Recapture probability and State change probability.

<p>Conditional Arnason-Schwarz model in which outcome probabilities are (S) survival, (p) recapture, (Ψ) state change, and the variables that can influence the outcomes are (g) site, (t) time in weeks, (to) state at previous capture, (f) state at capture. Panels (a) and (b) represent the two-disease-state model, <i>Bd</i> positive (Bd+) and <i>Bd</i> negative (Bd-), in which the best model was S(g)p(g*t)Ψ(to*f*t). Panels (c) and (d) represent the three-disease-state model, <i>Bd</i> negative (Bd-), low infection intensity of >350ZE (Low) and high infection intensity of >350ZE (High), in which the best model was S(g*f)p(g*to+t)Ψ(to*f). (a) Recapture probability per week in a two-disease-state model. Factors included in the best model for recapture probability were site and week, Error bars indicate 95% confidence interval. (b) Probability of changing state per week in a two-disease-state model. Factors included in the best model for state change probability were week, infection state at current capture, and infection state at previous capture, and error bars indicate 95% confidence interval. (c) Recapture probability per week in a three-disease-state model. Factors included in the best model for recapture probability were site, state of infection and week. Error bars indicate standard error, and only one error bar included for figure clarity. (d) Probability of changing state in a three-disease-state model, error bars indicate 95% confidence interval. Sites are Oglives Dam (OD) and Sponar’s Creek (SC).</p

Infection prevalence and intensity across sites for <i>Litoria verreauxii alpina</i>, <i>Crinia signifera</i> and <i>Cherax destructor</i>.

<p>(a) Prevalence of infection. Error bars indicate 95% confidence intervals. (*) indicates time-points where prevalence is significantly different at each site for <i>Litoria verreauxii alpina</i>, using Pearson’s Chi-Squared test. (b) Infection intensity transformed to log₁₀ scale. Error bars indicate standard error. Sites are Oglives Dam (OD) and Sponar’s Creek (SC).</p

AIC ranking for Conditional Arnason–Schwarz models.

<p>*Probabilities determined are (S) survival probability, (p) recapture probability, (Ψ) state change probability; and the variables that influence S, p and Ψ are (g) site, (t) time in weeks, (to) state of previous capture, (f) state of capture and no variable (.)</p><p>Model results for both the two-disease-state (<i>Bd</i> negative and <i>Bd</i> positive) and three-disease-state analysis (<i>Bd</i> negative, low <i>Bd</i> infection under 350ZE, and high <i>Bd</i> infection over 350ZE).</p

Disease state change over the course of the study.

<p>The proportion of recaptured individuals that changed disease state over the course of multiple recaptures between the two sites: Oglivies Dam and Sponar’s Creek. This table represents the data collected from the CMR study.</p

AIC ranking of best-fit POPAN models.

<p>* Outcome probabilities determined are (Φ) survival probability, (p) recapture probability, and (Pent) probability of entry into the population. These outcome probabilities are determined by the variable (t) time in weeks, or no variable (.).</p><p> Model results are for the two sites: Sponar’s Creek and Oglivies Dam.</p

Individual frog measurement data

This file contains measurement data for individual frogs, along with information on population origin and disease status for populations and individuals. Museum registration details refer to specimen I.D. for the Museum Victoria, Australia

Dataset 7.3 Liver matrix.isoforms.TPM.not_cross_norm

Dataset 7 contains the raw gene/transcript counts data for each frog tissue sample (Experiment B, n = 61) resulting from allocation of sequence reads to genes from the transcriptome assemblies. These data are contained in Dataset 7, as 12 individual tab-separated text files (.txt) [Data Citation 1]. The four files for each tissue type (skin, liver and spleen) represent raw (1) counts, (2) TMM.EXPR files, (3) TPM.not_cross_norm files, and (4) normalisation information (as per the standard output from RSEM). The first row of these files (1-3 above) represents frog ID, and the first element of all subsequent rows represents transcript/isoform ID

Dataset 7.2 Liver matrix.isoforms.TMM.EXPR

Dataset 7 contains the raw gene/transcript counts data for each frog tissue sample (Experiment B, n = 61) resulting from allocation of sequence reads to genes from the transcriptome assemblies. These data are contained in Dataset 7, as 12 individual tab-separated text files (.txt) [Data Citation 1]. The four files for each tissue type (skin, liver and spleen) represent raw (1) counts, (2) TMM.EXPR files, (3) TPM.not_cross_norm files, and (4) normalisation information (as per the standard output from RSEM). The first row of these files (1-3 above) represents frog ID, and the first element of all subsequent rows represents transcript/isoform ID

Dataset 7.1 Liver matrix.isoforms.counts

Dataset 7 contains the raw gene/transcript counts data for each frog tissue sample (Experiment B, n = 61) resulting from allocation of sequence reads to genes from the transcriptome assemblies. These data are contained in Dataset 7, as 12 individual tab-separated text files (.txt) [Data Citation 1]. The four files for each tissue type (skin, liver and spleen) represent raw (1) counts, (2) TMM.EXPR files, (3) TPM.not_cross_norm files, and (4) normalisation information (as per the standard output from RSEM). The first row of these files (1-3 above) represents frog ID, and the first element of all subsequent rows represents transcript/isoform ID

Dataset 5.2 Liver-filtered-condensed-transdecoder

Dataset 5 consists of de novo assembled transcriptomes for each tissue type from frogs in Experiment B (n = 61). These data are contained in Dataset 5, as six individual .fasta text files, including both nucleotide sequence assembly files and amino acid sequence assembly files (translated using TransDecoder) for each of the three tissue types (skin, liver and spleen) [Data Citation 1]. Descriptions of the sequence identifier lines are contained in the associated readme file