Fall 2021 | Harvard University
This discussion-based course will survey modern ideas about evolution and speciation, and how they have changed as a result of genomic approaches. As well as readings and discussions in class, the course will utilize some live online video sessions with major players in the field of evolutionary and comparative genomics.
General
Readings
Week 1: Sept 2 - Genome Assemblies and Do We Trust the Data?
Speaker: Tim Sackton (Harvard)
Reading Papers
Whibley, A., Kelley, J. L., & Narum, S. R. (2020). The changing face of genome assemblies: Guidance on achieving high-quality reference genomes. Molecular Ecology Resources, 21(2), 435–447.
Rhie, A., McCarthy, S.A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano‑Silva, M., Chow, W., Fungtammasan, A., Kim, J., Lee, C., Ko, B.J., Chaisson, M., Gedman, G.L., Cantin, L.J., Thibaud‑Nissen, F., Haggerty, L., Bista, I., Smith, M., and others (including Erich D. Jarvis) (2021). Towards complete and error‑free genome assemblies of all vertebrate species. Nature, 592(7856), 737–746.
Optional Readings
The Vertebrate Genomes Project: A Collection of Research Articles from Phase I of the Vertebrate Genomes Project. Nature Research (2021).
Week 2: Sept 9 - The Base of the Tree of Life
Speaker: Damien Devos (Sevilla, Spain)
Lecture Slide: The Tree of Life
Reading Papers
Devos, Damien P. (2021). Reconciling Asgardarchaeota Phylogenetic Proximity to Eukaryotes and Planctomycetes Cellular Features in the Evolution of Life. Molecular Biology and Evolution, 38(8), 3531–3542.
Stairs, Cody W., Dharamshi, Jarny E., Tamarit, Daniel, Eme, Laura, Jørgensen, Steffen L., Spang, Anja, & Ettema, Thijs J. G. (2020). Chlamydial Contribution to Anaerobic Metabolism During Eukaryotic Evolution. Science Advances, 6(48), eabb7258.
Optional Readings
Blais, Camille, & Archibald, John M. (2021).The past, present and future of the tree of life. Current Biology, 31(7), R314–R321. (Is it really a tree? What is a tree?)
Cavalier-Smith, Thomas, & Chao, Eunice E. Y. (2020). Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). Protoplasma, 257, 621–753. (A massive pro-one-domain theory of life, in 133 pages! Referred to by Devos. Tom Cavalier-Smith was a much loved, but often controversial figure in the field of the Tree of Life.)
Roger, Andrew J. (2021). Thomas Cavalier-Smith (1942–2021). Current Biology, 31(20), R977–R981. (Cavalier-Smith died soon after publishing the above paper.)
Woese, Carl R. (2002). On the evolution of cells. Proceedings of the National Academy of Sciences of the United States of America, 99(13), 8742–8747. (This paper is a classic. Earlier iterations of these ideas—often in PNAS—led to the rooting of the Tree of Life and the three-domain theory.)
Week 3: Sept 16 - Protist Diversity and the Origins of Multicellularity
Reading Papers
Baldauf, Sandra L., Romeralo, María, & Carr, Mathew. (2013). The evolutionary origin of animals and fungi (pp. 73–106). In G. Trueba & C. Montúfar (Eds.), Evolution from the Galapagos: Two Centuries after Darwin. Social and Ecological Interactions in the Galapagos Islands (Vol. 2).
Burki, Fabien, Roger, Andrew J., Brown, Matthew W., & Simpson, Alastair G. B. (2020). The New Tree of Eukaryotes. Trends in Ecology & Evolution, 35(1), 43–55.
Week 4: Sept 23 - Genomics and the Study of Introgression: Case Study in Heliconius Butterflies
Speaker: Simon H. Martin (Edinburgh)
Reading Papers
Martin, S.H., Dasmahapatra, K.K., Nadeau, N.J., Salazar, C., Walters, J.R., Simpson, F., Blaxter, M., Manica, A., Mallet, J., & Jiggins, C.D. (2013). Genome-wide evidence for speciation with gene flow in Heliconius butterflies. Genome Research, 23(11), 1817–1828.
Martin, S.H., Davey, J.W., Salazar, C., & Jiggins, C.D. (2019). Recombination rate variation shapes barriers to introgression across butterfly genomes. PLOS Biology, 17(2), e2006288.
Optional Readings
Martin, S.H., & Jiggins, C.D. 2017. Interpreting the Genomic Landscape of Introgression. Current Opinion in Genetics & Development 47:69-74.
Week 5: Sept 30 - Genomics of an Adaptive Radiation in Lake Victoria: The Role of Ancestral Hybridization
Speaker: Joana Meier (Cambridge, UK)
Reading Papers
Meier, J.I., Marques, D.A., Mwaiko, S., Wagner, C.E., Excoffier, L., & Seehausen, O. 2017. Ancient hybridization fuels rapid cichlid fish adaptive radiations. Nature Communications 8:14363
Meier, J.I., Sousa, V.C., Marques, D.A., Selz, O.M., Wagner, C.E., Excoffier, L., & Seehausen, O. (2017).
Demographic modelling with whole-genome data reveals parallel origin of similar Pundamilia cichlid species after hybridization. Molecular Ecology, 26(1), 123–141.
Option Readings
Marques, D.A., Meier, J.I., & Seehausen, O. (2019). A combinatorial view on speciation and adaptive radiation. Trends in Ecology & Evolution, 34(6), 531–544.
Richards, E.J., McGirr, J.A., Wang, J.R., et al., & Martin, C.H. (2021). A vertebrate adaptive radiation is assembled from an ancient and disjunct spatiotemporal landscape. Science, 373(6556), 1477–1481.
Week 6: Oct 7 - Genomic Stresses Due to Genome Doubling in Polyploid Flowering Plants
Speaker: Kirsten Bomblies (Zurich)
Reading Papers
Yant, L., Hollister, J.D., Wright, K.M., Arnold, B.J., Higgins, J.D., Franklin, F.C.H., & Bomblies, K. (2013).
Meiotic adaptation to genome duplication in Arabidopsis arenosa. Current Biology, 23(21), 2151–2156.
AND
a) This useful recent review of the topic of the evolutionary effects of gene duplication, except meiosis:
Bomblies, K. (2020). When everything changes at once: finding a new normal after genome duplication. Proceedings of the Royal Society B: Biological Sciences, 287 (1937), 20202154.
OR
b) This review paper on the importance of evolutionary adjustment for meiosis, and its relation to temperature:
Bomblies, K., Higgins, J.D., & Yant, L. 2015. Meiosis evolves: adaptation to external and internal environments. New Phytologist 208:306-323.
Week 7: Oct 14 - The Multispecies Coalescent and the Species Tree
Speaker: Scott Edwards (Harvard)
Reading Papers
Edwards, S.V. (2009). Is a new and general theory of molecular systematics emerging? Evolution, 63(1), 1–19.
Cloutier, A., Sackton, T.B., Grayson, P., Clamp, M., Baker, A.J., & Edwards, S.V. (2019). Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone. Systematic Biology, 68(6), 937–955.
Optional Readings
Liu, L., Anderson, C., Pearl, D., & Edwards, S.V. (2019). Modern Phylogenomics: Building Phylogenetic Trees Using the Multispecies Coalescent Model In: Anisimova, M. (Ed.), Evolutionary Genomics: Statistical and Computational Methods, 2nd ed., pp. 211–239. New York: Humana Press.
Week 8: Oct 21 - The Multispecies Coalescent with Introgression (MSci)
Speaker: Ziheng Yang (University College London)
Reading Papers
Flouri, T., Jiao, X., Rannala, B., & Yang, Z. 2020. A Bayesian Implementation of the Multispecies Coalescent Model with Introgression for Phylogenomic Analysis. Molecular Biology and Evolution 37:1211-1223.
Jiao, X., Flouri, T., & Yang, Z. 2021. Multispecies coalescent and its applications to infer species phylogenies and cross-species gene flow. National Science Review.
Week 9: Oct 28 -The Spectre of Too Many Species!
Speaker: Adam Leaché (University of Washington)
Reading Papers
Leaché, A.D., Zhu, T., Rannala, B., & Yang, Z. (2019). The Spectre of Too Many Species. Systematic Biology, 68(2), 168–181
Leaché, A.D., Davis, H.R., Singhal, S., Fujita, M.K., Lahti, M.E., & Zamudio, K.R. 2021. Phylogenomic Assessment of Biodiversity Using a Reference-Based Taxonomy: An Example With Horned Lizards (Phrynosoma). Frontiers in Ecology and Evolution 9:437.
Week 10: Nov 4 - Evolutionary Genomics of the Malaria Parasite, Plasmodium
Speaker: Lucy van Dorp (University College of London)
Reading Papers
Otto, T.D., Gilabert, A., Crellen, T., Böhme, U., Arnathau, C., Sanders, M., Oyola, S.O., Okouga, A.P., Boundenga, L., Willaume, E., Ngoubangoye, B., Moukodoum, N.D., Paupy, C., Durand, P., Rougeron, V., Ollomo, B., Renaud, F., Newbold, C., Berriman, M., & Prugnolle, F. 2018. Genomes of all known members of a Plasmodium subgenus [i.e. Laveriana, the subgenus that includes P. falciparum] reveal paths to virulent human malaria. Nature Microbiology 3:687-697.
and
van Dorp, L., Gelabert, P., Rieux, A., de Manuel, M., de-Dios, T., Gopalakrishnan, S., Carøe, C., Sandoval-Velasco, M., Fregel, R., Olalde, I., Escosa, R., Aranda, C., Huijben, S., Mueller, I., Marquès-Bonet, T., Balloux, F., Gilbert, M.T.P., & Lalueza-Fox, C. 2019. Plasmodium vivax Malaria Viewed through the Lens of an Eradicated European Strain. Molecular Biology and Evolution 37:773-785.
Week 11: Nov 11 - Understanding Selection in the Genome and the Ancestral Recombination Graph (ARG)
Speaker: Adam Siepel (Cold Spring Harbor)
Reading Papers
Hejase, H.A., Salman-Minkov, A., Campagna, L., Hubisz, M.J., Lovette, I.J., Gronau, I., & Siepel, A. 2020. Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps. Proceedings of the National Academy of Sciences of the United States of America 117:30554-30565.
Hejase, H.A., Dukler, N., & Siepel, A. 2020. From summary statistics to gene trees: methods for inferring positive selection. Trends in Genetics 36:243-258.
Comprehensive details of methods: Rasmussen, M.D., Hubisz, M.J., Gronau, I., & Siepel, A. 2014. Genome-Wide Inference of Ancestral Recombination Graphs. PLoS Genetics 10:e1004342.
Week 12: Nov 18 - Adaptation at the Molecular Level
Speaker: Michael Desai
Reading Papers
Phillips, A.M., Lawrence, K.R., Moulana, A., Dupic, T., Chang, J., Johnson, M.S., Cvijovic, I., Mora, T., Walczak, A.M., & Desai, M.M. 2021. Binding affinity landscapes constrain the evolution of broadly neutralizing anti-influenza antibodies. eLife 10:e71393.
Nguyen Ba, A.N., Lawrence, K.R., Rego-Costa, A., Gopalakrishnan, S., Temko, D., Michor, F., & Desai, M.M. 2021. Barcoded bulk QTL mapping reveals highly polygenic and epistatic architecture of complex traits in yeast. bioRxiv:2021.2009.2008.459513.
Week 13: Dec 2 - Evolution in Humans and Other Mammals
Speaker: Kelley Harris
Reading Papers
Harris, K., & Nielsen, R. (2016). The Genetic Cost of Neanderthal Introgression. Genetics, 203(2), 881–891.
Sasani, T.A., Ashbrook, D.G., Lu, L., Palmer, A.A., Williams, R.W., Pritchard, J.K., & Harris, K. 2021. A wild-derived antimutator drives germline mutation spectrum differences in a genetically diverse murine family. bioRxiv: 2021.2003.2012.435196
Sasani, T.A., Ashbrook, D.G., Beichman, A.C., Lu, L., Palmer, A.A., Williams, R.W., Pritchard, J.K., & Harris, K. (2021). A natural mutator allele shapes mutation spectrum variation in mice. bioRxiv.2021.03.12.435196v2