Genomics of Adaptation and Speciation
24.04.2017 - 24.07.2017

Prof. Dr. Jochen Wolf
Dr. Ricardo J Pereira


Course Description


Species formation has fascinated evolutionary biologists for centuries. How does natural selection lead to local adaptation? Can genetic incompatibilities maintain species borders? How do these processes interact during the continuum of species formation? These questions have remained unanswered largely due to the lack of genomic tools that can be applicable across species. The recent advent of high-throughput sequencing has unlocked these limitations and allows applications to virtually any kind of organism. In this seminar, we will discuss the most recent papers defining new benchmarks in genomics of speciation. We will discuss foundational theory supporting new research questions, advantages of current genomic methodologies, and the limitation defining future advances of the field.

In this master-level course, you will -
The program of this seminar covers essential topics on Adaptation and Speciation (see the program below). Each class consists of a short lecture introducing the core concepts of that topic, followed by the discussion of current papers. Each student selects a topic according to her/his own research interests, selects a paper from a suggested list or equivalent, and will lead its discussion. However, everyone is expected to read the selected paper and contribute to the discussion.


Prerequisites

Contact

Credit

3 ECTS, 2 SWS

Timing

Every week, Monday, 8:30-10:00

Location

Biozentrum B02.045

Grading

In order to pass, students have to attend to at least 11 of the 12 sessions and lead the discussion of one paper.
Everyone is expected to participate in the discussion.


Program (Summer semester 2017)



Class 1: Introduction to adaptation and speciation


Class 2: The geographic context of speciation - speciation with or without gene flow
Paper 1: Pinho, C., and J. Hey. 2010. Divergence with gene flow: Models and data. Ann. Rev. Ecol. Evol. Syst. 41:215–230.
Paper 2: Lamichhaney, S., J. Berglund, M. S. Almén, K. Maqbool, M. Grabherr, A. Martinez-Barrio, M. Promerová, C.-J. Rubin, C. Wang, N. Zamani, B. R. Grant, P. R. Grant, M. T. Webster, and L. Andersson. 2015. Evolution of Darwin’s finches and their beaks revealed by genome sequencing. Nature 518:371–375.

discussion leader: KW & WC



Class 3: Chromosomal speciation
Paper 1: Zanders, S. E., M. T. Eickbush, J. S. Yu, J.-W. Kang, K. R. Fowler, G. R. Smith, and H. S. Malik. 2014. Genome rearrangements and pervasive meiotic drive cause hybrid infertility in fission yeast. Elife 3:e02630–23.
Paper 2: Wright, K. M., D. Lloyd, D. B. Lowry, M. R. Macnair, and J. H. Willis. 2013. Indirect Evolution of Hybrid Lethality Due to Linkage with Selected Locus in Mimulus guttatus. PLoS Biol 11:e1001497.
Paper 3: Lai, Z., T. Nakazato, M. Salmaso, J. M. Burke, S. Tang, S. J. Knapp, and L. H. Rieseberg. 2005. Extensive chromosomal repatterning and the evolution of sterility barriers in hybrid sunflower species. Genetics 171:291–303. Genetics.

discussion leader: HG



Class 4: Genetic basis of prezygotic isolation
Paper 1: Seehausen, O., Y. Terai, I. S. Magalhaes, K. L. Carleton, H. D. J. Mrosso, R. Miyagi, I. Van Der Sluijs, M. V. Schneider, M. E. Maan, H. Tachida, H. Imai, and N. Okada. 2008. Speciation through sensory drive in cichlid fish. Nature 455:620–626.
Paper 2: Conte, G. L., and D. Schluter. 2013. Experimental confirmation that body size determines mate preference via phenotype matching in a stickback species pair. Evolution 67-5:1477–1484.
Paper 3: Higgie, M., S. Chenoweth, and M. W. Blows. 2000. Natural Selection and the Reinforcement of Mate Recognition. Science 290:519–521.

discussion leader: AB



Class 5: Genetic basis of post-zygotic intrinsic isolation
Paper 1: Tang, S., and D. C. Presgraves. 2009. Evolution of the Drosophila nuclear pore complex results in multiple hybrid incompatibilities. Science 323:779–782.
Paper 2: Corbett-Detig, R. B., J. Zhou, A. G. Clark, D. L. Hartl, and J. F. Ayroles. 2013. Genetic incompatibilities are widespread within species. Nature 504:135–137.

discussion leader: SC



Class 6: Cyto-nuclear incompatibilities: a special case of DMIs
Paper 1: Burton, R. S., R. J. Pereira, and F. S. Barreto. 2013. Cytonuclear Genomic Interactions and Hybrid Breakdown. Annu Rev Ecol Evol S 44:281–302.
Paper 2: Ellison, C. K., and R. S. Burton. 2008. Interpopulation hybrid breakdown maps to the mitochondrial genome. Evolution 62:631–638.
Paper 3: Brucker, R. M., and S. R. Bordenstein. 2013. The hologenomic basis of speciation: gut bacteria cause hybrid lethality in the genus Nasonia. Science, doi: 10.1126/science.1239053.

discussion leader: AW



Class 7: The genomic landscape of speciation
Paper 1: Vijay, N., C. M. Bossu, J. W. Poelstra, M. H. Weissensteiner, A. Suh, A. P. Kryukov, and J. B. W. Wolf. 2016. Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex. Nature Communications 7:1–10.
Paper 2: Poelstra, J. W., N. Vijay, C. M. Bossu, H. Lantz, B. Ryll, I. Mueller, V. Baglione, P. Unneberg, M. Wikelski, M. G. Grabherr, and J. B. W. Wolf. 2014. The genomic landscape underlying phenotypic integrity in the face of gene flow in crows. Science 344:1410–1414.

discussion leader: MB & HA



Class 8: The genetic basis of postzygotic extrinsic isolation
Paper 1: Dettman, J. R., C. Sirjusingh, L. M. Kohn, and J. B. Anderson. 2007. Incipient speciation by divergent adaptation and antagonistic epistasis in yeast. Nature 447:585.

discussion leader: LM



Class 9: The genetic basis of adaptation
Paper 1: Burke, M. K., G. Liti, and A. D. Long. 2014. Standing Genetic Variation Drives Repeatable Experimental Evolution in Outcrossing Populations of Saccharomyces cerevisiae. Molecular Biology and Evolution 31:3228–3239.
Paper 2: Savolainen, O., M. Lascoux, and J. Merilä. 2013. Ecological genomics of local adaptation. Nat Rev Genet 14:807–820.

discussion leader: BY & ZK



Class 10: Ecological Speciation: speciation with gene flow and divergent selection
Paper 1: Soria-Carrasco, V., Z. Gompert, A. A. Comeault, T. E. Farkas, T. L. Parchman, J. S. Johnston, C. A. Buerkle, J. L. Feder, J. Bast, T. Schwander, S. P. Egan, B. J. Crespi, and P. Nosil. 2014. Stick Insect Genomes Reveal Natural Selection's Role in Parallel Speciation. Science 344:738–742.
Paper 2: Jones, F. C., M. G. Grabherr, Y. F. Chan, P. Russell, E. Mauceli, J. Johnson, R. Swofford, M. Pirun, M. C. Zody, S. White, E. Birney, S. Searle, J. Schmutz, J. Grimwood, M. C. Dickson, R. M. Myers, C. T. Miller, B. R. Summers, A. K. Knecht, S. D. Brady, H. Zhang, A. A. Pollen, T. Howes, C. Amemiya, J. Baldwin, T. Bloom, D. B. Jaffe, R. Nicol, J. Wilkinson, E. S. Lander, F. Di Palma, K. Lindblad-Toh, and D. M. Kingsley. 2012. The genomic basis of adaptive evolution in threespine sticklebacks. Nature 484:55–61.

discussion leader: RH & MF



Class 11: Hybrid zones as windows into speciation and adaptation
Paper 1: Larson, E. L., J. A. Andres, S. M. Bogdanowicz, and R. G. Harrison. 2013. Differential introgression in a mosaic hybrid zone reveals candidate barrier genes. Evolution 67:3653–3661.
Paper 2: Nadeau, N. J., M. Ruiz, P. Salazar, B. Counterman, J. A. Medina, H. Ortiz-Zuazaga, A. Morrison, W. O. McMillan, C. D. Jiggins, and R. Papa. 2014. Population genomics of parallel hybrid zones in the mimetic butterflies, H. melpomene and H. erato. Genome Research 24:1316–1333. Cold Spring Harbor Lab.

discussion leader: AG & JV



Class 12: The evolutionary consequences of hybridization
Paper 1: Dasmahapatra, K. K., J. R. Walters, A. D. Briscoe, J. W. Davey, A. Whibley, N. J. Nadeau, A. V. Zimin, D. S. T. Hughes, L. C. Ferguson, S. H. Martin, C. Salazar, J. J. Lewis, S. Adler, S.-J. Ahn, D. A. Baker, S. W. Baxter, N. L. Chamberlain, R. Chauhan, B. A. Counterman, T. Dalmay, L. E. Gilbert, K. Gordon, D. G. Heckel, H. M. Hines, K. J. Hoff, P. W. H. Holland, E. Jacquin-Joly, F. M. Jiggins, R. T. Jones, D. D. Kapan, P. Kersey, G. Lamas, D. Lawson, D. Mapleson, L. S. Maroja, A. Martin, S. Moxon, W. J. Palmer, R. Papa, A. Papanicolaou, Y. Pauchet, D. A. Ray, N. Rosser, S. L. Salzberg, M. A. Supple, A. Surridge, A. Tenger-Trolander, H. Vogel, P. A. Wilkinson, D. Wilson, J. A. Yorke, F. Yuan, A. L. Balmuth, C. Eland, K. Gharbi, M. Thomson, R. A. Gibbs, Y. Han, J. C. Jayaseelan, C. Kovar, T. Mathew, D. M. Muzny, F. Ongeri, L.-L. Pu, J. Qu, R. L. Thornton, K. C. Worley, Y.-Q. Wu, M. Linares, M. L. Blaxter, R. H. Ffrench-Constant, M. Joron, M. R. Kronforst, S. P. Mullen, R. D. Reed, S. E. Scherer, S. Richards, J. Mallet, W. O. McMillan, C. D. Jiggins, and H. G. Consortium. 2012. Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature 487:94–98.
Paper 2: Meier, J. I., D. A. Marques, S. Mwaiko, C. E. Wagner, L. Excoffier, and O. Seehausen. 2017. Ancient hybridization fuels rapid cichlid fish adaptive radiations. Nature Communications 8:14363.

discussion leader: JL