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Males and females often differ in their fitness optima for shared traits that have a shared genetic basis, leading to sexual conflict. Morphologically differentiated sex chromosomes can resolve this conflict and protect sexually antagonistic variation, but they accumulate deleterious mutations. However, how sexual conflict is resolved in species that lack differentiated sex chromosomes is largely unknown. Here we present a chromosome-anchored genome assembly for rainbow trout (Oncorhynchus mykiss) and characterize a 55-Mb double-inversion supergene that mediates sex-specific migratory tendency through sex-dependent dominance reversal, an alternative mechanism for resolving sexual conflict. The double inversion contains key photosensory, circadian rhythm, adiposity and sex-related genes and displays a latitudinal frequency cline, indicating environmentally dependent selection. Our results show sex-dependent dominance reversal across a large autosomal supergene, a mechanism for sexual conflict resolution capable of protecting sexually antagonistic variation while avoiding the homozygous lethality and deleterious mutations associated with typical heteromorphic sex chromosomes. Methodology ReplicatesDescribe the experimental replicates, specifying number, type and replicate agreement. Sequencing depthDescribe the sequencing depth for each experiment, providing the total number of reads, uniquely mapped reads, length of reads and whether they were paired-or single-end. AntibodiesDescribe the antibodies used for the ChIP-seq experiments; as applicable, provide supplier name, catalog number, clone name, and lot number. Peak calling parametersSpecify the command line program and parameters used for read mapping and peak calling, including the ChIP, control and index files used. Data qualityDescribe the methods used to ensure data quality in full detail, including how many peaks are at FDR 5% and above 5-fold enrichment. SoftwareDescribe the software used to collect and analyze the ChIP-seq data. For custom code that has been deposited into a community repository, provide accession details. Flow Cytometry PlotsConfirm that:The axis labels state the marker and fluorochrome used (e.g. CD4-FITC).The axis scales are clearly visible. Include numbers along axes only for bottom left plot of group (a 'group' is an analysis of identical markers).All plots are contour plots with outliers or pseudocolor plots.A numerical value for number of cells or percentage (with statistics) is provided. Methodology Sample preparationDescribe the sample preparation, detailing the biological source of the cells and any tissue processing steps used. InstrumentIdentify the instrument used for data collection, specifying make and model number. SoftwareDescribe the software used to collect and analyze the flow cytometry data. For custom code that has been deposited into a community repository, provide accession details.Cell population abundance Describe the abundance of the relevant cell populations within post-sort fractions, providing details on the...

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Traits with different fitness optima in males and females cause sexual conflict when they have a shared genetic basis. Heteromorphic sex chromosomes can resolve this conflict and protect sexually antagonistic polymorphisms but accumulate deleterious mutations. However, many taxa lack differentiated sex chromosomes, and how sexual conflict is resolved in these species is largely unknown. Here we present a chromosome-anchored genome assembly for rainbow trout (Oncorhynchus mykiss) and characterize a 56 Mb double-inversion supergene that mediates sex-specific migration through sex-dependent dominance, a mechanism that reduces sexual conflict. The double-inversion contains key photosensory, circadian rhythm, adiposity, and sexual differentiation genes and displays frequency clines associated with latitude and temperature, revealing environmental dependence. Our results constitute the first example of sex-dependent dominance across a large autosomal supergene, a novel mechanism for sexual conflict resolution capable of protecting polygenic sexually antagonistic variation while avoiding the homozygous lethality and deleterious mutation load of heteromorphic sex chromosomes.

Major ecological realignments are already occurring in response to climate change. To be successful, conservation strategies now need to account for geographical patterns in traits sensitive to climate change, as well as climate threats to species-level diversity. As part of an effort to provide such information, we conducted a climate vulnerability assessment that included all anadromous Pacific salmon and steelhead ( Oncorhynchus spp.) population units listed under the U.S. Endangered Species Act. Using an expert-based scoring system, we ranked 20 attributes for the 28 listed units and 5 additional units. Attributes captured biological sensitivity, or the strength of linkages between each listing unit and the present climate; climate exposure, or the magnitude of projected change in local environmental conditions; and adaptive capacity, or the ability to modify phenotypes to cope with new climatic conditions. Each listing unit was then assigned one of four vulnerability categories. Units ranked most vulnerable overall were Chinook ( O . tshawytscha ) in the California Central Valley, coho ( O . kisutch ) in California and southern Oregon, sockeye ( O . nerka ) in the Snake River Basin, and spring-run Chinook in the interior Columbia and Willamette River Basins. We identified units with similar vulnerability profiles using a hierarchical cluster analysis. Life history characteristics, especially freshwater and estuary residence times, interplayed with gradations in exposure from south to north and from coastal to interior regions to generate landscape-level patterns within each species. Nearly all listing units faced high exposures to projected increases in stream temperature, sea surface temperature, and ocean acidification, but other aspects of exposure peaked in particular regions. Anthropogenic factors, especially migration barriers, habitat degradation, and hatchery influence, have reduced the adaptive capacity of most steelhead and salmon populations. Enhancing adaptive capacity is essential to mitigate for the increasing threat of climate change. Collectively, these results provide a framework to support recovery planning that considers climate impacts on the majority of West Coast anadromous salmonids.

Dam removal provides a valuable opportunity to measure the fluvial response to changes in both sediment supply and the processes that shape channel morphology. We present the first study of river response to the removal of a large (32‐m‐high) dam in a Mediterranean hydroclimatic setting, on the Carmel River, coastal California, USA. This before‐after/control‐impact study measured changes in channel topography, grain size, and salmonid spawning habitat throughout dam removal and subsequent major floods. During dam removal, the river course was re‐routed in order to leave most of the impounded sediment sequestered in the former reservoir and thus prevent major channel and floodplain aggradation downstream. However, a substantial sediment pulse occurred in response to base‐level fall, knickpoint migration, and channel avulsion through sediment in the former reservoir above the newly re‐routed channel. The sediment pulse advanced ~3.5 km in the first wet season after dam removal, resulting in decreased riverbed grain size downstream of the dam site. In the second wet season after dam removal, high flows (including a 30‐year flood and two 10‐year floods) transported sediment > 30 km downstream, filling pools and reducing cross‐channel relief. Deposition of gravel in the second wet season after dam removal enhanced salmonid spawning habitat downstream of the dam site. We infer that in dam removals where most reservoir sediment remains impounded and where high flows follow soon after dam removal, flow sequencing becomes a more important driver of geomorphic and fish‐habitat change than the dam removal alone. © 2018 John Wiley & Sons, Ltd.

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