Improving the gold standard in NCBI GenBank and related databases: DNA sequences from type specimens and type strains

Renner, Susanne S; Scherz, Mark D; Schoch, Conrad L; Gottschling, Marc; Vences, Miguel

doi:10.1093/sysbio/syad068

Cited by 3 publications

(1 citation statement)

References 48 publications

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“…Whenever possible, older specimens should not be used and historic vouchers should not be destroyed. In some cases, sequencing the type specimen of the species-which in many cases also is the oldest specimen-may be thought to be crucial 33,34 . However, some institutions may not allow destructive sampling of type specimens (see #3, above).…”

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The destructive sampling conundrum and guidelines for effective and ethical sampling of herbaria

Davis

2024

Preprint

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The use of herbaria for science and conservation is revolutionizing the discovery, exploration, and protection of biodiversity at unprecedented scopes and scales. The Global Metaherbarium—a digitally interlinked, open-access resource—is stimulating these efforts and helping to facilitate massive investigations that utilize aggregated digital derivatives of physical herbarium specimens. Simultaneously, the growing use of this virtual resource is expanding the use of physical collections by researchers from many scholarly domains who increasingly are sampling specimens for multiomic investigations (e.g., genomics, transcriptomics, metabolomics, proteomics, and microbiomics). These investigations are leading to new scientific insights and supporting the development of conservation actions, but they come with a substantial cost: the (partial) destruction of priceless and often irreplaceable specimens, which constitute a global heritage that should be permanently safeguarded for future reference. The absence of a comprehensive set of “best practices” for destructively sampling herbarium specimens leads to confusion and uncertainty from researchers and institutions alike and risks over-exploitation of precious collections when the research is executed. Here, we provide a set of best practices aimed at reducing these uncertainties and creating a framework for sustainably and ethically sampling herbarium specimens. Our recommendations are intended for two complementary but overlapping audiences—users and stewards—who together build, use, and protect herbarium collections.

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The destructive sampling conundrum and guidelines for effective and ethical sampling of herbaria

Davis

2024

Preprint

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The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation

Kosch,

Torres-Sánchez,

Liedtke

et al. 2024

Preprint

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Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomics resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomics resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, anti- predator strategies, and resilience and adaptive responses. They also serve as critical models for understanding widespread genomic characteristics, including evolutionary genome expansions and contractions given they have the largest range in genome sizes of any animal taxon and multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The advent of long-read sequencing technologies, along with computational techniques that enhance scaffolding capabilities and streamline computational workload is now enabling the ability to overcome some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC) in early 2023. This burgeoning community already has more than 282 members from 41 countries (6 in Africa, 131 in the Americas, 27 in Asia, 29 in Australasia, and 89 in Europe). The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and outline how the AGC can enable amphibian genomics research to “leap” to the next level.

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Lost in time: Unraveling the identity of Vitreorana parvula (Boulenger, 1895) (Anura: Centrolenidae)

ZUCCHETTI,

CASTROVIEJO-FISHER

2024

Zootaxa

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Vitreorana parvula was the first glassfrog described for the Atlantic Forest. The species, however, has become a taxonomic puzzle as the only known individual is the lectotype from the 19th century, which is not particularly well-preserved or accompanied by a detailed original description. To solve this problem, we collected topotypic specimens, as well as advertisement calls, tissue samples, and natural history data, and compared them to other Vitreorana species. Our results show clear morphological, acoustic, and genetic differences between V. parvula and other species of Vitreorana, except for V. uranoscopa. Following our results, we consider V. uranoscopa as a junior synonym of V. parvula and redescribe the species based on topotypic material, while summarizing relevant variation from across its distribution.

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Improving the gold standard in NCBI GenBank and related databases: DNA sequences from type specimens and type strains

Cited by 3 publications

References 48 publications

The destructive sampling conundrum and guidelines for effective and ethical sampling of herbaria

The destructive sampling conundrum and guidelines for effective and ethical sampling of herbaria

The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation

Lost in time: Unraveling the identity of Vitreorana parvula (Boulenger, 1895) (Anura: Centrolenidae)

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