W. John Kress's research while affiliated with Harvard University and other places

Publications (288)

Article
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Premise: Hedychium J.Koenig (Zingiberaceae) is endemic to the Indo-Malayan Realm and is known for its colorful and fragrant flowers. Historically, two different pollination syndromes characterize Hedychium: diurnal or bird pollination and nocturnal or moth pollination. In this study we aim to understand the evolution of nocturnal and diurnal flowe...
Article
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The community of biologists has been eager to realize the promise of DNA barcodes since the concept of a rapid method for genetic identification of species was first proposed in 2003 [...]
Article
The relationships between biome shifts and global environmental changes in temperate zone habitats have been extensively explored; yet, the historical dynamics of taxa found in the tropical rain forest (TRF) remain poorly known. This study aims to reconstruct the relationships between tropical rain forest shifts and global environmental changes thr...
Article
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DNA barcoding has transformed the fields of ecology, evolution, and conservation by providing a rapid and effective tool for species identification. The growth of DNA barcodes as a resource for biologists has followed advances in computational and sequencing technology that have enabled high-throughput barcoding applications. The global DNA barcode...
Article
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Many well-studied animal species use conspicuous, repetitive signals that attract both mates and predators. Orthopterans (crickets, katydids, and grasshoppers) are renowned for their acoustic signals. In Neotropical forests, however, many katydid species produce extremely short signals, totaling only a few seconds of sound per night, likely in resp...
Article
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The Indo-Malayan Realm is a biogeographic realm that extends from the Indian Subcontinent to the islands of Southeast Asia (Malay Archipelago). Despite being megadiverse, evolutionary hypotheses explaining taxonomic diversity in this region have been rare. Here, we investigate the role of geoclimatic events such as Himalayan orogeny and monsoon int...
Article
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The impact of humans on Earth's biodiversity varies across the Tree of Life. The extirpation and extinction of species is often determined by compatibility with human activities. Here we classify, where data are available, a significant portion (~30%) of vascular plant species as winners or losers with respect to this compatibility and show that cu...
Article
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November 2020 marked 2 y since the launch of the Earth BioGenome Project (EBP), which aims to sequence all known eukaryotic species in a 10-y timeframe. Since then, significant progress has been made across all aspects of the EBP roadmap, as outlined in the 2018 article describing the project’s goals, strategies, and challenges (1). The launch phas...
Article
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The Earth BioGenome Project (EBP) is an audacious endeavor to obtain whole-genome sequences of representatives from all eukaryotic species on Earth. In addition to the project’s technical and organizational challenges, it also faces complicated ethical, legal, and social issues. This paper, from members of the EBP’s Ethical, Legal, and Social Issue...
Article
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Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there on the origins of novelty and the con...
Article
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Green plants play a fundamental role in ecosystems, human health, and agriculture. As de novo genomes are being generated for all known eukaryotic species as advocated by the Earth BioGenome Project, increasing genomic information on green land plants is essential. However, setting standards for the generation and storage of the complex set of geno...
Preprint
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PREMISE Hedychium J.Koenig (ginger lilies: Zingiberaceae) is endemic to the Indo-Malayan Realm (IMR) and is known for its fragrant flowers. Two different pollination syndromes characterize the genus: diurnal or bird pollination and nocturnal or moth pollination systems. To date, no attempt has been undertaken to understand the evolution of floral t...
Article
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Ecology cannot yet fully explain why so many tree species coexist in natural communities such as tropical forests. A major difficulty is linking individual-level processes to community dynamics. We propose a combination of tree spatial data, spatial statistics and dynamical theory to reveal the relationship between spatial patterns and population-l...
Article
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DNA barcoding is an emerging molecular identification and classification technology that has been applied to medicinal plants since 2008. The application of this technique has greatly ensured the safety and effectiveness of medicinal materials. In this paper, we review the application of DNA barcoding and some related technologies over the past 10...
Chapter
Plants have been used to support healthy lifestyles throughout the world for thousands of years. Traditionally, consumer experience has driven the utility of specific plants through trusted, localized supply chains that were accountable in small regionalized communities. Contemporary supply chains are global, and very complex as botanical ingredien...
Article
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DNA barcoding is a valuable tool to support species identification with broad applications from traditional taxonomy, ecology, forensics, food analysis, and environmental science. We introduce Microfluidic Enrichment Barcoding (MEBarcoding) for plant DNA Barcoding, a cost-effective method for high-throughput DNA barcoding. MEBarcoding uses the Flui...
Article
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Green plants provide the foundation for the structure, function, and interactions among organisms in both tropical and temperate zones. To date, many investigations have revealed patterns and mechanisms that generate plant diversity at various scales and from diverse ecological perspectives. However, in the era of climate change, anthropogenic dist...
Article
In the Anthropocene, natural resource management approaches, including forestry, have been incorporating cross-disciplinary, multi-functional, and highly technological endeavors. Urban forestry has emerged as a way of adapting natural resource management to city settings. Here we propose a research agenda for more integrative urban forestry with du...
Article
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The Earth BioGenome Project (EBP) is a recently proposed international collaborative research initiative that aims to sequence the genomes of all ~1.5 million known eukaryotic species on Earth in 10 years. The project has been called “biology’s moonshot” because of its potential to transform our understanding of life on Earth, to provide new tools...
Article
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Applications of DNA barcoding include identifying species, inferring ecological and evolutionary relationships between species, and DNA metabarcoding. These applications require reference libraries that are not yet available for many taxa and geographic regions. We collected, identified, and vouchered plant specimens from Mpala Research Center in L...
Article
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Disturbance plays a key role in shaping forest composition and diversity. We used a community phylogeny and long-term forest dynamics data to investigate biotic and abiotic factors shaping tropical forest regeneration following both human and natural disturbance. Specifically, we examined shifts in seedling phylogenetic and functional (i.e., seed m...
Article
Many cases of rapid evolutionary radiations in plant and animal lineages are known; however phylogenetic relationships among these lineages have been difficult to resolve by systematists. Increasing amounts of genomic data have been sequentially applied in an attempt to resolve these radiations, dissecting their evolutionary patterns into a series...
Article
The mobile iPhone app Leafsnap, designed for the automatic identification of 220 tree species from the northeastern United States, was released to the public in 2011. In the first 3 years of its use, the app was downloaded by more than 1,500,000 users from five continents and 181 countries who recorded over 3,056,684 leaf images. The high levels of...
Article
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Increasing our understanding of Earth’s biodiversity and responsibly stewarding its resources are among the most crucial scientific and social challenges of the new millennium. These challenges require fundamental new knowledge of the organization, evolution, functions, and interactions among millions of the planet’s organisms. Herein, we present a...
Article
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Trade-offs among plant functional traits indicate diversity in plant strategies of growth and survival. The leaf economics spectrum (LES) reflects a trade-off between short-term carbon gain and long-term leaf persistence. A related trade-off, between foliar growth and anti-herbivore defense, occurs among plants growing in contrasting resource regim...
Conference Paper
Background: Plant DNA barcoding routinely uses more than one locus for species identification (rbcL, matK, psbA-trnH, and nrDNA ITS), which significantly increases sample handling, preparation time, and costs. Different primer pair combinations (ca. twelve) are necessary to amplify DNA barcode sequences from all major lineages of vascular plants, f...
Article
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Interactions among neighbors influence the structure of communities of sessile organisms. Closely related species tend to share habitat and resource requirements and to interact with the same mutualists and natural enemies so that the strength of interspecific interactions tends to decrease with evolutionary divergence time. Nevertheless, the degre...
Article
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Actions and priorities to connect the global community of plant scientists with the world's changing societies are today more imperative than ever. Environmental degradation, unsustainable resource use, and biodiversity loss all require integrated, collaborative solutions.
Article
Geographic isolation is the first step in insect herbivore diet specialization. Such specialization is postulated to increase insect fitness, but may simultaneously reduce insect ability to colonize novel hosts. During the Paleocene-Eocene, plants from the order Zingiberales became isolated either in the Paleotropics or in the Neotropics. During th...
Article
DNA barcodes have provided a new biological tool for organismal biologists to increase their understanding of the natural world. Over the last decade four plant DNA barcode markers, rbcL, matK, trnH-psbA, and ITS2, have been developed, tested, and used to address basic questions in systematics, ecology, evolutionary biology and conservation, includ...
Article
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DNA barcoding is a commonly used bio-technology in multiple disciplines including biology, environmental science, forensics and inspection, etc. Forest dynamic plots provide a unique opportunity to carry out large-scale, comparative, and multidisciplinary research for plant DNA barcoding. The paper concisely reviewed four previous progresses in Chi...
Article
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Closer collaboration among ecologists, systematists, and evolutionary biologists working in tropical forests, centred on studies within long-term permanent plots, would be highly beneficial for their respective fields. With a key unifying theme of the importance of vouchered collection and precise identification of species, especially rare ones, we...
Article
Premise of research. Rain forest ecosystems globally are synonymous with biodiversity, yet these vegetation communities vary widely in structure and composition. Historical biogeography and environment are thought to have significantly impacted Australian rain forest diversity and composition. Rain forest in Australia is extensively fragmented, and...
Data
PCR formulas. List of PCR mixtures and thermal profiles used for each locus. (DOCX)
Data
Supporting information. Specimen data and field observations. (DOCX)
Article
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Studies of forest dynamics plots (FDPs) have revealed a variety of negative density-dependent (NDD) demographic interactions, especially among conspecific trees. These interactions can affect growth rate, recruitment and mortality, and they play a central role in the maintenance of species diversity in these complex ecosystems. Here we use an equal...
Article
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The taxonomic status of a single island, narrow range endemic plant species from Palau, Micronesia (Timonius salsedoi) was assessed using DNA barcode markers, additional plastid loci, and morphology in order to verify its conservation status. DNA barcode loci distinguished T. salsedoi from all other Timonius species sampled from Palau, and were sup...
Data
DNA sequence list. List of GenBank accession numbers for all nucleotide sequences generated and used in the analysis. (XLSX)
Article
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Australia's Great Sandy Region is of international significance containing two World Heritage areas and patches of rainforest growing on white sand. Previous broad-scale analysis found the Great Sandy biogeographic subregion contained a significantly more phylogenetically even subset of species than expected by chance contrasting with rainforest on...
Data
Summary Table of details for all new additions to the SEQld rainforest barcode phylogeny. The species name, Genbank accession codes for each of the three DNA barcode markers used as well as the Queensland Herbarium (BRI) collector name or number which is used by BRI as specimen identifier as well as the BRI accession number where available at time...
Data
Summary of nine Orders, dates used and the reference pertaining to each (Shapcott et al., 2015) used to date the SEQ rainforest phylogenetic tree in the PATHd8 program. Where MRCA is the most recent common ancestor of the two taxa that span the clade being dated on the tree. (DOCX)
Article
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The Spectranomics approach to tropical forest remote sensing has established a link between foliar reflectance spectra and the phylogenetic composition of tropical canopy tree communities vis-à-vis the taxonomic organization of biochemical trait variation. However, a direct relationship between phylogenetic affiliation and foliar reflectance spectr...
Data
Statistical comparison of nectar volume, nectar concentration, number of bracts per inflorescence, and corolla length between plants of the red and yellow morphs of H. caribaea used in our experiments in 2012, 2013, and 2015. (DOC)
Data
Proportions (untransformed) of male and female visits to the yellow morph of H. caribaea alone and in competition. (XLS)
Data
Dye particles and pollen grains received versus flower order. (XLS)
Data
Proportions (untransformed) of dye transfers within Heliconia morphs for males alone, females alone, and males and females in competition. (XLS)
Data
Mean corolla lengths and mean numbers of dye particles received per plant for analyses of selection on corolla length for males alone, females alone, and males and females in competition. Prior to analysis we standardized corolla length to a mean equal to zero and to a variance equal to one and converted our fitness measure, mean dye particles rece...
Data
Number (Mean ± SE) of dye (open circles) and pollen grains (solid circles) deposited versus flower presentation order. (TIF)
Data
Suitability of powdered dyes as a proxy for pollen grains in Heliconia caribaea. We provide detailed statistics comparing (i) the slopes and intercepts of the regressions of dye particles/pollen grains received versus flower order and (ii) the number of dye particles or pollen grains received for flowers of a given order. (DOC)
Article
The critical thermal maximum (CTmax), the temperature at which motor control is lost in animals, has the potential to determine if species will tolerate global warming. For insects, tolerance to high temperatures decreases with latitude, suggesting that similar patterns may exist along elevational gradients as well. This study explored how CTmax va...
Article
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Carbon sequestration is a major ecosystem service provided by tropical forests. Especially in light of global climate change, understanding the drivers of forest productivity is of critical importance. Although abiotic conditions (e.g., precipitation) are known to influence forest productivity, ecological theory predicts that biodiversity may also...
Data
The breeding system of Zingiber densissimum. (DOC)
Data
A ventral pollinator (Amegilla zonata)’s foraging behaviour. The figure shows how pollen grains from the labellum of a flower are deposited on the stigma of other flowers. A ventral pollinator is retreating from a flower after probed nectar, with numerous pollen grains on the tongue, the head and forelegs of the pollinator. These pollen grains are...
Data
Pollination efficiency and pollen removal. (DOC)
Article
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Background and aims: Secondary pollen presentation (SPP), a floral mechanism of reproductive adaptation, has been described for more than 200 years, with nine types SPP recorded. However, few studies have been done experimentally to link the floral mechanism of SPP to its functional roles in pollination process. This study aims to describe a new S...
Article
Understanding how the relative importance of different community assembly processes changes during secondary succession of diverse systems remains elusive. Functional and phylogenetic approaches that place species along continuous axes of niche differentiation and evolutionary relatedness, however, are deepening our understanding of the mechanisms...
Article
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To determine how well DNA barcodes from the chloroplast region perform in forest dynamics plots (FDPs) from global CTFS-ForestGEO network, we analyzed DNA barcoding sequences of 1277 plant species from a wide phylogenetic range (3 FDPs in tropics, 5 in subtropics and 5 in temperate zone) and compared the rates of species discrimination (RSD). We qu...
Article
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Niche partitioning facilitates species coexistence in a world of limited resources, thereby enriching biodiversity. For decades, biologists have sought to understand how diverse assemblages of large mammalian herbivores (LMH) partition food resources. Several complementary mechanisms have been identified, including differential consumption of grass...
Article
Considerable debate focuses on whether invasive species establish and become abundant by being functionally and phylogenetically distinct from native species, leading to a host of invasion-specific hypotheses of community assembly. Few studies, however, have quantitatively assessed whether similar patterns of phylogenetic and functional similarity...