DOI: 10.5061/dryad.47d7wm3cf
title: Quantitative genetics of extreme insular dwarfing: the case of red deer (Cervus elaphus) on Jersey

description: Aim: The Island Rule – i.e. the tendency for body size to
 decrease in large mammals and increase in small mammals on islands has
 been commonly evaluated through macroecological or macroevolutionary,
 pattern-orientated approaches, which generally fail to model the
 microevolutionary processes driving either dwarfing or gigantism. Here, we
 seek to identify which microevolutionary process could have driven extreme
 insular dwarfism in the extinct dwarf red deer population on the island of
 Jersey. Location: Jersey, UK (Channel Islands).
 Taxon: Red deer ( Cervus elaphus) Methods: We applied an
 individual-based quantitative genetics model parameterized with red deer
 life-history data to study the evolution of dwarfism in Jersey’s deer,
 considering variations in island area and isolation through time due to
 sea level changes. Results: The body size of red deer on Jersey
 decreased fast early on, due to phenotypic plasticity, then kept
 decreasing almost linearly over time down to the actual body size of the
 Jersey deer (36 kg on average). Only 1% out of 10,000 replicates failed to
 reach that size in our simulations. The distribution of time to adaptation
 in these simulations was right-skewed, with a median of 395 generations
 (equivalent to roughly 4 ky years), with complete dwarfism effectively
 occurring in less than 6 ky 84.6% of times. About 72% of the variation in
 the time to adaptation between simulations was collectively explained by
 higher mutational variance, the number of immigrants from the continent
 after isolation, available genetic variance, heritability, and phenotypic
 plasticity. Main Conclusions: The extreme dwarfing of red deer on
 Jersey is an expected outcome of high mutational variance, high
 immigration rate, a wide adaptive landscape, low levels of inbreeding, and
 high phenotypic plasticity (in the early phase of dwarfing), all occurring
 within a time window of around 6 ky. Our model reveals how extreme
 dwarfism is a plausible outcome of common, well-known evolutionary
 processes.
description: The dataset was generated by an individual-based quantitative
 genetics model parameterized with red deer life-history data gathered from
 the literature. The changes of carrying capacity and colonization
 probability through time were calculated based on sea-level changes of
 Jersey Island (Lister 1995) and allometric equations proposed by Carbone
 & Gittleman (2002). Carbone, C., &
 Gittleman, J. L. (2002). A common rule for the scaling of carnivore
 density. Science, 295, 5563, 2273-2276. Lister, A.
 (1995). Sea-levels and the evolution of island endemics: the dwarf red
 deer of Jersey. In: Preece, R. (ed). Island Britain: a quaternary
 Perspective. Geological<br> Society Special Publications 96,
 151-172.
description: This zip directory contains the data, R codes, and simulation
 results required to reproduce analyses reported in the associated
 paper. <strong>Data</strong>
 The file contains folders for each simulation scenarios (1)
 Baseline, (2) constant_k, (3) no_plasticity, (4) no_recolonization and (5)
 no_reproduction_system. There is also a file named island_area.txt, which
 contains data of the island area (Kisl) and isolation (migr) changes
 through time. 
 <strong>Folders</strong> <strong style="color:rgb(14, 16, 26);background:transparent;margin-top:0pt;margin-bottom:0pt;">Baseline</strong> - Script to run baseline models. The baseline model includes non-constant carrying capacity, phenotypic plasticity, island recolonization, and sexual dimorphism.   <strong style="color:rgb(14, 16, 26);background:transparent;margin-top:0pt;margin-bottom:0pt;">constant_k</strong> - Script to run baseline models with constant carrying capacity through time<strong style="color:rgb(14, 16, 26);background:transparent;margin-top:0pt;margin-bottom:0pt;">.</strong>   <strong style="color:rgb(14, 16, 26);background:transparent;margin-top:0pt;margin-bottom:0pt;">no_plasticity</strong> - Script to run baseline models without phenotypic plasticity<strong style="color:rgb(14, 16, 26);background:transparent;margin-top:0pt;margin-bottom:0pt;">.</strong>   <strong style="color:rgb(14, 16, 26);background:transparent;margin-top:0pt;margin-bottom:0pt;">no_recolonization</strong> - Script to run baseline models without island recolonization.   <strong style="color:rgb(14, 16, 26);background:transparent;margin-top:0pt;margin-bottom:0pt;">no_reproduction_system</strong> - Script to run baseline models without sexual dimorphism.   All folders contain R codes to run simulations for each scenario and the tables of simulation results: <strong>AdaptSS_cervus_(scenario).R</strong> - Script to run adaptation through generations. The function AdaptSS runs a simulation of trait adaptation for each generation step and the function run_generation updates simulation's parameters for each generation and calls AdaptSS. <strong>parallel_function_cervus.R</strong> - Set simulation parameters and run simulations. <strong>Cervus_meanP.txt </strong>- Mean body size evolution through time. Rows are time steps and columns are simulation replicates. <strong>Cervus_results_(scenario).txt </strong>- Table of simulation results. Rows are simulation replicates and columns simulation outputs. <strong>Column Legend:</strong> h2 - heritability cv - phenotypic coefficient of variation vm -  mutational variance Ancestral - Initial trait meanK - mean carrying capacity Ni - initial population size Nrecol - number of recolonization Precol - probability of colonization w2 - Length of adaptive landscape time_adap - time until adaptation selgrad - selection gradient meanG -  mean genotype varG - genotypic variance N_end - Final population size F_Peak - adaptive landscape optimum (optimum trait) meanP - Final mean trait bp.max - maximum phenotypic plasticity bp - phenotypic plasticity