SEARCH · USGS Science

Results for “Genes”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,081 records · Page 60Linked to original sources

USGS2026

A chromosome-level genome assembly of a vernal pool specialist amphibian, the Western Spadefoot, Spea hammondii

We assembled and annotated a chromosome-level reference genome for the Western Spadefoot, Spea hammondii (Anura, Scaphiopodidae) representing one of only three amphibians included in the California Conservation Genomics Project (CCGP). Spea hammondii is a vernal pool breeding anuran native to California and northwestern Baja California which has undergone both range contractions and local extirpations across its distribution, primarily due to habitat loss and degradation and drought. The species is recognized by the state of California as a Species of Special Concern and is proposed for listing under the United States Endangered Species Act. Using the established CCGP pipeline, this S. hammondii genome was produced using Pacific Biosciences HiFi long-reads and Omni-C proximity ligation, resulting in a de novo genome assembly 1.14 Gb in length, distributed across 479 scaffolds (scaffold N50 = 120.8 Mb; largest scaffold = 183.6 Mb) with a BUSCO completeness score of 90.9% using a conserved tetrapod ortholog set. Our assembly shows high base accuracy (QV = 63.7) and low frameshift error in coding regions (QV 50.42). Annotation of this genome yielded 20,434 genes with a BUSCO completeness score of 94.7%. This reference genome, in combination with range-wide resequencing data from CCGP, will facilitate statewide population genomic assessments to delineate conservation units, quantify inbreeding and genomic load, and test for adaptive variation associated with vernal pool hydrology and drought tolerance, all of which are important considerations in the proposed federal listing.

BioRxiv↗

USGS2019

Migratory strategy explains differences in timing of female reproductive development in seasonally sympatric songbirds.

1. Divergent migratory strategies among populations can result in population-level differences in timing of reproduction (allochrony) and local adaptation. However, the mechanisms underlying among-population variation in timing are insufficiently understood, particularly in females. 2. We studied differences in reproductive development and its related mechanisms along the hypothalamic-pituitary-gonadal axis (HPG) in closely related migratory and sedentary (i.e., resident) female dark-eyed juncos (Junco hyemalis) living together in sympatry during early spring. We predicted that residents would be more reproductively developed than migrants. Alternatively, we predicted that females might exhibit similar reproductive development in response to the same environmental cue despite differences in migratory behavior. To compare their degree of reproductive development during seasonal sympatry and the underlying mechanisms of these differences, we collected ovarian and liver tissue in early spring prior to migration, and compared abundance of gene transcripts associated with reproduction using quantitative PCR. We also used stable hydrogen isotopes to infer relative breeding and wintering latitude of migrants. 3. We found more abundant transcripts for luteinizing hormone receptor and aromatase in addition to significantly heavier ovaries in residents than in migrants. Together these results suggest greater sensitivity and response to upstream endocrine stimulation in resident females. Transcript abundance for other receptors associated with reproduction, however, did not differ between populations. When comparing ovarian development within migrants, females with lower hydrogen isotopes (indicating higher breeding latitudes) had smaller ovaries, suggesting that longer-distance migrations may further delay reproductive development. 4. Based on differences in ovary mass and transcript abundance, we conclude that females that differ in migratory strategy also differ in timing of reproductive development. Differences in timing of reproductive development between migrant and resident females could drive reproductive isolation between populations. This study also reveals mechanisms that could drive allochrony and enable us to predict how seasonal organisms will respond to a changing world.

Functional Ecology↗

USGS2019

Extreme site fidelity as an optimal strategy in an unpredictable and homogeneous environment

1.Animal site fidelity structures space use, population demography and ultimately gene flow. Understanding the adaptive selection for site fidelity patterns provides a mechanistic understanding to both spatial and population processes. This can be achieved by linking space use with environmental variability (spatial and temporal) and demographic parameters. However, rarely is the environmental context that drives the selection for site fidelity behaviour fully considered. 2. We use ecological theory to understand whether the spatial and temporal variability in breeding site quality can explain the site fidelity behaviour and demographic patterns of Gunnison sage-grouse (Centrocercus minimus). We examined female site fidelity patterns across multiple spatial scales: proximity of consecutive year nest locations, space-use overlap within and across the breeding and brooding seasons, and fidelity to a breeding patch. We also examined the spatial and temporal variability in nest, chick, juvenile and adult survival. 3. We found Gunnison sage-grouse to be site faithful to their breeding patch, area of use within the patch and generally where they nest, suggesting an “Always Stay” site fidelity strategy. This is an optimal evolutionary strategy when site quality is unpredictable. Further, we found limited spatial variability in survival within age groups, suggesting little demographic benefit to moving among patches. We suggest Gunnison sage-grouse site fidelity is driven by the unpredictability of predation in a relatively homogeneous environment, the lack of benefits and likely costs to moving across landscape patches and leaving known lek and breeding/brooding areas. 4. Space use and demography are commonly studied separately. More so, site fidelity patterns are rarely framed in the context of ecological theory, beyond questions related to the win-stay:lose-switch rule. To move beyond describing patterns and understand the adaptive selection driving species movements and their demographic consequences require integrating movement, demography and environmental variability in a synthetic framework. 5. Site fidelity theory provides a coherent framework to simultaneously investigate the spatial and population ecology of animal populations. Using it to frame ecological questions will lead to a more mechanistic understanding of animal movement, spatial population structuring and meta-population dynamics.

Colorado↗

USGS2017

Effects of host species and environment on the skin microbiome of Plethodontid salamanders

The amphibian skin microbiome is recognized for its role in defence against pathogens, including the deadly fungal pathogen Batrachochytrium dendrobatidis (Bd). Yet, we have little understanding of evolutionary and ecological processes that structure these communities, especially for salamanders and closely related species. We investigated patterns in the distribution of bacterial communities on Plethodon salamander skin across host species and environments. Quantifying salamander skin microbiome structure contributes to our understanding of how host-associated bacteria are distributed across the landscape, among host species, and their putative relationship with disease. We characterized skin microbiome structure (alpha-diversity, beta-diversity and bacterial operational taxonomic unit [OTU] abundances) using 16S rRNA gene sequencing for co-occurring Plethodon salamander species (35 Plethodon cinereus , 17 Plethodon glutinosus , 10 Plethodon cylindraceus ) at three localities to differentiate the effects of host species from environmental factors on the microbiome. We sampled the microbiome of P. cinereus along an elevational gradient ( n = 50, 700–1,000 m a.s.l.) at one locality to determine whether elevation predicts microbiome structure. Finally, we quantified prevalence and abundance of putatively anti-Bd bacteria to determine if Bd-inhibitory bacteria are dominant microbiome members. Co-occurring salamanders had similar microbiome structure, but among sites salamanders had dissimilar microbiome structure for beta-diversity and abundance of 28 bacterial OTUs. We found that alpha-diversity increased with elevation, beta-diversity and the abundance of 17 bacterial OTUs changed with elevation (16 OTUs decreasing, 1 OTU increasing). We detected 11 putatively anti-Bd bacterial OTUs that were present on 90% of salamanders and made up an average relative abundance of 83% ( SD ± 8.5) per salamander. All salamanders tested negative for Bd. We conclude that environment is more influential in shaping skin microbiome structure than host differences in these congeneric species, and suggest that environmental characteristics that covary with elevation influence microbiome structure. High prevalence and abundance of anti-Bd bacteria may contribute to low Bd levels in these populations of Plethodon salamanders.

Journal of Animal Ecology↗

USGS2021

Genomic signatures of thermal adaptation are associated with clinal shifts of life history in a broadly distributed frog

Temperature is a critical driver of ectotherm life-history strategies, whereby a warmer environment is associated with increased growth, reduced longevity and accelerated senescence. Increasing evidence indicates that thermal adaptation may underlie such life-history shifts in wild populations. Single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) can help uncover the molecular mechanisms of temperature-driven variation in growth, longevity and senescence. However, our understanding of these mechanisms is still limited, which reduces our ability to predict the response of non-model ectotherms to global temperature change. In this study, we examined the potential role of thermal adaptation in clinal shifts of life-history traits (i.e. life span, senescence rate and recruitment) in the Columbia spotted frog Rana luteiventris along a broad temperature gradient in the western United States. We took advantage of extensive capture–recapture datasets of 20,033 marked individuals from eight populations surveyed annually for 14–18 years to examine how mean annual temperature and precipitation influenced demographic parameters (i.e. adult survival, life span, senescence rate, recruitment and population growth). After showing that temperature was the main climatic predictor influencing demography, we used RAD-seq data (50,829 SNPs and 6,599 putative CNVs) generated for 352 individuals from 31 breeding sites to identify the genomic signatures of thermal adaptation. Our results showed that temperature was negatively associated with annual adult survival and reproductive life span and positively associated with senescence rate. By contrast, recruitment increased with temperature, promoting the long-term viability of most populations. These temperature-dependent demographic changes were associated with strong genomic signatures of thermal adaptation. We identified 148 SNP candidates associated with temperature including three SNPs located within protein-coding genes regulating resistance to cold and hypoxia, immunity and reproduction in ranids. We also identified 39 CNV candidates (including within 38 transposable elements) for which normalized read depth was associated with temperature. Our study indicates that both SNPs and structural variants are associated with temperature and could eventually be found to play a functional role in clinal shifts in senescence rate and life-history strategies in R. luteiventris . These results highlight the potential role of different sources of molecular variation in the response of ectotherms to environmental temperature variation in the context of global warming.

Journal of Animal Ecology↗

USGS2019

Effect of permafrost thaw on plant and soil fungal community in the boreal forest: Does fungal community change mediate plant productivity response?

Permafrost thaw is leading to rapid shifts in boreal ecosystem function. Permafrost thaw affects soil carbon turnover through changes in soil hydrology, however, the biotic mechanisms regulating plant community response remain elusive. Here, we measured the response of fungal community composition and soil nutrient content in an intact permafrost plateau forest soil and an adjacent thermokarst bog using barcoded amplicon targeting ITS2 and 28S rRNA genes. Next, we used the soils from the permafrost plateau and the thermokarst bog as soil inoculum in a greenhouse experiment to measure whether shifts in fungal community and soil water level regulate plant productivity. Overall, we found that fungal community composition differed significantly between the thawed and intact permafrost sites, but soil nutrient content did not. Relative abundance of mycorrhizal fungal taxa decreased while relative abundance of putative fungal pathogens increased with permafrost thaw. In the greenhouse, we found that ecto- and arbuscular associated host plants had higher productivity in permafrost-intact soils relative to thawed soils. However, productivity of non-mycorrhizal tussock grass was more affected by soil water levels than soil communities. Our results suggest that fungal communities are crucial in mediating plant response to permafrost thaws inducing hydrology changes.

Alaska↗

USGS2022

What common-garden experiments tell us about climate responses in plants

Common garden experiments are indoor or outdoor plantings of species or populations collected from multiple distinct geographic locations, grown together under shared conditions. These experiments examine a range of questions for theory and application using a variety of methods for analysis. The eight papers of this special feature comprise a cross section of contemporary approaches, summarized and synthesized here by what they tell us about the relationships between climate-related trait spectra and fitness optima. Four of the eight papers are based on field experiments in prairie, desert, Mediterranean and boreal biomes. Representative of many common garden experiments, these experiments reveal consistent evidence of traits varying with population climate provenance, but evidence of a tradeoff between growth and tolerance traits or of consistent fitness optimization at home is scant, in contrast to trait theory. Two synthesis papers highlight dominant patterns of trait divergence, including for an exotic invasive species. One theoretical paper warned that unknown kinship relationships between populations can result in the misidentification of adaptive trait divergence. A third synthesis paper formulated novel and ambitious goals for common-garden studies through including measurement of response variables at multiple levels of biological organization. The featured papers discuss multiple avenues for improving common garden studies. Genomic analysis, together with the quantification of kinship relationships, will continue to reveal the influence of environmental drivers on gene selection. Measuring a more complete set of fitness traits, especially for traits related to regeneration, will permit the development of projection models to explicitly link trait spectra, climate patterns and fitness consequences. More standardized data reporting will additionally improve abilities to synthesize findings across experiments. Testing population performance in competition with other species will produce more robust fitness comparisons between genotypes, especially for slower-growing genotypes in higher-resource environments. Adding gardens in and beyond climatic edge locations will furthermore strengthen the understanding of population failure and species exclusion. Finally, there is unrealized potential in adding ecosystem-level observations to common-garden studies that will enhance integrative analysis across scales of biological organization and scientific domains. Synthesis . With novel, creative designs, data integration and synthesis, common garden experiments will continue to advance the understanding of trait ensembles interacting with climate across scales of biological organization, provide pivotal data for global change models and guide ecological applications such as restoration of habitats for rare and climate sensitive species.

Journal of Ecology↗

USGS2015

Organic matter quantity and source affects microbial community structure and function following volcanic eruption on Kasatochi Island, Alaska

In August 2008, Kasatochi volcano erupted and buried a small island in pyroclastic deposits and fine ash; since then, microbes, plants and birds have begun to re-colonize the initially sterile surface. Five years post-eruption, bacterial 16S rRNA gene and fungal internal transcribed spacer (ITS) copy numbers and extracellular enzyme activity (EEA) potentials were one to two orders of magnitude greater in pyroclastic materials with organic matter (OM) inputs relative to those without, despite minimal accumulation of OM (< 0.2%C). When normalized by OM levels, post-eruptive surfaces with OM inputs had the highest β-glucosidase, phosphatase, NAGase and cellobiohydrolase activities, and had microbial population sizes approaching those in reference soils. In contrast, the strongest factor determining bacterial community composition was the dominance of plants versus birds as OM input vectors. Although soil pH ranged from 3.9 to 7.0, and %C ranged 100×, differentiation between plant- and bird-associated microbial communities suggested that cell dispersal or nutrient availability are more likely drivers of assembly than pH or OM content. This study exemplifies the complex relationship between microbial cell dispersal, soil geochemistry, and microbial structure and function; and illustrates the potential for soil microbiota to be resilient to disturbance.

Alaska↗

USGS2022

Methanogenic archaea in subsurface coal seams are biogeographically distinct: An analysis of metagenomically-derived mcrA sequences

The production of methane as an end-product of organic matter degradation in the absence of other terminal electron acceptors is common, and has often been studied in environments such as animal guts, soils, and wetlands due to its potency as a greenhouse gas. To date however, the study of the biogeographic distribution of methanogens across coal seam environments has been minimal. Here, we show that coal seams are host to a diverse range of methanogens, which are distinctive to each geological basin. Based on comparisons to close relatives from other methanogenic environments, the dominant methanogenic pathway in these basins is hydrogenotrophic, with acetoclastic being a second major pathway in the Surat Basin. Finally, mcrA and 16S rRNA gene primer biases were predominantly seen to affect the detection of Methanocellales, Methanomicrobiales and Methanosarcinales taxa in this study. Subsurface coal methanogenic community distributions and pathways presented here provide insights into important metabolites and bacterial partners for in situ coal biodegradation.

Environmental Microbiology↗

USGS2013

Dryland soil microbial communities display spatial biogeographic patterns associated with soil depth and soil parent material

Biological soil crusts (biocrusts) are common to drylands worldwide. We employed replicated, spatially nested sampling and 16S rRNA gene sequencing to describe the soil microbial communities in three soils derived from different parent material (sandstone, shale, and gypsum). For each soil type, two depths (biocrusts, 0–1 cm; below-crust soils, 2–5 cm) and two horizontal spatial scales (15 cm and 5 m) were sampled. In all three soils, Cyanobacteria and Proteobacteria demonstrated significantly higher relative abundance in the biocrusts, while Chloroflexi and Archaea were significantly enriched in the below-crust soils. Biomass and diversity of the communities in biocrusts or below-crust soils did not differ with soil type. However, biocrusts on gypsum soil harbored significantly larger populations of Actinobacteria and Proteobacteria and lower populations of Cyanobacteria. Numerically dominant operational taxonomic units (OTU; 97% sequence identity) in the biocrusts were conserved across the soil types, whereas two dominant OTUs in the below-crust sand and shale soils were not identified in the gypsum soil. The uniformity with which small-scale vertical community differences are maintained across larger horizontal spatial scales and soil types is a feature of dryland ecosystems that should be considered when designing management plans and determining the response of biocrusts to environmental disturbances.

Utah↗

USGS2013

Variation in the hindgut microbial communities of the Florida manatee, Trichechus manatus latirostris over winter in Crystal River, Florida

The Florida manatee, Trichechus manatus latirostris, is a hindgut-fermenting herbivore. In winter, manatees migrate to warm water overwintering sites where they undergo dietary shifts and may suffer from cold-induced stress. Given these seasonally induced changes in diet, the present study aimed to examine variation in the hindgut bacterial communities of wild manatees overwintering at Crystal River, west Florida. Faeces were sampled from 36 manatees of known sex and body size in early winter when manatees were newly arrived and then in mid-winter and late winter when diet had probably changed and environmental stress may have increased. Concentrations of faecal cortisol metabolite, an indicator of a stress response, were measured by enzyme immunoassay. Using 454-pyrosequencing, 2027 bacterial operational taxonomic units were identified in manatee faeces following amplicon pyrosequencing of the 16S rRNA gene V3/V4 region. Classified sequences were assigned to eight previously described bacterial phyla; only 0.36% of sequences could not be classified to phylum level. Five core phyla were identified in all samples. The majority (96.8%) of sequences were classified as Firmicutes (77.3 ± 11.1% of total sequences) or Bacteroidetes (19.5 ± 10.6%). Alpha-diversity measures trended towards higher diversity of hindgut microbiota in manatees in mid-winter compared to early and late winter. Beta-diversity measures, analysed through permanova, also indicated significant differences in bacterial communities based on the season.

Florida↗

USGS2018

Biological connectivity of seasonally ponded wetlands across spatial and temporal scales

Many species that inhabit seasonally ponded wetlands also rely on surrounding upland habitats and nearby aquatic ecosystems for resources to support life stages and to maintain viable populations. Understanding biological connectivity among these habitats is critical to ensure that landscapes are protected at appropriate scales to conserve species and ecosystem function. Biological connectivity occurs across a range of spatial and temporal scales. For example, at annual time scales many organisms move between seasonal wetlands and adjacent terrestrial habitats as they undergo life‐stage transitions; at generational time scales, individuals may disperse among nearby wetlands; and at multigenerational scales, there can be gene flow across large portions of a species’ range. The scale of biological connectivity may also vary among species. Larger bodied or more vagile species can connect a matrix of seasonally ponded wetlands, streams, lakes, and surrounding terrestrial habitats on a seasonal or annual basis. Measuring biological connectivity at different spatial and temporal scales remains a challenge. Here we review environmental and biological factors that drive biological connectivity, discuss implications of biological connectivity for animal populations and ecosystem processes, and provide examples illustrating the range of spatial and temporal scales across which biological connectivity occurs in seasonal wetlands.

Journal of the American Water Resources Associatio↗

USGS2026

GT-Seq panel development for species identification and parentage analysis of closely related hybridising Scaphirhynchus sturgeons

Hatchery supplementation is vital for conserving dwindling fish populations. Effective augmentation requires distinguishing hatchery-origin from wild individuals and accurately identifying species, particularly in systems where closely related species coexist. Genetic monitoring is key to quantifying genetic differences, but conventional markers do not distinguish hybrids, especially backcrosses. Misidentifying hybrids in hatchery programs compromises wild gene pools because hatchery broodstock contributes to numerous offspring being released into the wild. Here, we present a workflow for developing and evaluating the Genotyping-in-Thousands by sequencing (GT-seq) single nucleotide polymorphism (SNP) panel for North American river sturgeons ( Scaphirhynchus spp.). This panel is designed to detect complex hybrid classes and to determine parent-offspring relationships. Our species identification panel (S-loci) contains 155 SNPs selected for high genetic differentiation (F ST ) between Pallid Sturgeon ( S. albus ) and Shovelnose Sturgeon ( S. platorynchus ), and the parentage assignment panel (P-loci) includes 112 SNPs with high heterozygosity within Pallid Sturgeon. Simulation analyses demonstrated that our GT-seq S-loci panel reliably classifies pure species, F1, F2 and backcross hybrids, even with up to 70% missing data. The P-loci panel achieves high-confidence parentage assignment with ≥ 80% typed loci, with performance influenced by the proportion of sampled parents. Overall, the novel Scaphirhynchus GT-seq panel developed in this study represents a robust and efficient tool for detecting hybridisation, assigning parentage and providing critical information for management decisions in ongoing Pallid Sturgeon conservation.

lower Mississippi River, Missouri River↗

USGS2022

Defining fine-scaled population structure among continuously distributed populations

Understanding wildlife population structure and connectivity can help managers identify conservation strategies, as structure can facilitate the study of population changes and habitat connectivity can provide information on dispersal and biodiversity. To facilitate the use of wildlife monitoring data for improved adaptive management, we developed a novel approach to define hierarchical tiers (multiple scales) of population structure. We defined population structure by combining graph theory with biological inference about dispersal capability (based on movement, gene flow, and habitat condition) and functional processes affecting movement (e.g. habitat selection across scales of landscape preferences). First, we developed least-cost paths between high fidelity sites (habitat patches) using a cost surface, informed from functional processes of habitat characteristics to account for resistance of inter-patch movements. Second, we combined the paths into a multi-path graph construct. Third, we used information on potential connectivity (dispersal distances) and functional connectivity (permeability of fragmented landscapes based on selection preferences) to decompose the graph into hierarchical tiers of connected subpopulations, denoting the degree that dispersal affected population structure. As a case study, we applied our approach across the greater sage-grouse ( Centrocercus urophasianus ) range, a species of conservation concern in western United States. We described the relative importance of local populations and where to potentially avoid landscape disturbances that may negatively affect population connectivity using centrality measures supported by graph theory, and we demonstrated close alignment of the resulting population structure with population densities. This method can be adapted for other species with site fidelity and used as a management tool to evaluate population trends and responses to landscape changes across different temporal and spatial scales.

Methods in Ecology and Evolution↗

USGS2024

Common-garden experiment reveals outbreeding depression and region-of-origin effects on reproductive success in a frequently translocated tortoise

Human-mediated animal movement can expose wildlife populations to novel environments. Phenotypic plasticity can buffer against the challenges presented by novel environments, while adaptation to local ecosystems may limit resilience in novel ecosystems. Outbreeding depression during the mixing of disparate gene pools can also reduce reproductive success after long-distance movement. Here, we use a ‘common-garden’ population of gopher tortoises ( Gopherus polyphemus ), translocated from numerous sites across the state of Florida, USA, to a mitigation site in the north-west (panhandle) region to assess whether geographic origin, outbreeding effects, and behavioral plasticity influence reproductive success in this threatened keystone species. We found that females from north-east Florida produced clutches with lower hatching success than females from other regions. We detected regional differentiation in nest site selection behavior in the common environment of the translocation site, though these differences did not mediate the regional effect on hatching success. We also found evidence for outbreeding depression: hatching success declined with increasing parental geographic and genetic distances, dropping from 93% to 67% across the range of observed parental genetic distances. Together, these results suggest that newly admixed populations may suffer reproductive costs due to historical population differentiation, and that undetected outbreeding depression could significantly hamper conservation efforts for this species and others undergoing a variety of human-mediated movements.

Florida↗

USGS2016

Challenge to the model of lake charr evolution: Shallow- and deep-water morphs exist within a small postglacial lake

All examples of lake charr ( Salvelinus namaycush ) diversity occur within the largest, deepest lakes of North America (i.e. > 2000 km 2 ). We report here Rush Lake (1.3 km 2 ) as the first example of a small lake with two lake charr morphs (lean and huronicus). Morphology, diet, life history, and genetics were examined to demonstrate the existence of morphs and determine the potential influence of evolutionary processes that led to their formation or maintenance. Results showed that the huronicus morph, caught in deep-water, had a deeper body, smaller head and jaws, higher eye position, greater buoyancy, and deeper peduncle than the shallow-water lean morph. Huronicus grew slower to a smaller adult size, and had an older mean age than the lean morph. Genetic comparisons showed low genetic divergence between morphs, indicating incomplete reproductive isolation. Phenotypic plasticity and differences in habitat use between deep and shallow waters associated with variation in foraging opportunities seems to have been sufficient to maintain the two morphs, demonstrating their important roles in resource polymorphism. Rush Lake expands previous explanations for lake charr intraspecific diversity, from large to small lakes and from reproductive isolation to the presence of gene flow associated with strong ecological drivers.

Biological Journal of the Linnean Society↗

USGS2017

Climate change and alpine stream biology: progress, challenges, and opportunities for the future

In alpine regions worldwide, climate change is dramatically altering ecosystems and affecting biodiversity in many ways. For streams, receding alpine glaciers and snowfields, paired with altered precipitation regimes, are driving shifts in hydrology, species distributions, basal resources, and threatening the very existence of some habitats and biota. Alpine streams harbour substantial species and genetic diversity due to significant habitat insularity and environmental heterogeneity. Climate change is expected to affect alpine stream biodiversity across many levels of biological resolution from micro- to macroscopic organisms and genes to communities. Herein, we describe the current state of alpine stream biology from an organism-focused perspective. We begin by reviewing seven standard and emerging approaches that combine to form the current state of the discipline. We follow with a call for increased synthesis across existing approaches to improve understanding of how these imperiled ecosystems are responding to rapid environmental change. We then take a forward-looking viewpoint on how alpine stream biologists can make better use of existing data sets through temporal comparisons, integrate remote sensing and geographic information system (GIS) technologies, and apply genomic tools to refine knowledge of underlying evolutionary processes. We conclude with comments about the future of biodiversity conservation in alpine streams to confront the daunting challenge of mitigating the effects of rapid environmental change in these sentinel ecosystems.

Biological Reviews↗

USGS2016

Risk and efficacy of human-enabled interspecific hybridization for climate-change adaptation: Response to Hamilton and Miller (2016)

Hamilton and Miller ( 2016 ) provide an interesting and provocative discussion of how hybridization and introgression can promote evolutionary potential in the face of climate change. They argue that hybridization—mating between individuals from genetically distinct populations—can alleviate inbreeding depression and promote adaptive introgression and evolutionary rescue. We agree that deliberate intraspecific hybridization (mating between individuals of the same species) is an underused management tool for increasing fitness in inbred populations (i.e., genetic rescue; Frankham 2015 ; Whiteley et al. 2015 ). The potential risks and benefits of assisted gene flow have been discussed in the literature, and an emerging consensus suggests that mating between populations isolated for approximately 50–100 generations can benefit fitness, often with a minor risk of outbreeding depression (Frankham et al. 2011 ; Aitken & Whitlock 2013 ; Allendorf et al. 2013 ).

Conservation Biology↗