Dates: September 2012 – February 2015
Project Title: Incorporating Hidden Markov models into ancestral state reconstruction methods
Jeremy Beaulieu (Ph.D. Ecology and Evolutionary Biology, Yale Univ., 2012) worked on extending and implementing new methods for identifying different rates of evolution in a binary character along different branches of a phylogeny. Biologists now have the capability of building large phylogenetic trees consisting of tens of thousands species, from which important comparative questions can be addressed. However, to the extent that biologists have applied large trees to comparative data, it is becoming clear that current methods make unrealistic assumptions about how character data are modeled. From a botanical standpoint, Dr. Beaulieu is interested combining biogeographic history with morphological character information to better understand patterns of lineage diversification and its consequences on the distribution of biodiversity. As part of his post-doctoral project, Dr. Beaulieu published a paper in Systematic Biology that illustrated a "Hidden Markov model" (HMM) allowing for the exploration of the evolution of growth form in the Campanulidae, an angiosperm clade, including the familiar composites (sunflowers and relatives), umbels (carrots and relatives), and Dipsacales (honeysuckles and relatives). Results from the Hidden Markov model indicated that branch-specific rates in the evolution of growth habit are a major feature of growth form evolution in campanulids. Dr. Beaulieu has made this method available by releasing an R package called corHMM. The publication led to an invitation to contribute a chapter in a forthcoming book on comparative methods.
Upon completion of his NIMBioS postdoctoral fellowship, Dr. Beaulieu began a postdoctoral fellowship with Drs. Brian O'Meara and Michael Gilchrist, where he is exploring the behavior of a new model for phylogenetic inference. The model applies more realistic processes in molecular evolution, particularly selection and drift. The goal is to use the new model to answer a long-standing phylogenetic question in plant evolution, particularly the role population size plays in the rates of molecular evolution between differing life history strategies.
LiveScience Profile Q&A with Dr. Beaulieu: Evolutionary patterns show biodiversity on earth
New models in the tree of life
Feature Story: Study offers clues to how plants evolved to cope with cold
Publications while at NIMBioS
Beaulieu JM and O'Meara BC. Extinction can be estimated from moderately-sized phylogenies. Evolution (In press).
Beaulieu JM, O'Meara BC. 2016. Detecting hidden diversification shifts in models of trait-dependent speciation and extinction. Systematic Biology, 65(4): 583-601. [Online]
Beaulieu JM, O'Meara BC, Crane P, Donoghue MJ. 2015. Heterogeneous Rates of Molecular Evolution and Diversification Could Explain the Triassic Age Estimate for Angiosperms. Systematic Biology, 64(5): 869-878 [a href="http://sysbio.oxfordjournals.org/content/early/2015/05/04/sysbio.syv027.short" target="_blank">Online]
Dornburg A, Moore J, Beaulieu JM, Eytan RI, Near TJ. 2015. The impact of shifts in marine biodiversity hotspots on patterns of range evolution: Evidence from the Holocentridae (squirrelfishes and soldierfishes). Evolution, 69(1): 146-161. [Online]
Cornwell et al. 2014. Functional distinctiveness of major plant lineages. Journal of Ecology, 102(2): 345-356. [Online]
Leslie AB, Beaulieu JM, Crane PR, Donoghue MJ. 2014. Cone size is related to branching architecture in conifers. New Phytologist, 203(4): 1119-1127. [Online]
Beaulieu JM and O'Meara BC. 2014. Hidden Markov models for studying the evolution of binary morphological character. In Modern Phylogenetic Comparative Methods and their Application in Evolutionary Biology – Concepts and Practice edited by L. Z. Garamszegi. [Online]
O'Meara BC and Beaulieu JM. 2014. Modeling stabilising selection: the attraction of Ornstein-Uhlenbeck models. In Modern Phylogenetic Comparative Methods and their Application in Evolutionary Biology – Concepts and Practice edited by L. Z. Garamszegi. [Online]
Zanne AE, Tank DC, Cornwell WK, Eastman JM, Smith SA, FitzJohn RG, McGlinn DJ, O'Meara BC, Moles AT, Reich PB, Royer DL, Soltis DE, Stevens PF, Westoby M, Wright IJ, Aarssen L, Bertin RI, Calaminus A, Govaerts R, Hemmings F, Leishman MR, Oleksyn J,Soltis PS, Swenson NG, Warman L, Beaulieu JM. 2014. Three keys to the radiation of angiosperms into freezing environments. Nature (published online 22 December 2013). [Online]
Beaulieu JM, O'Meara BC, Donoghue MJ. 2013. Identifying hidden rate changes in the evolution of a binary morphological character: The evolution of plant habit in campanulid angiosperms. Systems Biology, 62(5): 725-737. [Online]
Beaulieu JM, Tank DC, Donoghue MJ. 2013. A Southern Hemisphere origin for campanulid angiosperms, with traces of the break-up of Gondwana. BMC Evolutionary Biology, 13: 80. [Online]
Bossu CM, Beaulieu JM, Ceas PA, Near TJ. 2013. Explicit tests of palaeodrainage connections of southeastern North America and the historical biogeography of Orangethroat Darters (Percidae: Etheostoma: Ceasia). Molecular Ecology, 22(21): 5397-5417. [Online]
Lapiedra O, Sol D, Carranza S, Beaulieu JM. 2013. Behavioural changes and the adaptive diversification of pigeons and doves. Proceedings of the Royal Society B, 280(1755): 20122893. [Online].
Leslie AB, Beaulieu JM, Crane PR, Donoghue MJ. 2013. Explaining the distribution of breeding and dispersal syndromes in conifers. Proceedings of the Royal Society B: Biological Sciences, 280(1770): 20131812. [Online]
Beaulieu JM, Jhwueng DC, Boettiger C, O'Meara BC. 2012. Modeling stabilizing selection: Expanding the Ornstein-Uhlenbeck model of adaptive evolution. Evolution, 66(8): 2369-2383. [Online].
Presentations while at NIMBioS
Beaulieu J. July 2014. Exploring heterogeneity in binary character evolution. Botany 2014, Boise, ID
Beaulieu J. June 2014. Estimating how contemporary taxa will evolve in the future, to understand how island communities were assembled in the past. Evolution, Raleigh, NC
Beaulieu J. October 2013. Exploring the evolution of a very old and widespread angiosperm clade. 60th Systematics Symposium, St. Louis, MO
Beaulieu J. June 2013. Identifying hidden rate changes in the evolution of a binary morphological characte.r. Evolution, Snowbird, UT
Software/Data while at NIMBioS
Tank DC, Eastman JM, Beaulieu JM, Cornwell WK, Stevens PF, Zanne AE. 2013. Taxonomic lookup table containing clade-level mappings for 15.363 genera of Spermatophyta. Data from: Three keys to the radiation of angiosperms into freezing environments. Nature. Dryad Digital. [Online]
Tank DC, Eastman JM, Beaulieu JM, Smith SA. 2013. Phylogenetic resources. Data from: Three keys to the radiation of angiosperms into freezing environments. Nature. Dryad Digital. [Online]
Education, Outreach and Training
Data and Software while at NIMBioS
Zanne AE, Tank DC, Cornwell WK, Eastman JM, Smith SA, FitzJohn RG, McGlinn DJ, O'Meara BC, Moles AT, Reich PB, Royer DL, Soltis DE, Stevens PF, Westoby M, Wright IJ, Aarssen L, Bertin RI, Calaminus A, Govaerts R, Hemmings F, Leishman MR, Oleksyn J, Soltis PS, Swenson NG, Warman L, Beaulieu JM. 22 December 2013. Tree, data, and source code: Three keys to the radiation of angiosperms into freezing environments. [Online download] and [Interactive tree]
Plant evolution study shows how some plants prevent freezing. Guardian Express.
Largest evolutionary tree of flowering plants mapped. Business Standard.
These three coping mechanisms help deal with cold weather. International Science Times.
Study finds how flowering plants cope with the cold. Nature World News.