DOI: 10.5061/dryad.dv41ns28f
title: Complex residences and sociality: How coral structure and social environment influence occupation patterns in Gobiodon in Aquaria

description: Habitat size and complexity are two of many important characteristics that
 can have profound effects individual on survival, growth and reproduction.
 However, little is known about the influence these characteristics may
 have on sociality and how this may be altered in response to environmental
 stress. Amongst marine fishes, coral dwelling gobies are highly
 specialised cryptobenthic fish that live almost exclusively between the
 branches of Acropora corals, on which they rely for survival and
 reproduction. The study investigated whether grouping patterns and habitat
 choice decisions of a facultatively social species, Gobiodon
 quinquestrigatus, were influenced by habitat complexity and size. Corals
 structures were 3D printed with eco-friendly polymers to create high and
 low complexity Acropora structures allowing coral complexity and size to
 be precisely manipulated. Replicated trials consisted of three sequential
 24-hour treatments: 1) breeder pair only, 2) breeder pair with the
 addition of a subordinate, and 3) breeder pair and subordinate with a
 reduced size of the high complexity coral structure. All individuals were
 observed more frequently in the high complexity coral structure. Females
 chose the high complexity structure most frequently, with males and
 subordinates less likely to choose the high complexity structure. Breeders
 were more likely to choose the high complexity coral structure even when
 the size of the high complexity coral structure was reduced. Breeders were
 observed switching more frequently in their first round (breeder pair
 only) compared to the latter rounds when the subordinate was added and
 when the coral size was reduced. Breeder males switched marginally more
 than breeder females. However, subordinates performed the most switches
 consistently throughout the two rounds they were present. These results
 highlight the dynamic relationship between sociality and structural
 complexity in a habitat specialist reef fish, with implications for our
 understanding of social maintenance in response to climate change and
 habitat loss.
description: To examine whether the high complexity coral structure was chosen
 significantly more often than the low complexity structure and no-choice
 options, a chi-squared goodness of fit test was performed. All recordings
 12 hours post the addition of the individuals were included in the
 analysis, as it was at this point that the gobies appeared to settle
 within the trial tank. To examine the factors
 influencing host coral choice, two multinomial generalised linear mixed
 models were run. The first model examined the effect of sexual/social
 status on the choice of coral host, with group ID as a random factor.
  Note that the variable “sex” encompasses 3 categories, i.e., breeder
 male, breeder female, and subordinate non-breeder, and therefore reflects
 a combination of sex and status. This first model was run twice, with 1)
 breeder females as the reference category and 2) breeder males as the
 reference category, thus ensuring that comparisons between all present
 sexes could be observed. Only the choices made after the subordinate was
 added were used in the analyses, as this ensured all individuals were
 present at all time points used in the analysis. The second model examined
 the effect of trial round on host choice decisions, with group ID as a
 random effect. Each of the three trial rounds was represented by the
 recorded locations at 12 hours and 24 hours post commencement. The model
 was run in two stages: 1) the breeder pair only across all trial rounds,
 and 2) subordinates only across the second and third trial rounds. This
 division accommodated the fact that the subordinates were not present
 during the first trial round whilst also enabling comparisons between
 breeder and subordinate decisions to be examined. The location 12 hours
 post addition was used as the reference category for both status groups,
 respectively (breeder and subordinate), as there were very few choices
 made during the initial observation recorded immediately after
 addition. To examine the factors influencing the number
 of switches, generalised linear mixed models were used with sexual/social
 status, trial round, and their interaction as predictors of the number of
 switches performed (response). The analysis was conducted in three stages:
 1) breeder male and female only and during all rounds and, 2) breeder
 male, female and subordinate during the second and third trial rounds, and
 3) subordinate during the second and third rounds (however due to
 overfitting, a generalised linear model without a random factor was
 performed due to overfitting). This design was used due to the
 subordinates not being present during all rounds of the trial. A random
 factor of group identification was included in both analyses. The
 ‘Poisson’ distribution family was used in both models as the number of
 switches is a count variable. A negative binomial distribution was
 initially attempted, but the Poisson model was deemed a better fit to the
 data based on AIC values. The models were checked for overdispersion,
 homogeneity, and collinearity.
description: # Complex residences and sociality: How coral structure and social
 environment influence occupation patterns in Gobiodon in Aquaria
 [https://doi.org/10.5061/dryad.dv41ns28f](https://doi.org/10.5061/dryad.dv41ns28f) ## Description of the data and file structure The study investigated whether grouping patterns and habitat choice decisions of a facultatively social species, *Gobiodon quinquestrigatus*, were influenced by habitat complexity and size. Corals' structures were 3D printed with eco-friendly polymers to create high and low complexity *Acropora* structures, allowing coral complexity and size to be precisely manipulated. Replicated trials consisted of three sequential 24-hour treatments: 1) breeder pair only, 2) breeder pair with the addition of a subordinate, and 3) breeder pair and subordinate with a reduced size of the high complexity coral structure. The data included: | File | Info | | :--------------------- | :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | R\_Code.R | The R code file that can be used to run the analysis in R. | | R\_Output.pdf | A PDF of the code and the outputs that were generated when the analysis was conducted for investigating and cross-referencing. | | choiceMFS.csv | Data file containing the choices of the male and female individuals throughout the conducted trials. Utilised in the generalised multinomial linear mixed models. Trial variable is the number of the trial (1 to 16). Age is adult or subordinate. Sex.Mref, Sex.Fref and Sex.Sref are three columns that allow for the different sexes to be the reference category. Round is which of the rounds/treatments this row belongs to. Choice.highref, choice.nochoiceref, and choice.lowref are three columns that allow for each of the location categories to be used as the reference category for the multinomial analysis.  | | choiceMF.csv | Data file containing the choices of the male and female individuals throughout the conducted trials. Utilised in the generalised multinomial linear mixed models. Trial variable is the number of the trial (1 to 16). Age is adult or subordinate. Round is which of the rounds/treatments this row belongs to. Choice.highref, choice.nochoiceref, and choice.lowref are three columns that allow for each of the location categories to be used as the reference category for the multinomial analysis.  | | choiceS.csv | Data file containing the choices of the subordinate individuals throughout the conducted trials. Utilised in the generalised multinomial linear mixed models. Trial variable is the number of the trial (1 to 16). Age is adult or subordinate. Round is which of the rounds/treatments this row belongs to. Choice.highref, choice.nochoiceref, and choice.lowref are three columns that allow for each of the location categories to be used as the reference category for the multinomial analysis.  | | switch\_glm2adults.csv | Data file containing the details about the switch patterns of the adults across all three rounds. Utilised in the generalised linear models for switching patterns. Group.ID is the equivalent of trial in the above, and is the group trial ID. Individual what number individual they are. Sex is the sex of the individual. Age is the age of the individual. Round is which round of the trial was recorded. Switches is the number of switches conducted by the individual in that trial.  | | switch\_glm2r23.csv | Data file containing the details about the switch patterns of all individuals (male, female, and subordinate) only in the second and third rounds. Utilised in the generalised linear models for switching patterns. Group.ID is the equivalent of trial in the above, and is the group trial ID. Individual what number individual they are. Sex is the sex of the individual. Age is the age of the individual. Round is which round of the trial was recorded. Switches is the number of switches conducted by the individual in that trial.  | | switch\_glm2r23sub.csv | Data file containing the details about the switch patterns of the subordinates only across the second and third rounds. Utilised in the generalised linear models for switching patterns. Group.ID is the equivalent of trial in the above, and is the group trial ID. Individual what number individual they are. Sex is the sex of the individual. Age is the age of the individual. Round is which round of the trial was recorded. Switches is the number of switches conducted by the individual in that trial.  | | test.csv | This is the data file for the chi-squared test. No. is the number entry in the file. Sex is the sex status of the individual. Round is which round was recorded. Choice is the location of the individual during the round.  | ## Code/software All analyses were conducted in R (v4.2.1) (R Core Team, 2021), using the packages ‘mclogit’ (Elff, 2022), ‘nnet’ (Venables, Ripley and Venables, 2002), ‘memisc’ (Elff, 2023), ‘sJPlot’ (Lüdecke, 2023), ‘lme4’ (Bates *et al.*, 2015), ‘lmertest’ (Kuznetsova *et al.*, 2017) and ‘car’ (Fox and Weisberg, 2019).