DOI: 10.5061/dryad.1vhhmgqrt
title: Data from: Dietary-based developmental plasticity affects juvenile survival in an aquatic detritivore

description: Developmental plasticity is ubiquitous in natural populations, but the
 underlying causes and fitness consequences are poorly understood. For
 consumers, nutritional variation of juvenile diets is likely associated
 with plasticity in developmental rates, but little is known about how diet
 quality can affect phenotypic trajectories in ways that might influence
 survival to maturity and lifetime reproductive output. Here, we tested how
 the diet quality a freshwater detritivorous isopod (Asellus aquaticus), in
 terms of elemental ratios of diet (i.e. carbon : nitrogen : phosphorus; C
 :N: P), can affect (i) developmental rates of body size and pigmentation
 and (ii) variation in juvenile survival. We reared 1047 individuals, in a
 full-sib split family design (29 families), on either a high (low C : P, C
 :N) or low quality (high C : P, C : N), and quantified developmental
 trajectories of body size and pigmentation for every individual over 12
 weeks. Our diet contrast caused strong divergence in the developmental
 rates of pigmentation but not growth, culminating in a distribution of
 adult pigmentation spanning the broad range of phenotypes observed both
 within and among natural populations. Under low-quality diet, we found
 highest survival at intermediate growth and pigmentation rates. By
 contrast, survival under high-quality diet survival increased continuously
 with pigmentation rate, with longest lifespans at intermediate growth
 rates and high pigmentation rates. Building on previous work which
 suggests that visual predation mediates the evolution of cryptic
 pigmentation in A. aquaticus, our study shows how diet quality and
 composition can generate substantial phenotypic variation by affecting
 rates of growth and pigmentation during development in the absence of
 predation.
description: <strong>Common garden
 experiment </strong> Using a common
 garden experiment, we quantified the extent of variation in developmental
 rates of growth and pigmentation, and their effects on survival in
 <em>A. aquaticus </em>in response to diet composition
 (stoichiometric quality and tryptophan availability). To do so, we exposed
 1047 juvenile isopods from 29 families shortly after their birth (1-3
 days) to four different dietary contrasts: high elemental ratios (C:P and
 C:N, hereafter low quality [LQ] diet) and low elemental ratios (hereafter
 high-quality diet [HQ]), as well as each of these diet combinations
 crossed with a supplement (or not) of tryptophan. We measured growth,
 pigmentation and survival of each individual over the course of 12 weeks.
 For each family, half of the juveniles were randomly assigned to either
 low or high diet quality (full sib / split family design). For the eight
 families with the highest number of offspring (50-60 juveniles), we
 crossed the diet-quality treatment with a supplemental tryptophan
 treatment: in these eight families, 40 juveniles were randomly distributed
 among high- and low-quality treatments, and the remaining 10-20
 individuals among the two treatments with tryptophan
 supplement.  We used juvenile isopods from a total of
 29 successful matings (for details on isopod collection and breeding, and
 started the common garden experiment in three temporal blocks. Using small
 pipettes (for isopods bigger than ~5 mm we used soft steel forceps), we
 transferred an individual from its tube into a small container with lake
 water, and from there onto a flat tray containing lake water underneath a
 camera mounted on a camera stand. After taking the picture, we transferred
 each isopod into a new (autoclaved) tube with fresh lake water and a new
 food pellet. We repeated this procedure with every individual, yielding up
 to five phenotypic measurements for each developmental trajectory. We took
 pictures of isopods using a camera stand with a digital single lens reflex
 camera (Canon) and a 100- mm macro lens (Tamron). The tray was uniformly
 illuminated with an LED spot ring (Leica).  To quantify
 pigmentation and body size of isopods from the digital images, we applied
 computer vision techniques. For this purpose, we used the python package
 phenopype (https://mluerig.github.io/phenopype/). It uses thresholding
 algorithms to segment isopods from the image background, to then extract
 the phenotypic information from the pixels marking the animal (dorsal
 region of isopod torso = carapace, excluding legs and antennae). The
 greyscale values from these pixels were averaged and converted to a
 pigmentation scale from 0 (greyscale value of 255) to 1 (greyscale value
 of 0). Body size was measured as carapace length, excluding legs and
 antennae. <br> Statistical analyses 
 <strong>Statistical
 analysis</strong> Follow the script
 from top to bottom, do all steps to generate the following figures and
 accompanying statistics: (Fig 2) We
 tested for effects of diet composition and tryptophan supplement on
 developmental rates of body size and pigmentation, as well as survival
 over the course of the experiment using a series of generalized additive
 mixed models (GAM), using the “gamm” function in mgcv. We fit separate
 models each for body size (GAM1, Table1) and pigmentation (log
 transformed, GAM2), with time separated by diet contrast as the fixed
 effect and a thin plate spline term with time in weeks. Furthermore, we
 fit a GAM with a binomial distribution family to test for differences in
 survival as a binary dependent variable, and fixed effect and spline terms
 identical to the developmental rate models (GAM3, Table1). All three
 models contained nested random terms for family and individual, and used
 diet as a parametric component in the spline terms. 
 (Fig 3) In a further step, we tested for
 effects of diet composition and of juvenile phenotypes right after birth
 on growth and pigmentation rates and survival by performing a path
 analysis using Bayesian multilevel modelling. In a single model, we
 implemented three hierarchical levels, and included family as the grouping
 term, allowing us to estimate relative effect sizes of developmental rates
 and starting conditions on lifespan under all diet treatment contrasts
 (See supplement for details, Table S2). We applied both types of analysis
 in a complementary fashion: with separate additive models, we accounted
 for the nonlinearity in developmental rates, and with the path analysis we
 were able to disentangle complex interactions linking rearing conditions
 and juvenile traits through development with survival variation.
 (Fig 4) To test for interactions between
 growth and pigmentation on survival, we also applied a more complex
 multivariate GAM. To do so, we first converted measurements of body size
 and pigmentation up until week 6 (dashed line in figure 2) to a single
 linear slope per individual isopod (hereafter growth and pigmentation
 rate, respectively). We chose to calculate slopes from this time frame,
 because pigmentation and growth increased linearly to this point, and
 isopod survival up to this point was high. We then implemented an additive
 model (GAM4) with the “gam” function from mgcv, using lifespan (in weeks)
 as the dependent variable, single thin plate spline terms for growth and
 pigmentation rate, and a tensor smooth product term to test for the
 interaction (Table1). The model included family as a random effect, and
 the spline and tensor term included diet as a parametric component (See
 supplement for details).
description: Here we provide the data obtained from the image analysis
 pipeline (using phenopype: https://github.com/mluerig/phenopype). We
 provide a script from which the figures can be reproduced as an entry
 point to the comprehensive dataset. See the readme on how to get
 started.