Monday, January 20, 2020

Climate Was Pivotal To Out Of Africa Migration

Deserts were major barriers to human migration in the pre-Holocene era and deserts waxed and waned based upon shifts in climate over time historically. This is entirely expected, but important. 




Whilst an African origin for Anatomically Modern Humans is well established 1, the timings of their expansions into Eurasia are the subject to heated debate, due to the scarcity of fossils and the lack of suitably old ancient DNA 2. Here, we estimate potential timings and routes out of Africa by deriving anthropologically and ecologically plausible precipitation requirements for human existence, and applying them to high-resolution palaeoclimate reconstructions for the past 300k years. We find that exit routes and timings previously suggested based on archaeological and genetic evidence coincide precisely with the presence of sufficiently wet corridors into Eurasia, while the gaps between the proposed exit timings co-occur with periods of insufficient rainfall. This demonstrates the key role that palaeoclimatic conditions played for out-of-Africa expansions. The challenging environmental conditions outside of Africa that occurred between windows of potential contact, coupled with the lack of a demographic rescue effect from migration and possible competition with other hominins, likely explain the demise of early colonists prior to the large-scale colonisation of the world beginning from ∼65kya.
Robert M. Beyer, Mario Krapp, Anders Eriksson, Andrea Manica,"Windows out of Africa: A 300,000-year chronology of climatically plausible human contact with Eurasia" BioRxiv (January 14, 2020). doi: https://doi.org/10.1101/2020.01.12.901694

From the main text, which reasonably fairly sums up the evidence, omitting a couple of old dates in India (pre-dating the Toba eruption) and Myanmar and Indonesia (shortly after the Toba eruption), however.
The dating of most out-of-Africa fossils, and the dating of the split between Eurasian and African populations based on mitochondrial and whole-genome data 3,4 point to a major exit ∼65k years ago. However, archaeological findings in Saudi Arabia dated to at least 85k years ago 5, in Israel to at least ∼90k years ago 6, possibly ∼194k years ago 7, and in Greece dated back to ∼210k years ago 8 point to previous excursions from Africa, which might have reached as far as China 9. 
These, or another previous waves, might have also left a small genetic contribution (∼1%) found in modern inhabitants of Papua New Guinea 10. Further evidence for a possibly earlier exit comes from traces of geneflow from AMHs into Neanderthal, genetically dated to before 130k years ago, but could be as old as 270k years ago 11. Thus, AMHs likely had repeated periods when they were able to leave Africa, even though the timing and fate of those early waves is unclear.

Friday, January 17, 2020

Human Genetics 201

The rules of human genetics you learned in high school are a good first order approximation of how human genetics work. But, as we look closer, we are actually learning that human genetics are more complex.

* Some men are genetically pre-disposed to have more sons. There are genes that determine the sex ratio of a man's sperm output. So, some men are genetically pre-disposed to have sons, and other men are genetically pre-disposed to have daughters. This explains, for example, why after a war, more boys than girls are born. 
In many of the countries that fought in the World Wars, there was a sudden increase in the number of boys born afterwards. The year after World War I ended, an extra two boys were born for every 100 girls in the UK, compared to the year before the war started. The gene, which Mr Gellatly has described in his research, could explain why this happened. 
As the odds were in favour of men with more sons seeing a son return from the war, those sons were more likely to father boys themselves because they inherited that tendency from their fathers. In contrast, men with more daughters may have lost their only sons in the war and those sons would have been more likely to father girls. This would explain why the men that survived the war were more likely to have male children, which resulted in the boy-baby boom.
Also the natural sex ratio in humans is not 50-50 but 105-100, because the balances boys being more prone to die as children than girls, historically.)

The paper is:

Gellatly et al. "Trends in Population Sex Ratios May be Explained by Changes in the Frequencies of Polymorphic Alleles of a Sex Ratio Gene." Evolutionary Biology (Dec 11, 2008) DOI: 10.1007/s11692-008-9046-3

* Epigenetic markers can be inherited. The main form of genetic inheritance is in your genes, which are inherited from your ancestors ad infinitum, modified only by genetic mutations. During life, however, an organism's genes are "annotated", which tells those genes how to express themselves, most notably by a process known as DNA methylation. This is critical. The DNA in the cells in your ears need to know not to express as bone tissue, and your red blood cells need to know not to turn into white blood cells, for example, significant environmental exposures in life such as period of famine or intense fear also impact these annotations. Collectively, the annotations in your genome are called, rather unimaginatively, your epigenome.

Jean-Baptiste Lamarck thought that evolution was primarily driven by epigenetic responses to the environment being passed on to the next generation. And, mostly he was wrong. But, it turns out that he was not entirely wrong. The epigenome can be passed on in part to the next generation as well. A recent paper provides an example of this happening.

The paper is:

Sandra Catania, et al., 'Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase." Cell (2020). DOI: 10.1016/j.cell.2019.12.012

* Not all genes mutate at the same rate. We've actually know for a long time that certain parts of your genome (both different parts of your autosomal genome, and different parts of your mitochondrial genome) mutate at different rates. This makes determining the time frame in which two genomes diverged from each other based upon the number of mutations by which they differ much trickier than it was believed to be when this was first attempted.

* It is possible for your genome to change during your life.  An endogenous retrovirus, if you are infected by it, can permanently change your genes in a way that is passed on to your descendants. About 5%-8% of the human genome has its source in ERVs rather than parent to child inheritance. Viral infections with this effect are used for gene therapy. A bone marrow transplant can also change your genome. Also, of course, genetic mutations can arise by pure chance, and the risk of mutations can be enhanced by environmental conditions such as exposures to toxins.

* Not all cells in a person's body are necessarily identical. The phenomena is called genetic mosaicism if it arises in an organism arising from a single egg (often due to a mutation early in the developmental process), and genetic chimerism, in which two or more genotypes arise in one individual from the fusion of more than one fertilized zygote in the early stages of embryonic development (although many reasonably knowledgable people use the terms as interchangeable). Another way it commonly arises is in vitro fertilization. Also, it increasingly appears that when a woman is pregnant that some cells with genes of the fetus survive in the mother (also by implication, leaving cells with some genes that have an origin in the father in the mother.)

* Children do not receive exactly 50% of their genes from each parent, although it is close to 50-50. Some children receive a little more than 50% of their genes from their father, some a little less. You also can't tell which parent a child receives more genes from based upon appearance or other phenotypic traits, because the most obvious traits are governed by a very small share of the total genome. I've seen this, for example, in the genetic testing of my children and in the genetic testing of other siblings which I have seen. To be perfectly honest, I don't fully understand how this happens.