DOI: 10.5061/dryad.d51c5b0f9
title: Repeated evolution of cooperative breeding and life history traits in Tanganyikan cichlid fishes

description: 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.
description: # Repeated evolution of cooperative breeding and life history traits in
 Tanganyikan cichlid fishes Dataset DOI:
 [10.5061/dryad.d51c5b0f9](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.