Drosophila melanogaster is a model organism for the study of genetics and some laboratory populations have been bred for different life-history traits over the course of 30 years. Professor Michael Rose, of UC Irvine, began breeding flies with accelerated development in 1991 (600 generations ago). Doctoral student Molly Burke compared the experimental flies with a control group on a genome-wide basis. This is significant because it is the first time such a study of a sexually reproducing species has been done. Burke examined specific genes and also obtained "whole-genome resequencing data from Drosophila populations that have undergone 600 generations of laboratory selection for accelerated development." The results are noteworthy on several counts:
"For decades, most researchers have assumed that sexual species evolve the same way single-cell bacteria do: A genetic mutation sweeps through a population and quickly becomes "fixated" on a particular portion of DNA. But the UCI work shows that when sex is involved, it's far more complicated. "This research really upends the dominant paradigm about how species evolve," said ecology and evolutionary biology professor Anthony Long, the primary investigator."
Knowing the genome sequence of Drosophila has opened new avenues of research (Source here)
The researchers were looking for the fixation of positive mutations within the genome and within the whole population. This is referred to using the term "selection sweep". When it occurs, the new mutation at a base pair (a novel single nucleotide polymorphism or SNP) not only experiences replication to be transmitted to the descendants of the organism, but the gene pool of variation is effectively swept clean as the new mutation becomes dominant in the whole population. However, such sweeping was conspicuous by its absence.
"Recent research on evolutionary genetics has focused on classic selective sweeps, which are evolutionary processes involving the fixation of newly arising beneficialmutations. In a recombining region, a selected sweep is expected to reduce heterozygosity at SNPs flanking the selected site. [. . .] Notably, we observe no location in the genome where heterozygosity is reduced to anywhere near zero, and this lack of evidence for a classic sweep is a feature of the data regardless of window size."
The paper considers a range of possible explanations for the evidence obtained. First: "Classic sweeps may be occurring, but have had insufficient time to reach fixation." Second: "selection in these lines may generally act on standing variation, and not new mutations." Third, "selection coefficients associated with newly arising mutations are not static but in fact decrease over time." No conclusion is reached regarding these various options.
"Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles. This is notable because in wild populations we expect the strength of natural selection to be less intense and the environment unlikely to remain constant for ~600 generations. Consequently, the probability of fixation in wild populations should be even lower than its likelihood in these experiments. This suggests that selection does not readily expunge genetic variation in sexual populations, a finding which in turn should motivate efforts to discover why this is seemingly the case."
This empirical work is worth noting on two counts. First, we are here considering a mechanism that is central to Darwinian evolution. Positive natural selection of hereditable variation is the key (we are informed) to understanding how descent with modification occurs. However, the first set of empirical data relating to a sexually reproducing species does not confirm that modification works this way. This is why Long's comment is worth repeating: "This research really upends the dominant paradigm about how species evolve". Many scientists have long suspected that the Darwinian mechanisms are inadequate to account for large-scale transformation - these research findings provide empirical support for such doubts.
The other reason for taking an interest in this research is that the Darwinian paradigm has been widely used in the development of drugs for medical use. Whereas the classical view is that genes have specific functions, the new research supports the growing body of evidence that the norm is for genes to have pleiotropic effects. A novel SNP can then be expected to have not one, but many, effects. This has been underplayed by researchers of a darwinian persuasion.
"Based on that flawed paradigm, Rose noted, drugs have been developed to treat diabetes, heart disease and other maladies, some with serious side effects. He said those side effects probably occur because researchers were targeting single genes, rather than the hundreds of possible gene groups like those Burke found in the flies. Most people don't think of flies as close relatives, but the UCI team said previous research had established that humans and other mammals share 70 percent of the same genes as the tiny, banana-eating insect known as Drosophila melanogaster."
Genome-wide analysis of a long-term evolution experiment with Drosophila
Molly K. Burke, Joseph P. Dunham, Parvin Shahrestani, Kevin R. Thornton, Michael R. Rose and Anthony D. Long.
Nature, 467, 587-590, (30 September 2010) | doi: 10.1038/nature09352 (preprint)
Experimental evolution systems allow the genomic study of adaptation, and so far this has been done primarily in asexual systems with small genomes, such as bacteria and yeast. Here we present whole-genome resequencing data from Drosophila melanogaster populations that have experienced over 600 generations of laboratory selection for accelerated development. Flies in these selected populations develop from egg to adult ~20% faster than flies of ancestral control populations, and have evolved a number of other correlated phenotypes. On the basis of 688,520 intermediate-frequency, high-quality single nucleotide polymorphisms, we identify several dozen genomic regions that show strong allele frequency differentiation between a pooled sample of five replicate populations selected for accelerated development and pooled controls. On the basis of resequencing data from a single replicate population with accelerated development, as well as single nucleotide polymorphism data from individual flies from each replicate population, we infer little allele frequency differentiation between replicate populations within a selection treatment. Signatures of selection are qualitatively different than what has been observed in asexual species; in our sexual populations, adaptation is not associated with 'classic' sweeps whereby newly arising, unconditionally advantageous mutations become fixed. More parsimonious explanations include 'incomplete' sweep models, in which mutations have not had enough time to fix, and 'soft' sweep models, in which selection acts on pre-existing, common genetic variants. We conclude that, at least for life history characters such as development time, unconditionally advantageous alleles rarely arise, are associated with small net fitness gains or cannot fix because selection coefficients change over time.
Scientists Decode Genomes of Precocious Fruit Flies, ScienceDaily (September 19, 2010)
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