GENERAL INFORMATION

1. Paper Citation

Riquelme JD, Košćina T, León C, Morales CB, Hayes LD, Ebensperger LA (2025). Stability in foraging associations is linked to stability in communal use of burrows in degus. Behavioral Ecology.

2. Brief abstract

Consumers experience permanent and temporary changes in their associations with peers during foraging and when using refuge. We addressed whether individual associations during foraging contribute to long-term stability of associations when using refuges in group-living degus. We found that foraging associations during mating matched burrow use associations during mating and during offspring rearing. Most relevant, degus keeping stable associations when foraging also kept relatively more stable associations based on refuge use during offspring rearing.

3. Originators

Juan D. Riquelme de la Fuente

4. Contact information

Juan Riquelme, address: Avenida Libertador Bernardo O'Higgins 340. Edificio 210 piso 2 Santiago, email: jnriquelme@uc.cl

5. Date of data collection

Years: 2018-2019.

6. Geographic location(s) of data collection

Estación Experimental Germán Greve Silva (EEGGS; 33°23′S, 70°31′W; altitude 495 m), a field station of Universidad de Chile (central Chile). Rinconada, Maipú, Chile.

7. Information about funding sources that supported the collection and curation of the data

This research was supported by National Fund for Science and Technology (FONDECYT) grants 1170409 and 1210219 and the National Research and Development Agency (ANID, No. 21161585), and by National Science Foundation OISE grant no. 1854177.

ACCESS INFORMATION

1. Licenses/restrictions placed on the data

The dataset is released under the Creative Commons Zero (CC0) waiver, placing it in the public domain. The data may be freely reused without restriction. Citation of the original source is appreciated.

2. Data derived from other sources

None. All data were collected by the authors for this study.

DATA FILES AND VARIABLES

• WBA = Winter Burrow Associations (mating period)
• SBA = Spring Burrow Associations (offspring rearing period)
• WFA = Winter Foraging Associations (mating period)
• CF = Confusion effect (number of observations), relative to the sampling effort during burrow use.
• kin = Genetic relatedness matrices.

Files 1 to 32: Symmetric matrices containing IDs and values per dyad. Values represent either association indices (burrow use or foraging associations), genetic relatedness, or number of observed days (confusion effect), as appropriate for each matrix.

1 • 1F_WBA18_matrix.csv: Burrow use associations during mating, females 2018.

2 • 1F_WBA18CF.csv: Number of observed days per dyad.

3 • 1F_WFA18_matrix.csv: Foraging associations during mating, females 2018 (matched with burrow use associations during mating for comparison).

4 • 1kinF_WBA18.csv: Genetic relatedness matrix, females 2018 (matched with burrow use associations during mating for comparison).

5 • 1kinM_WBA18.csv: Genetic relatedness matrix, males 2018 (matched with burrow use associations during mating for comparison).

6 • 1M_WBA18_matrix.csv: Burrow use associations during mating, males 2018.

7 • 1M_WBA18CF.csv: Number of observed days per dyad.

8 • 1M_WFA18_matrix.csv: Foraging associations during mating, males 2018 (matched with burrow use associations during mating for comparison).

9 • 2F_SBA18_matrix.csv: Burrow use associations during offspring rearing, females 2018.

10 • 2F_SBA18CF.csv: Number of observed days per dyad.

11 • 2F_WFA18_matrix.csv: Foraging associations during mating, females 2018 (matched with burrow use associations during offspring rearing for comparison).

12 • 2kinF_SBA18.csv: Genetic relatedness matrix, females 2018 (matched with burrow use associations during offspring rearing for comparison).

13 • 2kinM_SBA18.csv: Genetic relatedness matrix, males 2018 (matched with burrow use associations during offspring rearing for comparison).

14 • 2M_SBA18_matrix.csv: Burrow use associations during offspring rearing, males 2018.

15 • 2M_SBA18CF.csv: Number of observed days per dyad.

16 • 2M_WFA18_matrix.csv: Foraging associations during mating, males 2018 (matched with burrow use associations during offspring rearing for comparison).

17 • 3F_WBA19_matrix.csv: Burrow use associations during mating, females 2019.

18 • 3F_WBA19CF.csv: Number of observed days per dyad.

19 • 3F_WFA19_matrix.csv: Foraging associations during mating, females 2019 (matched with burrow use associations during mating for comparison).

20 • 3kinF_WBA19.csv: Genetic relatedness matrix, females 2019 (matched with burrow use associations during mating for comparison).

21 • 3kinM_WBA19.csv: Genetic relatedness matrix, males 2019 (matched with burrow use associations during mating for comparison).

22 • 3M_WBA19_matrix.csv: Burrow use associations during mating, males 2019.

23 • 3M_WBA19CF.csv: Number of observed days per dyad.

24 • 3M_WFA19_matrix.csv: Foraging associations during mating, males 2019 (matched with burrow use associations during mating for comparison).

25 • 4F_SBA19_matrix.csv: Burrow use associations during offspring rearing, females 2019.

26 • 4F_SBA19CF.csv: Number of observed days per dyad.

27 • 4F_WFA19_matrix.csv: Foraging associations during mating, females 2019 (matched with burrow use associations during offspring rearing for comparison).

28 • 4kinF_SBA19.csv: Genetic relatedness matrix, females 2019 (matched with burrow use associations during offspring rearing for comparison).

29 • 4kinM_SBA19.csv: Genetic relatedness matrix, males 2019 (matched with burrow use associations during offspring rearing for comparison).

30 • 4M_SBA19_matrix.csv: Burrow use associations during offspring rearing, males 2019.

31 • 4M_SBA19CF.csv: Number of observed days per dyad.

32 • 4M_WFA19_matrix.csv: Foraging associations during mating, males 2019 (matched with burrow use associations during offspring rearing for comparison).

GBI files (asnipe format): Group-by-Individual matrices, where rows represent observation groups and columns represent individuals (1 = present, 0 = absent).

33 • gbi_1F_WBA18.csv: Burrow use associations for females during mating 2018.

34 • gbi_1M_WBA18.csv: Burrow use associations for males during mating 2018.

35 • gbi_2F_SBA18.csv: Burrow use associations for females during offspring rearing 2018.

36 • gbi_2M_SBA18.csv: Burrow use associations for males during offspring rearing 2018.

37 • gbi_3F_WBA19.csv: Burrow use associations for females during mating 2019.

38 • gbi_3M_WBA19.csv: Burrow use associations for males during mating 2019.

39 • gbi_4F_SBA19.csv: Burrow use associations for females during offspring rearing 2019.

40 • gbi_4M_SBA19.csv: Burrow use associations for males during offspring rearing 2019.

41 • DF_social_stability.csv

Information per focal individual, including social stability index, kinship, reproductive output, and derived metrics used in analyses.

Variables:

• JIS_BURROW: Stability in burrow use from mating through offspring rearing (JIS).

• ID: Unique identifier of each individual.

• SEX: Sex of the individuals (male or female).

• Mean_SFF: Average stability in foraging groups during mating (SFF).

• Mean_kinship: Mean kinship within foraging groups during mating.

• Strength: Intensity of foraging associations during mating.

• YEAR: For this analysis, this variable corresponds to the year 2019.

• N_pups: number of offspring produced by the individual.

• Delta_z_score: relative measure of social stability for each focal degu, comparing stability in burrow use (from the mating to offspring rearing, based on the JIS index), with the stability in foraging groups during mating (based on the SFF index). Z-scores were first calculated for each stability index (JIS and SFF), and the difference between them was used as the Delta z-score.

Additional files:

co-occurrence data used in association analyses (files 42–57) and data used for calculating the Mean SFF, Mean kinship, and Delta z-score (files 58–59).

Files 42-57 (co-occurrence data):

• Column 1: Date. Stored in Excel serial date number format (as used in Windows Excel). Each value corresponds to the calendar date of the observation.

• Column 2: Location. Unique identifier of the burrow (den site) where individuals were recorded.

• Column 3: Behaviour. Numeric code indicating the behavioral category recorded during the observation. In the foraging datasets, 1 indicates that the individual was foraging; in the burrow-use datasets, 1 indicates that the individual was present in the burrow.

• Column 4: Group. Identifier of a co-occurrence event. All individuals sharing the same Group value were observed together at the same location and time and are considered to belong to the same group for that observation event.

42 • gbi_1F_WBA18.xlsx: capture data for females during mating burrow use, 2018

43 • gbi_1F_WFA18.xlsx: co-occurrence data for females during mating foraging, 2018

44 • gbi_1M_WBA18.xlsx: capture data for males during mating burrow use, 2018

45 • gbi_1M_WFA18.xlsx: co-occurrence data for males during mating foraging, 2018

46 • gbi_2F_SBA18.xlsx: capture data for females during offspring rearing burrow use, 2018

47 • gbi_2F_WFA18.xlsx: co-occurrence data for females during mating foraging matched with offspring rearing burrow use, 2018.

48 • gbi_2M_SBA18.xlsx: capture data for males during offspring rearing burrow use, 2018

49 • gbi_2M_WFA18.xlsx: co-occurrence data for males during mating foraging matched with offspring rearing burrow use, 2018.

50 • gbi_3F_WBA19.xlsx: capture data for females during mating burrow use, 2019

51 • gbi_3F_WFA19.xlsx: co-occurrence data for females during mating foraging, 2019

52 • gbi_3M_WBA19.xlsx: capture data for males during mating burrow use, 2019

53 • gbi_3M_WFA19.xlsx: co-occurrence data for males during mating foraging, 2019

54 • gbi_4F_SBA19.xlsx: capture data for females during offspring rearing burrow use, 2019

55 • gbi_4F_WFA19.xlsx: co-occurrence data for females during mating foraging matched with offspring rearing burrow use, 2019.

56 • gbi_4M_SBA19.xlsx: capture data for males during offspring rearing burrow use, 2019

57 • gbi_4M_WFA19.xlsx: co-occurrence data for males during mating foraging matched with offspring rearing burrow use, 2019.

Files 58-59 (data for SFF and Delta z-score indices):

58 • Mean_SFF_and_Mean_kinship19.xlsx

• Column 1: Focal individual ID
• Column 2: Sex
• Column 3: Date
• Column 4: Video ID
• Column 5: Burrow use group ID
• Columns 6–11: Same foraging and burrow-use group (labeled in column as SAME FB). Each column represents a known individual from the focal individual's burrow-use group. Values indicate the total number of 30-second intervals the individual was present with the focal forager. Counts are summed across all observations, ranging from 0 (no co-occurrence) to positive integers (total co-occurrence intervals).
• Columns 12–17: Novel forager (labeled in column as NOVEL F). Each column represents an unknown individual from the focal individual's burrow-use group. Values indicate the total number of 30-second intervals the individual was present with the focal forager. Counts are summed across all observations, ranging from 0 (no co-occurrence) to positive integers (total co-occurrence intervals).
• Column 18: Total Same foraging-burrow (labeled in column as TOTAL FB). Total number of 30-second intervals in which, in a given video, the focal individual was with one or more known foragers from the burrow use group.
• Column 19: Total novel foragers (labeled in column as TOTAL NF). Total number of 30-second intervals in which, in a given video, the focal individual was with one or more novel (unknown) foragers from the burrow use group.
• Column 20: Sum of 30-second intervals in which known and unknown individuals from the burrow use group foraged together.
• Column 21: Social Foraging Familiarity index (SFF) for each video.
• Column 22: Overall within-group mean kinship, for each video.
• Column 23: Overall mean SFF experienced by the focal individual during the mating period, based on foraging and burrow-use data.
• Column 24: Overall mean kinship experienced by the focal individual during the mating period, based on foraging data only.
• Column 25: Focal individual ID.

59 • Delta_z_score_data19.xlsx

• Column 1: Focal individual ID
• Column 2: Social instability in burrow use (JIS)
• Column 3: JIS z-score
• Column 4: Mean social stability in foraging during mating (SFF)
• Column 5: SFF z-score
• Column 6: Delta z-score, relative to JIS and SFF

CODE SCRIPTS AND WORKFLOW

code 1:

Script name: MRQAP_analysis.R

MRQAP Analysis Script for Behavioral Ecology

This script allows loading association coefficient matrices and creating an MRQAP model, as well as evaluating the inclusion of confounding effects (number of observations per dyad for the response variable) and a null model. The script randomized matrices from the GBI table for each response variable, with 100,000 permutations, to evaluate whether the results differ from chance. Finally, the script performs a confirmatory Mantel test with 99,999 simulations. The main packages used are asnipe and vegan, with the functions mrqap.dsp, mrqap.custom.null, and mantel.test.

code 2:

Script name: GLM_analysis.R

Stability in foraging associations linked to stability in communal use of burrows in degus

This script allows fitting GLMs, evaluating term retention via Likelihood Ratio Tests, and checking model fit through residual analyses. These steps were carried out to:

Fit a model explaining JIS (social instability in burrow use).

Fit a model exploring whether the number of offspring produced is associated with the variation in JIS relative to SFF, using a Delta z-score.

Workflow

1. Run MRQAP_analysis.R - tests at the dyad level:

- Whether foraging associations predict burrow use associations during mating

- Whether foraging associations during mating predict burrow use associations during offspring rearing

2. Run GLM_analysis.R - tests at the focal individual level:

- Whether social stability during foraging predicts social stability in burrow use.

- Whether social stability in burrow use relative to social foraging stability during mating predicts the number of offspring produced.

SOFTWARE VERSIONS

R version 4.5.0 (2025-04-11)

loaded packages:

asnipe: version ‘1.1.17’, vegan: version ‘2.7.1’, ggplot2: version ‘3.5.2’, broom: version ‘1.0.8’, lme4: version ‘1.1.37’, glmmTMB: version ‘1.1.11’, ggeffects: version ‘1.4.28’, cowplot: version ‘1.2.0’, DHARMa: version ‘0.4.7’, qqplotr: version ‘0.0.6’, MuMIn: version ‘1.48.11’, ggrepel: version ‘0.9.6’, readr: version ‘2.1.5’, lmtest: version ‘0.9.40’, MASS: version ‘7.3.65’, grid: version ‘4.5.0’

REFERENCES

1. R Core Team (2024). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/

2. Farine, D.R. (2013). asnipe: Animal social network inference and permutations for ecologists. R package version 1.2. https://CRAN.R-project.org/package=asnipe

3. Oksanen, J., Blanchet, F.G., Friendly, M., Kindt, R., Legendre, P., McGlinn, D., et al. (2024). vegan: Community Ecology Package. R package version 2.7-8. https://CRAN.R-project.org/package=vegan

4. Brooks, M.E., Kristensen, K., van Benthem, K.J., Magnusson, A., Berg, C.W., Nielsen, A., et al. (2017). glmmTMB balances speed and flexibility among packages for zero-inflated generalized linear mixed modeling. The R Journal, 9(2), 378–400. https://journal.r-project.org/archive/2017/RJ-2017-066/index.html

5. Zeileis, A., Hothorn, T. (2002). Diagnostic checking in regression relationships. R News, 2(3), 7–10. https://CRAN.R-project.org/package=lmtest

6. Venables, W.N., Ripley, B.D. (2002). Modern Applied Statistics with S. 4th edition. Springer, New York. (Incluye el paquete MASS en R)