DOI: 10.5061/dryad.9s4mw6mpz
title: Multi-level in vivo selection of the biocontrol agent Akanthomyces muscarius, virulence, growth, sporulation, and variant data

description: Changes in parasite virulence are commonly expected to lead to trade-offs
 in other life history traits that can affect fitness. Understanding these
 trade-offs is particularly important if we want to manipulate the
 virulence of microbial biological control agents. Theoretically, selection
 across different spatial scales, i.e. between- and within-hosts, shapes
 these trade-offs. However, trade-offs are also dependent on parasite
 biology. Despite their applied importance the evolution of virulence in
 fungal parasites is poorly understood: virulence can be unstable in
 culture and commonly fails to increase in simple passage experiments. We
 hypothesized that manipulating selection intensity at different scales
 would reveal virulence trade-offs in a fungal pathogen of aphids,
 Akanthomyces muscarius. Starting with a genetically diverse stock we
 selected for speed of kill, parasite yield, or infectivity by manipulating
 competition within and between hosts and between populations of hosts over
 7 rounds of infection. We characterized ancestral and evolved lineages by
 whole genome sequencing and by measuring virulence, growth rate,
 sporulation, and fitness. While several lineages showed increases in
 virulence, we saw none of the trade-offs commonly found in
 obligately-killing parasites. Phenotypically similar lineages within
 treatments often shared multiple single-nucleotide variants, indicating
 strong convergent evolution. The most dramatic phenotypic changes were in
 the timing of sporulation and spore production in vitro. We found that
 early sporulation led to reduced competitive fitness but could increase
 the yield of spores on media, a trade-off characteristic of social
 conflict. Notably, the selection regime with the strongest
 between-population competition and lowest genetic diversity produced the
 most consistent shift to early sporulation, as predicted by social
 evolution theory. Multi-level selection therefore revealed social
 interactions novel to fungi and showed that these biocontrol agents have
 the genomic flexibility to improve multiple traits - virulence and spore
 production - that are often in conflict in other parasites.
description: # Multi-level in vivo selection of the biocontrol agent *Akanthomyces
 muscarius*, virulence, growth, sporulation, and variant data
 [https://doi.org/10.5061/dryad.9s4mw6mpz](https://doi.org/10.5061/dryad.9s4mw6mpz) Phenotypic and genomic data supporting the Plos Pathogens manuscript. ## Description of the data and file structure Data are contained in 7 Excel files and 1 vcf file. Treatment names: Within-host, between-host, and between-population are the same as speed, yield, and infectivity in some datasets. trt columns refer to individually evolving replicates belonging to each treatment (trt_type). **taqman_results_withrelfit_25032024:** Results of taqman assay, Sample BPI4 well E07 failed to amplify, hence NA values. FAM and VIC are fluorescence values for each corresponding dye. Content: cell description in software. Sample: sample name. Comb: a combination of competed lineages. Rep: replicate number. Treatment: Lineage belonging to each treatment competed against the common competitor (media1). Cq: quantification cycle (FAM). Total: Sum of fluorescence values (FAM+VIC). PropVIC and PropFAM: proportion of fluorescence for each dye per sample. RF_x and RF_y: Relative fitness derived from relative fluorescence units obtained via qPCR and calculated as v = x2(1-x1)/x1(1-x2), where x1 is the initial proportion of ancestral allele (present in both ancestor and between-population treataments) in the population and x2 is their final proportion. **surv_sel25032024_rename:** survivorship data for myzus persicae. Cup_rep: represent replicate aphid cups (replicate). Exp_rep: experiment repeated on different occasion. Death: day aphid death occured. Status: aphids dead (1) or alive (0). Trt_tpye: treatment. Trt: lineage. **brevi_surv25032022_rename**: survivorship data for brevycorine brassicae. Cup_rep: represent replicate aphid cups (replicate). Exp_rep: experiment repeated on different occasion. Death: day aphid death occured. Status: aphids dead (1) or alive (0). Trt_tpye: treatment. Trt: lineage. Dose: spore dose applied (spore/ml). **growth_25032022_rename:** Column letters represent diameter measure on agar plate. Trt_type: treatment. Treatment: lineage. Av_dia: average diameter of four subreplicates. dia_a, b, c and d are average diameters per subprep. Two measure was takent for each subprep each timepoint. **3dayspor25032022_rename:** Trt: lineage. Trt_type: treatment **sporulation25032022_rename:** Trt: lineage. Trt_type: treatment **GLM_sel_25032922_rename:** Trt: lineage. Trt_type: treatment. Cup_rep: represent replicate aphid cups (replicate). Exp_rep: experiment repeated on different occasion. Dead: number of dead aphids each day. Alive: number of alive aphid each day. Cum_mort: cumulative mortality. Sample_n: number of aphids per cup. **run.3.combined.IN.SNP.filtered.PASS.vcf:** Genetic variants found via GATK. For details see manuscript. ## Sharing/Access information Ancestral genome used for variant calling described in Erdos, Z., et al. (2023). "De novo genome assembly of Akanthomyces muscarius, a biocontrol agent of insect agricultural pests." *Access Microbiology* 5(6). Spray tower used for infections described in preprint: Laboratory sprayer for testing of microbial biocontrol agents: design and calibration Z. Erdos, P. Halswell, A. Matthews, B. Raymond