Michael J Donoghue

Yale University, New Haven, Connecticut, United States

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Publications (162)878.2 Total impact

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    ABSTRACT: Thuiller et al. analyzed the consequences of anticipated climate change on plant, bird, and mammal phylogenetic diversity (PD) across Europe. They concluded that species loss will not be clade specific across the Tree of Life, and that there will not be an overall decline in PD across the whole of Europe. We applaud their attempt to integrate phylogenetic knowledge into scenarios of future extinction but their analyses raise a series of concerns. We focus here on their analyses of plants.
    06/2014;
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    ABSTRACT: • Premise of the study: Despite recent progress, significant uncertainties remain concerning relationships among early-branching lineages within Viburnum (Adoxaceae), prohibiting a new classification and hindering studies of character evolution and the increasing use of Viburnum in addressing a wide range of ecological and evolutionary questions. We hoped to resolve these issues by sequencing whole plastid genomes for representative species and combining these with molecular data previously obtained from an expanded taxon sample.• Methods: We performed paired-end Illumina sequencing of plastid genomes of 22 Viburnum species and combined these data with a 10-gene data set to infer phylogenetic relationships for 113 species. We used the results to devise a comprehensive phylogenetic classification and to analyze the evolution of eight morphological characters that vary among early-branching lineages.• Key results: With greatly increased levels of confidence in most of the early branches, we propose a phylogenetic classification of Viburnum, providing formal phylogenetic definitions for 30 clades, including 13 with names recognized under the International Code of Nomenclature for Algae, Fungi, and Plants, eight with previously proposed informal names, and nine newly proposed names for major branches. Our parsimony reconstructions of bud structure, leaf margins, inflorescence form, ruminate endosperm, extrafloral nectaries, glandular trichomes, palisade anatomy, and pollen exine showed varying levels of homoplasy, but collectively provided morphological support for some, though not all, of the major clades.• Conclusions: Our study demonstrates the value of next-generation plastid sequencing, the ease of creating a formal phylogenetic classification, and the utility of such a system in describing patterns of character evolution.
    American Journal of Botany 06/2014; 101(6):1029-1049. · 2.59 Impact Factor
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    ABSTRACT: Biodiversity is a key to human well-being. However universally acknowledged, this reality is not appre-ciated as much as one might imagine or hope. Having achieved a high standing in the Convention on Biological Diversity (CBD) in 1992, biodiversity appears to have gradually fallen from that position in the 20 years since. This is evidenced by the fact that most discussions and actions in relation to the CBD have now shifted to sustainable development and ecosystem services (Daily 1997), instead of focusing more directly on biodiversity values themselves. One reason for this fall in status seems to be linked to issues about the actual definition of 'biodiversity', whether used in a broad sense, including the diversity of genes, species, communities and ecosystems, or more narrowly defined as the diversity of species alone. While the close link between biodiversity and 'ecosystem services' is undeniable, biodiversity itself has long recognized links to human well-being, including 'option values' (see later) that are sometimes neglected (Faith 2012). The conservation of biodiversity and all its values is fundamental to strategies aimed at achieving the long-term goal of sustainable development. The CBD definition of biodiversity captures the importance of considering variation and its values at multiple levels, including genetic and trait variation (http://www.cbd.int/convention/articles/default.shtml?a=cbd-02). A model that is explicitly evolutionary in nature provides the most coherent and powerful descriptor of biodiversity, and yet evolutionary thinking is generally neglected in most plans to manage our environment. It is critical, however, that an evolutionary perspective be incorporated into conservation planning (Hendry et al. 2010). 1. Evolution generates and maintains biodiversity and ecosystems Biodiversity is a product of evolution and, in the broadest sense, includes all biological variation on Earth, present and past. Organisms, the relationships among them, and the relationships between organisms and their abiotic environment are constantly changed by evolution. Given this, it might seem obvious that the principles of evolutionary biology should have a major role in regional planning for land or water uses as well as for managing ecosystems. Thus, an understanding of evolutionary processes necessarily comple-ments current emphasis on their ecological counterparts. It is easy to acknowledge that 'nothing in biology makes sense except in the light of evolution'. However, it is necessary to go beyond the generality of this statement and find ways to apply our understanding of evolutionary processes to the conservation and management of ecosystems (e.g. Sarkar and Margules 2002). 2. Incorporating evolution in the valuation of biodiversity for sustainable use
    Journal of Biosciences 06/2014; 39(3):1-5. · 1.76 Impact Factor
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    ABSTRACT: The relationship between branch diameter and leaf size has been widely used to understand how vegetative resources are allocated in plants. Branching architecture influences reproductive allocation as well, but fewer studies have explored this relationship at broad phylogenetic or ecological scales. In this study, we tested whether pollen-producing and seed-producing cone size scales with branch diameter in conifers, a diverse and globally distributed lineage of nonflowering seed plants. Branch diameter and cone size were analyzed using multiple regression models and evolutionary models of trait evolution for a data set of 293 extant conifer species within an explicit phylogenetic framework. Branch diameter is a strong predictor of cone size across conifer species, particularly for pollen cones and dry seed cones. However, these relationships are complex in detail because leaf morphology and seed dispersal biology influence the specific ways in which they are expressed. The ubiquity and strength of these scaling relationships across conifers suggest that reproductive and vegetative morphologies are coupled in the group, and it is therefore difficult to disentangle the evolution of cone size from the evolution of branching architecture.
    New Phytologist 05/2014; · 6.74 Impact Factor
  • Elisabeth J Forrestel, Michael J Donoghue, Melinda D Smith
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    ABSTRACT: The importance of fire in the creation and maintenance of mesic grassland communities is well recognized. Improved understanding of how grasses - the dominant clade in these important ecosystems - will respond to alterations in fire regimes is needed in the face of anthropogenically driven climate and land-use change. Here, we examined how grass communities shift in response to experimentally manipulated fire regimes at multiple levels of community diversity - taxonomic, phylogenetic and functional - in C4 -dominanted mesic savanna grassland sites with similar structure and physiognomy, yet disparate biogeographic histories. We found that the grass communities were similar in their phylogenetic response and aspects of their functional response to high fire frequency. Both sites exhibited phylogenetic clustering of highly abundant species in annually burned plots, driven by species of the Andropogoneae, and a narrow range of functional strategies associated with rapid post-fire regeneration in a high-light, nitrogen-limited environment. By examining multiple facets of diversity in a comparative context, we identified convergent phylogenetic and functional responses to altered fire regimes in two mesic savanna grasslands. Our results highlight the importance of a common filtering process associated with fire that is consistent across grasslands of disparate biogeographic histories and taxonomic representation.
    New Phytologist 05/2014; · 6.74 Impact Factor
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    ABSTRACT: Many major branches in the Tree of Life are marked by stereotyped body plans that have been maintained over long periods of time. One possible explanation for this stasis is that there are genetic or developmental constraints that restrict the origin of novel body plans. An alternative is that basic body plans are potentially quite labile, but are actively maintained by natural selection. We present evidence that the conserved floral morphology of a species-rich flowering plant clade, Malpighiaceae, has been actively maintained for tens of millions of years via stabilizing selection imposed by their specialist New World oil-bee pollinators. Nine clades that have lost their primary oil-bee pollinators show major evolutionary shifts in specific floral traits associated with oil-bee pollination, demonstrating that developmental constraint is not the primary cause of morphological stasis in Malpighiaceae. Interestingly, Malpighiaceae show a burst in species diversification coinciding with the origin of this plant-pollinator mutualism. One hypothesis to account for radiation despite morphological stasis is that although selection on pollinator efficiency explains the origin of this unique and conserved floral morphology, tight pollinator specificity subsequently permitted greatly enhanced diversification in this system.
    Proceedings of the National Academy of Sciences 04/2014; · 9.81 Impact Factor
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    D. A. Baum, M. J. Donoghue
    01/2014;
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    ABSTRACT: The leaf economics spectrum (LES) has been an organizing framework of plant functional ecology for the past decade. The LES describes a set of trade‐offs among traits related to plant carbon balance. Species with a long leaf life span (LLS) invest additional material for leaf protection and structural support and consequently tend to have a lower leaf photosynthetic rate per unit mass than species with a shorter LLS.While the LES is most apparent in comparing species with extreme differences in their traits, it has nonetheless been adopted as a general explanation of leaf trait variation at all scales and in all plants. It highlights the ‘trait‐based’ approach to plant ecology, which has generally used a small set of traits to predict whole organism and even whole ecosystem attributes. Few studies have investigated the relationships between LES traits and organismal attributes not directly related to carbon economy.We explored the LES in 32 deciduous woody species of Viburnum (Adoxaceae). We found no evidence for any mass‐based LES trade‐offs. Rather, on an area basis, photosynthetic rates were positively correlated with leaf mass per area (LMA); higher LMA was associated with greater investment in photosynthetic tissue, with most of the variation due to changes in the thickness of photosynthetic mesophyll.Species’ mean LLS varied between 19 and 26 weeks and was not correlated with other LES traits. Instead, LLS was strongly associated with the diverse set of whole‐plant branching patterns in Viburnum. In the most common growth pattern, LLS was significantly correlated with flowering time, because branches end in terminal inflorescences, and all leaves and inflorescences are pre‐formed in overwintering buds.Synthesis. Plants may recover the cost of their leaves early in the growing season, allowing LLS to vary independently of the plant carbon budget. In deciduous species, LLS may be strongly influenced by whole plant architecture, which, in Viburnum, is evolutionarily conserved. In general, positive area‐based LES trait relationships will limit the relevance of LLS to this spectrum and allow LLS to vary for reasons that are not directly related to carbon economy.
    Clinical and Experimental Allergy 01/2014; 102(2). · 5.43 Impact Factor
  • Jeremy M Beaulieu, Michael J Donoghue
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    ABSTRACT: With increases in both the size and scope of phylogenetic trees, we are afforded a renewed opportunity to address long-standing comparative questions, such as whether particular fruit characters account for much of the variation in diversity among flowering plant clades. Studies to date have reported conflicting results, largely as a consequence of taxonomic scale and a reliance on potentially conservative statistical measures. Here we examine a larger and older angiosperm clade, the Campanulidae, and infer the rates of character transitions among the major fruit types, emphasizing the evolution of the achene fruits that are most frequently observed within the group. Our analyses imply that campanulids likely originated bearing capsules, and that all subsequent fruit diversity was derived from various modifications of this dry fruit type. We also found that the preponderance of lineages bearing achenes is a consequence of not only being a fruit type that is somewhat irreversible once it evolves, but one that also seems to have a positive association with diversification rates. Although these results imply the achene fruit type is a significant correlate of diversity patterns observed across campanulids, we conclude that it remains difficult to confidently and directly view this character state as the actual cause of increased diversification rates.
    Evolution 11/2013; 67(11):3132-44. · 4.86 Impact Factor
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    ABSTRACT: People depend on benefits provided by ecological systems. Understanding how these ecosystem services - and the ecosystem properties underpinning them - respond to drivers of change is therefore an urgent priority. We address this challenge through developing a novel risk-assessment framework that integrates ecological and evolutionary perspectives on functional traits to determine species' effects on ecosystems and their tolerance of environmental changes. We define Specific Effect Function (SEF) as the per-gram or per capita capacity of a species to affect an ecosystem property, and Specific Response Function (SRF) as the ability of a species to maintain or enhance its population as the environment changes. Our risk assessment is based on the idea that the security of ecosystem services depends on how effects (SEFs) and tolerances (SRFs) of organisms - which both depend on combinations of functional traits - correlate across species and how they are arranged on the species' phylogeny. Four extreme situations are theoretically possible, from minimum concern when SEF and SRF are neither correlated nor show a phylogenetic signal, to maximum concern when they are negatively correlated (i.e., the most important species are the least tolerant) and phylogenetically patterned (lacking independent backup). We illustrate the assessment with five case studies, involving both plant and animal examples. However, the extent to which the frequency of the four plausible outcomes, or their intermediates, apply more widely in real-world ecological systems is an open question that needs empirical evidence, and suggests a research agenda at the interface of evolutionary biology and ecosystem ecology.
    Ecology and Evolution 09/2013; 3(9):2958-2975. · 1.66 Impact Factor
  • Erika J Edwards, Michael J Donoghue
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    ABSTRACT: Recent phylogenetic studies have documented high levels of conservatism in ecological traits that seem at odds with the traditional view that organisms can readily adapt to different environments. We highlight the need for a new level of rigour in interpreting such patterns from both organismal and biogeographical perspectives. A handful of closely studied systems are revealing a greater number of ecological transitions than anticipated, but these are typically phylogenetically clustered, suggesting that the relative ease or difficulty of such adaptations is strongly context-dependent. We believe that this differential evolutionary 'accessibility' to certain adaptations is pervasive across the tree of life and we illustrate this with reference to several important ecological syndromes in plants. Differential accessibility derives in large part from the attributes of the organisms themselves - certain traits may act as 'enablers' that increase the likelihood of particular innovations. So far, we have made minimal progress in identifying precursor traits that underlie the evolution of ecological syndromes, but we are hopeful that improved phylogenetic resolution will allow for a surge of new insight. However, the accessibility of particular adaptations also derives from external factors, such as the relative location and extent of certain habitats and the competitive ability of the lineages that already occupy them. Better understanding of where particular lineages have existed in the past, and of the adjacency or connectivity of different environments through time, will also be necessary to explain how both dispersal and ecological diversification have jointly contributed to the assembly of the world's ecosystems.
    Journal of Experimental Botany 08/2013; · 5.24 Impact Factor
  • Jeremy M Beaulieu, Brian C O'Meara, Michael J Donoghue
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    ABSTRACT: The growth of phylogenetic trees in scope and in size is promising from the standpoint of understanding a wide variety of evolutionary patterns and processes. With trees comprised of larger, older, and globally distributed clades, it is likely that the lability of a binary character will differ significantly among lineages, which could lead to errors in estimating transition rates and the associated inference of ancestral states. Here we develop and implement a new method for identifying different rates of evolution in a binary character along different branches of a phylogeny. We illustrate this approach by exploring the evolution of growth habit in Campanulidae, a flowering plant clade containing some 35,000 species. The distribution of woody versus herbaceous species calls into question the use of traditional models of binary character evolution. The recognition and accommodation of changes in the rate of growth form evolution in different lineages demonstrates, for the first time, a robust picture of growth form evolution across a very large, very old, and very widespread flowering plant clade.
    Systematic Biology 05/2013; · 12.17 Impact Factor
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    Jeremy M Beaulieu, David C Tank, Michael J Donoghue
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    ABSTRACT: BACKGROUND: New powerful biogeographic methods have focused attention on long-standing hypotheses regarding the influence of the break-up of Gondwana on the biogeography of Southern Hemisphere plant groups. Studies to date have often concluded that these groups are too young to have been influenced by these ancient continental movements. Here we examine a much larger and older angiosperm clade, the Campanulidae, and infer its biogeographic history by combining Bayesian divergence time information with a likelihood-based biogeographic model focused on the Gondwanan landmasses. RESULTS: Our analyses imply that campanulids likely originated in the middle Albian (~105 Ma), and that a substantial portion of the early evolutionary history of campanulids took place in the Southern Hemisphere, despite their greater species richness in the Northern Hemisphere today. We also discovered several disjunctions that show biogeographic and temporal correspondence with the break-up of Gondwana. CONCLUSIONS: While it is possible to discern traces of the break-up of Gondwana in clades that are old enough, it will generally be difficult to be confident in continental movement as the prime cause of geographic disjunctions. This follows from the need for the geographic disjunction, the inferred biogeographic scenario, and the dating of the lineage splitting events to be consistent with the causal hypothesis.
    BMC Evolutionary Biology 04/2013; 13(1):80. · 3.29 Impact Factor
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    ABSTRACT: The colors of fleshy fruits are considered to be a signal to seed-dispersing animals, but their diversity remains poorly understood. Using an avian color space to derive a sensory morphospace for fruit color, we tested four hypotheses of fruit color diversity: fruit colors occupy a limited area of the color space; they are less diverse than flower colors; fruit colors within localities are similar to each other; and fruit color diversity reflects phylogeny. The global fruit color diversity of 948 primarily bird-dispersed plant species and the color diversity of localities were compared with null models of random, unconstrained evolution of fruit color. Fruit color diversity was further compared with the diversity of 1300 flower colors. Tests of phylogenetic effects on fruit color were used to assess the degree of correspondence with phylogeny. Global and local fruit color diversity was limited compared with null models and fruits have achieved only half the color diversity of flowers. Interestingly, we found little indication of phylogenetic conservatism. Constraints resulting from the chemical properties of pigments probably limit global fruit and flower color diversity. Different types of selection on fruits and flowers may further explain the smaller color diversity of fruits.
    New Phytologist 02/2013; · 6.74 Impact Factor
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    ABSTRACT: Premise of research. Leaf mesophyll is often differentiated into a palisade layer with tightly packed, elongated cells (I-cells) and a spongy layer with loosely packed, complex shaped cells. An alternative palisade type, composed of branched H-cells, has evolved in a number of plant lineages. Viburnum (Adoxaceae) possesses both types of palisade, providing an opportunity to assess the significance of evolutionary switches between these forms. Methodology. An anatomical survey of 80 species spanning the Viburnum phylogeny permitted an analysis of palisade differences in relation to other characters. A geometric model of leaf mesophyll surface area for CO2 absorption correlated well with measured photosynthetic capacity in a subset of species, allowing us to infer shifts in photosynthetic function. Pivotal results. Ancestrally, viburnums probably produced a palisade with one layer of H-cells. Multiple transitions to two layers of H-cells (H2) and to one or two layers of I-cells (I1, I2) occurred. These shifts were correlated with increases in photosynthetic capacity, and H2 appear functionally equivalent to I1 with respect to CO2 absorption. Conclusions. Photosynthetic anatomy H2 and I1 palisade may represent alternative evolutionary solutions for increasing leaf CO2 absorption. Additionally, H-cells and I-cells might perform differently with respect to light absorption and/or drought tolerance. The evolution of I-palisade cells may thus have tracked movements into open environments, while H2 could increase photosynthetic capacity in the forest understory.
    International Journal of Plant Sciences 01/2013; 174(9):1277-1291. · 1.54 Impact Factor
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    ABSTRACT: The evolution of plants exhibiting different sexes, or dioecy, is correlated with a number of ecological and life-history traits such as woody growth form and animal-dispersed seeds, but the underlying causes of these associations are unclear. Previous work in seed plants has suggested that the evolution of fleshy cones or seeds may favour dioecy. In this study, we use a well-sampled molecular phylogeny of conifers to show that although dioecy and fleshiness strongly co-occur at the species level, this relationship has not resulted from numerous separate origins of this trait combination or from differential rates of diversification. Instead, we suggest that two character combinations-the ancestral dry-monoecious condition and the derived fleshy-dioecious condition-have persisted in conifers longer than other combinations over evolutionary time. The persistence of these trait combinations appears to reflect differences in the rate of successful transition into and out of these character states over time, as well as the geographical restriction of species with rare combinations and their consequent vulnerability to extinction. In general, we argue that such persistence explanations should be considered alongside 'key innovation' hypotheses in explaining the phylogenetic distribution of traits.
    Proceedings of the Royal Society B: Biological Sciences 01/2013; 280(1770):20131812. · 5.68 Impact Factor
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    ABSTRACT: Abstract Plant traits that mediate mutualistic interactions are widespread, yet few studies have linked their macroevolutionary patterns with the ecological interactions they mediate. Here we merged phylogenetic and experimental approaches to investigate the evolution of two common mutualistic plant traits, extrafloral nectaries (EFNs) and leaf domatia. By using the flowering plant clade Viburnum, we tested whether macroevolutionary patterns support adaptive hypotheses and conducted field surveys and manipulative experiments to examine whether ecological interactions are concordant with evolutionary predictions. Phylogenetic reconstructions suggested that EFN-bearing species are monophyletic, whereas the evolution of domatia correlated with leaf production strategy (deciduous or evergreen) and climate. Domatia were also more common in the EFN clade, suggesting that the two traits may jointly mediate ecological interactions. This result was further investigated in a common-garden survey, where plants with domatia and EFNs on the leaf blade had more mutualistic mites than plants with other trait combinations, and in manipulative field experiments, where the traits additively increased mutualist abundance. Taken together, our results suggest that mutualistic traits in Viburnum are not ecologically independent, as they work in concert to attract and retain mutualists, and their long-term evolution may be influenced by complex interactions among multiple traits, mutualists, and geography.
    The American Naturalist 10/2012; 180(4):450-63. · 4.55 Impact Factor
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    ABSTRACT: Fundamental differences in the distribution of oceans and landmasses in the Northern and Southern Hemispheres potentially impact patterns of biological diversity in the two areas. The evolutionary history of conifers provides an opportunity to explore these dynamics, because the majority of extant conifer species belong to lineages that have been broadly confined to the Northern or Southern Hemisphere during the Cenozoic. Incorporating genetic information with a critical review of fossil evidence, we developed an age-calibrated phylogeny sampling ∼80% of living conifer species. Most extant conifer species diverged recently during the Neogene within clades that generally were established during the later Mesozoic, but lineages that diversified mainly in the Southern Hemisphere show a significantly older distribution of divergence ages than their counterparts in the Northern Hemisphere. Our tree topology and divergence times also are best fit by diversification models in which Northern Hemisphere conifer lineages have higher rates of species turnover than Southern Hemisphere lineages. The abundance of recent divergences in northern clades may reflect complex patterns of migration and range shifts during climatic cycles over the later Neogene leading to elevated rates of speciation and extinction, whereas the scattered persistence of mild, wetter habitats in the Southern Hemisphere may have favored the survival of older lineages.
    Proceedings of the National Academy of Sciences 09/2012; 109(40):16217-21. · 9.81 Impact Factor
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    ABSTRACT: Strong latitudinal patterns in leaf form are well documented in floristic comparisons and palaeobotanical studies. However, there is little agreement about their functional significance; in fact, it is still unknown to what degree these patterns were generated by repeated evolutionary adaptation. We analysed leaf form in the woody angiosperm clade Viburnum (Adoxaceae) and document evolutionarily correlated shifts in leafing habit, leaf margin morphology, leaf shape and climate. Multiple independent shifts between tropical and temperate forest habitats have repeatedly been accompanied by a change between evergreen, elliptical leaves with entire margins and deciduous, more rounded leaves with toothed or lobed margins. These consistent shifts in Viburnum support repeated evolutionary adaptation as a major determinant of the global correlation between leaf form and mean annual temperature. Our results provide a new theoretical grounding for the inference of past climates using fossil leaf assemblages.
    Proceedings of the Royal Society B: Biological Sciences 07/2012; 279(1744):3905-13. · 5.68 Impact Factor

Publication Stats

7k Citations
878.20 Total Impact Points

Institutions

  • 2000–2014
    • Yale University
      • Department of Ecology and Evolutionary Biology
      New Haven, Connecticut, United States
    • University of Tasmania
      Hobart Town, Tasmania, Australia
  • 2011–2013
    • Brown University
      • Department of Ecology and Evolutionary Biology
      Providence, RI, United States
    • St. John's University
      • Department of Biological Sciences
      New York City, NY, United States
  • 2010
    • McGill University
      Montréal, Quebec, Canada
  • 2009–2010
    • National Evolutionary Synthesis Center
      Durham, North Carolina, United States
    • University of California, Berkeley
      • Department of Integrative Biology
      Berkeley, MO, United States
  • 1005–2009
    • Harvard University
      • Department of Organismic and Evolutionary Biology
      Cambridge, Massachusetts, United States
  • 2007
    • University of California, Santa Barbara
      Santa Barbara, California, United States
  • 2005
    • University of Michigan
      • Department of Ecology and Evolutionary Biology
      Ann Arbor, MI, United States
    • Stony Brook University
      • Department of Ecology and Evolution
      Stony Brook, NY, United States
    • Field Museum of Natural History
      • Department of Botany
      Chicago, IL, United States
  • 2003
    • Leiden University
      Leyden, South Holland, Netherlands
    • University of Texas at Austin
      • Department of Computer Science
      Texas City, TX, United States
    • University of Missouri
      • Biological Sciences
      Columbia, MO, United States
  • 2002
    • Washington State University
      • School of Biological Sciences
      Pullman, WA, United States
  • 1987–2000
    • University of California, Davis
      • Department of Evolution & Ecology
      Davis, California, United States
  • 1997
    • University of Maine
      Orono, Minnesota, United States
  • 1987–1991
    • The University of Arizona
      • Department of Ecology and Evolutionary Biology
      Tucson, AZ, United States