Data for: Does parasitoid species diversity promote protective symbiont diversity?
Data files
Mar 01, 2024 version files 286.70 KB
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basic.txt
29.92 KB
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mol.txt
204.28 KB
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R_code_final.Rmd
36.97 KB
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README.md
7.84 KB
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test.txt
7.71 KB
Abstract
How does diversity in nature come about? One factor contributing to this diversity are species interactions; diversity on one trophic level can shape diversity on lower or higher trophic levels. For example, parasite diversity enhances host immune diversity. Protective symbionts mediate host resistance and are therefore also engaged in reciprocal selection with their host’s parasites. Here, we applied experimental evolution in a well-known symbiont-aphid-parasitoid system to study whether parasitoid diversity contributes to maintaining symbiont diversity. We used caged populations of black bean aphids (Aphis fabae), containing uninfected individuals and individuals infected with different strains of the bacterial endosymbiont Hamiltonella defensa, which protects aphids against parasitoids. Over multiple generations, these populations were exposed to three different species of parasitoid wasps (Aphidius colemani, Binodoxys acalephae, or Lysiphlebus fabarum), simultaneous or sequential mixtures of these species, or no wasps. Surprisingly, we observed little selection for H. defensa in most treatments, even when it clearly provided protection against a fatal parasitoid infection. This seemed to be caused by high induced costs of resistance: aphids surviving parasitoid attacks suffered an extreme reduction in fitness. In marked contrast to previous studies looking at the effect of different genotypes of a single parasitoid species, we found little evidence for a diversifying effect of multiple parasitoid species on symbiont diversity in hosts.
README: Data for Does parasitoid species diversity promote protective symbiont diversity?
Experimental procedures
We conducted an experimental evolution experiment with 30 replicate populations (cages) over six generations each with the same initial composition of different haplotypes of the protective symbiont Hamiltonella defensa or no H. defensa. In each generation our artificial populations were exposed to different wasp species either individually or in combination. In each generation we collected data on aphid demographics and in generation three and six. In addition we conducted infection tests using each possible symbiont haplotype – parasitoid species combination.
Results
Contrary to our expectations we found little effect of parasitoid treatment on H. defensa composition.
Description of the data and file structure
basic.txt:
Data on aphid demographics collected during transfer in each generation.
- id1: Unique identifier for each pot-generation combination
- Generation: Generation
- Date: Day when sampling took place (DD/MM)
- ID: Identity of each cage
- ID-orig: in two cases replicates were lost very early in the experiments and replaced from another cage of the same treatments (see associated paper)
- ID_orig states the IDs of these cages. In all other cases ID and ID-orig are identical
- Pot: Identifier of each pot in each cage. In each cage we had three pots each containing a single plant
- Treatment: Experimental treatment; levels are: Baca: Cages exposed to Binodoxys acalephae; Lfab: Cages exposed to Lysiphlebus fabarum; Acol: Cages exposed Aphidius colemani; Sim: Cages simultaneously exposed to all three wasp species; Seq: Cages sequentially exposed to all three wasp species, i.e. t a single species in each generation. But alternating between generations.
- WaspLine: Wasp line used for this cage in this generation. Except for the Seq treatment this always corresponds to treatmen
- Block: In order to manage the work load, work was split over two consecutive days. Block indicates on which of these days each cage was handled
- N_aphids: Number of aphids
- N_mummies: Number of mummies
- L_stem: Plant length (cm)
- N_transferred: Number of aphids transferred to the next generation. We aimed for 10 aphids from each pot (30/ cage). Where this was not possible due to a lack of surviving aphids this number derivates from 10.
NA indicates that no data could be obtained for this replicate and column. In the remark column it indicates that nothing noteworthy happened in this replicate.
mol.txt:
Data on the presence/ absence and identity of H. Defensa collected in generation 3 and 6. Data for generation 0 presents the initial aphid composition.
- id1: Unique identifier for each pot-generation combination
- Generation: Generation
- ID: Identity of each cage
- pot: Identifier of each pot in each cage. In each cage we had three pots each containing a single plant
- Treatment: Experimental treatment; levels are: Baca: Cages exposed to Binodoxys acalephae; Lfab: Cages exposed to Lysiphlebus fabarum; Acol: Cages exposed Aphidius colemani; Sim: Cages simultaneously exposed to all three wasp species; Seq: Cages sequentially exposed to all three wasp species, i.e. t a single species in each generation. But alternating between generations.
- WaspLine: Wasp species used for this cage in this generation. Except for the Seq treatment this always corresponds to treatment
- plate: 96 well plate on which this sample was collected and processed
- col & row: Location on this place (column and row respectively)
- H0: H. defensa present or absent (H. defensa present=0, H.defensa absent=1)
- Hpos: H. defensa present or absent (H. defensa present=1, H.defensa absent=0)
- weakHam: Band for H. defensa in the diagnostic PCR weak
- H15: H. defensa haplotype 15? (yes=1, no=0)
- H76: H. defensa haplotype 76? (yes=1, no=0)
- Done: Molecular analysis of this sample complete? (yes=1, no=0)
- Use_pres: Data can be used to analyse the presence/ absence of H. defensa
- Use_haplo: Data can be used to analyse the haplotype identity of H. defensa. E.g. data in which sequencing failed had to be excluded.
test.txt:
Data for the experimental infection experiments
- Id: Unique identifier for each plant/ pot
- Time: Round of the experiment (pre vs. post experimental evolution experiment). Some experimental details differed between rounds (see accompanying paper)
- Symb: Haplotype of H. defensa present in aphids used in this replicate (H-: H. defensa free aphids, H15: H. defensa haplotyie H15, H76: H. defensa haplotype H76)
- Wasp: Wasp used for experimental exposure (Baca: Binodoxys acalephae; Lfab: Lysiphlebus fabarum; Acol Aphidius colemani)
- N_aphids1: Number of aphids prior to the addition of parasitoid wasps
- N_aphids2: Number of aphids 10 to 11 days after the addition of parasitoid wasps
- N_mummies: Number of mummies 10 to 11 days after the addition of parasitoid wasps
NA indicates that no data could be obtained for this replicate and column. In the remark column it indicates that nothing noteworthy happened in this replicate.
Code/Software
We used R, version 4.0.0 (2020-04-24) to analyse data. Scripts were written using R markdown (version 2.2) and run in R studio (version 2023.06.1). To run the code make sure that the files (basic.txt, mol.txt, & test.txt) are in your working directory.
The following packages were attached or loaded:
attached base packages:
stats, graphics, grDevices, utils, datasets, methods, base
other attached packages:
stringr_1.4.0, entropart_1.6-4, metacom_1.5.3, data.table_1.12.8,SpadeR_0.1.1, gmodels_2.18.1, DHARMa_0.3.2.0, factoextra_1.0.7,rcompanion_2.3.25, GLMMadaptive_0.7-0, magrittr_1.5, flextable_0.5.10,glmmTMB_1.0.1, vegan_2.5-6, permute_0.9-5, tidyr_1.1.0,taRifx_1.0.6.2, optimx_2020-4.2, lawstat_3.4, psyphy_0.1-9,blmeco_1.4, emmeans_1.4.7, dplyr_1.0.0, purrr_0.3.4,lmerTest_3.1-2, car_3.0-8, carData_3.0-4, fitdistrplus_1.1-1,officer_0.3.11, cowplot_1.0.0, gridExtra_2.3, reshape_0.8.8,plyr_1.8.6, Hmisc_4.4-0, Formula_1.2-3, lattice_0.20-41,multcomp_1.4-13, TH.data_1.0-10, MASS_7.3-51.5, survival_3.1-12,mvtnorm_1.1-1, lme4_1.1-23, Matrix_1.2-18, ggplot2_3.3.1
loaded via a namespace (and not attached):
readxl_1.3.1, uuid_0.1-4, backports_1.1.7,systemfonts_0.2.3, TMB_1.7.16, splines_4.0.0,digest_0.6.25, foreach_1.5.0, htmltools_0.4.0,gdata_2.18.0, checkmate_2.0.0, cluster_2.1.0,openxlsx_4.1.5, matrixStats_0.56.0, Kendall_2.2,sandwich_2.5-1, jpeg_0.1-8.1, colorspace_1.4-1,ggrepel_0.8.2, haven_2.3.1, xfun_0.14,crayon_1.3.4, libcoin_1.0-5, zoo_1.8-8,iterators_1.0.12, glue_1.4.1, gtable_0.3.0,abind_1.4-5, scales_1.1.1, bibtex_0.4.2.2,Rcpp_1.0.4.6, xtable_1.8-4, htmlTable_2.0.0,foreign_0.8-78, stats4_4.0.0, htmlwidgets_1.5.1,RColorBrewer_1.1-2, acepack_1.4.1, ellipsis_0.3.1,modeltools_0.2-23, farver_2.0.3, pkgconfig_2.0.3,nnet_7.3-13, multcompView_0.1-8, labeling_0.3,tidyselect_1.1.0, reshape2_1.4.4, munsell_0.5.0,cellranger_1.1.0, tools_4.0.0, generics_0.0.2,evaluate_0.14, EMT_1.1, arm_1.11-1,yaml_2.2.1, knitr_1.28, zip_2.0.4,coin_1.3-1, nlme_3.1-147, xml2_1.3.2,pbkrtest_0.4-8.6, compiler_4.0.0, rstudioapi_0.11,curl_4.3, png_0.1-7, tibble_3.0.1,statmod_1.4.34, DescTools_0.99.36, stringi_1.4.6,forcats_0.5.0, gdtools_0.2.2, nloptr_1.2.2.1,vctrs_0.3.0, pillar_1.4.4, lifecycle_0.2.0,Rdpack_1.0.0, lmtest_0.9-37, estimability_1.3,gbRd_0.4-11, R6_2.4.1, latticeExtra_0.6-29,rio_0.5.16, codetools_0.2-16, boot_1.3-24,gtools_3.8.2, withr_2.2.0, nortest_1.0-4,mgcv_1.8-31, expm_0.999-4, parallel_4.0.0,hms_0.5.3, grid_4.0.0, rpart_4.1-15,coda_0.19-3, minqa_1.2.4, rmarkdown_2.2,numDeriv_2016.8-1.1, base64enc_0.1-3
Methods
Data on aphid demograph from the experimental evolution experiments ("basic") was collected by counting aphids (roughly estimated by counting aphids in groups of ca. 10 individuals) and mummies (exact counts) and measuring plant size (i.e. total stem length of all plants) for each pot in each cage. Prior to data analysis, data for each cage was combined to obtain a single value for each cage in each generation (see associated paper for details).
To analyse H. Defensa composition ("mol") we first collected aphids at the end of generations 3 and 6, extracted their DNA, used diagnostic PCRs to amplify part of the bacterial 16S rRNA and part of H. defensa's murE gene for sequencing to distinguish H. defensa haplotypes. Data was recorded as either H. defensa absent or present and in the later case the identity of the haplotype. From this we calculate the proportion of H. defensa negative aphids and each H. defensa haplotype. This proportion was used in subsequent analysis (see associated paper for details).
Data on the experimental infection test ("test") was collected by counting aphids and mummies on each plant at different time points (see associated paper for details).