Data and code from: Disentangling the drivers of decadal body size decline in an insect population
Data files
Nov 02, 2023 version files 923.48 KB
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MidgeSize_data_and_code.zip
913.94 KB
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README.md
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Abstract
While climate warming is widely predicted to reduce body size of ectotherms, evidence for this trend is mixed. Body size depends not only on temperature but also on other factors, such as food quality and intraspecific competition. Because temperature trends or other long-term environmental factors may affect population size and food sources, attributing trends in average body size to temperature requires the separation of potentially confounding effects. We evaluated trends in the body size of the midge Tanytarsus gracilentus and potential drivers (water temperature, population size, and food quality) between 1977 and 2015 at Lake Mývatn, Iceland. Although temperatures increased at Mývatn over this period, there was only a slight (non-significant) decrease in midge adult body size, contrary to theoretical expectations. Using a state-space model including multiple predictors, body size was negatively associated with both water temperature and midge population abundance, and it was positively associated with 13C enrichment of midges (an indicator of favorable food conditions). The magnitude of these effects were similar, such that simultaneous changes in temperature, abundance, and carbon stable isotopic signature could counteract each other in the long-term body size trend. Our results illustrate how multiple factors, all of which could be influenced by global change, interact to affect average ectotherm body size.
README: Data and code for: Disentangling the drivers of decadal body size decline in an insect population
https://doi.org/10.5061/dryad.79cnp5j2m
This analysis had two major goals:
- characterize linear trends at Lake Mývatn, Iceland, between 1977 and 2015 in:
- midge (Tanytarsus gracilentus) wing lengths
- midge population size
- midge stable carbon isotopes (13C)
- air and water temperatures
- characterize the impact of population size, stable isotope signature, and water temperature on midge wing lengths.
To approach this problem, we employed state space models that account for temporal autocorrelation and measurement error. We assessed significance by using boostrapped likelihood ratio tests (2,000 simulations for each term).
Description of the data and file structure
This file consists of three subfolders: Data, Output, and Scripts.
Data includes the raw data on which the analyses were used.
- full_data_28Sep22.csv
- All data used in the analyses
| column | description | type | missing values |
|---|---|---|---|
| year | calendar year | numeric | NA |
| gen | the annual cohort when the midges emerged (Overwintering/ Summer) | character | NA |
| year2 | a unique numerical sequence for each generation (year + 0.5 for summer cohort) | numeric | NA |
| time | a sequence from the beginning of the dataset to the end of the dataset in decades | numeric | NA |
| mean.lengthmm | the average Tanytarsus gracilentus wing length in mm | numeric | NA |
| lengthmm.se | the standard error of the mean wing length of Tanytarsus gracilentus in mm | numeric | NA |
| n_wings | number of individuals on which the average wing length was calculated | numeric | NA |
| mean_wtemp | average water temperature during that midge generation, either observed or estimated for gaps (see paper for details) | numeric | NA |
| filled_using_airtemps | a logical describing whether water temperature was observed (FALSE) or estimated based on air temperatures (TRUE) used when gaps | logical | NA |
| nas_after_filling | There were a few occasions where some days could not be estimated from air temperatures. This logical indicates whether any days could not be estimated or were not observed. | logical | NA |
| d13C | carbon stable isotopes. See McCormick et al. (2022) for details | numeric | NA |
| n_iso | number of individuals used in the isotope analysis (pooled prior to stable isotope measurements) | numeric | NA |
| logcount | log transformed midge abundance in window traps | numeric | NA |
| gensummer | a binary reflecting whether the generation is part of the summer cohort | binary | NA |
| mean.lengthmm2 | same as mean.winglengthmm, but set to NA where isotope data are missing. | numeric | NA |
| d13C2 | same as d13C, but with missing values changed to 0. necessary for analysis. | numeric | 0* |
| logcountz | z transformed log count | numeric | NA |
| d13Cz | z transformed d13C, missing values set to 0 for for analysis (they are not estimated, so this has no impact on the analysis, but the method does not handle NAs in this matrix) | numeric | 0* |
| wtempanomz | z tranformed water temperature (z transformed within cohort). | numeric | NA |
trap_ids.csv
A spreadsheet that identifies the traps for which wing data are included for each generation.
Column Description Type missing values year calendar year numeric NA gen the annual cohort when the midges emerged (Overwintering/ Summer) character NA traps A list of traps used to generate the wing length data. Trap names come from Einarsson et al. 2004 character NA
old_wings.csv
- data from Einarsson et al. (2002). missing values = -100
- metadata in old_wings.xlsx
AnnualTemps.csv
a dataframe of air temperatures.
Column Description Type missing values year calendar year numeric NA iceoff the date on which we estimated when the lake was ice-free (see methods for description) yyyy-mm-dd NA iceon the date on which we estimated when the lake was ice covered yyyy-mm-dd NA nas_after_filling number of dates where there were no water temperatures (see above). logical NA ann_icefreewtemp average water temperature during the ice-free period for a given year in Celsius numeric NA est_ice_duration estimated duration of ice cover on the lake in days numeric NA time number of decades since the first sample numeric NA ann_airtemp average annual air temperature at Grimsstaðir in Celsius numeric NA ann_icefreewairtemp average annual air temperature at Grimsstaðir in Celsius during the period when the lake was ice-free numeric NA
Myvatn_Outlet_for_JamieBotsch_14sep2022.csv
a data frame containing water temperatures at the outlet (maintained by RAMY: https://ramy.is/).
Column Description Type missing values date calendar date dd.mm.08 blank JULIAN day of year 1-366 blank MONTH month of year numeric blank all others water temperature in Celsius numeric blank or -99
weatherstation_raw (not included. We could not confirm that it could be published under CC0)
Hourly weather data for Mývatn from the Icelandic Meteorological Office. Icelandic Meteorological Office 2022: Icelandic Meteorological Office Database, delivery no. 2022-09-16/GEJ01 - contact authors for a copy
Parameters Explanation missing values AR Year of observation NA D Wind direction (10 min average), degrees NA DAGUR Day of observation NA F Wind speed (10 min average), m/s NA FG Wind gust (maximum 3 secs value since last listing), m/s NA FX Maximum 10 min average wind speed, m/s NA KLST Hour of observation NA MAN Month of observation NA P Air pressure calculated down to sea level, hPa NA RH Humidity (1 min average),% NA STOD Station number NA T Air temperature (1 min average), °C NA TIMI Timestamp of observation NA TN Minimum temperature (lowest 1 min average value since last listing), °C NA TX Maximum temperature (maximum 1 min average since last listing), ° C NA
Grimsstadir_XXAvg.txt
- datafiles for average and monthly air temperatures at Grimsstaðir. Not included, but can be accessed through the below links.
Scripts includes all relevant code
- fit_trends.R includes code to fit SSMs to assess linear trends over time and to assess the significance of these trends
- plots.R includes code to make all figures
- TemperatureComp.R includes code comparing temperature at Grimsstaðir and Mývatn (both air and water temperatures).
- TVARSS_18Jan23.R contains code for performing a state space model per Ives and Dakos (2012)
- wing_analysis.R contains code to fit SSMs to wing length using predictor variables and to assess their significance.
- wing_comparison.R contains code comparing wing lengths used in the paper from wing lengths used in Einarsson et al. (2002) for years where data overlap
Outputs include all model outputs and bootstrapped results.
- Trends contains all outputs from the models estimating linear trends (XX_trends.RDS), p values from LRTs (trends_pvals.csv) and a folder containing the outputs from each of the bootstrapped LRTs (trends_bootstrapped_LRTs) with a file for each model.
- Wing contains all outputs from the full model relating wing length to z-scored predictors, p values from LRTs (wing_pvals.csv) and folders containing the outputs from each of the bootstrapped LRTs etiher with either only temperature or including population data (population size and carbon stable isotopes; NoFood and wing_boostrapped_LRTS, respectively).
External data sources
Long term air temperature data come from the Grimsstaðir weather station, maintained by the Icelandic Meteorological Office. IMO also provided hourly air temperatures at Mývatn.
- https://www.vedur.is/Medaltalstoflur-txt/Stod_495_Grimsstadir.ArsMedal.txt
- https://www.vedur.is/Medaltalstoflur-txt/Stod_495_Grimsstadir.ManMedal.txt
- Icelandic Meteorological Office Database delivery no. 2022-09-16/GEJ01.
Carbon stable isotopes come from McCormick et al. (2022).
- https://doi.org/10.6084/m9.figshare.c.6197266.v1
For comparison, wing lengths from Einarsson et al. (2002) are included.
Methods
Midges (Diptera: Chironomidae) were captured using window traps (Jónsson et al., 1986) at two locations around Lake Mývatn, Iceland. They were innumerated to species and separated into two cohorts (early summer and late summer), matching the voltinism pattern of the focal species (Tanytarsus gracilentus) which overwinter as larvae (Gardarsson et al., 2004; Lindegaard & Jónasson, 1979; Einarsson et al. 2002, 2004). Archived midges were used to measure carbon stable isotopes (McCormick et al. 2022) and wing lengths were measured from arculus to tip on 15-20 individuals per generation (where abundances were adequate). Because identifications of female midges is difficult and often impossible, the dataset includes only males. Air temperature data come from the Icelandic Meterological Office (https://www.vedur.is/). All processing to the data are included in scripts.