Does ecology shape geographical parthenogenesis? Evidence from the facultatively parthenogenetic stick insect Megacrania batesii
Data files
Apr 09, 2024 version files 29.98 KB
-
all_plant_morph_data.csv
-
chem_disper_with_poptype.csv
-
density_diversity_plant_locations.csv
-
disper_with_poptype.csv
-
README.md
Abstract
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.
README: 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.