DOI: 10.5061/dryad.brv15dvhd
title: Does ecology shape geographical parthenogenesis? Evidence from the facultatively parthenogenetic stick insect Megacrania batesii

description: Closely related sexual and parthenogenetic species often show distinct
 distribution patterns, known as geographical parthenogenesis. These
 patterns, characterized by a mosaic of separate sexual and parthenogenetic
 populations across their natural range, can also be found in facultative
 parthenogens – species in which every female is capable of both sexual and
 parthenogenetic reproduction. The underlying mechanisms driving this
 phenomenon in nature remain unclear. Features of the habitat, such as
 differences in host plant phenotypes or niche breadth, could favour sexual
 or asexual reproductive modes and thus help to explain geographical
 parthenogenesis in natural insect populations. Megacrania batesii is a
 facultatively parthenogenetic stick insect that displays geographical
 parthenogenesis in the wild. We aimed to explore whether sexual and
 parthenogenetic populations of M. batesii displayed niche differentiation
 or variations in niche breadth that could explain the separation of the
 two population types. To do this, we sampled host plants from across the
 range of M. batesii and quantified phenotypic traits that might affect
 palatability or accessibility for M. batesii, including leaf thickness,
 toughness, spike size and density, height, and chemical composition. We
 also quantified host plant density, which could affect M. batesii
 dispersal. We found little evidence of phenotypic differences between host
 plants supporting sexual versus asexual M. batesii populations, and no
 difference in host-plant density or niche breadth between the two
 population types. Our results suggest that habitat parameters do not play
 a substantial role in shaping patterns of geographical parthenogenesis in
 wild populations of M. batesii. Instead, population sex ratio variation
 could result from interactions between the sexes or dispersal dynamics.
description: # Does ecology shape geographical parthenogenesis? Evidence from the
 facultatively parthenogenetic stick insect *Megacrania batesii* Authors:
 Soleille M. Miller, Daniela Wilner, Jigmidmaa Boldbaatar, Russell
 Bonduriansky Pre-print: ### Summary of project: We collected morphological
 and chemical data for host plants of the facultatively parthenogenetic
 Australian phasmid Megacrania batesii. We first compared morphology and
 chemistry of host plants that were eaten and avoided by M. batesii and
 then looked at host plant differences between plants from sexual and
 parthenogenetic populations of M. batesii. Additionally we investigated
 whether all-female (asexual) populations of M. batesii were more likely to
 be found in more sparse habitats than their sexual counterparts. #### R
 version: R version 4.2.2 (2022-10-31 ucrt) #### R packages used: tidyverse
 (version 1.3.1): A collection of packages for data manipulation,
 exploration, and visualization in R. ggbiplot (version 0.55): A package
 for creating ggplot2-based biplots vegan (version 2.5-7): A package for
 community ecology analysis, including diversity indices, ordination
 methods, and more. ggdendro (version 0.1.23): A package for creating
 dendrograms and tree diagrams in R using ggplot2. lmerTest (version
 3.1-4): A package for computing p-values and confidence intervals for
 linear mixed-effects models fitted with lmer from the lme4 package. lme4
 (version 1.1-35.1): Linear Mixed-Effects Models using 'Eigen'
 and S4 gridExtra (version 2.3): Miscellaneous Functions for
 "Grid" Graphics performance (version 0.10.8): Assessment of
 Regression Models Performance ggplot2 (version 3.4.2): A system for
 creating graphics in R based on The Grammar of Graphics. ##
 Data: R script for all analyses including PCA, permutational
 modelling, and a multivariate homogeneity of groups dispersions test for
 host plant differentiation. #### List of files: 
 Niche_differentiation_analysis.v.3.qmd all_plant_morph_data.csv
 disper_with_poptype.csv chem_disper_with_poptype.csv
 density_diversity_plant_locations.csv ### File Descriptions: 
 Niche_differentiation_analysis.v.3.qmd - The only file needed to see all
 analyses in manuscript. Loads clean genetic dataset and runs all
 visualizations and statistics used in the manuscript.
 all_plant_morph_data.csv - Morphological and chemical phenotypes of host
 plants sampled in this study. Morphological traits obtained from either
 data collected in the field or photos taken in the field, chemical traits
 obtained from leaf cuttings from the field. Variables: ``` id Unique
 identifier of each sample date Date sample was collected full_pic_time
 Time the picture of the entire plant was taken num_id Numerical ID
 location_old Original location identifier (was changed to match Miller et
 al 2024) genetic_location Location of the plant sample (matching Miller et
 al 2024) poptype Whether this plant is in a habitat that hosts All-female
 (asex) or Mixed-sex (sex) M. batesii populations. megacrania_marks Whether
 this plant has visible chewmarks from M. batesii genus The genus of this
 plant: either Benstonea (b) or Pandanus (p) scale_picture The time that
 the picture of the plant spikes was taken morph_from_pics Morphotype of
 plant (unused in this analysis) height estimated height height_unit Unit
 of measurement of height variable thick1 First measure of leaf thickness
 thick2 Second measure of leaf thickness thick3 Third measure of leaf
 thickness avg_thick The average of the three measures of leaf thickness
 tough1 First measure of leaf toughness tough2 Second measure of leaf
 toughness tough3 Third measure of leaf toughness avg_tough The average of
 the three measures of leaf toughness chem. Whether or not this sample had
 a chemical analysis done N Nitrogen content of leaf; NA means no sample
 was taken from this plant for chemical analysis. C Carbon content of leaf;
 NA means no sample was taken from this plant for chemical analysis. H
 Hydrogen content of leaf; NA means no sample was taken from this plant for
 chemical analysis. S Sulfur content of leaf (not used); NA means no sample
 was taken from this plant for chemical analysis. notes Extra notes about
 sample morph_in_field_explained Explanation about the morphotype
 description from field spike.ang.mm Spike angle (in mm) spike.len.mm Spike
 length (in mm) spike.dist_bt.mm Distance between spikes (in mm)
 leaf.length leaf length (in pixels) leaf.width leaf width (in pixels)
 l.w.ratio The slenderness ratio (length/width) plume_perc The percentage
 of the plant that is edible for M. batesii ``` disper_with_poptype.csv -
 Distances of each plant to their genetic_location's group dispersion
 center for morphological data. Variables: ``` dist The distance to the
 group mean genetic_location The group identifier poptype Whether this
 plant is in a habitat that hosts All-female (asex) or Mixed-sex (sex) M.
 batesii populations. ``` chem_disper_with_poptype.csv - Distances of each
 plant to their genetic_location's group dispersion center for
 chemical data. Variables: ``` dist The distance to the group mean
 genetic_location The group identifier poptype Whether this plant is in a
 habitat that hosts All-female (asex) or Mixed-sex (sex) M. batesii
 populations. ``` density_diversity_plant_locations.csv - Data frame with
 information on the density of host plants for each quadrat at each
 location sampled. Variables: ``` location Original location identifier
 (was changed to match Miller et al 2024) pop Location of the plant
 quadtrat (matching Miller et al 2024) poptype Whether this quadrat is in a
 habitat that hosts All-female (asex) or Mixed-sex (sex) M. batesii
 populations. site The numerical identifier of the quadrat at each pop
 no.trees The number of host plants found in the quadrat size_sq.m The size
 of the quadrat in square meters morphotypes The number of morphotypes
 found in the quadrat (unused in this analysis) genus The dominant genus of
 the host plants found in this quadrat density The amount of host plants
 per sq meter ``` #### Data was not derived from another source Note: all
 files should be saved in the same directory as they will be called
 directly from the directory in which the Quarto document is in.