Data from: Do biological control agents adapt to local pest genotypes? A multi-year test across geographic scales
Data files
Aug 12, 2024 version files 52.61 KB
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2019_LA_RAW_DRYAD.csv
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2020_LA_RAW_DRYAD.csv
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2021_LA_RAW_DRYAD.csv
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2022_LA_RAW_DRYAD.csv
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README.md
Abstract
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.
README: Data from: Do biological control agents adapt to local pest genotypes? A multi-year test across geographic scales
https://doi.org/10.5061/dryad.00000009q
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 |
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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 |
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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 |
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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 |
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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
Methods
To test for local adaptation of P. penetrans, we collected paired samples of M. arenaria and P. penetrans 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 P. penetrans when paired with sympatric and allopatric M. arenaria 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.