Last night there was a bit of a discussion on twitter about whether or not reading 365 papers was a laudable, realistic, or even useful new years resolution. To be completely honest I’m not sure how much of a departure from my normal routine this would be. I tell new grad students all the time that they should be reading literature more than they are. I often recommend that they have a part of every day reserved for reading – this is what I do. However, I know that most of my reading is not consuming an entire paper. I like to think that I get the important bits as I look at figures and scan the discussion and results, but I also know that many times I am done with a paper just by reading the abstract.
If I had to make an informed estimate, I would say that reading a paper a day would not be any increase over my baseline. So my new years resolution is to keep track of papers that I read thoroughly, no promises on the final number. I’m not committing to reading every page either, but I will only count a paper if I feel like I have engaged enough to evaluate the science being presented. To keep the overhead low I am going to update this post by adding the citations and 1-2 sentences of my thoughts for each paper.
3) Hahn, Matthew W., and Luay Nakhleh. "Irrational exuberance for resolved species trees." Evolution (2015).
1) Sved, John A., Yizhou Chen, Deborah Shearman, Marianne Frommer, A. Stuart Gilchrist, and William B. Sherwin. "Extraordinary conservation of entire chromosomes in insects over long evolutionary periods." Evolution (2015).
- no new chromosomes in drosophila or tephritid flies
- possibly due to lack of telomerase
- suggest that this effect occurs across all diptera but cytogenetic evidence doesn't seem to support this and is not discussed.
2) Rovatsos, Michail, Jasna Vukić, Petros Lymberakis, and Lukáš Kratochvíl. "Evolutionary stability of sex chromosomes in snakes." In Proc. R. Soc. B, vol. 282, no. 1821, p. 20151992. The Royal Society, 2015.
- uses qPCR to look for a set of sex linked and autosomal genes across ~40 species.
- find that caenophidea all have the same genes sex linked on an X (sex specific portion)
- these genes are not sex linked in other groups of squamates that have differentiated sex chromosomes
- likely would miss any additions would have to look at many genes and still wouldn't catch unless the Y copy had been lost
3) Hahn, Matthew W., and Luay Nakhleh. "Irrational exuberance for resolved species trees." Evolution (2015).
- commentary suggesting that we shouldn't be trying to look at trait evolution with a single tree
- conflict among gene trees is telling us something possibly interesting and revealing
- bootstrap values are kinda pointless when it comes to phylogenomic datasets
- seems a bit pessimistic about the ability to overcome this problem by using Bayesian methods and modeling our trait evolution across a sample of trees.
4) Rundle, Howard D., and Michael C. Whitlock. "A genetic interpretation of ecologically dependent isolation." Evolution 55.1 (2001): 198-201.
- extends the lynch 1991 model (all autosomal loci approx. LCA) to include environmental dependent genetic effects. Lots of ways to extend this in SAGA.
5) Hangartner, Sandra, Anssi Laurila, and K. Räsänen. "The quantitative genetic basis of adaptive divergence in the moor frog (Rana arvalis) and its implications for gene flow." Journal of evolutionary biology 25.8 (2012): 1587-1599.
- Environmental dependent maternal and additive genetic effects contribute to divergence in trait (pH tolerance) Uses basic Rundle and Whitlock model above.
6) Edmands, Suzanne, and Julie K. Deimler. "Local adaptation, intrinsic coadaptation and the effects of environmental stress on interpopulation hybrids in the copepod Tigriopus californicus." Journal of Experimental Marine Biology and Ecology 303.2 (2004): 183-196.
4) Rundle, Howard D., and Michael C. Whitlock. "A genetic interpretation of ecologically dependent isolation." Evolution 55.1 (2001): 198-201.
- extends the lynch 1991 model (all autosomal loci approx. LCA) to include environmental dependent genetic effects. Lots of ways to extend this in SAGA.
5) Hangartner, Sandra, Anssi Laurila, and K. Räsänen. "The quantitative genetic basis of adaptive divergence in the moor frog (Rana arvalis) and its implications for gene flow." Journal of evolutionary biology 25.8 (2012): 1587-1599.
- Environmental dependent maternal and additive genetic effects contribute to divergence in trait (pH tolerance) Uses basic Rundle and Whitlock model above.
6) Edmands, Suzanne, and Julie K. Deimler. "Local adaptation, intrinsic coadaptation and the effects of environmental stress on interpopulation hybrids in the copepod Tigriopus californicus." Journal of Experimental Marine Biology and Ecology 303.2 (2004): 183-196.
- Shows no evidence of local adaptation but strong sugestion of coadaptation (coadapted gene complexes)
- Overwhelming pattern is F1s more fit F2s less fit - all relative to P1 and P2. So think this is likely dominance x dominance epistasis? Unfortunately data not availabe. No indication of local adaptation.
7) Erickson, David L., and Charles B. Fenster. "Intraspecific hybridization and the recovery of fitness in the native legume Chamaecrista fasciculata." Evolution 60.2 (2006): 225-233.
- F1 plants have low fitness but much of this is recovered by the F6
- Use an approach from Lynch and Walsh 1998 that sets up an expected phenotype measure accounting for addative and dominance and compares hybrids to this to test for role of epistasis.
- Not sure that I buy this as sold at the end - this as a source of adaptive variation that could favor homoploid hybrid speciation...
8) Egan, Scott P., and Daniel J. Funk. "Ecologically dependent postmating isolation between sympatric host forms of Neochlamisus bebbianae leaf beetles." Proceedings of the National Academy of Sciences 106.46 (2009): 19426-19431.
- Shows a strong pattern consistent with local adaptation for two races of leaf beetles.
- Would be perfect dataset for extending the Rundle and Whitlock 2001 model with SAGA
Writing these little notes up sucks! Just takes away time from additional reading/writing. Thinking that I will focus on this instead:
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