Genomics of Adaptation and Speciation
24.04.2017 - 24.07.2017
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, 8:30-10:00
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
- Historical perspective;
- Species: reality and concepts;
- Isolating barriers;
- Genomic methods in speciation.
- The geography of speciation;
- Demographic parameters of speciation;
- Genomic methods in the study of geographic structure.
: Pinho, C., and J. Hey. 2010. Divergence with gene flow: Models and data. Ann. Rev. Ecol. Evol. Syst. 41:215–230.
: 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.
: KW & WC
Class 3: Chromosomal speciation
- 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.
: 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.
: 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.
Class 4: Genetic basis of prezygotic isolation
- 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.
: 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.
: Higgie, M., S. Chenoweth, and M. W. Blows. 2000. Natural Selection and the Reinforcement of Mate Recognition. Science 290:519–521.
Class 5: Genetic basis of post-zygotic intrinsic isolation
- Post-zygotic and intrinsic mechanisms;
- Underdominance and DMIs;
- The two rules of speciation.
: Tang, S., and D. C. Presgraves. 2009. Evolution of the Drosophila nuclear pore complex results in multiple hybrid incompatibilities. Science 323:779–782.
: 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.
Class 6: Cyto-nuclear incompatibilities: a special case of DMIs
- Co-adaptation between genetic compartiments;
- Mismatch and hybrid breakdown;
- Mito-, Wolbachia-, and holobiont-incompatibilities.
: 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.
: Ellison, C. K., and R. S. Burton. 2008. Interpopulation hybrid breakdown maps to the mitochondrial genome. Evolution 62:631–638.
: 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.
Class 7: The genomic landscape of speciation
- 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.
: 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.
: MB & HA
Class 8: The genetic basis of postzygotic extrinsic isolation
- Underdominance in hybrids;
- Experimental evolution;
- Mesocosmos experiments.
: 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.
Class 9: The genetic basis of adaptation
- 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.
: Savolainen, O., M. Lascoux, and J. Merilä. 2013. Ecological genomics of local adaptation. Nat Rev Genet 14:807–820.
: BY & ZK
Class 10: Ecological Speciation: speciation with gene flow and divergent selection
- 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.
: 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.
: RH & MF
Class 11: Hybrid zones as windows into speciation and adaptation
- HWE and LD;
- Geographic and genomic clines;
- Admixture mapping.
: 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.
: 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.
: AG & JV
Class 12: The evolutionary consequences of hybridization
- 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.
: 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.