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.