Experimental and theoretical support for costs of plasticity and phenotype in a nematode cannibalistic trait
Data files
Oct 23, 2023 version files 1.55 MB
Abstract
Developmental plasticity is the ability of a genotype to express multiple phenotypes under different environmental conditions and has been shown to facilitate the evolution of novel traits. However, while the associated cost of plasticity, i.e., the loss in fitness due to the ability to express plasticity in response to environmental change, and the cost of phenotype, i.e., the loss of fitness due to expressing a fixed phenotype across environments, have been theoretically predicted, empirically such costs remain poorly documented and little understood. Here, we use a plasticity model system, hermaphroditic nematode Pristionchus pacificus, to experimentally measure these costs in wild isolates under controlled laboratory conditions. P. pacificus can develop either a bacterial feeding or predatory mouth morph in response to different external stimuli, with natural variation of mouth-morph ratios between strains. We first demonstrated the cost of phenotype by analyzing fecundity and developmental speed in relation to mouth morphs across the P. pacificus phylogenetic tree. Then, we exposed P. pacificus strains to two distinct microbial diets that induce strain-specific mouth-form ratios. Our results indicate that the plastic strain does shoulder a cost of plasticity, i.e., the diet-induced predatory mouth morph is associated with reduced fecundity and slower developmental speed. In contrast, the non-plastic strain suffers from the cost of phenotype since its phenotype does not change to match the unfavorable bacterial diet but shows increased fitness and higher developmental speed on the favorable diet. Furthermore, using a stage-structured population model based on empirically derived life history parameters, we show how population structure can alleviate the cost of plasticity in P. pacificus. The results of the model illustrate the extent to which the costs associated with plasticity and its effect on competition depend on ecological factors. This study provides support for costs of plasticity and phenotype based on empirical and modeling approaches.
README: Experimental and theoretical support for costs of plasticity and phenotype in a nematode cannibalistic trait
The software and data associated with Dardiry, Piscobulu, Kalirad & Sommer, Experimental and theoretical support for costs of plasticity and phenotype in a nematode predatory trait, Evolution Letters, Volume 7, Issue 1, 1 February 2023, Pages 48–57. This dataset contains the tabulated experimental data, the statistical analyses of the experimental data, and the computational model used in the manuscript. All the figures found in the manuscript can be generated using the code and the data found in this dataset.
Description of the data and file structure
The following scripts are included in this repository:
- digital_worm.py: The model written in Python 3.10
- main_figs_model.ipynb: The code with instructions to generate the main modeling figures.
- main_figs_exp.ipynb: The code with instructions to generate the main experimental figures, including the Bayesian statistical analyses associated with these figures.
- supp_figs.ipynb: The code with instructions to generate the supplementary figures
- digital_worm_n_dev_dif.py: A version of the model written in Python 3.10 in which the developmental speeds remain unchanged upon switching the diet. Used in supp_figs.ipynb.
The scripts above rely on the data found in raw_data.zip.
The raw_data.zip includes the following datasets:
- The developmental speed of the Pristionchus pacificus strains (RSC011,RSA076,RSC017, and RS5405) on the standard laboratory diet (E. coli OP50), measured as percentage of different developmental stages observed after 75 hours (raw_data/fig2/dev_speed_OP50_between_clades.xlsx).
- The fecundity of multiple P. pacificus strains from clade B and clade C on the standard laboratory diet (E. coli OP50). The fecundity was measured by counting the total number eggs laid by an adult worm during 7 days (raw_data/fig2/fecundity_between_strains.xlsx).
- The fecundity of multiple P. pacificus strains on the standard laboratory diet (E. coli OP50), where the mouth-form of the mother was assayed as well. The fecundity was measured by counting the total number eggs laid by an adult worm during 7 days (raw_data/fig2/fecundity_within_strain.xlsx).
- The percentage of adults with the predatory mouth form for multiple P. pacificus strains from clade B and clade C on the standard laboratory diet (E. coli OP50) (raw_data/fig2/mf_between_strains.xlsx).
- The percentage of adults with the predatory mouth form for multiple P. pacificus strains on the standard laboratory diet (E. coli OP50), including strains that only express the predatory mouth form (raw_data/fig2/mf_within_strains.xlsx)
- The developmental speed of the P. pacificus strains, RSC017, RS5405, and RSC019, on the standard laboratory diet (E. coli OP50) and the naturally Pristionchus-associated Novosphingobium sp. L76 (raw_data/fig3/dev_speed_novo_op50.xlsx).
- The fecundity of the P. pacificus strains, RSC017 and RS5405, on the standard laboratory diet (E. coli OP50) and the naturally Pristionchus-associated Novosphingobium sp. L76. The fecundity was measured by counting the total number eggs laid by an adult worm during 7 days (raw_data/fig3/fecundity_novo_op50.xlsx).
- The number of predatory adults of the P. pacificus strains, RSC017 and RS5405, on the standard laboratory diet (E. coli OP50) and the naturally Pristionchus-associated Novosphingobium sp. L76 (raw_data/fig3/MF_on_novo_op50.csv).
- The results of predation assay (the number of corpses observed at the end of the assay) for the P. pacificus strains, RSC017, RS5405, and RSC019, on the standard laboratory diet (E. coli OP50) (raw_data/fig4/Ecoli_killing.csv)
- The results of predation assay (the number of corpses observed at the end of the assay) for the \emph{P. pacifcus} strains, RSC017, RS5405, and RSC019, on the naturally Pristionchus-associated Novosphingobium sp. L76 (raw_data/fig4/Novo_killing.csv)
- The results of predation assay (the number of corpses observed at the end of the assay) and the percentage of predatory adults for multiple P. pacificus strains (raw_data/Killing_correlation.xlsx).
- Summary table of the number of predatory adults observed for multiple P. pacificus strains on the standard laboratory diet (E. coli OP50) (raw_data/MF_count.csv).
Variables used in the datasets
The definitions of the variables used in each dataset, in the order described above:
- Strain: the strain identifier for P. pacificus; Stage: the developmental stage of the observed worm; Percentage: the percentage of worms belonging to a specific stage after 75 hours of development; Clade: The phylogenetic clade of a worm.
- Progeny: The total number of eggs laid by an adult worm during a 7-day period; MF: mouth-from of the adult worm, non-predatory (St) or predatory (Eu). Clade: The phylogenetic clade of a worm.
- Strain: the strain identifier for P. pacificus; MF: mouth-from of the adult worm, non-predatory (St) or predatory (Eu); Fecundity: The total number of eggs laid by an adult worm during a 7-day period.
- Strain: the strain identifier for P. pacificus; Count: the number of predatory (Eu) adults observed out of 100; Clade: The phylogenetic clade of a worm.
- Strain: the strain identifier for P. pacificus; MF: percentage of the predatory (Eu) adults observed.
- Strain: the strain identifier for P. pacificus; Stage: the developmental stage of the observed worm; Percentage: the percentage of worms belonging to a specific stage after 75 hours of development; Condition: the bacterial diet on which the worms were grown.
- Strain: the strain identifier for P. pacificus; Total Progeny Count: The total number of eggs laid by an adult worm during a 7-day period; Culture Condition: the bacterial diet on which the worms were grown.
- Strain: the strain identifier for P. pacificus; Culture: the bacterial diet on which the worms were grown; Eu: number of the predatory (Eu) adults observed; Total: total number of worms observed; Prop: proportion of Eu adults (Eu/Total).
- Corpses: the number of corpses observed at the end of the killing assay on E. coli OP50.
- Corpses: the number of corpses observed at the end of the killing assay on Novosphingobium sp. L76.
- Strain: the strain identifier for P. pacificus; MF: proportion of Eu adults observed for a given strain; Corpses: the number of corpses observed at the end of the killing assay on E. coli OP50.
- Strain: the strain identifier for P. pacificus; Culture: the bacterial diet on which the worms were grown; Eu: number of the predatory (Eu) adults observed; Total: total number of worms observed; Prop: proportion of Eu adults (Eu/Total).
Sharing/Access information
The results published based on this repository can be found in the manuscript associated with this repository:
This dataset can also be found in a GitHub repository associated with the manuscript:
Code/Software
Software required to run the scripts provided in this repository: Python 3.10, IPython 8.4, Numpy 1.22.3, Matplotlib 3.5.1, Seaborn 0.11.2, Arviz 0.11.2, Pandas 1.4.3, Pymc3 3.11.4.
Methods
This dataset contains the following scripts:
- digital_worm.py: The model written in Python 3.10
- main_figs_model.ipynb: The code with instructions to generate the main modeling figures.
- main_figs_exp.ipynb: The code with instructions to generate the main experimental figures, including the Bayesian statistical analyses associated with these figures.
- raw_data.zip: The raw data required to generate main and supp figures.
- supp_figs.ipynb: The code with instructions to generat the supp figures
- digital_worm_n_dev_dif.py: A verison of the model written in Python 3.10 in which the developmental speeds remain unchanged upon switching the diet. Used in supp_figs.ipynb.
The dataset can be found in raw_data.zip
Usage notes
Software required to run the scripts provided in this repository: Pyhton 3.10, IPython 8.4, Numpy 1.22.3, Matplotlib 3.5.1, Seaborn 0.11.2, Arviz 0.11.2, Pandas 1.4.3, Pymc3 3.11.4