Climate warming extends the breeding interval between migratory and resident birds with asymmetric effects on their reproduction

Description of the data and file structureFiles and variablesA: climate.csvThis file contains the climatic information for the study area, to be used for the climwin analysis.A_temp： average temperatureH_temp：stands for maximum temperatureL_temp：indicates minimum temperatureRain：represents rainfallDate: corresponds to the dateB: JT (first)_climwin.csvC: JT (second)_climwinD: YF_climwinThese files contain the first-egg date data for the Japanese Tit (first and second brooding) and Yellow-rumped flycatcher.Date: first-egg datelaydate: Number of days from April 1 to the first egg date.year: The year in which the first egg was laid.E: firstegg_response_climate_LMMThis file contains the first-egg dates for the first and second breeding attempts of the Japanese tit and for the Yellow-rumped flycatcher across multiple years. It is used to analyze the differences in their phenological sensitivity to temperature changesFirstEgg: Number of days from April 1 to the first egg date.year: The year in which the first egg was laid.species: "titfirst" denotes the first brooding of Japanese tit. "titsecond" denotes the second brooding of Japanese tit. "flycatcher" denotes the Yellow-rumped flycatcher. temp: average temperatureF: JT (first)_breeding_performanceG: JT (second)_breeding_performanceH: YF_breeding_performanceThese files are used to analyze the effects of clutch interval and population density on the reproductive performance of the Japanese tit's first and second broods and the Yellow-rumped flycatcher.success:​ Reproductive success rate for the Japanese tit's first brood (F), second brood (G), and the Yellow-rumped flycatcher (H), respectively.clutch_size:​ Clutch size (number of eggs laid per nest) for the Japanese tit's first brood (F), second brood (G), and the Yellow-rumped flycatcher (H), respectively.clutch_interval:​ Breeding interval (in days) between the Yellow-rumped flycatcher and the Japanese tit.DSQ_density:​ Nest density (number of active nests) of the Japanese tit's first brood.DSQ2_density:​ Nest density (number of active nests) of the Japanese tit's second brood.BMJW_density:​ Nest density (number of active nests) of the Yellow-rumped flycatcher.temperature_success:​ Mean temperature within the optimal climate window (identified via climwin analysis) for explaining the reproductive success rate of the Japanese tit's first brood (F), second brood (G), and the Yellow-rumped flycatcher (H), respectively.temperature_clutch_size:​ Mean temperature within the optimal climate window (identified via climwin analysis) for explaining the clutch size of the Japanese tit's first brood (F), second brood (G), and the Yellow-rumped flycatcher (H), respectively.Code/softwareR 4.2.1library(climwin)#read fileclimate<-read.csv(E:/climate/climate.csv)bioclimate<- read.csv(E:/climate/JT(first)_climwin.csv)bioclimate2<- read.csv(E:/climate/JT(second)_climwin.csv)bioclimate3<- read.csv(E:/climate/YF_climwin.csv)#Identify the optimal climate window for the first egg-laying date in a breeding attempt of the Japanese tit.Masswin<-slidingwin(exclude=c(15,0),xvar=list(Temp=as.numeric(climate$A_Temp)),cdate=factor(climate$Date),bdate=factor(bioclimate$Date.FirstEgg.Site),baseline=lm(as.numeric(laydate)~1,data=bioclimate),cinterval="day",range=c(60,0),type="absolute",refday=c(24,4),stat="mean",func="lin")#Identify the optimal climate window for the first egg-laying date of the Japanese tit's second breeding attempt.Masswin2<-slidingwin(exclude=c(15,0),xvar=list(Temp=as.numeric(climate$A_Temp)),cdate=factor(climate$Date),bdate=factor(bioclimate2$Date.FirstEgg.Site),baseline=lm(as.numeric(laydate)~1,data=bioclimate),cinterval="day",range=c(90,0),type="absolute",refday=c(3,6),stat="mean",func="lin")#Identify the optimal climate window for the first egg-laying date of the Yellow-rumped flycatcherMasswin2<-slidingwin(exclude=c(15,0),xvar=list(Temp=as.numeric(climate$A_Temp)),cdate=factor(climate$Date),bdate=factor(bioclimate2$Date.FirstEgg.Site),baseline=lm(as.numeric(laydate)~1,data=bioclimate),cinterval="day",range=c(60,0),type="absolute",refday=c(24,5),stat="mean",func="lin")#read filex<-read.csv("E:/climate/firstegg_response_climate_LMM.csv")#analyze species-specific sensitivity of first-egg dates to temperature changes within their optimal climate windowsA<-with(x,{data.frame(FirstEgg,year,species=factor(species),temp)})gm215<-lmer(FirstEgg~temp+species+species*temp+(1|year),data=A,REML=T,control=lmerControl(optimizer="bobyqa"))summary(gm215)#read fileJT<-read.csv("E:/climate/JT(first)_breeding_performance.csv")JT2<-read.csv("E:/climate/JT(second)_breeding_performance.csv")YF<-read.csv("E:/climate/YF_breeding_performance.csv")JT_A<-with(JT,{data.frame(DSQ_density,BMJW_density,clutch_size,clutch_interval,clutch_bird,success,year=factor(year),temperature_clutch,temperature_success)})JT2_A<-with(JT2,{data.frame(DSQ2_density,BMJW_density,clutch_size,clutch_interval,clutch_bird,success,year=factor(year),temperature_clutch,temperature_success)})YF_A<-with(YF,{data.frame(DSQ_density,DSQ2_density,BMJW_density,clutch_size,clutch_interval,clutch_bird,success,year=factor(year),temperature_clutch,temperature_success)})#Effect of egg-laying interval on breeding performance of Japanese tit (frist brooding)JT_success<-lmer(success~DSQ_density+BMJW_density+clutch_interval+temperature_success+(1|year),data=JT_A,REML=T,control=lmerControl(optimizer="bobyqa"))JT_clutch_size<-lmer(clutch_size~DSQ_density+BMJW_density+clutch_interval+temperature_clutch+(1|year),data=JT_A,REML=T,control=lmerControl(optimizer="bobyqa"))summary(JT_success)summary(JT_clutch_size)#Effect of egg-laying interval on breeding performance of Japanese tit (second brooding)JT2_success<-lmer(success~DSQ2_density+BMJW_density+clutch_interval+temperature_success+(1|year),data=JT2_A,REML=T,control=lmerControl(optimizer="bobyqa"))JT2_clutch_size<-lmer(clutch_size~DSQ2_density+BMJW_density+clutch_interval+temperature_clutch+(1|year),data=JT2_A,REML=T,control=lmerControl(optimizer="bobyqa"))summary(JT2_success)summary(JT2_clutch_size)#Effect of egg-laying interval on breeding performance of Yellow-rumped flycatcherJT_success<-lmer(succss~DSQ_density+BMJW_density+DSQ2_density+clutch_interval+temperature_success+(1|year),data=YF_A,REML=T,control=lmerControl(optimizer="bobyqa"))JT_clutch_size<-lmer(clutch_size~DSQ_density+BMJW_density+DSQ2_density+clutch_interval+temperature_clutch+(1|year),data=YF_A,REML=T,control=lmerControl(optimizer="bobyqa"))summary(YF_success)summary(YF_clutch_size)