Article Alerts Archive – 2020

Most published solutions are computationally inefficient, incapable of running within a web browser, and focus on texts in English, thus omitting a substantial portion of biodiversity literature. An open‐source browser‐executable solution, Quaesitor, is presented in this article. Quaesitor automatically and efficiently identifies Latin scientific names in the 16 most common languages for biodiversity articles. The program will be a valuable tool for the mobilization of data contained within scanned specimen labels and biodiversity literature.

(Applications in Plant Sciences, July 31, 2020
NYBG Contact: Damon Little)

Applications in Plant Sciences Article

Follow these links for recent publications related to lichen biodiversity and conservation:

Caloplaca edwardiana (Teloschistaceae, Lichenized Ascomycetes), a new crustose species from the southern Appalachian Mountains of eastern North America
Description of a new narrowly endemic species names in honor of E.O. Wilson
(Senior Author: Graduate Student Jordan Hoffman)

The Bryologist 123(2): 255–234, July 10, 2020

The Bryologist Abstract

Field Guide to the Lichens of Great Smoky Mountains National Park
A 500 page all-in-one resource for Park exploration, with lichen distribution maps, tools for identification, vivid photographs and illustrations, and field notes.

University of Tennessee Press, March 2020

Amazon Book Information

A revision of Hypotrachyna subgenus Parmelinopsis (Parmeliaceae) in eastern North America
Revision of a group of charismatic macrolichens, with descriptions of three new species and one species that is reported from North America for the first time.

The Bryologist 123(2), 265-332, 10 July 2020

The Bryologist Abstract

Combing for Beach Broccoli: Surveys of the endemic macrolichen Cladonia submitis determines endangered status under IUCN guidelines
Documents the decline of a conspicuous macrolichen endemic to the Mid-Atlantic coast of eastern North America, and suggests and IUCN conservation status as Endangered.
(Senior Author: Graduate Student Jordan Hoffman)

Biodiversity and Conservation, May 12, 2020

Biodiversity and Conservation Abstract

Bacidia thiersiana (Ramalinaceae), a new species with lobaric acid widespread in southeastern North America
Description (with illustrations) of a new species from scattered locations throughout southeastern North America, including the southern Appalachian Mountains and Coastal Plain.

The Bryologist 123(1): 39-47, January 13, 2020

The Bryologist Abstract

The new species was discovered in the field and collected as part of NYBG’s ongoing floristic inventory of Myanmar’s northern forest complex.

(Phytotaxa, May 26, 2020
NYBG Contacts: Andrew Henderson, Kathleen Armstrong)

This volume documents the real world uses of the PhyloCode and will govern and apply to the names of clades, while species names will still be governed by traditional codes.

*Coverage for eight clades in the book derives from NYBG scientist Ken Karol’s ongoing research on the evolution and systematics of the green algae.

(CRC Press, August 2020
NYBG Contact: Kenneth G. Karol)

Amazon Book Information

The results supported the recognition of two new tribes, Litholobieae and Eriocnemeae.

(Phytotaxa, July 23, 2020
NYBG Contact: Fabián Michelangeli)

Phytotaxa Abstract

Many scientists have been involved in this program, including Roy Halling in identifying mushrooms, and Michael Balick, Daniel Atha, Rob Naczi and many others who have helped identify plants and provide taxonomic advice. In mid July the third edition of the Handbook of Poisonous and Injurious Plants was published, through the NYBG Press and our collaboration with Springer. Coauthored by Lewis S. Nelson, MD and Michael J. Balick, Ph.D., this new edition includes updates on toxic plants as well as the therapeutic interventions currently used in hospitals, both of which have changed since the publication of the second edition in 2007. With over 150 full-color photographs of potentially toxic and injurious plants inside and outside of the home, the Handbook is also useful for identifying and addressing concerns about cultivated species and those found in the wild. Dr. Nelson is a world-renowned toxicologist and Chair of the Department of Emergency Medicine and Director of the Division of Medical Toxicology at Rutgers New Jersey Medical School in Newark, New Jersey. He and Michael Balick are long-time collaborators, in both writing and teaching diverse audiences including medical professionals, undergraduate students, and the public.

(Springer/NYBG, July 2020
NYBG Contact: Michael Balick)

Springer Book Information

(American Midland Naturalist, July 2020
NYBG Contact: Rob Naczi)

American Midland Naturalist Abstract

Specifically, the article assesses how habitat loss likely impacted the climatic spaces occupied by the local species, the inferred composition of local communities and the spatial distribution of phylogenetic diversity and endemism. Using carefully curated point localities, phylogenetic data and parameterized models of species distributions, the authors generate maps of phylogenetic diversity, phylogenetic endemism and phylogenetic turnover for the entire Atlantic Forest. They map patterns of clade-specific diversity under complete preservation of forest, and then incorporate present-day deforestation patterns to provide a more realistic scenario. Instead of a singular pattern, three different reoccurring syndromes are described the flora and fauna of the Atlantic Forest. These patterns emerged irrespective of clade age and life history traits. General turnover patterns were highly consistent with previous analyses of species composition and panbiogeographical studies. Deforestation has altered the availability of climatic spaces in the Atlantic Forest, its biological communities and the distribution of evolutionary lineages in space. However, approximately 60% of the pre-Columbian climatic space persists in forest remnants, and today’s biological communities are estimated to be 45% similar to pre-deforestation times. The Atlantic Forest has been reduced to 8% of its once largely continuous range. However, the disproportionately large amounts of climate, community and lineage diversity that persist in remnants provide hope and support for conservation efforts that combine species occurrence and phylogenetic data. Inclusion of evolutionary thinking into strategic approaches to restoring Brazilian ecosystems could further conservation effectiveness by incorporating the adaptive potential of local assemblages in the face of further environmental shifts.

(Diversity and Distributions, July 2020
NYBG Contact: Fabián Michelangeli)

Diversity and Distributions Article

Robust automatic species identification algorithms using machine learning could accelerate species discovery. To encourage the development of an automatic species identification algorithm, the Herbarium 2019 data set was submitted to the Fine‐Grained Visual Categorization sub‐competition (FGVC6) hosted on the Kaggle platform. The data set focused on the flowering plant family Melastomataceae because of a large collection of imaged herbarium specimens (46,469 specimens representing 683 species) and taxonomic expertise in the family. As is common for herbarium collections, some species in this data set are represented by few specimens and others by many. In less than three months, the FGVC6 Herbarium 2019 Challenge drew 22 teams who entered 254 models for Melastomataceae species identification. The four best algorithms identified species with >88% accuracy. The FGVC competitions provide a unique opportunity for computer vision and machine learning experts to address difficult species‐recognition problems. The Herbarium 2019 Challenge brought together a novel combination of collections resources, taxonomic expertise, and collaboration between botanists and computer scientists.

(Applications in Plant Sciences, July 2020
NYBG Contacts: Damon Little, Melissa Tulig, Fabián Michelangeli, Barbara Ambrose)

Applications Article

The book provides a framework for how biodiversity can be detected and evaluated—focusing particularly on plants—using proximal and remotely sensed hyperspectral data and other tools such as LiDAR. The volume, whose chapters bring together a large cross-section of the biodiversity community engaged in these methods, attempts to establish a common language across disciplines for understanding and implementing remote sensing of biodiversity across scales.

*One chapter in the book, Predicting Patterns of Plant Diversity and Endemism in the Tropics Using Remote Sensing Data: A Study Case from the Brazilian Atlantic Forest (by Paz et al.), derives from NYBG’s ongoing participation in the Dimensions of Biodiversity: Brazilian Atlantic Forest research project. The chapter analyzes the distribution and phylogenetic data from three important plant groups in the megadiverse Atlantic Coastal Forest.

(Remote Sensing of Plant Biodiversity, June 2020
NYBG Contact: Fabián Michelangeli)

Springer Link Open Access Information

During systematic studies of Microchilus and Pelexia, it became apparent that two entities represented new species: Microchilus yungasensis from the Bolivian Yungas ecoregion, and Pelexia ocreatopsis from the Southern Amazon Humid Forests of Bolivia and Peru.

Brittonia, June, 2020
(NYBG Contact: Matthew Pace)

Brittonia Abstract

Nature Plants, June 22, 2020
(NYBG Contact: Ina Vandebroek)

Nature Plants Article

The largest families are Poaceae (56 species), Asteraceae (55), Rosaceae (27), Fabaceae (20), and Polygonaceae (17). The largest genera are Persicaria (8 species), Carex (7), Acer (7), Cyperus (6), Rubus (6), and Eragrostis (6). Seven species are ranked as rare, threatened, or endangered by New York Natural Heritage Program. Thirty-six species are listed as prohibited or regulated invasive species by New York State. All species are vouchered by herbarium specimens and silica-dried tissue samples at The New York Botanical Garden.

Journal of the Torrey Botanical Society, February, 2020

Journal of the Torrey Botanical Society Article

Cycads do not have axillary buds. Vegetative branching occurs via two processes, isotomous branching of the shoot apex, and adventitious branching from damaged regions and leaf bases. In addition, false isotomies can occur from equal adventitious branches on decapitated trunks; these are characterized by disruptions in the vasculature of the leaf base. Adventitious branching occurs via two pathways: branches can arise from meristematic tissue produced by a phellogen in the leaf bases, or branches can arise from lateral meristems (vascular cambium or phellogen) in damaged stems, or from the pith. This article is a great example of the insights that can be gained from ‘slice and dice’ botany, which is simple anatomical study using rudimentary cutting tools and phloroglucinol (a stain that reveals the presence of lignin).

International Journal of Plant Sciences, June, 2020
(NYBG Contact: Dennis Stevenson)

International Journal of Plant Sciences Abstract

Some highly diverse taxa, such as lichens, have received considerably less conservation attention, compared to plants and vertebrates. Here the authors present the results of a comprehensive demographic survey and IUCN risk assessment of Cladonia submitis, a conspicuous macrolichen endemic to the Mid-Atlantic coast of eastern North America, across the core of its range. The species was found at several new locations, but the species has disappeared from many locations where it once occurred. This decline, in conjunction with its restricted range, supports a status of Endangered under IUCN guidelines. While fire and sea level rise likely pose threats to the species, the most immediate threat is urbanization and alteration of coastal dunes. This study provides a basis for effective management strategies of this charismatic species whose core range consists of the densely populated region between the American cities of Boston and Washington, D.C.

Biodiversity and Conservation, May 2020
(NYBG Contacts: Jordan Hoffman & James Lendemer)

Biodiversity and Conservation Abstract

These characters are unusual in the genus and in Melastomataceae as a whole, and place the new species squarely in the B. purpusii group. Blakea ricardoi is a small shrub that differs from other species in the group by its longish peduncles, and leaves, bracts and peduncles that have course pubescence. The new species is named in honor of fellow melastomatologist and former NYBG graduate student, Ricardo Kriebel, Ph.D. (b. 1979).

Phytotaxa, May 2020
(NYBG Contact: Fabián Michelangeli)

Phytotaxa Abstract

The authors devised a new method for developing these genetic markers in groups for which they are not available. Their method involved selecting and identifying potential single copy nuclear genes by a two tier process using distantly related species of melastomes, by comparing transcriptomes to known genomes in other families, and then using genome skimming to find the full sequences for those loci. The study yielded potentially useful markers for phylogenetic studies of melastomes, and provided a general workflow for developing single-copy nuclear genes for other plant groups.

Applications in Plant Sciences, May 2020
(NYBG Contact: Fabián Michelangeli)

Applications Article

In Field Guide to the Lichens of Great Smoky Mountains National Park, the authors take on the formidable task of creating an all-in-one resource for Park exploration, including lichen distribution maps, tools for identification, vivid photographs and illustrations, and field notes. In the process, the authors create a touchstone for lichen taxonomy and ecology, and they inspire others—researchers as well as casual observers—to take interest in the incredible biodiversity of the Great Smoky Mountains. Biologists, botanists, visitors to the park, naturalists, and others interested in the flora and fauna of both the southern Appalachians and GSMNP will thoroughly enjoy this meticulously prepared field guide.

University of Tennessee Press, March 2020
(NYBG Contact: James Lendemer)

Amazon Book Listing

The authors suggest an alternative identity for the plant represented by k’an, which is the chib’ayal vine, Tynanthus guatemalensis (Bignoniaceae). Their argument is supported by the morphological and chemical characteristics of T. guatemalensis, which include cross-shaped stem anatomy similar to the k’an glyph, an allspice-like aroma, and yellow color. They examine other representations of the vine in Mayan tradition and suggest that the chib’ayal vine was used for its potent antidiabetic properties.

Heritage, April 2020
(NYBG Contact: Michael Balick)

Heritage Article

If you have ever been inside a grocery store, you have probably noticed the produce section. Mountains of lemons, piles of tomatoes, rows of cucumbers, several kinds of apples, and more. Some of these items you might know as fruits, and others as vegetables. But what is the difference between a fruit and a vegetable? When you eat an apple, strawberry, or peach, what part of the plant are you eating? This article explores our knowledge of fruits and how to properly identify them.

Frontiers for Young Minds: Science for kids, edited by kids, March 2020
(NYBG Contacts: Cecilia Zumajo, Barbara Ambrose)

Frontiers for Young Minds Article

Careful scrutiny of the North American data reveals that seven of the documented species are still extant, and seven of the species are not taxonomically distinct, thus appearing to reduce the number of North American extinctions from 38 to 24. However, the authors also note an additional 42 extinct taxa (28 species and 14 infraspecific taxa) that were overlooked in the original analysis, which brings the revised total for North America to 53 species (and 67 taxa). Therefore, based on North American data, the extinction rate is considerably greater for the United States and Canada than reported in the earlier study. The authors emphasize the importance of data quality, taxon concepts, inclusion of infraspecific taxa, and the taxonomic knowledge that is required to understand and document extinctions. These results suggest that careful scrutiny of global records will reveal similarly underestimated numbers of extinct species in other regions.

(Nature Ecology & Evolution, March 2020
NYBG Contact: Rob Naczi)

Nature Ecology & Evolution Article

With chapters on the Amazon and Caribbean forests, the Atlantic rainforests, the Andes, the Cerrado savannahs, the Caatinga drylands, the Chaco, and Mesoamerica – along with broad taxonomic coverage – this book summarizes a wide range of hypotheses, views, and methods concerning the processes and mechanisms of neotropical diversification. The range of perspectives presented makes the book a truly comprehensive, state-of-the-art publication on the topic, which will fascinate both scientists and general readers alike.

*Two chapters in the book derive from NYBG’s ongoing participation in the Dimensions of Biodiversity: Brazilian Atlantic Forest research project, and one of these chapters (Reginato & Michelangeli) generates an assessment of bioregions in eastern Brazil based on digitized herbarium specimen data.

(Neotropical Diversification: Patterns and Processes, April 2020
NYBG Contact: Fabian Michelangeli)

Springer Book Information

*Peres, E. A., R. Pinto-da-Rocha, L. G. Lohmann, F. A. Michelangeli, C. Y. Miyaki & A. C. Carnaval. 2020. Patterns of Species and Lineage Diversity in the Atlantic Rainforest of Brazil. In: Rull V, Carnaval AC (eds.) Neotropical Diversification: Patterns and Processes. Springer International Publishing, Cham, pp 415-447. doi:10.1007/978-3-030-31167-4_16

*Reginato, M. & F. A. Michelangeli. 2020. Bioregions of Eastern Brazil, Based on Vascular Plant Occurrence Data. In: Rull V, Carnaval AC (eds.) Neotropical Diversification: Patterns and Processes. Springer International Publishing, Cham, pp 475-494. doi:10.1007/978-3-030-31167-4_18

The two species were planted in gardens within the city of Xalapa-Enríquez, a distinctly urban area located within the broad distribution ranges of both species. The authors found obligate insect pollinators, two different species of beetles, associated with the pollen and ovulate cones of both cycad species (one pollinator with each cycad species), suggesting the maintenance of ecological interactions as they occur in the wild. Details of this gymnosperm–beetle pollination system, which is somewhat unexpected in urban areas, offer some encouragement for the conservation of species threatened by habitat loss.

Botany, April, 2020
(NYBG Contact: Dennis Stevenson)

Botany Abstract

The authors also compared the evolutionary rates and floral evolution in each of the areas for the two genera, which constitute the Ronnbergia alliance. The results suggested that the Ronnbergia alliance originated in the Atlantic Forest, followed by the origin of Ronnbergia after a long-distance dispersal event to the Pacific Forest. Wittmackia originated in the Atlantic Forest and later arrived to the Caribbean through a long-distance dispersal event to Jamaica. The authors suggest that the Caribbean is a much more dynamic area of diversification for the Ronnbergia alliance than the Atlantic Forest or the Pacific Forest.

Botanical Journal of the Linnean Society, April, 2020
(NYBG Contact: Fabián Michelangeli)

Bot J Linn Soc Abstract

This comparative study allowed the authors to examine the genetic control of ovule development across seed plants. The authors dissected the gene regulatory network involved in seed development and examined the evolutionary history of the gene lineages involved. Surprisingly, gene duplication is greater in the gymnosperms, which generally have a more simple (i.e., unitegmic) seed morphology. In addition, protein sequences indicate that ovule genes do not have similar roles across seed plants. This study provides a framework for molecular genetic analyses of non-model organisms.

Molecular Phylogenetics and Evolution, March 9, 2020
(NYBG Contacts: Cecilia Zumajo, Barbara Ambrose)

MPE Abstract

Based on a combination of plastid and nuclear loci, the new species is assigned to a small clade with Miconia paradoxa and M. michelangeliana. The three species in the “Paradoxa clade” can be recognized by a long list of (vegetative and reproductive) characters most readily appreciated by melastome specialists. The distinguishing features of the new species are concisely stated in the diagnosis: Miconia lucenae differs from Miconia paradoxa in having terete young branches (vs. strongly decussate-flattened in M. paradoxa), ciliate inner portion of the sepals (vs. eciliate), and lanceolate petals (vs. obovate). Miconia lucenae is endangered according to IUCN criteria.

Peer J, March 19, 2020
(NYBG Contact: Fabián Michelangeli)

Peer J Article

In this article, the authors performed phylogenomic analyses of bryophytes and relatives using both mitochondrial and plastid gene data sets, and investigated bryophyte plastome evolution. They tested for changes in plastid genes of a mycoheterotrophic liverwort (Aneura mirabilis) and a putatively mycoheterotrophic moss (Buxbaumia), and compared 15 bryophyte plastomes for major structural rearrangements.

Overall land‐plant relationships conflict weakly across analyses, but relationships within mosses, liverworts, and hornworts are largely congruent with previous studies. Relaxed purifying selection affects multiple plastid genes in mycoheterotrophic Aneura but not Buxbaumia, which leads the authors to cast doubt on the mycoheterophic status of the latter. Plastid genome structure is nearly invariant across bryophytes, but the tufA locus, presumed lost in embryophytes, is unexpectedly retained in several mosses. Autotrophic bryophyte plastomes, including Buxbaumia, hardly vary in overall structure.

American Journal of Botany, January, 2020
(NYBG Contact: Dennis Stevenson)

American Journal of Botany Abstract

Thyrsopteris cretacea is the first described mid-Cretaceous tree fern preserved in amber. It adds to the diversity previously ascribed to the Thyrsopteridaceae, which has been based on Eocene fossils, and it extends the fossil record of the family further back to the mid-Cretaceous. Most previous fossils of Thyrsopteridaceae have been from the Southern Hemisphere and are therefore considered Gondwanan. Thyrsopteris cretacea represents one of the few occurrences of the family in Laurasia.

Cretaceous Research, January, 2020
(NYBG Contact: Robbin Moran)

Cretaceous Research Article

They chose Merianieae (Melastomataceae) as the study system because the group is characterized by repeated independent shifts from an ancestral bee pollination syndrome to systems involving different vertebrate pollinators. In addition, all Merianieae have tubular anthers that are characteristic of highly-specialized buzz pollination. This study serves as a good test of more generalized hypotheses that have been used to explain increased evolutionary flexibility (evolvability) and evolutionary success. The authors suggest that modularity of flower structure, “may be key to the adaptive success of functionally specialized pollination systems by making flowers flexible (evolvable) for adaptation to changing selection regimes.”

Communications Biology, December 5, 2019
(NYBG Contact: Fabián Michelangeli

Communications Biology Article