DOI: 10.5061/dryad.8kprr4xwg
title: Limits to the evolution of herbicide escape and tolerance in the agricultural weed Amaranthus palmeri

description: In response to novel anthropogenic stresses, defense strategies including
 resistance, tolerance, and escape can evolve. However, if the evolution of
 one or more of these strategies is limited by weak natural selection or a
 lack of genetic variation, then a mixed strategy (e.g. resistance and
 tolerance) is unlikely to evolve. To determine the mechanisms that limit
 the evolution of defense strategies, we studied escape from and tolerance
 to glyphosate herbicide in Amaranthus palmeri, an agricultural weed that
 has evolved glyphosate resistance. We grew A. palmeri in fields planted
 with corn, soybean, or no crop; manipulated their exposure to glyphosate;
 and measured escape and tolerance. We did not detect selection or genetic
 variation for glyphosate escape in any agricultural environment,
 suggesting that a mixed strategy of resistance and escape is unlikely to
 evolve in A. palmeri. We also did not detect selection for glyphosate
 tolerance, but there was genetic variation for tolerance in a corn crop
 environment, suggesting the potential for a mixed strategy of resistance
 and tolerance to evolve in A. palmeri in only a subset of environments.
 These results suggest that exposure to herbicides is unlikely to cause the
 widespread evolution of a mixed defense strategy in agricultural weeds.
  
description: # Limits to the evolution of herbicide escape and tolerance in the
 agricultural weed Amaranthus palmeri Dataset DOI:
 [10.5061/dryad.8kprr4xwg](10.5061/dryad.8kprr4xwg) ## Description of the
 data and file structure Data and code for: Limits to the evolution of
 herbicide escape and tolerance in the agricultural weed *Amaranthus
 palmeri*. Submitted to Evolution. This package contains 14 files: 1\.
 “**survival.2017.csv**”: This file contains the data used to estimate
 selection on days to seedling emergence via survival for *Amaranthus
 palmeri* grown in 2017 a cultivated soybean field (Fig. 1; Table S2).  The
 columns are as follows:  -position: Unique number identifying each plant
 included in the data set -block: Identity of the field where each
 experimental plant was located (A, B, or C) -population: Identity of the
 population (Table S1) that an open-pollinated maternal family was
 collected from (HE (41.447092 -90.141592); CH (40.074505 -88.246533); EF
 (39.228864 -88.525873); MD-IL (38.691638, -90.021769); GA (37.629676
 -88.166345); PH (36.360356 -80.57341); MR (35.979622 -77.362871); UC
 (35.897903 -77.672789); TA (35.887358 -77.443634); WA (35.781702
 -78.352149); LI (35.726837 -80.313716); CL (35.674307 -78.512462); JO
 (35.669931 -78.49939); WI (35.60278 -78.071049); RA (35.55501 -80.013807);
 WN (35.310539 -78.078181); ON (34.90157 -77.607704); LB (34.897865
 -79.047614); MA (32.423982 -84.129029); DO (32.106095 -83.777492); WO
 (31.508744 -83.658883); CO (31.141031 -83.723125))  -treatment: S =
 sprayed with glyphosate herbicide; NS = not sprayed with glyphosate
 herbicide -emergence: Number of days from planting to seedling emergence
 -survival: 0 = either dead when fitness components were measured at the
 end of the growing season or alive but had not flowered. 1 = alive and had
 flowered when fitness components were measured at the end of the growing
 season 2\. “**survival.2018.csv**”: This file contains the data used to
 estimate genetic variation for and selection on days to seedling emergence
 via survival for *Amaranthus palmeri* grown in 2018 in either a cultivated
 corn field or a cultivated field not planted with a crop (Figs. 1-2; Table
 S2).  The columns are as follows:  -position: Unique number identifying
 each plant included in the data set -block: Identity of the field where
 each experimental plant was located (A, B, or C) -population: Identity of
 the population (Table S1) that an open-pollinated maternal family was
 collected from (HE (41.447092 -90.141592); CH (40.074505 -88.246533); EF
 (39.228864 -88.525873); MD-IL (38.691638, -90.021769); GA (37.629676
 -88.166345); PH (36.360356 -80.57341); MR (35.979622 -77.362871); UC
 (35.897903 -77.672789); TA (35.887358 -77.443634); WA (35.781702
 -78.352149); LI (35.726837 -80.313716); CL (35.674307 -78.512462); JO
 (35.669931 -78.49939); WI (35.60278 -78.071049); RA (35.55501 -80.013807);
 WN (35.310539 -78.078181); ON (34.90157 -77.607704); LB (34.897865
 -79.047614); MA (32.423982 -84.129029); DO (32.106095 -83.777492); WO
 (31.508744 -83.658883); CO (31.141031 -83.723125)) -crop: C = grown in a
 field planted with corn; NC = plant grown in a cultivated field not
 planted with a crop -treatment: S = sprayed with glyphosate herbicide; NS
 = not sprayed with glyphosate herbicide -emergence: Number of days from
 planting to seedling emergence -survival: 0 = either dead when fitness
 components were measured at the end of the growing season or alive but had
 not flowered. 1 = alive and had flowered when fitness components were
 measured at the end of the growing season -family: Unique number (1-30)
 identifying the open-pollinated maternal family that a plant is a member
 of 3\. “**inflor.2017.csv**”: This file contains the data used to estimate
 selection on days to seedling emergence via number of inflorescences and
 mean inflorescence length for *Amaranthus palmeri* grown in 2017 a
 cultivated soybean field (Fig. 1; Table S2).  The columns are as follows: 
 -Position: Unique number identifying each plant included in the data set
 -Block: Identity of the field where each experimental plant was located
 (A, B, or C) -Population: Identity of the population (Table S1) that an
 open-pollinated maternal family was collected from (HE (41.447092
 -90.141592); CH (40.074505 -88.246533); EF (39.228864 -88.525873); MD-IL
 (38.691638, -90.021769); GA (37.629676 -88.166345); PH (36.360356
 -80.57341); MR (35.979622 -77.362871); UC (35.897903 -77.672789); TA
 (35.887358 -77.443634); WA (35.781702 -78.352149); LI (35.726837
 -80.313716); CL (35.674307 -78.512462); JO (35.669931 -78.49939); WI
 (35.60278 -78.071049); RA (35.55501 -80.013807); WN (35.310539
 -78.078181); ON (34.90157 -77.607704); LB (34.897865 -79.047614); MA
 (32.423982 -84.129029); DO (32.106095 -83.777492); WO (31.508744
 -83.658883); CO (31.141031 -83.723125)) -Treatment: S = sprayed with
 glyphosate herbicide; NS = not sprayed with glyphosate herbicide
 -Num.Inflor: Number of inflorescences produced at the end of the growing
 season -Inflor.Len: Mean length in cm of the inflorescences produced on
 one haphazardly selected branch -Days.Emerge: Number of days from planting
 to seedling emergence 4\. “**inflor.2018.csv**”: This file contains the
 data used to estimate selection on days to seedling emergence via number
 of inflorescences and mean inflorescence length for *Amaranthus palmeri*
 grown in 2018 in either a cultivated corn field or a cultivated field not
 planted with a crop (Fig. 1; Table S2).  The columns are as follows: 
 -Position: Unique number identifying each plant included in the data set
 -Block: Identity of the field where each experimental plant was located
 (A, B, or C) -Population: Identity of the population (Table S1) that an
 open-pollinated maternal family was collected from (HE (41.447092
 -90.141592); CH (40.074505 -88.246533); EF (39.228864 -88.525873); MD-IL
 (38.691638, -90.021769); GA (37.629676 -88.166345); PH (36.360356
 -80.57341); MR (35.979622 -77.362871); UC (35.897903 -77.672789); TA
 (35.887358 -77.443634); WA (35.781702 -78.352149); LI (35.726837
 -80.313716); CL (35.674307 -78.512462); JO (35.669931 -78.49939); WI
 (35.60278 -78.071049); RA (35.55501 -80.013807); WN (35.310539
 -78.078181); ON (34.90157 -77.607704); LB (34.897865 -79.047614); MA
 (32.423982 -84.129029); DO (32.106095 -83.777492); WO (31.508744
 -83.658883); CO (31.141031 -83.723125))  -Crop: C = grown in a field
 planted with corn; NC = plant grown in a cultivated field not planted with
 a crop -Treatment: S = sprayed with glyphosate herbicide; NS = not sprayed
 with glyphosate herbicide -Days.Emerge: Number of days from planting to
 seedling emergence -Num.Inflor: Number of inflorescences produced at the
 end of the growing season -Inflor.Len: Mean length in cm of the
 inflorescences produced on one haphazardly selected branch 5\.
 “**tolerance.2018.csv**”: This file contains the data used to estimate
 genetic variation for (Fig. 3) and selection on tolerance for *Amaranthus
 palmeri* grown in 2018 in either a cultivated corn field or a cultivated
 field not planted with a crop.  The columns are as follows:  -position:
 Unique number identifying each plant included in the data set -block:
 Identity of the field where each experimental plant was located (A, B, or
 C) -population: Identity of the population (Table S1) that an
 open-pollinated maternal family was collected from (HE (41.447092
 -90.141592); CH (40.074505 -88.246533); EF (39.228864 -88.525873); MD-IL
 (38.691638, -90.021769); GA (37.629676 -88.166345); PH (36.360356
 -80.57341); MR (35.979622 -77.362871); UC (35.897903 -77.672789); TA
 (35.887358 -77.443634); WA (35.781702 -78.352149); LI (35.726837
 -80.313716); CL (35.674307 -78.512462); JO (35.669931 -78.49939); WI
 (35.60278 -78.071049); RA (35.55501 -80.013807); WN (35.310539
 -78.078181); ON (34.90157 -77.607704); LB (34.897865 -79.047614); MA
 (32.423982 -84.129029); DO (32.106095 -83.777492); WO (31.508744
 -83.658883); CO (31.141031 -83.723125)) -crop: C = grown in a field
 planted with corn; NC = plant grown in a cultivated field not planted with
 a crop -treatment: S = sprayed with glyphosate herbicide; NS = not sprayed
 with glyphosate herbicide -family: Unique number (1-30) identifying the
 open-pollinated maternal family that a plant is a member of
 -tot.inflor.len: Total inflorescence length for a plant, calculated as the
 number of inflorescences times the mean inflorescence length. Plants that
 did not survive have a total infloresence length of 0. 6\.
 “**emergence.2018.fam.inc.no.outliers.csv**”: This file contains the data
 used to estimate genetic correlations between tolerance and emergence for
 *Amaranthus palmeri* grown in 2018 in either a cultivated corn field or a
 cultivated field not planted with a crop when two outlier families were
 excluded (supplemental information). The columns are as follows: 
 -position: Unique number identifying each plant included in the data set
 -block: Identity of the field where each experimental plant was located
 (A, B, or C) -population: Identity of the population (Table S1) that an
 open-pollinated maternal family was collected from (HE (41.447092
 -90.141592); CH (40.074505 -88.246533); EF (39.228864 -88.525873); MD-IL
 (38.691638, -90.021769); GA (37.629676 -88.166345); PH (36.360356
 -80.57341); MR (35.979622 -77.362871); UC (35.897903 -77.672789); TA
 (35.887358 -77.443634); WA (35.781702 -78.352149); LI (35.726837
 -80.313716); CL (35.674307 -78.512462); JO (35.669931 -78.49939); WI
 (35.60278 -78.071049); RA (35.55501 -80.013807); WN (35.310539
 -78.078181); ON (34.90157 -77.607704); LB (34.897865 -79.047614); MA
 (32.423982 -84.129029); DO (32.106095 -83.777492); WO (31.508744
 -83.658883); CO (31.141031 -83.723125))  -crop: C = grown in a field
 planted with corn; NC = plant grown in a cultivated field not planted with
 a crop -treatment: S = sprayed with glyphosate herbicide; NS = not sprayed
 with glyphosate herbicide -emergence: Number of days from planting to
 seedling emergence -family: Unique number (1-30) identifying the
 open-pollinated maternal family that a plant is a member of 7\.
 “**tolerance.2018.no.outliers.csv**”: This file contains the data used to
 estimate genetic variation, selection, and tolerance for *Amaranthus
 palmeri* grown in 2018 in either a cultivated corn field or a cultivated
 field not planted with a crop after two outlier families were removed
 (supplemental information).  The columns are as follows:  -position:
 Unique number identifying each plant included in the data set -block:
 Identity of the field where each experimental plant was located (A, B, or
 C) -population: Identity of the population (Table S1) that an
 open-pollinated maternal family was collected from (HE (41.447092
 -90.141592); CH (40.074505 -88.246533); EF (39.228864 -88.525873); MD-IL
 (38.691638, -90.021769); GA (37.629676 -88.166345); PH (36.360356
 -80.57341); MR (35.979622 -77.362871); UC (35.897903 -77.672789); TA
 (35.887358 -77.443634); WA (35.781702 -78.352149); LI (35.726837
 -80.313716); CL (35.674307 -78.512462); JO (35.669931 -78.49939); WI
 (35.60278 -78.071049); RA (35.55501 -80.013807); WN (35.310539
 -78.078181); ON (34.90157 -77.607704); LB (34.897865 -79.047614); MA
 (32.423982 -84.129029); DO (32.106095 -83.777492); WO (31.508744
 -83.658883); CO (31.141031 -83.723125))  -crop: C = grown in a field
 planted with corn; NC = plant grown in a cultivated field not planted with
 a crop -treatment: S = sprayed with glyphosate herbicide; NS = not sprayed
 with glyphosate herbicide -family: Unique number (1-30) identifying the
 open-pollinated maternal family that a plant is a member of
 -tot.inflor.len: Total inflorescence length for a plant, calculated as the
 number of inflorescences times the mean inflorescence length. Plants that
 did not survive have a total infloresence length of 0. 8\.
 “**Script.emerge.2017.R”**: The R script used to estimate selection on
 days to seedling emergence for *Amaranthus palmeri* growing in cultivated
 field planted with a soybean crop in 2017 (Table S2) and calculate
 contrasts for graphing (Fig. 1). 9\. “**Script.emerge.2018.R**”: The R
 script used to estimate selection on days to seedling emergence for
 *Amaranthus palmeri* growing in either a cultivated corn field or a
 cultivated field not planted with a crop in 2018 (Table 1); calculate
 contrasts for graphing (Fig. 1); and compare and graph fitness between
 agricultural environments (Table S3; Fig. S3). 10\.
 “**Script.emerge.figure.R**”: The R script used to produce a graph of
 cumulative seedling emergence estimate selection on days to seedling
 emergence for *Amaranthus palmeri* growing in either a cultivated soybean
 field, a cultivated corn field, or a cultivated field not planted with a
 crop (Fig. S1). 11\. “**Script.tolerance.2018.R**”: The R script used to
 estimate genetic variation (Fig. 3) and selection for tolerance of
 *Amaranthus palmeri* growing in either a cultivated corn field or a
 cultivated field not planted with a crop in 2018. 12\.
 “**Script.gbye.corr.R**”: The R script used to estimate (1) genetic
 variation for days to seedling emergence (Fig. 2) and (2) genetic
 correlations for days to seedling emergence and tolerance (Fig. S2) for
 *Amaranthus palmeri* growing in either a cultivated corn field or a
 cultivated field not planted with a crop in 2018. 13\.
 “**Script.tolerance.2018.no.outliers.R**”: The R script used to estimate
 genetic variation, selection, and tolerance for *Amaranthus palmeri* grown
 in 2018 in either a cultivated corn field or a cultivated field not
 planted with a crop after two outlier families were removed (supplemental
 information). 14\. “**Fig.1.escape.R**”: The R script used to graph
 contrasts for selection for escape for *Amaranthus palmeri* grown in a
 cultivated soybean field, a cultivated corn field, or a cultivated field
 not planted with a crop (Fig. 1).