Different currencies for calculating resource phenology result in opposite inferences about trophic mismatches
Cite this dataset
Versluijs, Tom et al. (2024). Different currencies for calculating resource phenology result in opposite inferences about trophic mismatches [Dataset]. Dryad. https://doi.org/10.5061/dryad.3bk3j9kp3
Abstract
Shifts in phenology are among the key responses of organisms to climate change. When rates of phenological change differ between interacting species they may result in phenological asynchrony. Studies have found conflicting patterns concerning the direction and magnitude of changes in synchrony, which have been attributed to biological factors. A hitherto overlooked additional explanation is differences in the currency used to quantify resource phenology, such as abundance and biomass. Studying an insectivorous bird, Sanderling, and its prey, we show that the median date of cumulative arthropod biomass occurred, on average, 6.9 days after the median date of cumulative arthropod abundance. In some years this difference could be as large as 21 days. For 23 years, hatch dates of Sanderlings became less synchronized with the median date of arthropod abundance, but more synchronized with the median date of arthropod biomass. The currency-specific trends can be explained by our finding that mean biomass per arthropod specimen increased with date. Using a conceptual simulation, we show that estimated rates of phenological change for abundance and biomass can differ depending on temporal shifts in the size distribution of resources. We conclude that studies of trophic mismatch based on different currencies for resource phenology can be incompatible with each other.
README: Different currencies for calculating resource phenology result in opposite inferences about trophic mismatches
This online supplementary information contains five R-scripts and five data files.
DESCRIPTION OF THE DATA AND FILE STRUCTURE
R-SCRIPTS
- (0): Versluijs2022_Script_0-AuxilliaryFunctions.R A script containing auxiliary functions that are automatically sourced in Script 1 and Script 5. This script does not need to be run manually.
- (I): Versluijs2022_Script_1-ArthropodDataZAC_DataPreparation.R Script with data preparation steps for the arthropod dataset from Zackenberg containing pitfall data collected from 1996 to 2020. This adjusted data file is required as an input file for scripts II and III.
- (II): Versluijs2022_Script_2-ArthropodDataZAC_AddBiomass_NumbersvsBiomass.R To study whether the timing of the yearly arthropod peak at ZAC differs when depicted by arthropod numbers versus arthropod biomass, we first need to add estimates of biomass to the adjusted Zackenberg arthropod dataset from script I, because specimens were only counted and identified. In this script, we calculate these biomass estimates and add them to the adjusted Zackenberg arthropod pitfall dataset.
- (III): Versluijs2022_Script_3-Analysis_NumbersvsBiomass.R In this script, we analyse how estimates of the timing of the yearly arthropod peak at ZAC differ when calculated using arthropod numbers versus arthropod biomass. This script continues with the output file from script II.
- (IV): Versluijs2022_Script_4-Analysis_Simulation.R This script contains a simple conceptual simulation to assess how rates of phenological change might be impacted by the choice of currency for prey phenology. Note that this script can be run independently as it does not depend on input files (or output files of other scripts).
DATA FILE CONTENTS
- (I): Versluijs2022_Input_1-LengthBiomassRegressions.csv
- Allometric length-biomass regressions for 27 arthropod families were constructed based on pitfall data collected in Zackenberg in 2015 and in Knipovich in 2018.
- taxon: taxonomic group (generally corresponds to family level)
- n: the number of data points on which each allometric model was fitted and, if applicable, depicts in brackets the sample size before averaging within different length classes.
- Min (mm): Minimum length of specimen in [mm] used for fitting the regression
- Max (mm): Maximum length of specimen in [mm] used for fitting the regression
- B0: Intercept parameter of allometric length-biomass regression including, if applicable, in square brackets include 95% quantile confidence intervals calculated using non-parametric case-bootstrapping.
- B1: Slope parameter of allometric length-biomass regression including, if applicable, in square brackets include 95% quantile confidence intervals calculated using non-parametric case-bootstrapping.
- SF: Duan's smearing factor to correct back-transformed predictions for models with a log-transformed response variable.
- Level: indicates whether the regression was fitted on individual level measurements or average values for different length classes.
- Location: Location where specimens were collected (Knipovich (TAY) or Zackenberg (ZAC))
(II): DOWNLOAD_THIS_FILE_YOURSELF_FROM_ONLINE_GEM_PORTAL.csv
- IMPORTANT: This dataset is NOT provided in this Dryad repository due to conflicting licenses. It can be downloaded for free from the online GEM portal (https://data.g-e-m.dk/datasets?doi=10.17897/V285-Z265. When downloading this file, the date range needs to be specified as 1996-06-03 to 2020-08-26.
- This dataset corresponds to the arthropod emergence dataset collected at Zackenberg. It contains weekly data on arthropod numbers in permanent pitfall and flight-intercept traps at Zackenberg between 1996-06-03 and 2020-08-26. Arthropods have generally been identified to family-level taxonomic resolution. This dataset does not contain any information on each specimen's body length and/or biomass.
- Date = Date of sampling
- Hour = Start hour of sampling (UTC)
- PlotID = Plot ID
- Sorter = Name of labworker(s)
- Days A = Number of days the traps have been open in section A, or (in 1996) sections A-D combined. For Art1, A refers to the North chamber (2006-13). From 2014 onwards, A refers to the North-South chambers combined.
- Days B = Number of days the traps have been open in section B, or (in 1996) sections A-D combined. For Art1, B refers to the South chamber (2006-13). From 2014 onwards, B refers to the East-West chambers combined.
- Days C = Number of days the traps have been open in section C, or (in 1996) sections A-D combined. For Art1, C refers to the East chamber (2006-13).
- Days D = Number of days the traps have been open in section D, or (in 1996) sections A-D combined. For Art1, D refers to the West chamber (2006-13).
- Days E = Number of days the traps have been open in section E.
- Days F = Number of days the traps have been open in section F.
- Days G = Number of days the traps have been open in section G.
- Days H = Number of days the traps have been open in section H.
- Phylum = Phylum of the collected arthropod
- Order = Order of the collected arthropod
- Family = Family or super-family of the collected arthropod
- Genus = Genus of the collected arthropod
- Species = Species of the collected arthropod
- A = The number of collected individuals from section A, or (in 1996) sections A-D combined. For Art1, A refers to the North chamber (2006-13). From 2014 onwards, A refers to the North-South chambers combined.
- B = The number of collected individuals from section B, or (in 1996) sections A-D combined. For Art1, B refers to the South chamber (2006-13). From 2014 onwards, B refers to the East-West chambers combined.
- C = The number of collected individuals from section C, or (in 1996) sections A-D combined. For Art1, C refers to the East chamber (2006-13).
- D = The number of collected individuals from section D, or (in 1996) sections A-D combined. For Art1, D refers to the West chamber (2006-13).
- E = The number of collected individuals from section E.
- F = The number of collected individuals from section F.
- G = The number of collected individuals from section G.
- H = The number of collected individuals from section H.
- Field_remarks = Remarks from the field observer
- Sorting_remarks = Remarks from the sorter
- General_remarks = General remarks
(III): Versluijs2022_Input_3-ArthropodDataZAC_AddBiomass_PitfallZAC15.csv
- Datafile containing Zackenberg 2015 pitfall data. This dataset contains length and dry mass per specimen and is used for random sampling of lengths and/or biomass corresponding to the frequency in which they occur in this dataset.
- Area: Location where specimens were collected (Knipovich (TAY) or Zackenberg (ZAC))
- UTM_x: longitude coordinates of trapping location [UTM].
- UTM_y: latitude coordinates of trapping location [UTM].
- sample_ID: identifier for trap
- trap_type: type of trap (always yellow pitfall traps)
- year: trapping year
- month: trapping month
- day: trapping day
- taxon: taxonomic group (generally corresponds to family level)
- order: taxonomic order
- length_measured: length measured under stereomicroscope
- zoom: zoom-level of stereomicroscope
- length_conversion: conversion factor to go from length_measured to length_mm
- length_mm: body length of specimen [mm]
- length_class: grouping factor for individuals of similar length. If weights could not be measured individually then weights are based on averages for each level of length_class, which are where possible calculated separately for each trap and trapping day.
- weight_mg: dry weight of specimen [mg]
- weight_level: indicates whether weight measurements were done on an individual level, or weights are based on averages per length_class.
- analyzed_at: location and year of lab analysis
- identified_by: people/groups responsible for the identification of samples
- measurements_by: people responsible for measuring and weighing individuals
- Remarks: remarks
(IV): Versluijs2022_Input_4-ArthropodDataZAC_AddBiomass_PitfallTAY18.csv
- This data file contains Knipovich 2018 pitfall data; it only contains those taxa that were not present in the Zackenberg 2015 pitfall data (e.g. Tipulidae, Coleoptera). This dataset contains length and dry mass per specimen and is used for random sampling of lengths and/or biomass corresponding to the frequency in which they occur in this dataset.
- Area: Location where specimens were collected (Knipovich (TAY) or Zackenberg (ZAC))
- UTM_x: longitude coordinates of trapping location [UTM].
- UTM_y: latitude coordinates of trapping location [UTM].
- sample_ID: identifier for trap
- trap_type: type of trap (always yellow pitfall traps)
- year: trapping year
- month: trapping month
- day: trapping day
- taxon: taxonomic group (generally corresponds to family level)
- order: taxonomic order
- length_measured: length measured under stereomicroscope
- zoom: zoom-level of stereomicroscope
- length_conversion: conversion factor to go from length_measured to length_mm
- length_mm: body length of specimen [mm]
- length_class: grouping factor for individuals of similar length. If weights could not be measured individually then weights are based on averages for each level of length_class, which are where possible calculated separately for each trap and trapping day.
- weight_mg: dry weight of specimen [mg]
- weight_level: indicates whether weight measurements were done on an individual level, or weights are based on averages per length_class.
- analyzed_at: location and year of lab analysis
- identified_by: people/groups responsible for the identification of samples
- measurements_by: people responsible for measuring and weighing individuals
- Remarks: remarks
(V): Versluijs2022_Input_5-ArthropodDataZAC_AddBiomass_StickyTrapZAC19-21.csv
- Datafile containing arthropod sticky trap data collected in Zackenberg in 2019 and 2021. This datafile contains lengths per specimen and is used for random sampling of lengths corresponding to the frequency in which they occur in this dataset.
- Sample: unique identifier to the label of the sticky trap
- Order: taxonomic order
- Family: taxonomic family
- Subgroup: taxonomic subgroup (combination of multiple families)
- Length_measured: length measured under stereomicroscope
- Zoom: zoom level when measuring
- length_mm: actual body length of specimen [mm]
- Trap_type: Type of sticky trap (Large: ST_Large, or Small: ST_Small)
- Bino: model of stereo microscope
- Remarks: remarks
(VI): Versluijs2022_Input_6-Analysis_NumbersvsBiomass_SanderlingHatchdates.csv
- Datafile with Sanderling hatch dates based on nests and broods found in Zackenberg between 1996 and 2021.
- fateID = unique identifier corresponding to the column in our database
- NestID = ID of nest or brood
- Year = Year in which nest was found
- source = hatch date was defined from data obtained during the nesting phase ('nest') or the brood phase ('brood')
- hatched = did the nest hatch (i.e. is the exact hatching date known and not estimated)
- medianhatchday = hatch date in the day of the year
- Remarks = Remarks
SHARING/ACCESS INFORMATION
Dataset number II (i.e. the arthropod emergence dataset for Zackenberg) is not included in this Dryad repository and can be accessed at the following permanent location: https://doi.org/10.17897/V285-Z265.
Methods
To evaluate how our choice of currency for prey phenology will affect our perception of a phenological mismatch, we introduce a model system: the breeding phenology of an arctic shorebird, Sanderling (Calidris alba), and the phenology of their arthropod prey. We derive measures of arthropod phenology in terms of abundance and biomass (with the latter inferred using allometric length-biomass regressions). For this purpose, we analyzed 23 years of arthropod and bird data collected at Zackenberg. In addition, we use a simple simulation to assess how rates of phenological change are affected by the choice of currency for prey phenology. Since 1996 arthropod communities have been sampled throughout the snow-free season at Zackenberg, northeast Greenland (74°28' N, 20°34' W). To calculate annual seasonal trends in arthropod biomass at Zackenberg we first calculated the average number of specimens caught per taxonomic group per day per trap. This we did for each day of the time window during which a trap was active. These data only comprise counts of arthropods but do not contain measurements of the length or weight of individual specimens. Therefore, to calculate trends in biomass we first allocated a length to each specimen by sampling from an additional dataset containing taxon-specific length distributions. Once a length was allocated to each specimen, we calculated each specimen’s biomass using taxon-specific length-biomass regressions. For each year, we then computed daily estimates of total arthropod biomass by summing daily biomass estimates of all taxonomic groups and averaging them across all active traps. Using this adjusted dataset we then calculated the median date of cumulative arthropod numbers and the median date of cumulative arthropod biomass for each year. In addition, we assessed hatching dates of Sanderlings in Zackenberg by visiting nests or inferred this from egg flotation data or chick weights. We then calculated an annual estimate of mismatch by subtracting (I) the median date of arthropod abundance, and (II) the median date of arthropod biomass from the median hatch date of Sanderling chicks. We then assessed trends in the degree and direction of mismatch depending on the chosen currency by inspecting the slope of linear models. We used case-bootstrapping to calculate 95% quantile confidence intervals for all statistics. In addition, we used a simple conceptual simulation to assess how rates of phenological change might be impacted by the choice of currency when calculating resource phenology.
Usage notes
This Dryad repository contains five R-scripts (i.e. script 0, I, II, II, and IV). Script 0 is automatically sourced in the other scripts and does not need to be run manually. Script IV is a standalone script that does not require input files. In contrast, scripts I, II, and III rely on six data files as input. Five of these input files (i.e. I, III, IV, V, and VI) are provided in this Dryad repository. One input file (II) is not provided in this Dryad repository due to conflicting licenses. This file can be downloaded for free from the Greenland Ecosystem Monitoring webpage at the following permanent location https://data.g-e-m.dk/datasets?doi=10.17897/V285-Z265. When downloading this file, the date range needs to be specified as 1996-06-03 to 2020-08-26. All six input files need to be placed in the same working directory as the R-scripts. In addition to these six input files, scripts I, II, and III also require input files that are generated as output in the other R-scripts. It is therefore essential to run all scripts in order of their numbering (from I to III) to generate these output files. Output files are automatically stored in the same working directory as the R-script. For a detailed description of the R-scripts and input files, see the supplemented README.MD file. Meta-data for the output files that are generated in-script can be found in the code of the R-script.
Funding
Dutch Research Council, Award: ALWOP.432
Dutch Research Council, Award: ALWPP.2016.044
Dutch Research Council, Award: VI.C.182.060
Dutch Research Council, Award: 886.15.207
Waddenfonds, Award: WF209925
European Research Council, Award: 856506—LIFEPLAN, ERC-synergy grant
Academy of Finland, Award: VEGA 322266