Demand-resource mismatch explains body shrinkage in a migratory shorebird
Data files
Apr 04, 2025 version files 61.15 MB
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1._chicks.csv
37.14 KB
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10._snowmelt_Taimyr.csv
58.88 MB
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11._isotopes_arthropods_Taimyr.csv
2.10 KB
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12._juveniles_Mauritania.csv
44.63 KB
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13._chicks_data.csv
286.26 KB
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14._adults_Mauritania.csv
69.87 KB
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2._SI_data_Taimyr.csv
1.40 KB
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3._Barcoding_Taimyr.csv
13.81 KB
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4._pitfall_arthropod_specimens_Taimyr.csv
291.28 KB
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5._pitfall_station_metadata_Taimyr.csv
2.90 KB
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6._pitfall_status_Taimyr.csv
45.84 KB
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7._biomass_length_Taimyr.csv
1.84 KB
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8._snowmelt_Knipovich.csv
102 B
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9._temperature_Knipovich.csv
1.46 MB
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README.md
14.09 KB
Abstract
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.
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:
- chicks.csv
- SI_data_Taymyr.csv
- Barcoding_Taymyr.csv
- pitfall_arthropod_specimens_Taymyr.csv
- pitfall_station_metadata_Taymyr.csv
- pitfall_status_Taymyr.csv
- biomass_length_Taymyr.csv
- snowmelt_Knipovich.csv
- temperature_Knipovich.csv
- snowmelt_Taimyr.csv
- isotopes_arthropods_Taimyr.csv
- juveniles_Mauritania.csv
- chicks_data.csv
- adults_Mauritania.csv
Scripts include:
- Taimyr_analyses.R
- Tipulidae_traps.R
- SI mixing model script.R
- Structural_Equation_Model.R
- MAIN.R
- 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.