A framework for estimating the determinants of spatial and temporal variation in vital rates and inferring the occurrence of unobserved extreme events

We develop a general framework that combines long-term tag–recapture data and powerful statistical and modelling techniques to investigate how population, environmental and climate factors determine variation in vital rates and population dynamics in an animal species, using as a case study the population of brown trout living in Upper Volaja (Western Slovenia). This population has been monitored since 2004. Upper Volaja is a sink, receiving individuals from a source population living above a waterfall. We estimate the numerical contribution of the source population on the sink population and test the effects of temperature, population density and extreme events on variation in vital rates among 2647 individually tagged brown trout. We found that individuals dispersing downstream from the source population help maintain high population densities in the sink population despite poor recruitment. The best model of survival for individuals older than juveniles includes additive effects of birth cohort and sampling occasion. Fast growth of older cohorts and higher population densities in 2004–2005 suggest very low population densities in the late 1990s, which we hypothesize were caused by a flash flood that strongly reduced population size and created the habitat conditions for faster individual growth and transient higher population densities after the extreme event.


Figure S1
Title: Maximum annual rainfall. Legend: Maximum annual rainfall recorded in the rainfall station closest to Upper Volaja (Kobarid) along with loess smoothing (gray area delimits 95% CI). Maximum daily rainfall was recorded on November 7 th 1997. Daily rainfall similar to that of 1997 was recorded on December 25 th 2009 (247 mm)

Figure S2
Title: Boxplots of water temperature. Legend: Boxplots of water temperature recorded (by month) in Upper Volaja between 2004 and 2014. Dashed lines enclose the range of temperatures allowing growth and the thick solid line identifies the temperature for maximum growth according to Elliott et al. (1995).

Figure S3
Title: Individual growth trajectories. Legend: Individual growth trajectories of brown trout and prediction of the growth model of growth trajectory of the average fish in Eq. (2) in the main text (see Avg in Table ESM 6).

Figure S4
Title: Partial effects on growth. Legend: Partial effects on growth between sampling occasions (mm day -1 ) of L and GDDs-by-Season as predicted by the best GAMM model.  Legend: Estimates of number and density of fish alive, and probability of capture in each Year and Month for fish aged 0+ (0) or 1+ and older (1). P_Est, P_Se = point estimate and standard error of probability of capture; N_Obs = number of fish sampled; N_Est, N_LCI, N_UCI = point estimate and lower and upper 95% CI of number of fish. D_Est, D_LCI, D_UCI = point estimate and lower and upper 95% CI of density of fish (fish ha -1 ). There was complete recruitment failure in 2014.

Table S4
Title: Proportion of "late incomers". Legend: Proportion of "late incomers" present in the population each year in September. We applied the same ratio of "late incomers" to total number of fish found for cohorts born after the start of sampling to cohorts born before the start of sampling (from 2000 to 2003). Early.inc = "early incomers", i.e. fish that were either born in Upper Volaja or came into Upper Volaja before age 1+ in September. FP_Coh = number of fish from cohorts born before the start of sampling. N.tot = total number of fish aged 1+ or older sampled each Septebmer. Late.inc = "late incomers", i.e. fish that were born in AW and came into Upper Volaja when 1+ in September or older. Prop.late.inc = proportion of "late incomers" in Upper Volaja each year in September.

Table S5
Title: vBGF parameters. Legend: Predictors of vBGF parameters and k (Constant = no predictors except for individual random effects), number of parameters, and AIC of the tested growth models (dataset Data W ; only September data).
Text S1 Title: Estimating the proportion of "early incomers" and "late incomers" Legend: Not applicable.
Text S2 Title: Details on estimation of growth models Legend: Not applicable.
Text S3 Title: Details on survival models for tagged individuals Legend: Not applicable.
Text S4 Title: Details on survival models for juveniles Legend: Not applicable.