DOI: 10.5061/dryad.t1g1jwt7c
title: Deer grazing drove an assemblage-level evolution of plant dwarfism in an insular system

description: 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.
description: # 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)