DOI: 10.5061/dryad.3n5tb2rqb
title: Demand-resource mismatch explains body shrinkage in a migratory shorebird

description: Recent observations of body size declines in animal populations have given
 rise to discussions whether or not this is related to climate
 change-induced temperature increases, with which the body size changes
 would follow Bergmann’s rule. Although the debate is ongoing, the limited
 thermal benefits of currently observed size reductions make it unlikely
 that temperature increase shapes a direct selection pressure. Food
 constraints during early-life development, which could be caused by
 mismatches between available resources and energetic demands, could cause
 smaller body sizes too. Here we investigate whether a decrease in body
 size, observed in a migratory shorebird the red knot (Calidris canutus
 canutus) at their West-African non-breeding grounds over two decades, is
 linked to developmental plasticity during chick growth in the High Arctic.
 To do so, we combined datasets from both the wintering and breeding
 grounds on body size measurements (during chick growth and in fully-grown
 juveniles), food availability, and diet inferred from stable isotopes
 deposited in feathers grown as chicks. From 2003 to 2021, stable-isotope
 ratios revealed a decline in the dietary contribution of crane flies
 (Tipulidae, Diptera), the key food of growing chicks in the Arctic. On the
 breeding grounds we observed that while the emergence of adult crane flies
 advanced along with earlier snowmelt dates, red knots did not adjust the
 timing of breeding, and this resulted in an increasing mismatch with the
 demands of growing chicks. As a result, chicks grew slower and, as
 observed on the wintering grounds, reached smaller final body sizes. Our
 results imply that increasing resource-demand mismatches may lead to body
 shrinkage via plasticity during development. In this study the increasing
 mismatch was linked with climate warming; the presented causal chain may
 explain other recent examples of body size reductions as well.
description: READ ME file for data and analyses appearing in: "Demand-resource
 mismatch explains body shrinkage in a migratory shorebird" Oortwijn,
 T., Lameris, T.K., Zhemchuzhnikov, M.K., Dekinga, A., ten Horn, J.,
 Kutcherov, D., Lisovski, S., Piersma, T., Rakhimberdiev, R., Soloviev,
 M.Y., Spaans, B., Syroechkovsky, E.E., Tomkovich, P.S., Zhemchuzhnikova,
 E., van Gils, J.A. --- The data is analysed using 5 scripts and 13 data
 files (of which 1 data file (no. 13) generated in the scripts). Data files
 include: 1. chicks.csv 2. SI_data_Taymyr.csv 3. Barcoding_Taymyr.csv 4.
 pitfall_arthropod_specimens_Taymyr.csv 5.
 pitfall_station_metadata_Taymyr.csv 6. pitfall_status_Taymyr.csv 7.
 biomass_length_Taymyr.csv 8. snowmelt_Knipovich.csv 9.
 temperature_Knipovich.csv 10. snowmelt_Taimyr.csv 11.
 isotopes_arthropods_Taimyr.csv 12. juveniles_Mauritania.csv 13.
 chicks_data.csv 14. adults_Mauritania.csv Scripts include: 1.
 Taimyr_analyses.R 2. Tipulidae_traps.R 3. SI mixing model script.R 4.
 Structural_Equation_Model.R 5. MAIN.R 6. Adult_analysis.R \--- DATA ---
 METADATA 1. chicks.csv This file contains biometric measurements of
 chicks, collected at the study site Knipovich Bay, Russia in
 1990,1991,2018,2019 **BroodID** ID number of the brood (all chicks hatched
 from the same nest) **Ring** Ring number of individual chick **Recap**
 whether or not the capture is a recapture event (1) or a first capture (0)
 **Year** Year of study **AGE** age of the chick in days since hatch
 **Hatchdate.observed** hatch date observed in the field **Mass** body mass
 in grams **Bill** bill length (from base to tip) in mm **Tarsus** tarsus
 length in mm **Wing** wing length in mm **P10.total** length of 10th
 primary feather in mm **Date** date of capture, formatted as dd/mm/yyyy
 **Time** time of capture, using local Krasnoyarsk time (GMT + 7)
 **date_time1** combined date and time of capture **sex** sex as determined
 from DNA analyses, either unknown (u), male (m) or female (f)
 **shit_pool_ID** ID of feacal sample (pooled per brood) **shit_single_ID**
 ID of feacal sample from single chick) **Brood_Year_ID** ID number
 combining brood ID and Year **aknown** whether or not age is known (1) or
 unknown (0) METADATA 2. SI_data_Taimyr.csv This file contains stable
 isotope values as measured in feathers, down feathers, red blood cells and
 plasma of red knots, samples in Knipovich Bay, Russia in 2018 and 2019.
 The estimated fraction of tipulids in the diet (estimated from stable
 isotope mixing model) is also included. **year** Study year **sample**
 sample ID **d15N** stable isotope value of d15N **Tipmean** fraction of
 tipulidae in diet as estimated from stable isotope mixing model (mean)
 METADATA 3. Barcoding_data_Taimyr.csv This file contains the fractional
 number of reads per family for all faecal samples analysed using DNA
 barcoding **Field_ID** sample ID **Field_ID2** sample ID (short version
 without location label) **Year** year of study **Species** shorebird
 species from which feacal sample was taken **Dropping** Dry weight,(g) dry
 weight of dropping grams **Remarks** **include** whether or not to include
 in final analysis (as some of the samples are subsamples from a single
 sample, see remarks) **count_families** number of families found in sample
 **family** ID of family identification **Unassigned** Fraction of reads
 unassigned to any family **Chironomidae** and all remaining columns in
 file Fraction of reads assigned to a family METADATA 4.
 pitfall_arthropod_specimens_Taimyr.csv This file contains information on
 the identification of arthropod specimens and their length, sampled in
 pitfall traps in Knipovich Bay, Russia, 2018 and 2019. **row.ID** ID
 number of row **poskey** ID of sample **order** identified arthropod order
 (Ara = Araneae, Clm = Colembola, Col = Coleoptera, Dip = Diptera, Hap =
 Haplotoxida, Hym = Hymenoptera, Lep = Lepidoptera, Ori = Oribatida, Ple =
 Plecoptera) family identified arthropod family (Car = Carabidae, Chr =
 Chrysomelidae, Sta = Staphylinidae, Ant = Antomyiidae, Bol =
 Bolitophilidae, Cal = Calliphoridae, Chi = Chironomidae, Emp = Empididae,
 Mus = Muscidae, Myc = Mycetophilidae, Sca = Scathophagidae, Sci =
 Sciaridae, Syr = Syrphidae, Tip = Tipulidae, Tri = Trichoceridae, Lum, Dia
 = Diapriidae, Lum = Lumbricidae, Ich = Ichneumonidae, Mym = Mymaridae, Ten
 = Tenthredinidae, Noc = Noctuoidea, Nym = Nymphalidae, Pap =
 Papilionoidea, Nem = Nemouridae) **larva** whether specimens were in
 larval (y) or imago stage (n) **length** length (average of three) of
 specimens in mm **n** number of specimens captured in pitfall METADATA 5.
 pitfall_station_metadata_Taimyr.csv This file contains metadata on the
 pitfall sampling stations in Knipovich Bay, Russia, 2018 and 2019.
 **station.type** type of stations, with three types: grid (in grids of 10
 traps with 400m intervals, sampled every 5 days), transect (900m transect
 with 100m intervals, sampled every 5 days), daily (100m transect with 25m
 intervals, sampled daily) **station.no** ID of sampling station
 **grid.no** ID of grid **x** x coordinates (in UTM 47) **y** y coordinates
 (in UTM 47) **elevation** elevation (m above sea level)
 **snowmelt.date.2018** date when pitfall trap location was free of snow in
 2018 **snowmelt.date.2019** date when pitfall trap location was free of
 snow in 2019 METADATA 6. pitfall_status_Taimyr.csv This file contains
 metadata on the daily status of pitfall stations: whether these were
 sampled or not and at which interval. **station.type** type of stations,
 with three types: grid (in grids of 10 traps with 400m intervals, sampled
 every 5 days), transect (900m transect with 100m intervals, sampled every
 5 days), daily (100m transect with 25m intervals, sampled daily)
 **station.no** ID of sampling station **date** date **year** study year
 **poskey** ID of sample **status** status, whether pitfall location was
 still covered with snow (snow) or flooded (water), whether it was placed
 (placed) or sampled (sampled) **interval** interval in days at which
 pitfall station was sampled METADATA 7. biomass_length_Taimyr.csv This
 file contains the biomass - length relationships which we used to estimate
 biomass of arthropod specimens. These data are published in Versluijs et
 al. 2023. In addition, we used biomass - length relationships from older
 literature based on arthropods in temperate environments. Detailed
 information on this can be found in the methods section and in the
 R-script. **Order** arthropod order **Family** arthropod family **n**
 sample size of measured specimens **min** minimum length (mm) **max**
 maximum length (mm) **B0** intercept value for mass - length relationship
 **B1** coefficient value for mass - length relationship **sf** smearing
 factor used to backtransform predictions for models with natural
 log-transformed response variable **Level** whether the allometric model
 was fit on individual level measurements or average values for different
 length classes **Model** model description **Location** Knipovich Bay,
 Russia (KNP) or Zackenberg, Greenland (ZAC) **model** ID of model type
 **order_2** arthropod order (using abbreviations corresponding to METADATA
 file 4) **family_2** arthropod family (using abbreviations corresponding
 to METADATA file 4) METADATA 8. snowmelt_Knipovich.csv This file contains
 data on the date at which the tundra at our study site in Knipovich Bay,
 Russia was 50% snowfree, including satellite-derived data as well as
 observed data from the field. **year** study year **snowmelt_satellite**
 date of 50% snowmelt as measured from satellite data **snowmelt_observed**
 date of 50% snowmelt as observed in the field METADATA 9.
 temperature_Knipovich.csv This file contains temperature data downloaded
 from the NCEP database of temperatures at the study site Knipovich Bay,
 Russia **date** date **time** time (UTC) **date_time** date and time
 combined **temp** temperature (Kelvin) METADATA 10. snowmelt_Taimyr.csv
 This file contains dates of snowmelt in spring from the whole breeding
 range of red knots, canutus-subspecies. Each line is a grid cell within
 this range, see Materials and Methods for more details. **year** year
 **sm** day of year in which grid cell became 50% snow free METADATA 11.
 isotopes_arthropods_Taimyr.csv This file contains stable nitrogen values
 from several arthropods families from Taimyr. **Sample** sample name
 **Family** arthropod family name of sample **d15N** d15N value of sample
 (after correction, using certified standards, see Materials and Methods)
 METADATA 12. juveniles_Mauritania.csv This file contains data on juvenile
 red knots, caught and measured in Banc d'Arguin, Mauritania. Each row
 contains data on one individual. **Ring** individual code **Hatchyear**
 year in which the individual hatched **d15N** d15N of 6th primary covert
 of the juvenile plumage (so containing dietary information from tundra,
 when this feather was grown as chick) **Tipmean** estimated proportion of
 crane flies in diet (based on stable isotope mixing model with d15N from
 feather sample) **TipSD** standard deviation of estimated proportion of
 crane flies in diet (based on stable isotope mixing model with d15N from
 feather sample) **Sex** sex, determined from DNA analyses **Wing** wing
 length (to nearest mm) **Bill** bill length (to nearest 0.1 mm) **Tarsus**
 diagonal tarsus length (to nearest 0.1 mm) **PC1** first principal
 component of three body size measures METADATA 13 chicks_data.csv This
 file contains all calculations on data from Knipovich study site,
 including calculations on chick growth, diet, arthropod availability and
 snowmelt. This file is generated in the script
 "Taimyr_analyses.r". The first columns are equal to those in 1.
 chicks.csv, others are described below. **iso_tipulids** estimated
 proportion of crane flies in diet (based on stable isotope mixing model
 with d15N from feather sample) **snowmelt** date of 50% snowmelt as
 measured from satellite data (day of the year) **snowmelt_observed** date
 of 50% snowmelt as observed in the field (day of the year)
 **predict.age.P10.plotted** predicted age based on P10 (days)
 **predicted.age** corrected predicted age, set negative values to zero
 (days) **Hatchdate.predicted** predicted hatch date based on predicted age
 (days) **age.plotted** age, observed age when known, predicted age when
 unknown (days) **age.plotted.numeric** copy of previous column
 **Hatchdate.plotted** hatch date, observed when known, predicted when
 unknown **Hatchdate.plotted.jun** hatch date in June days
 **Hatchdate.plotted.jul** hatch date as day of the year **mean_bill** mean
 bill length of a juvenile (mm) **predicted_bill** predicted bill length
 based on age (mm) **res_bill_2** residuals of bill length as residuals
 divided by predicted value bill measured bill length (mm) **res_bill_3**
 another method to determine growth reductions, used for visualization
 **tarsus, mass, pc1** previous 5 columns are repeated for tarsus (mm),
 mass (g) and pc1 (first principal component of bill, tarsus and mass)
 **pc1_0** the 5 same columns, but now for pc1 with chick with body size of
 '0' added **rel_hatchdate** hatch date relative to date of
 snowmelt (days) **tip_pool** relative abundance of tipulids in the diet
 pooled per brood **tip_single** relative abundance of tipulids in the diet
 of a single individual **diet** per arthropod group (abbreviations
 specified in metadata 4) relative abundance in the diet **jul.date** day
 of the year **s** per arthropod group (abbreviations specified in metadata
 4) daily biomass (mg) per pitfall **f** per arthropod group (abbreviations
 specified in metadata 4) fraction compared to total biomass **select** per
 arthropod group (abbreviations specified in metadata 4) IVLEV index
 **Hatchdate.posixct** hatch date in POSIXct format **avg.temp** mean
 temperature of period 3 days before catch moment METADATA 14.
 adults_Mauritania.csv This file contains data on adult red knots, caught
 and measured in Banc d'Arguin, Mauritania. Each row contains data on
 one individual. **Ring** individual code **Year** year in which the
 individual was caught **Month** month in which the individual was caught
 **Sex** sex, determined from DNA analyses **Wing** wing length (to nearest
 mm) **Bill** bill length (to nearest 0.1 mm) **Tarsus** diagonal tarsus
 length (to nearest 0.1 mm) \--- SCRIPTS --- *Taimyr_analyses.R* This
 script uses data files 1 - 9 and 12 to calculate growth curves of chicks,
 their hatch date relative to snow melt and links their diet to data on
 available arthropods (from pitfall traps). It also connects to data on
 stable isotopes in feathers and temperature data. At the end of the
 script, supplemental analyses are included supporting the supplemental
 text on sex-specific growth curve effects. *Tipulidae_traps.R* This script
 uses data files 4 - 6 to calculate the date at which peak numbers of
 Tipulidae are found in pitfall traps, relative to the date of snowmelt,
 and to generate figure 3a. *SI mixing model script.R* This script uses
 data files 2, 11 and 12 to construct stable-isotope mixing models using
 simmr to estimate the proportion of crane flies consumed by red knots. The
 first part uses primary coverts (feathers) from juveniles, collected in
 Mauritania, and the second part uses body feathers from chicks, collected
 in Taimyr. The sources for the model are 7 insect families, that are most
 consumed by chicks in Taimyr (based on DNA barcoding of feces).
 *Structural_Equation_Model.R* This script uses data files 10 and 12 to
 analyze the data using structural equation models. *MAIN.R* This script
 contains all of the statistical tests and is used to generate the main
 figures (with the exception of figure 3a, which is generated in script
 Tipulidae_traps.R) *Adult_analysis.R* This script uses data files 12 and
 14 to analyze body size changes in adult and juvenile red knots.