Water availability drives instream conditions and life-history of an imperiled desert fish: A case study to inform water management.

In arid ecosystems, available water is a critical, yet limited resource for human consumption, agricultural use, and ecosystem processes-highlighting the importance of developing management strategies to meet the needs of multiple users. Here, we evaluated how water availability influences stream thermal regimes and life-history expressions of Lahontan cutthroat trout (Oncorhynchus clarkii henshawi) in the arid Truckee River basin in the western United States. We integrated air temperature and stream discharge data to quantify how water availability drives stream temperature during annual spawning and rearing of Lahontan cutthroat trout. We then determined how in situ stream discharge and temperature affected adult spawning migrations, juvenile growth opportunities, and duration of suitable thermal conditions. Air temperatures had significant, large effects (+) on stream temperature across months; the effects of discharge varied across months, with significant effects (-) during May through August, suggesting increased discharge can help mitigate temperatures during seasonally warm months. Two models explained adult Lahontan cutthroat trout migration, and both models indicated that adult Lahontan cutthroat trout avoid migration when temperatures are warmer (~ > 12 °C) and discharge is higher (~ > 50 m3*s-1). Juvenile size was best explained by a quadratic relationship with cumulative degree days (CDD; days>4 °C) as size increased with increasing CDDs but decreased at higher CDDs. We also found an interaction between CDDs and discharge explaining juvenile size: when CDDs were low, higher discharge was associated with larger size, but when CDDs were high, higher discharge was associated with smaller size. Stream temperatures also determined the duration of juvenile rearing, as all juvenile emigration ceased at temperatures >24.4 °C. Together, our results illustrated how stream discharge and temperature shape the life-history of Lahontan cutthroat trout at multiple stages and can inform management actions to offset warming temperatures and facilitate life-history diversity and population resilience.

Assessing thermal adaptation using family-based association and FST outlier tests in a threatened trout species.

Discovering genetic markers associated with phenotypic or ecological characteristics can improve our understanding of adaptation and guide conservation of key evolutionary traits. The Lahontan cutthroat trout (Oncorhynchus clarkii henshawi) of the northern Great Basin Desert, USA, demonstrated exceptional tolerance to high temperatures in the desert lakes where it resided historically. This trait is central to a conservation hatchery effort to protect the genetic legacy of the nearly extinct lake ecotype. We genotyped full-sibling families from this conservation broodstock and samples from the only two remaining, thermally distinct, native lake populations at 4,644 new single nucleotide polymorphisms (SNPs). Family-based genome-wide association testing of the broodstock identified nine and 26 SNPs associated with thermal tolerance (p < 0.05 and p < 0.1), measured in a previous thermal challenge experiment. Genes near the associated SNPs had complex functions related to immunity, growth, metabolism and ion homeostasis. Principal component analysis using the thermotolerance-related SNPs showed unexpected divergence between the conservation broodstock and the native lake populations at these loci. FST outlier tests on the native lake populations identified 18 loci shared between two or more of the tests, with two SNPs identified by all three tests (p < 0.01); none overlapped with loci identified by association testing in the broodstock. A recent history of isolation and the complex genetic and demographic backgrounds of Lahontan cutthroat trout probably limited our ability to find shared thermal tolerance loci. Our study extends the still relatively rare application of genomic tools testing for markers associated with important phenotypic or environmental characteristics in species of conservation concern.

Hierarchical multi-population viability analysis.

Population viability analysis (PVA) uses concepts from theoretical ecology to provide a powerful tool for quantitative estimates of population dynamics and extinction risks. However, conventional statistical PVA requires long-term data from every population of interest, whereas many species of concern exist in multiple isolated populations that are only monitored occasionally. We present a hierarchical multi-population viability analysis model that increases inference power from sparse data by sharing information among populations to assess extinction risks while accounting for incomplete detection and sampling biases with explicit observation and sampling sub-models. We present a case study in which we customized this model for historical population monitoring data (1985-2015) from federally threatened Lahontan cutthroat trout populations in the Great Basin, USA. Data were counts of fish captured during backpack electrofishing surveys from locations associated with 155 isolated populations. Some surveys (25%) included multi-pass removal sampling, which provided valuable information about capture efficiency. GIS and remote sensing were used to estimate August stream temperatures, peak flows, and riparian vegetation condition in each population each year. Field data were used to derive an annual index of nonnative trout densities. Results indicated that population growth rates were higher in colder streams and that nonnative trout reduced carrying capacities of native trout. Extinction risks increased with more environmental stochasticity and were also related to population extent, water temperatures, and nonnative densities. We developed a graphical user interface to interact with the fitted model results and to simulate future habitat scenarios and management actions to assess their influence on extinction risks in each population. Hierarchical multi-population viability analysis bridges the gap between site-level field observations and population-level processes, making effective use of existing datasets to support management decisions with robust estimates of population dynamics, extinction risks, and uncertainties.

Return of a giant: DNA from archival museum samples helps to identify a unique cutthroat trout lineage formerly thought to be extinct.

Currently one small, native population of the culturally and ecologically important Lahontan cutthroat trout (Oncorhynchus clarkii henshawi, LCT, Federally listed) remains in the Truckee River watershed of northwestern Nevada and northeastern California. The majority of populations in this watershed were extirpated in the 1940s due to invasive species, overharvest, anthropogenic water consumption and changing precipitation regimes. In 1977, a population of cutthroat trout discovered in the Pilot Peak Mountains in the Bonneville basin of Utah, was putatively identified as the extirpated LCT lacustrine lineage native to Pyramid Lake in the Truckee River basin based on morphological and meristic characters. Our phylogenetic and Bayesian genotype clustering analyses of museum specimens collected from the large lakes (1872-1913) and contemporary samples collected from populations throughout the extant range provide evidence in support of a genetically distinct Truckee River basin origin for this population. Analysis of museum samples alone identified three distinct genotype clusters and historical connectivity among water bodies within the Truckee River basin. Baseline data from museum collections indicate that the extant Pilot Peak strain represents a remnant of the extirpated lacustrine lineage. Given the limitations on high-quality data when working with a sparse number of preserved museum samples, we acknowledge that, in the end, this may be a more complicated story. However, the paucity of remnant populations in the Truckee River watershed, in combination with data on the distribution of morphological, meristic and genetic data for Lahontan cutthroat trout, suggests that recovery strategies, particularly in the large lacustrine habitats should consider this lineage as an important part of the genetic legacy of this species.