DOI: 10.5061/dryad.00000009q
title: Data from: Do biological control agents adapt to local pest genotypes? A multi-year test across geographic scales

description: Parasite local adaptation has been a major focus of (co)evolutionary
 research on host-parasite interactions. Studies of wild host-parasite
 systems frequently find that parasites paired with local, sympatric host
 genotypes perform better than parasites paired with allopatric host
 genotypes. In contrast, there are few such tests in biological control
 systems to establish whether biological control parasites commonly perform
 better on sympatric pest genotypes. This knowledge gap prevents the
 optimal design of biological control programs: strong local adaptation
 could argue for the use of sympatric parasites to achieve consistent pest
 control. To address this gap, we tested for local adaptation of the
 biological control bacterium Pasteuria penetrans to the root-knot nematode
 Meloidogyne arenaria, a global threat to a wide range of crops. We
 measured the probability and intensity of P. penetrans infection on
 sympatric and allopatric M. arenaria over the course of four years. Our
 design accounted for variation in adaptation across scales by conducting
 tests within and across fields, and we isolated the signature of parasite
 adaptation by comparing parasites collected over the course of the growing
 season. Our results are largely inconsistent with local adaptation of P.
 penetrans to M. arenaria: in three of four years, parasites performed
 similarly well in sympatric and allopatric combinations. In one year,
 however, infection probability was 28% higher for parasites paired with
 hosts from their sympatric plot, relative to parasites paired with hosts
 from other plots within the same field. These mixed results argue for
 population genetic data to characterize the scale of gene flow and genetic
 divergence in this system. Overall, our findings do not provide strong
 support for using P. penetrans from local fields to enhance biological
 control of Meloidogyne.
description: To test for local adaptation of <em>P.
 penetrans</em>, we collected paired samples of <em>M. arenaria
 </em>and <em>P. penetrans</em> from six sites each year.
 Because the strength of local adaptation can vary with spatial scale, we
 collected samples from six plots within a single field in 2019 and 2020
 and from six fields in 2021 and 2022. Each year, we compared the
 performance of <em>P. penetrans</em> when paired with
 sympatric and allopatric <em>M. arenaria</em> by measuring
 proxies for infection probability (attachment rate) and intensity
 (attachment load). In 2019 and 2020, we isolated the signature of parasite
 adaptation by comparing local adaptation of early-, mid-, and late-season
 parasites.
description: # Data from: Do biological control agents adapt to local pest genotypes? A
 multi-year test across geographic scales
 **Includes 4 data sets,
 one for each year/experiment. Data sets provide the number of spores
 attached to individual nematodes in replicate flasks (rows) of sympatric
 and allopatric treatments, designated by attributes in initial columns:**
 2019_LA_RAW_AR.csv data from the 2019 LA and time shift experiment, small
 spatial scale 2020_LA_RAW_AR.csv data from the 2020 LA and time shift
 experiment, small spatial scale 2021_LA_RAW_AR.csv data from the 2021 LA
 experiment, large spatial scale 2022_LA_RAW_AR.csv data from the 2022 LA
 experiment, large spatial scale ## Description of the data and file
 structure **Metadata for csv data files** | **Column Name** |
 **Descriptor** | | :-------------- |
 :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Year | Year of experiment (2019, 2020, 2021 or 2022) | | Block | groups replicates by experimental block, for 2021 and 2022 | | Rep | replicate flask for a combination | | Host\_ID | Host site (plot or field) - see Site IDs tab | | Parasite\_ID | Site of origin for host sample (plot or field) - see Site IDs tab | | Season | Site of origin for parasite sample (plot or field) - see Site IDs tab | | Time | Sampling point for parasite sample, relative to host sample: in 2019 and 2020, past = early-season parasite sample; present = mid-season parasite sample; future = late-season parasite sample; in 2021 and 2022, host and parasite samples were both taken at the end of the season, at a shared time point, thus labeled as "present" | | Sympatric | 0 = allopatric, 1 = sympatric, meaning host and parasite samples were collected from the same site | | A and on | Spores counted on individual nematodes; arranged in long format, so all nematodes counted for a single replicate flask are in a single row, distributed across A+ columns | **IDs used for field collection sites:** 2019 and 2020: plots of the Tubbs Field at the Gibbs Farm, small scale experiment | **Plot** | **Host\_ID** | **Parasite\_ID** | | :------- | :----------- | :--------------- | | 104 | RKN104 | P104 | | 117 | RKN117 | P117 | | 206 | RKN206 | P206 | | 305 | RKN305 | P305 | | 312 | RKN312 | P312 | | 410 | RKN410 | P410 | 2021: fields at multiple farms, larger-scale experiment | **Farm** | **Field** | **Host\_ID** | **Parasite\_ID** | | :--------- | :------------ | :----------- | :--------------- | | Blackshank | Lower Field 2 | 11 | 11 | | Blackshank | Lower Field 5 | 7 | 7 | | Blackshank | Upper Field 3 | 12 | 12 | | Gibbs | Tubbs | 8 | 8 | | Gibbs | Kemerait | 10 | 10 | | Lang | | 9 | 9 | 2022: fields at multiple farms, larger-scale experiment | **Farm** | **Field** | **Host\_ID** | **Parasite\_ID** | | :--------- | :------------ | :----------- | :--------------- | | Blackshank | Lower Field 1 | 1 | 1 | | Blackshank | Lower Field 2 | 2 | 2 | | Blackshank | Lower Field 3 | 3 | 3 | | Blackshank | Lower Field 4 | 4 | 4 | | Blackshank | Upper Field 3 | 5 | 5 | | Blackshank | Upper Field 4 | 6 | 6 | ## Code/Software **6 R code files are included for analyzing the data** 00_import.r data import and cleaning 01_summaryfuns.r functions for summarizing data in subsequent code files 02_2019.r analysis codes for 2019 experiment 03_2020.r analysis codes for 2020 experiment 04_2021.r analysis codes for 2021 experiment 05_2022.r analysis codes for 2022 experiment