Michael J. Donoghue

Yale University, New Haven, Connecticut, United States

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Publications (221)1194.51 Total impact

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    ABSTRACT: Madagascar’s rain forests are characterized by extreme and uneven patterns of species richness and endemicity, the biogeographic and evolutionary origins of which are poorly understood. Here we use a time-calibrated phylogeny of a dominant group of trees in Madagascar’s eastern rain forests, Canarium, and related Burseraceae (Canarieae), to test biogeographic hypotheses regarding the origin and radiation of the flora of this unique biome. Our findings strongly support the monophyly of Malagasy Canarium, suggesting that this clade represents a previously undocumented in situ radiation. Contrary to expectations of dispersal from Africa during the Oligocene, concurrent with the formation of Madagascar’s rain forest biome, our analyses support a late Miocene origin for Malagasy Canarium, probably by long distance dispersal from Southeast Asia. Our study illustrates the importance of considering long distance dispersal as a viable explanation for clades with pantropical distributions diversifying subsequent to the Oligocene, and it highlights the formation of the Indo-Australian Archipelago and associated fast-moving equatorial surface currents, suggesting an under-appreciated evolutionary link among tropical centers of endemism. We postulate that the relatively recent establishment and radiation of Canarium in Madagascar may have been facilitated by the highly stochastic climates associated with these forest ecosystems.
    Full-text · Article · Dec 2015 · BMC Evolutionary Biology
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    ABSTRACT: An introductory textbook of plant systematics.
    No preview · Book · Nov 2015
  • Erika J Edwards · Jurriaan M de Vos · Michael J Donoghue

    No preview · Article · May 2015 · Nature
  • Jeremy M Beaulieu · Brian C O'Meara · Peter Crane · Michael J Donoghue
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    ABSTRACT: Dating analyses based on molecular data imply that crown angiosperms existed in the Triassic, long before their undisputed appearance in the fossil record in the Early Cretaceous. Following a re-analysis of the age of angiosperms using updated sequences and fossil calibrations, we use a series of simulations to explore the possibility that the older age estimates are a consequence of (i) major shifts in the rate of sequence evolution near the base of the angiosperms and/or (ii) the representative taxon sampling strategy employed in such studies. We show that both of these factors do tend to yield substantially older age estimates. These analyses do not prove that younger age estimates based on the fossil record are correct, but they do suggest caution in accepting the older age estimates obtained using current relaxed-clock methods. Although we have focused here on the angiosperms, we suspect that these results will shed light on dating discrepancies in other major clades. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
    No preview · Article · May 2015 · Systematic Biology
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    ABSTRACT: Integration influences patterns of trait evolution, but the relationship between these patterns and the degree of trait integration is not well understood. In order to explore this further, we study a specialized pollination mechanism in conifers whose traits are linked through function but not development. This mechanism depends on interactions among three characters: pollen that is buoyant, ovules that face downward at pollination, and the production of a liquid droplet that buoyant grains float through to enter the ovule. We use a well-sampled phylogeny of conifers to test correlated evolution among these characters and specific sequences of character change. Using likelihood models of character evolution, we find that pollen morphology and ovule characters evolve in a concerted manner, where the flotation mechanism breaks down irreversibly following changes in orientation or drop production. The breakdown of this functional constraint, which may be facilitated by the lack of developmental integration among the constituent traits, is associated with increased trait variation and more diverse pollination strategies. Although this functional "release" increases diversity in some ways, the irreversible way in which the flotation mechanism is lost may eventually result in its complete disappearance from seed plant reproductive biology. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    Full-text · Article · Apr 2015 · Evolution
  • Michael J Donoghue · Michael J Sanderson
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    ABSTRACT: I. II. III. IV. V. VI. References SUMMARY: We review the empirical phylogenetic literature on plant diversification, highlighting challenges in separating the effects of speciation and extinction, in specifying diversification mechanisms, and in making convincing arguments. In recent discussions of context dependence, key opportunities and landscapes, and indirect effects and lag times, we see a distinct shift away from single-point/single-cause 'key innovation' hypotheses toward more nuanced explanations involving multiple interacting causal agents assembled step-wise through a tree. To help crystalize this emerging perspective we introduce the term 'synnovation' (a hybrid of 'synergy' and 'innovation') for an interacting combination of traits with a particular consequence ('key synnovation' in the case of increased diversification rate), and the term 'confluence' for the sequential coming together of a set of traits (innovations and synnovations), environmental changes, and geographic movements along the branches of a phylogenetic tree. We illustrate these concepts using the radiation of Bromeliaceae. We also highlight the generality of these ideas by considering how rate heterogeneity associated with a confluence relates to the existence of particularly species-poor lineages, or 'depauperons.' Many challenges are posed by this re-purposed research framework, including difficulties associated with partial taxon sampling, uncertainty in divergence time estimation, and extinction. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.
    No preview · Article · Mar 2015 · New Phytologist
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    ABSTRACT: We used a near-complete phylogeny for the angiosperm clade Viburnum to assess lineage diversification rates, and to examine possible morphological and ecological factors driving radiations. Maximum-likelihood and Bayesian approaches identified shifts in diversification rate and possible links to character evolution. We inferred the ancestral environment for Viburnum and changes in diversification dynamics associated with subsequent biome shifts. Viburnum probably diversified in tropical forests of Southeast Asia in the Eocene, with three subsequent radiations in temperate clades during the Miocene. Four traits (purple fruits, extrafloral nectaries, bud scales and toothed leaves) were statistically associated with higher rates of diversification. However, we argue that these traits are unlikely to be driving diversification directly. Instead, two radiations were associated with the occupation of mountainous regions and a third with repeated shifts between colder and warmer temperate forests. Early-branching depauperate lineages imply that the rare lowland tropical species are 'dying embers' of once more diverse lineages; net diversification rates in Viburnum likely decreased in these tropical environments after the Oligocene. We suggest that 'taxon pulse' dynamics might characterize other temperate plant lineages. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.
    Full-text · Article · Feb 2015 · New Phytologist
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    Elisabeth J. Forrestel · Michael J. Donoghue · Melinda D. Smith
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    ABSTRACT: 1.Grazing and fire are disturbances integral to the evolution and maintenance of savanna grasslands. Humans are altering or completely eliminating these disturbance regimes at a global scale, with important consequences for savanna ecosystem structure and function. It is unknown whether the alteration of these disturbance regimes will have similar effects on grass communities of savanna grasslands in different geographic regions that vary in their biogeographic and evolutionary histories, as well as in the diversity of extant grazers.2.Here we examined the effects of large herbivore loss on different aspects of grass community structure – taxonomic, phylogenetic, and functional – across a range of fire frequencies in C4-dominated mesic savanna grassland sites of North America (Konza Prairie Biological Station, Kansas, USA) and South Africa (Kruger National Park). The goal of the study was to determine whether the loss of large herbivores exerted a consistent effect on the grass communities of two physiognomically similar grasslands with different biogeographic and grazing histories.3.The removal of large herbivores resulted in divergent responses in the grass communities at Konza and Kruger that was consistent across fire treatments. At Konza, there was a rapid and significant response to grazing exclusion while the response was muted, and transient at Kruger. Functional syndromes associated with grazing resistance were generally conserved across sites, and it was the functional strategies of the dominant species at each site that drove the divergent responses. Further, our study supports the hypothesis that grazing and aridity may be selective forces that act in parallel as those species that were grazing resistant also occupied drier niches.4.Synthesis: Our study demonstrates that savanna grassland communities with different biogeographic and grazing histories respond differently to the removal of large herbivores, and that climate, fire, and grazing are interactive forces in maintaining savanna grassland diversity and function. We show that the functional attributes of the dominant grasses, which are in part driven by the biogeographic and grazing history experienced, are the most relevant in predicting the response of savanna ecosystems to the loss of large herbivores.This article is protected by copyright. All rights reserved.
    Full-text · Article · Feb 2015 · Journal of Ecology
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    Full-text · Dataset · Jan 2015
  • Michael J. Donoghue · Erika J. Edwards
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    ABSTRACT: What factors influence whether a lineage can successfully transition into a new biome, and why have some biome shifts been more frequent than others? To orient this line of research we develop a conceptual framework in which the likelihood of a biome shift is a function of (a) exposure to contrasting environments over time, (b) the evolutionary accessibility of relevant adaptations, and (c) changing biotic interactions. We evaluate the literature on biome shifts in plants in relation to a set of hypotheses on the size, connectedness, and absolute age of biomes, as well as on the adaptability of particular lineages and ecological interactions over time. We also critique the phylogenetic inference of past biomes and a "global" model-based approach to biome evolution. More robust generalizations about biome shifts will require detailed studies of well-sampled and well-resolved clades, accounting for changes in the relevant abiotic and biotic factors through time.
    No preview · Article · Nov 2014 · Annual Review of Ecology Evolution and Systematics
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    ABSTRACT: Background/Question/Methods Phenology is a powerful indicator of plant responses to climate change. Earlier spring flowering and leafing have been widely reported as spring temperatures increase, but studies of late season phenological changes are still uncommon. We conducted a six-year phenological monitoring program for 35 species of Viburnum in a common garden setting at the Arnold Arboretum, Jamaica Plain, Massachusetts. This monitoring period included normal weather years and two of the warmest years on record for the area (2010 and 2012). In order to document fall phenological changes in addition to spring advancement, we monitored plants from bud break to senescence. We noted phenological abnormalities in the fall in addition to an extension of the growing season: certain species initiated a second flush of growth late in the season. We tracked the fate of these prematurely-opened buds to assess the consequences for reproductive potential of this abnormal phenological behavior. Results/Conclusions All species shifted their spring phenology earlier in warmer years as compared with normal weather years. A subset of species shifted fall senescence later. A surprising 76% of species also exhibited at least a limited second phenological flush late in the growing season. Among these closely related species, there is a great deal of variability in degree of responsiveness to elevated temperatures. Some of this variability is explained by the morphological character of naked buds, present in three lineages representing independent transitions from the tropics to the temperate zone. Species with naked buds were significantly more likely than scale-bud species to initiate a late-season second flush of growth. Their late-opened buds were also disproportionately likely to survive through the winter and provide limited spring reproductive potential. Number of buds opened in fall ranged from zero or very few (eg, V. dentatum) to 22% (V. cassinoides). Across all species in which reproductive buds opened in fall, spring flower number was significantly reduced in fall-opened inflorescences when compared to normal spring inflorescences. This reduction in reproductive potential in the year following climate-driven abnormal fall phenology introduces a new concern regarding negative consequences of species responses to warming climates.
    No preview · Conference Paper · Aug 2014
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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.
    Full-text · Article · Jun 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.
    Full-text · Article · Jun 2014 · American Journal of Botany
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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
    Full-text · Article · Jun 2014 · Journal of Biosciences
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    Andrew B Leslie · Jeremy M Beaulieu · Peter R Crane · Michael J Donoghue
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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.
    Full-text · Article · May 2014 · New Phytologist
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    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.
    Full-text · Article · May 2014 · New Phytologist
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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.
    Full-text · Article · Apr 2014 · Proceedings of the National Academy of Sciences
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    Erika J. Edwards · David S. Chatelet · Lawren Sack · Michael J. Donoghue
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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.
    Full-text · Article · Mar 2014 · Journal of Ecology
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    D. A. and Baum · Michael J. Donoghue
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    ABSTRACT: Several different ''phylogenetic'' species concepts have been proposed, and we consider how to choose among them. There appear to be two main approaches. ''Character-based'' concepts define species on the possession of characters, whereas ''history-based'' concepts are based on historical. relatedness. Under the latter view, characters may be used to discover species in practice but they are not viewed as defining attributes of species. To illustrate the distinction we discuss a character-based approach utilizing ''diagnostic'' characters and a history-based approach using genetic coalescence. We argue that the choice between character- and history-based concepts is primarily determined by one's understanding of systematics. If the goal of systematics is simply to describe the hierarchical distribution of characters (''pattern cladistics''), a character-based definition of species is required. In contrast, if systematics is concerned with inferring the evolutionary relationships of organisms (''evolutionary phylogenetics''), a history-based definition of species is needed. We hold the view that phylogenetic systematics is concerned with evolutionary history and therefore we maintain that a phylogenetic species concept should be history-based.
    Full-text · Article · Jan 2014 · Systematic Botany
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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.
    No preview · Article · Nov 2013 · International Journal of Plant Sciences

Publication Stats

18k Citations
1,194.51 Total Impact Points


  • 2000-2015
    • Yale University
      • Department of Ecology and Evolutionary Biology
      New Haven, Connecticut, United States
    • University of Tasmania
      Hobart Town, Tasmania, Australia
  • 2014
    • University of Wisconsin–Madison
      • Department of Botany
      Madison, Wisconsin, United States
  • 1986-2009
    • Harvard University
      • Department of Organismic and Evolutionary Biology
      Cambridge, Massachusetts, United States
  • 2005
    • University of Chicago
      Chicago, Illinois, United States
  • 2004
    • University of Toronto
      Toronto, Ontario, Canada
  • 2003
    • Stockholm University
      Tukholma, Stockholm, Sweden
    • University of Missouri
      • Biological Sciences
      Columbia, MO, United States
  • 2001
    • Duke University
      • Department of Biology
      Durham, North Carolina, United States
  • 1990-1999
    • University of California, Berkeley
      • Department of Plant and Microbial Biology
      Berkeley, California, United States
  • 1995
    • Tottori Mycological Institute
      TTJ, Tottori, Japan
  • 1987-1993
    • University of California, Davis
      • Department of Evolution & Ecology
      Davis, California, United States
  • 1992
    • Indiana University Bloomington
      • Department of Biology
      Bloomington, Indiana, United States
  • 1986-1992
    • The University of Arizona
      • Department of Ecology and Evolutionary Biology
      Tucson, AZ, United States
  • 1984
    • San Diego State University
      San Diego, California, United States