Independent Study: Geography of Speciation — Fall 2017

This is an independent reading course that I have designed for Kevin Hawkins and Jessica McLaughlin, two PhD student in my lab. It is tailored to give them an historical, broad, and also deep perspective on the current state of thinking about the geography of speciation, especially as it relates to birds (since Kevin and Jessica’s dissertations focus on speciation in a New World birds). While many of these readings would be considered canonical, they also represent papers/systems (e.g. Heliconius) that have influenced my thinking about speciation. Many obvious papers were excluded because of Jessica and Kevin’s existing familiarity with the topic.

For the independent study, I will be meeting with the students once a week for 60 minutes. During that meeting we will discuss the three papers. 24 hours before our meeting, the students will provide me:

  • A printed copy of each paper that shows highlighting and annotations.
  • A summary of the paper. In the style of Jonathan Tonkin
  • A list of three key points of observations. Written in sentence style. Two to four sentences per observation.

Jessica, Kevin and I will meet once a week, for 11 weeks. Time and day of the week to be determined.

Week 1: The Canonical View of the Geography of Speciation

  1. Coyne and Orr, Chapters 1 & 2
  2. Coyne and Orr, Chapters 3 & 4

Week 2: Alternatives to Allopatric Speciation

  1. Endler, J.A., 1982. Problems in distinguishing historical from ecological factors in biogeography. American Zoologist, 22(2), pp.441-452.
  2. Patton, J.L. and Smith, M.F., 1992. MtDNA phylogeny of Andean mice: a test of diversification across ecological gradients. Evolution, pp.174-183.
  3. Jiggins, C.D. and Mallet, J., 2000. Bimodal hybrid zones and speciation. Trends in Ecology & Evolution, 15(6), pp.250-255.
  4. Smith, T.B., Wayne, R.K., Girman, D.J. and Bruford, M.W., 1997. A role for ecotones in generating rainforest biodiversity. Science, 276(5320), pp.1855-1857.

Week 3: Phylogenetics and Speciation

  1. Avise, J.C., Arnold, J., Ball, R.M., Bermingham, E., Lamb, T., Neigel, J.E., Reeb, C.A. and Saunders, N.C., 1987. Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annual review of ecology and systematics, 18(1), pp.489-522.
  2. Losos, J.B. and Glor, R.E., 2003. Phylogenetic comparative methods and the geography of speciation. Trends in Ecology & Evolution, 18(5), pp.220-227.
  3. Edwards, S.V., Kingan, S.B., Calkins, J.D., Balakrishnan, C.N., Jennings, W.B., Swanson, W.J. and Sorenson, M.D., 2005. Speciation in birds: genes, geography, and sexual selection. Proceedings of the National Academy of Sciences, 102(suppl 1), pp.6550-6557.
  4. Fitzpatrick, B.M. and Turelli, M., 2006. The geography of mammalian speciation: mixed signals from phylogenies and range maps. Evolution, 60(3), pp.601-615.
  5. Elias, M., Joron, M., Willmott, K., Silva‐Brandao, K.L., Kaiser, V., Arias, C.F., Piñerez, L.G., Uribe, S., Brower, A.V.Z., Freitas, A.V.L. and Jiggins, C.D., 2009. Out of the Andes: patterns of diversification in clearwing butterflies. Molecular Ecology, 18(8), pp.1716-1729.

Week 4: The Importance of the Pleistocene for Speciation in North American Birds

  1. Klicka, J. and Zink, R.M., 1997. The importance of recent ice ages in speciation: a failed paradigm. Science, 277(5332), pp.1666-1669.
  2. Avise, J.C. and Walker, D.E., 1998. Pleistocene phylogeographic effects on avian populations and the speciation process. Proceedings of the Royal Society of London B: Biological Sciences, 265(1395), pp.457-463.
  3. Klicka, J. and Zink, R.M., 1999. Pleistocene effects on North American songbird evolution. Proceedings of the Royal Society of London B: Biological Sciences, 266(1420), pp.695-700.
  4. Hewitt, G., 2000. The genetic legacy of the Quaternary ice ages. Nature, 405(6789), pp.907-913.
  5. Good, J.M., Hird, S., Reid, N., Demboski, J.R., Steppan, S.J., MARTIN‐NIMS, T.R. and Sullivan, J., 2008. Ancient hybridization and mitochondrial capture between two species of chipmunks. Molecular Ecology, 17(5), pp.1313-1327. Not avian, but important for Jessica and Kevin’s work

Week 5: Contemporary studies of North American Avian Speciation

  1. Milá, B., McCormack, J.E., Castañeda, G., Wayne, R.K. and Smith, T.B., 2007. Recent postglacial range expansion drives the rapid diversification of a songbird lineage in the genus Junco. Proceedings of the Royal Society of London B: Biological Sciences, 274(1626), pp.2653-2660.
  2. Klicka, J., Spellman, G.M., Winker, K., Chua, V. and Smith, B.T., 2011. A phylogeographic and population genetic analysis of a widespread, sedentary North American bird: The Hairy Woodpecker (Picoides villosus). The Auk, 128(2), pp.346-362.
  3. Toews, D.P., Taylor, S.A., Vallender, R., Brelsford, A., Butcher, B.G., Messer, P.W. and Lovette, I.J., 2016. Plumage genes and little else distinguish the genomes of hybridizing warblers. Current Biology, 26(17), pp.2313-2318.
  4. Bay, R.A. and Ruegg, K., 2017, March. Genomic islands of divergence or opportunities for introgression?. In Proc. R. Soc. B (Vol. 284, No. 1850, p. 20162414). The Royal Society.
  5. Good, J.M., Vanderpool, D., Keeble, S. and Bi, K., 2015. Negligible nuclear introgression despite complete mitochondrial capture between two species of chipmunks. Evolution, 69(8), pp.1961-1972. Follow up to Good et al. 2008.

Week 6: Phenotypic vs. Genetic Differentiation in Neotropical Birds

  1. Bates, J.M., Hackett, S.J. and Goerck, J.M., 1999. High levels of mitochondrial DNA differentiation in two lineages of antbirds (Drymophila and Hypocnemis). The Auk, pp.1093-1106.
  2. Aleixo, A., 2004. Historical diversification of a terra-firme forest bird superspecies: a phylogeographic perspective on the role of different hypotheses of Amazonian diversification. Evolution, 58(6), pp.1303-1317.
  3. Weir, J.T., Faccio, M.S., Pulido‐Santacruz, P., Barrera‐Guzmán, A.O. and Aleixo, A., 2015. Hybridization in headwater regions, and the role of rivers as drivers of speciation in Amazonian birds. Evolution, 69(7), pp.1823-1834.
  4. Winger, B.M. and Bates, J.M., 2015. The tempo of trait divergence in geographic isolation: avian speciation across the Marañon Valley of Peru. Evolution, 69(3), pp.772-787.

Week 7: Hybridization in North American Birds

  1. Harrison, R.G., Rand, D.M. and Wheeler, W.C., 1987. Mitochondrial DNA variation in field crickets across a narrow hybrid zone. Molecular Biology and Evolution, 4(2), p.144.
  2. Mallet, J., 2005. Hybridization as an invasion of the genome. Trends in ecology & evolution, 20(5), pp.229-237.
  3. Carling, M.D. and Brumfield, R.T., 2008. Haldane’s rule in an avian system: using cline theory and divergence population genetics to test for differential introgression of mitochondrial, autosomal, and sex‐linked loci across the Passerina bunting hybrid zone. Evolution, 62(10), pp.2600-2615.
  4. Seneviratne, S.S., Davidson, P., Martin, K. and Irwin, D.E., 2016. Low levels of hybridization across two contact zones among three species of woodpeckers (Sphyrapicus sapsuckers). Journal of Avian Biology, 47(6), pp.887-898
  5. van Els, P., Spellman, G.M., Smith, B.T. and Klicka, J., 2014. Extensive gene flow characterizes the phylogeography of a North American migrant bird: Black-headed Grosbeak (Pheucticus melanocephalus). Molecular phylogenetics and evolution, 78, pp.148-159.

Week 8: Heliconius as a model for studying the geography of speciation, part 1

  1. Jiggins, C.D., McMillan, W.O., Neukirchen, W. and Mallet, J., 1996. What can hybrid zones tell us about speciation? The case of Heliconius erato and H. himera (Lepidoptera: Nymphalidae). Biological Journal of the Linnean Society, 59(3), pp.221-242.
  2. Jiggins, C.D., Naisbit, R.E., Coe, R.L. and Mallet, J., 2001. Reproductive isolation caused by colour pattern mimicry. Nature, 411(6835), pp.302-305.
  3. Naisbit, R.E., Jiggins, C.D., Linares, M., Salazar, C. and Mallet, J., 2002. Hybrid sterility, Haldane’s rule and speciation in Heliconius cydno and H. melpomene. Genetics, 161(4), pp.1517-1526.

Week 9: Heliconius as a model for studying the geography of speciation, part 2

  1. Beltrán, M., Jiggins, C.D., Bull, V., Linares, M., Mallet, J., McMillan, W.O. and Bermingham, E., 2002. Phylogenetic discordance at the species boundary: comparative gene genealogies among rapidly radiating Heliconius butterflies. Molecular Biology and Evolution, 19(12), pp.2176-2190.
  2. Bull, V., Beltrán, M., Jiggins, C.D., McMillan, W.O., Bermingham, E. and Mallet, J., 2006. Polyphyly and gene flow between non-sibling Heliconius species. BMC biology, 4(1), p.11.
  3. Pardo-Diaz, C., Salazar, C., Baxter, S.W., Merot, C., Figueiredo-Ready, W., Joron, M., McMillan, W.O. and Jiggins, C.D., 2012. Adaptive introgression across species boundaries in Heliconius butterflies. PLoS Genet, 8(6), p.e1002752.

Week 10: Heliconius as a model for studying the geography of speciation, part 2

  1. Nadeau, N.J., Martin, S.H., Kozak, K.M., Salazar, C., Dasmahapatra, K.K., Davey, J.W., Baxter, S.W., Blaxter, M.L., Mallet, J. and Jiggins, C.D., 2013. Genome‐wide patterns of divergence and gene flow across a butterfly radiation. Molecular Ecology, 22(3), pp.814-826.
  2. Rosser, N., Kozak, K.M., Phillimore, A.B. and Mallet, J., 2015. Extensive range overlap between heliconiine sister species: evidence for sympatric speciation in butterflies?. BMC evolutionary biology, 15(1), p.125. (I especially want to see a careful review of the idea that the culture of ornithologists and lepidopterists contributes to fundamental ly-different ideas of how speciation works)
  3. Merot, C., Salazar, C., Merrill, R.M., Jiggins, C.D., & Joron, M. 2017. What shapes the continuum of reproductive isolation? Lessons from Heliconius butterflies. Proc. Roy Soc B 284:20170335.

Week 11: Contemporary views on the role of habitat variation in primary diversification

  1. Benham, P.M. and Witt, C.C., 2016. The dual role of Andean topography in primary divergence: functional and neutral variation among populations of the hummingbird, Metallura tyrianthina. BMC evolutionary biology, 16(1), p.22.
  2. Winger, B.M., 2017. Consequences of divergence and introgression for speciation in Andean cloud forest birds. Evolution.
  3. Alcaide, M., Scordato, E.S., Price, T.D. and Irwin, D.E., 2014. Genomic divergence in a ring species complex. Nature, 511(7507), pp.83-85.

Week 12: Where we are now, part 1

  1. Harrison, R.G. and Larson, E.L., 2014. Hybridization, introgression, and the nature of species boundaries. Journal of Heredity, 105(S1), pp.795-809.
  2. Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N. and Bierne, N., 2016. Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS biology, 14(12), p.e2000234.
  3. Edwards, S.V., Potter, S., Schmitt, C.J., Bragg, J.G. and Moritz, C., 2016. Reticulation, divergence, and the phylogeography–phylogenetics continuum. Proceedings of the National Academy of Sciences, 113(29), pp.8025-8032.
  4. Zamudio, K.R., Bell, R.C. and Mason, N.A., 2016. Phenotypes in phylogeography: Species’ traits, environmental variation, and vertebrate diversification. Proceedings of the National Academy of Sciences, 113(29), pp.8041-8048.

Week 13: Where we are now, part 2

  1. Guerrero, Rafael F., and Matthew W. Hahn.2017. Speciation as a sieve for ancestral polymorphism. Online Early Molecular Ecology.
  2. Smith BT, Seeholzer GF, Harvey MG, Cuervo AM, Brumfield RT. 2017. A latitudinal phylogeographic diversity gradient in birds. PLoS Biology 15(4):e2001073.
  3. Hooper, D.M., 2016. Range overlap drives chromosome inversion fixation in passerine birds. bioRxiv, p.053371.
  4. Davidson J.H. and Balakrishnan C.N., 2016. Gene regulatory evolution during speciation in a songbird. G3: Genes, Genomes, Genetics 6: 1357-1364.


Do you love Neotropical birds?
Do you love field expeditions in Latin America?
Want to do some serious genomics in one of the nation’s best university-based natural history museums?

I am recruiting 1-2 PhD students to join my lab in the Ornithology Department of the Sam Noble Museum at University of Oklahoma for the Fall 2017. Students should be willing to take a creative leadership role in the comparative genomics of secondary contact and speciation in Neotropical birds. These positions would involve considerable time in the field on expeditions in Latin America to collect birds, supported by the Sam Noble Oklahoma Museum Department of Ornithology.

The ideal student will have previous Latin American ornithological field experience, as well as the ability to understand and speak Spanish. Students from Latin America are particularly encouraged to apply. These projects will consist of developing genomic datasets from massively-parallel sequencing efforts (i.e. next gene sequencing) at the University of Oklahoma. Strong computational skills in UNIX, R and Python are a real plus. However, all potential students with strong field, lab, and museum ornithological skills are encouraged to contact me.

Students can undertake projects in two areas where we have existing datasets: either in the comparative genomics of secondary contact of lowlands birds (see Secondary Contact Project) or in the genomics of species isolation of Lampornis hummingbirds (see Lampornis Genomics Project), or the student can develop her/his own project. We have active funding for field research in Bolivia and Peru as well, so projects in this area could be developed.

Students in our lab are enrolled in either the Biology or closely allied Ecology and Evolutionary Biology PhD program, but maintain offices and a lab home in the Ornithology Department at the Sam Noble Oklahoma Museum of Natural History. The Ornithology Department consists of a fast-growing ornithological collection, state-of-the-art molecular genomics labs (capable of doing all NGS preparations including ddRAD-Seq, hybrid capture, and whole genome sequencing), multiple bioinformatics Linux workstations (as well as access to the OU Supercomputer), and an impressive ornithological research library.

OU Biology/EEB has a strong focus on “geographical ecology”, and our group participates in the Geographical Ecology working group, which is organized by Mike Kaspari (tropical community ecology), and includes the following faculty: Katie Marske (phylogeography) Katie Marshall (physiological ecology), Dan Allen (stream and riparian ecology) and Cam Siler (herpetology and systematics). Collectively, our group provides a rich environment for students to interact with these and other talented faculty and students in the Geographical Ecology working group and throughout the Biology department.

We are also allied with the Oklahoma Biological Survey, which has considerable strengths in ornithology. This includes Jeff Kelly’s lab, Eli Bridge’s group, and Jeremy Ross’s lab. Collectively, this makes OU among the best universities for ornithology in the country.

Funding for graduate students is currently available in the form of 10-month teaching assistantships with reasonable stipends, full tuition waivers and excellent health care coverage. In addition, students can expect to be funded during the summer by the OU Sutton Avian Research Scholarships, Adams Scholarships, and Curatorial Assistantships in Ornithology at the Sam Noble Museum. Our lab has existing funds for field expeditions and specimen collection, and there are several funding sources on campus and elsewhere for the development of next-generation genomic datasets. Norman is an amazing college town, and the cost of living is quite reasonable for graduate students.

Interested students should contact me (mjmiller@ou.edu) with a brief summary of your research interests and relevant experiences and attach a CV. All prospective students must also apply through the OU Biology Graduate Program by mid December. Candidates from groups underrepresented in STEM are encouraged to apply. Se habla español aqui!

05 Jun 2016

We’ve arrived in Norman! Our group is settling in to Norman, the University of Oklahoma, and the Sam Noble Oklahoma Museum of Natural History.

Over the summer, we will begin our first Great Plains collecting trip, return to Panama to export tissue duplicates back to our SNOMNH lab, and welcome Kevin and Krisangel to the group. It’s also a time for me to finish all the old manuscripts that have been lingering.