Formulaic Unpublished Names: The need for a TDWG standard and for the inclusion of such names in apps such as iNaturalist

Names are essential for communication. In biodiversity we have a nomenclature system that has stood the test of time (around 270 years) and, despite some shortcomings, it works. However, the world has changed. Extinction rates have increased rapidly in recent times and are rising at ever increasing rates due to climate change and human neglect. As a result, we need to do everything we can to protect the species that remain and, to do that, we need to be able to communicate about those species. The publishing process is slow, and there is a dearth of taxonomists, so the formal publication for many of these species, especially in the tropics and the New World, cannot keep up with the ever-increasing known unpublished species. It is estimated (Chapman 2009) that only about 16% of the world’s species have been described. In plants that figure is around 65% described, with 35% still undescribed. Many of these are known, and many are threatened, but unless we give them names, we cannot adequately communicate about them, exchange data on them, or add them into conservation legislation. This includes being able to identify photos, etc. in citizen science apps such as iNaturalist, which can be important in determining ranges, identifying new taxa, and for taxonomists and other researchers.In the 1980s, Australia developed a formulaic naming system for undescribed plant species (Chapman 2005). The formulaic name follows the format: \" sp. ()\" e.g., \"Prostanthera sp. Somersbey (B.J.Conn 4024)\". This was universally adopted in Australia in the 1990s, and allowed, from 1999, the inclusion of these undescribed taxa in the legislated National and State threatened species lists. As of May 2022, there were 41 such taxa listed in the Australian Environment Protection and Biodiversity Conservation Act 1999 (EPBC Act). Such formulaic names can be synonymised as new names are formally described. A more detailed discussion of the formulaic method was given on pages 20-21 in Chapman (2005).Some have said that this is a trivial issue, but it is not trivial, and we will give evidence of this by looking at just one small part of the world – Western Australia – where there are currently 987 currently accepted undescribed taxa out of an estimated flora of about 13,000 that use this formulaic naming system (https://florabase.dpaw.wa.gov.au/). That is around 7.5% of all plant species in the state. Of these 987 taxa, over 50% are listed as Conservation Priority taxa (calculated from the florabase reference).This is not just an Australian problem, or just a plant problem, and thus we need such a system formalised into a TDWG standard. This would allow for consistency across the globe and across life kingdoms and allow for the transfer of data through data aggregators such as the Global Biodiversity Information Facility (GBIF). We also need citizen science apps such as iNaturalist to allow for the inclusion of such names in their taxonomies, otherwise we lose a lot of important information on some of the most valuable and threatened taxa in the world.While looking at the benefits, we must also look at some of the drawbacks e.g., physical piracy of rare taxa, and taxonomic piracy. It has been suggested that in some taxonomic groups, tying a formula name to a voucher, and especially where there is a link to a photo on iNaturalist, could encourage taxon pirates to describe and publish the taxa as new taxa in self-published journals without having examined any material. These issues need to be discussed, but we believe they are not reasons to deny support of the concept of formulaic names, even if different formats are needed for different taxonomic groups

Prostanthera volucris DArTseq SNP dataset

This dataset includes molecular data and associated metadata supporting the analysis of Prostanthera volucris (Lamiaceae) as a new, distinct species in the Central Tablelands. Samples of 3 taxa for this study were collected from across New South Wales, Australia. Analysis code can be found at https://github.com/rpodonnell/ASB_PE

A global growth-form database for 143,616 vascular plant species

For the majority of plant species in the world, we know little about their functional ecology, and not even one of the most basic traits—the species’ growth habit. To fill the gap in availability of compiled plant growth-form data, we have assembled what is, to our knowledge, the largest global database on growth-form as a plant trait. We have, with extensive error checking and data synthesis, assembled a growth-form database from 163 data sources for 143,616 vascular plant species from 445 different plant families. This is 38.6% of the currently accepted vascular plant diversity. For our database, we have chosen seven categories to cover the majority of the diversity in plant growth forms: aquatic plants, epiphytes, hemiepiphytes, climbing plants, parasitic plants, holo-mycoheterotrophs, and freestanding plants. These categories were used because we were able to reconcile the wealth of existing definitions and types of growth-form information available globally to them clearly and unequivocally, and because they are complementary with existing databases. Plants in the database were designated into a category if their adult growth form fit the criterion. We make available two databases: first, the complete data set, including species for which there is currently conflicting information, and second, a consensus data set, where all available information supports one categorization. Of the plant species for which we found information, 103,138 (72%) are freestanding, 21,110 (15%) are epiphytes, and 4,046 (3%) are parasites. Our growth-form data can be used to produce useful summary statistics by clade. For example, current data suggests that half of pteridophytes are epiphytic, that all hemiepiphytes are eudicots, and that there are no parasitic monocots, gymnosperms, or pteridophytes. Growth form is a crucial piece of fundamental plant-trait data with implications for each species’ ecology, evolution, and conservation, and thus this data set will be useful for a range of basic and applied questions across these areas of research. No copyright or proprietary restrictions are associated with the use of this data set, other than citation of the present Data Paper. A static version of this dataset is provided as Supporting Information, and a living and updating version of the dataset is available in a GitHub repository

Molecular phylogenetic analysis of the Prostanthera phylicifolia (Lamiaceae) assemblage resolves relationships of the 'Critically Endangered' P. gilesii and other putative new species

Prostanthera gilesii Althofer ex. B.J.Conn & T.C.Wilson is a critically endangered species from the Central Tablelands of New South Wales. A conservation management strategy is currently underway for this species, whose phylogenetic affinities are not known. Morphologically, P. gilesii resembles P. phylicifolia F.Muell. and a population of uncertain identity from Evans Crown Nature Reserve in the Central Tablelands of New South Wales known as P. sp. Evans Crown (G.M.Taseski NSW1055966). The taxonomy of P. phylicifolia, however, is unclear. Prostanthera phylicifolia was described from populations in the Victorian Alps and Monaro; however, populations spanning from Victoria to southern Queensland have been variously identified as either P. phylicifolia or P. scutellarioides (R.Br.) Briq. despite substantial geographic disjunctions and morphological dissimilarity. To examine the relationship between populations identified as P. phylicifolia, P. gilesii and P. sp. Evans Crown, nuclear (external transcribed spacer, ETS) and chloroplast (trnH-psbA intergenic spacer) regions were sequenced and combined with an existing Prostanthera dataset and analysed with maximum-likelihood and Bayesian-inference methods. Prostanthera gilesii and P. sp. Evans Crown were recovered as sister taxa within a clade consisting of populations morphologically similar to the type of P. phylicifolia from the Victorian Alps and Snowy Mountains, Monaro and Southern Tablelands of New South Wales. Populations from northern New South Wales and southern Queensland identified as P. phylicifolia or P. scutellarioides were recovered as an assemblage of unrelated clades. The molecular phylogeny supports P. gilesii and P. phylicifolia as closely related as hypothesised based on morphology and supports P. sp. Evans Crown as a population which requires additional study to assess its taxonomic status

A global growth‐form database for 143,616 vascular plant species

For the majority of plant species in the world, we know little about their functional ecology, and not even one of the most basic traits—the species’ growth habit. To fill the gap in availability of compiled plant growth-form data, we have assembled what is, to our knowledge, the largest global database on growth-form as a plant trait. We have, with extensive error checking and data synthesis, assembled a growth-form database from 163 data sources for 143,616 vascular plant species from 445 different plant families. This is 38.6% of the currently accepted vascular plant diversity. For our database, we have chosen seven categories to cover the majority of the diversity in plant growth forms: aquatic plants, epiphytes, hemiepiphytes, climbing plants, parasitic plants, holo-mycoheterotrophs, and freestanding plants. These categories were used because we were able to reconcile the wealth of existing definitions and types of growth-form information available globally to them clearly and unequivocally, and because they are complementary with existing databases. Plants in the database were designated into a category if their adult growth form fit the criterion. We make available two databases: first, the complete data set, including species for which there is currently conflicting information, and second, a consensus data set, where all available information supports one categorization. Of the plant species for which we found information, 103,138 (72%) are freestanding, 21,110 (15%) are epiphytes, and 4,046 (3%) are parasites. Our growth-form data can be used to produce useful summary statistics by clade. For example, current data suggests that half of pteridophytes are epiphytic, that all hemiepiphytes are eudicots, and that there are no parasitic monocots, gymnosperms, or pteridophytes. Growth form is a crucial piece of fundamental plant-trait data with implications for each species’ ecology, evolution, and conservation, and thus this data set will be useful for a range of basic and applied questions across these areas of research. No copyright or proprietary restrictions are associated with the use of this data set, other than citation of the present Data Paper. A static version of this dataset is provided as Supporting Information, and a living and updating version of the dataset is available in a GitHub repository

AusTraits: a curated plant trait database for the Australian flora

INTRODUCTION AusTraits is a transformative database, containing measurements on the traits of Australia’s plant taxa, standardised from hundreds of disconnected primary sources. So far, data have been assembled from > 250 distinct sources, describing > 400 plant traits and > 26,000 taxa. To handle the harmonising of diverse data sources, we use a reproducible workflow to implement the various changes required for each source to reformat it suitable for incorporation in AusTraits. Such changes include restructuring datasets, renaming variables, changing variable units, changing taxon names. While this repository contains the harmonised data, the raw data and code used to build the resource are also available on the project’s GitHub repository, http://traitecoevo.github.io/austraits.build/. Further information on the project is available in the associated publication and at the project website austraits.org. Falster, Gallagher et al (2021) AusTraits, a curated plant trait database for the Australian flora. Scientific Data 8: 254, https://doi.org/10.1038/s41597-021-01006-6 CONTRIBUTORS The project is jointly led by Dr Daniel Falster (UNSW Sydney), Dr Rachael Gallagher (Western Sydney University), Dr Elizabeth Wenk (UNSW Sydney), and Dr Hervé Sauquet (Royal Botanic Gardens and Domain Trust Sydney), with input from > 300 contributors from over > 100 institutions (see full list above). The project was initiated by Dr Rachael Gallagher and Prof Ian Wright while at Macquarie University. We are grateful to the following institutions for contributing data Australian National Botanic Garden, Brisbane Rainforest Action and Information Network, Kew Botanic Gardens, National Herbarium of NSW, Northern Territory Herbarium, Queensland Herbarium, Western Australian Herbarium, South Australian Herbarium, State Herbarium of South Australia, Tasmanian Herbarium, Department of Environment, Land, Water and Planning, Victoria. AusTraits has been supported by investment from the Australian Research Data Commons (ARDC), via their “Transformative data collections” (https://doi.org/10.47486/TD044) and “Data Partnerships” (https://doi.org/10.47486/DP720) programs; fellowship grants from Australian Research Council to Falster (FT160100113), Gallagher (DE170100208) and Wright (FT100100910), a grant from Macquarie University to Gallagher. The ARDC is enabled by National Collaborative Research Investment Strategy (NCRIS). ACCESSING AND USE OF DATA The compiled AusTraits database is released under an open source licence (CC-BY), enabling re-use by the community. A requirement of use is that users cite the AusTraits resource paper, which includes all contributors as co-authors: Falster, Gallagher et al (2021) AusTraits, a curated plant trait database for the Australian flora. Scientific Data 8: 254, https://doi.org/10.1038/s41597-021-01006-6 In addition, we encourage users you to cite the original data sources, wherever possible. Note that under the license data may be redistributed, provided the attribution is maintained. The downloads below provide the data in two formats: austraits-3.0.2.zip: data in plain text format (.csv, .bib, .yml files). Suitable for anyone, including those using Python. austraits-3.0.2.rds: data as compressed R object. Suitable for users of R (see below). Both objects contain all the data and relevant meta-data. AUSTRAITS R PACKAGE For R users, access and manipulation of data is assisted with the austraits R package. The package can both download data and provides examples and functions for running queries. STRUCTURE OF AUSTRAITS The compiled AusTraits database has the following main components: austraits ├── traits ├── sites ├── contexts ├── methods ├── excluded_data ├── taxanomic_updates ├── taxa ├── definitions ├── contributors ├── sources └── build_info These elements include all the data and contextual information submitted with each contributed datasets. A schema and definitions for the database are given in the file/component definitions, available within the download. The file dictionary.html provides the same information in textual format. Full details on each of these components and columns are contained within the definition. Similar information is available at http://traitecoevo.github.io/austraits.build/articles/Trait_definitions.html and http://traitecoevo.github.io/austraits.build/articles/austraits_database_structure.html. CONTRIBUTING We envision AusTraits as an on-going collaborative community resource that: Increases our collective understanding the Australian flora; and Facilitates accumulation and sharing of trait data; Builds a sense of community among contributors and users; and Aspires to fully transparent and reproducible research of the highest standard. As a community resource, we are very keen for people to contribute. Assembly of the database is managed on GitHub at traitecoevo/austraits.build. Here are some of the ways you can contribute: Reporting Errors: If you notice a possible error in AusTraits, please post an issue on GitHub. Refining documentation: We welcome additions and edits that make using the existing data or adding new data easier for the community. Contributing new data: We gladly accept new data contributions to AusTraits. See full instructions on how to contribute at http://traitecoevo.github.io/austraits.build/articles/contributing_data.html

AusTraits, a curated plant trait database for the Australian flora

International audienceWe introduce the austraits database-a compilation of values of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 448 traits across 28,640 taxa from field campaigns, published literature, taxonomic monographs, and individual taxon descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological attributes (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual-and species-level measurements coupled to, where available, contextual information on site properties and experimental conditions. This article provides information on version 3.0.2 of AusTraits which contains data for 997,808 trait-by-taxon combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data, which also provides a template for other national or regional initiatives globally to fill persistent gaps in trait knowledge