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Progress 2019

Evolution@home results facilitate refining the previous analysis of genomic decay from Muller's ratchet in the Amazon molly - and further comments on progress.

 

New analysis enabled by evolution@home results in the Amazon molly genome paper

The Amazon molly genome has been sequenced, not least motivated by the question how this small asexual fish manages to stay alive for so long. This question was first qualitatively investigated in 2008 by an evolution@home model as implemented in Simulator005. The latest study sequenced and compared a few dozen genomes to investigate, whether paternal introgression of new genetic material contributes to the long-term survival of this all-female fish. Using the evolution@home results database of global computing results made it easy to analyze the potential impact of such new material on genomic decay. The effects turn out to be subtle. For more details, see the online material of the new study (in comparison with the previous evolution@home study):

  • Update on Muller's ratchet in the fish Amazon molly - to investigate potential paternal introgression (using evolution@home results):
    • Wesley C. Warren, Raquel García-Pérez, Sen Xu, Kathrin P. Lampert, Domitille Chalopin, Matthias Stöck, Laurence Loewe, Yuan Lu, Lukas Kuderna, Patrick Minx, Michael J. Montague, Chad Tomlinson, LaDeana W. Hillier, Daniel N. Murphy, John Wang, Zhongwei Wang, Constantino Macias Garcia, Gregg C. W. Thomas, Jean-Nicolas Volff, Fabiana Farias, Bronwen Aken, Ronald B. Walter, Kim D. Pruitt, Tomas Marques-Bonet, Matthew W. Hahn, Susanne Kneitz, Michael Lynch & Manfred Schartl (2018) "Clonal polymorphism and high heterozygosity in the celibate genome of the Amazon molly", Nature Ecology & Evolution 2:669–679 (with extensive supplementary material, discussing genomic decay from Muller's ratchet in 'Note 6 & Fig. 7', pages 10-12 & 19-22). Open Access at:  PDF  |  Main DOI | Main PDF | Supplement PDF  - accompanied by a News & Views article: "Genomic health in an asexual fish", see here
  • First study quantifying Muller's ratchet in the fish Amazon molly (using evolution@home results) - see news here.
    • Loewe L & Lamatsch D (2008) "Quantifying the threat from Muller's ratchet in the Amazon molly (Poecilia formosa)", BMC Evolutionary Biology 8:88. (20 pages). Designated as ‘highly accessed’ by BMC.  PDF  |  Journal

Thank You to all who have been contributing to the computing results used in this important analysis!

 

Progress with developing a stable evolution@home platform serving broader research in biology


Evolution@home has been steadily expanding the range of questions, models, and parameter combinations in evolutionary biology that can be analyzed by computations spanning many orders of magnitude in computational complexity (see the 2007 paper on how to decide what to put out for solving by global computing). This work has gain much breadth, width, and depth by the NSF-funded development of a prototype for the Evolvix modeling language that is being developed for facilitating computation in evolutionary systems biology. 
The ongoing experiences with running evolution@home have been of critical importance for exploring feasible long-term stable designs for Evolvix; they enabled a perspective that Evolvix could otherwise not have adopted. In return, Evolvix has been very informative and effective in finding long-term solutions for long-standing problems that have been reducing the efficiency of evolution@home research computing.
Therefore, the partnership continues in order to develop an entirely new, long-term stable foundation for 

  • Evolvix as a modeling and general-purpose programming language that will eventually have distributed and global computing built-in, so users can focus on coding & the science, and for
  • Evolution@home as a global-computing system that will eventually run on a programing language that was made to support it (alleviating many administrational burdens of distributing work across computers worldwide.
There are lots of exciting developments behind the scenes! Here is not the time and pace to cover them; they will shared as research proceeds. Suffice to say that none of this would be possible without you, so:
 
 

Thank You to all who have been contributing to what makes evolution@home do useful work!

 
 
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