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PremiseThe ability to sequence genome‐scale data from herbarium specimens would allow for the economical development of data sets with broad taxonomic and geographic sampling that would otherwise not be possible. Here, we evaluate the utility of a basic double‐digest restriction site–associatedDNAsequencing (ddRADseq) protocol usingDNAs from four genera extracted from both silica‐dried and herbarium tissue. MethodsDNAs fromDraba,Boechera,Solidago, andIlexwere processed with a ddRADseq protocol. The effects ofDNAdegradation, taxon, and specimen age were assessed. ResultsAlthough taxon, preservation method, and specimen age affected data recovery, large phylogenetically informative data sets were obtained from the majority of samples. DiscussionThese results suggest that herbarium samples can be incorporated into ddRADseq project designs, and that specimen age can be used as a rapid on‐site guide for sample choice. The detailed protocol we provide will allow users to pursue herbarium‐based ddRADseq projects that minimize the expenses associated with fieldwork and sample evaluation.
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A new phenological metric for use in pheno‐climatic models: A case study using herbarium specimens of Streptanthus tortuosus
PremiseHerbarium specimens have been used to detect climate‐induced shifts in flowering time by using the day of year of collection (DOY) as a proxy for first or peak flowering date. Variation among herbarium sheets in their phenological status, however, undermines the assumption thatDOYaccurately represents any particular phenophase. Ignoring this variation can reduce the explanatory power of pheno‐climatic models (PCMs) designed to predict the effects of climate on flowering date. MethodsHere we present a protocol for the phenological scoring of imaged herbarium specimens using an ImageJ plugin, and we introduce a quantitative metric of a specimen's phenological status, the phenological index (PI), which we use inPCMs to control for phenological variation among specimens ofStreptanthus tortuosus(Brassicaceeae) when testing for the effects of climate onDOY. We demonstrate that includingPIas an independent variable improves model fit. ResultsIncludingPIinPCMs increased the modelR2relative toPCMs that excludedPI; regression coefficients for climatic parameters, however, remained constant. DiscussionOur protocol provides a simple, quantitative phenological metric for any observed plant. IncludingPIinPCMs increasesR2and enables predictions of theDOYof any phenophase under any specified climatic conditions.
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- Award ID(s):
- 1802301
- PAR ID:
- 10461304
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- Applications in Plant Sciences
- Volume:
- 7
- Issue:
- 7
- ISSN:
- 2168-0450
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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