different mutation rates in different human populations

well this seems important! via race/history/evolution notes, an abstract from the society for molecular biology and evolution 2014 conference (in puerto rico! – teh scientists are always good to themselves whenever they can be (~_^) ):

Evidence for different mutation rates across human populations
Ron Do, David Reich
Department of Genetics, Harvard Medical School, Boston, USA

Although mutation rates (per base pair) have clearly changed across primate evolution, many analyses continue to assume that all present-day human populations have the same mutation rates. Recently, William Amos analyzed 1000 Genomes Project and Complete Genomics sequences and found evidence of significantly higher divergence rates on African than on non-African lineages since separation (W. Amos, PLoS One 4, e63048). The detected pattern was strongest in genomic regions of high polymorphism rate, a pattern that the author hypothesized was due to ‘heterozygote instability’, whereby gene conversion events surrounding heterozygous sites increase the mutation rate. To further test this observation, we measured the relative accumulation of mutations in lineages drawn from two different populations, using 25 deep genome sequences generated according to the same experimental protocol using the Illumina technology. We carried out pairwise comparisons of five sub-Saharan African (Dinka, Mandenka, Mbuti, San, Yoruba) and eight Non-African populations (Australian, Dai, French, Han, Karitiana, Mixe, Papuan, Sardinian) on all divergent sites. We observed statistically significant differences in the relative accumulation of mutations for many pairs of African and Non-African populations. Among the strongest differences is significantly more lineage-specific mutations in Mbuti than in Han Chinese (R=1.044, standard error (SE) =0.0015). On average, we observed about 1% more mutations on African lineages compared to Non-African lineages. We also observed some significant differences across non-African populations, with the Han Chinese who have experienced extreme expansions in population size associated with agriculture having more mutations than the Karitiana, a hunter-gatherer population from Amazonia who did not experience such expansions (R=1.015, SE=0.0014). The results are consistent across both European and African segments of the human reference sequence, so are not an artifact of reference sequence bias. Taken together, these results support the view that per-base pair mutation rates may be dynamically and substantially changing across humans.


wrt to greater number of mutations in african lineages: polygamy (and, therefore, older fathers)? life in the tropics?

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evolution likes it hot

i posted about this before, but the topic came up in conversation recently, so i thought i’d post about it again:

“Evolution faster when it’s warmer”
24 June 2009

“Climate could have a direct effect on the speed of ‘molecular evolution’ in mammals, according to a study.

“Researchers have found that, among pairs of mammals of the same species, the DNA of those living in warmer climates changes at a faster rate.

“These mutations – where one letter of the DNA code is substituted for another – are a first step in evolution.

“The study, reported in Proceedings of the Royal Society B, could help explain why the tropics are so species-rich….

“The idea that microevolution happens faster in warmer environments is not new. But this is the first time the effect has been shown in mammals, which regulate their own body temperature.

“‘The result was unexpected,’ said Len Gillman from Auckland University of Technology, who led the study.

“‘We have previously found a similar result for plant species and other groups have seen it in marine animals. But since these are “ectotherms” – their body temperature is controlled directly by the environment – everyone assumed that the effect was caused by climate altering their metabolic rate….’

“‘We suspected the same effect might be happening in mammals, because seasonal changes affect the animals’ activity,’ Dr Gillman told BBC News.

“He and his team compared the DNA of 130 pairs of mammals, looking at genetically similar ‘sister species’ – where each of the pair lived at a different latitude or elevation.

“They tracked changes in one gene that codes for a protein known as cytochrome b, comparing the same gene in each of the pair of mammals to a “reference” gene in a common ancestor.

“By looking for mutations in the DNA code for this gene – each point where one letter in the code was substituted for another – the researchers were able to see which of the two mammals had ‘microevolved’ faster.

“Animals living in environments where the climate was warmer, had about 1.5 times more of these substitutions than the animals living in cooler environments.

“Dr Gillman explained that, at higher latitudes where environments are colder and less productive, animals often conserve their energy – hibernating or resting to reduce their metabolic activity.

“‘In warmer climates annual metabolic activity is likely to be greater, so this will lead to more total cell divisions per year in the germline.’

“These results support the idea that high tropical biodiversity is caused by faster rates of evolution in warmer climates.”

here’s the original research article: Latitude, elevation and the tempo of molecular evolution in mammals

one of the first things that popped into my mind — right after cool! — when hearing about this a few years ago was: so what could this mean for the out-of-africa (ooa) theory? one of the foundational pillars of ooa is that, because genetic variation is greatest in africans, they must be some of the oldest populations on earth ’cause they’ve acquired so many, many mutations — therefore, everyone else prolly came ooa:

“A 10-year study published in 2009 analyzed the patterns of variation at 1,327 DNA markers of 121 African populations, 4 African American populations, and 60 non-African populations. The research showed that there is more human genetic diversity in Africa than anywhere else on Earth….

“Human genetic diversity decreases in native populations with migratory distance from Africa and this is thought to be the result of bottlenecks during human migration, which are events that temporarily reduce population size. It has been shown that variations in skull measurements decrease with distance from Africa at the same rate as the decrease in genetic diversity. These data support the Out of Africa theory over the multiregional origin of modern humans hypothesis.”

but if genetic variation might be increased just by living in a hot climate … well … then what?

more recently, davidski over at eurogenes posted about this paper the other day: An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People. turns out african americans have a lot more rare genetic variants than europeans — and northern europeans have the least of all:

could the differences be related to the fact that these people’s ancestors came from different latitudes/climates and, so, their mutation rates were different? dunno. maybe.

previously: here’s my question

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