systematics, evolution, biogeography

How are species related, how have they evolved, why do they occur where they do? We study these questions mostly in plants, especially in the Hengduan Mountains of China and environs. We also tackle conceptual and methodological issues in phylogenetics and macroevolution.

Join the lab

I accept PhD students through the Committee on Evolutionary Biology at the University of Chicago, and can co-advise graduate students at the University of Illinois at Chicago. Undergraduates, postdocs, sabbatical visitors: please inquire (funding may be possible through Field Museum internships and scholarships).

People

Richard Ree

Associate Curator of Flowering Plants, Field Museum
Faculty Associate, U. Chicago Committee on Evolutionary Biology
Lecturer, U. Chicago Biological Sciences Collegiate Division

Yaowu Xing

Boyd Postdoctoral Fellow

diversification; historical biogeography; tempo and mode of assembly of the Hengduan Mountains flora

Christie Ziegler

Research assistant

Ivy development; multi-regime models of discrete character evolution

Alumni

Graduate students

Matthew Nelsen
Deren Eaton
Traci Kantarski
Jacqueline Van De Viere

Postdocs

Lyndon Coghill
Olena Peregrym
Wen-Bin Yu
Jipei Yue
Norbert Cordiero
Yingwei Wang

Interns

Megan Vats (Loyola)
Joshua Stevens-Stein (U. Chicago)
David Park (IMSA)
Jim Li (IMSA)
Brian Wray (NEIU)
Ciera Martinez (NEIU)
Diana Jolles

Publications

Yu, W-B, M-L Liu, H Wang, RR Mill, RH Ree, J-B Yang, and D-Z Li. 2015. “Towards a comprehensive phylogeny of the large temperate genus Pedicularis (Orobanchaceae), with an emphasis on species from the Himalaya-Hengduan Mountains.” BMC Plant Biology 15 (1). doi:10.1186/s12870-015-0547-9.
Hinchliff, CE, SA Smith, JF Allman, JG Burleigh, R Chaudhary, LM Coghill, KA Crandall, J Deng, BT Drew, R Gazis, K Gude, DS Hibbett, LA Katz, HD Laughinghouse, EJ McTavish, PE Midford, CL Owen, RH Ree, JA Rees, DE Soltis, T Williams, and KA Cranston. 2015. “Synthesis of phylogeny and taxonomy into a comprehensive tree of life.” Proceedings of the National Academy of Sciences 112 (41): 12764–69. doi:10.1073/pnas.1423041112.
Ree, RH, and AL Hipp. 2015. “Inferring phylogenetic history from restriction site associated DNA (RADseq).” In Next-Generation Sequencing in Plant Systematics, edited by E Hörandl and MS Appelhans. Regnum Vegetabile 158. Königstein: Koeltz Scientific Books.
Meseguer, AS, JM Lobo, RH Ree, DJ Beerling, and I Sanmartín. 2014. “Integrating fossils, phylogenies, and niche models into biogeography to reveal ancient evolutionary history: the case of Hypericum (Hypericaceae).” Systematic Biology, November, syu088. doi:10.1093/sysbio/syu088.
Winger, BM, FK Barker, and RH Ree. 2014. “Temperate origins of long-distance seasonal migration in New World songbirds.” PNAS 111 (33): 12115–20. doi:10.1073/pnas.1405000111.
Tkach, N, RH Ree, P Kuss, M Röser, and MH Hoffmann. 2014. “High mountain origin, phylogenetics, evolution, and niche conservatism of Arctic lineages in the hemiparasitic genus Pedicularis (Orobanchaceae).” Molecular Phylogenetics and Evolution 76 (July): 75–92. doi:10.1016/j.ympev.2014.03.004.
Elkington, BG, K Sydara, A Newsome, CH Hwang, DC Lankin, C Simmler, JG Napolitano, RH Ree, JG Graham, C Gyllenhaal, S Bouamanivong, O Souliya, GF Pauli, SG Franzblau, and DD Soejarto. 2014. “New Finding of an Anti-TB Compound in the Genus Marsypopetalum (Annonaceae) from a Traditional Herbal Remedy of Laos.” Journal of Ethnopharmacology 151 (2): 903–11. doi:10.1016/j.jep.2013.11.057.
Ree, RH. 2014. “Using phylogenies to study phenotypic evolution: comparative methods and tests of adaptation.” In The Princeton Guide to Evolution, edited by JB Losos. Princeton; Oxford: Princeton University Press.
Wen, J, RH Ree, SM Ickert-Bond, Z Nie, and V Funk. 2013. “Biogeography: Where do we go from here?” Taxon 62 (5): 912–27. doi:10.12705/625.15.
Eaton, DAR, and RH Ree. 2013. “Inferring Phylogeny and Introgression Using RADseq Data: An Example from Flowering Plants (Pedicularis: Orobanchaceae).” Systematic Biology 62 (5): 689–706. doi:10.1093/sysbio/syt032.
Beaulieu, JM, RH Ree, J Cavender-Bares, GD Weiblen, and MJ Donoghue. 2012. “Synthesizing Phylogenetic Knowledge for Ecological Research.” Ecology 93 (8s): S4–13. doi:10.1890/11-0638.1.
Eaton, DAR, CB Fenster, J Hereford, S-Q Huang, and RH Ree. 2012. “Floral Diversity and Community Structure in Pedicularis (Orobanchaceae).” Ecology 93 (8s): S182–94. doi:10.1890/11-0501.1.
Webb, CO, and RH Ree. 2012. “Historical biogeography inference in Malesia.” In Biotic Evolution and Environmental Change in Southeast Asia, edited by DJ Gower. The Systematics Association Special Volume Series, v. 82. Cambridge: The Systematics Association: Cambridge University Press.
Yu, W-B, P-H Huang, RH Ree, M-L Liu, D-Z Li, and H Wang. 2011. “DNA barcoding of Pedicularis L. (Orobanchaceae): evaluating four universal barcode loci in a large and hemiparasitic genus.” Journal of Systematics and Evolution 49 (September): 425–37. doi:10.1111/j.1759-6831.2011.00154.x.
Goldberg, EE, LT Lancaster, and RH Ree. 2011. “Phylogenetic inference of reciprocal effects between geographic range evolution and diversification.” Systematic Biology 60 (4): 451–65. doi:10.1093/sysbio/syr046.
Vila, R, CD Bell, R Macniven, B Goldman-Huertas, RH Ree, CR Marshall, Z Bálint, K Johnson, D Benyamini, and NE Pierce. 2011. “Phylogeny and palaeoecology of Polyommatus Blue butterflies show Beringia was a climate-regulated gateway to the New World.” Proceedings of the Royal Society B: Biological Sciences 278: 2737–44. doi:10.1098/rspb.2010.2213.
Branco, S, and RH Ree. 2010. “Serpentine soils do not limit mycorrhizal fungal diversity.” PLoS ONE 5 (7): e11757. doi:10.1371/journal.pone.0011757.
Eckert, CG, S Kalisz, MA Geber, R Sargent, E Elle, P-O Cheptou, C Goodwillie, MO Johnston, JK Kelly, DA Moeller, E Porcher, RH Ree, M Vallejo-Marín, and AA Winn. 2010. “Plant mating systems in a changing world.” Trends in Ecology & Evolution 25 (1): 35–43. doi:10.1016/j.tree.2009.06.013.
Goodwillie, C, RD Sargent, CG Eckert, E Elle, MA Geber, MO Johnston, S Kalisz, DA Moeller, RH Ree, M Vallejo-Marin, and AA Winn. 2010. “Correlated evolution of mating system and floral display traits in flowering plants and its implications for the distribution of mating system variation.” New Phytologist 185 (1): 311–21. doi:10.1111/j.1469-8137.2009.03043.x.
Salvo, G, SYW Ho, G Rosenbaum, RH Ree, and E Conti. 2010. “Tracing the temporal and spatial origins of island endemics in the Mediterranean region: a case study from the citrus family (Ruta L., Rutaceae).” Systematic Biology 59 (6): 705–22. doi:10.1093/sysbio/syq046.
Xie, L, WL Wagner, RH Ree, PE Berry, and J Wen. 2009. “Molecular phylogeny, divergence time estimates, and historical biogeography of Circaea (Onagraceae) in the Northern Hemisphere.” Molecular Phylogenetics and Evolution 53 (3): 995–1009. doi:10.1016/j.ympev.2009.09.009.
Zhang, D-C, DE Boufford, RH Ree, and H Sun. 2009. “The 29°N latitudinal line: an important division in the Hengduan Mountains, a biodiversity hotspot in southwest China.” Nordic Journal of Botany 27 (5): 405–12. doi:10.1111/j.1756-1051.2008.00235.x.
Santos, JC, LA Coloma, K Summers, JP Caldwell, RH Ree, and DC Cannatella. 2009. “Amazonian amphibian diversity is primarily derived from late Miocene Andean lineages.” PLoS Biology 7 (3): e56 EP – . doi:10.1371/journal.pbio.1000056.
Ree, RH, and I Sanmartín. 2009. “Prospects and challenges for parametric models in historical biogeographical inference.” Journal of Biogeography 36 (7): 1211–20. doi:10.1111/j.1365-2699.2008.02068.x.
Yue, J-P, H Sun, DA Baum, J-H Li, IA Al-Shebaz, and RH Ree. 2009. “Molecular phylogeny of Solms-Laubachia (Brassicaceae) S.l., based on multiple nuclear and plastid DNA sequences, and its biogeographic implications.” Journal of Systematics and Evolution 47 (5): 402–15.
Clark, JR, RH Ree, ME Alfaro, MG King, WL Wagner, and EH Roalson. 2008. “A comparative study in ancestral range reconstruction methods: retracing the uncertain histories of insular lineages.” Systematic Biology 57 (5): 693–707. doi:10.1080/10635150802426473.
Ree, R, and S Smith. 2008. “Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis.” Systematic Biology 57 (1): 4–14.
Yue, J, K Feldheim, H Sun, and RH Ree. 2008. “Ten microsatellite loci from Solms-laubachia eurycarpa (Brassicaceae).” Molecular Ecology Resources 8 (5): 1023–25. doi:10.1111/j.1755-0998.2008.02141.x.
Sargent, RD, C Goodwillie, S Kalisz, and RH Ree. 2007. “Phylogenetic evidence for a flower size and number trade-Off.” American Journal of Botany 94 (12): 2059–62. doi:10.3732/ajb.94.12.2059.
Fine, PVA, and RH Ree. 2006. “Evidence for a time-integrated species-area effect on the latitudinal gradient in tree diversity.” The American Naturalist 168 (6): 796–804. doi:10.1086/508635.
Ree, RH, BR Moore, CO Webb, and MJ Donoghue. 2005. “A likelihood framework for inferring the evolution of geographic range on phylogenetic trees.” Evolution 59 (11): 2299–2311.
Ree, RH. 2005. “Detecting the historical signature of key innovations using stochastic models of character evolution and cladogenesis.” Evolution 59 (2): 257–65.
Ree, RH. 2005. “Phylogeny and the evolution of floral diversity in Pedicularis (Orobanchaceae).” International Journal of Plant Sciences 166 (4): 595–613. doi:10.1086/430191.
Ree, RH, HL Citerne, M Lavin, and QCB Cronk. 2004. “Heterogeneous selection on LEGCYC paralogs in relation to flower morphology and the phylogeny of Lupinus (Leguminosae).” Molecular Biology and Evolution 21 (2): 321–31. doi:10.1093/molbev/msh022.
Sanderson, MJ, AC Driskell, RH Ree, O Eulenstein, and S Langley. 2003. “Obtaining maximal concatenated phylogenetic data sets from large sequence databases.” Molecular Biology and Evolution 20 (7): 1036–42. doi:10.1093/molbev/msg115.
Donoghue, MJ, and RH Ree. 2000. “Homoplasy and developmental constraint: a model and an example from Plants.” American Zoologist 40 (5): 759–69.
Ree, RH, and MJ Donoghue. 1999. “Inferring rates of change in flower symmetry in asterid angiosperms.” Systematic Biology 48 (3): 633. doi:10.1080/106351599260201.
Ree, RH, and MJ Donoghue. 1998. “Step matrices and the interpretation of homoplasy.” Systematic Biology 47 (4): 582–88. doi:10.1080/106351598260590.
Donoghue, MJ, RH Ree, and DA Baum. 1998. “Phylogeny and the evolution of flower symmetry in the Asteridae.” Trends in Plant Science 3 (8): 311–17. doi:10.1016/S1360-1385(98)01278-3.
Ree, RH. 1997. “Pollen flow, fecundity, and the adaptive significance of heterostyly in Palicourea padifolia (Rubiaceae).” Biotropica 29 (3): 298–308.

CODE/DATA

LAGRANGE: likelihood analysis of geographic range evolution

For reconstructing dispersal dynamics and ancestral range-inheritance scenarios on phylogenies. Implements the DEC model—see Ree and Smith (2008).

A web-based analysis configurator is available for the original Python code. Stephen Smith wrote a separate standalone C++ version, which is much faster; I've written a Cython wrapper for it, exposing its internals to Python. Someday I hope to marry the web configurator with the Cython code.

Biodiversity of the Hengduan Mountains

A specimen database of plants and fungi from the mountains of south-central China, in long-term collaboration with David Boufford at the Harvard University Herbaria. Contains many photos of specimens and localities in the field.

IVY: interactive visual phylogenetics

A Python library for manipulating phylogenetic trees and data, with a somewhat unique focus on visualizations that are interactive simultaneously using a GUI (Matplotlib) and command line (IPython).

Developed primarily for internal use in the lab (until I find the time to write proper documentation and tutorials; Christie has been helping with this). Meanwhile see the source code and the fledgling documentation.

BLOG

Congratulations Deren!

Mon 18 April 2016

Lab alum Deren Eaton will be joining the Ecology and Evolution faculty at Columbia University in NYC! Deren's work since leaving the lab has focused on the use of RADseq in systematics and evolutionary research, especially via development of pyRAD and related software.

Let's hope he finds time ...

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New Pelican site

Wed 09 March 2016

Old Wordpress site got hacked and redirected to a Russian porn site, and of course, I was notified of this by a prospective student. Static site generation from now on...

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