Who We Are and How We Got Here
David Reich, 2018, Cedar Mill Library, 572.86
This book is fascinating as geneology, less so as vaguely-described technology and molecular biology.
Enough bone remains in ancient skeletal DNA to reconstruct partial genomes with SNP sequencing. The vast majority of the DNA in these bones is decay micro-organisms, but the specificity of SNP matching to lab-synthesized targets allows researchers like Reich and his colleagues at Harvard to map ancient migrations and genetic interminglings.
The book is about geneology, and is vague about the nuts-and-bolts details of the sequencing technology and statistical estimations of validity. It does not discuss why genomes change. It mentions rate of change estimates, but does not tell us why the genomic clock ticks at the rate it does. The book is for a general audience, who care more about lineage than machinery.
I read about 50%, and skimmed and sampled the rest.
The Book I Want to Read
Co-evolution with pathogens will probably turn out to be the biggest story that ancient DNA can tell us. Wild speculation follows:
Why bury or dispose of human remains? Not so that anthropologists and geneticists can dig them up and study them. Why not eat corpses instead? I imagine that some humans discovered long ago that this gave the consumer the same disease, and that handling the artifacts of the deceased sometimes caused disease also ( though funerary endocannibalism persisted among the Fore people of Papua New Guinea into the middle 20th century). Leaving a corpse lying around would attract predators who might learn that humans are tasty, or amplify the disease pathogens. Burial is time consuming but helps the survivors survive.
Grief is attributed to some animals like elephants, who are reputed to remain around dead companions for days. Perhaps this permits an elephant to kill predators that are attracted to elephant meat, before those predators attack baby elephants. When the elephant corpse rots sufficiently, predators learn that elephant meat tastes awful and causes illness. Perhaps human corpse-related behaviors evolved for similar practical survival reasons, embellished with ritual and superstition millenia later.
Pathogens are the dominant human predator, and the strongest driver of human genetic evolution. Retroviruses copy themselves into human DNA, and sometimes into germ-line DNA. Chromosome pairs cross over during meiosis prophase; that exchanges genes, but most importantly it can slice retroviral sequences in half, neutralizing the virus and allowing the zygote to survive - with new bits of genetic machinery for evolution to act on. A huge part of our ancestry may be viral fragments, selected from the small fraction of viral proteins that accidentally help build a better animal. Conversely, recombination may also help a retrovirus lineage incorporate useful animal proteins.
Most useful changes won't be animal shape and behavior, but tweaks to the immune system to resist or recover from bacterial infection and other genetically separate parasites. The DNA of those parasites coexist with the human DNA that Reich focuses on, and his techniques are designed to exclude them.
My guess is that gene flow through retroviruses can be measured with the similar techniques to Reich's lab, though the DNA palette and the number of SNP targets on a test chip would need to be vastly expanded. Humans are a small fraction of all animal life, and a vanishingly small fraction millenia ago - the pathogens did most of their evolving in other animals. So, while the focus on human migration and ancestry is an interesting paragraph, the whole story of human evolution is a pathogen history book, part of the vast encyclopedia of vertebrate evolution.
I hope researchers like Reich learn to read more of the entire encyclopedia. We learn a lot from animal testing, but we can predict the next chapter in our own evolution from the genetic history of all animals and all pathogens. Humans are decimated by "great plagues" a few times per millenia; our next may be a super-influenza, burning through third-world slums and Manhattan high-rises. Human evolution may be the response to a thousand horrendous plagues since the genetic divergence from Erectus, Neanderthal and Denisovan.