Tuesday, October 27, 2015

"Ancestors in Our Genome" - Eugene E. Harris

The following review now posted on Amazon.


Somewhere between a coffee table book and a textbook, Eugene E. Harris’s new work is an excellent introduction both to the human evolution story and to genetics itself. Here’s a chapter summary.

Chapter 1: Looks Can Be Deceiving

The author recalls his experiences as an anthropologist post-grad in the 1990s. These were the years of the ‘morphology-molecules’ wars. Where should we look to reconstruct the tree of life, anatomy or genetics?  Reliance on anatomy is undermined by convergent evolution: structures which suggest a close relationship between two species can mislead. The war was eventually won by genetics, and the author was soon getting his head around genomics and population genetics.

Chapter 2: Many Trees in the Forest

You can build gene-trees (going back in time) for a target gene found in different species by looking at sequence differences (base substitutions, insertions and deletions). This looks a good way to determine ‘genetic closeness’ between species – except that different genes give different answers!

It turns out that the gene-tree and the species-tree are rather different things: the species tree emerges when looking at the aggregate of mutations and divergences between many different genes. Affordable whole-genome sequencing transformed the genetic synthesis of evolutionary descent trees. The key population genetics concept used here is that of gene coalescence, and specifically coalescence time (typically thousands or millions of years).

Chapter 3: The Great Divorce

How and when did humans and chimpanzees part ways?  Think of this as looking for the coalescence time for genes which differ between humans and our closest living cousins. It turns out that an important variable in computing this is the ‘effective population size’ of ancestral groups.

This is another key concept of population genetics, relating to the number of individuals breeding in a ‘model population’ which would create the same population genetic diversity as we see today. The author suggests that, as a rough rule of thumb, actual populations are around three times the size of calculated effective populations, as many individuals do not leave descendants. The answer, by the way, is not known for certain but is of the order of four million years.

Chapter 4: A Population Crash in the Past

The effective population size of humans (based on existing genetic diversity) is rather small – around 10,000 individuals. This is one fifth to one tenth the effective population size of the common ancestor to humans and chimpanzees and indeed that of deeper ancestral populations which also evolved into gorillas and orang-utans.  This has consequences in terms of genetic drift and a weakening of positive and negative (purifying) natural selection. Humans have more slightly detrimental DNA than our cousin species, which translates into an increased propensity to disease.

Chapter 5: What Can the Genome Tell Us about Being Human?

We share a great deal of genetic commonality with chimpanzees, and indeed other apes and monkeys. Our differences are the result of mutations in our genomes (and, of course, those of the other species), amplified by positive natural selection. How do we look at human and cousin genomes for evidence of adaptation?

Most obviously there are human physiological differences in areas such as larger brains, loss of fur, bipedalism and speech. Unfortunately we know next to nothing about what most genes actually do so we can’t just take the sets of genomes (ours, chimpanzees, etc) and read off the differences. Instead we use the statistical tools of population genetics to identify areas of the human genome showing signs of recent selection. The author explains what has been found so far.

Chapter 6: The Genomic Origins of Modern Humans

As we sequenced more individuals across the world, we learned more about the original exodus from Africa and the signature of multiple founder effects: genetic diversity decreases rapidly in populations geographically furthest away. Whole genome analyses build up a complex picture of migration histories.

Chapter 7: The Ongoing Evolutionary Journey

Humans now cover most of the planet, but as they expanded they encountered new stresses, differences in: temperature, humidity, foods, disease-causing pathogens, intensity of ultra-violet light, altitude etc. These varied demands created selective pressures for further evolutionary change and that change was sometimes in the form of a small number of point mutations as in the classic Mendelian model (lactose tolerance and malarial resistance are examples). The process by which a beneficial mutation spreads through a population is called a selective sweep. This population genetics concept is explained in detail, as is the methods of seeking evidence of such ‘hard sweeps’ in genomes taken from different populations across the world.

Most traits, however, such as height are quantitative, normally being distributed in the population as a bell-shaped curve. This is an indicator that the traits are under the control of many hundreds of genes, each of small effect. It’s evident, for example, that different human populations have varying average height. An adaptation process which changes the frequency of many alleles to modify the overall distribution of a quantitative trait (such as height) between populations is called a soft sweep. This is even harder to detect in genomic analyses, requiring extremely large sample sizes.

Chapter 8: Kissing Cousins – Clues in Ancient Genomes

In this final chapter we’re led into the murky depths of Neanderthal and Denisovan genomics, and hybridisation between these archaic hominid lineages and modern humans. A very detailed discussion follows, which highlights just how much more there is to learn.

In conclusion, this is an excellent book to understand the state of the art (2015) in human evolution over the last, say, ten million years. As a bonus you get an extremely clear conceptual overview of the main concepts of population genetics. The author avoids the mathematics, which sometimes makes his arguments look rather arbitrary, but after reading his account you are in a much better place to study population genetics in detail.

A final remark: there is always a worry reading books on genetics, human evolution and population differences that one is going to get an agenda - propaganda rather than science. The reader may rest assured – this book is thoroughly scientific, and Henry Harpending was one of the pre-publication reviewers.