Appendix II – Representing Tissue Conditions in Metadata for Quality Control

This appendix provides a brief discussion and examples of the IHerbSpec approach for recording metadata pertaining to sources of biological and herborization variation that affect spectral data. As explained in Section 6.1 Sources of Variation, we aim to capture biological variation that is scientifically meaningful, but the degraded nature of herbarium specimens requires a careful assessment and annotation of tissue quality and sources of contamination. The Tissue Metadata fields of developmentalStage, hasGlue, hasNonGlueContamination, measurementFlags, and tissueNotes Table 4.3 are designed to support quality control of spectral data and enable downstream filtering.

The codes for enumerating the developmentalStage fields are provided in Table 4.4, and the codes for measurementFlags are described in Table 4.6.

Technicians should also be aware that some taxa (e.g. Myrtaceae) or tropical collections in general may naturally exhibit discoloration or non-flat, deformed surfaces (e.g., Gasteranthus atratus). Such characteristics do not necessarily indicate tissue degradation and poor-quality spectral data. In addition, some taxa exhibit more pronounced discoloration during herborization as a result of their biology, and such discoloration should not be interpreted as evidence of poor preservation condition. Some traits also covary; for example, young leaves wilt and become discolored faster and are more challenging to press and dry flat, so they may more often be scored as moderately or poorly preserved.

As a reminder, measurementFlags pertain only to the measurement area, not the whole tissue unit (e.g., leaf). Since suitable measurement areas of tissues (see decision tree in Fig. 6.1) will not contain any contaminants, pathogens, or other damage, technicians should not be enumerating any codes in the measurementFlags field. This could differ in projects collecting measurements pertaining to extended uses of the specimen, e.g., symbionts, degradation, etc., that might be measuring tissue areas with these other features.

The specimens and metadata examples in Table A1 have been selected to guide consistent scoring of these fields during spectral measurement and promote metadata consistency across projects. Note that the images do not specify the exact measurement area corresponding to these metadata fields (as is done in the IHerbSpec Metadata Spreadsheet for specimen NEBC_00651639 shown in main text Fig. 2.2).

Table A1: Select Metadata Fields and Scoring for Representative Specimens.

This table provides example metadata records for herbarium specimens, illustrating how to score key fields related to tissue condition and contamination. The fields developmentalStage, hasGlue, hasNonGlueContamination, and measurementFlags refer specifically to the measurement area. Broader observations about the specimen or other tissues can be recorded in tissueNotes (see Table 4.3). Linked specimen images are included, though they do not indicate the precise measurement area corresponding to each metadata record. This table can be downloaded on the Protocol home page.

herbariumCode_specimenID	`developmentalStage`	`hasGlue`	`hasNonGlueContamination`	`measurementFlags`	`tissueNotes`
A_00631088	`mature`	`TRUE`	`FALSE`	`MediumPreservation`	discolored
A_00672503	`mature`	`FALSE`	`TRUE`	`GoodPreservation`	PathogenPresent
A_00746288	`mature`	`TRUE`	`FALSE`	`MediumPreservation`	Discolored. Glue on loose leaf in measurement area.
A_00772865	`young`	`FALSE`	`FALSE`	`PoorPreservation`	Measured leaves uneven, mottled, discolored, breakage
A_2613405	`mature`	`FALSE`	`FALSE`	`MediumPreservation`
A_2614928	`mature`	`uncertain`	`TRUE`	`PoorPreservation`	OrganismPresent
AAU_A.S.Barfod48062	`mature`	`FALSE`	`TRUE`	`MediumPreservation`	MidveinPresent
AAU_I.A.Chacon1199	`mature`	`FALSE`	`TRUE`	`MediumPreservation`	AlcoholPresent
AAU_R.C.Moran6023	`mature`	`FALSE`	`TRUE`	`GoodPreservation`	AlcoholPresent
ALF_035514	`mature`, `young`	`FALSE`	`FALSE`	`GoodPreservation`
ECON_00338371	`young`	`FALSE`	`FALSE`	`MediumPreservation`	Discolored, wrinkled. Specimen burnt but not in target area.
GH_00611866	`mature`	`FALSE`	`FALSE`	`MediumPreservation`	Discolored specimen
INPA_142198	`mature`	`FALSE`	`FALSE`	`MediumPreservation`	discolored, herbivory on specimen
INPA_179322	`mature`	`FALSE`	`FALSE`	`GoodPreservation`
INPA_184434	`mature`	`FALSE`	`FALSE`	`MediumPreservation`	Herbivory on specimen, necrotic leaf
INPA_187932	`mature`	`FALSE`	`FALSE`	`MediumPreservation`	burnt leaves on specimen
INPA_203125	`mature`	`FALSE`	`FALSE`	`MediumPreservation`	discolored, wrinkled leaves
INPA_218399	`mature`	`TRUE`	`FALSE`	`PoorPreservation`	discolored, herbivory, wrinkled and burnt leaves
INPA_264413	`mature`	`FALSE`	`FALSE`	`GoodPreservation`
INPA_267597	`mature`	`FALSE`	`FALSE`	`GoodPreservation`
INPA_275373	`mature`	`FALSE`	`FALSE`	`MediumPreservation`	discolored, mold, grayish spots on older leaves specimen
INPA_278882	`mature`	`FALSE`	`TRUE`	`MediumPreservation`	AlcoholPresent
INPA_4628	`mature`	`FALSE`	`TRUE`	`PoorPreservation`	PreservativePresent
INPA_59178	`mature`	`TRUE`	`TRUE`	`PoorPreservation`	PathogenPresent
INPA_72939	`mature`	`TRUE`	`TRUE`	`PoorPreservation`	FungusPresent
INPA_97794	`mature`	`FALSE`	`FALSE`	`MediumPreservation`	wrinkled leaves
INPA264208	`mature`	`FALSE`	`FALSE`	`MediumPreservation`	Measurement area not flat. Herbivory on sheet
M_PU681750	`mature`	`FALSE`	`uncertain`	`MediumPreservation`	Discolored; Alcohol preservation suspected.
MIN_332436	`mature`	`FALSE`	`FALSE`	`MediumPreservation`	MidveinPresent
MIN_370477	`mature`	`FALSE`	`FALSE`	`PoorPreservation`	discolored, wrinkled leaves
MIN_588200	`mature`	`FALSE`	`FALSE`	`GoodPreservation`
NEBC_00634726	`young`	`FALSE`	`FALSE`	`PoorPreservation`	Measurement area leaves uneven, discolored
NEBC_00636882	`uncertain`	`FALSE`	`TRUE`	`PoorPreservation`	PathogenPresent
NEBC_00651639	`mature`	`FALSE`	`FALSE`	`GoodPreservation`
NEBC_00677096	`mature`	`FALSE`	`TRUE`	`MediumPreservation`	PathogenPresent
NEBC_00695035	`mature`	`FALSE`	`FALSE`	`GoodPreservation`
NEBC_00746092	`mature`	`FALSE`	`TRUE`	`MediumPreservation`	PathogenPresent
NEBC_00898559	`mature`	`FALSE`	`FALSE`	`GoodPreservation`
NEBC_02618198	`mature`	`FALSE`	`FALSE`	`MediumPreservation`	Dark spots on measured leaf
NEBC_02618743	`mature`	`FALSE`	`FALSE`	`GoodPreservation`
NY_00042623	`mature`	`TRUE`	`FALSE`	`GoodPreservation`
NY_00043385	`mature`	`FALSE`	`TRUE`	`MediumPreservation`	PathogenPresent
NY_00194824	`mature`	`FALSE`	`FALSE`	`GoodPreservation`
NY_00402473	`mature`	`TRUE`	`FALSE`	`MediumPreservation`	MoldPresent
NY_00709210	`mature`	`FALSE`	`TRUE`	`MediumPreservation`	PathogenPresent
NY_01163859	`mature`	`TRUE`	`FALSE`	`MediumPreservation`	Discolored; herbivory on specimen
NY_02498899	`mature`	`TRUE`	`FALSE`	`MediumPreservation`	Discolored
NY_02499746	`mature`	`FALSE`	`TRUE`	`PoorPreservation`	MoldPresent
P_00391795	`mature`	`FALSE`	`uncertain`	`MediumPreservation`	wrinkled leaves; possible chemical preservative.
P_05198525	`mature`	`FALSE`	`TRUE`	`PoorPreservation`	FungusPresent
P_05198660	`mature`	`FALSE`	`TRUE`	`MediumPreservation`	AlcoholPresent

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Browse additional parts and appendices below

Part 1 – Overview
Part 2 – Measurement and Metadata Workflow
Part 3 – Filename Conventions and Formats
Part 4 – Metadata and Databasing
Part 5 – Instrumentation and Materials Guidelines
Part 6 – Selecting Tissues for Spectral Measurement
References
Appendix I – Number of Measurements per Tissue
Appendix II – Tissue Metadata for Quality Control