DOI: 10.5061/dryad.k98sf7mn6
title: Data and code from: Large-scale source-sink dynamics in <em>Tachycineta bicolor</em> breeding in nest-boxes across eastern Canada's farmlands

description: 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.
description: # Code and data from: Large-scale source-sink dynamics in Tachycineta
 bicolor breeding in nest-boxes across eastern Canada's farmlands 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](mailto:fanie.pelletier@usherbrooke.ca)
 Gabriel Pigeon - Université du Québec en Abitibi-Témiscamingue -
 [gabriel.pigeon@uqat.ca](mailto: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