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opencc-zeroDec 2018View details →

Data from: A rangewide herbarium-derived dataset indicates high levels of gene flow in black cherry (Prunus serotina)

Aim: Isolation by Distance (IBD) is a genetic pattern in which populations geographically closer to one another are more genetically similar to each other than populations which are farther apart. Black cherry (Prunus serotina Ehrh.) (Rosaceae) is a forest tree species widespread in eastern North America, and found sporadically in the southwestern United States, Mexico, and Guatemala. IBD has been studied in relatively few North American plant taxa, and no study has rigorously sampled across the range of such a widespread species. In this study, IBD and overall genetic structure were assessed in eastern black cherry (P. serotina Ehrh. subsp. serotina), the widespread subspecies of eastern North America. Location: Eastern North America Taxon: Prunus serotina Ehrh. Rosaceae Methods: Dense sampling across the entire range of eastern black cherry was made possible by genotyping 15 microsatellite loci in 439 herbarium samples from all portions of the range. Mantel tests and STRUCTURE analyses were performed to evaluate the hypothesis of IBD and genetic structure. Results: Mantel tests demonstrated significant but weak IBD, while STRUCTURE analyses revealed no clear geographic pattern of genetic groups. Main conclusions: The modest geographic/genetic structure across the eastern black cherry range suggests widespread gene flow in this taxon. This is consistent with P. serotina's status as a disturbance-associated species. Further studies should similarly evaluate IBD in species characteristic of low-disturbance forests.

opencc-zeroDec 2014View details →

Data from: Next-generation sampling: pairing genomics with herbarium specimens provides species-level signal in Solidago (Asteraceae)

Premise of the study: The ability to conduct species delimitation and phylogeny reconstruction with genomic data sets obtained exclusively from herbarium specimens would rapidly enhance our knowledge of large, taxonomically contentious plant genera. In this study, the utility of genotyping by sequencing is assessed in the notoriously difficult genus Solidago (Asteraceae) by attempting to obtain an informative single-nucleotide polymorphism data set from a set of specimens collected between 1970 and 2010. Methods: Reduced representation libraries were prepared and Illumina-sequenced from 95 Solidago herbarium specimen DNAs, and resulting reads were processed with the nonreference Universal Network-Enabled Analysis Kit (UNEAK) pipeline. Multidimensional clustering was used to assess the correspondence between genetic groups and morphologically defined species. Results: Library construction and sequencing were successful in 93 of 95 samples. The UNEAK pipeline identified 8470 single-nucleotide polymorphisms, and a filtered data set was analyzed for each of three Solidago subsections. Although results varied, clustering identified genomic groups that often corresponded to currently recognized species or groups of closely related species. Discussion: These results suggest that genotyping by sequencing is broadly applicable to DNAs obtained from herbarium specimens. The data obtained and their biological signal suggest that pairing genomics with large-scale herbarium sampling is a promising strategy in species-rich plant groups.

publicMay 2016View details →

Data from: Next-generation sampling: pairing genomics with herbarium specimens provides species-level signal in Solidago (Asteraceae)

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publicMar 2019View details →

Data from: Bolstering species delimitation in difficult species complexes by analyzing herbarium and common garden morphological data: a case study using the New Zealand native Myosotis pygmaea species group (Boraginaceae)

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publicJan 2019View details →

Data from: A rangewide herbarium-derived dataset indicates high levels of gene flow in black cherry (Prunus serotina)

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dryad28/100

Data from: Robust DNA isolation and high-throughput sequencing library construction for herbarium specimens

Herbaria are an invaluable source of plant material that can be used in a variety of biological studies. The use of herbarium specimens is associated with a number of challenges including sample preservation quality, degraded DNA, and destructive sampling of rare specimens. In order to more effectively use herbarium material in large sequencing projects, a dependable and scalable method of DNA isolation and library preparation is needed. This paper demonstrates a robust, beginning-to-end protocol for DNA isolation and high-throughput library construction from herbarium specimens that does not require modification for individual samples. This protocol is tailored for low quality dried plant material and takes advantage of existing methods by optimizing tissue grinding, modifying library size selection, and introducing an optional reamplification step for low yield libraries. Reamplification of low yield DNA libraries can rescue samples derived from irreplaceable and potentially valuable herbarium specimens, negating the need for additional destructive sampling and without introducing discernible sequencing bias for common phylogenetic applications. The protocol has been tested on hundreds of grass species, but is expected to be adaptable for use in other plant lineages after verification. This protocol can be limited by extremely degraded DNA, where fragments do not exist in the desired size range, and by secondary metabolites present in some plant material that inhibit clean DNA isolation. Overall, this protocol introduces a fast and comprehensive method that allows for DNA isolation and library preparation of 24 samples in less than 13 hours, with only 8 hours of active hands-on time with minimal modifications.

opencc-zeroDec 2017View details →

dryad28/100

Data from: The changing uses of herbarium data in an era of global change: an overview using automated content analysis

Widespread specimen digitization has greatly enhanced the use of herbarium data in scientific research. Publications using herbarium data have increased exponentially over the last century. Here, we review changing uses of herbaria through time with a computational text analysis of 13,702 articles from 1923 to 2017 that quantitatively complements traditional review approaches. Although maintaining its core contribution to taxonomic knowledge, herbarium use has diversified from a few dominant research topics a century ago (e.g., taxonomic notes, botanical history, local observations), with many topics only recently emerging (e.g., biodiversity informatics, global change biology, DNA analyses). Specimens are now appreciated as temporally and spatially extensive sources of genotypic, phenotypic, and biogeographic data. Specimens are increasingly used in ways that influence our ability to steward future biodiversity. As we enter the Anthropocene, herbaria have likewise entered a new era with enhanced scientific, educational, and societal relevance.

opencc-zeroSep 2019View details →

Figure 5 from: Zhao Y, Zhao F, Paton AJ, Xiao J-F, Chen Y-P, Xiang C-L (2024) Using scanning electron microscopy and molecular data to discover a new species from old herbarium collections: The case of Phlomoides henryi (Lamiaceae, Lamioideae). PhytoKeys 238: 127-146. https://doi.org/10.3897/phytokeys.238.117180

Figure 5 Phlomoides henryi Y.Zhao & C.L.Xiang A habitat B plant with linear-tuberous roots C inflorescence D verticillaster E flowers F dissected flower G appendages at base of posterior filaments H fruiting calyces I dissected calyces J bracts K floral leaves L stem leaves. Photographs by Yue Zhao, except C by Li Chen.

Figure 4 from: Zhao Y, Zhao F, Paton AJ, Xiao J-F, Chen Y-P, Xiang C-L (2024) Using scanning electron microscopy and molecular data to discover a new species from old herbarium collections: The case of Phlomoides henryi (Lamiaceae, Lamioideae). PhytoKeys 238: 127-146. https://doi.org/10.3897/phytokeys.238.117180

Figure 4 SEM of both sides of leaves of Phlomoides henryi and related species A, BP. henryiC, DP. bracteosaE, FP. brevifloraG, HP. macrophyllaI, JP. nyalamensisK, LP. tibeticaM, NP. milingensisO, PP. rotataA, C, E, G, I, K, M, OSEM of adaxial leaves B, D, F, H, J, L, N, PSEM of abaxial leaves.

Figure 2 from: Zhao Y, Zhao F, Paton AJ, Xiao J-F, Chen Y-P, Xiang C-L (2024) Using scanning electron microscopy and molecular data to discover a new species from old herbarium collections: The case of Phlomoides henryi (Lamiaceae, Lamioideae). PhytoKeys 238: 127-146. https://doi.org/10.3897/phytokeys.238.117180

Figure 2 Different types of trichomes of PhlomoidesA short simple non-glandular trichomes (P. macrophylla) B short simple non-glandular trichomes (P. breviflora) C long simple non-glandular trichomes (P. henryi) D symmetrically non-glandular stellate (P. breviflora) E non-glandular stellate with central long branch (P. bracteosa) F bi- or trifurcate non-glandular stellate (P. nyalamensis) G sub-sessile/ sessile glandular trichomes (P. macrophylla) H simple glandular trichomes of (P. bracteosa) I branched glandular trichomes (P. breviflora).

Figure 1 from: Zhao Y, Zhao F, Paton AJ, Xiao J-F, Chen Y-P, Xiang C-L (2024) Using scanning electron microscopy and molecular data to discover a new species from old herbarium collections: The case of Phlomoides henryi (Lamiaceae, Lamioideae). PhytoKeys 238: 127-146. https://doi.org/10.3897/phytokeys.238.117180

Figure 1 Phylogeny of Phlomoides inferred by Bayesian Inference (BI), based on the combined plastid dataset cpDNA. Support values displayed on the branches follow the order BI-PP/ML-BS (" * " indicates PP = 1.00 or BS = 100%, "-" indicates incongruent relationship between BI and ML tree.

Figure 3 from: Zhao Y, Zhao F, Paton AJ, Xiao J-F, Chen Y-P, Xiang C-L (2024) Using scanning electron microscopy and molecular data to discover a new species from old herbarium collections: The case of Phlomoides henryi (Lamiaceae, Lamioideae). PhytoKeys 238: 127-146. https://doi.org/10.3897/phytokeys.238.117180

Figure 3 Photos of bracts, SEM of bracts of Phlomoides henryi and related species A, BP. henryiC, DP. bracteosaE, FP. brevifloraG, HP. macrophyllaI, JP. nyalamensisK, LP. tibeticaM, NP. milingensisO, PP. rotata. A, C, E, G, I, K, M, O photos of bracts B, D, F, H, J, L, N, PSEM of bracts.

Supplementary material 1 from: Vissers J, Bosch FV, Bogaerts A, Cocquyt C, Degreef J, Diagre D, de Haan M, De Smedt S, Engledow H, Ertz D, Fabri R, Godefroid S, Hanquart N, Mergen P, Ronse A, Sosef M, Stévart T, Stoffelen P, Vanderhoeven S, Groom Q (2017) Scientific user requirements for a herbarium data portal. PhytoKeys 78: 37-57. https://doi.org/10.3897/phytokeys.78.10936

Gathered needs per type of researcher :

Figure 1 from: Vissers J, Bosch FV, Bogaerts A, Cocquyt C, Degreef J, Diagre D, de Haan M, De Smedt S, Engledow H, Ertz D, Fabri R, Godefroid S, Hanquart N, Mergen P, Ronse A, Sosef M, Stévart T, Stoffelen P, Vanderhoeven S, Groom Q (2017) Scientific user requirements for a herbarium data portal. PhytoKeys 78: 37-57. https://doi.org/10.3897/phytokeys.78.10936

Figure 1 - Stakeholders interacting with the Botanic Garden Meise and potentially using its data portal. The stakeholders prefixed by the words 'internal' refer to those that work at the Botanic Garden, whereas those referred to as 'external' refer to researchers in other institutions.

Figure 3 from: Vissers J, Bosch FV, Bogaerts A, Cocquyt C, Degreef J, Diagre D, de Haan M, De Smedt S, Engledow H, Ertz D, Fabri R, Godefroid S, Hanquart N, Mergen P, Ronse A, Sosef M, Stévart T, Stoffelen P, Vanderhoeven S, Groom Q (2017) Scientific user requirements for a herbarium data portal. PhytoKeys 78: 37-57. https://doi.org/10.3897/phytokeys.78.10936

Figure 3 - A summary of the data elements mentioned by the different researcher types, showing which data elements researchers had in common and which were unique. This does not mean that any particular data element is not of interest to another group, only that it did not arise in the series of interviews. Details of these data elements can be found in the supplementary information. The full list of common data elements is listed in Table 2.

Figure 2 from: Vissers J, Bosch FV, Bogaerts A, Cocquyt C, Degreef J, Diagre D, de Haan M, De Smedt S, Engledow H, Ertz D, Fabri R, Godefroid S, Hanquart N, Mergen P, Ronse A, Sosef M, Stévart T, Stoffelen P, Vanderhoeven S, Groom Q (2017) Scientific user requirements for a herbarium data portal. PhytoKeys 78: 37-57. https://doi.org/10.3897/phytokeys.78.10936

Figure 2 - A user experience researcher using affinity diagramming to cluster user requirements from the results of the interviews.

opencc-zeroJan 2024View details →

Linked collectors and determiners for: Janet Cosh Herbarium (WOLL) AVH data.

Natural history specimen data linked to collectors and determiners held within, "Janet Cosh Herbarium (WOLL) AVH data". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/2002f5f5-a2b6-43ee-bcc7-44811ae22acb">https://bionomia.net/dataset/2002f5f5-a2b6-43ee-bcc7-44811ae22acb</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/2002f5f5-a2b6-43ee-bcc7-44811ae22acb">https://gbif.org/dataset/2002f5f5-a2b6-43ee-bcc7-44811ae22acb</a>. Formatted as a Frictionless Data package.