The National Center for Biotechnology Information (NCBI) Taxonomy includes organism names and classifications for every sequence in the nucleotide and protein sequence databases of the International Nucleotide Sequence Database Collaboration. Since the last review of this resource in 2012, it has undergone several improvements. Most notable is the shift from a single SQL database to a series of linked databases tied to a framework of data called NameBank. This means that relations among data elements can be adjusted in more detail, resulting in expanded annotation of synonyms, the ability to flag names with specific nomenclatural properties, enhanced tracking of publications tied to names and improved annotation of scientific authorities and types. Additionally, practices utilized by NCBI Taxonomy curators specific to major taxonomic groups are described, terms peculiar to NCBI Taxonomy are explained, external resources are acknowledged and updates to tools and other resources are documented. Database URL: https://www.ncbi.nlm.nih.gov/taxonomy.

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NCBI Taxonomy: a comprehensive update on curation, resources and tools.

An updated inventory of the vascular flora alien to Italy, providing details on the occurrence at regional level, is presented. The checklist includes 1597 species, subspecies, and hybrids, distributed in 725 genera and 152 families; 2 taxa are lycophytes, 11 ferns and fern allies, 33 gymnosperms, and 1551 angiosperms. 157 taxa are archaeophytes and 1440 neophytes. The alien taxa currently established in Italy are 791 (570 naturalized and 221 invasive), while 705 taxa are casual aliens, 4 are not assessed, 7 are of unknown regional distribution, 47 have not been confirmed in recent times, 3 are considered extinct or possibly extinct in the country, and 40 are doubtfully occurring in Italy. This checklist allows to establish an up-to-date number (9792) of taxa constituting the whole (native and alien) Italian flora.

/pdf/an-updated-checklist-of-the-vascular-flora-native-to-italy-2tuf9mb3d4.pdf

An updated checklist of the vascular flora native to Italy

The Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.

/pdf/notes-outline-and-divergence-times-of-basidiomycota-41rounhft0.pdf

Notes, outline and divergence times of Basidiomycota

Premise of the study For the past one billion years, green plants (Viridiplantae) have dominated global ecosystems, yet many key branches in their evolutionary history remain poorly resolved. Using the largest analysis of Viridiplantae based on plastid genome sequences to date, we examined the phylogeny and implications for morphological evolution at key nodes. Methods We analyzed amino acid sequences from protein-coding genes from complete (or nearly complete) plastomes for 1879 taxa, including representatives across all major clades of Viridiplantae. Much of the data used was derived from transcriptomes from the One Thousand Plants Project (1KP); other data were taken from GenBank. Key results Our results largely agree with previous plastid-based analyses. Noteworthy results include (1) the position of Zygnematophyceae as sister to land plants (Embryophyta), (2) a bryophyte clade (hornworts, mosses + liverworts), (3) Equisetum + Psilotaceae as sister to Marattiales + leptosporangiate ferns, (4) cycads + Ginkgo as sister to the remaining extant gymnosperms, within which Gnetophyta are placed within conifers as sister to non-Pinaceae (Gne-Cup hypothesis), and (5) Amborella, followed by water lilies (Nymphaeales), as successive sisters to all other extant angiosperms. Within angiosperms, there is support for Mesangiospermae, a clade that comprises magnoliids, Chloranthales, monocots, Ceratophyllum, and eudicots. The placements of Ceratophyllum and Dilleniaceae remain problematic. Within Pentapetalae, two major clades (superasterids and superrosids) are recovered. Conclusions This plastid data set provides an important resource for elucidating morphological evolution, dating divergence times in Viridiplantae, comparisons with emerging nuclear phylogenies, and analyses of molecular evolutionary patterns and dynamics of the plastid genome.

https://bsapubs.onlinelibrary.wiley.com/doi/epdf/10.1002/ajb2.1048

Plastid phylogenomic analysis of green plants: A billion years of evolutionary history.

Bill Dunmire previously collaborated with Gail Tierney in two delightful books on the plants and people of the southwestern United States (1995. Wild Plants of the Pueblo Province; 1997. Wild Plants and Native Peoples of the Four Corners). Alone Bill has written this engaging and information-packed volume on the arrival and impact of plants that the Europeans brought to the New World. Much previously has been written of New World contributions to Old World lives. Now that has been balanced with details of the other part of the story. This book outlines the history of Spanish colonization in the New World and the arrival with them of their favorite plants. The story begins with the status of life in Spain on the cusp of American exploration and contrasts that with foods and worldviews in Mexico and what became the southwestern United States. Chapters 4–6 tell of the ‘‘pathways’’ to the New World between 1492 and 1521, with discussions of Spanish agricultural arrival and the associated trade systems and livestock. Then, it explains how the Spanish first brought their culture, religion, and plants into Mexico, New Mexico, Arizona, and Texas before discussing either Florida or California. There is a Master Plant List (pp. 315–324), a Glossary, a Sources providing data supporting each chapter (pp. 329–342), a Selected Bibliography (pp. 343–362) of ca. 400 titles, and an Index. Most chapters are introduced with a map (13 total) showing the points needed for orientation and understanding movements by people. Also scattered throughout are sketches of tools and other items of the period, and many chapters end in discussions of individual cultivated plants, with drawings of each. All illustrations were created by Bill’s wife, Evangeline L. Dunmire. Most of the black-and-white photographs were taken by the author. The only color in the book is on the cover, featuring photos of the courtyard garden at the Parroquia de San Luis Obispo in Texcoco, grapes, plums, and a traditional farmer harvesting her safflower. The quality of these makes me wish that all pictures were in color. There are 12 tables providing various information on the plants pertinent to the individual chapters. The data packed into these tables on the 158 Old World species in the master list is wonderful. Nowhere else is there as much information about so many topics on these species and their arrival in the New World. Dunmire clearly worked long and hard on compiling these data and presents them in a lucid, compact format. Since the New and Old World plants became intermingled in indigenous and European-derived cultures, he has included pertinent New World species in the second part of the master list (57 spp.). Bill has a delightful twist that brings the history of these plants into the modern world in the Epilogue (pp. 309–314). He highlights two individuals, Anita Chavez and Rudy Perea, as representatives of traditional agriculture who continue growing many of the Mediterranean and American plants together in modern New Mexico. This is a thoroughly researched and readable book that will interest all readers of this journal. I strongly recommend it!

https://bioone.org/journals/economic-botany/volume-59/issue-2/0013-0001(2005)059[0198:TPOM]2.0.CO;2/The-Pteridophytes-of-Mexico/10.1663/0013-0001(2005)059[0198:TPOM]2.0.CO;2.pdf

The Pteridophytes of Mexico

Phylogeny has long informed pteridophyte classification. As our ability to infer evolutionary trees has improved, classifications aimed at recognizing natural groups have become increasingly predic ...

Alison M. Paul

Papers

A community-derived classification for extant lycophytes and ferns