Geology topics

Andrew R. Whiteley

Publications and source records attributed to Andrew R. Whiteley.

At least 19 recordsLinked to original sources

USGS2023

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

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.

Molecular Ecology Resources↗

USGS2023

Connecting research and practice to enhance the evolutionary potential of species under climate change

Resource managers have rarely accounted for evolutionary dynamics in the design or implementation of climate change adaptation strategies. We brought the research and management communities together to identify challenges and opportunities for applying evidence from evolutionary science to support on-the-ground actions intended to enhance species' evolutionary potential. We amalgamated input from natural-resource practitioners and interdisciplinary scientists to identify information needs, current knowledge that can fill those needs, and future avenues for research. Three focal areas that can guide engagement include: (1) recognizing when to act, (2) understanding the feasibility of assessing evolutionary potential, and (3) identifying best management practices. Although researchers commonly propose using molecular methods to estimate genetic diversity and gene flow as key indicators of evolutionary potential, we offer guidance on several additional attributes (and their proxies) that may also guide decision-making, particularly in the absence of genetic data. Finally, we outline existing decision-making frameworks that can help managers compare alternative strategies for supporting evolutionary potential, with the goal of increasing the effective use of evolutionary information, particularly for species of conservation concern. We caution, however, that arguing over nuance can generate confusion; instead, dedicating increased focus on a decision-relevant evidence base may better lend itself to climate adaptation actions.

Conservation Science and Practice↗

USGS2023

Identifying mechanisms underlying individual body size increases in a changing, highly seasonal environment: The growing trout of West Brook

As air temperature increases, it has been suggested that smaller individual body size may be a general response to climate warming. However, for ectotherms inhabiting cold, highly seasonal environments, warming temperatures may increase the scope for growth and result in larger body size. In a long-term study of individual brook trout Salvelinus fontinalis and brown trout Salmo trutta inhabiting a small stream network, individual lengths increased over the course of 15 years. As size-selective gains and losses to the population acted to reduce body sizes and mean body size at first tagging in the autumn (<60 mm) were not observed to change substantially over time, the increase in body size was best explained by higher individual growth rates. For brook trout, increasing water temperatures during the spring (when both trout species accomplish most of their total annual growth) was the primary driver of growth rate for juvenile fish and the environmental factor which best explained increases in individual body size over time. For brown trout, by contrast, reduction in and subsequent elimination of juvenile Atlantic salmon Salmo salar midway through the study period explained most of the increases in juvenile growth and body size. In addition to these major trends, a considerable amount of interannual variation in trout growth and body size was explained by other abiotic (stream flow) and biotic (population density) factors with the direction and magnitude of these effects differing by season, age-class and species. For example, stream flow was the dominant growth rate driver for adult fish with strong positive effects in the summer and autumn, but flow variation could not explain increases in body size as we observed no trend in flow. Overall, our work supports the general contention that for high-latitude ectotherms, increasing spring temperatures associated with a warming climate can result in increased growth and individual body size (up to a point), but context-dependent change in other factors can substantially contribute to both interannual variation and longer-term effects.

Massachusetts↗

USGS2023

Effects of freshwater residence time on reproductive success in anadromous alewife (Alosa pseudoharengus): climate change implications

Earlier spring warming and anadromous fish migrations prompted by climate change are linked to shorter freshwater residency. Impacts of phenological change on anadromous fish populations are poorly understood with limited studies focused on iteroparous non-salmonids. We assessed freshwater residence time and reproductive success in an iteroparous clupeid, alewife ( Alosa pseudoharengus ) using a pedigree analysis and otolith-based spawning dates from captured juveniles. The primary objectives were to (1) estimate adult spawning duration in a freshwater pond (freshwater residence time) and (2) evaluate adult freshwater residence time, arrival date, length, sex, and reproductive success across 2 years in one system. Estimated freshwater residence times varied widely (1–64 days), and longer residence times were associated with earlier arrival dates, higher reproductive success, and more mating events. Longer freshwater residence times may allow alewife to spawn with more mates, produce more gametes, and experience a range of spawning and nursery conditions. Plasticity in alewife freshwater residence time could support earlier and shorter migration periods but may result in lower reproductive output if adults spend less time in freshwater ponds.

Massachusetts↗

USGS2022

Population genetics of Brook Trout (Salvelinus fontinalis) in the southern Appalachian Mountains

Broad-scale patterns of genetic diversity for Brook Trout remain poorly understood across their endemic range in the eastern United States. We characterized variation at 12 microsatellite loci in 22,020 Brook Trout among 836 populations from Georgia, USA to Quebec, Canada to the western Great Lakes region. Within-population diversity was typically lower in the southern Appalachians relative to the mid-Atlantic and northeastern regions. Effective population sizes in the southern Appalachians were often very small, with many estimates less than 30 individuals. The population genetics of Brook Trout in the southern Appalachians are far more complex than a conventionally held simple “northern” versus “southern” dichotomy would suggest. Contemporary population genetic variation was consistent with geographic expansion of Brook Trout from Mississippian, mid-Atlantic, and Acadian glacial refuges, as well as differentiation among drainages within these broader clades. Genetic variation was pronounced among drainages (57.4% of overall variation occurred among Hydrologic Unit Code (HUC)10 or larger units) but was considerable even at fine spatial scales (13% of variation occurred among collections within HUC12 drainage units). Remarkably, 87.2% of individuals were correctly assigned to their collection of origin. While comparisons with fish from existing major hatcheries showed impacts of stocking in some populations, genetic introgression did not overwhelm the signal of broad-scale patterns of population genetic structure. Although our results reveal deep genetic structure in Brook Trout over broad spatial extents, fine-scale population structuring is prevalent across the southern Appalachians. Our findings highlight the distinctiveness and vulnerability of many Brook Trout populations in the southern Appalachian Mountains and have important implications for wild Brook Trout management. To facilitate application of our findings by conservation practitioners, we provide an interactive online visualization tool to allow our results to be explored at management relevant scales.

North Carolina, Virginia, West Virginia↗

USGS2022

Cohort strength and body size in co-occurring salmonids in a small stream network: Variation in space and time

Trout and salmon commonly coexist in stream networks. Exploring similarities and differences among species can help explain coexistence and invasive ability. Here, we describe spatial distribution, cohort strengths and size-at-age of three co-occurring species in a small stream network. Spatial distributions varied dramatically among species; native brook trout occupied all stream reaches, naturalized brown trout were found in the mainstem and lower portions of tributaries and fry-stocked Atlantic salmon were limited to the mainstem. Size-at-age also differed among species, Atlantic salmon were consistently the smallest, brook trout were intermediate in size and brown trout were the largest. Despite size differences, mean lengths of brook trout and brown trout were highly correlated among years. Cohort strengths varied considerably across years but were also highly correlated for the two trout species, suggesting strong environmental control on cohort strength and a reduced role for species interactions. At low densities, we observed strong negative effects of density on body sizes and weaker effects otherwise. Overall, these results suggest differences in spatial distribution combined with similarities in response to environmental variation contribute to species coexistence in this small steam network.

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS2021

Supporting the adaptive capacity of species through more effective knowledge exchange with conservation practitioners

There is an imperative for conservation practitioners to facilitate the ability of biodiversity to adapt to accelerating environmental change. Evolutionary biologists are well-positioned to inform the development of evidence-based management strategies that will effectively support the adaptive capacity of species and ecosystems. Conservation practitioners increasingly accept that management practices must change, but harbor concerns about how to apply recommended changes to their management contexts. Given the goodwill from both conservation practitioners and evolutionary biologists, we believe there is opportunity to accelerate the required changes by promoting closer collaboration between these two groups. We highlight how evolutionary biologists can harness lessons learned via the evidence-based conservation movement to make a substantive contribution to the development of effective conservation management practices. These lessons include: 1) recognising why practitioners do and do not use scientific evidence; 2) building an evidence base that will influence management decisions; 3) translating theory into a format that conservation practitioners can use to inform management practices; and 4) developing strategies for effective knowledge exchange. Although efforts will be required on both sides, we believe there are rewards for both practitioners and evolutionary biologists, not least of which is fostering practices that will help support the long-term persistence of species.

Evolutionary Applications↗

USGS2021

Feeling the squeeze: Adult run size and habitat availability limit juvenile river herring densities in lakes

Maximum densities of juvenile river herring (Alewife Alosa pseudoharengus and Blueback Herring A. aestivalis ) vary among freshwater lakes, likely due to densities of adult spawners. Differences in habitat availability and lake water quality may also contribute to variation in juvenile river herring productivity between populations, yet these relationships have not been tested across a large geographic scope. In this study we investigated relationships between juvenile river herring densities and (1) spawning adult river herring densities, (2) lake habitat availability, and (3) lake water quality in 29 freshwater lakes in the northeastern USA. Purse seines were used at night to sample juvenile river herring monthly in June–August 2014 and 2015, with concurrent collection of lake-specific physical (e.g., lake surface area, mean depth, depth to thermocline), chemical (e.g., nitrogen, phosphorus, dissolved organic carbon [DOC]), and biological (chlorophyll a , adult spawning density) data. Spawning adult density (number of adults per surface area of lake) explained 66.6% of the variation in juvenile densities using a generalized additive model. Juvenile densities increased with increasing adult density, peaking at roughly 1,000 adults/ha, and then declined at higher adult densities, suggesting a limit to carrying capacity in juvenile production. Linear mixed-effects models revealed that differences in water quality and habitat across lakes explained additional variation in juvenile densities. Specifically, DOC was negatively related to juvenile densities, suggesting that DOC limits the amount of suitable, well-oxygenated epilimnion habitat available to juvenile river herring in late summer. Our results can be used to help understand expected juvenile production based on adult density within a lake, to inform expectations about juvenile growth and survival, and to understand the mechanisms for how changes in habitat availability and water quality affect river herring populations.

Connecticut, Maine, Massachusetts, New Hampshire, ↗

USGS2021

Climate change and expanding invasive species drive widespread declines of native trout in the northern Rocky Mountains, USA

Climate change and invasive species are major threats to native biodiversity, but few empirical studies have examined their combined effects at large spatial and temporal scales. Using 21,917 surveys collected over 30 years, we quantified the impacts of climate change on the past and future distributions of five interacting native and invasive trout species throughout the northern Rocky Mountains, USA. We found that the occupancy of native bull trout and cutthroat trout declined by 18 and 6%, respectively (1993–2018), and was predicted to decrease by an additional 39 and 16% by 2080. However, reasons for these occupancy reductions markedly differed among species: Climate-driven increases in water temperature and decreases in summer flow likely caused declines of bull trout, while climate-induced expansion of invasive species largely drove declines of cutthroat trout. Our results demonstrate that climate change can affect ecologically similar, co-occurring native species through distinct pathways, necessitating species-specific management actions.

Montana↗

USGS2021

Influence of water temperature and biotic interactions on the distribution of westslope cutthroat trout (Oncorhynchus clarkii lewisi) in a population stronghold under climate change

Climate warming is expected to have substantial impacts on native trout across the Rocky Mountains, but there is little understanding of how these changes affect future distributions of co-occurring native fishes within population strongholds. We used mixed-effects logistic regression to investigate the role of abiotic (e.g., temperature) and biotic factors (bull trout presence, Salvelinus confluentus ) on distributions of westslope cutthroat trout ( Oncorhynchus clarkii lewisi ; WCT) in the North Fork Flathead River, USA and Canada. The probability of WCT presence increased with stream temperature and decreased with channel gradient and bull trout presence, yet the effect of bull trout was reduced with increasing pool densities. Combining this model with spatially explicit stream temperature projections, we predict a 29% increase in suitable habitat under high emissions through 2075, with gains at mid-elevation sites predicted to exceed bull trout thermal tolerances and high-elevation sites expected to become more thermally suitable for WCT. Our study illustrates the importance of considering abiotic and biotic drivers to assess species response to climate change, helping to guide local-scale climate adaptation and management.

Alberta, British Columbia, Montana↗

USGS2020

Evaluation of genetic structuring within GIS‐derived Brook Trout management units

Delineation of management units across broad spatial scales can help to visualize population structuring and identify conservation opportunities. Geographical information system (GIS) approaches can be useful for developing broad‐scale management units, especially when paired with field data that can validate the GIS‐based delineations. Genetic data can be useful for evaluating whether management units accurately represent population structuring. The Eastern Brook Trout Joint Venture, a regionwide collaborative group, delineated patch‐based management units for Brook Trout Salvelinus fontinalis by using GIS approaches to inform conservation strategies across the eastern United States. The objectives of this research were to (1) evaluate how well the patches predicted Brook Trout genetic structuring in Connecticut, USA; (2) modify the patches as needed to represent contemporary genetic structuring; and (3) identify catchment‐ and patch‐scale riverscape characteristics that predict genetic diversity. Patches with dams and high levels of upstream impervious surfaces (>3%) had increased intrapatch genetic structuring, which we incorporated into our revised patch delineation algorithm. Patch area and catchment area were the best predictors of genetic diversity, suggesting the importance of maintaining connectivity and incorporating patch‐scale processes into conservation actions. The modified patch layer could be used as the basis for Brook Trout management units to help predict population structuring in the absence of watershed‐scale genetic data, allowing opportunities for Brook Trout conservation to be identified.

Connecticut↗

USGS2019

Evaluating the effects of barriers on Slimy Sculpin movement and population connectivity using novel sibship-based and traditional genetic metrics

Population genetics-based approaches can provide robust and cost-effective ways to assess the effects of potential barriers, including dams and road-stream crossings, on the passage and population connectivity of aquatic organisms. Determining the best way to apply and modify genetic tools for different species and situations is essential for making these genetics-based approaches broadly applicable to fisheries and aquatic habitat management. Here, we used multiple genetic approaches to assess the movement and population structure of Slimy Sculpin Cottus cognatus at two road-stream crossings in Michigan and one dam in Massachusetts, USA. We captured and genotyped individual sculpin and assessed movement and population connectivity by using (1) a sibship-based approach, where the presence and proportional distribution of siblings on either side of a barrier indicates population connectivity and the possible direction of movement (i.e., presumed movement from higher to lower proportions), and (2) two Bayesian genetic assignment approaches (STRUCTURE and BayesAss) to identify migrants across potential barriers based on individual population assignment probabilities. We also used traditional genetic metrics to assess within-population genetic variation and among-population genetic divergence. At all three locations, we found evidence for sculpin movement across the potential barrier based on sibship reconstruction, but small family sizes limited the ability of this approach to provide robust estimates of the rate and direction of movement. At two sites, a lack of genetic differentiation between above- and below-barrier populations limited the effectiveness of the genetic assignment methods for identifying possible migrants. At the third site, reduced upstream allelic diversity and effective number of breeders resulted in high genetic differentiation (FST) between above- and below-barrier populations, and both sibship and genetic assignment methods provided strong evidence of limited connectivity and bias against upstream movement. Overall, combining approaches and metrics may help overcome the limitations of any one method and maximize the value of datasets for genetics-based monitoring and assessment.

Massachusetts, Michigan↗

USGS2019

Larger body size and earlier run timing increase alewife reproductive success in a whole lake experiment

Environmental conditions can influence biological characteristics like phenology and body size with important consequences for organismal fitness. Examining these fitness consequences under natural conditions through genetic pedigree reconstruction offers a lens into potential population responses to changing environments. Over three years (2013-2015), we introduced adult alewife (Alosa pseudoharengus), anadromous, iteroparous clupeids, into one Massachusetts (USA) lake to complete the first detailed examination of this species’ mating system and assess relationships between body size, reproductive timing, and seasonal reproductive success. We reconstructed pedigrees using 15 microsatellites and genotypes from all possible parents and samples of naturally produced offspring within four months of hatching. Within each of the three study years, spawning adults had multiple mates and spawned multiple times. Larger females that arrived earlier had higher reproductive success. Declining body size and altered migration timing over time, through an influence on reproductive success, can influence population vital rates and productivity.

Massachusetts↗

USGS2019

Daily estimates reveal fine-scale temporal and spatial variation in fish survival across a stream network

Environmental drivers of population vital rates, such as temperature and precipitation, often vary at short time scales, and these fluctuations can have important impacts on population dynamics. However, relationships between survival and environmental conditions are typically modeled at coarse temporal scales, ignoring the role of daily environmental variation in survival. Our goal was to determine the importance of fine-scale temporal variation in survival to population dynamics of stream salmonids. We extended the Cormack–Jolly–Seber model to estimate daily survival rates from seasonal samples of individually marked brook trout ( Salvelinus fontinalis ) in a stream network. Daily variation in temperature and flow were strongly associated with survival, but relationships varied between juvenile and adult trout and among streams. In all streams, juveniles had higher mortality in warm, low-flow conditions, but in the two larger streams, cold, high-flow conditions also reduced juvenile survival. Adult survival decreased during low flows, particularly in the fall spawning period. Differing survival responses among stream network components to short-term environmental events created shifts in optimal location for maximum survival across life stages, seasons, and years.

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS2018

Three visualization approaches for communicating and exploring PIT tag data

As the number, size and complexity of ecological datasets has increased, narrative and interactive raw data visualizations have emerged as important tools for exploring and understanding these large datasets. As a demonstration, we developed three visualizations to communicate and explore passive integrated transponder tag data from two long-term field studies. We created three independent visualizations for the same dataset, allowing separate entry points for users with different goals and experience levels. The first visualization uses a narrative approach to introduce users to the study. The second visualization provides interactive cross-filters that allow users to explore multi-variate relationships in the dataset. The last visualization allows users to visualize the movement histories of individual fish within the stream network. This suite of visualization tools allows a progressive discovery of more detailed information and should make the data accessible to users with a wide variety of backgrounds and interests.

Maine, Massachusetts↗

USGS2018

Precision and relative effectiveness of a purse seine for sampling age-0 river herring in lakes

Stock assessments for anadromous river herring, collectively Alewife Alosa pseudoharengus and Blueback Herring A. aestivalis , lack adequate demographic information, particularly with respect to early life stages. Although sampling adult river herring is increasingly common throughout their range, currently no standardized, field‐based, analytical methods exist for estimating juvenile abundance in freshwater lakes. The objective of this research was to evaluate the relative effectiveness and sampling precision of a purse seine for estimating densities of age‐0 river herring in freshwater lakes. We used a purse seine to sample age‐0 river herring in June–September 2015 and June–July 2016 in 16 coastal freshwater lakes in the northeastern USA. Sampling effort varied from two seine hauls to more than 50 seine hauls per lake. Catch rates were highest in June and July, and sampling precision was maximized in July. Sampling at night (versus day) in open water (versus littoral areas) was most effective for capturing newly hatched larvae and juveniles up to ca. 100 mm TL. Bootstrap simulation results indicated that sampling precision of CPUE estimates increased with sampling effort, and there was a clear threshold beyond which increased effort resulted in negligible increases in precision. The effort required to produce precise CPUE estimates, as determined by the CV, was dependent on lake size; river herring densities could be estimated with up to 10 purse‐seine hauls (one‐two nights) in a small lake (<50 ha) and 15–20 hauls (two‐three nights) in a large lake (>50 ha). Fish collection techniques using a purse seine as described in this paper are likely to be effective for estimating recruit abundance of river herring in freshwater lakes across their range.

North American Journal of Fisheries Management↗

USGS2017

No evidence for ecological segregation protecting native trout from invasive hybridization

We appreciate the comments of Young et al. (2017) on our recent paper (Muhlfeld et al., 2017) concerning spatiotemporal dynamics of hybridization between native westslope cutthroat trout ( Oncorhynchus clarkii lewisi ; WCT) and introduced coastal rainbow trout ( Oncorhynchus mykiss irideus ; RBT). Nevertheless, we believe there is no evidence for “ecological segregation” protecting WCT from hybridization with invasive RBT. Here we consider their three major arguments for ecological segregation and find their conclusions invalid.

Global Change Biology↗

USGS2017

Experimental test of genetic rescue in isolated populations of brook trout

Genetic rescue is an increasingly considered conservation measure to address genetic erosion associated with habitat loss and fragmentation. The resulting gene flow from facilitating migration may improve fitness and adaptive potential, but is not without risks (e.g., outbreeding depression). Here, we conducted a test of genetic rescue by translocating ten (five of each sex) brook trout ( Salvelinus fontinalis ) from a single source to four nearby and isolated stream populations. To control for the demographic contribution of translocated individuals, ten resident individuals (five of each sex) were removed from each recipient population. Prior to the introduction of translocated individuals, the two smallest above-barrier populations had substantially lower genetic diversity, and all populations had reduced effective number of breeders relative to adjacent below-barrier populations. In the first reproductive bout following translocation, 31 of 40 (78%) translocated individuals reproduced successfully. Translocated individuals contributed to more families than expected under random mating and generally produced larger full-sibling families. We observed relatively high (>20%) introgression in three of the four recipient populations. The translocations increased genetic diversity of recipient populations by 45% in allelic richness and 25% in expected heterozygosity. Additionally, strong evidence of hybrid vigour was observed through significantly larger body sizes of hybrid offspring relative to resident offspring in all recipient populations. Continued monitoring of these populations will test for negative fitness effects beyond the first generation. However, these results provide much-needed experimental data to inform the potential effectiveness of genetic rescue-motivated translocations.

Virginia↗