Data and code from: Large-scale source-sink dynamics in Tachycineta bicolor breeding in nest-boxes across eastern Canada's farmlands
Data files
Feb 10, 2026 version files 219.21 KB
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CMRdata.Rdata
165.97 KB
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DataCMR_csv.zip
30.36 KB
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README.md
3.04 KB
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ReadMe.txt
2.83 KB
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S3_Rscript_CMR.R
13.79 KB
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S4_Rscript_CrossVal.R
3.23 KB
Abstract
Many wild species are declining due to human driven environmental changes, including landscape transformation due to agricultural intensification. This is especially true for insects and their avian predators worldwide. To understand how populations respond to human-induced environmental changes, detailed data on survival, reproduction and dispersal are essential especially in declining populations where immigration can buffer local declines. We used multi-state Capture-Mark-Recapture (CMR) models and 14 years of data (2006-2019) on individually marked Tree Swallows (Tachycineta bicolor (Vieillot, 1808)) breeding on farmlands in southern Québec, Canada, to quantify the effects of agricultural intensity, local weather, and interspecific competition on vital rates and population growth. Annual population growth rates were strongly influenced by immigration and adult return rates. Nest site competition from House Sparrows (Passer domesticus (Linnaeus, 1758)), primarily present in intensively cultivated landscapes, was the main factor driving the observed decline in productivity and adult return rates. Our results suggest that intensively cultivated farmlands act as population sinks, making them unsustainable for Tree Swallows without immigration. Our findings highlight the importance of considering both landscape context and population connectivity when assessing demographic processes. They also underscore the need to study multiple populations over large geographic regions to identify drivers of large-scale declines.
by Le Vaillant, Justine, Pigeon, Gabriel, Houle, Carolyne, Garant Dany, Bélisle, Marc & Pelletier, Fanie, in Canadian Journal of Zoology, 2026
Data
Code for conducting CMR analysis of survival and reproduction of tree swallows in southern Quebec, given their environment
Corresponding authors
Fanie Pelletier - Université de Sherbrooke - fanie.pelletier@usherbrooke.ca
Gabriel Pigeon - Université du Québec en Abitibi-Témiscamingue - gabriel.pigeon@uqat.ca
File list
- ReadMe.txt: current file
- CMRdata.Rdata : all data used
- DataCMR_csv.zip: content of the above Rdata, but transformed into csv tables for compatibility
- S3_Rscript_CMR.R: script to run the model
- S4_Rscript_CrossVal.R: script used for cross-validation
Data Description
Const (list)
- nb.t: number of years (14)
- nb.id: number of marked individual (6677)
- age: matrix of age class (1: nestling,2:Second years, 3: after second year) [ID, year]
- DF: constant used in scaled inverse-wishart prior
- zero: vector of 0s . means of the multivariate normal distributions used for random effects
- first: time of first capture for all individuals
- firstMat: same as first, but filtered to remove ids of nestlings that never returned.
- iMat: vector of index for individuals in firstMat
- nb.mat: length of iMat (2056)
- W: identity matrix
- nb.farm: number of farms (40)
- D: matrix of distance between farms (in km)
- Dsq: square root of D
Dat (list)
- obs: observation matrix [ID, year]: 1 = seen & no reproductive success, 2 = seen & sucessfully reproduced, 3 = not Seen
- state: Matrix of known states [ID,year]: 0 = unborn, 1 = no reproductive success, 2 = sucessfully reproduced, 3 = dead, NA = unknown
- nbFledge: Matrix of the number of nestling that fledged [ID, year]
- imi: matrix of the number of immigrant females of age class second year (first colomn) and after second year (second colomn) per year (rows)
- farm: matrix [ID, year] of the farm where the individual was captured or recaptured
- x.farmYrEnv: array of environmental variables [farm, year, variable]
all variables were standardized.
variables:
- meanTemp.rearing: mean temperature during rearing period
- precip.rearing: total precipitation duriong rearing periode
- coldSnap.rearing: number of cold snaps during rearing period
- hosp: number of nestbox on farm with house sparrow occupation
- IA: index of agricultural intesification
- prec:cold: product of precip.rearing and coldSnap.rearing
- prec:IA: product of precip.rearing and IA
- IA:cold: product of IA and coldSnap.rearing
- triple product of IA, coldSnap.rearing and precip.rearing
envScalingPar (data.frame)
useful to back transform to original scale
- var: environmental variable
- mean: mean used during the standardization
- sd: sd used during the standardization
