Stolzfus and Yampolsky 2009 & Nielsen 2009
Fri Oct 23 2009
Climbing Mount Probable: Mutation as a Cause of Nonrandomness in Evolution
The classic view of evolution as ‘‘shifting gene frequencies’’ in the Modern Synthesis literally means that evolution is the modulation of existing variation (‘‘standing variation’’), as opposed to a ‘‘new mutations’’ view of evolution as a 2-step process of mutational origin followed by acceptance-or-rejection (via selection and drift). The latter view has received renewed attention, yet its implications for evolutionary causation still are not widely understood. We review theoretical results showing that this conception of evolution allows for a role of mutation as a cause of nonrandomness, a role that could be important but has been misconceived and associated misleadingly with neutral evolution. Specifically, biases in the introduction of variation, including mutational biases, may impose predictable biases on evolution, with no necessary dependence on neutrality. As an example of how important such effects may be, we present a new analysis partitioning the variance in mean rates of amino acid replacement during human–chimpanzee divergence to components of codon mutation and amino acid exchangeability. The results indicate that mutational effects are not merely important but account for most of the variance explained. The challenge that such results pose for comparative genomics is to address mutational effects as a necessary part of any analysis of causal factors. To meet this challenge requires developing knowledge of mutation as a biological process, understanding how mutation imposes propensities on evolution, and applying methods of analysis that incorporate mutational effects.
AND
ADAPTIONISM—30 YEARS AFTER GOULD AND LEWONTIN
Gould and Lewontin’s 30-year-old critique of adaptionism fundamentally changed the discourse of evolutionary biology. However, with the influx of new ideas and scientific traditions from genomics into evolutionary biology, the old adaptionist controversies are being recycled in a new context. The insight gained by evolutionary biologists, that functional differences cannot be equated to adaptive changes, has at times not been appreciated by the genomics community. In this comment, I argue that even in the presence of both functional data and evidence for selection from DNA sequence data, it is still difficult to construct strong arguments in favor of adaptation. However, despite the difficulties in establishing scientific arguments in favor of specific historic evolutionary events, there is still much to learn about evolution from genomic data.
Additional Reading: The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme
The classic view of evolution as ‘‘shifting gene frequencies’’ in the Modern Synthesis literally means that evolution is the modulation of existing variation (‘‘standing variation’’), as opposed to a ‘‘new mutations’’ view of evolution as a 2-step process of mutational origin followed by acceptance-or-rejection (via selection and drift). The latter view has received renewed attention, yet its implications for evolutionary causation still are not widely understood. We review theoretical results showing that this conception of evolution allows for a role of mutation as a cause of nonrandomness, a role that could be important but has been misconceived and associated misleadingly with neutral evolution. Specifically, biases in the introduction of variation, including mutational biases, may impose predictable biases on evolution, with no necessary dependence on neutrality. As an example of how important such effects may be, we present a new analysis partitioning the variance in mean rates of amino acid replacement during human–chimpanzee divergence to components of codon mutation and amino acid exchangeability. The results indicate that mutational effects are not merely important but account for most of the variance explained. The challenge that such results pose for comparative genomics is to address mutational effects as a necessary part of any analysis of causal factors. To meet this challenge requires developing knowledge of mutation as a biological process, understanding how mutation imposes propensities on evolution, and applying methods of analysis that incorporate mutational effects.
AND
ADAPTIONISM—30 YEARS AFTER GOULD AND LEWONTIN
Gould and Lewontin’s 30-year-old critique of adaptionism fundamentally changed the discourse of evolutionary biology. However, with the influx of new ideas and scientific traditions from genomics into evolutionary biology, the old adaptionist controversies are being recycled in a new context. The insight gained by evolutionary biologists, that functional differences cannot be equated to adaptive changes, has at times not been appreciated by the genomics community. In this comment, I argue that even in the presence of both functional data and evidence for selection from DNA sequence data, it is still difficult to construct strong arguments in favor of adaptation. However, despite the difficulties in establishing scientific arguments in favor of specific historic evolutionary events, there is still much to learn about evolution from genomic data.
Additional Reading: The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme