Scientists in Europe and the US are challenging the traditional notion of human evolution. For the past 35 years, geneticists have designated classic selective sweeps, when a beneficial genetic mutation quickly spreads through the human population, as the primary drivers of human evolution. However, a study published in Science suggests that such events may have been rare, with little influence on the history of our species. Instead, it claims that smaller changes in multiple genes may have been the primary driver of changes in human phenotypes, and calls for new models to retrace the genetic steps of evolution.
After examining the sequences of nearly 200 human genomes, researchers said they found new evidence arguing against selective sweeps as the dominant mode of human adaptation.
'Our findings suggest that recent human adaptation has not taken place through the arrival and spread of single changes of large effect, but through shifts of frequency in many places of the genome,' says co-author Dr Molly Przeworski, a professor of Human Genetics and Ecology and Evolution at the University of Chicago in the US. 'It suggests that human adaptation, like most common human diseases, has a complex genetic architecture.'
Under the classic selective sweep model, a new and advantageous gene appears, spreading quickly through the population. Because of its rapid rise, the gene becomes fixed in the genome with less variation than a gene that spreads more slowly. Geneticists have used this model to look for genetic segments surrounded by 'troughs' of low variation, the theoretical footprint of a selective sweep.
Applying the model has identified more than 2,000 genes - equivalent to around 10% of the human genome - suggesting that selective sweeps were a frequent occurrence that drove the evolution of humans away from their primate ancestors.
'The selective sweep model was introduced in 1974 and has pretty much been the central model ever since,' Dr Przeworski says. 'It is fair to say that it is the model behind almost every scan for selection done to date, in humans or in other organisms.'
However, areas of low diversity around gene segments might also be generated by other evolutionary mechanisms. To test whether selective sweeps were the predominant cause of these troughs, the team used data from 179 subjects in the 1000 Genomes Project, an international effort to catalogue human variation.
'This is really a groundbreaking dataset that allowed this type of analysis to be done for the very first time,' says Professor Ryan Hernandez of Bioengineering and Therapeutic Sciences at University of California at San Francisco (UCSF).
The research team looked at genes with human-specific substitutions, where the nucleotide sequence was different from close primate relatives. 'Phenotypic variation in humans isn't as simple as we thought it would be,' Dr Hernandez explains. 'The idea that human adaptation might proceed by single changes at the amino acid level is quite a nice idea, and it's great that we have a few concrete examples of where that occurred, but it's too simplistic a view.'
Further evidence against common selective sweeps was provided by comparing genome variation in different populations. Because Nigerian, European, and Chinese/Japanese populations separated roughly 100,000 years ago and subsequently adapted to different environments, frequent selective sweeps would be expected to fix clear genetic differences between the populations.
Dr Przeworski concludes, 'These findings call into question how much more there is to find using the selective sweep approach, and should also make us skeptical of how many of the findings to date will turn out to be validated'.
Experts from Israel and the UK contributed to this study.
After examining the sequences of nearly 200 human genomes, researchers said they found new evidence arguing against selective sweeps as the dominant mode of human adaptation.
'Our findings suggest that recent human adaptation has not taken place through the arrival and spread of single changes of large effect, but through shifts of frequency in many places of the genome,' says co-author Dr Molly Przeworski, a professor of Human Genetics and Ecology and Evolution at the University of Chicago in the US. 'It suggests that human adaptation, like most common human diseases, has a complex genetic architecture.'
Under the classic selective sweep model, a new and advantageous gene appears, spreading quickly through the population. Because of its rapid rise, the gene becomes fixed in the genome with less variation than a gene that spreads more slowly. Geneticists have used this model to look for genetic segments surrounded by 'troughs' of low variation, the theoretical footprint of a selective sweep.
Applying the model has identified more than 2,000 genes - equivalent to around 10% of the human genome - suggesting that selective sweeps were a frequent occurrence that drove the evolution of humans away from their primate ancestors.
'The selective sweep model was introduced in 1974 and has pretty much been the central model ever since,' Dr Przeworski says. 'It is fair to say that it is the model behind almost every scan for selection done to date, in humans or in other organisms.'
However, areas of low diversity around gene segments might also be generated by other evolutionary mechanisms. To test whether selective sweeps were the predominant cause of these troughs, the team used data from 179 subjects in the 1000 Genomes Project, an international effort to catalogue human variation.
'This is really a groundbreaking dataset that allowed this type of analysis to be done for the very first time,' says Professor Ryan Hernandez of Bioengineering and Therapeutic Sciences at University of California at San Francisco (UCSF).
The research team looked at genes with human-specific substitutions, where the nucleotide sequence was different from close primate relatives. 'Phenotypic variation in humans isn't as simple as we thought it would be,' Dr Hernandez explains. 'The idea that human adaptation might proceed by single changes at the amino acid level is quite a nice idea, and it's great that we have a few concrete examples of where that occurred, but it's too simplistic a view.'
Further evidence against common selective sweeps was provided by comparing genome variation in different populations. Because Nigerian, European, and Chinese/Japanese populations separated roughly 100,000 years ago and subsequently adapted to different environments, frequent selective sweeps would be expected to fix clear genetic differences between the populations.
Dr Przeworski concludes, 'These findings call into question how much more there is to find using the selective sweep approach, and should also make us skeptical of how many of the findings to date will turn out to be validated'.
Experts from Israel and the UK contributed to this study.
