Mutation and evolution

Category: Research

  • Mutation-biased adaptation reaches the mainstream

    The most recent issue of PNAS includes a report by Galen, et al linking enhanced mutation at a CpG site to altitude adaptation in Andean house wrens (Troglodytes aedon), based on clear biogeographic and biochemical evidence of adaptation.  I’ve been waiting for this, both in the narrow sense that I’ve been waiting for this particular study…

  • Some comments on Pachter’s P value prize

    In late May, Lior Pachter posted a blog entitled Pachter’s P-value prize, offering a cash prize for providing a probability calculation (P value) based on a “justifiable” null model for the claim of Kellis, Birren and Lander, 2004, hereafter KBL, that some results from an analysis of yeast duplicate genes “strikingly” favored the classic…

  • Revolt of the clay: updated evidence

    In a previous post called “The revolt of the clay“, I described four different ways to think about the role of variation as a process with a predictably non-random impact on the outcome of evolution.  The main point was to draw attention to my favorite idea, about biases in the introduction of variation as…

  • The revolt of the clay: an initial progress report

    A “chance” encounter Earlier this month I was contacted by a reporter writing a piece on the role of chance in evolution.   I responded that I didn’t work on that topic, but if he was interested in predictable non-randomness due to biases in variation, then I would be happy to…

  • Amino acid exchangeability: condensing data from mutation-scanning experiments

    I just had to post the image below because it’s so cool. Here’s the backstory.  A decade ago, Lev Yampolsky and I did a meta-analysis of mutation-scanning experiments– studies that systematically change amino acids in proteins, and measure the effects.  Based on about 10,000 experimental exchanges, we computed an “EX” measure…

  • Mendelian-Mutationism: the Forgotten Evolutionary Synthesis

    What is Mendelian-mutationism?  And why do we argue in a recent paper in that it represents a forgotten evolutionary synthesis (Stoltzfus and Cable, 2014, Mendelian-Mutationism: The Forgotten Evolutionary Synthesis. J Hist Biol. doi:10.1007/s10739-014-9383-2)? For me, the story started a long time ago with our theoretical demonstration (graph at right) that bias in the…

  • The surprising case of origin-fixation models

    In a recent QRB paper with David McCandlish, we review the form, origins, uses, and implications of models (e.g., the familiar K = 4Nus) that represent evolutionary change as a 2-step process of (1) the introduction of a new allele by mutation, followed by (2) its fixation or loss. What could…

  • Going global with phylogeny: the tree-for-all hackathon

    Earlier this year, the Open Tree of Life project made the first public release of its synthetic tree of 2.5 million species (from ~4000 source trees), and announced a web services API (Application Programming Interface) providing programmatic access to a continually updated set of resources: a synthetic tree covering millions of species a database of thousands of source trees a reference taxonomy used…