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1. Variable hybridization outcomes in trout are predicted by historical fish stocking and environmental context

   https://doi.org/10.1111/mec.15175  

   Mandeville, Elizabeth G. ; Walters, Annika W. ; Nordberg, Brittany J. ; Higgins, Karly H. ; Burckhardt, Jason C. ; Wagner, Catherine E. ( August 2019 , Molecular Ecology)

   Hybridization can profoundly affect the genomic composition and phenotypes of closely related species, and provides an opportunity to identify mechanisms that maintain reproductive isolation between species. Recent evidence suggests that hybridization outcomes within a species pair can vary across locations. However, we still do not know how variable outcomes of hybridization are across geographic replicates, and what mechanisms drive that variation. In this study, we described hybridization outcomes across 27 locations in the North Fork Shoshone River basin (Wyoming, USA) where native Yellowstone cutthroat trout and introduced rainbow trout co‐occur. We used genomic data and hierarchical Bayesian models to precisely identify ancestry of hybrid individuals. Hybridization outcomes varied across locations. In some locations, only rainbow trout and advanced backcrossed hybrids towards rainbow trout were present, while trout in other locations had a broader range of ancestry, including both parental species and first‐generation hybrids. Later‐generation intermediate hybrids were rare relative to backcrossed hybrids and rainbow trout individuals. Using an individual‐based simulation, we found that outcomes of hybridization in the North Fork Shoshone River basin deviate substantially from what we would expect under null expectations of random mating and no selection against hybrids. Since this deviation implies that some mechanisms of reproductive isolation function to maintain parental taxa and a diversity of hybrid types, we then modelled hybridization outcomes as a function of environmental variables and stocking history that are likely to affect prezygotic barriers to hybridization. Variables associated with history of fish stocking were the strongest predictors of hybridization outcomes, followed by environmental variables that might affect overlap in spawning time and location.

    

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2. Multiple lines of evidence reveal complex rainbow trout responses to stream habitat enhancements

   https://doi.org/10.1111/fwb.13592  

   Collins, Scott F. ; Baxter, Colden V. ( July 2020 , Freshwater Biology)

   Habitat enhancements seek to ameliorate the detrimental effects of environmental degradation and take many forms, but usually entail structural (e.g. logs, cribs, reefs) or biogenic (e.g. carrion additions, vegetation plantings, fish stocking) augmentations with the intent of increasing fish annual production (i.e. accrual of new fish biomass through time). Whether efforts increase fish production or simply attract fish has long been subject to debate.

   Streams of the Pacific Northwest are commonly targeted for habitat enhancements to mitigate for the detrimental effects of dams and other forms of habitat degradation on Pacific salmon. Nutrient mitigation (i.e. the practice of artificially fertilising freshwaters) is a form of biogenic habitat enhancement that attempts to mimic the enrichment effects of a natural Pacific salmon spawning event. This approach assumes nutrient augmentations alleviate nutrient limitation of primary producers and/or food limitation of primary and secondary consumers, culminating in increased fish production.

   We conducted a multi‐year manipulative experiment and tracked responses of interior rainbow trout (Oncorhynchus mykiss) to annual additions of Pacific salmon carcasses as part of an effort to enhance the productivity of salmonid populations in streams where salmon runs have been lost. We employed an integrated approach to partition the mechanisms driving numerical responses of trout populations across timescales, to assess population turnover, and to track responses to habitat enhancements across individual to population level metrics.

   Short‐term numerical increases by trout were shaped by immigration and subsequently via retention of individuals within treatment reaches. As trout moved into treated stream reaches, individuals foraged, grew, and subsequently moved to other locations such that short‐term increases in fish numbers did not persist from year to year. All told, additions of salmon carcasses alleviated apparent food limitation and thereby increased secondary production of rainbow trout. However, at an annual time scale, increased production manifested as larger individual fish, not more fish within treated reaches. Fish movements and high population turnover within treated stream reaches apparently led to the subsequent dispersal of increased fish production.

   We found multiple lines of evidence that indicated that annual additions of salmon carcasses aggregated rainbow trout and enhanced their annual production. Through this replicated management experiment, we documented dynamic individual and population level responses to a form of stream habitat manipulation across weekly and annual timescales.

    

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3. Parallel introgression and selection on introduced alleles in a native species

   https://doi.org/10.1111/mec.15097  

   Bay, Rachael A. ; Taylor, Eric B. ; Schluter, Dolph ( June 2019 , Molecular Ecology)

   As humans cause the redistribution of species ranges, hybridization between previously allopatric species is on the rise. Such hybridization can have complex effects on overall fitness of native species as new allelic combinations are tested. Widespread species introductions provide a unique opportunity to study selection on introgressed alleles in independent, replicated populations. We examined selection on alleles that repeatedly introgressed from introduced rainbow trout (Oncorhynchus mykiss) into native westslope cutthroat trout (Oncorhynchus clarkii lewisi) populations in western Canada. We found that the degree of introgression of individual single nucleotide polymorphisms from the invasive species into the native is correlated between independent watersheds. A number of rainbow trout alleles have repeatedly swept to high frequency in native populations, suggesting parallel adaptive advantages. Using simulations, we estimated large selection coefficients up to 0.05 favoring several rainbow trout alleles in the native background. Although previous studies have found reduced hybrid fitness and genome‐wide resistance to introgression in westslope cutthroat trout, our results suggest that some introduced genomic regions are strongly favored by selection. Our study demonstrates the utility of replicated introductions as case studies for understanding parallel adaptation and the interactions between selection and introgression across the genome. We suggest that understanding this variation, including consideration of beneficial alleles, can inform management strategies for hybridizing species.

    

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4. A new genomic resource to enable standardized surveys of SNPs across the native range of brook trout ( Salvelinus fontinalis )

   https://doi.org/10.1111/1755-0998.13853  

   Mamoozadeh, Nadya R. ; Whiteley, Andrew R. ; Letcher, Benjamin H. ; Kazyak, David C. ; Tarsa, Charlene ; Meek, Mariah H. ( August 2023 , Molecular Ecology Resources)

   Understanding how genetic diversity is distributed across spatiotemporal scales in species of conservation or management concern is critical for identifying large‐scale mechanisms affecting local conservation status and implementing large‐scale biodiversity monitoring programmes. However, cross‐scale surveys of genetic diversity are often impractical within single studies, and combining datasets to increase spatiotemporal coverage is frequently impeded by using different sets of molecular markers. Recently developed molecular tools make surveys based on standardized single‐nucleotide polymorphism (SNP) panels more feasible than ever, but require existing genomic information. Here, we conduct the first survey of genome‐wide SNPs across the native range of brook trout (Salvelinus fontinalis), a cold‐adapted species that has been the focus of considerable conservation and management effort across eastern North America. Our dataset can be leveraged to easily design SNP panels that allow datasets to be combined for large‐scale analyses. We performed restriction site‐associated DNA sequencing for wild brook trout from 82 locations spanning much of the native range and domestic brook trout from 24 hatchery strains used in stocking efforts. We identified over 24,000 SNPs distributed throughout the brook trout genome. We explored the ability of these SNPs to resolve relationships across spatial scales, including population structure and hatchery admixture. Our dataset captures a wide spectrum of genetic diversity in native brook trout, offering a valuable resource for developing SNP panels. We highlight potential applications of this resource with the goal of increasing the integration of genomic information into decision‐making for brook trout and other species of conservation or management concern.

    

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5. Functional traits and drought strategy predict leaf thermal tolerance

   https://doi.org/10.1093/conphys/coad085  

   Valliere, Justin M. ; Nelson, Kekoa C. ; Martinez, Marco Castañeda ; Tomlinson, ed., Sean ( November 2023 , Conservation Physiology)

   Heat stress imposes an important physiological constraint on native plant species—one that will only worsen with human-caused climate change. Indeed, rising temperatures have already contributed to large-scale plant mortality events across the globe. These impacts may be especially severe in cities, where the urban heat island effect amplifies climate warming. Understanding how plant species will respond physiologically to rising temperatures and how these responses differ among plant functional groups is critical for predicting future biodiversity scenarios and making informed land management decisions. In this study, we evaluated the effects of elevated temperatures on a functionally and taxonomically diverse group of woody native plant species in a restored urban nature preserve in southern California using measurements of chlorophyll fluorescence as an indicator of leaf thermotolerance. Our aim was to determine if species’ traits and drought strategies could serve as useful predictors of thermotolerance. We found that leaf thermotolerance differed among species with contrasting drought strategies, and several leaf-level functional traits were significant predictors of thermotolerance thresholds. Drought deciduous species with high specific leaf area, high rates of transpiration and low water use efficiency were the most susceptible to heat damage, while evergreen species with sclerophyllous leaves, high relative water content and high water use efficiency maintained photosynthetic function at higher temperatures. While these native shrubs and trees are physiologically equipped to withstand relatively high temperatures in this Mediterranean-type climate, hotter conditions imposed by climate change and urbanization may exceed the tolerance thresholds of many species. We show that leaf functional traits and plant drought strategies may serve as useful indicators of species’ vulnerabilities to climate change, and this information can be used to guide restoration and conservation in a warmer world.

    

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