Data from: Development time, survival, and performance of Lepidoptera reared at constant temperatures
Data files
Aug 04, 2023 version files 807.90 KB
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BreadthDPS.csv
3.81 KB
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DevelopmentTable.csv
26.19 KB
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HighLimitsDPS.csv
4.69 KB
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LowLimitsDPS.csv
5.11 KB
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PerformanceTable.csv
15.63 KB
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PhysiologyDatabaseVersion5.ods
716.23 KB
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README.txt
18.90 KB
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SurvivalTable.csv
17.36 KB
Aug 04, 2023 version files 806.87 KB
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BreadthDPS.csv
3.81 KB
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DevelopmentTable.csv
26.19 KB
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HighLimitsDPS.csv
4.69 KB
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LowLimitsDPS.csv
5.11 KB
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PerformanceTable.csv
15.63 KB
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PhysiologyDatabaseVersion5.ods
716.23 KB
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README.md
17.87 KB
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SurvivalTable.csv
17.36 KB
Abstract
This dataset is a compilation of lepidopteran development and survival rates measured at constant temperatures in the laboratory and reported in peer-reviewed publications. We compiled these data to reconstruct thermal performance curves. Thermal performance curves (TPCs) depict variation in vital rates in response to temperature and have been an important tool to understand ecological and evolutionary constraints on the thermal sensitivity of ectotherms. TPCs allow for the calculation of indicators of thermal tolerance, such as minimum, optimum, and maximum temperatures that allow for a given metabolic function. However, these indicators are computed using only responses from surviving individuals, which can lead to underestimation of deleterious effects of thermal stress, particularly at high temperatures. We advocate for an integrative framework for assessing thermal sensitivity, which combines both vital rates and survival probabilities, and focuses on the temperature interval that allows for population persistence. Using a collated data set of lepidopteran development rate and survival measured on the same individuals, we showed (see associated publication) that development rate is generally limiting at low temperatures, while survival is limiting at high temperatures. We also uncover differences between life stages and across latitudes, with extended survival at lower temperatures in temperate regions. Our combined performance metric demonstrates similar thermal breadth in temperate and tropical individuals, an effect that only emerges from integration of both development and survival trends. We discuss the benefits of using this framework in future predictive and management contexts.
https://doi.org/10.5061/dryad.qjq2bvqk4
Reference Information
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Provenance for this README
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* File name: README_insect_thermal_sensitivity.txt
* Authors: Mariana Abarca, Anna L. Parker, Elise A. Larsen, James Umbanhowar, Chandra Earl, Robert Guralnick, Joel Kingsolver, Leslie Ries
* Date Created: 2022-03-16
* Date Modified: 2023-08-02
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* Dataset Title: Development time, survival, and performance of Lepidoptera reared at constant temperatures.
* Associated manuscript: Abarca M, Parker A L, Larsen E A, Umbanhowar J, Earl C, Guralnick R, Kingsolver J, Rees L. How development and survival combine to determine the thermal sensitivity of insects. PLOS ONE. PONE-D-23-02122R1.
Overview
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* Data on development time and/or survival of immature stages of Lepidoptera were compiled from published peer-reviewed articles reporting development time and/or survival of insects in the order Lepidoptera (butterflies and moths) reared at constant temperatures in the laboratory. In manuscript “How development and survival combine to determine the thermal sensitivity of insects” we analyzed subsets of these data. Here we include the complete data set product of the literary search, the “full” and “analytical” data sets (see manuscript for definitions of these sets and rationale for their use), and the scripts to obtain and reproduce analyses of the “full” and “analytical” data sets.
Table of contents
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Data files
* PhysiologyDatabaseVersion5.ods
* PerformanceTable.csv
* SurvivalTable.csv
* DevelopmentTable.csv
* BreadthDPS.csv
* HighLimitsDPS.csv
* LowLimitsDPS.csv
Scripts
* DR1_variablecalculation.Rmd (R script)
* S1_variablecalculation.Rmd (R script)
* P1_variablecalculation.Rmd (R script)
* DR2_analyses.Rmd (R script)
* P2-analyses.Rmd (R script)
* S2_analyses.Rmd (R script)
* AnalysesDPS.Rmd (R script)
* GTRG_Unpartitioned_constrain.raxml.bestTree.tre (Unrooted, undated phylogeny from RAxML used to test for phylogenetic autocorrelation in R)
* FcC_supermatrix.fas (Supermatrix FASTA file containing raw, concatenated sequence data for 102 species across 8 loci used as input into RAxML)
File details
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Details for : PhysiologyDatabaseVersion5.ods
* Description: a spreadsheet with two sheets: “WorkingTable” and “PaperLevelData” This file contains development and performance data of Lepidoptera reared at constant temperatures that was extracted from peer-reviewed publications as well as information about the articles where these data were published.
* “WorkingTable”- Variables:
* set (numeric) Unique identifier of each analysis unit: N groups of larvae reared at N different temperature treatments but otherwise equivalent (same study, host, photoperiod, sex)
* year (numeric) year the study was conducted
* id (numeric) unique article identifier
* cite (text) Matches citation column in PaperLevelData table
* sp (text) Species
* family (text) taxonomic family
* status (text) Non-mutually exclusive categories to describe the species status as described by the authors of the articles, there are 14 possible values: pest migratory forestpest biocontrol pest/biocontrol silk ornamental insectivorous research wild parasitoid nopest tea endangered
* lifestage (text) Life stage at which development time was measured, there are 49 possible values: adult egg eggtoadultdeath eggtoegg eggtoemergence eggtoinstar2 eggtoinstar3 eggtoinstar4 eggtoinstar5 eggtooviposition eggtopupa eggtopupation hatchtoadult hatchtoemergence hatchtoprepupa hatchtopupa instar1 instar1&instar2 instar1to3 instar1toinstar4completion instar2 instar2topupa instar3 instar3&instar4 instar3topupa instar4 instar5 instar6 instar7 instar7-8 instar8 larva larvatoadult larvatoemergence larvatopupa lastInstar oviposition to 4th molt oviposition to 5thmolt oviposition to first motl oviposition to second molt oviposition to third molt ovipositionto6thmolt pre-oviposition prepupa prepupapupa prepupatoemergence pupa secondinstartoemergence secondinstartopupation
* sex (text) sex of the individuals assessed in each case, there are three options: male, female, both
* host (text) text indicating the host plant identity: common or scientific name of plant species or artificial diet, “NA” and “no” correspond to eggs (who do not feed), “nd” for studies that did not disclose that information
* photoperiod (text) hours of light out of 24 hours. Eg 8 means 8L:16D, “nd” for studies that do not report it
* temp (numeric) temperature in degrees Celsius
* regime (text) only one value: “constant” which denotes constant temperature regimes
* dt (numeric) development time in days
* se (numeric) standard error of development time if reported
* sd (numeric) standard deviation of development time if reported
* survival (numeric) percentage of surviving individuals
* survivalsd (numeric) standard deviation of percent survival if reported
* survivalse (numeric) standard error of percent survival if reported
* n (numeric) sample size as/if reported. It often corresponds to initial sample size (before mortality), but not all the times.
* c1 (text) notes that help differentiating among sets or offer miscellaneous clarification
* idaid (text) notes that help differentiating among sets or offer miscellaneous clarification
* c2 (text) notes that help differentiating among sets or offer miscellaneous clarification
* c3 (text) notes that help differentiating among sets or offer miscellaneous clarification
* photo (numeric) hours of light out of 24 hours, “NA” corresponds to missing numeric values
* dr.naive (numeric) development rate obtained as: 1/dt
* dr (numeric) Adjusted development time according to the following rationale: Development time can be a missing value denoted by “NA” because 1) it was not measured at a given temperature or 2) all individuals died. The calculation of development rate in this table was corrected so it is 0 when both dt == NA and survival == 0
* lat (numeric) latitude in decimal numbers
* lon (numeric) longitude in decimal numbers
* locality (text) name of the locality as reported by authors
* quality (text) Indicates precision of location data. It can be as detailed as indicated by authors (country to gps coordinates) “combination” indicates authors combined individuals from multiple localities in the same set, “inferred” corresponds to the location of the affiliation institution of authors (only when no other data reported) “NA” corresponds to cases where no inference was possible. See manuscript text for details.
* “PaperLevelData”- Variables:
* Year (numeric) Publication year
* PaperID (numeric) unique article identifier
* Citation (text) Summary citation matching “Cite” in “WorkingTable”
* Author (text) Last name of first author
* StateProvRegion (text) Site where study was conducted or specimens were collected
* Country.ies (text) Country/countries where study was conducted/ specimens were collected
* Continent.s (text) Continent where study was conducted/specimens were collected
* Missing data codes: “NA”
* Details for: PerformanceTable.csv
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* set (numeric) Unique identifier of a “set” see manuscript for a definition and rationale.
* Pmin (numeric) Minimum temperature at which performance as defined in manuscript was observed.
* Pmax (numeric) Maximum temperature at which performance as defined in manuscript was observed.
* Pl (numeric) Minimum temperature in degrees Celsius that allows for 50% performance as defined in manuscript.
* Ph (numeric) Maximum temperature in degrees Celsius that allows for 50% performance as defined in manuscript.
* Pbreadth (numeric) Difference between Ph and Pl in degrees Celsius- this is the length of the interval that allows for performance values equal or greater than 50%
* Pgradecold (text)- complete/incomplete indicates whether sets had a complete curve rise (see manuscript for explanation and rationale)
* Pgradehot (text) - complete/incomplete indicates whether sets had a complete curve fall (see manuscript for explanation and rationale)
* sp (text) - Species
* family (text) - Taxonomic family
* lifestage (text) - ontogenetic life stage at which performance was assessed: egg, larva, pupa, eggtoemergence (from egg to adult emergence).
* lat (numeric) latitude in decimal numbers
* lon (numeric) longitude in decimal numbers
* locality (text) name of the locality as reported by authors
* quality (text) Indicates precision of location data. It can be as detailed as indicated by authors (country to gps coordinates) “combination” indicates authors combined individuals from multiple localities in the same set, “inferred” corresponds to the location of the affiliation institution of authors (only when no other data reported) “NA” corresponds to cases where no inference was possible. See manuscript text for details.
* Missing data codes: “NA”
* Details for: SurvivalTable.csv
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* set (numeric) Unique identifier of a “set” see manuscript for a definition and rationale.
* Smin (numeric) Minimum temperature at which survival as defined in manuscript was observed.
* Smax (numeric) Maximum temperature at which survival as defined in manuscript was observed.
* Sl (numeric) Minimum temperature that allowed for survival of at least 50% of individuals
* Sh (numeric) Maximum temperature that allowed for survival of at least 50% of individuals
* Sbreadth (numeric) Difference between Sh and Sl in degrees Celsius- this is the length of the interval that allows for survival of at least 50% of individuals.
* Sgradecold (text)complete/incomplete indicates whether sets had a complete curve rise (see manuscript for explanation and rationale)
Sgradehot (text) complete/incomplete indicates whether sets had a complete curve fall (see manuscript for explanation and rationale)
sp (text) - Species
family (text) - Taxonomic family
lifestage (text) - ontogenetic life stage at which performance was assessed: egg, larva, pupa, eggtoemergence (from egg to adult emergence).
lat (numeric) latitude in decimal numbers
lon (numeric) longitude in decimal numbers
locality (text) name of the locality as reported by authors
quality (text) Indicates precision of location data. It can be as detailed as indicated by authors (country to gps coordinates) “combination” indicates authors combined individuals from multiple localities in the same set, “inferred” corresponds to the location of the affiliation institution of authors (only when no other data reported) “NA” corresponds to cases where no inference was possible. See manuscript text for details.
Missing data codes: “NA”
* Details for: DevelopmentTable.csv
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* set (numeric) Unique identifier of a “set” see manuscript for a definition and rationale.
* Dl (numeric) Minimum temperature that allows for development at 50% or higher of the maximum rate (see manuscript for explanation and rationale).
* Dh (numeric) Minimum temperature that allows for development at 50% or higher of the maximum rate (see manuscript for explanation and rationale).
* Dbreadth (numeric) Difference between Dh and Dl in degrees Celsius- this is the length of the interval that allows for development time at or greater than 50% efficiency (see manuscript for details).
* gradecold (text)complete/incomplete indicates whether sets had a complete curve rise (see manuscript for explanation and rationale)
* gradehot (text) complete/incomplete indicates whether sets had a complete curve fall (see manuscript for explanation and rationale)
* sp (text) - Species
* family (text) - Taxonomic family
* lifestage (text) - ontogenetic life stage at which performance was assessed: egg, larva, pupa, eggtoemergence (from egg to adult emergence).
* lat (numeric) latitude in decimal numbers
* lon (numeric) longitude in decimal numbers
* locality (text) name of the locality as reported by authors
* quality (text) Indicates precision of location data. It can be as detailed as indicated by authors (country to gps coordinates) “combination” indicates authors combined individuals from multiple localities in the same set, “inferred” corresponds to the location of the affiliation institution of authors (only when no other data reported) “NA” corresponds to cases where no inference was possible. See manuscript text for details.
Missing data codes: “NA”
* Details for: BreadthDPS.csv
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* This table includes sets for which the calculation of all three breadth variables: development, survival and performance can be calculated.
* set (numeric) Unique identifier of a “set” see manuscript for a definition and rationale.
* Dbreadth (numeric) Difference between Dh and Dl in degrees Celsius- this is the length of the interval that allows for development time at or greater than 50% efficiency (see manuscript for details).
* sp (text) - Species
* family (text) - Taxonomic family
* lifestage (text) - ontogenetic life stage at which performance was assessed: egg, larva, pupa, eggtoemergence (from egg to adult emergence).
* lat (numeric) latitude in decimal numbers
* lon (numeric) longitude in decimal numbers
* locality (text) name of the locality as reported by authors
* quality (text) Indicates precision of location data. It can be as detailed as indicated by authors (country to gps coordinates) “combination” indicates authors combined individuals from multiple localities in the same set, “inferred” corresponds to the location of the affiliation institution of authors (only when no other data reported) “NA” corresponds to cases where no inference was possible. See manuscript text for details.
* Pbreadth (numeric) Difference between Ph and Pl in degrees Celsius- this is the length of the interval that allows for performance values equal or greater than 50%
* Sbreadth (numeric) Difference between Sh and Sl in degrees Celsius- this is the length of the interval that allows for survival of at least 50% of individuals.
Missing data codes: “NA”
* Details for: HighLimitsDPS.csv
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* set (numeric) Unique identifier of a “set” see manuscript for a definition and rationale.
* Dh (numeric) Minimum temperature that allows for development at 50% or higher of the maximum rate (see manuscript for explanation and rationale).
* sp (text) - Species
* family (text) - Taxonomic family
* lifestage (text) - ontogenetic life stage at which performance was assessed: egg, larva, pupa, eggtoemergence (from egg to adult emergence).
* lat (numeric) latitude in decimal numbers
* lon (numeric) longitude in decimal numbers
* locality (text) name of the locality as reported by authors
* quality (text) Indicates precision of location data. It can be as detailed as indicated by authors (country to gps coordinates) “combination” indicates authors combined individuals from multiple localities in the same set, “inferred” corresponds to the location of the affiliation institution of authors (only when no other data reported) “NA” corresponds to cases where no inference was possible. See manuscript text for details.
* Ph (numeric) Maximum temperature in degrees Celsius that allows for 50% performance as defined in manuscript.
* Sh (numeric) Maximum temperature that allowed for survival of at least 50% of individuals
Missing data codes: “NA”
* Details for:LowLimitsDPS.csv
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* set (numeric) Unique identifier of a “set” see manuscript for a definition and rationale.
* sp (text) - Species
* family (text) - Taxonomic family
* lifestage (text) - ontogenetic life stage at which performance was assessed: egg, larva, pupa, eggtoemergence (from egg to adult emergence).
* lat (numeric) latitude in decimal numbers
* lon (numeric) longitude in decimal numbers
* locality (text) name of the locality as reported by authors
* quality (text) Indicates precision of location data. It can be as detailed as indicated by authors (country to gps coordinates) “combination” indicates authors combined individuals from multiple localities in the same set, “inferred” corresponds to the location of the affiliation institution of authors (only when no other data reported) “NA” corresponds to cases where no inference was possible. See manuscript text for details.
* Pl (numeric) Minimum temperature in degrees Celsius that allows for 50% performance as defined in manuscript.
* Sl (numeric) Minimum temperature that allowed for survival of at least 50% of individuals
Missing data codes: “NA”
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Steps to reproduce analyses described in manuscript ÒHow development and survival combine to determine the thermal sensitivity of insectsÓ
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1. Generate D, S and P variables as defined in manuscript
Data:
PhysiologyDatabaseVersion5.xlsx
Scripts:
DR1_variablecalculation.Rmd
S1_variablecalculation.Rmd
P1_variablecalculation.Rmd
2. Analyses of Òfull data setÓ
Data (output from scripts above plus phylogenetic tree):
PerformanceTable.csv
SurvivalTable.csv
DevelopmentTable.csv
GTRG_Unpartitioned_constrain.raxml.bestTree.tre
Scripts:
DR2_analyses.Rmd
P2-analyses.Rmd
S2_analyses.Rmd
3. Analyses of Òanalytical data setÓ
Data:
BreadthDPS.csv
HighLimitsDPS.csv
LowLimitsDPS.csv
Scripts:
AnalysesDPS.Rmd
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END OF README
Data was extracted from scientific publications and entered in the "WorkingTable" which was subsequently processed (using provided scripts, see methods in associated publication) to create the rest of the data tables included here.