Dataset of diverse evolutionary pathways shape cichlid egg size in Lake Tanganyika
Data files
Oct 28, 2025 version files 358.16 KB
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b1_pruned.tre
273.84 KB
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data_cichlid.csv
10.75 KB
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lifehistorytraits_rawdata.csv
18.04 KB
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pop2_backbone_Tanga.tre
29.89 KB
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RbS_test_for_MB.csv
998 B
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RbS_test_for_SB.csv
1.11 KB
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README.md
11.52 KB
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trait.csv
7.77 KB
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use.tree
4.23 KB
Oct 30, 2025 version files 358.62 KB
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b1_pruned.tre
273.84 KB
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data_cichlid.csv
10.75 KB
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lifehistorytraits_rawdata.csv
18.04 KB
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pop2_backbone_Tanga.tre
29.89 KB
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RbS_test_for_MB.csv
998 B
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RbS_test_for_SB.csv
1.11 KB
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README.md
11.98 KB
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trait.csv
7.77 KB
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use.tree
4.23 KB
Abstract
Optimal egg size is a classic and important concept in life history theory. Here, we examined the ecological factors affecting egg size, using a comparative analysis of 83 cichlid species from Lake Tanganyika, which employ either a mouth-brooding or substrate-brooding. The two strategies differ substantially in regard to spatial limitations and food availability for offspring, potentially leading to divergent responses to the ecological factors influencing egg size. We observed a strong negative correlation between egg size and egg number in species that exhibit mouth-brooding, but not in substrate-brooding cichlids. Our results suggest that the importance of the relationship between clutch size and egg size varies substantially between these two types of parental care. Interestingly, in mouth-brooding species, we found that egg size increases when offspring exhibit external feeding behaviors (grazing behavior). We also demonstrate that substrate-brooding species with shorter periods of parental care typically produced larger eggs, compared to species with relatively longer periods of parental care. Overall, our results demonstrate that behavioral differences, including parental care type and duration, play an important but often overlooked role in the evolution of egg size across species.
Description of files and variables:
File: data_cichlid.csv
Description: dataset including mouth- and substrate-brooding cichlids (n = 83 species).
Variables
- species: Species Code. The name corresponds to the phylogenetic tree data.
- samplesize: Number of mature females we caught.
- tribe: The tribe to which the species belonged.
- broodtype: brooding type (mouth- or substrate-brooding)
- care_sex: sexes mainly provide parental care
- parentalcare_dulation: duration of parental care. For mouth-brooders, data collection for parental care period was not conducted; therefore, missing data are indicated as NA.
- guarding: sexes provide brood guarding (BI: biparental guarding, MG: maternal guarding, NG: no guarding)
- bodyweight: mean body weight of matured females (g)
- gonalweight: mean weight of ovary in matured females (g)
- clutchsize: the mean number of eggs in ovary
- eggsize: the maen size of matured egg in ovary (mm)
- SL: mean standard length (mm)
- gonadfreeBW: mean body size (= bodyweight-gonalweight)
- logES: log 10 transfered eggsize
- logCS: log 10 transfered clutchsize
- logBW: log 10 transfered gonadfreeBW
File: trait.csv
Description: dataset including mouth- and substrate-brooding cichlids (n = 87 species).
Variables
- species: Species Code. The name corresponds to the phylogenetic tree data.
- samplesize: Number of mature females we caught.
- tribe: The tribe to which the species belonged.
- broodtype: brooding type (mouth- or substrate-brooding)
- care_sex: sexes mainly provide parental care. Data of some species is missing because of luck of life history knowledge.
- guarding: sexes provide brood guarding (BI: biparental guarding, MG: maternal guarding, NG: no guarding). Data of some species is missing because of luck of life history knowledge.
- bodyweight: mean body weight of matured females (g)
- gonalweight: mean weight of ovary in matured females (g)
- clutchsize: the mean number of eggs in ovary
- eggsize: the mean size of matured egg in ovary (mm)
- SL: mean standard length (mm)
- gonadfreeBW: mean body size (= bodyweight-gonalweight)
File: pop2_backbone_Tanga.tre
Description: Phylogenetic tree containing all species used in the study
File: use.tree
Description: Phylogenetic tree created by combining pop2_backbone_Tanga.tre and b1_pruned.tre
File: b1_pruned.tre
Description: Phylogenetic tree published by Ronco et al. 2021. This phylogenetic tree was used to create the use.tree
File: lifehistorytraits_rawdata.csv
Description: Raw data before averaging of cichlid fishes in Lake Tanganyika
Variables
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name: scientific names
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name2: Species Code. The name corresponds to the phylogenetic tree data.
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SL_f: standard length (mm)
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eggnum: the number of eggs in ovary
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eggsize: the size of matured egg in ovary (mm)
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fBW: body weight of matured females (g)
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gonadweight: weight of ovary in matured females (g)
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gonad_free_BW: body size (= bodyweight-gonalweight)
NA indicates data due to measurement errors.
File: RbS_test_for_SB.csv
Description: data set for post-hoc Rate_by_state test in substrate-brooders.
Variables
- species: scientific names
- egg size: log 10 transfered egg size
- care_duration: parental care duration (longer: species with longer parental care, shorter: species with shorter parental care)
File: RbS_test_for_MB.csv
Description: data set for post-hoc Rate_by_state test in mouth-brooders.
Variables
- species: scientific names
- guarding: presence or absence of grazing behavior (P: presence, A: absence)
- egg size: log 10 transfered egg size
File: MCMCGLMM(Figure3_5).R (in Zenodo)
Description: R code to reproduce the analysis by Phylogenetic MCMC GLMM. This R code corresponds to the analysis associated with Figures 3, 4, and 5.
File: RbS_test_for_SB.R (in Zenodo)
Description: R code to reproduce the analysis by Rate_by_state test for substrate-brooders.
File: RbS_test_for_MB.R (in Zenodo)
Description: R code to reproduce the analysis by Rate_by_state test for mouth-brooders.
File: other_analysis.R (in Zenodo)
Description: R code to reproduce the analyses other than the MCMC and Rate_by_state tests. This code was accidentally deleted from Zenodo during dataset adjustments and was re-added on October 30.
File: MCMCGLMM_results.pdf
Description: Figures showing the results of the MCMC. We created Figures 3, 4, and 5 by editing these figures.
Code/software
- R (R Core Team (2024))
Access information
Software with packages or sources used in this study
- R Core Team (2024). R: A Language and Environment for Statistical Computing_. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/.
- Hadfield, J. D. (2010). MCMC Methods for Multi-Response Generalized Linear Mixed Models: The MCMCglmm R Package. Journal of Statistical Software, 33(2), 1–22.
- Plummer M, Best N, Cowles K, Vines K (2006). “CODA: Convergence Diagnosis and Output Analysis for MCMC.” R News, 6(1), 7–11.
Information of Phylogenetic trees
- Ronco, F., Matschiner, M., Böhne, A., Boila, A., Büscher, H.H., El Taher, A., et al. (2021). Drivers and dynamics of a massive adaptive radiation in cichlid fishes. Nature, 589, 76–81.
References where life history information was provided
- Balshine, Sigal, et al. "Correlates of group size in a cooperatively breeding cichlid fish (Neolamprologus pulcher)." Behavioral Ecology and Sociobiology 50 (2001): 134-140.
- Heg, Dik, and Zina Bachar. "Cooperative breeding in the Lake Tanganyika cichlid Julidochromis ornatus." Environmental Biology of Fishes 76 (2006): 265-281.
- Heg, Dik, Zina Bachar, and Michael Taborsky. "Cooperative breeding and group structure in the Lake Tanganyika cichlid Neolamprologus savoryi." Ethology 111.11 (2005): 1017-1043.
- Ito, Munehiko H., Motoomi Yamaguchi, and Nobuyuki Kutsukake. "Sex differences in intrasexual aggression among sex-role-reversed, cooperatively breeding cichlid fish Julidochromis regani." Journal of Ethology 35 (2017): 137-144.
- Keenleyside, Miles H., ed. Cichlid fishes: behaviour, ecology and evolution. Vol. 2. Springer Science & Business Media, 1991.
- Kohda, M. "Does male‐mating attack in the herbivorous cichlid, Petrochromis polyodon, facilitate the coexistence of congeners?" Ecology of Freshwater Fish 4.4 (1995): 152-159
- Kohler, Uwe. Zur Struktur und Evolution des Sozialsystems von Neolamprologus multifasciatus (Cichlidae, Pisces), dem kleinsten Schneckenbuntbarsch des Tanganjikasees. Shaker, 1998.
- Konings AD. "Tanganyika Cichlids in their natural habitat 4th edition". Cichlid press. ISBN 978-1-932892-26-0
- Kuwamura, T. "The evolution of parental care and mating systems among Tanganyikan cichlids." Fish communities in lake Tanganyika (1997): 57-86.
- Kuwamura, Tetsuo. "Biparental mouthbrooding and guarding in a Tanganyikan cichlid Haplotaxodon microlepis." Japanese Journal of Ichthyology 35.1 (1988): 62-68
- Matsumoto, Kazunori, and Masanori Kohda. "Male foraging avoidance in female feeding territories in a harem polygynous cichlid in Lake Tanganyika." Journal of Ethology 25 (2007): 21-27.
- Morita, M., et al. "Bower‐building behaviour is associated with increased sperm longevity in Tanganyikan cichlids." Journal of evolutionary biology 27.12 (2014): 2629-2643.
- Nagoshi, M., and Y. Yanagisawa. "Parental care patterns and growth and survival of dependent offspring in cichlids." Fish Communities in Lake Tanganyika (1997): 175-192.
- Ochi, Haruki, and Yasunobu Yanagisawa. "Sand-transfer behavior outside the nest by guarding parents of the Tanganyikan cichlid, Neolamprologus caudopunctatus." Ichthyological Research 46 (1999): 419-422.
- Ochi, Haruki. "Maintenance of separate territories for mating and feeding by males of a maternal mouthbrooding cichlid, Gnathochromis pfefferi, in Lake Tanganyika." Japanese Journal of Ichthyology 40.2 (1993a): 173-182.
- Ochi, Haruki. "Mate monopolization by a dominant male in a multi-male social group of a mouthbrooding cichlid, Ctenochromis horei." Japanese Journal of Ichthyology 40.2 (1993b): 209-218.
- Ochi, Haruki. "Mating systems of two midwater-spawning cichlids, Cyprichromis microlepidotus and Paracyprichromis brieni, in Lake Tanganyika." Ichthyological Research 43 (1996): 239-246.
- Ota, Kazutaka, and Masanori Kohda. "Maternal food provisioning in a substrate-brooding African cichlid." PloS one 9.6 (2014): e99094.
- Saeki, Taiga, et al. "Kin-structured cooperatively breeding groups due to limited dispersal in the obligate shell-brooding cichlid Neolamprologus meeli." Behavioral Ecology and Sociobiology 76.7 (2022): 89.
- Sato, T., and M. M. Gashagaza. "Shell-brooding cichlid fishes of Lake Tanganyika: their habitats and mating systems." Fish Communities in Lake Tanganyika (1997): 219-240.
- Sato, Tetsu. "Active accumulation of spawning substrate: a determinant of extreme polygyny in a shell-brooding cichlid fish." Animal Behaviour 48.3 (1994): 669-678.
- Satoh, S. "First Report of Maternal Interference Behaviour towards Sibling Aggression in the Shell-brooding Cichlid Lamprologus ornatipinnis (Cichlidae)." Journal of Ichthyology (2021): 1-5.
- Satoh, Shun, et al. "Bi-parental mucus provisioning in the scale-eating cichlid Perissodus microlepis (Cichlidae)." Biological Journal of the Linnean Society 128.4 (2019): 926-935.
- Satoh, Shun, et al. "Cooperative breeding in Neolamprologus bifasciatus, a cichlid fish inhabiting the deep reefs of Lake Tanganyika." Ecology of Freshwater Fish 31.4 (2022): 640-649.
- Satoh, Shun, et al. "Dynamics of sibling aggression of a cichlid fish in Lake Tanganyika." Hydrobiologia 832 (2019): 201-213
- Satoh, Shun, Takashi Hotta, and Masanori Kohda. "Maternal care-providing cichlid Neolamprologus furcifer selectively focuses on high-threat carnivorous intruders, limiting attention to other threats." Frontiers in Ecology and Evolution 9 (2021): 616810.
- Sturmbauer, Christian, et al. "Variation of territory size and defense behavior in breeding pairs of the endemic Lake Tanganyika cichlid fish Variabilichromis moorii." Patterns and Processes of Speciation in Ancient Lakes: Proceedings of the Fourth Symposium on Speciation in Ancient Lakes, Berlin, Germany, September 4–8, 2006. Springer Netherlands, 2009.
- Sunobe, Tomoki, and Hiroyuki Munehara. "Mating system and kin relationship between adults and young in the shell-brooding cichlid fish Neolamprologus meeli in Lake Tanganyika." Journal of Ethology 21 (2003): 87-92.
- Taborsky, Michael. "Broodcare helpers in the cichlid fish Lamprologus brichardi: their costs and benefits." Animal Behaviour 32.4 (1984): 1236-1252.
- Takahashi, T., and M. Hori. "Description of a new Lake Tanganyikan cichlid fish of the genus Cyprichromis (Perciformes: Cichlidae) with a note on sexual dimorphism." Journal of Fish Biology 68.SB (2006): 174-192.
- Takahashi, Tetsumi, Michio Hori, and Kazuhiro Nakaya. "New species of Cyprichromis (Perciformes: Cichlidae) from Lake Tanganyika, Africa." Copeia 2002.4 (2002): 1029-1036.
- Tanaka, Hirokazu, et al. "Group composition, relatedness, and dispersal in the cooperatively breeding cichlid Neolamprologus obscurus." Behavioral ecology and sociobiology 69 (2015): 169-181.
- Yamagishi, Satoshi, and Masanori Kohda. "Is the cichlid fish Julidochromis marlieri polyandrous?" Ichthyological Research 43 (1996): 469-471.
- Yanagisawa, Yasunobu. "Social organization of a polygynous cichlid Lamprologus furcifer in Lake Tanganyika." Japanese Journal of Ichthyology 34.1 (1987): 82-90.
Change log:
Changes since October 28, 2025: the code hosted on Zenodo was slightly adjusted resulting in a new data version, but there are not meaningful changes. The README was updated to reflect this.
Egg size, clutch size (i.e., the number of eggs released during a single spawning event), and adult female body mass were measured in 47 mouth-brooding (belonging to 11 tribes) and 40 substrate-brooding cichlid species (belonging to 2 tribes), all endemic to Lake Tanganyika, in East-Central Africa. The sexually mature female specimens were obtained mainly from local fishermen and fish markets (n = 62 species, n = 161 individuals) and from field sampling using a fine-mesh gill net, hand nets, and SCUBA (n = 19 species, n = 73 individuals). The captured fish were euthanized by overdosing with anesthetic (MS-222, Wako Pure Chemical Industries) and stored in a freezer until measurements were taken. Given the relatively small sample size of females carrying mature eggs collected during the field survey, we also used samples stored at Osaka Metropolitan University (n = 10 species, n = 22 individuals) and the Hokkaido University Museum (n = 7 species, n = 13 individuals). Standard length (in mm), body mass (i.e., gonad-free body weight to 0.001 g), and ovary mass (to 0.001 g) were measured. Mature eggs were distinguishable from immature eggs in the ovary based on coloration and size and were counted using a tally counter and preserved in 5% formalin. Immature eggs found in the same ovary were not included in the total and omitted from the analyses. In each clutch we randomly selected five eggs or used all eggs if the clutch size was smaller than five, to measure the mean egg size. Eggs were photographed using a digital camera equipped with a stereomicroscope (HD212; AMscope, USA), and the long and short diameter was measured on each egg to an accuracy of 0.01 mm using Image J ver. 1.52q software (Schneider et al. 2012). The mean value of the long and short diameter was used to define the mean egg size. In total, measurements were taken from 1326 eggs from 269 female individuals representing 87 species.
Literature survey
Information on parental care, i.e., brooding type - mouth or substrate-brooding, care type- maternal parental or biparental care, duration of parental care, and presence or absence of grazing behavior, was collected from the literature.
For 44 of 47 mouth-brooding species, we collated data on care type (biparental or maternal care) and grazing behavior (present or absent; Yanagisawa 1985, 1986; Kuwamura 1988b, 1997). We predicted that the acquisition of external food resources by offspring (i.e., grazing behavior) may allow for a reduction in egg yolk sac investment and consequently a reduction in egg size. Although we gained life history trait data from the field for Baileychromis centropomoides, Paracyprichromis nigripinnis, and Xenotilapia nigrolabiata, we were unable to determine care type or the presence/absence of grazing behavior due to limited ecological descriptions of these species in the literature.
For 39 of 40 substrate-brooding species, we collected information on care type (biparental or maternal care) and the duration of parental care (short or long). In this study, we defined the parental care period as days from the spawning event to dispersal and broadly classified the duration of parental care as either “shorter” or “longer”, based on the literature. Some cichlid species in Lake Tanganyika exhibit extremely short periods of parental care, often less than 20 days after hatching, while others have comparatively longer periods, ranging from 66–130 days . As far as we are aware, an intermediate period of parental care, between 20 and 65 days, has not been reported in any Lake Tanganyikan substrate-brooding species. Therefore, we defined species exhibiting parental care behaviors for ≤ 20 days as having “shorter” (n = 7 species) and > 20 days as having “longer” (n = 32 species) parentalcare duration. Information on parental care duration was lacking in one species Neolamprologus mustax again due to limited ecological descriptions.
Phylogenetic tree
To account for the effects of phylogeny, we included in our analyses a modified time calibrated phylogenetic tree of the cichlids that have radiated in Lake Tanganyika (Ronco et al. 2021). We pruned the Ronco et al. (2021) tree using the ‘droptip’ function in R ver 4.4.0 (R Core Team. 2024) package ape (Paradis et al. 2004) down to 85 species, excluding Oreochromis tanganicae and Tylochromis polylepis from our initial sample size of 87 species. We then obtained divergence ages of O. tanganicae and T. polylepis, which secondarily invaded Lake Tanganyika from a time estimated phylogenetic tree targeting representatives of all cichlid tribes (Ronco et al. 2021). These divergence ages were integrated into the previously pruned phylogenetic tree, resulting in a tree representing all 87 species used in our study. The ancestral states of egg size were estimated in phytools (Revell 2024) to visualize the posterior probabilities of each trait condition of mean egg size of species, along the branches of the cichlid phylogeny in Lake Tanganyika.
Phylogenetic signal life-history traits
We calculated phylogenetic signals for egg size, clutch size, and female body mass with the ‘phylosig’ function in the R package phytools. We note that measurement error can lead to an underestimation of the strength of phylogenetic signals and potentially obscure patterns of phylogenetic correlation among species in univariate cases. Therefore, for the 62 species for which repeated data were available, the strength of the phylogenetic signal was calculated, considering intraspecific variation. Each trait value was log10-transformed and the mean for all species and standard error for available species were calculated and used in the analysis.
Phylogenetic comparative analyses
We used Bayesian phylogenetic mixed model analyses (BPMM; R package “MCMCglmm”) to investigate the effects of brooding strategy (i.e. mouth- and substrate-brooding) and various parental care traits on the trade-off between clutch size and egg size. In each model, we fitted the pruned phylogenetic tree with 87 species as a random effect.
First, we used BPMM to investigate the effect of brooding strategy on mean egg size We fitted a model mean with egg size (log10-transformed) as the response variable and brooding type (mouth- or substrate brooding), mean clutch size (log10-transformed), mean female body mass (log10-transformed), and their interactions as fixed effects. The pruned phylogenetic tree was fitted as a random effect. The error distribution for the continuous variables followed a Gaussian distribution and were consequently standardized to facilitate the comparison of regression coefficients among the fixed effects. We used the uninformative priors for the random effect and the residual variance (inverse-Wishart distribution, nu = 1/2, V = 0.002) and non-informative priors for the fixed effects. The MCMC was performed with 205000 total iterations, a burn-in of 5000, and a thinning interval of 100 was applied. We evaluated model convergence based on the visual examination of trace plots. The model convergence was also checked by running the MCMC chain independently and using the Gelman-Rubin's diagnostic was less than 1.1 using the 'gelman.diag' function in the R package coda (Plummer et al. 2006). For all fixed effects, random effects and residuals, the effective sample size exceeded 1000. We also computed the variance inflation factor (VIF) to assess collinearity between log-transformed clutch size and body mass. The VIF for each fixed effect was lower than 10 (Clutch size = 8.26, female body mass = 4.96, brooding type = 1.75, clutch size: brooding type = 8.45, female body mass: brooding type = 4.67).
Next, since egg size variation was likely to account for different ecological conditions between mouth- and substrate brooders, we ran BPMMs separately for mouth-brooding and substrate-brooding species to investigate factors influencing variation in egg size within brooding strategies. For mouth-brooding species, we fitted a model with mean egg size as the response variable and with mean clutch size, mean female body mass, grazing behavior (presence or absence), and care type (biparental or maternal mouth-brooding) as explanatory variables, omitting any two-way interaction terms. For substrate-brooding species, we fitted a model with mean egg size as the response variable and with mean clutch size, mean female body mass, parental care duration (short or long), and care type (biparental or maternal brood guarding) as explanatory variables, again omitting any two-way interactions. The phylogenetic tree, isolated to either mouth-brooding or substrate-brooding species was incorporated as a random effect in each model. All other model components were conducted the same as described above.