Estimating Cohort Survival through Tributaries for Salmonid Populations with Variable Ages at Migration

Abstract

Survival of juvenile anadromous Pacific salmonids from their earliest age of seaward movement ("outmigration") through the tributaries that connect their rearing grounds to larger-order rivers ("cohort survival") is an important yet often unmonitored factor in the complex life history of these species. Populations with variable age at out-migration (e.g., steelhead Oncorhynchus mykiss) or multiple juvenile rearing strategies (e.g., Chinook Salmon O. tshawytscha) raise particular challenges in survival monitoring. A multiple-state release-recapture model is presented to estimate cohort survival for salmonid species with variable age at out-migration and demonstrated in two case studies. Annual releases of fish tagged with passive integrated transponder (PIT) tags from the same brood year (cohort) and their detections by instream PIT-tag detection arrays in tributaries and at hydroelectric dams are used to estimate survival through tributaries and the age composition of juvenile migrants reaching downstream sites. The 2010 cohort of Chinook Salmon from the Chiwawa River in Washington State had estimated survival of 0.59 to the middle Wenatchee River array in Tumwater Dam Reservoir (river distance of 30 km) and 0.12 to McNary Dam (364 km) on the Columbia River. The age composition shifted from 60.1% subyearlings at the Wenatchee River array to 100% yearlings at McNary Dam, reflecting the use of the Wenatchee River as a nonnatal rearing area, whereas McNary Dam is in the migratory corridor. The 2010 cohort of steelhead from the Twisp River in Washington State had estimated survival from the yearling stage of 0.30 to Rocky Reach Dam (146 km from the Twisp River mouth) on the Columbia River and 0.17 to McNary Dam (439 km). The low survival to the Columbia River resulted from both mortality and adoption of a resident life history and reflects the diverse population structure in the Twisp River.

Migration and survival of Okanagan River Sockeye Salmon Oncorhynchus nerka, 2012–2019

“…Sockeye Salmon smolts emigrating from Cultus Lake in the unimpounded Fraser River have considerably lower survival rates of ≈ 50 to 70% per 100 km over 4 years of monitoring, though different technologies were used in the evaluation [65]. Other salmonids in the region also have lower smolt survival in mainstem [68] or tributary habitats [6]. While these estimates are not directly comparable, they do suggest that Okanagan Sockeye have relatively high rates of survival during the juvenile outmigration.…”

Generation of multistate release–recapture models using a graphic user interface (GUI)

“…Buchanan et al [21] used a three-dimensional multistate model to describe the downriver migration of juvenile steelhead over multiple age classes that included possible residualization as they migrated to the ocean. The current version of Program Branch can be used to depict the fully parameterized model of Buchanan et al [21] but not special cases where parameter values are shared across release groups. Refinements to Program Branch will permit setting migration and/or detection parameters common across migrant groups.…”

“…Steelhead (anadromous Rainbow Trout Oncorhynchus mykiss) in the Columbia River Basin are listed as threatened under the Endangered Species Act of 1973, and their juvenile seaward migrations have been studied for years using passive integrated transponder (PIT) tags [21,[31][32][33]. Recently focus has shifted to the adult spawning migration.…”

“…Perry et al [19] and Buchanan et al [20] have used multistate models to characterize survival through the complex migration pathways in the Sacramento-San Joaquin River Delta of California for juvenile Chinook salmon and steelhead (Oncorhynchus mykiss). Buchanan et al [21] also estimated in-stream survival of juvenile steelhead that migrate through tributaries between 1 and 6 years of age using multistate models.…”

A Bayesian nested patch occupancy model to estimate steelhead movement and abundance

“…However, existing approaches are limited in their ability to deal with complex spatial structure (e.g., multiple levels of nested patches) when implemented in a Bayesian framework. Previous researchers have modeled the movement of tagged animals in a nested spatial structure; however, these works use a maximum likelihood framework and are limited in spatial complexity relative to the model we propose (Buchanan and Skalski 2010, Buchanan et al 2015).…”