Data from: Molecular evidence reveals unsustainable harvest of wild orchids
Data files
Mar 21, 2026 version files 85.05 MB
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README.md
6.85 KB
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species_occurrences.csv
14.40 KB
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species_ranges.pdf
64.78 MB
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species_ranges.zip
1.77 MB
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target_sequences.zip
18.45 MB
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tuber_measurements.csv
39.66 KB
Abstract
Human use of wild species has long reshaped biodiversity, but the historical dynamics of exploitation are often poorly documented. In the eastern Mediterranean, orchids are harvested for the production of salep, a traditional beverage made of dried orchid tubers. Pharmaceutical and natural history museums harbour collections of these tubers dating back centuries, but their provenance and species identity remain largely unknown. Here, salep tubers spanning nearly 200 years were analyzed using target capture of orchid-specific loci to identify the likely source among 80 regional candidate species. Our approach confidently identifies up to 85 % of highly degraded tubers, enabling temporal and spatial reconstructions of harvesting patterns. We reveal a rapid expansion in the diversity of collected species in recent decades that is linked to variation in flowering time. Longer harvesting seasons and universally declining tuber sizes are consistent with a scenario of intensifying exploitation. Species distribution models indicate that salep diversity sold on markets today exceeds local orchid availability, implying long-distance trade, while comparative phylogenomics identifies lineages that are increasingly targeted today and at elevated risk of future depletion. Combined, our results show that traditional salep orchid populations are declining, driving shifts toward new species and harvesting territories. This escalating trade poses a significant and growing threat to orchid diversity.
Dataset DOI: 10.5061/dryad.mpg4f4rf5
Description of the data and file structure
This dataset contains:
- The assembled sequences of 205 orchid loci targeted by the Orchidinae-205 bait kit, for 7 species not previously included in the original reference dataset (Veltman et al., 2024) and 178 historical and contemporary orchid tubers identified in this study. Only individuals with a coverage of at least 40 % (~150-330kb) are included.
- Weight and size measurements of all individual tubers belonging to the collections from which tubers were selected for sequencing.
- Range maps of 80 candidate species occurring in the study region (Greece, Turkey and Iran) that could be targets for orchid harvesting, and the corresponding shape files.
- Occurrence records of orchids observed during fieldwork in Iran (2013-2014), that served as input for species distribution models in addition to publicly available occurrence records from GBIF (https://www.gbif.org/).
Files and variables
File: species_occurrences.csv
Description: Occurrence records of Iranian orchid species that could be targets for salep harvesting, based on field observations. Together with publicly available records from GBIF, these occurrence records were used as input for species distribution modelling and continued spatial analyses in R, yielding range maps for 80 out of 85 candidate species.
Variables
- Species: Name of the observed species (based on the GBIF backbone taxonomy).
- Latitude: Latitude of observed species in decimal degrees.
- Longitude: Longitude of observed species in decimal degrees.
- Elevation: Elevation of observed species in meters (m) above sea level. Occurrences for which elevations were not recorded are indicated with "n/a".
File: species_ranges.pdf
Description: PDF with species range maps for 80 orchid species that could be targets for salep harvesting. The maps were generated in R from the shapefiles in species_ranges.zip. Species with insufficient occurrence records or model quality are not included.
File: species_ranges.zip
Description: Shapefiles used for spatial analysis in R, describing the geographic distribution of 80 orchid species that could be targets for salep harvesting. The distributions were inferred by 1) species distribution modelling with MaxEnt and 2) applying a custom habitat suitability threshold for each species that yielded the range map most closely resembling known species distributions based on expert knowledge (Kühn et al., 2019). Species with insufficient occurrence records or model quality are not included.
File: target_sequences.zip
Description: Target sequences for the Orchidinae-205 loci (Veltman et al., 2024) of 7 degraded leaf samples and 178 dried salep tubers collected in different centuries. The files are separated into two folders:
- de-novo: these files were generated with HybPiper (Johnson et al., 2016), which first sorts the on-target reads into their respective target loci by mapping against a previously published target reference file (Veltman et al., 2024) and subsequently performs de novo sequence assembly of each locus and identifies intron-exon boundaries. Only exon sequences were used. This was done for 17 tuber sequences with relatively high quality quality DNA and sufficiently long reads to perform assembly.
- reference-guided: these files were generated by mapping trimmed reads of each sample to the exon sequences of the closest reference species (i.e. the one with the highest mapping rate) in the same target reference file (Veltman et al., 2024), followed by SNP-calling, conversion to FASTA format, and subsequent masking of zero coverage regions. This done for all samples in Table S3 of the supplementary table, including the remaining 161 tubers and 7 degraded leaf samples for which the DNA was too short to assemble it with Hybpiper.
File: tuber_measurements.csv
Description: This file contains the weight and size measurements of all 1192 intact orchid tubers that were collected and analysed in the context of this study. Only a subset of these tubers were sequenced.
Variables
- Collection: The collection code used throughout the study (metadata available in Tables S1 and S2).
- Weight (g): Weight of the tuber, measured in grammes with a precision scale.
- Length (mm), Width (mm) and Depth (mm): size of the tuber, measured in millimetres with a caliper at two decimal points precision, along three dimensions.
- LxWxD: the product of the tuber size measurements along all three dimensions (an estimate of it's total size in cubic millimetres).
- DNA sample: Sample numbers of tubers from which DNA was extracted. Tubers from which no DNA was extracted are indicated with "n/a".
Code/software
The shapefiles can be opened in R with the 'sf' package. The target sequences can be viewed in a standard text editor.
Access information
Data was derived from the following sources:
- The target reference sequences used for reference-guided assembly of the raw sequencing reads are available in Veltman, Margaretha (2024). Data from: Orchidinae-205: A new genome-wide custom bait set for studying the evolution, systematics, and trade of terrestrial orchids [Dataset]. Dryad. https://doi.org/10.5061/dryad.sj3tx96bn.
- Additional occurrence records of candidate species that were used for species distribution modelling and range map construction were downloaded from GBIF (https://www.gbif.org/).
Other publicly accessible locations of the data:
- Raw sequencing reads used to perform reference-guided assembly of the target sequences is publicly available on the NCBI Sequence Read Archive under project number PRJNA1403031.
References
- Johnson, M. G., Gardner, E. M., Liu, Y., Medina, R., Goffinet, B., Shaw, A. J., Zerega, N. J. C., & Wickett, N. J. (2016). HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment. Applications in Plant Sciences, 4(7), 1600016. https://doi.org/10.3732/apps.1600016.
- Kühn, R., Pedersen, H., and Cribb, P. (2019). Field Guide to the Orchids of Europe and the Mediterranean (Kew Publishing).
- Veltman, M.A., Anthoons, B., Schrøder-Nielsen, A., Gravendeel, B., and de Boer, H.J. (2024). Orchidinae-205: A new genome-wide custom bait set for studying the evolution, systematics, and trade of terrestrial orchids. Molecular Ecology Resources 24, e13986. https://doi.org/10.1111/1755-0998.13986.