Nancy Knowlton

Smithsonian Institution, Washington, Washington, D.C., United States

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Publications (98)742.15 Total impact

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    ABSTRACT: Many cnidarians host endosymbiotic dinoflagellates from the genus Symbiodinium. It is generally assumed that the symbiosis is mutualistic, where the host benefits from symbiont photosynthesis while providing protection and photosynthetic substrates. Diverse assemblages of symbiotic gorgonian octocorals can be found in hard bottom communities throughout the Caribbean. While current research has focused on the phylo- and population genetics of gorgonian symbiont types and their photo-physiology, relatively less work has focused on biogeochemical benefits conferred to the host and how these benefits vary across host species. Here we examine this symbiosis among 11 gorgonian species collected in Bocas del Toro, Panama. By coupling light and dark bottle incubations (P/R) with (13)C-bicarbonate tracers, we quantified the link between holobiont oxygen metabolism with carbon assimilation and translocation from symbiont to host. Our data show that P/R varied among species, and was correlated with colony morphology and polyp size. Sea fans and sea plumes were net autotrophs (P/R>1.5), while nine species of sea rods were net heterotrophs with most below compensation (P/R<1.0). (13)C assimilation corroborated the P/R results, and maximum δ(13)Chost values were strongly correlated with polyp size, indicating higher productivity by colonies with high polyp SA:V. A survey of gorgonian-Symbiodinium associations revealed that productive species maintain specialized, obligate symbioses and are more resistant to coral bleaching, whereas generalist and facultative associations are common among sea rods that have higher bleaching sensitivities. Overall, productivity and polyp size had strong phylogenetic signals with carbon fixation and polyp size showing evidence of trait covariance.The ISME Journal advance online publication, 19 May 2015; doi:10.1038/ismej.2015.71.
    The ISME Journal 05/2015; DOI:10.1038/ismej.2015.71 · 9.27 Impact Factor
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    ABSTRACT: We describe Symbiodinium necroappetens sp. nov. found predominantly in diseased or thermally damaged tissues in some reef corals of the Greater Caribbean. Small, albeit fixed, differences in the ribosomal DNA (ITS2 and LSU) and cytochrome b (cob) indicate that S. necroappetens is evolutionarily separate, but closely related to S. microadriaticum (members of Clade A). However, haplotype sequences of the non-coding region of the psbA minicircle are highly divergent, signifying that the degree of genetic divergence between these sibling lineages is far greater than indicated by changes in rDNA. Small morphological differences also support the delineation of this species. The Kofoidian plate formula for S. necroappetens (x-plate, EAV, 4′, 5a, 8′′, 9-11s, 21c, 6′′′, 2′′′′, PE) is generally the same as described for S. microadriaticum, except for the number of cingulum plates (21 vs 22-24), but plate shapes and configurations differ. Nuclear and mitochondrial volumes calculated from ultrastructural serial sections (published previously) also distinguish it from S. microadriaticum and S. pilosum. There are significant physiological differences in the response of S. necroappetens to high pCO2 and thermal stress when compared with S. microadriaticum, indicating that large functional differences exist even among closely related species. This species appears to be necrotrophic rather than mutualistic. Before it was recognized as a distinct entity, reports on its ecology contributed to the supposition that members of Clade A Symbiodinium were opportunistic. Available evidence indicates that S. necroappetens exists at low environmental background levels, but may ‘proliferate’ selectively in artificial growth media, or emerge opportunistically in bleached coral colonies during early recovery from severe stress, or in diseased necrotic tissues, especially in colonies of the Orbicella (formerly Monstastraea) annularis complex. However, S. necroappetens fails to persist at detectable levels as populations of the typical symbiont recover. The description of this species raises awareness of the broad functional and ecological diversity exhibited by members of this large dinoflagellate genus.
    European Journal of Phycology 04/2015; 50(2):223-238. DOI:10.1080/09670262.2015.1025857 · 2.34 Impact Factor
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    Matthieu Leray, Nancy Knowlton
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    ABSTRACT: Documenting the diversity of marine life is challenging because many species are cryptic, small, and rare, and belong to poorly known groups. New sequencing technologies, especially when combined with standardized sampling, promise to make comprehensive biodiversity assessments and monitoring feasible on a large scale. We used this approach to characterize patterns of diversity on oyster reefs across a range of geographic scales comprising a temperate location [Virginia (VA)] and a subtropical location [Florida (FL)]. Eukaryotic organisms that colonized multilayered settlement surfaces (autonomous reef monitoring structures) over a 6-mo period were identified by cytochrome c oxidase subunit I barcoding (>2-mm mobile organisms) and metabarcoding (sessile and smaller mobile organisms). In a total area of ∼15.64 m(2) and volume of ∼0.09 m(3), 2,179 operational taxonomic units (OTUs) were recorded from 983,056 sequences. However, only 10.9% could be matched to reference barcodes in public databases, with only 8.2% matching barcodes with both genus and species names. Taxonomic coverage was broad, particularly for animals (22 phyla recorded), but 35.6% of OTUs detected via metabarcoding could not be confidently assigned to a taxonomic group. The smallest size fraction (500 to 106 μm) was the most diverse (more than two-thirds of OTUs). There was little taxonomic overlap between VA and FL, and samples separated by ∼2 m were significantly more similar than samples separated by ∼100 m. Ground-truthing with independent assessments of taxonomic composition indicated that both presence-absence information and relative abundance information are captured by metabarcoding data, suggesting considerable potential for ecological studies and environmental monitoring.
    Proceedings of the National Academy of Sciences 02/2015; 112(7). DOI:10.1073/pnas.1424997112 · 9.81 Impact Factor
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    ABSTRACT: Global species richness, whether estimated by taxon, habitat, or ecosystem, is a key biodiversity metric. Yet, despite the global importance of biodiversity and increasing threats to it (e.g., [1-4]), we are no better able to estimate global species richness now than we were six decades ago [5]. Estimates of global species richness remain highly uncertain and are often logically inconsistent [5]. They are also difficult to validate because estimation of global species richness requires extrapolation beyond the number of species known [6-13]. Given that somewhere between 3% and >96% of species on Earth may remain undiscovered [4], depending on the methods used and the taxa considered, such extrapolations, especially from small percentages of known species, are likely to be highly uncertain [13, 14]. An alternative approach is to estimate all species, the known and unknown, directly. Using expert taxonomic knowledge of the species already described and named, those already discovered but not yet described and named, and those still awaiting discovery, we estimate there to be 830,000 (95% credible limits: 550,000-1,330,000) multi-cellular species on coral reefs worldwide, excluding fungi. Uncertainty surrounding this estimate and its components were often strongly skewed toward larger values, indicating that many more species on coral reefs is more plausible than many fewer. The uncertainties revealed here should guide future research toward achieving convergence in global species richness estimates for coral reefs and other ecosystems via adaptive learning protocols whereby such estimates can be tested and improved, and their uncertainties reduced, as new knowledge is acquired. Copyright © 2015 Elsevier Ltd. All rights reserved.
    Current Biology 01/2015; DOI:10.1016/j.cub.2014.12.022 · 9.92 Impact Factor
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    ABSTRACT: Modern coral taxonomy has begun to resolve many long-standing problems in traditional systematics stemming from its reliance on skeletal macromorphology. By integrating examinations of colony, corallite, and subcorallite morphology with the molecular sequence data that have proliferated in the last decade, many taxa spread across the scleractinian tree of life have been incorporated into a rigorous classification underpinned by greater phylogenetic understanding. This monograph focuses on one of the most challenging clades recovered to date – its disarray epitomized by the informal name ‘Bigmessidae’. This group of predominantly Indo-Pacific species previously comprised families Merulinidae, Faviidae, Pectiniidae, and Trachyphylliidae, but in a recent study these have been incorporated within Merulinidae. We studied 84 living merulinid species by examining morphological traits at three different scales of coral skeletal structure − macromorphology, micromorphology, and microstructure − to construct a morphological matrix comprising 44 characters. Data were analysed via maximum parsimony and also transformed onto a robust molecular phylogeny under the parsimony and maximum likelihood criteria. Comparisons amongst morphological character types suggest that although many characters at every scale are homoplastic, some to a greater extent than others, several can aid in distinguishing genus-level clades. Our resulting trees and character analyses form the basis of a revised classification that spans a total of 139 species contained within 24 genera. The tree topologies necessitate the synonymization of Barabattoia as Dipsastraea, and Phymastrea as Favites. Furthermore, Astrea and Coelastrea are resurrected, and one new genus, Paramontastraea Huang & Budd gen. nov., is described. All the genera in Merulinidae, along with the monotypic Montastraeidae and Diploastraeidae, are diagnosed based on the characters examined. The integrative classification system proposed here will form the framework for more accurate biodiversity estimates and guide the taxonomic placement of extinct species. © 2014 The Linnean Society of London
    Zoological Journal of the Linnean Society 06/2014; 171(2). DOI:10.1111/zoj.12140 · 2.72 Impact Factor
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    ABSTRACT: Explaining patterns of commonness and rarity is fundamental for understanding and managing biodiversity. Consequently, a key test of biodiversity theory has been how well ecological models reproduce empirical distributions of species abundances. However, ecological models with very different assumptions can predict similar species abundance distributions, whereas models with similar assumptions may generate very different predictions. This complicates inferring processes driving community structure from model fits to data. Here, we use an approximation that captures common features of “neutral” biodiversity models—which assume ecological equivalence of species—to test whether neutrality is consistent with patterns of commonness and rarity in the marine biosphere. We do this by analyzing 1,185 species abundance distributions from 14 marine ecosystems ranging from intertidal habitats to abyssal depths, and from the tropics to polar regions. Neutrality performs substantially worse than a classical nonneutral alternative: empirical data consistently show greater heterogeneity of species abundances than expected under neutrality. Poor performance of neutral theory is driven by its consistent inability to capture the dominance of the communities’ most-abundant species. Previous tests showing poor performance of a neutral model for a particular system often have been followed by controversy about whether an alternative formulation of neutral theory could explain the data after all. However, our approach focuses on common features of neutral models, revealing discrepancies with a broad range of empirical abundance distributions. These findings highlight the need for biodiversity theory in which ecological differences among species, such as niche differences and demographic trade-offs, play a central role.
    Proceedings of the National Academy of Sciences 05/2014; early edition. DOI:10.1073/pnas.1406664111 · 9.81 Impact Factor
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    Science 05/2014; 344(6186):814-815. DOI:10.1126/science.344.6186.814 · 31.48 Impact Factor
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    Science 05/2014; 344(6186):814-815. · 31.48 Impact Factor
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    ABSTRACT: Over 95% of all metazoan (animal) species comprise the “invertebrates,” but very few genomes from these organisms have been sequenced. We have, therefore, formed a “Global Invertebrate Genomics Alliance” (GIGA). Our intent is to build a collaborative network of diverse scientists to tackle major challenges (e.g., species selection, sample collection and storage, sequence assembly, annotation, analytical tools) associated with genome/transcriptome sequencing across a large taxonomic spectrum. We aim to promote standards that will facilitate comparative approaches to invertebrate genomics and collaborations across the international scientific community. Candidate study taxa include species from Porifera, Ctenophora, Cnidaria, Placozoa, Mollusca, Arthropoda, Echinodermata, Annelida, Bryozoa, and Platyhelminthes, among others. GIGA will target 7000 noninsect/nonnematode species, with an emphasis on marine taxa because of the unrivaled phyletic diversity in the oceans. Priorities for selecting invertebrates for sequencing will include, but are not restricted to, their phylogenetic placement; relevance to organismal, ecological, and conservation research; and their importance to fisheries and human health. We highlight benefits of sequencing both whole genomes (DNA) and transcriptomes and also suggest policies for genomic-level data access and sharing based on transparency and inclusiveness. The GIGA Web site (http://giga.nova.edu) has been launched to facilitate this collaborative venture.
    Journal of Heredity 01/2014; 105(1):1-18. · 1.97 Impact Factor
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    ABSTRACT: Over 95% of all metazoan (animal) species comprise the “invertebrates,” but very few genomes from these organisms have been sequenced. We have, therefore, formed a “Global Invertebrate Genomics Alliance” (GIGA). Our intent is to build a collaborative network of diverse scientists to tackle major challenges (e.g., species selection, sample collection and storage, sequence assembly, annotation, analytical tools) associated with genome/transcriptome sequencing across a large taxonomic spectrum. We aim to promote standards that will facilitate comparative approaches to invertebrate genomics and collaborations across the international scientific community. Candidate study taxa include species from Porifera, Ctenophora, Cnidaria, Placozoa, Mollusca, Arthropoda, Echinodermata, Annelida, Bryozoa, and Platyhelminthes, among others. GIGA will target 7000 noninsect/nonnematode species, with an emphasis on marine taxa because of the unrivaled phyletic diversity in the oceans. Priorities for selecting invertebrates for sequencing will include, but are not restricted to, their phylogenetic placement; relevance to organismal, ecological, and conservation research; and their importance to fisheries and human health. We highlight benefits of sequencing both whole genomes (DNA) and transcriptomes and also suggest policies for genomic-level data access and sharing based on transparency and inclusiveness. The GIGA Web site (http://giga.nova.edu) has been launched to facilitate this collaborative venture.
    Journal of Heredity 12/2013; 105(1):1-18. · 1.97 Impact Factor
  • C Hurt, K Silliman, A Anker, N Knowlton
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    ABSTRACT: Divergent natural selection driven by competition for limited resources can promote speciation, even in the presence of gene flow. Reproductive isolation is more likely to result from divergent selection when the partitioned resource is closely linked to mating. Obligate symbiosis and host fidelity (mating on or near the host) can provide this link, creating ideal conditions for speciation in the absence of physical barriers to dispersal. Symbiotic organisms often experience competition for hosts, and host fidelity ensures that divergent selection for a specific host or host habitat can lead to speciation and strengthen pre-existing reproductive barriers. Here, we present evidence that diversification of a sympatric species complex occurred despite the potential for gene flow and that partitioning of host resources (both by species and by host habitat) has contributed to this diversification. Four species of snapping shrimps (Alpheus armatus, A. immaculatus, A. polystictus and A. roquensis) are distributed mainly sympatrically in the Caribbean, while the fifth species (A. rudolphi) is restricted to Brazil. All five species are obligate commensals of sea anemones with a high degree of fidelity and ecological specificity for host species and habitat. We analysed sequence data from 10 nuclear genes and the mitochondrial COI gene in 11-16 individuals from each of the Caribbean taxa and from the only available specimen of the Brazilian taxon. Phylogenetic analyses support morphology-based species assignments and a well-supported Caribbean clade. The Brazilian A. rudolphi is recovered as an outgroup to the Caribbean taxa. Isolation-migration coalescent analysis provides evidence for historical gene flow among sympatric sister species. Our data suggest that both selection for a novel host and selection for host microhabitat may have promoted diversification of this complex despite gene flow.
    Molecular Ecology 07/2013; DOI:10.1111/mec.12398 · 5.84 Impact Factor
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    ABSTRACT: Benefits humans rely on from the ocean – marine ecosystem services – are increasingly vulnerable under future climate. This paper reviews how three valued services have, and will continue to, shift under climate change: (1) capture fisheries, (2) food from aquaculture, and (3) protection from coastal hazards such as storms and sea-level rise. Climate adaptation planning is just beginning for fisheries, aquaculture production, and risk mitigation for coastal erosion and inundation. A few examples are highlighted, showing the promise of considering multiple ecosystem services in developing approaches to adapt to sea-level rise, ocean acidification, and rising sea temperatures.Ecosystem-based adaptation in fisheries and along coastlines and changes in aquaculture practices can improve resilience of species and habitats to future environmental challenges. Opportunities to use market incentives – such as compensation for services or nutrient trading schemes – are relatively untested in marine systems. Relocation of communities in response to rising sea levels illustrates the urgent need to manage human activities and investments in ecosystems to provide a sustainable flow of benefits in the face of future climate change.
    Marine Policy 07/2013; 40:154–159. DOI:10.1016/j.marpol.2013.01.009 · 2.62 Impact Factor
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    Conservation Biology 05/2013; 27(5). DOI:10.1111/cobi.12080 · 4.32 Impact Factor
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    ABSTRACT: Ancient DNA (aDNA) provides powerful evidence for detecting the genetic basis for adaptation to environmental change in many taxa. Among the greatest of changes in our biosphere within the last century is rapid anthropogenic ocean warming. This phenomenon threatens corals with extinction, evidenced by the increasing observation of widespread mortality following mass bleaching events. There is some evidence and conjecture that coral-dinoflagellate symbioses change partnerships in response to changing external conditions over ecological and evolutionary timescales. Until now, we have been unable to ascertain the genetic identity of Symbiodinium hosted by corals prior to the rapid global change of the last century. Here, we show that Symbiodinium cells recovered from dry, century old specimens of 6 host species of octocorals contain sufficient DNA for amplification of the ITS2 subregion of the nuclear ribosomal DNA, commonly used for genotyping within this genus. Through comparisons with modern specimens sampled from similar locales we show that symbiotic associations among several species have been static over the last century, thereby suggesting that adaptive shifts to novel symbiont types is not common among these gorgonians, and perhaps, symbiotic corals in general.
    PLoS ONE 02/2013; 8(2):e55057. DOI:10.1371/journal.pone.0055057 · 3.53 Impact Factor
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    ABSTRACT: The United States is an ocean nation—our past, present, and future are inextricably connected to and dependent on oceans and marine resources. Marine ecosystems provide many important services, including jobs, food, transportation routes, recreational opportunities, health benefits, climate regulation, and cultural heritage that affect people, communities, and economies across the United States and internationally every day. There is a wealth of information documenting the strong linkages between the planet’s climate and ocean systems, as well as how changes in the climate system can produce changes in the physical, chemical, and biological characteristics of ocean ecosystems on a variety of spatial and temporal scales. There is relatively little information on how these climate-driven changes in ocean ecosystems may have an impact on ocean services and uses, although it is predicted that ocean-dependent users, communities, and economies will likely become increasingly vulnerable in a changing climate. Based on our current understanding and future projections of the planet’s ocean systems, it is likely that marine ecosystems will continue to be affected by anthropogenic-driven climate change into the future. This review describes how these impacts are set in motion through a suite of changes in ocean physical, chemical, and biological components and processes in U.S. waters and the significant implications of these changes for ocean users and the communities and economies that depend on healthy oceans. U.S. international partnerships, management challenges, opportunities, and knowledge gaps are also discussed. Effectively preparing for and responding to climate-driven changes in the ocean will require both limiting future change through reductions of greenhouse gases and adapting to the changes that we can no longer avoid.
    Oceanography and marine biology 01/2013; 51:71-192. · 11.08 Impact Factor
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    ABSTRACT: Molecular analyses are transforming our understanding of the evolution of scleractinian corals and conflict with traditional classification, which is based on skeletal morphology. A new classification system, which integrates molecular and morphological data, is essential for documenting patterns of biodiversity and establishing priorities for marine conservation, as well as providing the morphological characters needed for linking present-day corals with fossil species. The present monograph is the first in a series whose goal is to develop such an integrated system. It addresses the taxonomic relationships of 55 Recent zooxanthellate genera (one new) in seven families (one new), which were previously assigned to the suborder Faviina (eight genera are transferred to incertae sedis). The present monograph has two objectives. First, we introduce the higher-level classification system for the 46 genera whose relationships are clear. Second, we formally revise the taxonomy of those corals belonging to the newly discovered family-level clade (restricted today to the western Atlantic and Caribbean regions); this revised family Mussidae consists of ten genera (one of which is new) and 26 species that were previously assigned to the 'traditional' families Faviidae and Mussidae. To guide in discovering morphologic characters diagnostic of higher-level taxa, we mapped a total of 38 morphologic characters [19 macromorphology, eight micromorphology, 11 microstructure] onto a molecular tree consisting of 67 species [22 Indo-Pacific and seven Atlantic species in the traditional family Faviidae; 13 Indo-Pacific and ten Atlantic species in the traditional family Mussidae; 13 species in the traditional families Merulinidae (5), Pectiniidae (7), and Trachyphylliidae (1); two Atlantic species of traditional Montastraea], and trace character histories using parsimony. To evaluate the overall effectiveness of morphological data in phylogeny reconstruction, we performed morphology-based phylogenetic analyses using 27 (80 states) of the 38 characters, and compared morphological trees with molecular trees. The results of the ancestral state reconstructions revealed extensive homoplasy in almost all morphological characters. Family-and subfamily-level molecular clades [previously identified as XVII-XXI] are best distinguished on the basis of the shapes of septal teeth and corresponding microstructure. The newly revised family Mussidae (XXI) has septal teeth with regular pointed tips (a symplesiomorphy) and a stout blocky appearance. It has two subfamilies, Mussinae and Faviinae. The subfamily Mussinae is distinguished by spine-shaped teeth and widely spaced costoseptal clusters of calcification centres. The subfamily Faviinae is distinguished by blocky, pointed tricorne or paddle-shaped teeth with elliptical bases, transverse structures such as carinae that cross the septal plane, and well-developed aligned granules. Defining diagnostic characters for the broader data set is more challenging. In analyses of taxonomic subsets of the data set that were defined by clade, morphological phylogenetic analyses clearly distinguished the families Mussidae (XXI) and Lobophylliidae (XIX), as well as the two subfamilies of Mussidae (Mussinae, Faviinae), with one exception (Homophyllia australis). However, analyses of the entire 67-species data set distinguished the family Lobophylliidae (XIX), but not the Merulinidae (XVII) and not the newly defined Mussidae (XXI), although the subfamily Mussinae was recovered as monophyletic. Some lower-level relationships within the Merulinidae (XVII) agree with molecular results, but this particular family is especially
    Zoological Journal of the Linnean Society 11/2012; 166(166):466-529. DOI:10.1111/j.1096-3642.2012.00855.x · 2.72 Impact Factor
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    ABSTRACT: In broadcast spawners, prezygotic reproductive isolation depends on differences in the spatial and temporal patterns of gamete release and gametic incompatibility. Typically, gametic incompatibility is measured in no-choice crosses, but conspecific sperm precedence (CSP) can prevent hybridization in gametes that are compatible in the absence of sperm competition. Broadcast spawning corals in the Montastraea annularis species complex spawn annually on the same few evenings. Montastraea franksi spawns an average of 110 min before M. annularis, with a minimum gap of approximately 40 min. Gametes are compatible in no-choice heterospecific assays, but it is unknown whether eggs exhibit choice when in competition. Hybridization depends on either M. franksi eggs remaining unfertilized and in proximity to M. annularis when the latter species spawns or M. franksi sperm remaining in sufficient viable concentrations when M. annularis spawns. We found that the eggs of the early spawning M. franksi demonstrate strong CSP, whereas CSP appears to be lacking for M. annularis eggs. This study provides evidence of diverging gamete affinities between these recently separated species and suggests for the first time that selection may favour CSP in earlier spawning species when conspecific sperm is diluted and aged and is otherwise at a numeric and viability disadvantage with heterospecific sperm.
    Journal of Evolutionary Biology 10/2012; 25(12). DOI:10.1111/j.1420-9101.2012.02625.x · 3.48 Impact Factor

Publication Stats

10k Citations
742.15 Total Impact Points

Institutions

  • 2008–2015
    • Smithsonian Institution
      • Department of Invertebrate Zoology
      Washington, Washington, D.C., United States
  • 2012
    • Academia Sinica
      • Biodiversity Research Center
      T’ai-pei, Taipei, Taiwan
  • 2000–2012
    • University of California, San Diego
      • • Center for Marine Biodiversity and Conservation
      • • Marine Biology Research Division
      San Diego, California, United States
  • 1992–2008
    • Smithsonian Tropical Research Institute
      Ciudad de Panamá, Panamá, Panama
  • 2002–2006
    • San Diego State University
      • Department of Biology
      San Diego, California, United States
    • Natural History Museum, London
      Londinium, England, United Kingdom
  • 2001–2003
    • National University (California)
      San Diego, California, United States
  • 1995
    • Australian Institute of Marine Science
      Townsville, Queensland, Australia