DOI: 10.5061/dryad.jm63xsj6t
title: Spatial covariation of fish population vital rates in a stream network

description: Animal populations are spatially structured in heterogeneous landscapes,
 in which local patches with differing vital rates are connected by
 dispersal of individuals to varying degrees. Although there is evidence
 that vital rates differ among local populations, much less is understood
 about how vital rates covary among local patches in spatially
 heterogeneous landscapes. In this study, we conducted a 9-year annual
 mark-recapture survey to characterize spatial covariation of survival and
 growth for two Japanese native salmonids, white-spotted charr (Salvelinus
 leucomaenis japonicus) and red-spotted masu salmon (Oncorhynchus masou
 ishikawae), in a headwater stream network composed of distinctly different
 tributary and mainstem habitats. Spatial structure of survival and growth
 differed by species and age class, but results provided support for
 negative covariation between vital rates, where survival was higher in the
 tributary habitat but growth was higher in the mainstem habitat. Thus,
 neither habitat was apparently more important than the other, and local
 habitats with complementary vital rates may make this spatially structured
 population less vulnerable to environmental change (i.e., portfolio
 effect). Despite the spatial structure of vital rates and possibilities
 that fish can exploit spatially distributed resources, movement of fish
 was limited due partly to a series of low-head dams that prevented
 upstream movement of fish in the study area. This study shows that spatial
 structure of vital rates can be complex and depend on species and age
 class, and this knowledge is likely paramount to elucidating dynamics of
 spatially structured populations.
description: Field surveys
 were conducted annually (the third weekend of October) in 2009–2017. Fish
 were captured using a backpack electrofishing unit (300–400 V DC, model
 12B or LR20, Smith-Root, Inc., Vancouver, WA, USA) and 3-mm mesh dip nets.
 Two passes of electrofishing were conducted for fish density estimates of
 each section with a depletion method (Zippen 1958). Captured fish were
 anaesthetised with phenoxyethanol (ca. 0.5 ml/L water), measured for fork
 length (FL: nearest 1 mm), and were marked individually with visible
 implant elastomer tags (Northwest Marine Technology Inc., WA, USA) or
 their individual code was recorded if recaptured. A unique combination of
 four elastomer colours were subcutaneously administered to the forehead of
 each individual. All captured fish with FL &gt; 43 mm were marked.
 During each year of the study, juveniles (young-of-the-year, YOY) and
 adults (age 1+ and older) were distinguished based on
 length-frequency histograms. For individuals which cannot be assigned to
 an age class due to their intermediate body size, a few scales were taken
 using a scalpel and the annuli were counted. All fish were returned alive
 to the capture site (&lt; 20 m for mainstem, &lt; 40 m for
 tributaries) after recovering from anaesthesia. All captured individuals
 retained at least two of the four elastomer colours, and were marked again
 with the lost colour(s). We identified all individuals uniquely based on
 species, sex, body size, and study section at mark (i.e., asymmetrical
 movement at dams).
description: A multi-state Cormack-Jolly-Seber (CJS) model was developed to infer state-specific annual survival, capture and transition probabilities for charr and salmon. States were defined based on age (juveniles and adults) and location (tributary, mainstem connected, and mainstem fragmented). Because locations were considered states, the state-transition probability referred to the movement probability among locations, which varied by age. To account for imperfect recapture of individuals, a state-space model was developed, composed of an ecological model following the state transitions over time and an observation model linking the true states to observed data. Data were formatted in a two-dimensional array (<i>y<sub>i,t</sub></i>), where rows indicated individuals (<i>i</i>) and columns indicated annual sampling occasions (<i>t</i>). Elements of the array were observed states defined by age and location. A unique combination of ages (juvenile and adult) and locations (tributary, mainstem connected and mainstem fragmented) resulted in six states (1 = juveniles in tributary; 2 = juveniles in mainstem connected; 3 = juveniles in mainstem fragmented; 4 = adults in tributary; 5 = adults in mainstem connected; and 6 = adults in mainstem fragmented). In addition, sampling occasions on which individuals were not detected were coded as 7. Prior to fitting multi-state CJS models to data, we used the R2ucare package (Gimenez et al. 2018) to confirm that there was no evidence for trap-dependence (p &gt; 0.27), transience (p = 1.00), and memory of past states (p &gt; 0.35) in either charr or salmon.