Spring 2025 | Harvard University
Speciation, or the origin of species, has been a controversial topic ever since Darwin's 1859 book. Even in the genomic era we are now experiencing, speciation is a frequent topic that demands attention. In this course, we will cover in approximate order:
• History of ideas in speciation; pre-Darwin, Darwin & Wallace, 1930-1940s, recent.
• What are species? Species concepts and species delimitation.
• What is needed to understand speciation? The population genetics of gene flow, and genetic divergence via mutation, drift, and selection
• The concept of reproductive isolation
• Brief introduction to coalescent theory and the multi-species coalescent
• The geography of speciation, including allopatric, parapatric, and sympatric speciation
• Ecological "races" and ecological speciation
• Behavioral divergence and mate choice, including "reinforcement"
• Hybrid inviability and hybrid sterility between species
• Idealized population genetic models of speciation
• Chromosomal evolution, genomic rearrangements, and speciation
• Speciation: caused by natural selection or by genetic drift?
• Beyond the species: macroevolution and diversification
General
Reading and Lecture Notes
Lecture 01: What Is Speciation? Darwin's Origin of Species
Lecture Slides: What is speciation? Darwin and the “Origin of Species”
Reading
Darwin, C., 1859. On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. London: John Murray. (Chapters 2, 3, 4).
For reference: Complete facsimile Origin of Species
Lecture 02: What Are Species? Concepts of Species
Lecture Slide: What are species? Concepts of species
Reading
Darwin, C., 1859. On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. London: John Murray. (Chapters 2, 3 & 4: “The Struggle for Existence” and “Natural Selection”).
Optional Readings
Mayr, E., 1970. Populations, species, and evolution. Cambridge, MA: Harvard University Press. (Chapter 2).
Mallet, J., et al., 2024. Species, concepts of. In: S.M. Scheiner, ed. Encyclopedia of biodiversity. 3rd ed. Vol. 7. Oxford: Elsevier, pp. 531–545.
Lecture 03: Discussion – What on Earth Was Darwin on About?
Essential Reading
Darwin, C., 1859. On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. London: John Murray. Chapters 2–4: "The Struggle for Existence" and "Natural Selection" (extracts).
Supplementary Reading
Mallet, J. (2008). Mayr’s view of Darwin: was Darwin wrong about speciation? Biological Journal of the Linnean Society, 95(1), 3–16.
Lecture 04: The Speciation Continuum: Subspecies and Ecological "Races"
Lecture Slides: The speciation continuum: ecological races
Essential Readings
Johnson, S.D. (2025). Pollination ecotypes and the origin of plant species. Proceedings of the Royal Society B: Biological Sciences, 292:20242787.
Mallet, J. (2008). Hybridization, ecological races, and the nature of species: empirical evidence for the ease of speciation. Philosophical Transactions of the Royal Society B: Biological Sciences, 363(1506), 2971–2986.
Lecture 05: Levels of Selection and the "Shifting Balance"
Optional Readings
Okasha, S. (2008).The Units and Levels of Selection In: Sarkar, S. and Plutynski, A. (eds.) A Companion to the Philosophy of Biology, pp. 138–156. Oxford: Wiley-Blackwell.
Lewontin, R.C. (1970). The Units of Selection. Annual Review of Ecology and Systematics, 1, pp.1–18.
Lecture 06: Discussion – Species Continuum and Species Concepts
Required Readings
Johnson, S.D. (2025). Pollination ecotypes and the origin of plant species. Proceedings of the Royal Society B: Biological Sciences, 292, 20242787.
Mallet, J. (2008). Hybridization, ecological races, and the nature of species: empirical evidence for the ease of speciation. Philosophical Transactions of the Royal Society B: Biological Sciences, 363, pp.2971–2986.
Additional Reading (Optional)
Stankowski, S. and Ravinet, M. (2021). Defining the speciation continuum. Evolution, 75(6), pp.1256–1273.
Lowry, D.B. (2012). Ecotypes and the controversy over stages in the formation of new species. Biological Journal of the Linnean Society, 106(2), pp.241–257.
Lecture 07: Population Structure, Gene Flow, Clines
Lecture Slides: Evolution in space and time
Readings
Barton, N.H. and Hewitt, G.M. (1989). Adaptation, speciation and hybrid zones. Nature, 341, pp.497–503.
Lecture 08: Studying Species: "Reproductive Isolation"
Lecture Slides: Studying Species: Reproductive isolation
Lecture 09: Discussion: Population Structure of Species and Reproductive Isolation
Required Readings
Barton, N.H. and Hewitt, G.M. (1989) Adaptation, speciation and hybrid zones. Nature, 341, pp. 497–503.
Coyne, J.A. and Orr, H.A. (2004) Speciation. Chapter 2: Studying Speciation, pp. 55–82. Sunderland, MA: Sinauer Associates.
Optional Readings
Ramsey, J., Bradshaw, H.D. and Schemske, D.W. (2003) Components of reproductive isolation between the monkeyflowers Mimulus lewisii and M. cardinalis (Phrymaceae). Evolution, 57, pp. 1520–1534.
Sobel, J.M. and Chen, G.F. (2014) Unification of methods for estimating the strength of reproductive isolation. Evolution, 68, pp. 1511–1522.
Westram, A.M., Stankowski, S., Surendranadh, P. and Barton, N. (2022) What is reproductive isolation? Journal of Evolutionary Biology, 35, pp. 1143–1164.
Mallet, J. and Mullen, S.P. (2022) Reproductive isolation is a heuristic, not a measure: a commentary on Westram et al., 2022. Journal of Evolutionary Biology, 35, pp. 1175–1182.
Lecture 10: Hybrid Sterility and Inviability: Postzygotic Isolation
Lecture Slides: Hybrid sterility and hybrid inviability: "postzygotic isolation"
Lecture 11: Discussion – MCZ Bird Museum Visit
Required Reading
Reifová, R., Ament‑Velásquez, S.L., Bourgeois, Y., Coughlan, J., Kulmuni, J., Lipinska, A.P., Okude, G., Stevison, L., Yoshida, K. & Kitano, J. (2023). Mechanisms of intrinsic postzygotic isolation: from traditional genic and chromosomal views to genomic and epigenetic perspectives. Cold Spring Harbor Perspectives in Biology, 15(10), a041607.
Optional Reading
Orr, H.A. (2005). The genetic basis of reproductive isolation: insights from Drosophila. Proceedings of the National Academy of Sciences USA, 102(Suppl 1), 6522–6526.
Lecture 12: Guest Lecture – Kerry L. Shaw (Cornell): Mate Choice, Sexual Selection and Speciation
Lecture 13: "Reinforcement" via Assortative Mating
Lecture 14: Discussion: Sexual Selection, Mate Choice, and "Pre-zygotic isolation"
Required Reading
Shaw, K.L., Cooney, C.R., Mendelson, T.C., Ritchie, M.G., Roberts, N.S. & Yusuf, L.H. (2024). How important is sexual isolation to speciation? Cold Spring Harbor Perspectives in Biology.
Hopkins, R., Guerrero, R.F., Rausher, M.D. & Kirkpatrick, M. (2014). Strong Reinforcing Selection in a Texas Wildflower Current Biology, 24, 1995–1999.
Lecture 15: Allopatry, Sympatry, and Parapatry in Speciation
Lecture Slides: Allopatry, Parapatry, and Sympatry in Speciation
Lecture 16: Sympatric Speciation
Lecture Slides: Sympatric Speciation
Lecture 17: Discussion: Geography of Speciation
Required Readings
Price, T. (2008). Speciation in Birds. Chapter 2. Greenwood Village, Colorado: Roberts & Co.
Bolnick, D.I. & Fitzpatrick, B.M. (2007). Sympatric Speciation: Models and Empirical Evidence. Annual Review of Ecology, Evolution, and Systematics, 38, pp.459–487.
Lecture 18: Selection vs. Drift in Speciation; Founder Events
Lecture Slides: Selection vs. Drift in Speciation
Lecture 19: Hybridization and Introgression Among Species: Why the "Tree of Life" is a Network
Lecture 20: Discussion - Selection vs. Drift in Speciation; Hybridization and Introgression
Required Readings
Coyne, J.A. & Orr, H.A. (2004). Speciation by Drift. In: Speciation, Chapter 11, pp. 387–396. Sunderland, MA: Sinauer Associates.
Grant, P.R. & Grant, B.R. (1992). Hybridization of Bird Species. Science, 256, 193–197.
Optional Readings
Carson, H.L. & Templeton, A.R. (1984). Genetic Revolutions in Relation to Speciation Phenomena: The Founding of New Populations Annual Review of Ecology and Systematics, 15, 97–131.
Barton, N.H. & Charlesworth, B. (1984). Genetic Revolutions, Founder Effects, and Speciation. Annual Review of Ecology and Systematics, 15, 133–164.
Lecture 21: Mathematical Models of Speciation
Lecture Slides: Theories of Speciation
Lecture 22: Experiments on Speciation
Lecture Slides: Experiments on Speciation
Lecture 23: Paragraphs on Experiments and Theory; and DISCUSSION/FIELD TRIP: The Mammal Collection
Lecture 24: Chromosomal Evolution and Speciation
Lecture Slides: Chromosomal Evolution and Speciation
Required Reading
Lucek, K., Giménez, M.D., Joron, M., Rafajlović, M., Searle, J.B., Walden, N., Westram, A.M. & Faria, R. (2023). The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution. Cold Spring Harbor Perspectives in Biology, 15(11), a041447.
Lecture 25: Hybrid Speciation
Lecture Slides: Hybrid Speciation
Lecture 26: Discussion - Chromosomes and hybrid speciation
Required Readings
Rieseberg, L.H. (2001). Chromosomal rearrangements and speciation. Trends in Ecology & Evolution, 16(7), 351–358.
Schumer, M., Rosenthal, G.G. & Andolfatto, P. (2014). How common is homoploid hybrid speciation? Evolution, 68(6), 1553–1560.
OPTIONAL - for reference:
The "party line" on the shifting balance since 1997 is that drift is almost never involved in adaptive evolution and speciation, and this now seems to be the general belief. This was largely laid down by: Coyne, J.A., Barton, N.H., & Turelli, M. 1997. Perspective: a critique of Sewall Wright's shifting balance theory of evolution. Evolution 51: 643-671.
But see these papers arguing "don't throw the baby out with the bathwater"!:
Whitlock, M.C., & Phillips, P.C. 2000. The exquisite corpse: a shifting view of the shifting balance. Trends in Ecology & Evolution 15:347-348.
Lenormand, T., Roze, D., & Rousset, F. 2009. Stochasticity in evolution. Trends in Ecology and Evolution 24:157-165.
Mallet, J. 2010. Shift happens! Evolution of diversity in warning colour and mimicry. Ecological Entomology 35:90-104.
Also, hybrid speciation, a general review:
Abbott, R.J., & Rieseberg, L.H. 2021. Hybrid speciation, Pages 1-8 Encyclopaedia of Life Sciences: Evolution and Diversity of LIfe. 2: 1-12. Chichester, John Wiley & Sons Ltd.
Lecture 27: Ecological Speciation and Adaptive Radiation
Lecture Slides: Adaptive Radiation & Ecological Speciation
Lecture 28: Guest Lecture – Valeria Schmidt (TF): Speciation in Phlox
Lecture 29: Discussion: Adaptive Radiation in Animals and Plants
Required Readings
Losos, J.B., Jackman, T.R., Larson, A., de Queiroz, K. & Rodríguez‑Schettino, L. (1998). Contingency and Determinism in Replicated Adaptive Radiations of Island Lizards. Science, 279(5359), 2115–2118.
Cutter, A.D. (2019). Reproductive transitions in plants and animals: selfing syndrome, sexual selection and speciation. New Phytologist, 224(3), 1080–1094.
Lecture 30: Phylogeny, its Estimation, Tree Thinking, and the Coalescent
Lecture Slides: Phylogenetic trees Methods and interpretation
Lecture 31: Guest Lecture – Mallet: Speciation in Heliconius Butterflies
Rosser, N., Seixas, F., Queste, L.M., Cama, B., Mori‑Pezo, R., Kryvokhyzha, D., Nelson, M., Waite‑Hudson, R., Goringe, M., Costa, M., Elias, M., Mendes Eleres de Figueiredo, C., Freitas, A.V.L., Joron, M., Kozak, K., Lamas, G., Martins, A.R.P., McMillan, W.O., Ready, J., … Dasmahapatra, K.K. (2024). Hybrid speciation driven by multilocus introgression of ecological traits. Nature 628, 811–817.
Lecture 32: Discussion – MCZ Insect Collections Visit
Lecture 33: Macroevolution? Punctuated Equilibrium? Species Selection
Lecture 34: The Evolution of Us: Speciation of Hominins
Lecture Slides: The Evolution of Us: Modern Evolution and Speciation
Lecture 35: Final Discussion
Harris, D.N., Platt, A., Hansen, M.E.B., Fan, S., McQuillan, M.A., Nyambo, T., Mpoloka, S.W., Mokone, G.G., Belay, G., Fokunang, C., Njamnshi, A.K. & Tishkoff, S.A. (2023). Diverse African genomes reveal selection on ancient modern human introgressions in Neanderthals. Current Biology, 33(22), pp. 4905–4916.e5.
Recommended Textbooks and Readings
(Available on reserve at the Mayr Library – as of January 22, 2025)
General Books on Evolution
Futuyma, D. J., & Kirkpatrick, M. (2024). Evolution (5th ed.). Sinauer Associates.
Emlen, D. J., & Zimmer, C. (2019). Evolution: Making sense of life (3rd ed.). Macmillan.
Bergstrom, C. T., & Dugatkin, L. A. (2023). Evolution (3rd ed.). W. W. Norton & Company.
Books on Speciation
Mayr, E. (1970). Populations, species, and evolution. Harvard University Press.
Howard, D. J., & Berlocher, S. H. (Eds.). (1998). Endless forms: Species and speciation. Oxford University Press.
Schluter, D. (2000). The ecology of adaptive radiation. Oxford University Press.
Nosil, P. (2012). Ecological speciation. Oxford University Press.
Barraclough, T. G. (2019). The evolutionary biology of species. Oxford University Press.
Peichel, C. L., Bolnick, D. I., Brännström, Å., Dieckmann, U., & Safran, R. J. (Eds.). (2024). Speciation. Cold Spring Harbor Perspectives in Biology. (Available online as individual articles; full volume on order.)