Data and code from: Ontogenetic trophic differentiation in the Amur softshell turtle (Pelodiscus maackii) from a temperate large-river system
Data files
Sep 04, 2026 version files 56.14 KB
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Body_Size_and_Sex_Distribution_Data.xlsx
9.58 KB
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Diet_Data.xlsx
13.38 KB
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Figure_2.R
3.15 KB
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Figure_3a_3c.R
4.68 KB
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Figure_4_PCoA.R
4.41 KB
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Figure_S2.R
3.65 KB
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README.md
6.33 KB
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Table_1.R
2.80 KB
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Table_2.R
4.41 KB
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Table_S2.R
3.75 KB
Abstract
The Amur softshell turtle (Pelodiscus maackii) has undergone severe population declines across northeastern China, yet its trophic ecology remains poorly understood. Because ontogenetic dietary shifts can generate size-structured functional roles within food webs, clarifying diet across life stages is critical for both ecological inference and conservation. We examined diet composition and ontogenetic trophic differentiation in a remnant population of P. maackii from the midstream Ussuri River (China side) using stomach content analysis. Samples were obtained opportunistically from incidental fishery bycatch and market-derived remains collected between July 2022 and October 2025. Diet was quantified using frequency of occurrence and volumetric contribution of five functional prey categories and analysed with multivariate ordination and permutation-based tests, generalized additive models along a continuous body-mass gradient, and niche overlap indices. Across 41 individuals with non-empty stomachs, diet composition differed strongly among ontogenetic stages, whereas no sex-specific differences were detected after accounting for body mass. Juveniles exhibited diverse, invertebrate-dominated diets, particularly freshwater snails, while fish increased sharply with body size and dominated the diets of subadult and adult turtles. Dietary richness and within-group variability declined with ontogeny, and niche overlap was lowest between juveniles and adults but high among older stages. Together, these results demonstrate pronounced size-structured trophic differentiation in P. maackii, indicating that population declines or size-selective losses may have disproportionate consequences for riverine food-web structure and function.
Dataset DOI: 10.5061/dryad.z8w9ghxw3
Overview
This dataset contains the individual-level data and R scripts used for the analyses, tables, and figures associated with the article. The study examines ontogenetic dietary differentiation in the Amur softshell turtle (Pelodiscus maackii) using stomach content data.
The dietary dataset contains 41 individuals with non-empty stomachs. Individuals were assigned to four ontogenetic groups: - J = Juvenile - S = Small subadult - L = Large subadult - A = Adult
Sample sizes were: - Juvenile: n = 10 - Small subadult: n = 7 - Large subadult: n = 9 - Adult: n = 15
Data files
File: Diet_Data.xlsx
Description: Contains the individual-level dietary data used for analyses of dietary
composition, dietary niche overlap, PERMANOVA, multivariate dispersion,
principal coordinates analysis (PCoA), and associated tables and
figures.
The workbook contains two worksheets:
- Sheet1: dietary composition expressed as proportions on a 0--1 scale. This sheet is used in all R analyses.
- Sheet2: the same dietary composition expressed a percentages on a 0--100 scale for ease of interpretation.
Main variables
- Age: ontogenetic group (J, S, L, or A)
- weight: body mass in kg
- sex: sex (F = female; M = male; blank/NA where not determined or not applicable)
- fish: proportional contribution of fish
- decapods: proportional contribution of freshwater decapods
- odonate: proportional contribution of aquatic insect larvae
- snail: proportional contribution of freshwater snails
- terrestrial: proportional contribution of terrestrial invertebrates
File: Body_Size_and_Sex_Distribution_Data.xlsx
Description: Contains individual-level body-size and sex data used to generate Figure 2.
Main variables
- Age: ontogenetic group (J, S, L, or A)
- weight: body mass
- sex: sex (F = female; M = male; blank/NA where not determined or not applicable)
R scripts
File: Figure_2.R
Description: Generates Figure 2 showing the distribution of individuals among
body-mass intervals and sex categories, with four ontogenetic classes indicated.
File: Figure_3a_3c.R
Description: Generates the dietary-composition panels of Figure 3. Figure 3a
summarizes mean dietary composition among ontogenetic groups, and Figure 3c generates the Amundsen-style prey-specific abundance plot using frequency of occurrence (FO) and prey-specific abundance.
File: Figure_4_PCoA.R
Description: Performs PCoA using Bray--Curtis dissimilarities and generates Figure 4. Dietary composition is visualized by ontogenetic group and sex. Group centroids are calculated, and age-group centroids are connected to illustrate the ontogenetic dietary trajectory.
File: Figure_S2.R
Description: Generates Supplementary Figure S2. Figure S2a shows distance of individual diets to their group dietary centroid (multivariate dispersion), and Figure S2b shows pairwise Bray--Curtis dietary dissimilarities among ontogenetic groups.
File: Table_1.R
Description: Calculates dietary metrics presented in Table 1, including frequency of
occurrence (FO), proportional dietary contribution, and index of
relative importance (IRI).
File: Table_2.R
Description: Calculates dietary niche overlap using Pianka's niche overlap index with a null-model randomization procedure (999 permutations) and Morisita--Horn overlap with 95% confidence intervals obtained by bootstrap resampling (1,000 iterations).
File: Table_S2.R
Description: Performs overall PERMANOVA using Bray--Curtis dissimilarities and 999
permutations, tests of homogeneity of multivariate dispersion, descriptive statistics for distance to group dietary centroid, and pairwise PERMANOVA comparisons with Holm adjustment of P-values.
Data coding
Ontogenetic groups
- J = Juvenile
- S = Small subadult
- L = Large subadult
- A = Adult
Sex
- F = Female
- M = Male
- NA/blank = sex not determined or not applicable
Dietary categories
- fish = Fish
- decapods = Freshwater decapods
- odonate = Aquatic insect larvae
- snail = Freshwater snails
- terrestrial = Terrestrial invertebrates
Software and R packages
Analyses and figures were produced in R. Depending on the script, packages include vegan, tidyverse, readxl, patchwork, knitr, kableExtra, scales, showtext, and grid.
Reproducibility
Place the two Excel data files and all R scripts in the same working directory before running the scripts.
All analyses based on Diet_Data.xlsx explicitly use Sheet1, containing dietary proportions on a 0--1 scale. Scripts use relative paths for input data and output files.
The ontogenetic coding throughout the dataset and scripts is J, S, L, and A, where L denotes Large subadult.
Some figure scripts specify Times New Roman using a Windows font path. Users on other operating systems may need to modify the font path or font configuration. This affects figure formatting only and does not affect statistical analyses.
Some analyses use permutation or bootstrap procedures. Exact resampled P-values or bootstrap confidence-interval endpoints may vary slightly among runs unless a random-number seed is specified. Observed statistics calculated directly from the data are unaffected.
Missing data
Missing sex values are retained as NA/blank where sex was not determined or was not applicable. Analyses involving sex exclude individuals with missing sex information as specified in the relevant scripts. Dietary analyses use complete observations for required dietary variables.
Data availability and citation
These data and scripts are provided to support transparency and reproducibility of the analyses reported in the associated article. Users should cite the associated Ecology and Evolution article and the Dataset DOI: 10.5061/dryad.z8w9ghxw3
Contact
For questions regarding the data or R code, please contact the corresponding author listed in the associated publication.