One thousand plant transcriptomes and the phylogenomics of green plants
The green plant tree of life is built upon many evolutionary innovations, and plants have come a long way since they began as single-celled organisms one billion years ago. Plants have transitioned from water to land and managed to become the beautiful, towering, flowering and fruiting beings that are the backbone of life on earth.
Plants have complex life histories—creating vascular systems, waxy cuticles, spores, seeds and flowers. These innovations define key turning points in the history of green plants, and they are what separate the major plant groups: green algae, mosses and liverworts, ferns, gymnosperms and flowering plants.
The One Thousand Plant Transcriptomes Initiative, also known as the 1KP initiative, is a global collaboration of nearly 200 plant scientists, including NYBG’s Dr. Dennis Stevenson. “This long term project integrates field work, herbarium research, and living collections with the latest in laboratory and information sciences as an international collaboration,” Dr Stevenson said. For almost 10 years, this group has been attempting to sequence the genes of one thousand plants, spanning every plant family on the tree of life. The publication of these sequences, 1,147 in total, brings science significantly closer to understanding how the tree of life works in the plant kingdom. By examining the similarities and differences in genes, we can more fully understand how plants created evolutionarily significant transitions.
Nature, October 23, 2019
Tales of the discovery of new plant species: Dacryodes
Thousands of new species of plants and fungi have been described by NYBG researchers in recent decades, contributing to a total of more than 2,000 new plant species named by scientists each year. The most important contributions to these totals result from thorough systematic study of taxa (monographs and revisions).
As an example of such work, Douglas Daly and collaborators recently described 19 new species of Dacryodes (Burseraceae) in two separate publications as part of an ongoing systematic study of the neotropical representatives of the genus. The story of the discovery of these new species illustrates several important points about botanical exploration. Most of the newly described species are known from a single collection, and none is known from more than a handful of specimens, demonstrating how much we are limited by what we do not know. Scrutiny of the history of these collections also indicates declining numbers of collections in the past 25 years, suggesting that prospects for receiving additional material of these species in the near future are slim. In the end, we have to work with the material we have, and the authors make a strong case for describing new species even when specimens are limited. Studies like this serve as a plea for botanical exploration, and they highlight the importance of herbaria as rich sources of information about undiscovered plant diversity.
Brittonia, June, 2019
Brittonia, September, 2019
Biodiversity of Pantepui: The Pristine "Lost World" of the Neotropical Guiana Highlands
This book provides the most updated and comprehensive knowledge on the biota, origin, and evolution of the Pantepui biogeographical province. It synthesizes historical information and recent discoveries, covering the main biogeographic patterns, evolutionary trends, and conservation efforts.
Written by international experts on the biodiversity of this pristine land, this book explores what makes Pantepui a unique natural laboratory to study the origin and evolution of Neotropical biodiversity under the influence of only natural drivers.
Botanists estimate that the Pantepui flora consists of 2579 species of vascular plants confined to a relatively small area of 5000 square kilometers, with approximately 34% species endemism. The most recent information, summarized in Chapter 6 (“Vascular Plants and Bryophytes”), represents a modest increase in species diversity, and a slight decline in endemism, compared with earlier reports.
Riina, R., P. E. Berry, O. Huber, & F. A. Michelangeli. 2019. Vascular plants and bryophytes. In: Biodiversity of Pantepui: The Pristine “Lost World” of the Neotropical Guiana Highlands. V. Rull, T. Vegas-Vilarrúbia, O. Huber & C. Señaris (eds.). Academic Press, London. Pp: 121-147. ISBN: 978-0-12-815591-2.
A taxonomically broad metagenomic survey suggests cystobasidiomycete yeasts are not ubiquitous across all lichens
This American Journal of Botany cover article describes the results of a broad metagenomic survey for lichen‐associated cystobasidiomycete yeasts to determine the extent to which lichens represent dynamic metacommunities, versus the traditional view of lichens as binary symbiont pairs.
Lichens are fungi that enter into obligate symbioses with photosynthesizing organisms (algae, cyanobacteria). Traditional narratives of lichens as binary symbiont pairs have given way to their recognition as dynamic metacommunities. Basidiomycete yeasts, particularly of the genus Cyphobasidium, have been inferred to be widespread and important components of lichen metacommunities. Yet, the presence of basidiomycete yeasts across a wide diversity of lichen lineages has not previously been tested.
The authors searched for lichen‐associated cystobasidiomycete yeasts in newly generated metagenomic data from 413 samples of 339 lichen species spanning 57 families and 25 orders. The data set was generated as part of a large‐scale project to study lichen biodiversity gradients in the southern Appalachian Mountains Biodiversity Hotspot of southeastern North America. The authors detected cystobasidiomycete yeasts in nine taxa, representing 2.7% of all species sampled. Despite the need to reconceptualize lichens as dynamic metacommunities, the failure to detect cystobasidiomycetes in 97.3% (330 species) of the sampled species suggests that basidiomycete yeasts are not ubiquitous in lichens.
American Journal of Botany (cover story), August 9, 2019
Lichen conservation in North America: a review of current practices and research in Canada and the United States
The authors review the current state of lichen conservation in Canada and the United States. Through detailed case studies, they document threats, review the legal frameworks for protection, and provide a summary of actions that must be taken to accelerate lichen conservation.
Biodiversity and Conservation, August 2, 2019
Phylogenetics, morphology and circumscription of Cambessedesieae: a new Neotropical tribe of Melastomataceae
The most recent article in a long series of installments focused on systematics of the Melastomataceae addresses placement of Cambessedesia and genera of the ‘Merianthera and allies clade’. The genera of this clade are exclusively neotropical with centers of species diversity in the Atlantic Forest and Cerrado of Brazil.
To address the relationships of this group of genera, the authors analyzed DNA markers of three plastid genes (atpF-atpH, psbK-psbL and trnS-trnG), two ribosomal spacers (nrETS and nrITS), and a segment of a low-copy nuclear gene (waxy). Based on the results, the authors recognize the new tribe Cambessedesieae, which consists of Cambessedesia, Merianthera and an expanded Huberia (including Behuria and Dolichoura).
Botanical Journal of the Linnean Society, July, 2019
The Plant Ontology facilitates comparisons of plant development stages across species
This article represents the latest installment of the ongoing Plant Ontology (PO) project, an NSF-supported initiative that aims to develop a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and developmental stages for use by botanists in a diversity of fields.
The paper describes the structure of the ontology and the design principles the authors used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind the revision and expansion of the PO to cover development stages for all plants, particularly the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, the authors examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, the authors identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation database (http://www.planteome.org) make plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution.
Frontiers in Plant Science, June 4, 2019
The gradual loss of African indigenous vegetables in tropical America
In this review, the authors trace the trajectories of 12 prominent African indigenous vegetables (AIVs) in tropical America, in order to better understand the diffusion of their culinary and ethnobotanical uses by the African diaspora. The 12 AIVs were selected from African reference works and preliminary reports of their presence in the Americas.
A review of the historical and contemporary literature, and consultation with scholars, shows that the culinary uses of most of these vegetables have been gradually lost. Two noteworthy exceptions include okra (Abelmoschus esculentus) and callaloo (Amaranthus viridis), although the latter is not the species used in Africa and callaloo has only risen to prominence in Jamaica since the 1960s. Nine of the 12 AIVs found refuge in the African-derived religions Candomblé and Santería, where they remain ritually important. In explaining why these AIVs did not survive in the diets of the New World African diaspora, the authors point to the sociocultural, economic, and environmental forces that have shaped—and continue to shape—these foodways and cuisines since the Atlantic slave trade. Because these vegetables are neglected and underutilized species (NUS) that represent the biocultural heritage of the African diaspora in the Americas, their culinary traditions merit intensified scholarly attention and conservation efforts.
Economic Botany, April 3, 2019
Revisiting the classification of Melastomataceae: Habit and fruit evolution
Bertolonieae (Melastomataceae) have traditionally comprised more than 100 Neotropical species in a dozen genera. However, recent phylogenetic analyses have shown that Bertolonieae are not monophyletic, which implies that suites of morpholocial and ecological features have evolved independently in unrelated groups of Melastomataceae.
The authors conducted molecular phylogenetic analyses in order to evaluate tribal and generic limits, reconstruct morphological patterns, and identify clades in the tribe Bertolonieae. Bertolonieae as traditionally recognized were recovered in four major lineages across the tree, and Bertolonieae are recircumscribed here to include only the genus Bertolonia. Geographical and morphological congruence in the results suggests that the convergence of morphological characters historically used to identify Bertolonieae s.l. may be explained by different lineages around the world that occupy similar habitats (i.e., mostly shaded and moist herbaceous layers under the rainforest canopy). Dependence on water for seed dispersal and limited dispersability may also explain the restriction of the taxa to such similar habitats.
Botanical Journal of the Linnean Society, May, 2019
Habitat quality and disturbance drive lichen species richness in a temperate biodiversity hotspot
Relatively little is known about how lichens–obligate symbiotic organisms–respond to disturbance. Successful establishment and development of lichens require a minimum of two compatible yet usually unrelated species to be present in an environment, suggesting disturbance might be particularly detrimental.
To address this gap, the authors focused on lichens, which are obligate symbiotic organisms that function as hubs of trophic interactions. The investigation was conducted in the southern Appalachian Mountains, USA. The authors conducted complete biodiversity inventories of lichens (all growth forms, reproductive modes, substrates) across 47, 1-ha plots to test classic models of responses to disturbance (e.g., linear, unimodal).
The analyses recovered a strong, positive, linear relationship between lichen biodiversity and habitat quality: lower levels of disturbance correlate to higher species diversity. With few exceptions, additional variables failed to significantly explain variation in diversity among plots for the 509 total lichen species. Strong, detrimental impacts of disturbance on lichen biodiversity raises concerns about conservation and land management practices that fail to incorporate complete estimates of biodiversity, especially from ecologically important organisms such as lichens.
Oecologia, May 15, 2019
Genetic mechanisms underlying perianth epidermal elaboration of Aristolochia ringens (Aristolochiaceae)
The authors studied the morpho-anatomical and molecular basis of perianth elaboration of Aristolochia ringens. The study provides the first large scale analysis of perianth genes in Aristolochia and presents an overall view of the transcriptomic profiles in three well-differentiated portions of the perianth.
Candidate genes were identified that are likely involved in epidermal tissue development, metabolic functioning, and cell proliferation, and that were linked to observed morpho-anatomical patterning throughout the three perianth portions. The three CINCINNATA copies found are differentially expressed in the three perianth portions likely controlling rates of cell proliferation. Although particular biological roles of a number of candidate genes here identified in the Aristolochia perianth have not been characterized, the results provide an important platform to further investigate the molecular networks of epidermal-specific developmental processes and differential cell proliferation.
Flora, April, 2019
Biodiversity recovery of Neotropical secondary forests
This large team of authors assessed how tree species richness and composition recover during secondary succession across gradients in environmental conditions and anthropogenic disturbance in an unprecedented multisite analysis for the Neotropics. Secondary forests recover remarkably fast in species richness but slowly in species composition.
Secondary forests take a median time of five decades to recover the species richness of old-growth forest (80% recovery after 20 years) based on rarefaction analysis. Full recovery of species composition takes centuries (only 34% recovery after 20 years). A dual strategy that maintains both old-growth forests and species-rich secondary forests is therefore crucial for biodiversity conservation in human-modified tropical landscapes.
Science Advances, March 6, 2019
First record of Usnea (Parmeliaceae) growing in New York City in nearly 200 years
During a series of lichen surveys in New York City, the authors found a single thallus of Usnea on one very large, old red oak (Quercus rubra) at Woodlawn Cemetery in the Bronx. The individual was too poorly developed to identify by its morphology and chemistry, so they used a DNA barcoding approach.
Molecular data confidently assigned the thallus as Usnea mutabilis. Finding this thallus was highly notable, as it is the first report of an Usnea from New York City since 1824.
Journal of the Torrey Botanical Society, February 25, 2019
Pleistocene range expansions might explain striking disjunctions between eastern Brazil, Andes and Mesoamerica in Leandra
Most species of Leandra are narrow endemics, but a few present striking disjunct distributions between eastern Brazil and Andes or Mesoamerica. The authors used Climatic Niche Modeling to better understand the distributions of the species in this clade.
The results suggest that disjunct distributions in Leandra may have been shaped by cyclical range expansions during colder Pleistocene periods, followed by local extinctions during warmer interglacial periods. The results also support a short‐dispersion/stepping‐stone migration scenario to account for the observed disjunctions in this clade.
Journal of Systematics and Evolution, January 24, 2019
From plant ontology to gene ontology and back
In this article, NYBG scientists Dennis Stevenson and Cecilia Zumajo explore terminology related to structures of the seed, addressing the question of which of the two integuments in the angiosperms is the equivalent of the single integument in the gymnosperms.
In angiosperms, the gene INNER NO OUTER (INO) is involved in the proper development of the outer integument but not in the inner integument and in ino mutants there is no outer integument. INO genes are angiosperm specific as no orthologs have been found in gymnosperms. Thus, it appears that the inner integument of the angiosperms is equivalent –homologous- to the single integument of the gymnosperms and the PO terms can be revised accordingly.
Current Plant Biology, October 4, 2018
Patterns of biodiverse, understudied groups do not mirror those of the surrogate groups that set conservation priorities
The authors–two NYBG curators and the first-author graduate student–conducted biodiversity inventories of lichens, woody plants, and sedges at 32 sites on the Mid-Atlantic Coastal Plain of eastern North America between November 2012 and June 2015.
They then compared alpha diversity and community assemblages of each organismal group across the sites, and compared selected minimal reserve sets in order to visualize biodiversity patterns and assess whether specific components of vascular plants (sedges and woody plants) serve as an effective surrogate for lichens. The results show a lack of congruence between species richness patterns across organismal groups and suggest that the mechanisms that shape patterns of diversity are not identical. An important conclusion is that identifying and incorporating specific biodiversity indicators for understudied groups in conservation policy is necessary if the protection of such groups is to be ensured.
Biodiversity and Conservation, August 22, 2017
Traditional lifestyles, transition and implications for healthy aging
A team of researchers including New York Botanical Garden scientist Michael Balick has found that citizens of a Pacific island nation who are in transition between traditional, agrarian communities and modernized areas are more likely to have unhealthful lifestyles than those living in either traditional or modernized communities.
The findings from the study of residents of the state of Pohnpei in the Federated States of Micronesia have important implications that are applicable to the greater global population, including the United States, given that contemporary western society is transitional at its core.
The PLOS ONE article was published by an interdisciplinary research group that includes authors from The New York Botanical Garden, Southern Arizona VA Health Care System, North Carolina State University, American Academy of Family Physicians, Columbia University, Conservation Society of Pohnpei, Federated States of Micronesia (FSM), The Nature Conservancy—Micronesia Office, and University of Hawaii at Manoa.
PLOS ONE, March 12, 2019
The first complete plastid genomes of Melastomataceae are highly structurally conserved
NYBG scientists Fabian Michelangeli and Marcelo Reginato report the first full plastid sequences of Melastomataceae, compare general features of the sampled plastomes to other sequenced Myrtales, and survey the plastomes for highly informative regions for phylogenetics.
Melastomataceae plastomes are no exception for the general patterns observed in the genomic structure of land plant chloroplasts, being highly conserved and structurally similar to most other Myrtales. Despite the fact that the full plastome phylogeny shares most of the clades with the previously widely used and reduced data set, some changes are still observed and bootstrap support is higher. The plastome data set presented here is a step towards phylogenomic analyses in the Melastomataceae and will be a useful resource for future studies.
Peer J, November 29, 2016
Science Magazine: This lily’s cousin is an ear of corn
As different as they seem, corn, daylilies, towering palm trees, and diminutive lady’s slipper orchids have a lot in common. Now, a new genetic study published by 20 authors including NYBG’s Dr. Dennis Stevenson reveals why: Even though all of these plants are landlubbers today, their ancestor lived in water.
Science, November 5, 2018