As rivers warm, cold‐water fish species may alleviate thermal stress by moving into localized thermal refuges such as cold‐water plumes created by cool tributary inflows. We quantified use of two tributary confluence plumes by juvenile steelhead,Oncorhynchus mykiss, throughout the summer, including how trout positioned themselves in relation to temperature within confluence plumes. At two confluences, Cedar and Elder creeks, along the South Fork Eel River, California, USA, we monitored temperatures using in situ logger grids throughout summer 2016. Fish were counted within confluences via snorkel surveys five times a day on 5 days at each site. We found diel and seasonal dependence on confluence use by steelhead, especially at the Cedar Creek confluence, where mainstem temperatures exceeded 28°C. At this site, fish moved into the confluence on the warmest days and warmest times of the day. Fish observed within the Cedar Creek confluence plume were most common in locations between 20–22°C, rather than the coldest locations (14.5°C). At Elder Creek, where mainstem temperatures remained below 24°C, there was little relationship between mainstem temperature and steelhead presence in the confluence plume. At both sites, steelhead distribution within plumes was influenced by spatial variation of temperature and mean temperature in surveyed grid cells. Our results show that cool tributaries flowing into warmer mainstem reaches (over 24°C) likely create important thermal refuges for juvenile steelhead. As mainstem rivers warm with climate change, cool‐water tributary inputs may become more important for sustaining cold‐water salmonids near the southern end of their range.

Landscape permeability is often explored spatially, but may also vary temporally. Landscape permeability, including partial barriers, influences migratory animals that move across the landscape. Partial barriers are common in rivers where barrier passage varies with streamflow. We explore the influence of partial barriers on the spatial and temporal distribution of migration‐linked genotypes ofOncorhynchus mykiss, a salmonid fish with co‐occurring resident and migratory forms, in tributaries to the South Fork Eel River, California, USA, Elder and Fox Creeks. We genotyped >4,000 individuals using RAD‐capture and classified individuals as resident, heterozygous or migratory genotypes using life history‐associated loci. Across four years of study (2014–2017), the permeability of partial barriers varied across dry and wet years. In Elder Creek, the largest waterfall was passable for adults migrating up‐river 4–39 days each year. In this stream, the overall spatial pattern, with fewer migratory genotypes above the waterfall, remained true across dry and wet years (67%–76% of migratory alleles were downstream of the waterfall). We also observed a strong relationship between distance upstream and proportion of migratory alleles. In Fox Creek, the primary barrier is at the mouth, and we found that the migratory allele frequency varied with the annual timing of high flow events. In years when rain events occurred during the peak breeding season, migratory allele frequency was high (60%–68%), but otherwise it was low (30% in two years). We highlight that partial barriers and landscape permeability can be temporally dynamic, and this effect can be observed through changing genotype frequencies in migratory animals.

Environmental DNA (eDNA) metabarcoding approaches to surveillance have great potential for advancing biodiversity monitoring and fisheries management. For eDNA metabarcoding, having a genetic reference sequence identified to fish species is vital to reduce detection errors. Detection errors will increase when there is no reference sequence for a species or when the reference sequence is the same between different species at the same sequenced region of DNA. These errors will be acute in high biodiversity systems like the Mekong River Basin, where many fish species have no reference sequences and many congeners have the same or very similar sequences. Recently developed tools allow for inspection of reference database coverage and the sequence similarity between species. These evaluation tools provide a useful pre-deployment approach to evaluate the breadth of fish species richness potentially detectable using eDNA metabarcoding. Here we combined established species lists for the Mekong River Basin, resulting in a list of 1345 fish species, evaluated the genetic library coverage across 23 peer-reviewed primer pairs, and measured the species specificity for one primer pair across four genera to demonstrate that coverage of genetic reference libraries is but one consideration before deploying an eDNA metabarcoding surveillance program. This analysis identifies many of the eDNA metabarcoding knowledge gaps with the aim of improving the reliability of eDNA metabarcoding applications in the Mekong River Basin. Genetic reference libraries perform best for common and commercially valuable Mekong fishes, while sequence coverage does not exist for many regional endemics, IUCN data deficient, and threatened fishes.

Climate change is expected to increase weather extremes and variability, including more frequent weather whiplashes or extreme swings between severe drought and extraordinarily wet years. Shifts in precipitation patterns will alter stream flow regimes, affecting critical life history stages of sensitive aquatic organisms. Understanding how threatened fish species, such as steelhead/rainbow trout (Oncorhynchus mykiss), are affected by stream flows in years with contrasting environmental conditions is important for their conservation. Here, we report how extreme wet and dry years, from 2015 to 2018, affected stream flow patterns in two tributaries to the South Fork Eel River, California, USA, and aspects of O. mykiss ecology, including over‐summer fish growth and body condition as well as spring out‐migration timing. We found that stream flow patterns differed across years in the timing and magnitude of large winter–spring flow events and in summer low‐flow levels. We were surprised to find that differences in stream flows did not impact growth, body condition, or timing of out‐migration of O. mykiss. Fish growth was limited in the late summer in these streams (average of 0.02 ± 0.05 mm/d), but was similar across dry and wet years, and so was end‐of‐summer body condition and pool‐specific biomass loss from the beginning to the end of the summer. Similarly, O. mykiss migrated out of tributaries during the last week of March/first week of April regardless of the timing of spring flow events. We suggest that the muted response to inter‐annual hydrologic variability is due to the high quality of habitat provided by these unimpaired, groundwater‐fed tributaries. Similar streams that are likely to maintain cool temperatures and sufficient base flows, even in the driest years, should be a high priority for conservation and restoration efforts.

Migration is a complex trait that often has genetic underpinnings. However, it is unclear if migratory behaviour itself is inherited (direct genetic control), or if the decision to migrate is instead the outcome of a set of physiological traits (indirect genetic control). For steelhead/rainbow trout ( Oncorhynchus mykiss ), migration is strongly linked to a large genomic region across their range. Here, we demonstrate a shared allelic basis between early life growth rate and migratory behaviour. Next, we demonstrate that early life growth differs among resident/migratory genotypes in wild juveniles several months prior to migration, with resident genotypes achieving a larger size in their first few months of life than migratory genotypes. We suggest that the genetic basis of migration is likely indirect and mediated by physiological traits such as growth rate. Evolutionary benefits of this indirect genetic mechanism likely include flexibility among individuals and persistence of life-history diversity within and among populations.