How taxonomic change influences forecasts of the Linnean shortfall (and what we can do about it)?

Journal of Biogeography, Journal Year: 2024, Volume and Issue: 51(8), P. 1365 - 1373

Published: March 8, 2024

Abstract The gap between the number of described species and that actually exist is known as Linnean shortfall fundamental importance for biogeography conservation. Unsurprisingly, there have been many attempts to quantify its extent different taxa regions. In this Perspective , we argue such forecasts remain highly problematic because does depend not only on rates exploration (sampling undescribed taxa) which estimates commonly based but also taxonomic change (lumping splitting). These changes concepts adopted information methods used delimit species. Commonly estimating unknown (e.g. discovery curves, taxon ratios) can underestimate or overestimate if they do effectively account trends change. A further complication history well documented most typically available in biodiversity databases. Moreover, wide geographic variation adoption delimitation mean comparison even same regions may be unreliable. Given high likelihood future major taxa, propose two main strategies consider influence species: (i) a conservative approach shortfall, restricting analysis groups where taxonomies are relatively stable (ii) explicitly incorporating metrics into models estimates. short, relevant will achieved by accounting dynamic nature process itself.

Language: Английский

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APCalign: an R package workflow and app for aligning and updating flora names to the Australian Plant Census

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 5, 2024

Abstract Here we present “APCalign”, an R package and accompanying browser-sourced application to align update scientific names for Australian vascular plants the most likely currently accepted name using Plant Census (APC) or a in Names Index (APNI). Scientific are label assigned unique taxon concepts by community, but this common terminology is useful if concept consistently referred same name. These links can be broken due either spelling mistakes taxonomic changes. Automated tools required resolve lists, aligning updating long lists of possibly erroneous names. It essential that specific APC/APNI developed, as these specify endorsed national-level nomenclature used government legislation include uniquely phrase names, absent global datasets. To input within APC APNI, “APCalign” works progressively through sequence checks combine different permutations name, exact versus fuzzy matches, matches consider entire subset words, character strings indicate only resolved genus family. The aligned then, when possible, updated APC. This should facilitate all research outputs require diverse merged outdated updated.

Language: Английский

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The 5 ‘D’s of Taxonomy: A User’s Guide

The Quarterly Review of Biology, Journal Year: 2024, Volume and Issue: 99(3), P. 131 - 156

Published: Aug. 16, 2024

Language: Английский

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A taxonomic revision and conservation assessments of Thesium Section Frisea (Subgenus Frisea, Santalaceae)

South African Journal of Botany, Journal Year: 2025, Volume and Issue: 178, P. 280 - 306

Published: Jan. 30, 2025

Language: Английский

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Commentary on "Preliminary Species Hypotheses" in Entomological Taxonomy: A Global Data and FAIR Infrastructure Perspective

Biodiversity Data Journal, Journal Year: 2025, Volume and Issue: 13

Published: Feb. 10, 2025

What if early taxonomic findings were treated like preprints, open to iterative improvement or managed with practices from the open-source community, such as Git branching, merging and patch management? Prompted by Buckley's article Charting a Future for Entomological Taxonomy in New Zealand (2024), this commentary explores these possibilities context of biodiversity informatics. In response need rapid, scalable monitoring, Buckley introduces preliminary species hypotheses (PSH) bridge between quick identification tools rigorous Linnaean system, leveraging DNA barcoding AI-assisted image recognition produce provisional classifications that can later be validated. Expanding on Buckley’s framework, emphasises critical role data linking, versioning integration support evolving data. Borrowing software practices, I explore idea managing PSH an infrastructure treats each update versioned "commit", which tracked, refined integrated over time. Drawing insights FAIR (Findable, Accessible, Interoperable, Reusable) principles Digital Extended Specimens, identify requirements PSH, including robust standards, persistent identifiers interoperability global repositories. Additionally, Taxonomic Data Objects offer model dynamically integrating into adaptable taxonomies evolve new tools. By positioning within open, infrastructure-focused advocates scalable, hypothesis-driven meets modern conservation needs, bridging traditional emerging taxonomy.

Language: Английский

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Phylogenetic Assessment of Gazella bennettii: A Genetic Framework for the Conservation of the Endangered Jebeer in Iran

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(2)

Published: Feb. 1, 2025

ABSTRACT The chinkara ( Gazella bennettii , Sykes 1831) exhibits a broad distribution from Iran to India and has been categorized into five species: G. christyi salinarum representing the Indian chinkara, fuscifrons shikarii pertaining Iranian (jebeer). This classification within “ Gazelle group” is solely based on morphological data, lacking genetic information. To investigate potential presence of multiple species group determine subspecific variations, we sampled jebeer in conducted phylogenetic analyses using cytochrome b COI, sequences two nuclear introns (CHD2 ZNF618). Our mitochondrial data revealed significant divergence group,” identifying lineages: lineage (jebeer) (chinkara). Estimates time suggest that split between occurred approximately 0.895 million years ago, possibly associated with vicariant event caused by Indus River. These findings have important implications for assessing conservation statuses IUCN Red List because an endangered currently grouped together non‐threatened one (chinkara) under same global assessment, which underestimates true status jebeer. In Iran, haplotype map can serve as fundamental framework guiding efforts across protected areas captive breeding centers. Therefore, recommend any future management plan should be these treat lineages separately.

Language: Английский

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Potential transoceanic dispersal of Geodia cf. papyracea and six new tetractinellid sponge species descriptions within the Hawaiian reef cryptofauna

PeerJ, Journal Year: 2025, Volume and Issue: 13, P. e18903 - e18903

Published: Feb. 17, 2025

Kāne'ohe Bay has historically been known for the introduction of alien species from Caribbean and Western Indo-Pacific. Recent efforts that explore reef cryptofauna have shown in addition to diversity non-indigenous species, patch environments are rich with undescribed species. Here we integrate molecular phylogeny systematics distinguish introduced those potentially native or endemic. We focus on order Tetractinellida document potential transoceanic dispersal Geodia papyracea Hawai'i. Our integrative approach allowed us describe new Stelletta (Stelletta kela sp. nov., hokunalohia kuhapa hokuwanawana apapaola nov.) one Stryphnus (Stryphnus huna nov.); all collected via use Autonomous Reef Monitoring Structures. Specimens were barcoded using 28S COI markers, providing insights into phenotypic plasticity sponges phylogenetic placement these based morphological characters. Using both traditional taxonomy enhances accuracy identification classification, contributing a broader understanding sponge biodiversity within Hawaiian archipelago.

Language: Английский

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Taxonomy Resolver: A Python package for building and filtering taxonomy trees

The Journal of Open Source Software, Journal Year: 2025, Volume and Issue: 10(106), P. 7604 - 7604

Published: Feb. 21, 2025

Language: Английский

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Including Funga in Brazilian environmental impact reports

Biological Conservation, Journal Year: 2025, Volume and Issue: 305, P. 111095 - 111095

Published: March 15, 2025

Language: Английский

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Global hotspots of butterfly diversity are threatened in a warming world

Nature Ecology & Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: March 24, 2025

Insects are in decline and threatened by climate change, yet lack of globally comprehensive information limits the understanding management this crisis. Here we uncover a strong concentration butterfly diversity rare rapidly shrinking high-elevation climates. Integrating phylogenetic geographic range data for 12,119 species, find that global centres richness, rarity unusually concentrated tropical subtropical mountain systems. Two-thirds assessed species primarily dwelling mountains hold 3.5 times more hotspots (top 5%) than lowlands. These only partially overlap with those ants, terrestrial vertebrates vascular plants (14-36%), while is uniquely above 2,000 m elevation. We project up to 64% temperature niche space butterflies realms will erode 2070, geographically restricted conditions potentially turning these from refugia traps diversity. Our study identifies critical conservation priorities underscores need quantitative assessments at least select insect groups help mitigate biodiversity loss warming world.

Language: Английский

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