Deer grazing drove an assemblage-level evolution of plant dwarfism in an insular system
Data files
Mar 29, 2024 version files 1.91 MB
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InputFiles_GeneticAnalysis.zip
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Morphodata_All_20240326.csv
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NconcentrationDataSub_20240327.csv
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README.md
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Species-pairData20240327.csv
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VoucherList.csv
Abstract
Plant dwarfism, a syndrome characterised by a significant reduction in plant height and organ size, is a widely observed pattern of stress-tolerant life-form evolution that results from local adaptation to harsh environmental conditions. The drivers of assemblage-level dwarfism have primarily been attributed to abiotic factors, such as low temperature, aridity, poor soil fertility, or frequent fires. While biotic factors such as grazing pressure from herbivores can contribute to the establishment of plant dwarfism, these factors have rarely been tested at assemblage levels. Focusing on a dwarf plant assemblage comprising over 80 taxa on a small continental island in Japan with a high deer density, we hypothesised that historical deer grazing could also be a factor contributing to the large-scale convergent evolution of dwarfism. To test this hypothesis, we measured the size of 1,908 individual plants of 40 taxa-pairs, comprising both palatable and unpalatable pairs from the island and their counterpart taxa from neighbouring regions, and sought to assess which factors (i.e. low solar radiation, estimated divergence time, low nutrient conditions, and grazing pressure from deer) may have contributed to the formation of the dwarf plant assemblage on the island. We also performed genetic analysis to infer the timeframes for the establishment of dwarf taxa. Statistical analyses revealed that plant size was significantly reduced mainly among the palatable taxa growing on the island, with preferential grazing by deer being identified as the most significant factor influencing plant size. Furthermore, genetic analyses revealed that dwarf ecotypes may have evolved over tens of thousands of years.
Synthesis: To the best of our knowledge, this study is the first to demonstrate that interactions with herbivores can shape the assemblage-level convergence of plant dwarfism. These findings enhance our current understanding of the formation of plant functional diversity.
README: Deer grazing drove an assemblage-level evolution of plant dwarfism in an insular system
Raw morphological data, leaf N concentration, and input file for LM analysis and genetic analyses are included. We also show the BioProject ID of raw read data of MIG-seq analysis deposited in NCBI.
Description of the Data and file structure
Morphodata_All_20240326.csv
Raw morphological data
- Taxapair: Name of the taxa pair
- Yakushima_alpine_or_counterpart: Binary population code (1: Yakushima alpine taxa, 0: counterpart taxa)
- Lat: latitude
- Lon: Longitude
- Alt: Altitude (m)
- Taxon name: Scientific name of taxon
- SpecimenSheetNO: Specimen sheet number or voucher number
- Locality: Name of collection sites
- IndividualID: Plant individual ID in the sheet
- Leafsize: Measured length of leaf (mm)
- Plantheight: Measured length of plant height (mm)
- IndexTrait: Used traits for statistical analyses of leaf size or plant height
- Preference: deer preference of the taxa-pair, preferable or non-preferable.
NconcentrationDataSub.csv
Raw data of leaf Nitrogen concentration
- Taxapair: Name of the taxa pair
- Yakushima_alpine_or_counterpart: Population information Yakushima alpine or counterpart taxa
- Preference: deer preference of the taxa-pair, preferable or non-preferable.
- IndividualID: Sample id
- mg: Measured weight (mg)
- Nvalues: Measured amount of nitrogen (mg)
- N%: leaf nitrogen concentration (%)
- C%: leaf carbon concentration (%)
Species-pairData20230607sub.csv
Input file for LM analysis
- Taxapair: Name of the taxa pair
- Y_N: Number of individuals of Yakushima alpine taxa used for morphological measurement
- Y_mean: Mean plant size of Yakushima alpine tax a (mm)
- C_N: Number of individuals of counterpart taxa used for morphological measurement
- C_mean: Mean plant size of counterpart taxa (mm)
- Preference: deer preference of the taxa-pair, preferable or non-preferable.
- DivTime: Estimated divergence time (years)
- Nratio: Rate of leaf nitrogen concentration calculated by dividing the mean leaf nitrogen concentration of the Yakushima alpine taxon by that of its counterpart taxon
- Index: The relative plant size of each taxa-pair was calculated by dividing the mean plant height or leaf size of the Yakushima alpine taxon by that of its counterpart taxon
- MATdiff: The difference of mean annual temperature for the collection localities of the Yakushima alpine and the counterpart taxa (10^-1 °C)
- APdiff: The difference of annual precipitation for the collection localities of the Yakushima alpine and the counterpart taxa (10^-1 mm)
- ATSPdiff: The difference in sunshine duration (hours) for the collection localities of the Yakushima alpine and the counterpart taxa (10^-1 hour)
VoucherList.csv
Voucher information of materials
- Taxapair: Name of the taxa pair
- Taxon name: Scientific name of taxon
- Yakushima_alpine_or_counterpart: Population information Yakushima alpine or counterpart taxa
- Voucher: Voucher code (all specimens are deposited to TUS), and NA means measurements are conducted only using deposited specimens or living materials
InputFiles_GeneticAnalysis.zip
Input files for fastsimcoal2 and StairwayPlot2
Sharing/Access Information
Links to other publicly accessible locations of the data: The National Center for Biotechnology Information (BioProject ID: PRJNA862386)