser extent East Asia. Or, Villabruna populations were intrusive to the Near East, and possibly East Asia, or there were mediating populations between. It is all somewhat unclear. Then the Villabruna populations, which become Mesolithic hunter-gatherers, are overwhelmed by Near Eastern groups, which have very exotic ancestry unrelated to all other non-Africans (Basal Eurasian). Finally, the Neolithic groups are overwhelmed by populations from the steppe, who are themselves compounds of very distinct elements.

2019-09-30: We can also detect missing species, or genetic ghosts if you will

Genes from an extinct “ghost ape” live on in modern bonobos. Because apes have their natural habitat in the trees of the rainy tropical forest, with an acidic soil where the organic matter decomposes very quickly, the fossil record for our closest relatives is poor, but genetic data in living bonobos could help fill in gaps. Similar, but different: David Gokhman summoned a ghost, using information for 32 skeletal features encoded in DNA that was extracted from a pinky bone. DNA reveals first look at enigmatic human relative, providing more details of the physical structure of Denisovans.

2023-01-17: Using DNA to study parental age differences. Amazing.

The research used genetic mutations in modern human DNA to create a timeline of when people have tended to conceive children over the past 250 ka, since our species first emerged. 26.9 years was the overall average age of conception during the past 250 ka. But breaking this down by sex showed that men averaged 30.7 years when they conceived a child, compared with 23.2 years for women. The numbers fluctuated over time, but the model suggested that men consistently had children later in life than women.

70 ka Human bottleneck

From one of my favorite projects, the Genographic Project.

Human beings may have had a brush with extinction 70 ka BP. The human population at that time was reduced to small isolated groups in Africa, apparently because of drought. The number of early humans may have shrunk as low as 2k before numbers began to expand again in the early Stone Age.

2023-08-31: And an even more severe, earlier bottleneck

Human ancestors in Africa were pushed to the brink of extinction 900 ka BP. It suggests a drastic reduction in the population of our ancestors well before our species, Homo sapiens, emerged. The population of breeding individuals was reduced to 1280 and didn’t expand again for 117 ka. “98.7% of human ancestors were lost”. The fossil record in Africa and Eurasia between 950 ka and 650 ka BP is patchy and that “the discovery of this bottleneck may explain the chronological gap”. “Of greater surprise is the estimated length of time that this small group survived. If this is correct, then one imagines that it would require a stable environment with sufficient resources and few stresses to the system.”

Neanderthals

Pääbo may have the entire Neanderthal genome sequenced in the next 18 months.

2009-02-13: Draft Genome is announced. Bookmarked also for the nice facial reconstruction.

2009-05-17: We ate them

Neanderthals met a violent end at our hands and in some cases we ate them

2010-09-28: The cloning arguments are nothing new, but I was struck by

There were no cities when the Neanderthals went extinct, and at their population’s peak there may have only been 10k of them spread across Europe. A cloned Neanderthal might be missing the genetic adaptations we have evolved to cope with the world’s greater population density, whatever those adaptations might be. But, not everyone agrees that Neanderthals were so different from modern humans that they would automatically be shunned as outcasts.

2013-08-16: Neanderthal leather-working

Excavations of Neanderthal sites 40 ka BP have uncovered a kind of tool that leather workers still use to make hides more lustrous and water resistant. The bone tools, known as lissoirs, had previously been associated only with modern humans. The latest finds indicate that Neanderthals and modern humans might have invented the tools independently.

2016-05-25: 176 ka ago is unimaginably old. This is more than 15x older than Gobekli Tepe.

After drilling into the stalagmites and pulling out cylinders of rock, the team could see an obvious transition between 2 layers. On one side were old minerals that were part of the original stalagmites; on the other were newer layers that had been laid down after the fragments were broken off by the cave’s former users. By measuring uranium levels on either side of the divide, the team could accurately tell when each stalagmite had been snapped off for construction.

Their date? 176 ka ago, give or take a few millennia. “When I announced the age to Jacques, he asked me to repeat it because it was so incredible”. Outside Bruniquel Cave, the earliest, unambiguous human constructions are just 20 ka old. Most of these are ruins—collapsed collections of mammoth bones and deer antlers. By comparison, the Bruniquel stalagmite rings are well-preserved and far more ancient.

2016-05-27: More Neanderthal than human

In some spots of our genome, we are more Neanderthal than human. the sequences we inherited from archaic hominins helped us survive and reproduce

2017-01-15: Neanderthals Were People, Too

For millenniums, some scientists believe, before modern humans poured in from Africa, the climate in Europe was exceptionally unstable. The landscape kept flipping between temperate forest and cold, treeless steppe. The fauna that Neanderthals subsisted on kept migrating away, faster than they could. Though Neanderthals survived this turbulence, they were never able to build up their numbers. (Across all of Eurasia, at any point in history, “there probably weren’t enough of them to fill a stadium.”) With the demographics so skewed, even the slightest modern human advantage would be amplified tremendously: a single innovation, something like sewing needles, might protect just enough babies from the elements to lower the infant mortality rate and allow modern humans to conclusively overtake the Neanderthals. And yet Stringer is careful not to conflate innovation with superior intelligence. Innovation, too, can be a function of population size. “We live in an age where information, where good ideas, spread like wildfire, and we build on them. But it wasn’t like that 50 ka ago.” The more members your species has, the more likely 1 member will stumble on a useful new technology — and that, once stumbled upon, the innovation will spread; you need sufficient human tinder for those sparks of culture to catch.

2017-09-05: 200 ka Neanderthal Glue

As far back as 200 ka ago Neanderthals were using a tar-based adhesive to glue axe heads and spears to their handles. Researchers have attempted to recreate the Neander-glue, which could help scientists figure out just how technologically sophisticated the species was. Archaeologists have found lumps of adhesive tar likely made from birch bark at Neanderthal sites in Italy and Germany. But just how they made the substance puzzled researchers, especially because they did it without the aid of ceramic pots, which were used by later cultures to produce large quantities of tar.

2019-06-12: Did Neanderthals Speak?

Neanderthals had the anatomical properties to create the sounds that could form the basis of speech, though any words they produced would have sounded a bit unfamiliar to modern human ears

2020-03-04: long distance Neanderthals

Their intercontinental odyssey over 1000s of kilometers is a rarely observed case of long-distance dispersal in the Paleolithic and highlights the value of stone tools as culturally informative markers of ancient population movements.

2022-11-19: Interbreeding in Africa

The human-like Y chromosome entered the Neanderthal gene pool well before the migration out of Africa 80ka BP – perhaps 270ka BP. Which means that many of the Neanderthals that those migrants encountered must have already had human-like Y chromosomes! The Neanderthal Y chromosome and mitochondrial DNA are 2 new lines of evidence that point to a much more complex and ancient relationship between us and our closest cousins than we otherwise would have known.

2023-12-15: A new book, The Naked Neanderthal, looks interesting

Next, he explores evidence from skeletal remains for butchery and cannibalism of the dead in Neanderthal communities at Moula Guercy. Some researchers have proposed that such findings are a sign of starvation — evidence that Neanderthals were not able to adapt to the warm Eemian forests. Slimak concludes instead that these behaviors were a natural part of hominin social interactions, citing growing evidence from both archaeology and primatology that such practices were relatively common among humans right through prehistory.
Humans temporarily replaced local Neanderthals 54ka BP over an extraordinarily short time — potentially less than 1 year. The author uses this to argue that extermination, rather than assimilation, is the most likely explanation for the Neanderthals’ eventual extinction.