DOI: 10.5061/dryad.gqnk98sxp
title: Rapid wing size evolution of African fig fly (Zaprionus indianus) following temperate colonization

description: Invasive species often encounter novel selective pressures in their
 invaded range, and understanding their potential for rapid evolution is
 critical for developing effective management strategies. Zaprionus
 indianus is an invasive drosophilid native to Africa that reached Florida
 in 2005 and likely re-establishes temperate North American populations
 each year. We addressed two evolutionary questions in this system: first,
 do populations evolve phenotypic changes in the generations immediately
 following colonization of temperate environments? Second, does Z. indianus
 evolve directional phenotypic changes along a latitudinal cline? We
 established isofemale lines from wild collections across space and time
 and measured twelve ecologically relevant phenotypes, using a reference
 population as a control. Z. indianus evolved smaller wings following
 colonization, suggesting early colonizers have larger wings, but smaller
 wings are favorable after colonization. No other phenotypes changed
 significantly following colonization or across latitudes, but we did see
 significant post-colonization changes in principal components of all
 phenotypes. We documented substantial laboratory evolution and effects of
 the laboratory environment across multiple phenotypes, emphasizing the
 importance of controlling for both possibilities when conducting common
 garden studies. Our results demonstrate the potential for rapid adaptation
 in Z. indianus, which could contribute to its success and expansion
 throughout invaded ecosystems.
description: Fitness-related and morphological phenotypes were measured for
 lab-reared<em> Zaprionus indianus </em>flies derived from
 wild-caught flies. We started isofemale lines from flies collected at
 different times and locations and compared the phenotypes of those lines.
 The data archived here include the raw phenotypic measurements and
 relavent metadata about each sample, as well as processed data including
 line means. The code for analysis and plotting is also included. See Gray,
 Rakes, et al for detailed methodological information. 
description: # Data for: Rapid wing size evolution in African fig flies (Zaprionus
 indianus) following temperate colonization The following dataset contains
 the phenotypic data and analysis code for a study assessing rapid
 evolution in the invasive drosophilid Z. indianus in the eastern United
 States. This study compared phenotypes of lab-reared flies derived from
 isofemale lines collected early in the growing season, late in the season,
 and across 4 locations spanning 15 degrees latitude. Principal
 Investigator Contact Information Name: Priscilla Erickson Institution:
 University of Richmond Address: 138 UR Drive, Richmond, VA, 23173, USA
 Email: [perickso@richmond.edu](mailto:perickso@richmond.edu) ## List of
 analyses and their corresponding files (.csv files are found on Dryad, .R
 files are found on Zenodo) 1. CCRT * CCRT_merge_clean.R This file contains
 the code utilized in the CCRT analysis. * latitude_CCRT.csv This file
 contains the raw data utilized in the latitude CCRT analysis. *
 seasonal_CCRT.csv This file contains the raw data utilized in the seasonal
 CCRT analysis. 2. Diapause * Diapause_analysis_clean_Weisburg.R This file
 contains the code utilized in the diapause analysis. * latitude_DIA.csv
 This file contains the raw data utilized in the latitude diapause
 analysis. * seasonal_DIA.csv This file contains the raw data utilized in
 the seasonal diapause analysis. 3. Fecundity * fecundity_analysis_clean.R
 This file contains the code utilized in the fecundity analysis. *
 latitude_FEC.csv This file contains the raw data utilized in the latitude
 fecundity analysis. * seasonal_FEC.csv This file contains the raw data
 utilized in the seasonal fecundity analysis. 4. Freeze Survival *
 Freeze_Tolerance_clean_Weisburg.R This file contains the code utilized in
 the freeze survival analysis. * latitude_FS.csv This file contains the raw
 data utilized in the latitude freeze survival analysis. * seasonal_FS.csv
 This file contains the raw data utilized in the seasonal freeze survival
 analysis. 5. Pupation * pupation_analysis_clean.R This file contains the
 code utilized in the pupation analysis. * latitude_PUP.csv This file
 contains the raw data utilized in the latitude pupation analysis. *
 seasonal_PUP.csv This file contains the raw data utilized in the seasonal
 pupation analysis. 6. Starvation * starvation_analysis_clean.R This file
 contains the code utilized in the starvation analysis. *
 latitude_STARV.csv This file contains the raw data utilized in the
 latitude starvation analysis. * seasonal_STARV.csv This file contains the
 raw data utilized in the seasonal starvation analysis. 7. Summary Analysis
 * Summary_AnalysisWithManova_clean.R This file contains the code utilized
 when conducting PCA. * all_lines_means.csv This file contains the mean
 values for each phenotype by isofemale line. * DiaAdjust_seasonal.csv This
 file contains the logit transformed values for each diapuause measurement
 for each seasonal isofemale line. * DiaAdjust_lat.csv This file contains
 the logit transformed values for each diapuause measurement for each
 latitudinal isofemale line. * FSAdjust_seasonal.csv This file contains the
 logit transformed values for freeze survival for each seasonal isofemale
 line. * FSAdjust_lat.csv This file contains the logit transformed values
 for freeze survival for each latitudinal isofemale line. 8. Summary
 Figures * Summary_Graphs_clean.R This file contains the code utilized the
 construct the figures with all phenotypes displayed. * latitude_means.csv
 This file contains the mean values and SEs for each latitudinal
 population. * seasonal_means.csv This file contains the mean values and
 SEs extracted from the seasonal models for each experimental group. *
 sex_means.csv This file contains the mean values and SEs extracted from
 the wild-derived seasonal and latitude models for each trait where sex
 could be recorded. * Effect_Size_Model_Outputs.csv This file contains the
 effect sizes and SEs extracted from the seasonal models for each
 experimental group. 9. Wing & Thorax * wt_analysis_clean.R This file
 contains the code utilized in the wing and thorax analysis. *
 latitude_WT.csv This file contains the raw data utilized in the latitude
 wing and thorax analysis. * seasonal_WT.csv This file contains the raw
 data utilized in the seasonal wing and thorax analysis. ## Description of
 the data and file structure Description of columns that appear frequently
 * line: The nomenclature used to denote each unique isofemale line. The
 alphabetical abbreviation indicates which orchard the lineage was
 established from (see population column). * vial: The replicate vial
 number that a fly was placed in when conducting a particular phenotypic
 assay. * sex: The sex of the fly (M=male, F=female). * batch: The batch
 that a fly was a part of during a particular phenotypic assay. *
 population: Where the founding individuals for each isofemale line were
 collected from. * CM = Carter Mountain Orchard, Charlottesville, VA * HPO
 = Hanover Peach Orchard, Richmond, VA * CT = Lyman Orchard, Middlefield,
 CT * PA = Linvilla Orchard, Media, PA * HCGA/GA = Hillcrest Orchard,
 Ellijay, GA * FL = Fruit and Spice Park, Homestead, FL * 24.2 = An inbred
 line used as a control for all assays * control: A binary variable
 indicating whether or not an individual belonged to the inbred control
 line (0 = experimental, 1 = control). * Control: Indicates which
 experimental group the data in the row belong to. * Wild-Derived Lines *
 Lab Evolution Lines * Inbred Control * edate: An integer variable starting
 with zero for the first day a given phenotypic assay was set up within a
 batch. Description of columns that appear across all seasonal files *
 season: Indicates when the founding individuals for each isofemale line
 were collected, during either the Early (colonizing) or Late (established)
 collection. * redo: A binary variable identifying individuals from lines
 collected early in the season that were re-phenotyped alongside flies from
 the late season to test for lab adapatation (0 = not re-phenotyped, 1 =
 early line that was re-phenotyped). * redo_lines: A binary variable
 identifying all lines that were utilized in the lab evolution analysis
 (whether in the early or late dataset)(0 = line was not part of the
 analysis, 1 = line was part of the analysis) . * orchard: Specifies which
 orchard in VA that the founding individuals for each isofemale line were
 collected from (CM = Carter Mountain, HPO = Hanover Peach Orchard).
 Description of the column that appears across all latitude files * lat:
 The latitude of the colleciton location (numeric). Description of the
 column that is unique to CCRT files * CCRT (chill coma recovery time): The
 number of seconds it took a fly to recover from a cold-induced comatose
 state. Description of the columns that are unique to Diapause files * Fly:
 A numerical count denoting each fly from a particular line and edate. *
 Stage: The stage of the most advanced ovariole for each fly (see King
 1970). * st8: A binary variable identifying those indiviuals that were in
 diapause using stage 8 as the cutoff (0=non-diapause, 1=diapause). * st10:
 A binary variable identifying those indiviuals that were in diapause using
 stage 10 as the cutoff (0=non-diapause, 1=diapause). * st14: A binary
 variable identifying those indiviuals that were in diapause using stage 14
 as the cutoff (0=non-diapause, 1=diapause). Description of the column that
 is unique to Fecundity files * eggs: The number of eggs laid by a single
 female fly in a 48 hour experiment. Description of the columns that are
 unique to Freeze Survival files * survival: A binary variable indicating
 whether or not that individual survived a 45 minute cold shock treatment
 (0 = dead, 1 = alive). * prop_survived_line: The proportion of flies that
 survived the cold shock treatment for each line. Description of the column
 that is unique to Pupation files * time: The number of days it took for
 the individual to pupate. Description of the column that is unique to
 Starvation files * time: The number of days an individual fly survived
 under starvation conditions. Description of the columns that are unique to
 Wing & Thorax files * number: A numerical count denoting each
 replicate fly measured from a particular line. * thorax: The thorax
 measurement for each fly in mm. * wing_size: The wing size mearsurement
 for each fly (geometric mean of major and minor radii of an ellipse fitted
 to the wing) in mm. * wing_shape: The wing shape measurement for each fly
 (minor/major). * wing_load: The wing:thorax ratio for each fly. *
 maj_radius: The measurement of the major radius of an ellipse fitted to
 the wing of each fly. * min_radius: The measurement of the minor radius of
 an ellipse fitted to the wing of each fly. Description of the columns that
 are unique to Summary Analysis files, which summarize phenotypic data per
 isofemale line * CCRT: The mean CCRT for each line. * prop_dia_st8: The
 proportion of flies that were in diapause using stage 8 as the cutoff for
 each line. * prop_dia_st10: The proportion of flies that were in diapause
 using stage 10 as the cutoff for each line. * prop_dia_st14: The
 proportion of flies that were in diapause using stage 14 as the cutoff for
 each line. * eggs: The mean number of eggs laid for each line. *
 prop_survived_line: The proportion of flies that survived the cold shock
 treatment for each line. * pup_time: The mean pupation time for each line.
 * starv_time: The mean starvation time for each line. * wing_size: The
 mean wing size for each line. * wing_shape: The mean wing shape for each
 line. * wing_load: The mean wing:thorax ratio for each line. * thorax: The
 mean thorax length for each line. * Population: Indicates which large
 experimental group the line belonged to or if it was a control. * 24.2
 (inbred control) * Early * Late * CT * PA * GA * FL * Grouping: Signifies
 which large experimental group the line belonged to. * Early * Late *
 Latitude * prop_diast8_line_adjust: The logit transformed value of the
 proportion of flies in diapause for each line when using stage 8 as the
 cutoff. * prop_diast10_line_adjust: The logit transformed value of the
 proportion of flies in diapause for each line when using stage 10 as the
 cutoff. * prop_diast14_line_adjust: The logit transformed value of the
 proportion of flies in diapause for each line when using stage 14 as the
 cutoff. * prop_FS_adjust: The logit transformed value of the proportion of
 flies that survived the cold shock treatment for each line. *
 n_flies_line: The number of flies in each line used in a particular
 phneotypic analysis. Description of the columns that are unique to Summary
 Figures files * phenotype: Specifies which phenotype the data in the row
 refers to. * grouping: Signifies which large experimental group the data
 belongs to. * Wild-Derived Lines (seasonal_means) * Lab Evolution
 (seasonal_means) * Inbred Control (seasonal_means) * Post-Colonization
 (sex_means) * Latitude (sex_means) * emmean: The estimated mean for each
 phenotype extracted from the model. * SE: The standard error extracted
 from the model. * significance: Identifies those rows that had a
 significant change after Bonferroni correction. * mean: The mean
 phenotypic value for each latitudinal population. * se: The standard error
 calculated for each latitudinal population. * Effect_Size: The effect size
 extracted from the model. * Phenotype: Specifies which phenotype the data
 in the row refers to. * Population: Signifies which large experimental
 group the data belongs to. * Wild-Derived Lines (seasonal) * Lab Evolution
 (seasonal) * Inbred Control (seasonal) * Significance: Identifies those
 rows that had a significant change after Bonferroni correction. ##
 Sharing/Access information Links to other publicly accessible locations of
 the data: *
 [https://doi.org/10.5061/dryad.gqnk98sxp](https://doi.org/10.5061/dryad.gqnk98sxp) Data was derived from the following sources: * All data was produced from experiments conducted by the Erickson lab at the University of Richmond ## Code/Software All data was analyzed in R with the scripts attached.