DOI: 10.25338/b81s7c
title: Data and analysis from: Two centuries of monarch butterfly collections reveal contrasting effects of range expansion and migration loss on wing traits

description: Migratory animals exhibit traits that allow them to exploit seasonally
 variable habitats. In environments where migration is no longer
 beneficial, such as oceanic islands, migration-association traits may be
 selected against or be under relaxed selection. Monarch butterflies are
 best known for their continent-scale migration in North America but have
 repeatedly become established as non-migrants in the tropical Americas and
 on Atlantic and Pacific Islands. These replicated non-migratory
 populations provide natural laboratories for understanding the rate of
 evolution of migration-associated traits. We measured &gt;6,000 museum
 specimens of monarch butterflies collected from 1856 to the present, as
 well as contemporary wild-caught monarchs from around the world. We
 determined (1) how wing morphology varies across the monarch’s global
 range, (2) whether initial long-distance founders were particularly suited
 for migration and (3) whether recently-established non-migrants show
 evidence for contemporary phenotypic evolution. We further reared
 &gt;1,000 monarchs from six populations around the world under
 controlled conditions and measured migration-associated traits. Historical
 specimens show that (1) initial founders are well-suited for long-distance
 movement and (2) loss of seasonal migration is associated with reductions
 in forewing size and elongation. Monarch butterflies raised in a common
 garden from four derived non-migratory populations exhibit
 genetically-based reductions in forewing size, consistent with a previous
 study. Our findings provide a compelling example of how
 migration-associated traits may be favored during the early stages of
 range expansion, and also the rate of reductions in those same traits upon
 loss of migration.
description: This repository contains two sets of analyses and raw data. The
 first folder ("monarch_morphology_primary_analysis") contains
 the raw data and code used for generating all of the analyses and figures
 reported in the main manuscript. The second folder
 ("RAFM_and_DRIFTSEL") contains raw data and code used for some
 of the analyses reported in the supplementary materials.
 The first file "wings_04.25.20.csv" contains all
 measurements from museum and contemporary wild caught monarch specimens.
 The measurement protocol is described in the manuscript. The raw data file
 includes the following columns: Index:
 variable for sorting purposes. SampleID: unique
 identifier for each individual butterfly. Collection:
 refers to the ID of the collection from which images were
 taken. Region: refers to the broad geographic region
 from which the monarch butterfly was collected. Regions include North
 America, Central America, South America, the Caribbean, Pacific Islands,
 and the Atlantic. Country/Archipelago: refers to the
 country or archipelago from which butterflies were collected.
 Island/State: refers to the individual island or state from
 which butterflies were collected. County/District:
 refers to the county or district from which butterflies were
 collected. Site/City: refers to the site or city from
 which butterflies were collected. exact_location:
 variable describing whether the locality information is sufficient to
 provide pinpointed GPS coordinates to be used in analysis
 lon: decimal longitude, generated using the geocode
 function lat: decimal latitude, generated using the
 geocode function overwintering?: variable describing
 whether butterflies were collected from known overwintering sites in North
 America Wild-Caught?: variable to distinguish
 butterflies that were reared or collected as eggs, larvae, or
 pupae image_type: variable describing the imaging
 procedure. "scan" refers to butterflies that were dissected and
 had their wings imaged using a flatbed scanner. "photo" refers
 to butterflies that were photographed in standard pinning position.
 "satscan" is specific to the Natural History Museum (London)
 collection as refers to images that were generated as satscans, which
 involves whole drawer-level imaging. smoothing:
 variable describing whether forewing perimeter was measured using the
 "spline fit" or "interpolate" option in
 ImageJ Host_plant: variable describing host plant ID,
 if known, for reared monarchs. Not important for analysis.
 Collection_Date: refers to the date of collection for monarchs,
 in the form YYYYMMDD. In cases where month or day of collection is
 unknown, the MM and DD fields are left as "00"
 Sex: variable describing butterfly sex
 LLength: left forewing length LWidth: left
 forewing width LArea: left forewing area
 LPerimeter: left forewing perimeter
 RLength: right forewing length RWidth:
 right forewing width RArea: right forewing
 area RPerimeter: right forewing perimeter
 observer: refers to the individual who conducted the
 measurements. &gt;95% of entries were measured by the first author
 (MF). The second and third files
 ("adult_morphology.csv" and "thorax_abdomen_mass.csv")
 are measurements from common-garden reared monarchs. The details of
 rearing are provided in thorough detail in Freedman et al. (2020),
 <em>Evolution</em>. The raw data file includes the following
 columns: Cat.ID: unique identifier for
 butterflies Index: sorting variable
 Year: year in which rearing occurred (2017 or 2018)
 Date: the date on which caterpillars were added to host
 plants Usage: refers whether a given host plant was
 being used for the first or second time Plant.ID:
 unique identifier for host plants Species: host plant
 species Pop: host plant population
 GH: refers to the identity of the greenhouse in which
 butterflies were reared Group: refers to the position
 of the plants on the bench within each greenhouse
 Mon.Pop: monarch population identity ID:
 maternal family identity Caterpillar: the index of
 caterpillars on each host plant Weight: weight (in g)
 on day 8 of development Pupation: date of
 pupation Eclosion: date of eclosion
 Env.weight: weight of glassine envelope in which adults were
 weighed Total.weight: weight of glassine envelope and
 enclosed butterfly together. Adult butterfly mass determined as the
 difference between this and previous column (see column 34).
 Sex: butterfly sex OE: infection status
 with the protozoan parasite Ophryocystis elektroschirrha, on an
 approximate log(10) scale LLength: left forewing
 length LWidth: left forewing width
 LArea: left forewing area LPerimeter: left
 forewing perimeter RLength: right forewing
 length RWidth: right forewing width
 RArea: right forewing area RPerimeter:
 right forewing perimeter RHWArea: right hindwing area
 (not used in analysis) HW.Mass: right hindwing mass
 (not used in analysis) days_to_pupation: time
 difference between caterpillar placement and pupation, in days
 days_to_eclosion: time difference between caterpillar placement
 and eclosion, in days maternal_family: combination of
 Mon.Pop and ID columns, gives unique identifier for each maternal
 family emergence_weight: mass of butterflies (in g)
 ~6 hours after eclosion infection_status: considered
 infected if log(10) OE spore counts &gt;= 2, uninfected if &lt;=
 2 infection_status_binomial: same as previous column,
 but with 1/0 sym.allo: refers to whether host plant
 species and monarch population are sympatric or allopatric
 The thorax/abdomen mass file comes from the same
 experiment and includes the following columns: 
 Index: sorting variable, matches with
 adults_morphology  Cat.ID: identifier, matches with
 adults_morphology, used to merge files Eclosion:
 eclosion date Sex: butterfly sex
 thorax: mass of dried thoracic tissue in g
 abdomen: mass of dried abdominal tissue in g
 fresh: refers to whether butterflies were frozen immediately
 post-eclosion (fresh = "yes") or were kept alive in envelopes
 subsequent to eclosion (fresh = "no"). Only fresh specimens were
 used for analysis. Additional .csv files
 includes in this repository are associated with the RAFM and driftsel
 analyses reported in the Supplementary Information. Files included in the
 "RAFM_and_DRIFTSEL" folder are as follows: 
 flt_snps_clean.RDS -- this file contains called
 genotypes RAFM_1000SNPs_10000_theta.csv -- this is a
 single output run from RAFM reporting the theta parameter, which is used
 for generating the ancestry/coancestry matrix shown in Figure S4a. The
 remaining .csv files are all quantitative trait inputs for the driftsel
 analysis monarchs_rafm.R -- code for generating the
 ancestry/coancestry matrix reported in the supplementary
 information RAFM.R -- code associated with the R
 admixture F model DRIFTSEL -- folder containing
 driftsel analyses 
 analysis_quant.traits_drifstel_monarchs.R -- code for
 implementing the driftsel model driftsel.r -- the
 underlying driftsel model
 viztraits_driftsel_monarchs.R -- code for creating the drift
 ellipses shown in the supplementary information
 input_data -- folder containing quantitative trait data used in
 driftsel models 
 complete_driftsel_raw_data.csv
 complete_monarch_covariates_driftsel.csv
 complete_monarch_traits_driftsel.csv
 complete_monarchs_pedigree_driftsel.csv 
  
description: All analyses were conducted in R, and scripts are available here.
 The primary script that contains all analyses reported in the main text of
 the paper is global_monarch_wing_morphology.R. Remaining scripts are
 associated with the RAFM and driftsel analyses reported in the
 Supplementary Information.