https://doi.org/10.5061/dryad.5x69p8ddp

Description of the data and file structure

Files and variables

note that the file labels are congruent between files and therefore not described extra for every file*

In general: (Rare) empty cells mean missing values as something happened during the measuring process and the value could not be reconstructed. Except for the breeding data in the file 'Life_history_traits' - see below.

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File: Experiment_details.xlsx

Description: Experimental details are given.

variable labels explained:

• 'generation': generation of selection from 0 (start) to 2 (second generation of artificial selection
• 'replicate': the experiment was run in 3 independent replicates each containing one predation and one control line
• 'sex': males or females
• 'days_inexp_tank': number of days the fish spent in the selection tank
• 'tank_id': we uesd 6 tanks for this Experiment each with a unique number (1-6)
• 'breeding time': number of days the fish were kept in pairs to let them breed
• 'place' : country where the fish were kept

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File: Length_BP_F2.xlsx

Description: standard length of breeding pairs of the F2 generation

variable labels explained:

• 'treatment': two levels: either control (kept in safe space) or predation (exposed to predator)
• 'replicate': the experiment was run in 3 independent replicates each containing one predation and one control line
• 'BP': breeding pair number - identifier of breeding pair
• 'generation': what number of selective generations those fish are in. 'F2' means 2nd generation of selection.
• 'sex': males or females
• 'standard_length_mm' standard length of the fish (tip of the snout to end of caudal peduncle, in mm.

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File: Length_F2.xlsx

Description: standard length of F2 generation

File with length of fish from predation lines at various time points

tabs of file:

Variable labels explained (labels the same for all sheets):

• 'number': running number
• 'fish_nr': identifier number of individual fish
• 'timing': before (or after) selection - coincides with sheet names
• 'photo type': were fish photographed individually or in groups
• 'treatment': two levels: either control (kept in safe space) or predation (exposed to predator)
• 'replicate': the experiment was run in 3 independent replicates each containing one predation and one control line
• 'length_cm': body length of fish

• 'standard_length_mm' standard length of the fish (tip of the snout to end of caudal peduncle, in mm.
• 'standard_length_cm' standard length of the fish (tip of the snout to end of caudal peduncle, in cm.

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File: Life_history_traits.xlsx

Description: life history traits of F3 generation

empty cells in 'fry_number' mean no reproduction in that pair for that brood --> also no 'interval_brood' possible, hence also empty cell. The higher the brood number, the less likely that any pair has a value in the 'fry_number'. But, for example, pair 3C18 had 6 broods, that means it has a fry number in all 6 'brood' 'fry_number cells'.

variable labels explained:

• 'generation': generation of selection from 0 (start) to 2 (second generation of artificial selection)
• 'treatment': predation (P) or control (C) treatment of selection
• 'pair_id': number of a pair in a given group
• 'id': individual identifying code for a given pair. e.g.: '1P2" means second pair in replicate one, predation treatment
• 'fry_yes_no' did the pair produce offspring at all
• 'brood': number of brood.
• 'fry_number': number of offspring produced
• 'interval_brood': number of days between this and the last brood

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File: Offspring_traits_juveniles.xlsx

Description: morphological traits of F4 juveniles

variable labels explained:

• 'ID': running identifying number of individual measured
• 'tank_ID': number of the tank the fish came from
• 'day': day the fish was measured
• 'date': date the fish was measured
• 'treatment': either control (C) or predation (P) selection treatment
• 'rep': number of replicate
• 'BP_nr': number of the breeding pair
• 'clutch_size': number of siblings in the clutch of the measured animal
• 'fish_nr': always 3 fish per clutch measured (1, 2, 3)
• 'size_mm': body size in mm
• 'id': individual identifying code for a given pair. e.g.: '1P2" means second pair in replicate one, predation treatment

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File: Offspring_traits_female_adults.xlsx

Description: morphological traits of F4 adult females

variable labels explained:

(most variables like above, here the extra variables)

All measures in mm or mm2*

• 'body_area': are of body surface measured from picture
• 'tail_length'": length of the tail
• 'eye_size_x': width of the eye
• 'eye_size_y': height of the eye
• 'full length': total body length
• 'weight_mg': weight of the fish in mg
• 'eye_area': surface of the eye area

File: offspring_traits_male_adults.xlsx

Description: morphological traits of F4 adult males

variable labels explained:

(most variables like above in females, here the extra variables)

All measures in mm or mm2*

• 'body_area': body area
• 'gonopodium_size': length of the gonopodium in mm
• 'full_length': total body length including tail
• 'area_black': surface area of black colouration on that fish
• 'area_orange': surface area of orange colouration on that fish
• 'area_iridescent': surface area of iridescent colouration on that fish

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R code implementation

R_code_life_history_25-09-24.Rmd

This data repository contains the R Markdown file used to analyse life-history and offspring trait data associated with the accompanying dataset. The code performs data import, preprocessing, statistical analyses, and figure generation.

Software Requirements

R version:

  R ≥ 4.2.0

Recommended environment:

  RStudio Desktop (for knitting the R Markdown file)

R Package Requirements

We used the following CRAN packages:

tidyverse, readxl, lme4, lmerTest, glmmTMB, emmeans, car, DHARMa, performance, ggplot2, ggpubr, cowplot, FactoMineR, factoextra, sjPlot, kableExtra

Packages are loaded within the script. All packages are available from CRAN.

Data Inputs

Input data are Excel files (.xlsx).

File paths are specified directly in the R Markdown file and must be updated by the user to reflect the local location of the data files.

Required input files include life-history trait data and offspring trait data for juvenile and adult females.

Running the Code

1. Install R (≥ 4.2.0) and required packages.

2. Update file paths in R_code_life_history_25-09-24.Rmd to point to the local data files.

3. Open the R Markdown file in RStudio.

4. Run code chunks sequentially or knit the document to HTML.

• All analyses are fully scripted in a single R Markdown file.
• Results are reproducible given the same input data, R version, and package versions.
• Minor numerical differences may occur across operating systems or R versions.

For questions regarding the data or code, please refer to the associated publication and senior author Alexander Kotrschal, alexander.kotrschal@wur.nl.