DOI: 10.5061/dryad.9zw3r22pw
title: Data from: Repeated evolution of photoperiodic plasticity by different genetic architectures during recurrent colonizations in a butterfly

description: In cases of recurrent colonization of similar habitats from the same base
 population, it is commonly expected that repeated phenotypic adaptation is
 caused by parallel changes in genetic variation. However, it is becoming
 increasingly clear that similar phenotypic variation may also evolve by
 alternative genetic pathways. Here we explore the repeated evolution of
 photoperiodic plasticity for diapause induction across Swedish populations
 of the Speckled wood butterfly Pararge aegeria. This species has colonized
 Scandinavia at least twice and population genomic results show that one of
 the candidate regions associated with spatial variation in photoperiodism
 is situated on the Z-chromosome. Here we assay hybrid crosses between
 several populations that differ in photoperiodic plasticity for sex-linked
 inheritance of the photoperiodic reaction norm. We find that while a cross
 between more distantly related populations from the two different
 colonization events shows strong sex-dependent inheritance of
 photoperiodic plasticity, a cross between two more closely related
 populations within the oldest colonization range shows no such effect. We
 conclude that the genotype-phenotype map for photoperiodic plasticity
 varies across these populations and that similar local phenotypic
 adaptation has evolved during recurrent colonization events by partly
 non-parallel genetic changes.
description: The data is combined from the current experiment and the
 experiment from the article: Pruisscher, P., Nylin, S., Gotthard, K. and
 Wheat, C.W., 2018. Genetic variation underlying local adaptation of
 diapause induction along a cline in a butterfly. <em>Molecular
 ecology</em>, <em>27</em>(18), pp.3613-3626. 
description: # Repeated evolution of photoperiodic plasticity by different genetic
 architectures during recurrent colonizations in a butterfly
 [https://doi.org/10.5061/dryad.9zw3r22pw](https://doi.org/10.5061/dryad.9zw3r22pw) ## Description of the data and file structure This file contains information about the data files used in the manuscript entitled “Repeated evolution of photoperiodic plasticity by different genetic architectures during recurrent colonizations in a butterfly”. Descriptions of the data and explanations for each column in the data tables are given under each file name below. ### Files and variables #### File: means1\_LARVAL\_DECISION.csv **Description:** The proportion of individuals inducing diapause in the larval decision within each treatment for every genotype (GG, SS, CC). ##### Variables * pop: the genotype, either GG (Gotland), SS (Stockholm) or CC (the reciprocal crosses of GG and SS) * treatm: the photoperiodic treatment of either 17, 17.4, 17.8, 18.2 or 18.6 hours of light. * mean: the proportion that induced diapause #### File: means1\_PUPAL\_DECISION.csv **Description:** The proportion of individuals inducing diapause in the pupal decision within each treatment for every genotype (GG, SS, CC). ##### Variables * pop: the genotype, either GG (Gotland), SS (Stockholm) or CC (the reciprocal crosses of GG and SS) * treatm: the photoperiodic treatment of either 17, 17.4, 17.8, 18.2 or 18.6 hours of light. * mean: the proportion that induced diapause #### File: means2\_LARVAL\_DECISION.csv **Description:** The proportion of individuals inducing diapause in the larval decision within each treatment, for every genotype (GS, SG), while taking sex into account. ##### Variables * treatm: the photoperiodic treatment of either 17, 17.4, 17.8, 18.2 or 18.6 hours of light. * cross: the genotype, either GS (mother from Gotland and father from Stockholm) or SG (mother from Stockholm and father from Gotland) * sex: the sex (F: female, M: male) * mean: the proportion that induced diapause #### File: means2\_PUPAL\_DECISION.csv **Description:** The proportion of individuals inducing diapause in the pupal decision within each treatment, for every genotype (GS, SG), while taking sex into account. ##### Variables * treatm: the photoperiodic treatment of either 17, 17.4, 17.8, 18.2 or 18.6 hours of light. * cross: the genotype, either GS (mother from Gotland and father from Stockholm) or SG (mother from Stockholm and father from Gotland) * sex: the sex (F: female, M: male) * mean: the proportion that induced diapause #### File: MF\_PUPAL\_DECISION\_SG\_GS.csv **Description:** Binary data for comparing the pupal decision of the reciprocal hybrid crosses, taking sex into account (the main question of the manuscript). ##### Variables * Treatment: the photoperiod treatment the individual was subjected to, either 17, 17.4, 17.8, 18.2 or 18.6 hours of light. * Cross: the genotype of the individual, either GS (mother from Gotland and father from Stockholm) or SG (mother from Stockholm and father from Gotland) * Mother: id of the individual’s mother * Sex: the sex of the individual (F: female, M: male) * Diapause: whether the individual decided to diapause (1) or not (0) #### File: MF\_LARVAL\_DECISION\_SG\_GS.csv **Description:** Binary data for comparing the larval decision of the reciprocal hybrid crosses, taking sex into account (the main question of the manuscript). ##### Variables * Treatment: the photoperiod treatment the individual was subjected to, either 17, 17.4, 17.8, 18.2 or 18.6 hours of light. * Cross: the genotype of the individual, either GS (mother from Gotland and father from Stockholm) or SG (mother from Stockholm and father from Gotland) * Mother: id of the individual’s mother * Sex: the sex of the individual (F: female, M: male) * Diapause: whether the individual decided to diapause (1) or not (0) #### File: MF\_SS\_GG\_GS\_SG\_PUPAL\_DECISION.csv **Description:** Binary data of the pupal decision of the Gotland and Stockholm populations and their reciprocal hybrid crosses, taking sex into account. ##### Variables * treatment: the photoperiod treatment the individual was subjected to, either 17, 17.4, 17.8, 18.2 or 18.6 hours of light. * cross: the genotype of the individual, either GS (mother from Gotland and father from Stockholm), SG (mother from Stockholm and father from Gotland), SS (Stockholm) or GG (Gotland). * mother: id of the individual’s mother * sex: the sex of the individual (F: female, M: male) * diapause: whether the individual decided to diapause (1) or not (0) * cross_sex: the cross and sex combined, for instance GGM for a male from Gotland. #### File: Pop\_GG\_SS\_C\_LARVAL\_DECISION.csv **Description:** Binary data for comparing the larval decision of the Gotland and Stockholm populations and their reciprocal hybrid crosses combined. ##### Variables * Treatment: the photoperiod treatment the individual was subjected to, either 17, 17.4, 17.8, 18.2 or 18.6 hours of light. * Cross: the genotype of the individual, either GG (Gotland), SS (Stockholm) or CC (the reciprocal crosses of GG and SS) * Mother: id of the individual’s mother * Sex: the sex of the individual (F: female, M: male) * Diapause: whether the individual decided to diapause (1) or not (0) #### File: Pop\_GG\_SS\_C\_PUPAL\_DECISION\_2.csv **Description:** Binary data for comparing the pupal decision of the Gotland and Stockholm populations and their reciprocal hybrid crosses combined. ##### Variables * treatment: the photoperiod treatment the individual was subjected to, either 17, 17.4, 17.8, 18.2 or 18.6 hours of light. * diapause: whether the individual decided to diapause (1) or not (0) * cross_new: the genotype of the individual, either GG (Gotland), SS (Stockholm) or CC (the reciprocal crosses of GG and SS) #### File: Pop\_GG\_SS\_C\_PUPAL\_DECISION.csv **Description:** Binary data for comparing the pupal decision of the Gotland and Stockholm populations and their reciprocal hybrid crosses combined. ##### Variables * Treatment: the photoperiod treatment the individual was subjected to, either 17, 17.4, 17.8, 18.2 or 18.6 hours of light. * Cross: the genotype of the individual, either GG (Gotland), SS (Stockholm) or CC (the reciprocal crosses of GG and SS) * Mother: id of the individual’s mother * Sex: the sex of the individual (F: female, M: male) * Diapause: whether the individual decided to diapause (1) or not (0) #### File: Compare\_to\_Prui\_LARVAL\_DECISION.csv **Description:** Binary data for comparing the larval decision of the reciprocal hybrid crosses from the present study to the study by Pruisscher et al. 2018. ##### Variables * Exp: the study the individual originates from, the current study (A) or the study by Pruisscher et al. 2018 (P) * Direction: the direction is based on the father of the individual’s origin. N for north and S for south. For instance, an individual from the GS cross has a father from Stockholm. Since, Stockholm is further north in Sweden than Gotland, that individual is categorized as N. * Cross: the genotype of the individual, either GS (mother from Gotland and father from Stockholm), SG (mother from Stockholm and father from Gotland), SU X SK (mother from Sundsvall and father from Skåne) or SK X SU (mother from Skåne and father from Sundsvall) * Sex: the sex of the individual (F: female, M: male) * Diapause: whether the individual decided to diapause (1) or not (0) #### File: 36D\_Pop\_GG\_SS\_C\_LARVAL\_DECISION.csv **Description:** Binary data for comparing the the larval decision of the Gotland and Stockholm populations and their reciprocal hybrid crosses combined. However, the larval decision to diapause is based on the larval development time being &gt;36 days instead of &gt;40 days since hatching. ##### Variables * treatment: the photoperiod treatment the individual was subjected to, either 17, 17.4, 17.8, 18.2 or 18.6 hours of light. * cross: the genotype of the individual, either GG (Gotland), SS (Stockholm) or CC (the reciprocal crosses of GG and SS) * mother: id of the individual’s mother * sex: the sex of the individual (F: female, M: male) * diapause: whether the individual decided to diapause (1) or not (0) #### File: Correlation\_of\_decisions.csv **Description:** Binary data for assessing any correlation between larval and pupal decisions. ##### Variables * larval decision: whether the individual decided to diapause (1) or not (0) in the larval decision * pupal decision: whether the individual decided to diapause (1) or not (0) in the pupal decision #### File: 36D\_MF\_LARVAL\_DECISION\_SG\_GS.csv **Description:**  Binary data for comparing the larval decision of the reciprocal hybrid crosses, taking sex into account (the main question of the manuscript). However, the larval decision to diapause is based on the larval development time being &gt;36 days instead of &gt;40 days since hatching. ##### Variables * treatment: the photoperiod treatment the individual was subjected to, either 17, 17.4, 17.8, 18.2 or 18.6 hours of light. * cross: the genotype of the individual, either GS (mother from Gotland and father from Stockholm) or SG (mother from Stockholm and father from Gotland) * mother: id of the individual’s mother * sex: the sex of the individual (F: female, M: male) * diapause: whether the individual decided to diapause (1) or not (0) #### File: 44D\_Compare\_to\_Prui\_LARVAL\_DECISION.csv **Description:** Binary data for comparing the larval decision of the reciprocal hybrid crosses from the present study to the study by Pruisscher et al. 2018. However, the larval decision to diapause is based on the larval development time being &gt;44 days instead of &gt;40 days since hatching.  ##### Variables * Exp: the study the individual originates from, the current study (A) or the study by Pruisscher et al. 2018 (P) * Direction: the direction is based on the father of the individual’s origin. N for north and S for south. For instance, an individual from the GS cross has a father from Stockholm. Since, Stockholm is further north in Sweden than Gotland, that individual is categorized as N. * Cross: the genotype of the individual, either GS (mother from Gotland and father from Stockholm), SG (mother from Stockholm and father from Gotland), SU X SK (mother from Sundsvall and father from Skåne) or SK X SU (mother from Skåne and father from Sundsvall) * Sex: the sex of the individual (F: female, M: male) * Diapause: whether the individual decided to diapause (1) or not (0) #### File: 44D\_Pop\_GG\_SS\_C\_LARVAL\_DECISION.csv **Description:** Binary data for comparing the larval decision of the Gotland and Stockholm populations and their reciprocal hybrid crosses combined. However, the larval decision to diapause is based on the larval development time being &gt;44 days instead of &gt;40 days since hatching.  ##### Variables * treatment: the photoperiod treatment the individual was subjected to, either 17, 17.4, 17.8, 18.2 or 18.6 hours of light. * cross: the genotype of the individual, either GG (Gotland), SS (Stockholm) or CC (the reciprocal crosses of GG and SS) * mother: id of the individual’s mother * sex: the sex of the individual (F: female, M: male) * diapause: whether the individual decided to diapause (1) or not (0) #### File: 44D\_MF\_LARVAL\_DECISION\_SG\_GS.csv **Description:** Binary data for comparing the larval decision of the reciprocal hybrid crosses, taking sex into account (the main question of the manuscript). However, the larval decision to diapause is based on the larval development time being &gt;44 days instead of &gt;40 days since hatching.  ##### Variables * treatment: the photoperiod treatment the individual was subjected to, either 17, 17.4, 17.8, 18.2 or 18.6 hours of light. * cross: the genotype of the individual, either GS (mother from Gotland and father from Stockholm) or SG (mother from Stockholm and father from Gotland) * mother: id of the individual’s mother * sex: the sex of the individual (F: female, M: male) * diapause: whether the individual decided to diapause (1) or not (0) #### File: 36D\_Compare\_to\_Prui\_LARVAL\_DECISION.csv **Description:** Binary data for comparing the larval decision of the reciprocal hybrid crosses from the present study to the study by Pruisscher et al. 2018. However, the larval decision to diapause is based on the larval development time being &gt;36 days instead of &gt;40 days since hatching.  ##### Variables * Exp: the study the individual originates from, the current study (A) or the study by Pruisscher et al. 2018 (P) * Direction: the direction is based on the father of the individual’s origin. N for north and S for south. For instance, an individual from the GS cross has a father from Stockholm. Since, Stockholm is further north in Sweden than Gotland, that individual is categorized as N. * Cross: the genotype of the individual, either GS (mother from Gotland and father from Stockholm), SG (mother from Stockholm and father from Gotland), SU X SK (mother from Sundsvall and father from Skåne) or SK X SU (mother from Skåne and father from Sundsvall) * Sex: the sex of the individual (F: female, M: male) * Diapause: whether the individual decided to diapause (1) or not (0) #### File: Compare\_to\_Prui\_PUPAL\_DECISION.csv **Description:** Binary data for comparing the pupal decision of the reciprocal hybrid crosses from the present study to the study by Pruisscher et al. 2018. ##### Variables * Exp: the study the individual originates from, the current study (A) or the study by Pruisscher et al. 2018 (P) * Direction: the direction is based on the father of the individual’s origin. N for north and S for south. For instance, an individual from the GS cross has a father from Stockholm. Since, Stockholm is further north in Sweden than Gotland, that individual is categorized as N. * Cross: the genotype of the individual, either GS (mother from Gotland and father from Stockholm), SG (mother from Stockholm and father from Gotland), SU X SK (mother from Sundsvall and father from Skåne) or SK X SU (mother from Skåne and father from Sundsvall) * Sex: the sex of the individual (F: female, M: male) * Diapause: whether the individual decided to diapause (1) or not (0) #### File: MF\_SS\_GG\_GS\_SG\_LARVAL\_DECISION.csv **Description:** Binary data of the larval decision of the Gotland and Stockholm populations and their reciprocal hybrid crosses, taking sex into account. ##### Variables * treatment: the photoperiod treatment the individual was subjected to, either 17, 17.4, 17.8, 18.2 or 18.6 hours of light. * cross: the genotype of the individual, either GS (mother from Gotland and father from Stockholm), SG (mother from Stockholm and father from Gotland), SS (Stockholm) or GG (Gotland). * mother: id of the individual’s mother * sex: the sex of the individual (F: female, M: male) * diapause: whether the individual decided to diapause (1) or not (0) * cross_sex: the cross and sex combined, for instance GGM for a male from Gotland. #### File: Pop\_GG\_SS\_C\_LARVAL\_DECISION\_2.csv **Description:** Binary data for comparing the larval decision of the Gotland and Stockholm populations and their reciprocal hybrid crosses combined. ##### Variables * treatment: the photoperiod treatment the individual was subjected to, either 17, 17.4, 17.8, 18.2 or 18.6 hours of light. * diapause: whether the individual decided to diapause (1) or not (0) * cross_new: the genotype of the individual, either GG (Gotland), SS (Stockholm) or CC (the reciprocal crosses of GG and SS) ## Code/software All analyses were carried out using R version 4.1.2 for Windows. Script: ALL chosen models, necessary packages: Matrix, carData, partR2, vcd Script: Sensitivity_test, necessary packages: Matrix, carData Script: Larval_decision_figures, necessary packages: ggplot2 Script: Pupal_decision_figures, necessary packages: ggplot2 Script: Comparison_across_studies, necessary packages: ggplot2 Script: CI_figures