Recently I worked quite heavily on figuring out how to extract variance components for analyzing Qst. Here is a summary of the useful web resources that I found helpful. The between-population and within-population variance can be extracted from phenotypic data mainly in 3 ways. The most straightforward approach is to use ANOVA. For how to use ANOVA to partition variance…
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Career day Daphnia body parts
Here is the answer to the Daphnia body parts! I hope you enjoyed this learning experience!
Useful links for Kallisto and Sleuth RNA-seq analysis
I recently compiled a list of websites that are very useful for me to understand the Kallisto and Sleuth RNA-seq workflow. First, we should always check the official resources first. https://pachterlab.github.io/sleuth/walkthroughs Some walk-through examples. https://groups.google.com/forum/#!forum/kallisto-sleuth-users User group support for Sleuth https://github.com/pachterlab/sleuth/issues Reported issues with Sleuth https://galaxyproject.org/tutorials/rb_rnaseq/ Below are some resources I collected while I learn about RNA-seq analysis and Kallisto/Sleuth…
Lab meeting 4/10/2018
Swatantra: Hickey, D. A., & Golding, G. B. (2018). The advantage of recombination when selection is acting at many genetic Loci. Journal of Theoretical Biology, 442, 123–128. https://doi.org/10.1016/j.jtbi.2018.01.018 In this paper the authors revisited the classic Fisher-Muller models of recombination by numerical simulations. They simulated the fate of newly arised asexual clone in a population of sexually reproducing clones, in…
Lab meeting 4/3/2018
Papers we discussed. Trung: Metzger, C. M. J. A., Luijckx, P., Bento, G., Mariadassou, M. & Ebert, D. The Red Queen lives: Epistasis between linked resistance loci. Evolution 70, 480–487 (2016). Among the major hypotheses explaining the origin and maintance of sexual reproduction and recombination is the Red Queen hypothesis. Although the Red Queen dynamic is used in many theoretical…
Lab meeting 3/27/2018
Papers discussed. Trung Gherbi, H. et al. Homologous recombination in planta is stimulated in the absence of Rad50. EMBO Rep 2, 287–291 (2001). Gherbi was able to produce plants that express the hyper-recombination phenotype by suppressing the nonhomologous end joining (NHEJ) pathway that is used by cells to repair double stranded breaks (DSB). It would be interesting to see if…
2018 Sampling Trip to Arlington Drying Bed Ponds
During this Spring Break, our lab made a short trip to the Drying Bed in Arlington. This is our first time sampling Daphnia in Texas. This site is a waste water treatment facility and there are a few large ponds. These ponds probably exist all year long and are different from the temporary ponds that I used to sample a…
Lab meeting 2/20/2018
Marelize Lynch M, Gutenkunst R, Ackerman M, Spitze K, Ye Z, Maruki T, & Jia Z (2017) Population Genomics of Daphnia pulex. Genetics 206:315-332. Swatantra Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols…
Lab meeting 1/30/2018
Trung: Cowgill, U. M., Williams, D. M. & Esquivel, J. B. Effects of Maternal Nutrition on Fat Content and Longevity of Neonates of Daphnia magna. Journal of Crustacean Biology 4, 173–190 (1984). Comment: In the wake of several algae collapses and restarts in our own lab, information of the effects of maternal nutrition on their offspring would be useful. The…
Lab meeting 12/6/2017
Kenny Kruppert, S., Horstmann, M., Weiss, L. C., Schaber, C. F., Gorb, S. N. and Tollrian, R. (2016), Push or Pull? The light-weight architecture of the Daphnia pulex carapace is adapted to withstand tension, not compression. Journal of Morphology, 277: 1320–1328. doi:10.1002/jmor.20577 Comments: This paper is interesting because to has great images on the carapace of the daphnia. They went into detail…