Mark W. Chase

University of Western Australia, Perth City, Western Australia, Australia

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Publications (450)1479.37 Total impact

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    Steven Dodsworth · Mark W. Chase · Andrew R. Leitch ·

    Botanical Journal of the Linnean Society 12/2015; DOI:10.1111/boj.12357 · 2.53 Impact Factor
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    ABSTRACT: Due to its special geological history, the New Caledonian Archipelago is a mosaic of soil types, and in combination with climatic conditions this results in a heterogeneous environment across relatively small distances. A group of over 20 endemic species of Diospyros (Ebenaceae) has rapidly and recently radiated on the archipelago after a single long-distance dispersal event. Most of the Diospyros species in the radiating group are morphologically and ecologically well differentiated, but they exhibit low levels of DNA variability. To investigate the processes that shaped the diversification of this group we employed restriction site associated DNA sequencing (RADseq). Over 8,400 filtered SNPs generally confirm species delimitations and produce a well-supported phylogenetic tree. Our analyses document local introgression, but only a limited potential for gene flow over longer distances. The phylogenetic relationships point to an early regional clustering among populations and species, indicating that allopatric speciation with respect to macrohabitat (i.e., climatic conditions) may have had a role in the initial differentiation within the group. A later, more rapid radiation involved divergence with respect to microhabitat (i.e., soil preference). Several sister species in the group show a parallel divergence in edaphic preference. Searches for genomic regions that are systematically differentiated in this replicated phenotypic divergence pointed to loci potentially involved in ion binding and cellular transport. These loci appear meaningful in the context of adaptations to soil types that differ in heavy-metal and mineral content. Identical nucleotide changes affected only two of these loci, indicating that introgression may have played a limited role in their evolution. Our results suggest that both allopatric diversification and (parapatric) ecological divergence shaped successive rounds of speciation in the Diospyros radiation on New Caledonia.
    Systematic Biology 10/2015; DOI:10.1093/sysbio/syv076 · 14.39 Impact Factor
  • André Schuiteman · Mark Chase ·
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    ABSTRACT: It is argued that a broad and expanded circumscription of Maxillaria is to be preferred over a narrower one that necessitates the recognition of many segregate genera. These more narrowly circumscribed genera are often difficult to diagnose, increasing the risk of misidentifications, especially when material is only identified to genus level. The genera of the Maxillaria alliance as recognised in Genera orchidacearum are treated as sections of an expanded genus Maxillaria. Cryptocentrum, Cyrtidiorchis, Mormolyca, Pityphyllum, and Trigonidium are here included in Maxillaria. Criteria for generic delimitation are discussed, the necessary combinations are made, and a key to the sections as well as a provisional checklist of the 634 species of Maxillaria arranged according to section are provided. Maxillaria prolifera is shown to be the correct name for M. pendens. Maxillaria humilis is a new combination for M. gracilis.
    Phytotaxa 09/2015; 225(1):001-078. DOI:10.11646/phytotaxa.225.1.1 · 1.32 Impact Factor
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    ABSTRACT: High-throughput sequencing data have transformed molecular phylogenetics and a plethora of phylogenomic approaches are now readily available. Shotgun sequencing at low genome coverage is a common approach for isolating high-copy DNA, such as the plastid or mitochondrial genomes, and ribosomal DNA. These sequence data, however, are also rich in repetitive elements that are often discarded. Such data include a variety of repeats present throughout the nuclear genome in high copy number. It has recently been shown that the abundance of repetitive elements has phylogenetic signal and can be used as a continuous character to infer tree topologies. In the present study, we evaluate repetitive DNA data in tomatoes (Solanum section Lycopersicon) to explore how they perform at the inter- and intraspecific levels, utilizing the available data from the 100 Tomato Genome Sequencing Consortium. The results add to previous examples from angiosperms where genomic repeats have been used to resolve phylogenetic relationships at varying taxonomic levels. Future prospects now include the use of genomic repeats for population-level analyses and phylogeography, as well as potentially for DNA barcoding.
    Biological Journal of the Linnean Society 07/2015; DOI:10.1111/bij.12612 · 2.26 Impact Factor
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    ABSTRACT: Recently, DNA barcoding has emerged as an effec- tive tool for species identification. This has the poten- tial for many useful applications in conservation, such as biodiversity inventories, forensics and trade sur- veillance. It is being developed as an inexpensive and rapid molecular technique using short and standard- ized DNA sequences for species identification.
    Lankesteriana 06/2015; 7(1-2). DOI:10.15517/lank.v7i1-2.19502
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    ABSTRACT: Conservation biologists have only finite resources, and so must prioritise some species over others. The EDGE-listing approach ranks species according to their combined evolutionary distinctiveness and degree of threat, but ignores the uncertainty surrounding both threat and evolutionary distinctiveness. We develop a new family of measures for species, which we name EDAM, that incorporates evolutionary distinctiveness, the magnitude of decline, and the accuracy with which decline can be predicted. Further, we show how the method can be extended to explore phyogenetic uncertainty. Using the vascular plants of Britain as a case study, we find that the various EDAM measures emphasise different species and parts of Britain, and that phylogenetic uncertainty can strongly affect the prioritisation scores of some species.
    PLoS ONE 05/2015; 10(5):e0126524. DOI:10.1371/journal.pone.0126524 · 3.23 Impact Factor
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    ABSTRACT: Speciation in angiosperms can be accompanied by changes in floral colour that may influence pollinator preference and reproductive isolation. This study investigates whether changes in floral colour can accompany polyploid and homoploid hybridization, important processes in angiosperm evolution. Spectral reflectance of corolla tissue was examined for 60 Nicotiana (Solanaceae) accessions (41 taxa) based on spectral shape (corresponding to pigmentation) as well as bee and hummingbird colour perception in order to assess patterns of floral colour evolution. Polyploid and homoploid hybrid spectra were compared with those of their progenitors to evaluate whether hybridization has resulted in floral colour shifts. Floral colour categories in Nicotiana seem to have arisen multiple times independently during the evolution of the genus. Most younger polyploids displayed an unexpected floral colour, considering those of their progenitors, in the colour perception of at least one pollinator type, whereas older polyploids tended to resemble one or both of their progenitors. Floral colour evolution in Nicotiana is weakly constrained by phylogeny, and colour shifts do occur in association with both polyploid and homoploid hybrid divergence. Transgressive floral colour in N. tabacum has arisen by inheritance of anthocyanin pigmentation from its paternal progenitor while having a plastid phenotype like its maternal progenitor. Potentially, floral colour evolution has been driven by, or resulted in, pollinator shifts. However, those polyploids that are not sympatric (on a regional scale) with their progenitor lineages are typically not divergent in floral colour from them, perhaps because of a lack of competition for pollinators. © The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email:
    Annals of Botany 05/2015; 115(7). DOI:10.1093/aob/mcv048 · 3.65 Impact Factor
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    ABSTRACT: Resolution of evolutionary relationships among some monocot orders remains problematic despite the application of various taxon and molecular locus sampling strategies. In this study we sequenced and analysed a fragment of the low-copy, nuclear phytochrome C (PHYC) gene and combined these data with a previous multigene data set (four plastid, one mitochondrial, two nuclear ribosomal loci) to determine if adding this marker improved resolution and support of relationships among major lineages of monocots. Our results indicate the addition of PHYC to the multigene dataset increases support along the backbone of the monocot tree, although relationships among orders of commelinids remain elusive. We also estimated divergence times in monocots by applying newly evaluated fossil calibrations to our resolved phylogenetic tree. Inclusion of early-diverging angiosperm lineages confirmed the origin of extant monocots c. 131 Mya and strengthened the hypothesis of recent divergence times for some lineages, although current divergence time estimation methods may inadequately model rate heterogeneity in monocots. We note significant shifts in diversification in at least two monocot orders, Poales and Asparagales. We describe patterns of diversification in the context of radiation of other relevant plant and animal lineages. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, ●●, ●●–●●.
    Botanical Journal of the Linnean Society 04/2015; 178(3). DOI:10.1111/boj.12260 · 2.53 Impact Factor
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    Félix Forest · Keith A Crandall · Mark W Chase · Daniel P Faith ·
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    ABSTRACT: Evolutionary studies have played a fundamental role in our understanding of life, but until recently, they had only a relatively modest involvement in addressing conservation issues. The main goal of the present discussion meeting issue is to offer a platform to present the available methods allowing the integration of phylogenetic and extinction risk data in conservation planning. Here, we identify the main knowledge gaps in biodiversity science, which include incomplete sampling, reconstruction biases in phylogenetic analyses, partly known species distribution ranges, and the difficulty in producing conservation assessments for all known species, not to mention that much of the effective biological diversity remains to be discovered. Given the impact that human activities have on biodiversity and the urgency with which we need to address these issues, imperfect assumptions need to be sanctioned and surrogates used in the race to salvage as much as possible of our natural and evolutionary heritage. We discuss some aspects of the uncertainties found in biodiversity science, such as the ideal surrogates for biodiversity, the gaps in our knowledge and the numerous available phylogenetic diversity-based methods. We also introduce a series of cases studies that demonstrate how evolutionary biology can effectively contribute to biodiversity conservation science. © 2015 The Author(s) Published by the Royal Society. All rights reserved.
    Philosophical Transactions of The Royal Society B Biological Sciences 02/2015; 370(1662). DOI:10.1098/rstb.2014.0002 · 7.06 Impact Factor
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    ABSTRACT: Since the last classification of Orchidaceae in 2003, there has been major progress in the determination of relationships, and we present here a revised classification including a list of all 736 currently recognized genera. A number of generic changes have occurred in Orchideae (Orchidoideae), but the majority of changes have occurred in Epidendroideae. In the latter, almost all of the problematic placements recognized in the previous classification 11 years ago have now been resolved. In Epidendroideae, we have recognized three new tribes (relative to the last classification): Thaieae (monogeneric) for Thaia, which was previously considered to be the only taxon incertae sedis; Xerorchideae (monogeneric) for Xerorchis; and Wullschlaegelieae for achlorophyllous Wullschlaegelia, which had tentatively been placed in Calypsoeae. Another genus, Devogelia, takes the place of Thaia as incertae sedis in Epidendroideae. Gastrodieae are clearly placed among the tribes in the neottioid grade, with Neottieae sister to the remainder of Epidendroideae. Arethuseae are sister to the rest of the higher Epidendroideae, which is unsurprising given their mostly soft pollinia. Tribal relationships within Epidendroideae have been much clarified by analyses of multiple plastid DNA regions and the low-copy nuclear gene Xdh. Four major clades within the remainder of Epidendroideae are recognized: Vandeae/Podochileae/Collabieae, Cymbidieae, Malaxideae and Epidendreae, the last now including Calypsoinae (previously recognized as a tribe on its own) and Agrostophyllinae s.s. Agrostophyllinae and Collabiinae were unplaced subtribes in the 2003 classification. The former are now split between two subtribes, Agrostophyllinae s.s. and Adrorhizinae, the first now included in Epidendreae and the second in Vandeae. Collabiinae, also probably related to Vandeae, are now elevated to a tribe along with Podochileae. Malaxis and relatives are placed in Malaxidinae and included with Dendrobiinae in Malaxideae. The increased resolution and content of larger clades, recognized here as tribes, do not support the ‘phylads’ in Epidendroideae proposed 22 years ago by Dressler. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 177, 151–174.
    Botanical Journal of the Linnean Society 02/2015; 177(2). DOI:10.1111/boj.12234 · 2.53 Impact Factor
  • John V Freudenstein · Mark W Chase ·
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    ABSTRACT: The largest subfamily of orchids, Epidendroideae, represents one of the most significant diversifications among flowering plants in terms of pollination strategy, vegetative adaptation and number of species. Although many groups in the subfamily have been resolved, significant relationships in the tree remain unclear, limiting conclusions about diversification and creating uncertainty in the classification. This study brings together DNA sequences from nuclear, plastid and mitochrondrial genomes in order to clarify relationships, to test associations of key characters with diversification and to improve the classification. Sequences from seven loci were concatenated in a supermatrix analysis for 312 genera representing most of epidendroid diversity. Maximum-likelihood and parsimony analyses were performed on this matrix and on subsets of the data to generate trees and to investigate the effect of missing values. Statistical character-associated diversification analyses were performed. Likelihood and parsimony analyses yielded highly resolved trees that are in strong agreement and show significant support for many key clades. Many previously proposed relationships among tribes and subtribes are supported, and some new relationships are revealed. Analyses of subsets of the data suggest that the relatively high number of missing data for the full analysis is not problematic. Diversification analyses show that epiphytism is most strongly associated with diversification among epidendroids, followed by expansion into the New World and anther characters that are involved with pollinator specificity, namely early anther inflexion, cellular pollinium stalks and the superposed pollinium arrangement. All tested characters show significant association with speciation in Epidendroideae, suggesting that no single character accounts for the success of this group. Rather, it appears that a succession of key features appeared that have contributed to diversification, sometimes in parallel. © The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email:
    Annals of Botany 01/2015; 115(4). DOI:10.1093/aob/mcu253 · 3.65 Impact Factor
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    ABSTRACT: Since its launch in 2009 Phytotaxa has grown to be the leading journal in taxonomic botany, publishing the greatest number of articles, pages, and new names. It has replaced Taxon as the top journal by volume and total citation to current papers but not impact factor. More than just a journal, Phytotaxa has made it easier for authors to publish in botanical taxonomy and has improved access to publication for disadvantaged authors. This is reflected in it gaining ‘market share’ from biodiversity-rich BRIC countries, which have invested in their taxonomic capacity. It could also reflect a shift away from Europe & US as main descriptors of plant diversity. We believe that Phytotaxa has been well accepted by the taxonomic community because it is free at point of publication (barrier-free to authors of all income brackets), flexible (unlimited issues and pages) and rapidly indexed with an impact factor that is relatively high for a taxonomic journal. Phytotaxa thus meets the needs of the broadest group of taxonomists who survive based on publication number and impact factor, and who do not have access to funds to support open-access publication. We suggest that it is eminently feasible to fully describe and typify all plant diversity using the Linnean system, but that do so in a timely manner and so meet Society’s needs in the face of the mass-extinction of biodiversity and climate change. Phytotaxa will work with all taxonomists to continue to promote taxonomy as a scientific discipline.
    Phytotaxa 12/2014; 191(1):1-9. DOI:10.11646/phytotaxa.191.1.1 · 1.32 Impact Factor
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    ABSTRACT: Phylogenetic relationships of the pantropical and polyphyletic family Icacinaceae were investigated, focusing on the Old World vining genera. Plastid ndhF, rbcL and matK sequences from taxa representing 32 of the 36 currently recognized genera were analysed with maximum parsimony and Bayesian methods. As in previous studies, our results show that the family is divided into several poorly resolved groups. An evaluation of the traditional tribal classification revealed Iodeae as polyphyletic and the monogeneric Sarcostigmateae as sister to a monophyletic Phytocreneae (with the inclusion of Rhyticaryum). In Iodeae, the monospecific, eastern Malesian Polyporandra was embedded in the Old World Iodes. A strongly supported clade containing Phytocreneae plus Rhyticaryum was present in the Icacina group. The tropical African genera Chlamydocarya and Polycephalium were embedded in the Old World Pyrenacantha. Further relationships in the family and potential synapomorphic characters of the clades are discussed. New combinations are made for Polyporandra and Chlamydocarya/Polycephalium spp., which are formally synonymized with Iodes and Pyrenacantha, respectively. Conclusions about family-level relationships (and circumscription) cannot be reached with these data because of several weakly supported inter-relationships between some clades, such as Cassinopsis, Platea/Calatola and the Emmotum group. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176, 277–294.
    Botanical Journal of the Linnean Society 11/2014; 176(3). DOI:10.1111/boj.12205 · 2.53 Impact Factor
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    Taxon 10/2014; 63(5). DOI:10.12705/635.22 · 3.30 Impact Factor
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    ABSTRACT: A large proportion of genomic information, particularly repetitive elements, is usually ignored when researchers are using next-generation sequencing. Here we demonstrate the usefulness of this repetitive fraction in phylogenetic analyses, utilizing comparative graph-based clustering of next-generation sequence reads, which results in abundance estimates of different classes of genomic repeats. Phylogenetic trees are then inferred based on the genome-wide abundance of different repeat types treated as continuously varying characters; such repeats are scattered across chromosomes and in angiosperms can constitute a majority of nuclear genomic DNA. In six diverse examples, five angiosperms and one insect, this method provides generally well-supported relationships at interspecific and intergeneric levels that agree with results from more standard phylogenetic analyses of commonly used markers. We propose that this methodology may prove especially useful in groups where there is little genetic differentiation in standard phylogenetic markers. At the same time as providing data for phylogenetic inference, this method additionally yields a wealth of data for comparative studies of genome evolution.
    Systematic Biology 09/2014; 64(1). DOI:10.1093/sysbio/syu080 · 14.39 Impact Factor
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    ABSTRACT: Recent molecular phylogenetic studies in Chrysobalanaceae as well as new analyses presented in this study cast doubt on the monophyly of the three largest genera in the family, Couepia, Hirtella and Licania. Couepia, a Neotropical genus, had species appearing in four separate clades, the majority of species sequenced, however, form a highly supported clade, referred to here as core Couepia (including the type species). These results lend support to a revised taxonomy of the genus, and to resolve Couepia as monophyletic the following taxonomic changes are here proposed: Couepia recurva should be transferred to Hirtella, C. platycalyx transferred to Licania, C. longipendula and C. dolichopoda transferred to Acioa, and a new genus, Gaulettia, is proposed to accommodate species of the Gaulettia clade and allies.
    Phytotaxa 06/2014; 172(2):176–200. DOI:10.11646/phytotaxa.172.3.2 · 1.32 Impact Factor
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    ABSTRACT: Similar to other species-rich taxa in the Indo-Australian Archipelago, taxonomy of the genus Aglaia (mahogany family, Meliaceae) remains problematic. This study aims to evaluate taxonomic concepts within Aglaia based on the largest dataset to-date. We analyzed sequences of 237 accessions of Aglaia and representatives of all other genera of the tribe Aglaieae, including nuclear ribosomal ITS, the trnL-trnF intron and intergenic spacer, the atpF intron and the petD region comprising the petB-petD spacer, the petD-5' exon and the petD intron (all but the first from the plastid genome). Our analyses were set both in maximum likelihood and Bayesian frameworks, which (1) supported paraphyly of Aglaia and Aphanamixis; (2) demonstrated polyphyly of previously described sections for Aglaia; and (3) suggested delimitation problems with of 57% of the morphologically "variable species" and all "complex species". In general, there were more genetic entities than species described, which shows that the taxonomy of this group is more complex than has sometimes been previously assumed. For some species, morphological variation suggests the existence of more variants, subspecies or species within various taxa. Furthermore, our study detected additional phylogenetic entities that were geographically distinct, occurring on either side of Wallace's Line but not on both sides. The delineation of these inter-specific taxa needs further investigation by taking into account the morphological variation within and between populations across the entire distribution.
    Molecular Phylogenetics and Evolution 04/2014; 73(1). DOI:10.1016/j.ympev.2014.01.025 · 3.92 Impact Factor
  • Maarten J M Christenhusz · Mark W Chase ·
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    ABSTRACT: Background and AimsThroughout the history of fern classification, familial and generic concepts have been highly labile. Many classifications and evolutionary schemes have been proposed during the last two centuries, reflecting different interpretations of the available evidence. Knowledge of fern structure and life histories has increased through time, providing more evidence on which to base ideas of possible relationships, and classification has changed accordingly. This paper reviews previous classifications of ferns and presents ideas on how to achieve a more stable consensus.ScopeAn historical overview is provided from the first to the most recent fern classifications, from which conclusions are drawn on past changes and future trends. The problematic concept of family in ferns is discussed, with a particular focus on how this has changed over time. The history of molecular studies and the most recent findings are also presented.Key ResultsFern classification generally shows a trend from highly artificial, based on an interpretation of a few extrinsic characters, via natural classifications derived from a multitude of intrinsic characters, towards more evolutionary circumscriptions of groups that do not in general align well with the distribution of these previously used characters. It also shows a progression from a few broad family concepts to systems that recognized many more narrowly and highly controversially circumscribed families; currently, the number of families recognized is stabilizing somewhere between these extremes. Placement of many genera was uncertain until the arrival of molecular phylogenetics, which has rapidly been improving our understanding of fern relationships. As a collective category, the so-called 'fern allies' (e.g. Lycopodiales, Psilotaceae, Equisetaceae) were unsurprisingly found to be polyphyletic, and the term should be abandoned. Lycopodiaceae, Selaginellaceae and Isoëtaceae form a clade (the lycopods) that is sister to all other vascular plants, whereas the whisk ferns (Psilotaceae), often included in the lycopods or believed to be associated with the first vascular plants, are sister to Ophioglossaceae and thus belong to the fern clade. The horsetails (Equisetaceae) are also members of the fern clade (sometimes inappropriately called 'monilophytes'), but, within that clade, their placement is still uncertain. Leptosporangiate ferns are better understood, although deep relationships within this group are still unresolved. Earlier, almost all leptosporangiate ferns were placed in a single family (Polypodiaceae or Dennstaedtiaceae), but these families have been redefined to narrower more natural entities.Conclusions Concluding this paper, a classification is presented based on our current understanding of relationships of fern and lycopod clades. Major changes in our understanding of these families are highlighted, illustrating issues of classification in relation to convergent evolution and false homologies. Problems with the current classification and groups that still need study are pointed out. A summary phylogenetic tree is also presented. A new classification in which Aspleniaceae, Cyatheaceae, Polypodiaceae and Schizaeaceae are expanded in comparison with the most recent classifications is presented, which is a modification of those proposed by Smith et al. (2006, 2008) and Christenhusz et al. (2011). These classifications are now finding a wider acceptance and use, and even though a few amendments are made based on recently published results from molecular analyses, we have aimed for a stable family and generic classification of ferns.
    Annals of Botany 02/2014; 113(4). DOI:10.1093/aob/mct299 · 3.65 Impact Factor

Publication Stats

26k Citations
1,479.37 Total Impact Points


  • 2013-2015
    • University of Western Australia
      • School of Plant Biology
      Perth City, Western Australia, Australia
  • 1996-2015
    • Royal Botanic Gardens, Kew
      • Jodrell Laboratory
      TW9, England, United Kingdom
  • 2003-2013
    • University of Vienna
      • Department of Systematic and Evolutionary Botany
      Wien, Vienna, Austria
  • 2001-2009
    • Natural History Museum, London
      • Department of Botany
      Londinium, England, United Kingdom
    • Florida Museum of Natural History
      Gainesville, Florida, United States
  • 2008
    • University of Adelaide
      Tarndarnya, South Australia, Australia
    • København Zoo
      København, Capital Region, Denmark
  • 2006
    • Aarhus University
      Aarhus, Central Jutland, Denmark
  • 2005
    • University of Oslo
      Kristiania (historical), Oslo, Norway
  • 2004
    • Concordia University–Ann Arbor
      Ann Arbor, Michigan, United States
    • Indiana University Bloomington
      • Department of Biology
      Bloomington, IN, United States
  • 2002-2004
    • The Ohio State University
      • Department of Evolution, Ecology, and Organismal Biology
      Columbus, OH, United States
    • Trinity College Dublin
      • Department of Botany
      Dublin, Leinster, Ireland
  • 1992-2003
    • University of North Carolina at Chapel Hill
      • Department of Biology
      North Carolina, United States
  • 1998-2001
    • University of Wisconsin–Madison
      • Department of Botany
      Madison, Wisconsin, United States
    • Harvard University
      Cambridge, Massachusetts, United States
  • 1997-2001
    • Washington State University
      • School of Biological Sciences
      پولمن، واشینگتن, Washington, United States
  • 2000
    • University of London
      • School of Biological Sciences
      Londinium, England, United Kingdom
    • University of Reading
      Reading, England, United Kingdom
    • Royal Botanic Garden Edinburgh
      Edinburgh, Scotland, United Kingdom
    • Melbourne Water
      Melbourne, Victoria, Australia
  • 1994
    • Lebanon Valley College
      Annville, Pennsylvania, United States
  • 1993
    • University of Wisconsin - Milwaukee
      • Department of Biological Sciences
      Milwaukee, Wisconsin, United States
    • University of Toronto
      Toronto, Ontario, Canada
  • 1989
    • University of Michigan
      • Department of Biology
      Ann Arbor, Michigan, United States
  • 1988
    • University of Washington Seattle
      Seattle, Washington, United States