Repeated evolution of cooperative breeding and life history traits in Tanganyikan cichlid fishes
Data files
Feb 11, 2026 version files 418.66 KB
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05_BEAST_RAxML.tre
273.84 KB
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ancestral_states_reconstruction.R
3.04 KB
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ASR_niger_non.csv
3.05 KB
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ASR_niger_removal.csv
3.05 KB
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ASR.csv
3.05 KB
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data_for_cooperative_breeding.xlsx
18.87 KB
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data_indi_rev.xlsx
59.53 KB
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data_PPA.csv
2.67 KB
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Phylogenetic_path_analysis.R
1.02 KB
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R_analysis.R
13.92 KB
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README.md
7.61 KB
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sp.data.csv
9.39 KB
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sp.df.ave.csv
3.27 KB
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species.trait.rdata
1.84 KB
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tanga_Lamp_list.csv
5.87 KB
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tr4PPA.tree
1.57 KB
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tree_new.tre
7.07 KB
Abstract
Cooperative breeding is a complex social system in the animal kingdom where offspring receive care not only from their parents but also from other group members. However, the life history traits related to the evolutionary transition toward this complex system are still poorly understood. This study investigated the evolutionary transition from non-cooperativeto cooperative breeding in lamprologine cichlid fishes endemic to Lake Tanganyika using phylogenetic comparative methods. Ancestral state reconstruction revealed that the evolutionary transition from non-cooperative to cooperative breeding occurred at least seven times independently. Comparative analyses using life history data obtained from field observations and sampling and literature review showed an evolutionary link between cooperative breeding and clutch size or body size but not egg size; both clutch and body sizes were smaller in cooperative breeders. These findings suggested the evolutionary scenario that cooperative breeding first evolved in smaller species, most likely because of ecological constraints, such as an increased predation risk, followed by a reduction in clutch size. These results highlight the impact of predation risk on life history traits and how it mediates the transition toward a complex social organization.
Dataset DOI: 10.5061/dryad.d51c5b0f9
Description of the data and file structure
Files and variables
File: species_df.xlsx
Description: Averaged data on life history traits of target species.
File: sp.data.csv
Description: A dataset of life history traits for Tanganyika cichlids. This dataset includes field data obtained through this project and data obtained from FishBase.
Variables
- phylo: taxon name to for connecting to the phylogenetic tree
- BodyWeight_log_mean_female: meam log-transfer body weight of female breeders
- BodyWeight_log_mean_male: meam log-transfer body weight of male breeders
- EggSize_log_mean: mean log-transfer egg size
- ClutchSize_log_mean: mean log-transfer clutch size (number of eggs)
- habitat: breeding habitats of each species
- Species: scientific name
- cooperative_brooder: Whether the species engaing cooperative breeding (0= no, 1 = yes, NA=missing data)
- FBname: common name of species discrived in FaceBase
- FB_Length: Body size discrived in FishBase (in cm).
- FB_LTypeMaxM: Masurement method of FB_Length (TL = total length, SL = standard length , NA =missing data)
File: sp.df.ave.csv
Description: A dataset averaging the traits obtained from each field site.
Variables
- species and phylo: taxon name to for connecting to the phylogenetic tree
- BodyWeight_log_mean_female: meam log-transfer body weight of female breeders
- BodyWeight_log_mean_male: meam log-transfer body weight of male breeders
- EggSize_log_mean: mean log-transfer egg size
- ClutchSize_log_mean: mean log-transfer clutch size (number of eggs)
- habitat2: breeding habitats of each species
- CB: Whether the species engaing cooperative breeding (0= no, 1 = yes)
File: tanga_Lamp_list.csv
Description: A list of the species we studied is explicitly provided in this dataset, as the scientific names recorded during our data collection from FishBase often did not align with those used in Ronco et al. (2021).
Variables
- SpeciesID: Species name used in the phylogenetic tree
- Species_inFishbase: scientific names used in the FishBase
- Species_inRonco2022: scientific names used in the Ronco et al. 2021
File: 05_BEAST_RAxML.tre
Description: Phylogenetic tree published by Ronco et al. (2021). This tree represents the evolutionary relationships among the taxa included in their study, providing insights into lineage divergence and genetic relatedness. It can be used for comparative analyses, visualization of phylogenetic structure, and as a reference for downstream evolutionary or molecular studies.
File: data_indi_rev.xlsx
Description: Individual-level trait data collected in the field.
Variables
- species: scientific name
- name: taxon name to for connecting to the phylogenetic tree
- CB: Whether the species engaing cooperative breeding (0= no, 1 = yes)
- Shell: Whether the species engaing shell-brooding (0= no, 1 = yes)
- shell_facultative: Whether the species engaing facultative shell-brooding
- SL_f: standard length (in mm)
- eggnum: the number of eggs (= clutch size)
- eggsize: mean egg size in mm
- egg_volume: mean egg volume
- BW: body weight (in g)
- observer: The name of the person who captured that individual
- population: The location where that individual was captured
- gonadweight: gonad weight of (in g)
- gonad_free_BW: body weight - ovary weight of female (in g)
- habitat: habitat type
- sex: male or female
- reasoning of breeders: Why did you determine that individual to be a mature specimen?
File :species.trait.rdata
Description: R script data used for data collection in Fishbase
- phylo – unique code for each species
- BodyWeight_log_mean_female – Log-transformed mean body weight of adult females
- BodyWeight_log_mean_male – Log-transformed mean body weight of adult males
- EggSize_log_mean – Log-transformed mean egg size
- ClutchSize_log_mean – Log-transformed mean clutch size (number of eggs per reproductive event)
- CB – A categorical or binary variable (0/1). Based on the context, this could indicate a trait such as cavity brooding vs. non-cavity brooding or another reproductive behavior
- habitat2 – Habitat type or ecological category of the species, e.g., “rocky area,” “crevices and caves,” “facultative shell-brooder,” etc
File: R_analysis.R
Description:The R environment we used. Readers can use this project file to reproduce our analysis environment.
File: ASR_niger_non.csv
Description: Dataset used for ancestral trait reconstruction; N. niger is included as a non-cooperative breeding species.
Variables
- species: Name matching to phylogenetic tree data
- social_system: cooperative breeding species or non-cooperative breeding species. Taxa that were not the subject of our study and species with unknown social status are shown as NA.
File: ASR_niger_removal.csv
Description: Dataset used for ancestral trait reconstruction; N. niger is removed from dataset.
Variables
- species:Name matching to phylogenetic tree data
- social_system: cooperative breeding species or non-cooperative breeding species. Taxa that were not the subject of our study and species with unknown social status are shown as NA.
File: ASR.csv
Description: Dataset used for ancestral trait reconstruction in main analysis. Neolamprologus niger is included this dataset as cooperative breeder.
Variables
- species: Name matching to phylogenetic tree data
- social_system: cooperative breeding species or non-cooperative breeding species. Taxa that were not the subject of our study and species with unknown social status are shown as NA.
File: data_PPA.csv
Description: Dataset used for phylogenetic path analysis. Each life history data set was averaged.
Variables
- Name: name of species
- CB: social system (cooperative or non-cooperative breeders)
- eggnum: mean clutch size (the number of ovary)
- gonadfree_bodyweight_female: mean body weight (BW).
- N: stable isotope ratio dscrived in Ronco et al. (2021)
- CS: log transformed clutch size
- BS: log transformed BW
File: tr4PPA.tree
Description: Phylogenetic tree data used for phylogenetic path analysis (PPA), which allows the study of causal relationships among traits while accounting for shared evolutionary history.
File: tree_new.tre
Description: Phylogenetic tree data used for ancestral trait reconstruction (ATR), which infers the likely traits of ancestral species based on the traits observed in their descendants.
File: data_for_cooperative_breeding.xlsx
Description: Averaged life history data sampling at field.
File: ancestral_states_reconstruction.R
Description: R script for ancestral states reconstruction for social evolution among cichlid fishes. Used in conjunction with ASR.csv (traits data) and tree_new.tre (phylogenetic tree data), the results of our analysis can be reproduced.
File: Phylogenetic_path_analysis.R
Description: R script for phylogenetic path analysis (PPA) for social evolution among cichlid fishes. Used in conjunction with data_PPA.csv (traits data) and tr4PPA.tree (phylogenetic tree data), the results of our analysis can be reproduced.
Code/software
- R ver 4.4.0 RStudio (Software capable of running R) is used for statistical analysis and data visualization.