Towards a global list of accepted species II. Consequences of inadequate taxonomic list governance

Thomson, Scott; Thiele, Kevin R.; Conix, Stijn; Christidis, Les; Costello, Mark J.; Hobern, Donald; Nikolaeva, Svetlana; Pyle, Richard L.; Dijk, Peter Paul van; Weaver, Haylee J.; Zachos, Frank E.; Zhang, Zhi‐Qiang; Garnett, Stephen T.

doi:10.1007/s13127-021-00518-8

Cited by 19 publications

(21 citation statements)

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“…Taxonomic discord is a primary source of difference in data because diatom taxonomic concepts are fluid, insufficient, and often contradictory 26 . Lack of stable and universally accepted taxonomic concepts in many groups of organisms is known for its negative impacts on both fundamental and applied research that uses taxonomic data 27 , 28 but is especially problematic in microscopic organisms such as diatoms that have relatively few diagnostic morphological characters. Several remedies have been suggested for reducing taxonomic consistency in future diatom projects 26 , 29 , but post-hoc harmonization is necessary for collating already existing datasets produced by different researchers.…”

Section: Background and Summarymentioning

confidence: 99%

A harmonized dataset of sediment diatoms from hundreds of lakes in the northeastern United States

et al. 2022

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Sediment diatoms are widely used to track environmental histories of lakes and their watersheds, but merging datasets generated by different researchers for further large-scale studies is challenging because of taxonomic discrepancies caused by rapidly evolving diatom nomenclature and taxonomic concepts. We collated five datasets of lake sediment diatoms from the Northeastern USA using a harmonization process which included updating synonyms, tracking the identity of inconsistently identified taxa, and grouping those that could not be resolved taxonomically. Each harmonization step led to an increase in variation explained by environmental variables and a parallel reduction of variation attributable to taxonomic inconsistency. To maximize future use of the data and underlying specimens we provide the original and harmonized counts for 1327 core samples from 607 lakes, name translation schemes, sample metadata, specimen museum locations, and the Northeast Lakes Voucher Flora, which is a set of light microscope images grouped into 1154 morphological operational taxonomic units. Post-hoc harmonization enables data quality control when other approaches (e.g., upfront management of taxonomic consistency) are not possible.

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Section: Background and Summarymentioning

confidence: 99%

A harmonized dataset of sediment diatoms from hundreds of lakes in the northeastern United States

et al. 2022

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“…because it is reclassified or its name is replaced), or even if the spelling of its name subtly changes, serious legal ramifications may arise. Thomson et al (2021) provide a more detailed discussion and specific examples of these cases.…”

Section: A List Of What Exactly?mentioning

confidence: 99%

“…Accommodating names (as represented by TNUs) for higher taxa is necessary for embedding a classification scheme within the global list, and accommodating lower taxonomic ranks is important for certain groups (especially vertebrates and plants) where such taxonomic divisions can have important conservation implications (e.g. Thomson et al, 2021).…”

Section: Granularitymentioning

confidence: 99%

“…This debate led to the formation of a Working Group on the governance of taxonomic lists, supported by the International Union of Biological Sciences (IUBS), and focused on developing a consensus view on the issues that initiated the debate (Garnett et al, 2020a(Garnett et al, , 2020b. Other papers in this Special Issue discuss the taxonomic context (Thiele et al, 2021), governance (Lien et al, 2021), case studies (Thomson et al, 2021), issues related to independence and stakeholder inclusion (Conix et al, 2021), and role of the Catalogue of Life (Hobern et al, 2021) for creating a global list of accepted species.…”

Section: Introductionmentioning

confidence: 99%

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Towards a global list of accepted species V. The devil is in the detail

et al. 2021

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A consensus among biologists has been growing in recent years for the development of a global list of accepted species (and other taxa). To date, much discussion has focused on visions for how such a list would benefit many scientific and societal disciplines. Less emphasis has been placed on understanding the many technical challenges of compiling and maintaining such a list. Challenges include details of implementation such as defining what each entry on the list represents, the scope (taxonomic breadth), granularity (only species, all taxonomic ranks, unnamed operational taxonomic units), and level of confidence in the status of individual list entries. The specific properties and minimum information requirements of list items need to be defined, and a process for ensuring accuracy, consistency, and noting uncertainties, needs to be adopted. Perhaps the greatest technical challenge is in developing the procedures by which the global list is created, updated, and maintained. Considerations of how to incorporate obscure and newly described taxa, the extent and specific implementation of a review process, and mechanisms for arbitrating disputes or alternative taxonomic viewpoints will need to be addressed through an open and transparent process with broad engagement from multiple communities. Details concerning how the global list can be accessed, how it will be maintained, and the way in which the list and its contents are properly cited need to be determined. Many of these issues have been considered and sometimes solved by the Catalogue of Life, which should serve as the core foundation for the actual implementation of any global list of species.

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“…taxID) and taxonomic names in the biodiversity domain, in a manner that is harmonised across repositories. This is exemplified by issues raised regarding the pressing need for collaborative efforts to build a common taxonomic framework ( Thiele et al 2021 ; Thomson et al 2021 ; Conix et al 2021 ; Lien et al 2021 ; Pyle et al 2021 ; Hobern et al 2021 ). This would provide tools to deal with synonyms and updates, it would enable better understanding of the meaning of a taxonomic name through access to taxonomic treatments, and it would facilitate annotations and links with external data.…”

Section: Introductionmentioning

confidence: 99%

Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR

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Adam-Blondon

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et al. 2022

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Threats to global biodiversity are increasingly recognised by scientists and the public as a critical challenge. Molecular sequencing technologies offer means to catalogue, explore, and monitor the richness and biogeography of life on Earth. However, exploiting their full potential requires tools that connect biodiversity infrastructures and resources. As a research infrastructure developing services and technical solutions that help integrate and coordinate life science resources across Europe, ELIXIR is a key player. To identify opportunities, highlight priorities, and aid strategic thinking, here we survey approaches by which molecular technologies help inform understanding of biodiversity. We detail example use cases to highlight how DNA sequencing is: resolving taxonomic issues; Increasing knowledge of marine biodiversity; helping understand how agriculture and biodiversity are critically linked; and playing an essential role in ecological studies. Together with examples of national biodiversity programmes, the use cases show where progress is being made but also highlight common challenges and opportunities for future enhancement of underlying technologies and services that connect molecular and wider biodiversity domains. Based on emerging themes, we propose key recommendations to guide future funding for biodiversity research: biodiversity and bioinformatic infrastructures need to collaborate closely and strategically; taxonomic efforts need to be aligned and harmonised across domains; metadata needs to be standardised and common data management approaches widely adopted; current approaches need to be scaled up dramatically to address the anticipated explosion of molecular data; bioinformatics support for biodiversity research needs to be enabled and sustained; training for end users of biodiversity research infrastructures needs to be prioritised; and community initiatives need to be proactive and focused on enabling solutions. For sequencing data to deliver their full potential they must be connected to knowledge: together, molecular sequence data collection initiatives and biodiversity research infrastructures can advance global efforts to prevent further decline of Earth’s biodiversity.

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Towards a global list of accepted species II. Consequences of inadequate taxonomic list governance

Cited by 19 publications

References 42 publications

A harmonized dataset of sediment diatoms from hundreds of lakes in the northeastern United States

A harmonized dataset of sediment diatoms from hundreds of lakes in the northeastern United States

Towards a global list of accepted species V. The devil is in the detail

Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR

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