Genomics of Adaptation and Speciation
winter semester 2017
16 Oct 2017 - 10 Feb 2018
Prof. Dr. Jochen Wolf
Dr. Ricardo J Pereira
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 -
- Get familiar with long standing questions and theory on speciation research;
- Understand the advantages and limitations of new genomics methods;
- Identify opportunities for future research.
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
However, everyone is expected to
the selected paper and
- Population Genetics;
- pereira AT bio.lmu.de
- j.wolf AT bio.lmu.de
3 ECTS, 2 SWS
Every week, Monday, 10:00-11:30
In order to pass, students can miss a maximum of 1 session, and lead the discussion of one paper (i.e. presentation of an article).
Grading is based both on the presentation and on the student's participation in the discussion during the other sessions.
Below there's a description of the topics addressed in each discussion session, along with a list of key concepts and suggested papers.
Students are free to suggest papers beyond this list, as long as it covers the same topic and one of the key concepts.
The estimated dates of discussion sessions and the initials of the initials of the discussion leader/s are marked below, but note that these are subjected to changes during the course of the semester.
23 Oct 2017; led by: CC
- The geography of speciation;
- Demographic parameters of speciation;
- Genomic methods in the study of geographic structure.
Meier, J. I., Sousa, V. C., Marques, D. A., Selz, O. M., Wagner, C. E., Excoffier, L., & Seehausen, O. (2016). Demographic modelling with whole-genome data reveals parallel origin of similar Pundamiliacichlid species after hybridization. Molecular Ecology, 26(1), 123–141. http://doi.org/10.1111/mec.13838 link
Pinho, C., and J. Hey. 2010. Divergence with gene flow: Models and data. Ann. Rev. Ecol. Evol. Syst. 41:215–230. link
Sousa, V., & Hey, J. (2013). Understanding the origin of species with genome-scale data: modelling gene flow. Nature Reviews Genetics, 14(6), 404–414. http://doi.org/10.1038/nrg3446 link
30 Oct 2017; led by: JKC
- Post-zygotic and intrinsic mechanisms;
- Underdominance and DMIs;
- The two rules of speciation.
Masly, J. P., & Presgraves, D. C. (2007). High-resolution genome-wide dissection of the two rules of speciation in Drosophila. PLoS Biology, 5(9), e243. http://doi.org/10.1371/journal.pbio.0050243 link
Tang, S., and D. C. Presgraves. 2009. Evolution of the Drosophila nuclear pore complex results in multiple hybrid incompatibilities. Science 323:779–782. link
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. link
Presgraves, D. C. (2010). The molecular evolutionary basis of species formation. Nature Reviews Genetics, 11(3), 175–180. http://doi.org/10.1038/nrg2718 link
Presgraves, D. C. (2008). Sex chromosomes and speciation in Drosophila. Trends in Genetics, 24(7), 336–343. http://doi.org/10.1016/j.tig.2008.04.007 link
6 Nov 2017; led by: IR
- Co-adaptation between genetic compartiments;
- Mismatch and hybrid breakdown;
- Mito-, Wolbachia-, and holobiont-incompatibilities.
Ellison, C. K., and R. S. Burton. 2008. Interpopulation hybrid breakdown maps to the mitochondrial genome. Evolution 62:631–638. link
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.link
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. link
Rand, D. M., Haney, R. A., & Fry, A. J. (2004). Cytonuclear coevolution: the genomics of cooperation. Tree, 19(12), 645–653. link
Bordenstein, S. R., & Theis, K. R. (2015). Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes. PLoS Biology, 13(8), e1002226–23. http://doi.org/10.1371/journal.pbio.1002226 link
13 Nov 2017; led by LN
- Pre-mating and pre-zygotic mechanisms;
- Sexual selection and assortative mating;
- Sensory drive.
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. link
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. link
Higgie, M., S. Chenoweth, and M. W. Blows. 2000. Natural Selection and the Reinforcement of Mate Recognition. Science 290:519–521. link
Kirkpatrick, M., & Ravigne, V. (2002). Speciation by natural and sexual selection: Models and experiments. American Naturalist, 159(S3), S22–S35. http://doi.org/10.1086/338370. link
Maan, M. E., & Seehausen, O. (2011). Ecology, sexual selection and speciation. Ecology Letters, 14(6), 591–602. http://doi.org/10.1111/j.1461-0248.2011.01606.x. link
20 Nov 2017; led by SN
- Adaptation to the ecological environment;
- Divergent Natural selection and fitness trade-offs;
- Fitness landscape.
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. link
Tenaillon, O., Barrick, J. E., Ribeck, N., Deatherage, D. E., Blanchard, J. L., Dasgupta, A., et al. (2016). Tempo and mode of genome evolution in a 50,000-generation experiment. Nature, 536(7615), 165–170. http://doi.org/10.1038/nature18959 link
Lang, G. I., Rice, D. P., Hickman, M. J., Sodergren, E., Weinstock, G. M., Botstein, D., & Desai, M. M. (2013). Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations. Nature, 500(7464), 571–574. http://doi.org/10.1038/nature12344 link
Savolainen, O., M. Lascoux, and J. Merilä. 2013. Ecological genomics of local adaptation. Nat Rev Genet 14:807–820. link
Burke, M. K. 2012. How does adaptation sweep through the genome? Insights from long-term selection experiments. Proc Biol Sci 279:5029. link
Elena, S. F., and R. E. Lenski. 2003. Microbial genetics: Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat Rev Genet 4:457. Nature Publishing Group. link
27 Nov 2017; led by CG
- Underdominance in hybrids;
- Experimental evolution;
- Mesocosmos experiments.
Barrett, R. D. H., Rogers, S. M., & Schluter, D. (2008). Natural selection on a major armor gene in threespine stickleback. Science, 322(5899), 255–257. http://doi.org/10.1126/science.1159978 link
McBride, C. S., & Singer, M. C. (2010). Field Studies Reveal Strong Postmating Isolation between Ecologically Divergent Butterfly Populations. PLoS Biology, 8(10), e1000529–17. http://doi.org/10.1371/journal.pbio.1000529 link
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. link
4 Dec 2017; led by RiS
- Chromosomal rearrangements;
- Meiotic drive.
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. link
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. link
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. link
11 Dec 2017; led by RaS & ZK
- The genic view of speciation;
- Heterogeneity of gene flow;
- Hitchhiking and linked selection.
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. link
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. link
18 Dec 2017; led by EL & SL
- Ecological divergence;
- Reproductive isolation.
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. link
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. link
Riesch, R., Muschick, M., Lindtke, D., Villoutreix, R., Comeault, A. A., Farkas, T. E., et al. (2017). Transitions between phases of genomic differentiation during stick-insect speciation. Nature Publishing Group, 1, 1–13. http://doi.org/10.1038/s41559-017-0082 link
15 Jan 2018; led by MO
- Reinforcement vs speciation reversal;
- Adaptive introgression;
- Hybrid speciation.
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. link
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. link
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. link
Abbott, R., Albach, D., Ansell, S., Arntzen, J. W., Baird, S. J. E., Bierne, N., et al. (2013). Hybridization and speciation. Journal of Evolutionary Biology, 26(2), 229–246. http://doi.org/10.1111/j.1420-9101.2012.02599.x link
22 Jan 2018; led by GM & AP
- HWE and LD;
- Geographic and genomic clines;
- Admixture mapping.
Singhal, S., & Bi, K. (2017). History cleans up messes: The impact of time in driving divergence and introgression in a tropical suture zone. Evolution, 25, 4692–12. http://doi.org/10.1111/evo.13278 link
Turner, L. M., & Harr, B. (2014). Genome-wide mapping in a house mouse hybrid zone reveals hybrid sterility loci and Dobzhansky-Muller interactions. Elife, 3, 4803–25. http://doi.org/10.7554/eLife.02504 link
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. link
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. link
Gompert, Z., & Mandeville, E. G. (2017). Analysis of Population Genomic Data from Hybrid Zones. Annual Review of Ecology. http://doi.org/10.1146/annurev-ecolsys-110316-022652 link