DOI: 10.5061/dryad.95x69p8tw
title: Environmental vs. biotic filtering: what if species traits contribute to both?

description: This study introduced a novel approach to explore the contribution of
 species traits to environmental and biotic filtering and, in turn, to
 community assembly. This approach assumes that a species trait can be
 associated with both the α component of the niche (describing resource use
 within communities) and its β component (describing position along
 environmental gradients). Using data from 26 lacustrine fish communities
 in the Yangtze River basin, China, and a series of traits based on
 large-scale habitat preference, trophic resources use, micro-habitat
 partitioning, and predation, we observed that all traits were
 over-dispersed within communities, the signature of environmental
 filtering. However, besides this dominant pattern, we observed that
 species dissimilar in traits related to resource use or habitat
 partitioning and similar in habitat requirement were more likely to
 coexist, as niche theory predicts. Acknowledging the dual role of traits
 offers a more nuanced understanding of community assembly rules.
description: # Environmental vs. biotic filtering: what if the species traits
 contribute to both?
 [https://doi.org/10.5061/dryad.95x69p8tw](https://doi.org/10.5061/dryad.95x69p8tw) ## Description of the data and file structure ### **Part 1 – Null model analysis (Pairs-Null model.zip)** This folder contains all input and output files used for running the null model in the software **Pairs** (Ulrich 2008). The executable program `Pairs.exe` is **not** included. The original software can be obtained from: Ulrich, W. (2008). *Pairs—a FORTRAN program for studying pair-wise species associations in ecological matrices.* URL: [http://www.keib.umk.pl/pairs](http://www.keib.umk.pl/pairs) --- #### **Input files** * **Input-26lakes-all species.txt** Presence/absence data matrix directly formatted for use in *Pairs*. * **Input-26lakes-all species.xlsx** Same data as above, but in spreadsheet form for clarity. Rows = species, columns = lakes, values = 1 (presence) / 0 (absence). --- #### **Output files** (produced by *Pairs*) * **output-CoocPairs.txt** Summary statistics of the matrix and the null model results, including observed and simulated values, Z-scores, confidence limits, and null model parameters. * **output-Matrix.txt** Packed representation of the original data matrix and the last randomized matrix from the null model run. * **output-Pairs.txt** Detailed pairwise association statistics for all species pairs, including observed values, expected values under the null model, standard deviations, Z-scores, and probability levels. * **output-SigPairs.txt** List of significant species pairs, with counts of significant associations per score class and expected numbers from randomized matrices. ## **Part 2. Original data of the study** **Fish abundance+Environmental.csv** This file contains abundance data for all fish species and measurements of environmental variables across all study lakes. Environmental variables are grouped into four categories: * **Eutrophication**: * *Total phosphorus* (mg/L; measured using standard water chemistry protocols) — Indicates nutrient enrichment; a key driver of algal growth and primary productivity. * *Chlorophyll a* (µg/L; measured via spectrophotometry) — Proxy for phytoplankton biomass and trophic status. * *Secchi depth* (m; measured with a Secchi disk) — Indicator of water transparency and, indirectly, algal or sediment load. * **Land use** (derived from catchment land use maps in ArcGIS): * *Agricultural* (%) — Reflects nutrient and pesticide runoff potential. * *Grassland* (%) — May buffer runoff and influence sediment/nutrient input. * *Pond* (%) — Indicates aquaculture pressure or altered hydrology. * **Lake morphology**: * *Lake area* (km²; extracted from satellite maps) — Affects habitat heterogeneity and potential for species coexistence. * *Maximum water depth* (m; measured using a handheld depth sounder) — Influences thermal stratification, oxygen levels, and habitat depth range. * *Shoreline development index* (unitless; calculated as shoreline length/circumference of a circle with equal area) — Proxy for habitat complexity and littoral zone extent. * **Fishery** (based on questionnaire data from 2019): * *Fishery yield* (kg/ha/year) — Represents fishing pressure and harvest intensity. * *Annual stocking amounts* (kg/ha/year) — Reflects degree of human intervention via fish introductions. * *Feed-fertilizer input levels* (ordinal score 0–4; 0 = none, 4 = intensive input) — Indicates intensity of aquaculture and potential nutrient loading. --- **Species pair-PRED.csv** Matrix representing predator–prey relationships between fish species pairs: * 1 = presence of a predator–prey relationship * 0 = absence of such a relationship. --- **Species pair-SES.csv** This file contains Standardized Effect Size (SES) values of species pair associations derived from the null model analysis (Pairs software). These SES values are z-scored contribution metrics reflecting the strength and significance of species pairwise associations relative to randomized expectations. The SES data were calculated based on the raw output from the file `output-Pairs.txt` (see Part 1). This file is used to assess the ecological significance of species interactions beyond random chance. --- **Species traits.csv** Functional traits of fish species, with details as follows: * **Life history strategy**: * *Maximum standard length* (cm; maximum value from published records) — Determines life history strategy, trophic position, metabolic rates, and overall energetics. * *Parental care index* (ordinal 0–4; 0 = no care, 1 = special placement of zygotes, 2 = nesting without protection, 3 = nesting with one-parent protection, 4 = nesting with biparental protection) — Reflects degree of investment in individual offspring. * **Feeding**: * *Trophic guild* (factor: TG1–TG7; herbivore, algivore, detritivore, omnivore, zooplanktivore, zoobenthivore, piscivore) — Indicates energy flow pathways. * *Trophic level* (numeric; range 2–4.5) — Describes position in the food web and nutrient budget. * **Habitat use**: * *Habitat preference* (factor: HP1–HP4; eurytopic, rheophilic, limnophilic, potamodromous) — Reflects tolerance to hydrological conditions. * *Vertical position* (factor: VP1–VP3; demersal, near demersal, pelagic) — Indicates habitat use within the water column. * **Taxonomy**: * *Genus* — Reflects phylogenetic differences at the genus level. * *Family* — Reflects phylogenetic differences at the family level. ## **Part 3 PCA1-9.CSV** This file contains the results of Principal Component Analysis (PCA) conducted in R, formatted as a matrix with species as rows and principal components as columns. Each column represents one principal component axis summarizing trait variation among species. The column headers include species names to indicate data for each species. * **PCA1:** The first principal component, explaining the largest proportion of variance in species traits. * **PCA2:** The second principal component, orthogonal to PCA1, capturing additional variation. * **PCA3:** The third principal component, representing further trait variability. * **PCA4:** The fourth principal component, capturing remaining variance components. * **PCA5:** The fifth principal component. * **PCA6:** The sixth principal component. * **PCA7:** The seventh principal component. * **PCA8:** The eighth principal component. * **PCA9:** The ninth principal component. All these principal components together summarize the multivariate functional trait space of the fish species, facilitating downstream ecological analyses. ## **Part 4 R scripts of all analyses** Contains all analysis scripts used in the study, calling the above CSV files as inputs. Scripts are run in **R**. **Citation:** Feng, K., et al. (2025). Dataset for: *Environmental vs. biotic filtering: what if species traits contribute to both?* Dryad Digital Repository. [https://doi.org/10.5061/dryad.95x69p8tw](https://doi.org/10.5061/dryad.95x69p8tw)