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- Apr 22, 2013
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"In the last few years, two paradigms underlying human evolution have crumbled. Modern humans have not totally replaced previous hominins without any admixture, and the expected signatures of adaptations to new environments are surprisingly lacking at the genomic level. Here we review current evidence about archaic admixture and lack of strong selective sweeps in humans. We underline the need to properly model differential admixture in various populations to correctly reconstruct past demography. We also stress the importance of taking into account the spatial dimension of human evolution, which proceeded by a series of range expansions that could have promoted both the introgression of archaic genes and background selection."
"Until recently, the out-of-Africa model of human evolution was favoured by most genetic analyses, but this model collapsed when the sequencing of the Neanderthal genome revealed that 1%–3% of the genome of Eurasians was of Neanderthal origin. At the same time, refined analyses of modern human genomic data [1]–[3] have changed our view of evolutionary forces acting on our genome."
"Most methods aiming at detecting recent episodes of selection in humans have been designed under the paradigm that adaptations were mainly driven by classical positive selection"
"Several lines of evidence support the past action of positive selection, such as increased levels of population differentiation in or close to genic regions [3], [37], increased diversity with distance from coding regions [38], or lower diversity and increased population differentiation in regions of low recombination where selective sweep should be more efficient [8], [39]–[41].
And now the kicker (Positive selection is a mechanism of natural selection):"Most methods aiming at detecting recent episodes of selection in humans have been designed under the paradigm that adaptations were mainly driven by classical positive selection"
"Several lines of evidence support the past action of positive selection, such as increased levels of population differentiation in or close to genic regions [3], [37], increased diversity with distance from coding regions [38], or lower diversity and increased population differentiation in regions of low recombination where selective sweep should be more efficient [8], [39]–[41].
"However, this paradigm has been recently eroded as it has been realized that our genome does not show many sites that are fixed between human populations [2], [38], and that fixed differences are always between populations from different continents [3], suggesting that strong adaptive events rarely occurred in response to local adaptation."
"Because background selection can explain most aspects of human genetic diversity, it does not mean that adaptive events driven by positive selection have not occurred in recent or past human evolution (e.g., [49]), but they might not be that widespread and detecting their signal might be more difficult than anticipated."
"As James F. Crow would have put it, in human evolution the questions have remained the same but the answers have changed. Genomics has revealed that the genome of Eurasians is partly of archaic origin, and genome-wide patterns of diversity have not revealed expected signals of adaptive selection in humans. The sequencing of additional archaic hominins should be helpful to distinguish between alternative scenarios of admixture, infer the timing and the geographic location of admixture events, and assess human migration routes over Eurasia. Archaic admixture can also seriously impact estimated human demography, which should be revisited to account for differential introgression among human populations. Scenarios of human evolution need to be geographically coherent and integrate range expansions during which deleterious mutations can readily surf and accumulate on wave fronts, giving later fuel to background selection. Whereas our view of human evolution has drastically changed over the past few years, it would be pretentious to believe we now know the true history of modern humans and that we have identified all selective forces that have shaped the diversity of our genome. However, progress in the analysis of modern and ancient genomes is likely to soon provide the data that will allow us to test complex scenarios of human evolution and contrast the role of various selective forces that are currently or were acting in our genome."
http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002837"Because background selection can explain most aspects of human genetic diversity, it does not mean that adaptive events driven by positive selection have not occurred in recent or past human evolution (e.g., [49]), but they might not be that widespread and detecting their signal might be more difficult than anticipated."
"As James F. Crow would have put it, in human evolution the questions have remained the same but the answers have changed. Genomics has revealed that the genome of Eurasians is partly of archaic origin, and genome-wide patterns of diversity have not revealed expected signals of adaptive selection in humans. The sequencing of additional archaic hominins should be helpful to distinguish between alternative scenarios of admixture, infer the timing and the geographic location of admixture events, and assess human migration routes over Eurasia. Archaic admixture can also seriously impact estimated human demography, which should be revisited to account for differential introgression among human populations. Scenarios of human evolution need to be geographically coherent and integrate range expansions during which deleterious mutations can readily surf and accumulate on wave fronts, giving later fuel to background selection. Whereas our view of human evolution has drastically changed over the past few years, it would be pretentious to believe we now know the true history of modern humans and that we have identified all selective forces that have shaped the diversity of our genome. However, progress in the analysis of modern and ancient genomes is likely to soon provide the data that will allow us to test complex scenarios of human evolution and contrast the role of various selective forces that are currently or were acting in our genome."
I think they are sending a message with that opening statement. Darwin's prediction of an out-of-Africa model has been debunked, and "the expected signatures of adaptations to new environments are surprisingly lacking at the genomic level." Darwin's theory says that: a species adapt or change to their environment, yet, in the peer-reviewed scientific journal PLOS, the article asserts a species NOT adapting to their environment?????
Yes, our view of evolution has drastically changed.
