Model source files

This file contains the source files of the model used in the article. This model is an object-oriented model that has been implemented in Borland Delphi

Environmental spatial structure for three degrees of spatial autocorrelation α.

<p>(a) α = 0. (b) α = 5. (c) α = 10. The landscape size is 25 cells by 25 cells. Dark cells represent high environmental values E_i and light cells low values.</p

Dispersal kernel for three different species dispersal abilities δ_s.

<p>δ_s = 0.20 (plain line), δ_s = 1.00 (dashed line) and δ_s = 3.54 ( = δ_max, maximal value in this study) (dotted line).</p

Species persistence and mean abundance as a function of their dispersal ability.

<p>On the left y-axis (continuous line) is represented the species persistence probability (proportion of replicates in which the species has survived) while the right y-axis (dashed line) shows the species mean abundances (computed only on the replicates in which the species has survived). (a) Generalist species (σ_s = 0.5) with very high adult survival rate (ψ_s = 0.95), in the presence of a low disturbance rate (T = 0.01) in an uncorrelated environment (α = 0). (b) Generalist species (σ_s = 0.5) with high adult survival rate (ψ_s = 0.5), in the presence of a medium disturbance rate (T = 0.1) in an uncorrelated environment (α = 0).</p

Parameter values used for the simulations.

<p>°only when T>0.</p

Dominant dispersal strategies for the generalist species (σ_s = 0.5).

<p>Most abundant dispersal strategy as a function of spatial autocorrelation α, adult survival rate ψ_s, and disturbance rate T. (a) Influence of spatial autocorrelation when ψ_s = 0 and T = 0. (b) Influence of spatial autocorrelation and survival rate when T = 0. (c) Influence of spatial autocorrelation, adult survival and disturbance rate. Each box represents the distribution of the n = 50 replicates. Results for the specialist species are presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034733#pone.0034733.s001" target="_blank">Figure S1</a>.</p

XML for EBSP analysis

XML file used in BEAST for the Extended Bayesian Skyline Plot (EBSP) analysis of H. amphibius, based on control region, cytochrome-b and nuclear HMG-2 sequence

Sequence alignments

FASTA alignments of all H. amphibius' sequences included in this study: mitochondrial control region ("Hippo_CR_all.fas"), cytochome-B ("Hippo_cytB_all.fas") and nuclear HMG-2 (Hippo_Nucl_all.fas"). Taxon ID are listed in Supplementary Table S1

XML file for molecular calibration analysis

XML file used in BEAST for the molecular calibration analysis of CR H. amphibius sequences, using the split with H. liberiensis (sequence OGR) as a reference

Codes used for EBSP simulation analyses

Set of codes used for generating simulated datasets and performing EBSP analyses. File "ms_beast.R" runs the coalescent simulator MS (via package "phyclust" providing a R version of MS) to generate sequences from the template file "testalt_template" and create XML input files for use in BEAST. File "run.sh" runs these XML inputs in BEAST. File "plots.R" is used to visualize generated skyline plots