The informative value of museum collections for ecology and conservation: A comparison with target sampling in the Brazilian Atlantic forest

Tarli, Vitor Dias; Grandcolas, Philippe; Pellens, Roseli

doi:10.1371/journal.pone.0205710

Cited by 12 publications

(8 citation statements)

References 47 publications

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“…These data proved to be extremely useful for identifying species in a more recent exploration of native parasitoid biodiversity across North America (e.g., Abram et al, 2020). There are additional uses for DROP: curated specimen collections may be used to document species distributions, phenology, understand microevolutionary patterns, observe the effects of climate change, and detect and track biological invasions (Funk, 2018;Schilthuizen et al, 2015;Tarli et al, 2018).…”

Section: From Molecular Mechanisms To Ecosystem Structurementioning

confidence: 99%

DROP: Molecular voucher database for identification of Drosophila parasitoids

Lue

Buffington

Scheffer

et al. 2021

Molecular Ecology Resources

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Molecular identification is increasingly used to speed up biodiversity surveys and laboratory experiments. However, many groups of organisms cannot be reliably identified using standard databases such as GenBank or BOLD due to lack of sequenced voucher specimens identified by experts. Sometimes a large number of sequences are available, but with too many errors to allow identification. Here we address this problem for parasitoids of Drosophila by introducing a curated open-access molecular reference database, DROP (Drosophila parasitoids). Identifying Drosophila parasitoids is specimens are identified by taxonomists and vetted through direct comparison with primary type material. To initiate DROP, we curated 154 laboratory strains, 853 vouchers, 545 DNA sequences, 16 genomes, 11 transcriptomes, and 6 proteomes drawn from a total of 183 operational taxonomic units (OTUs): 113 described Drosophila parasitoid species and 70 provisional species. We found species richness of Drosophila parasitoids to be acutely underestimated and provide an updated taxonomic catalogue for the community. DROP offers accurate molecular identification and improves crossreferencing between individual studies that we hope will catalyze research on this diverse and fascinating model system. Our effort should also serve as an example for researchers facing similar molecular identification problems in other groups of organisms.

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Section: From Molecular Mechanisms To Ecosystem Structurementioning

confidence: 99%

DROP: Molecular voucher database for identification of Drosophila parasitoids

Lue

Buffington

Scheffer

et al. 2021

Molecular Ecology Resources

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“…The vast amounts of specimens of seagrasses deposited in herbaria can serve as a historical lens into the ecological processes by which presentday seagrass diversity arose, are maintained, and may evolve in the future. However, occurrence records archived in herbaria and museums are non-randomly collected over space and time, and thus present biases and uncertainties that can complicate ecological inferences (e.g., Boakes et al, 2010;Meyer et al, 2016;Daru et al, 2018;Dias Tarli et al, 2018). As a consequence, the use of occurrence records has not fully permeated the field of global change biology.…”

Section: Knowledge Gaps In Seagrass Sampling Practicesmentioning

confidence: 99%

Impediments to Understanding Seagrasses’ Response to Global Change

Rock

Daru

2021

Front. Mar. Sci.

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Uncertainties from sampling biases present challenges to ecologists and evolutionary biologists in understanding species sensitivity to anthropogenic climate change. Here, we synthesize possible impediments that can constrain research to assess present and future seagrass response from climate change. First, our knowledge of seagrass occurrence information is prevalent with biases, gaps and uncertainties that can influence inferences on species response to global change. Second, research on seagrass diversity has been focused on species-level metrics that can be measured with data from the present – but rarely accounting for the shared phylogenetic relationships and evolutionary distinctiveness of species despite species evolved and diversified from shared ancestors. Third, compared to the mass production of species occurrence records, computational tools that can analyze these datasets in a reasonable amount of time are almost non-existent or do not scale well in terms of computer time and memory. These impediments mean that scientists must work with incomplete information and often unrepresentative data to predict how seagrass diversity might change in the future. We discuss these shortfalls and provide a framework for overcoming the impediments and diminishing the knowledge gaps they generate.

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“…These data proved to be extremely useful for identifying species in a more recent exploration of native parasitoid biodiversity across North America (e.g., Abram et al, 2020). There are additional uses for DROP: curated specimen collections may be used to document species distributions, phenology, understand micro-evolutionary patterns, observe the effects of climate change, and detect and track biological invasions (Funk, 2018;Schilthuizen et al, 2015;Tarli et al, 2018).…”

Section: From Molecular Mechanisms To Ecosystem Structurementioning

confidence: 99%

DROP: Molecular voucher database for identification ofDrosophilaparasitoids

Lue

Buffington

Scheffer

et al. 2021

Preprint

View full text Add to dashboard Cite

Molecular identification is increasingly used to speed up biodiversity surveys and laboratory experiments. However, many groups of organisms cannot be reliably identified using standard databases such as GenBank or BOLD due to lack of sequenced voucher specimens identified by experts. Sometimes a large number of sequences are available, but with too many errors to allow identification. Here we address this problem for parasitoids of Drosophila by introducing a curated open-access molecular reference database, DROP (Drosophila parasitoids). Identifying Drosophila parasitoids is challenging and poses a major impediment to realize the full potential of this model system in studies ranging from molecular mechanisms to food webs, and in biological control of Drosophila suzukii. In DROP (http://doi.org/10.5281/zenodo.4519656), genetic data are linked to voucher specimens and, where possible, the voucher specimens are identified by taxonomists and vetted through direct comparison with primary type material. To initiate DROP, we curated 154 laboratory strains, 853 vouchers, 545 DNA sequences, 16 genomes, 11 transcriptomes, and 6 proteomes drawn from a total of 183 operational taxonomic units (OTUs): 113 described Drosophila parasitoid species and 70 provisional species. We found species richness of Drosophila parasitoids to be acutely underestimated and provide an updated taxonomic catalogue for the community. DROP offers accurate molecular identification and improves cross-referencing between individual studies that we hope will catalyze research on this diverse and fascinating model system. Our effort should also serve as an example for researchers facing similar molecular identification problems in other groups of organisms.

show abstract

The informative value of museum collections for ecology and conservation: A comparison with target sampling in the Brazilian Atlantic forest

Cited by 12 publications

References 47 publications

DROP: Molecular voucher database for identification of Drosophila parasitoids

DROP: Molecular voucher database for identification of Drosophila parasitoids

Impediments to Understanding Seagrasses’ Response to Global Change

DROP: Molecular voucher database for identification ofDrosophilaparasitoids

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