EvoGen Journal Club Schedule - ie2/evogen_journalclub Wiki

Fall 2021

Readings on Genetic Conflict. Zoom link here. 4-5PM Friday.

October 1: Organizational Meeting

October 8: Self-study/reading

Suggested paper: Rice, WR. 2013. Nothing in Genetics Makes Sense Except in Light of Genomic Conflict. Annu. Rev. Ecol. Evol. Syst. 44:217-237. https://www.annualreviews.org/doi/10.1146/annurev-ecolsys-110411-160242

October 15: Shola A.

Discussion Paper: Rice, WR. 2013. Nothing in Genetics Makes Sense Except in Light of Genomic Conflict. Annu. Rev. Ecol. Evol. Syst. 44:217-237. https://www.annualreviews.org/doi/10.1146/annurev-ecolsys-110411-160242

October 22:Michael S.

Discussion Paper: de Oliveira, J.L., Morales, A.C., Stewart, B. et al. Conditional expression explains molecular evolution of social genes in a microbe. Nat Commun 10, 3284 (2019). https://doi.org/10.1038/s41467-019-11237-2

October 29: Sabrina M.

Discussion Paper: Courret C, Chang C-H, Wei KH-C, Montchamp-Moreau C, Larracuente AM. 2019. Meiotic drive mechanisms: lessons from Drosophila. Proc. R. Soc. B 286: 20191430. http://dx.doi.org/10.1098/rspb.2019.1430

November 5:

November 12: Hope H.

Discussion Paper: Incompatibility between mitochondrial and nuclear genomes during oogenesis results in ovarian failure and embryonic lethality https://journals.biologists.com/dev/article/144/13/2490/48163/Incompatibility-between-mitochondrial-and-nuclear

November 19:

November 26: Thanksgiving break

No journal club

December 3: Murillo

Summer 2021

Exploring publications in predatory journals 3:30-4:30 Friday at Washburne Park

Spring 2021

Readings on determinants of genetic diversity II. 3:30-4:30 on Fridays.

Zoom: https://uoregon.zoom.us/j/91467161735?pwd=TUpoQnVsSno5aGRCcjVlS3huQ0lBZz09

April 2th: Organizational Meeting

April 9th: Zach S.

Discussion Paper: Johnson, M. S. et al. Phenotypic and molecular evolution across 10,000 generations in laboratory budding yeast populations. Elife 10, 1–28 (2021). DOI: 10.7554/eLife.63910

April 16th: Sabrina M.

Discussion Paper: Cooper TF (2007) Recombination Speeds Adaptation by Reducing Competition between Beneficial Mutations in Populations of Escherichia coli. PLOS Biology 5(9): e225. https://doi.org/10.1371/journal.pbio.0050225

Additional Companion Paper: de Visser JAGM (2007) Bacterial Solutions to the Problem of Sex. PLOS Biology 5(9): e245. https://doi.org/10.1371/journal.pbio.0050245

April 23rd: Shola A.

Discussion Paper: Eickbush, M. T., Young, J. M. & Zanders, S. E. Killer meiotic drive and dynamic evolution of the WTF gene family. Mol. Biol. Evol. 36, 1201–1214 (2019).

Review Article: McLaughlin, R. N. & Malik, H. S. Genetic conflicts: the usual suspects and beyond. J. Exp. Biol. 220, 6–17 (2017).

April 30th:Hope H.

Discussion Paper: Liu, J. & Robinson-Rechavi, M. Adaptive evolution of animal proteins over development: Support for the Darwin selection opportunity hypothesis of evo-devo. Mol. Biol. Evol. 35, 2862–2872 (2018).

May 7th: Gillia P.

Discussion Paper: Rousselle, M., Simion, P., Tilak, M. K., Figuet, E., Nabholz, B., & Galtier, N. (2020). Is adaptation limited by mutation? A timescale-dependent effect of genetic diversity on the adaptive substitution rate in animals. PLoS genetics, 16(4), e1008668.

May 14th: Shola A.

Discussion Paper:Cai JJ, Petrov DA. Relaxed purifying selection and possibly high rate of adaptation in primate lineage-specific genes. Genome Biol Evol. 2010 Jul 12;2:393-409. doi: 10.1093/gbe/evq019. PMID: 20624743; PMCID: PMC2997544.

May 21st: Claire G.:

Discussion Paper: Habrich, AK, Lawrence, ER, Fraser, DJ. Varying genetic imprints of road networks and human density in North American mammal populations. Evol Appl. 2020; 00: 1– 14. https://doi.org/10.1111/eva.13232

May 28th: Shannon S.

Discussion Paper: Sheldon EL, Schrey A,Andrew SC, Ragsdale A, Griffith SC. 2018Epigenetic and genetic variation among threeseparate introductions of the house sparrow(Passerdomesticus)into Australia.R.Soc.opensci.5:172185.http://dx.doi.org/10.1098/rsos.172185

June 4th: Sabrina M.

Discussion Paper: Caterpillars evolved from onychophorans by hybridogenesis Donald I. Williamson Proceedings of the National Academy of Sciences Nov 2009, 106 (47) 19901-19905; DOI: 10.1073/pnas.0908357106

End of term discussion & planning for Summer**

Winter 2021

Discussion Paper:Readings on determinants of genetic diversity. 3:30-4:30 on Fridays.

January 8: Organizational meeting

January 15: Andy

Lewontin, R. C. (1974). The genetic basis of evolutionary change. New York: Columbia University Press. Part 1: Chapter 5 pgs

January 22: Gilia

Lewontin, R. C. (1974). The genetic basis of evolutionary change. New York: Columbia University Press. Part 2: Chapter 5 pgs

January 29: Sabrina

Discussion Paper: Allaby RG, Ware RL, Kistler L. A re-evaluation of the domestication bottleneck from archaeogenomic evidence. Evol Appl. 2019;12:29–37. https://doi.org/10.1111/eva.1268

February 5: Hope

Discussion Paper: Masel, J. Cryptic genetic variation is enriched for potential adaptations. Genetics 172, 1985–1991 (2006). https://www.genetics.org/content/172/3/1985

February 12: Savanah

Discussion Paper: Marsden, C. D. et al (2016). Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs. Proceedings of the National Academy of Sciences, 113(1), 152-157.

https://www.pnas.org/content/113/1/152.short

February 19: LyAndra

Discussion Paper: Storz, J. F. et al. The role of mutation bias in adaptive molecular evolution: Insights from convergent changes in protein function. bioRxiv (2019)

doi:10.1101/580175

February 26: Shannon

Discussion Paper: Teixeira, J. C. & Huber, C. D. Dismantling a dogma: The inflated significance of neutral genetic diversity in conservation genetics. arXiv 118, 1–10 (2020)

https://www.pnas.org/content/pnas/118/10/e2015096118.full.pdf

March 5: CANCELLED

**March 12: **

March 19th: CANCELLED

Fall 2020

Readings on Conservation Genetics. 3:30-4:30 Friday

October 2: Organizational Meeting

October 9: Claire G.

DISCUSSION PAPER: Grossen, C., Guillaume, F., Keller, L. F., & Croll, D. (2020). Purging of highly deleterious mutations through severe bottlenecks in Alpine ibex. Nature communications, 11(1), 1-12.

REVIEW (OPTIONAL): Frankham, R. (2005). Genetics and extinction. Biological conservation, 126(2), 131-140.

October 16: Savanah B.

DISCUSSION PAPER: Baiz, M. D., Tucker, P. K., & Cortés‐Ortiz, L. (2019). Multiple forms of selection shape reproductive isolation in a primate hybrid zone. Molecular ecology, 28(5), 1056-1069.

REVIEW (OPTIONAL): Quilodrán, C. S., Montoya-Burgos, J. I., & Currat, M. (2020). Harmonizing hybridization dissonance in conservation. Communications Biology, 3(1), 1-10.

October 23: Zach

Discussion Paper" Fitzpatrick, S. W., Bradburd, G. S., Kremer, C. T., Salerno, P. E., Angeloni, L. M., & Funk, W. C. (2020). Genomic and Fitness Consequences of Genetic Rescue in Wild Populations. Current Biology, 30(3), 517-522.e5. https://doi.org/10.1016/j.cub.2019.11.062

Review: Frankham, R. (2015), Genetic rescue of small inbred populations: meta‐analysis reveals large and consistent benefits of gene flow. Mol Ecol, 24: 2610-2618. doi:10.1111/mec.13139

October 30: Shola

DISCUSSION PAPER: Yi, X., Donner, D. M., Marquardt, P. E., Palmer, J. M., Jusino, M. A., Frair, J., Lindner, D. L., & Latch, E. K. (2020). Major histocompatibility complex variation is similar in little brown bats before and after white-nose syndrome outbreak. Ecology and Evolution, 10(18), 10031–10043. https://doi.org/10.1002/ece3.6662

REVIEW: Carlson, S. M., Cunningham, C. J., & Westley, P. A. H. (2014). Evolutionary rescue in a changing world. Trends in Ecology and Evolution, 29(9), 521–530. https://doi.org/10.1016/j.tree.2014.06.005

November 6: Naomi and Anneliese

Discussion Paper: Patrik Nosil, Romain Villoutreix, Clarissa F. de Carvalho, Jeffrey L. Feder, Thomas L. Parchman and Zach Gompert. Ecology shapes epistasis in a genotype–phenotype–fitness map for stick insect colour. https://doi.org/10.1038/s41559-020-01305-y

November 13: Gilia

Kyriazis, C. C., Wayne, R. K., & Lohmueller, K. E. (2020). Strongly deleterious mutations are a primary determinant of extinction risk due to inbreeding depression. bioRxiv, 678524. https://www.biorxiv.org/content/10.1101/678524v2.full

Ralls, K., Sunnucks, P., Lacy, R. C., & Frankham, R. (2020). Genetic rescue: a critique of the evidence supports maximizing genetic diversity rather than minimizing the introduction of putatively harmful genetic variation. Biological Conservation, 251, 108784. https://doi.org/10.1016/j.biocon.2020.108784

November 20: Lauren

Discussion Paper: Narwhal Genome Reveals Long-Term Low Genetic Diversity despite Current Large Abundance Size iScience 2019

December 4: NIH RCR Module