W. John Kress’s research while affiliated with Smithsonian Institution and other places

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Publications (305)


Fig. 1 | DSI is "mixed together" in a global dataset regardless of UN fora. Left side of the diagram: taxonomic distribution across 8 phylogenetic groups organized in a cladogram based on their phylogeny relative to the last universal common ancestor, LUCA and 2 groups without taxonomic information. "Virus" and "Other eukaryota" are non-monophyletic groups. The dashed and faded line connecting viruses to LUCA indicates uncertainties in the phylogenetic relationship of the group. The thickness of the lines connecting the two sides of the diagram is proportional to the number of sequences assigned to each taxonomic category and UN fora. Right side of the diagram: assignment of sequences to relevant UN fora based on absolute number of sequence entries in the database. DSI are color-coded indicating whether a country tag was explicitly indicated in the ENA metadata of each individual entry (yellow) as country of origin or if the tag was missing (blue). In parentheses, the percentage relative to the total dataset. See Supplementary Note 1 for details. Created in BioRender. Faggionato, D. (2024) BioRender.com/w04m281.
Fig. 2 | Two proposed models for harmonization between UN fora. A Option 1 -One house with one door and four windows. B Option 2 -One house with four doors and four windows. Inside the house lies the open database ecosystem with the DSI of relevance to all different UN fora without jurisdictional sub-division. Doors indicate trigger points for monetary benefits and windows indicate how the monetary benefits will be delivered to the relevant UN fora. The house represents the DSI benefit-sharing mechanism and not database infrastructures. Created in BioRender. Internationalisation, S. (2024) BioRender.com/h63v844 (A) and BioRender.com/u09u989 (B).
Fig. 3 | Flowcharts of two possible scenarios for benefit-sharing distribution under Option 2. Scenario A: development of a new variety of an ITPGRFA Annex I plant that is resistant to a fungus that falls under the CBD. Although DSI of both the Annex I plant and the CBD-relevant fungi have been used, the DSI-related benefits resulting from the use of the new plant variety will stream to the ITPGRFA fund. In scenario B: identification of a bacterial strain in soil that falls under the scope of the CBD that promotes the growth of an ITPGRFA Annex I plant under stress conditions. Although DSI of both the bacterium and the plant have been instrumental to the discovery, the DSI-related benefits generated by the use of the bacteria strain will stream to the CBD fund. DSI Digital Sequence Information, GR physical Genetic Resource. Created in BioRender. Faggionato, D. (2024) BioRender.com/m52p511 (A) and BioRender.com/u21i840 (B).
Harmonize rules for digital sequence information benefit-sharing across UN frameworks
  • Article
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October 2024

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75 Reads

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W John Kress

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As multiple UN fora develop parallel rules for sharing benefits from digital sequence information, we urge better coordination. International policymakers should focus on harmonizing new benefit-sharing rules to ensure open access to data, database interoperability, and better benefit-sharing outcomes.

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Demography of the understory herb Heliconia acuminata (Heliconiaceae) in an experimentally fragmented tropical landscape

November 2023

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27 Reads

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1 Citation

Habitat fragmentation remains a major focus of research by ecologists decades after being put forward as a threat to the integrity of ecosystems. While studies have documented myriad biotic changes in fragmented landscapes, including the local extinction of species from fragments, the demographic mechanisms underlying these extinctions are rarely known. However, many of them—especially in lowland tropical forests—are thought to be driven by one of two mechanisms: (1) reduced recruitment in fragments resulting from changes in the diversity or abundance of pollinators and seed dispersers or (2) increased rates of individual mortality in fragments due to dramatically altered abiotic conditions, especially near fragment edges. Unfortunately, there have been few tests of these potential mechanisms due to the paucity of long‐term and comprehensive demographic data collected in both forest fragments and continuous forest sites. Here we report 11 years (1998–2009) of demographic data from populations of the Amazonian understory herb Heliconia acuminata (LC Rich.) found at Brazil's Biological Dynamics of Forest Fragments Project (BDFFP). The data set comprises >66,000 plant × year records of 8586 plants, including 3464 seedlings established after the first census. Seven populations were in experimentally isolated fragments (one in each of four 1‐ha fragments and one in each of three 10‐ha fragments), with the remaining six populations in continuous forest. Each population was in a 50 × 100 m permanent plot, with the distance between plots ranging from 500 m to 60 km. The plants in each plot were censused annually, at which time we recorded, identified, marked, and measured new seedlings, identified any previously marked plants that died, and recorded the size of surviving individuals. Each plot was also surveyed four to five times during the flowering season to identify reproductive plants and record the number of inflorescences each produced. These data have been used to investigate topics ranging from the way fragmentation‐related reductions in germination influence population dynamics to statistical methods for analyzing reproductive rates. This breadth of prior use reflects the value of these data to future researchers. In addition to analyses of plant responses to habitat fragmentation, these data can be used to address fundamental questions in plant demography and the evolutionary ecology of tropical plants and to develop and test demographic models and tools. Though we welcome opportunities to collaborate with interested users, there are no restrictions on the use of this data set. However, we do request that those using the data for teaching or research purposes inform us of how they are doing so and cite this paper and the data archive when appropriate. Any publication using the data must also include a BDFFP Technical Series Number in the Acknowledgments. Authors can request this series number upon the acceptance of their article by contacting the BDFFP's Scientific Coordinator or E. M. Bruna.


Figure 2. The scaling of the probability of extinction. a, The extinction probability í µí±ƒí µí±ƒ 0 í µí±›í µí±› (í µí±¡í µí±¡, í µí±í µí± 0 )
Figure 3. Reinterpretation of the invasion criterion to consider demographic stochsticity. We start each species with N0 = 50 individuals, all other species are assumed to be quasi-stationary, and we used the birth-death model (equations 12, 13) parameterized for 720 species of the 21 ForestGEO plots to estimate the probability P0(t, 50) of local extinction after t = 200 timesteps (1000 years). a, Geographic variation in the mean reduction of the extinction probability due to the spatial crowding mechanism for scenario 1 (where con-and heterospecifics compete equally) relative to the corresponding neutral model (eq. 2a). b, Geographic variation in the proportion of species that behave near-neutral for scenario 1 (i.e., í µí±ƒí µí±ƒ 0 (í µí±¡í µí±¡, 50)/í µí±ƒí µí±ƒ 0
Characteristics of the selected forest plots.
Latitudinal scaling of aggregation with abundance and its consequences for coexistence in species rich forests

May 2023

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557 Reads

The complex spatial structure and dynamics of ecological communities continue to defy explanation by simple principles despite decades of attention from ecologists and theoreticians. For example, the relationship between plant spatial distributions and species coexistence is often challenging to resolve in empirical settings. By analysing the spatial patterns of trees in 21 large forest plots we find a general and strong latitudinal gradient in the relationship between conspecific aggregation and abundance of tree species, with stronger negative abundance-dependency as latitude increases. To derive theoretical expectations for how interactions between multiple spatial pattern and processes can impact species coexistence, we incorporate the observed spatial patterns together with neighbourhood crowding competition into a mathematical model to estimate the local extinction risk of species. Strikingly, we find simple relationships that predict species local extinction risk from their demography and spatial distribution. Compared to a corresponding non-spatial analysis, accounting for spatial patterns reduces the 1000-year extinction risk on average by 52% when species invade from low abundances of 50 individuals. Additionally, based on their current abundances, only 8% of the species had an extinction risk greater than 5%. Our approach opens up new avenues for integrating observed spatial patterns with multiple ecological processes into mathematical theory. Our results demonstrate that emerging spatial patterns can contribute substantially to coexistence in species-rich forests, emphasizing the need to understand the interacting multiple processes under-pinning spatial patterns in greater detail than has previously been appreciated.


Heat tolerance (critical temperature, T15 and temperature at which fluorescence decreases 50%, T50) in 39 Zingiberales at La Selva Biological Station, Costa Rica. Error bars indicate standard deviation, boxes indicate standard error and the central line represents the average for each species. Box colours indicate habitat use for each species: Old growth forest (OGF), secondary forest (SF) and open areas (OA). Asterisks indicate exotic species. Picture of Canna tuerckheimii was provided by JM Chaves‐Fallas. Species abbreviations as in Table S2.
Heat tolerance of Zingiberales families at La Selva Biological Station, Costa Rica. (a) Critical temperature (T15). (b) Temperature at which fluorescence decreases 50% (T50). Plant families: Musaceae (MU), Heliconaceae (HE), Zingiberaceae (ZI), Costaceae (CO), Cannaceae (CA) and Marantaceae (MA). Error bars indicate standard deviation, boxes indicate standard error and the central line represents the average for each plant family. N.S., no significant differences.
Heat tolerance of Zingiberales in open areas, secondary and old growth forest. (a) Critical temperature (T15). (b) Temperature at which fluorescence decreases 50% (T50). Error bars indicate standard deviation, boxes indicate standard error and the central line represents the average for each habitat. N.S., no significant differences.
Heat tolerance of native and exotic Zingiberales at La Selva Biological Station, Costa Rica. (a) Critical temperature (T15). (b) Temperature at which fluorescence decreases 50% (T50). Error bars indicate standard deviation, boxes indicate standard error and the central line is the average for native or exotic species. *p < 0.05. N.S., no significant differences.
Evolutionary history constrains heat tolerance of native and exotic tropical Zingiberales

October 2022

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118 Reads

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2 Citations

Tropical wet forest plants experience relatively stable temperatures throughout the year. However, tropical forests represent a mosaic of habitats characterized by different temperatures. Heat tolerances are expected to be adapted to temperatures specific to their habitats. Although heat tolerance of species sharing similar environments is expected to be similar, it is also possible that heat tolerance is constrained by evolutionary history because closely related species usually display similar physiologies. When exotic species are introduced to novel communities, colonization may be facilitated by their previous adaptation to high temperatures and other physiological, genetic and demographic traits, which may grant them some competitive advantage. Increasing temperatures may represent a strong environmental filter affecting community assembly, and higher heat tolerances could facilitate the persistence of exotic species in novel environments. Using a community of 32 native and 7 exotic Zingiberales species from different tropical habitats in Costa Rica, Central America, we aim to answer the following questions: (a) does evolutionary history constrain heat tolerance? (b) do plants in the same habitat display similar heat tolerances? (c) do the heat tolerances of exotic species differ from those of native species? We measured temperature‐dependent changes in photosynthetic fluorescence to determine the temperature at which the first sign of damage to photosystem II is observed (T15), and the temperature at which the fluorescence of photosystem II is reduced by 50% (T50). Using a community phylogeny, we tested for phylogenetic signal in T15 and T50. In addition, we tested for differences in heat tolerance among Zingiberales from old growth, secondary forests and open areas, as well as between native and exotic species. Our results support (a) a significant phylogenetic signal (Pagel's λ) for both T15 and T50, (b) communities from open areas displayed similar photosynthetic heat tolerance compared to species from old growth and secondary forests, and (c) exotic Zingiberales are marginally tolerant to high temperatures than native species, but only for T15. Our results suggest that evolutionary history constraints heat responses of native and exotic Zingiberales in a warming world. Read the free Plain Language Summary for this article on the Journal blog.


Floral evolution and pollinator diversification in Hedychium : Revisiting Darwin's predictions using an integrative taxonomic approach

July 2022

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377 Reads

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2 Citations

American Journal of Botany

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 flowers, and to test its putative association with lineage diversification in Hedychium. Methods: A molecular tree of Hedychium was used as a scaffold upon which we estimated ancestral character-states, phylogenetic signals, and correlations for certain categorical and continuous floral traits. Further, we employed phylomorphospace and trait-dependent diversification rate estimation analyses to understand phenotypic evolution and associated lineage diversification in Hedychium. Results: Although floral color and size lacked any association with specific pollinators, white or pale flowers were most common in the early branching clades, when compared to bright-colored flowers which were more widely represented in the most derived clade IV. Five categorical and two continuous characters were identified to have informative evolutionary patterns which also emphasized that ecology may have played a critical role in the diversification of Hedychium. Conclusions: From our phylogenetic analyses and ecological observations, we conclude that specializations in pollinator interactions are rare in the hyperdiverse clade IV, thus challenging the role of both moth-specialization and bird-specialization as central factors in the diversification of Hedychium. However, our results also suggest that clade III (predominantly island clade) may show specializations, and future studies should investigate ecological and pollinator interactions, along with inclusion of new traits such as floral fragrance and anthesis time. This article is protected by copyright. All rights reserved.



Historical biogeography of the gingers and its implications for shifts in tropical rain forest habitats

May 2022

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243 Reads

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7 Citations

Journal of Biogeography

Aim 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 through the patterns of historical biogeography of a pantropical family of monocots, the Zingiberaceae. Location Global. Taxon Zingiberaceae. Methods We sampled DNA sequences (nrITS, trn K, trn L‐ trn F and psb A‐ trn H) from GenBank for 77% of the genera, including 30% of species, in the Zingiberaceae. Global fossil records of the Zingiberaceae were collected from literatures. Rates of speciation, extinction and diversification were estimated based on phylogenetic data and fossil records through methods implemented in BAMM. Ancestral ranges were estimated using single‐tree BioGeoBEARS and multiple‐trees BioGeoBEARS in RASP. Dispersal rate through time and dispersal rate among regions were calculated in R based on the result of ancestral estimation. Results The common ancestor of the Zingiberaceae likely originated in northern Africa during the mid‐Cretaceous, with later dispersal to the Asian tropics. Indo‐Burma, rather than Malesia, was likely a provenance of the common ancestor of Alpinioideae–Zingiberoideae. Several abrupt shifts of evolutionary rates from the Palaeocene were synchronized with sudden global environmental changes. Main conclusions Integrating phylogenetic patterns with fossil records suggests that the Zingiberaceae dispersed to Asia through drift of the Indian Plate from Africa in the late Palaeocene. Formation of island chains, land corridors and warming temperatures facilitated the emigration of the Zingiberaceae to a broad distribution across the tropics. Moreover, dramatic fluctuations of the speciation rate of Zingiberoideae appear to have been synchronized with global climate fluctuations. In general, the evolutionary history of the Zingiberaceae broadens our understanding of the association between TRF shifts in distribution and past global environmental changes, especially the origin of TRF in Southeast Asia.



Figure 1. Numbers of species and DNA barcodes across the Tree of Life. The number of species in
The Expanding Role of DNA Barcodes: Indispensable Tools for Ecology, Evolution, and Conservation

March 2022

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551 Reads

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79 Citations

Diversity

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 database is expanding to represent the diversity of species on Earth thanks to efforts by international consortia and expanding biological collections. Today, DNA barcoding is instrumental in advancing our understanding of how species evolve, how they interact, and how we can slow down their extirpation and extinction. This review focuses on current applications of DNA barcode sequences to address fundamental lines of research, as well as new and expanding applications of which DNA barcoding will play a central role.


Citations (66)


... According to Xie et al. (2022), it has various characteristics resulting from strictly cultural aspects. Therefore, preserving the forests that host the greatest heliconia diversity is a very important task (Benítez-Malvido et al., 2014;Bruna et al., 2023). Since heliconias are a shared property in rural landscapes, studying the biotic and abiotic factors that influence their establishment is fundamental, along with the preservation of their rural landscapes. ...

Reference:

Heliconias (Heliconiaceae) in rural landscapes
Demography of the understory herb Heliconia acuminata (Heliconiaceae) in an experimentally fragmented tropical landscape

... Our results are inconsistent with some previous observations of phylogenetic signal in photosynthetic heat tolerance. For example, Hernández et al. (2022) found that evolutionary history constrained photosynthetic heat tolerance among 39 species within six families in the order Zingiberales. Zhu et al. (2018) reported higher T crit in species from warmer biomes in a common garden study of 62 species. ...

Evolutionary history constrains heat tolerance of native and exotic tropical Zingiberales

... Furthermore, the GC-biases of matK gene with specific preference (>0.5) might be the particular feature for subgenus Crassula. Due to rapid evolutionary rate, high universality, and significant interspecific divergence, the matK gene has been broadly used in plant evolutionary studies as one of the core DNA barcodes [9,10,[81][82][83][84]. ...

Floral evolution and pollinator diversification in Hedychium : Revisiting Darwin's predictions using an integrative taxonomic approach

American Journal of Botany

... As a distinctive identifying marker to detect and classify species, DNA barcodes are gene sequences of between 400 and 800 base pairs (bp) that are https://plantsciencetoday.online taken from a specified region of the genome (1)(2)(3). Using these brief DNA segments and techniques that have been authorised by international agencies, DNA barcoding is a tool for species identification that builds a worldwide record of living things (4)(5)(6). It is reported that the first accurate (100 %) identification of 200 closely related Lepidopteran species using the mitochondrial cytochrome c oxidase, I (COI) region (4,5). ...

Plant DNA Barcodes, Community Ecology, and Species Interactions

Diversity

... Subsequent studies using the same markers (Kress & al., 2005(Kress & al., , 2007De Boer & al., 2018;Le & al., 2022) share a similar topology, albeit with slightly varying taxon sampling. A similar topology was also found in a phylogeny with dense taxon sampling using ITS and three plastid regions (trnK, trnL-trnF, psbA-trnH), used by Zhao & al. (2022) for a biogeographic study. The biogeographic implications of the phylogenetic topologies in the above studies and the formal analysis of Zhao & al. (2022) indicate a South-East Asian origin for the Alpinioideae clade followed by dispersal to Africa, followed by back dispersal from Africa to India and the Neotropics. ...

Historical biogeography of the gingers and its implications for shifts in tropical rain forest habitats
  • Citing Article
  • May 2022

Journal of Biogeography

... Many species remain understudied, and without a comprehensive understanding of the biodiversity within these ecosystems, it will be challenging to protect them effectively. DNA barcoding offers a promising tool for identifying and cataloguing marine species, contributing to a more accurate understanding of marine biodiversity and helping to guide conservation efforts (Gostel and Kress, 2022). ...

The Expanding Role of DNA Barcodes: Indispensable Tools for Ecology, Evolution, and Conservation

Diversity

... These highlight potential challenges and opportunities for each species in the future (Engler et al. 2009). On a global scale, analyses have shown that species not exploited by humans may be at risk of becoming losers in the face of climate change and may even face the threat of extinction (Kress and Krupnick 2022). Among the species in our study, L. gaudinii stands out as particularly vulnerable due to its hybridisation potential and limited avenues for escaping it. ...

Lords of the biosphere: Plant winners and losers in the Anthropocene

... The Coleoptera 44 , Hemiptera 45 and Lepidoptera 46 include many specialist herbivorous species, whereas the Orthoptera includes generalist herbivores with broader plant diets 51,52 . Diversity of the Araneae and Hymenoptera may be indirectly correlated with leaf herbivory through their dependence on predation or parasitism of leaf-feeding invertebrates. ...

Patterns of Herbivory in Neotropical Forest Katydids as Revealed by DNA Barcoding of Digestive Tract Contents

Diversity

... The Indian plate, the land portion of which comprises the Indian subcontinent, was part of the Gondwanan supercontinent 150 million years ago (Ma) (Jokat et al. 2003), before separating from Africa 130-110 Ma (Morley 2003, Lomolino et al. 2017, then Madagascar and the Seychelles 99-66 Ma (Ashton and Gunatilleke 1987, Plummer et al. 1998, Lomolino et al. 2017, and then drifting northwards and colliding with Eurasia 55-42 Ma (Ashton andGunatilleke 1987, Briggs 2003). Dramatic climatic shifts during its northward journey resulted in the loss of many endemic plant lineages (Morley 1998(Morley , 2000(Morley , 2003, but the region might have played a key role in the diversification of species-rich plant families in Asia, such as Dipterocarpaceae and Zingiberaceae (e.g., Karanth 2006, Ashokan et al., 2022 as the recipient of long-distance dispersals (e.g., Zhao et al. 2022); the site of rapid in situ radiations (e.g., Surveswaran et al. 2021) and as 'a biogeographical raft' (Zhao et al. 2022). Certainly, biotic exchanges following collision with Eurasia would have had profound effects on the composition of the flora of that region (e.g., Mani 1974, Conti et al. 2002, Karanth 2006, Sen et al. 2019, but most biogeographic studies involving the Indian plate have focused on animals, with plants examined only rarely (e.g., Sen et al. 2019, Zhao et al. 2022. ...

Himalayan orogeny and monsoon intensification explain species diversification in an endemic ginger (Hedychium: Zingiberaceae) from the Indo-Malayan Realm
  • Citing Article
  • February 2022

Molecular Phylogenetics and Evolution

... Indigenous knowledge and the genetic resources of orchids often originate from biodiverse regions inhabited by indigenous communities. The principles of prior informed consent and benefit-sharing must be adhered to, respecting the rights of these communities and ensuring that they benefit from the scientific and commercial use of their biological resources (Sherkow et al., 2022). ...

Ethical, legal, and social issues in the Earth BioGenome Project

Proceedings of the National Academy of Sciences