EES Seminar and Discussion Course 3, Winter Semester 13/14

Instructors Niels Dingemanse, Dirk Metzler

Presentations given in the seminar

Nov 4 (De): Drug resitance in HIV

Long (S):

Beerenwinkel, N., Montazeri, H., Schuhmacher, H., Knupfer, P., von Wyl, V., Furrer, H., Battegay, M., Hirschel, B., Cavassini, M., Vernazza, P., Bernasconi, E., Yerly, S., Boni, J., Klimkait, T., Cellerai, C., & Gunthard, H. F. (2013). The Individualized Genetic Barrier Predicts Treatment Response in a Large Cohort of HIV-1 Infected Patients.. PLoS Comput Biol, 9(8), e1003203.

Short (H)

Pennings, P. S. (2012). Standing genetic variation and the evolution of drug resistance in HIV.. PLoS Comput Biol, 8(6), e1002527.

Nov 11 (H): Evolution of reproduction strategies in social insects

Long (C):

Boomsma, J. J. (2013). Beyond promiscuity: mate-choice commitments in social breeding.. Philos Trans R Soc Lond B Biol Sci, 368(1613), 20120050.

Short (De):

Purcell, J., & Chapuisat, M. (2013). Bidirectional shifts in colony queen number in a socially polymorphic ant population.. Evolution, 67(4), 1169-80.

Nov 18 (Di): Evolution of responsiveness

Long (L):

Wolf, M., Van Doorn, G. S., & Weissing, F. J. (2011). On the coevolution of social responsiveness and behavioural consistency.. Proc Biol Sci, 278(1704), 440-8.

Short (F):

Laskowski, K. L., & Bell, A. M. (2013). Competition avoidance drives individual differences in response to a changing food resource in sticklebacks.. Ecol Lett, 16(6), 746-53.

Nov 25 (L): Social network evolution

Long (Di):

Aplin, L. M., Farine, D. R., Morand-Ferron, J., Cole, E. F., Cockburn, A., & Sheldon, B. C. (2013). Individual personalities predict social behaviour in wild networks of great tits (Parus major).. Ecol Lett,.

Short (S):

Lea, A. J., Blumstein, D. T., Wey, T. W., & Martin, J. G. (2010). Heritable victimization and the benefits of agonistic relationships.. Proc Natl Acad Sci U S A, 107(50), 21587-92.

Dec 2 (J): Critique of ENCODE

Long (De):

Graur, D., Zheng, Y., Price, N., Azevedo, R. B., Zufall, R. A., & Elhaik, E. (2013). On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE.. Genome Biol Evol, 5(3), 578-90.

Short (L):

Doolittle, W. F. (2013). Is junk DNA bunk? A critique of ENCODE.. Proc Natl Acad Sci U S A, 110(14), 5294-300.

Eddy, S. R. (2013). The ENCODE project: missteps overshadowing a success.. Curr Biol, 23(7), R259-61.

Dec 9 (C): Evolution of genomes

Long (H):

Simola, D. F., Wissler, L., Donahue, G., Waterhouse, R. M., Helmkampf, M., Roux, J., Nygaard, S., Glastad, K. M., Hagen, D. E., Viljakainen, L., Reese, J. T., Hunt, B. G., Graur, D., Elhaik, E., Kriventseva, E. V., Wen, J., Parker, B. J., Cash, E., Privman, E., Childers, C. P., Munoz-Torres, M. C., Boomsma, J. J., Bornberg-Bauer, E., Currie, C. R., Elsik, C. G., Suen, G., Goodisman, M. A., Keller, L., Liebig, J., Rawls, A., Reinberg, D., Smith, C. D., Smith, C. R., Tsutsui, N., Wurm, Y., Zdobnov, E. M., Berger, S. L., & Gadau, J. (2013). Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality.. Genome Res, 23(8), 1235-47.

Short (J):

Ghiselli, F., Milani, L., Guerra, D., Chang, P. L., Breton, S., Nuzhdin, S. V., & Passamonti, M. (2013). Structure, transcription, and variability of metazoan mitochondrial genome: perspectives from an unusual mitochondrial inheritance system.. Genome Biol Evol, 5(8), 1535-54.

Jan 20 (L):

Long (J):

Caudy, A. A., Guan, Y., Jia, Y., Hansen, C., Desevo, C., Hayes, A. P., Agee, J., Alvarez-Dominguez, J. R., Arellano, H., Barrett, D., Bauerle, C., Bisaria, N., Bradley, P. H., Breunig, J. S., Bush, E., Cappel, D., Capra, E., Chen, W., Clore, J., Combs, P. A., Doucette, C., Demuren, O., Fellowes, P., Freeman, S., Frenkel, E., Gadala-Maria, D., Gawande, R., Glass, D., Grossberg, S., Gupta, A., Hammonds-Odie, L., Hoisos, A., Hsi, J., Hsu, Y. H., Inukai, S., Karczewski, K. J., Ke, X., Kojima, M., Leachman, S., Lieber, D., Liebowitz, A., Liu, J., Liu, Y., Martin, T., Mena, J., Mendoza, R., Myhrvold, C., Millian, C., Pfau, S., Raj, S., Rich, M., Rokicki, J., Rounds, W., Salazar, M., Salesi, M., Sharma, R., Silverman, S., Singer, C., Sinha, S., Staller, M., Stern, P., Tang, H., Weeks, S., Weidmann, M., Wolf, A., Young, C., Yuan, J., Crutchfield, C., McClean, M., Murphy, C. T., Llinas, M., Botstein, D., Troyanskaya, O. G., & Dunham, M. J. (2013). A new system for comparative functional genomics of Saccharomyces yeasts.. Genetics, 195(1), 275-87.

Short (C):

Forstmeier, W., & Schielzeth, H. (2011). Cryptic multiple hypotheses testing in linear models: overestimated effect sizes and the winner's curse.. Behav Ecol Sociobiol, 65(1), 47-55.

Feb 3 (F): Whole-genome analyses in population genetics

Long presentation (L):

Campo, D., Lehmann, K., Fjeldsted, C., Souaiaia, T., Kao, J., & Nuzhdin, S. V. (2013). Whole-genome sequencing of two North American Drosophila melanogaster populations reveals genetic differentiation and positive selection. Mol Ecol,.

Short (Di):

Tucker, A. E., Ackerman, M. S., Eads, B. D., Xu, S., & Lynch, M. (2013). Population-genomic insights into the evolutionary origin and fate of obligately asexual Daphnia pulex.. Proc Natl Acad Sci U S A, 110(39), 15740-5.

Feb 10 (S): How accurately can we infer bottlenecks from genetic data?

Long (F):

Peery, M. Z., Kirby, R., Reid, B. N., Stoelting, R., Doucet-Beer, E., Robinson, S., Vasquez-Carrillo, C., Pauli, J. N., & Palsboll, P. J. (2012). Reliability of genetic bottleneck tests for detecting recent population declines.. Mol Ecol, 21(14), 3403-18.

Short (L):

Hoban, S. M., Gaggiotti, O. E., & Bertorelle, G. (2013). The number of markers and samples needed for detecting bottlenecks under realistic scenarios, with and without recovery: a simulation-based study.. Mol Ecol, 22(13), 3444-50.

Peery, M. Z., Reid, B. N., Kirby, R., Stoelting, R., Doucet-Beer, E., Robinson, S., Vasquez-Carrillo, C., Pauli, J. N., & Palsbo, L. L. (2013). More precisely biased: increasing the number of markers is not a silver bullet in genetic bottleneck testing.. Mol Ecol, 22(13), 3451-7.

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web page last updated: Dirk Metzler, Dec 13, 2013