Geology topics

Gordon Luikart

Publications and source records attributed to Gordon Luikart.

At least 37 records · Page 2Linked to original sources

USGS2017

Legacy introductions and climatic variation explain spatiotemporal patterns of invasive hybridization in a native trout

Hybridization between invasive and native species, a significant threat to worldwide biodiversity, is predicted to increase due to climate-induced expansions of invasive species. Long-term research and monitoring are crucial for understanding the ecological and evolutionary processes that modulate the effects of invasive species. Using a large, multi-decade genetics dataset (N = 582 sites, 12,878 individuals) with high-resolution climate predictions and extensive stocking records, we evaluate the spatiotemporal dynamics of hybridization between native cutthroat trout and invasive rainbow trout, the world’s most widely introduced invasive fish, across the northern Rocky Mountains of the United States. Historical effects of stocking and contemporary patterns of climatic variation were strongly related to the spread of hybridization across space and time. The probability of occurrence, extent of, and temporal changes in hybridization increased at sites in close proximity to historical stocking locations with greater rainbow trout propagule pressure, warmer water temperatures, and lower spring precipitation. Although locations with warmer water temperatures were more prone to hybridization, cold sites were not protected from invasion; 58% of hybridized sites had cold mean summer water temperatures (<11 ° C). Despite cessation of stocking over 40 years ago, hybridization increased over time at half (50%) of the locations with long-term data, the vast majority of which (74%) were initially non-hybridized, emphasizing the chronic, negative impacts of human-mediated hybridization. These results show that effects of climate change on biodiversity must be analyzed in the context of historical human impacts that set ecological and evolutionary trajectories.

Global Change Biology↗

USGS2016

Vive la résistance: genome-wide selection against introduced alleles in invasive hybrid zones

Evolutionary and ecological consequences of hybridization between native and invasive species are notoriously complicated because patterns of selection acting on non-native alleles can vary throughout the genome and across environments. Rapid advances in genomics now make it feasible to assess locus-specific and genome-wide patterns of natural selection acting on invasive introgression within and among natural populations occupying diverse environments. We quantified genome-wide patterns of admixture across multiple independent hybrid zones of native westslope cutthroat trout and invasive rainbow trout, the world's most widely introduced fish, by genotyping 339 individuals from 21 populations using 9380 species-diagnostic loci. A significantly greater proportion of the genome appeared to be under selection favouring native cutthroat trout (rather than rainbow trout), and this pattern was pervasive across the genome (detected on most chromosomes). Furthermore, selection against invasive alleles was consistent across populations and environments, even in those where rainbow trout were predicted to have a selective advantage (warm environments). These data corroborate field studies showing that hybrids between these species have lower fitness than the native taxa, and show that these fitness differences are due to selection favouring many native genes distributed widely throughout the genome.

Proceedings of the Royal Society B: Biological Sci↗

USGS2016

Assessments of species' vulnerability to climate change: From pseudo to science

Climate change vulnerability assessments (CCVAs) are important tools to plan for and mitigate potential impacts of climate change. However, CCVAs often lack scientific rigor, which can ultimately lead to poor conservation prioritization and associated ecological and economic costs. We discuss the need to improve comparability and consistency of CCVAs and either validate their findings or improve assessment of CCVA uncertainty and sensitivity to methodological assumptions.

Biodiversity and Conservation↗

USGS2016

Accounting for adaptive capacity and uncertainty in assessments of species’ climate-change vulnerability

Climate change vulnerability assessments (CCVAs) are valuable tools for assessing species’ vulnerability to climatic changes, yet failure to include measures of adaptive capacity and to account for sources of uncertainty may limit their effectiveness. Here, we provide a more comprehensive CCVA approach that incorporates all three elements used for assessing species’ climate change vulnerability: exposure, sensitivity, and adaptive capacity. We illustrate our approach using case studies of two threatened salmonids with different life histories – anadromous steelhead trout ( Oncorhynchus mykiss ) and non-anadromous bull trout ( Salvelinus confluentus ) – within the Columbia River Basin, USA. We identified general patterns of high vulnerability in low-elevation and southernmost habitats for both species. However, vulnerability rankings varied widely depending on the factors (climate, habitat, demographic, and genetic) included in the CCVA and often differed for the two species at locations where they were sympatric. Our findings illustrate that CCVA results are highly sensitive to data inputs and that spatial differences can complicate multi-species conservation. Our results highlight how CCVAs should be considered within a broader conceptual and computational framework for refining hypotheses, guiding research, and comparing plausible scenarios of species’ vulnerability for ongoing and projected climate change.

Columbia River Basin↗

USGS2016

Genetic status and conservation of Westslope Cutthroat Trout in Glacier National Park

Invasive hybridization is one of the greatest threats to the persistence of Westslope Cutthroat Trout Oncorhynchus clarkii lewisi . Large protected areas, where nonhybridized populations are interconnected and express historical life history and genetic diversity, provide some of the last ecological and evolutionary strongholds for conserving this species. Here, we describe the genetic status and distribution of Westslope Cutthroat Trout throughout Glacier National Park, Montana. Admixture between Westslope Cutthroat Trout and introduced Rainbow Trout O. mykiss and Yellowstone Cutthroat Trout O. clarkii bouvieri was estimated by genotyping 1,622 fish collected at 115 sites distributed throughout the Columbia, Missouri, and South Saskatchewan River drainages. Currently, Westslope Cutthroat Trout occupy an estimated 1,465 km of stream habitat and 45 lakes (9,218 ha) in Glacier National Park. There was no evidence of introgression in samples from 32 sites along 587 km of stream length (40% of the stream kilometers currently occupied) and 17 lakes (2,555 ha; 46% of the lake area currently occupied). However, nearly all (97%) of the streams and lakes that were occupied by nonhybridized populations occurred in the Columbia River basin. Based on genetic status (nonnative genetic admixture ≤ 10%), 36 Westslope Cutthroat Trout populations occupying 821 km of stream and 5,482 ha of lakes were identified as “conservation populations.” Most of the conservation populations ( N = 27; 736 km of stream habitat) occurred in the Columbia River basin, whereas only a few geographically restricted populations were found in the South Saskatchewan River ( N = 7; 55 km) and Missouri River ( N = 2; 30 km) basins. Westslope Cutthroat Trout appear to be at imminent risk of genomic extinction in the South Saskatchewan and Missouri River basins, whereas populations in the Columbia River basin are widely distributed and conservation efforts are actively addressing threats from hybridization and other stressors. A diverse set of pro-active management approaches will be required to conserve, protect, and restore Westslope Cutthroat Trout populations in Glacier National Park throughout the 21st century.

Glacier National Park↗

USGS2016

SNP discovery in candidate adaptive genes using exon capture in a free-ranging alpine ungulate

Identification of genes underlying genomic signatures of natural selection is key to understanding adaptation to local conditions. We used targeted resequencing to identify SNP markers in 5321 candidate adaptive genes associated with known immunological, metabolic and growth functions in ovids and other ungulates. We selectively targeted 8161 exons in protein-coding and nearby 5′ and 3′ untranslated regions of chosen candidate genes. Targeted sequences were taken from bighorn sheep ( Ovis canadensis ) exon capture data and directly from the domestic sheep genome ( Ovis aries v. 3; oviAri3). The bighorn sheep sequences used in the Dall's sheep ( Ovis dalli dalli ) exon capture aligned to 2350 genes on the oviAri3 genome with an average of 2 exons each. We developed a microfluidic qPCR-based SNP chip to genotype 476 Dall's sheep from locations across their range and test for patterns of selection. Using multiple corroborating approaches ( lositan and bayescan ), we detected 28 SNP loci potentially under selection. We additionally identified candidate loci significantly associated with latitude, longitude, precipitation and temperature, suggesting local environmental adaptation. The three methods demonstrated consistent support for natural selection on nine genes with immune and disease-regulating functions (e.g. Ovar-DRA, APC, BATF2, MAGEB18), cell regulation signalling pathways (e.g. KRIT1, PI3K, ORRC3), and respiratory health (CYSLTR1). Characterizing adaptive allele distributions from novel genetic techniques will facilitate investigation of the influence of environmental variation on local adaptation of a northern alpine ungulate throughout its range. This research demonstrated the utility of exon capture for gene-targeted SNP discovery and subsequent SNP chip genotyping using low-quality samples in a nonmodel species.

Molecular Ecology Resources↗

USGS2016

Loss of genetic diversity and increased subdivision in an endemic Alpine Stonefly threatened by climate change

Much remains unknown about the genetic status and population connectivity of high-elevation and high-latitude freshwater invertebrates, which often persist near snow and ice masses that are disappearing due to climate change. Here we report on the conservation genetics of the meltwater stonefly Lednia tumana (Ricker) of Montana, USA, a cold-water obligate species. We sequenced 1530 bp of mtDNA from 116 L. tumana individuals representing “historic” (>10 yr old) and 2010 populations. The dominant haplotype was common in both time periods, while the second-most-common haplotype was found only in historic samples, having been lost in the interim. The 2010 populations also showed reduced gene and nucleotide diversity and increased genetic isolation. We found lower genetic diversity in L. tumana compared to two other North American stonefly species, Amphinemura linda (Ricker) and Pteronarcys californica Newport. Our results imply small effective sizes, increased fragmentation, limited gene flow, and loss of genetic variation among contemporary L. tumana populations, which can lead to reduced adaptive capacity and increased extinction risk. This study reinforces concerns that ongoing glacier loss threatens the persistence of L. tumana, and provides baseline data and analysis of how future environmental change could impact populations of similar organisms.

Montana↗

USGS2016

Identification of landscape features influencing gene flow: How useful are habitat selection models?

Understanding how dispersal patterns are influenced by landscape heterogeneity is critical for modeling species connectivity. Resource selection function (RSF) models are increasingly used in landscape genetics approaches. However, because the ecological factors that drive habitat selection may be different from those influencing dispersal and gene flow, it is important to consider explicit assumptions and spatial scales of measurement. We calculated pairwise genetic distance among 301 Dall's sheep (Ovis dalli dalli) in southcentral Alaska using an intensive noninvasive sampling effort and 15 microsatellite loci. We used multiple regression of distance matrices to assess the correlation of pairwise genetic distance and landscape resistance derived from an RSF, and combinations of landscape features hypothesized to influence dispersal. Dall's sheep gene flow was positively correlated with steep slopes, moderate peak normalized difference vegetation indices (NDVI), and open land cover. Whereas RSF covariates were significant in predicting genetic distance, the RSF model itself was not significantly correlated with Dall's sheep gene flow, suggesting that certain habitat features important during summer (rugged terrain, mid-range elevation) were not influential to effective dispersal. This work underscores that consideration of both habitat selection and landscape genetics models may be useful in developing management strategies to both meet the immediate survival of a species and allow for long-term genetic connectivity.

Evolutionary Applications↗

USGS2016

Genomics reveals historic and contemporary transmission dynamics of a bacterial disease among wildlife and livestock

Whole-genome sequencing has provided fundamental insights into infectious disease epidemiology, but has rarely been used for examining transmission dynamics of a bacterial pathogen in wildlife. In the Greater Yellowstone Ecosystem (GYE), outbreaks of brucellosis have increased in cattle along with rising seroprevalence in elk. Here we use a genomic approach to examine Brucella abortus evolution, cross-species transmission and spatial spread in the GYE. We find that brucellosis was introduced into wildlife in this region at least five times. The diffusion rate varies among Brucella lineages (B3 to 8 km per year) and over time. We also estimate 12 host transitions from bison to elk, and 5 from elk to bison. Our results support the notion that free-ranging elk are currently a self-sustaining brucellosis reservoir and the source of livestock infections, and that control measures in bison are unlikely to affect the dynamics of unrelated strains circulating in nearby elk populations.

Nature Communications↗

USGS2016

Applications of genetic data to improve management and conservation of river fishes and their habitats

Environmental variation and landscape features affect ecological processes in fluvial systems; however, assessing effects at management-relevant temporal and spatial scales is challenging. Genetic data can be used with landscape models and traditional ecological assessment data to identify biodiversity hotspots, predict ecosystem responses to anthropogenic effects, and detect impairments to underlying processes. We show that by combining taxonomic, demographic, and genetic data of species in complex riverscapes, managers can better understand the spatial and temporal scales over which environmental processes and disturbance influence biodiversity. We describe how population genetic models using empirical or simulated genetic data quantify effects of environmental processes affecting species diversity and distribution. Our summary shows that aquatic assessment initiatives that use standardized data sets to direct management actions can benefit from integration of genetic data to improve the predictability of disturbance–response relationships of river fishes and their habitats over a broad range of spatial and temporal scales.

Fisheries↗

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↗

USGS2016

Climate variables explain neutral and adaptive variation within salmonid metapopulations: The importance of replication in landscape genetics

Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal how human stressors influence population connectivity, genetic diversity and persistence. We used riverscape genetics modelling to assess whether climatic and habitat variables were related to neutral and adaptive patterns of genetic differentiation (population-specific and pairwise F ST ) within five metapopulations (79 populations, 4583 individuals) of steelhead trout ( Oncorhynchus mykiss ) in the Columbia River Basin, USA. Using 151 putatively neutral and 29 candidate adaptive SNP loci, we found that climate-related variables (winter precipitation, summer maximum temperature, winter highest 5% flow events and summer mean flow) best explained neutral and adaptive patterns of genetic differentiation within metapopulations, suggesting that climatic variation likely influences both demography (neutral variation) and local adaptation (adaptive variation). However, we did not observe consistent relationships between climate variables and F ST across all metapopulations, underscoring the need for replication when extrapolating results from one scale to another (e.g. basin-wide to the metapopulation scale). Sensitivity analysis (leave-one-population-out) revealed consistent relationships between climate variables and F ST within three metapopulations; however, these patterns were not consistent in two metapopulations likely due to small sample sizes ( N = 10). These results provide correlative evidence that climatic variation has shaped the genetic structure of steelhead populations and highlight the need for replication and sensitivity analyses in land and riverscape genetics.

Columbia River Basin↗

USGS2015

Multiple estimates of effective population size for monitoring a long-lived vertebrate: An application to Yellowstone grizzly bears

Effective population size ( N e ) is a key parameter for monitoring the genetic health of threatened populations because it reflects a population's evolutionary potential and risk of extinction due to genetic stochasticity. However, its application to wildlife monitoring has been limited because it is difficult to measure in natural populations. The isolated and well-studied population of grizzly bears ( Ursus arctos ) in the Greater Yellowstone Ecosystem provides a rare opportunity to examine the usefulness of different N e estimators for monitoring. We genotyped 729 Yellowstone grizzly bears using 20 microsatellites and applied three single-sample estimators to examine contemporary trends in generation interval (GI), effective number of breeders ( N b ) and N e during 1982–2007. We also used multisample methods to estimate variance ( N eV ) and inbreeding N e ( N eI ). Single-sample estimates revealed positive trajectories, with over a fourfold increase in N e (≈100 to 450) and near doubling of the GI (≈8 to 14) from the 1980s to 2000s. N eV (240–319) and N eI (256) were comparable with the harmonic mean single-sample N e (213) over the time period. Reanalysing historical data, we found N eV increased from ≈80 in the 1910s–1960s to ≈280 in the contemporary population. The estimated ratio of effective to total census size ( N e /N c ) was stable and high (0.42–0.66) compared to previous brown bear studies. These results support independent demographic evidence for Yellowstone grizzly bear population growth since the 1980s. They further demonstrate how genetic monitoring of N e can complement demographic-based monitoring of N c and vital rates, providing a valuable tool for wildlife managers.

Idaho, Montana, Wyoming↗

USGS2015

Genetic diversity is related to climatic variation and vulnerability in threatened bull trout

Understanding how climatic variation influences ecological and evolutionary processes is crucial for informed conservation decision-making. Nevertheless, few studies have measured how climatic variation influences genetic diversity within populations or how genetic diversity is distributed across space relative to future climatic stress. Here, we tested whether patterns of genetic diversity (allelic richness) were related to climatic variation and habitat features in 130 bull trout ( Salvelinus confluentus ) populations from 24 watersheds (i.e., ~4–7th order river subbasins) across the Columbia River Basin, USA. We then determined whether bull trout genetic diversity was related to climate vulnerability at the watershed scale, which we quantified on the basis of exposure to future climatic conditions (projected scenarios for the 2040s) and existing habitat complexity. We found a strong gradient in genetic diversity in bull trout populations across the Columbia River Basin, where populations located in the most upstream headwater areas had the greatest genetic diversity. After accounting for spatial patterns with linear mixed models, allelic richness in bull trout populations was positively related to habitat patch size and complexity, and negatively related to maximum summer temperature and the frequency of winter flooding. These relationships strongly suggest that climatic variation influences evolutionary processes in this threatened species and that genetic diversity will likely decrease due to future climate change. Vulnerability at a watershed scale was negatively correlated with average genetic diversity ( r = −0.77; P < 0.001); watersheds containing populations with lower average genetic diversity generally had the lowest habitat complexity, warmest stream temperatures, and greatest frequency of winter flooding. Together, these findings have important conservation implications for bull trout and other imperiled species. Genetic diversity is already depressed where climatic vulnerability is highest; it will likely erode further in the very places where diversity may be most needed for future persistence.

Global Change Biology↗

USGS2015

Dispersal and selection mediate hybridization between a native and invasive species

Hybridization between native and non-native species has serious biological consequences, but our understanding of how dispersal and selection interact to influence invasive hybridization is limited. Here, we document the spread of genetic introgression between a native (Oncorhynchus clarkii) and invasive (Oncorhynchus mykiss) trout, and identify the mechanisms influencing genetic admixture. In two populations inhabiting contrasting environments, non-native admixture increased rapidly from 1984 to 2007 and was driven by surprisingly consistent processes. Individual admixture was related to two phenotypic traits associated with fitness: size at spawning and age of juvenile emigration. Fish with higher non-native admixture were larger and tended to emigrate at a younger age—relationships that are expected to confer fitness advantages to hybrid individuals. However, strong selection against non-native admixture was evident across streams and cohorts (mean selection coefficient against genotypes with non-native alleles (s) ¼ 0.60; s.e. ¼ 0.10). Nevertheless, hybridization was promoted in both streams by the continuous immigration of individuals with high levels of non-native admixture from other hybrid source populations. Thus, antagonistic relationships between dispersal and selection are mediating invasive hybridization between these fish, emphasizing that data on dispersal and natural selection are needed to fully understand the dynamics of introgression between native and non-native species. .

Proceedings of the Royal Society B↗

USGS2015

Landscape community genomics: understanding eco-evolutionary processes in complex environments

Extrinsic factors influencing evolutionary processes are often categorically lumped into interactions that are environmentally (e.g., climate, landscape) or community-driven, with little consideration of the overlap or influence of one on the other. However, genomic variation is strongly influenced by complex and dynamic interactions between environmental and community effects. Failure to consider both effects on evolutionary dynamics simultaneously can lead to incomplete, spurious, or erroneous conclusions about the mechanisms driving genomic variation. We highlight the need for a landscape community genomics (LCG) framework to help to motivate and challenge scientists in diverse fields to consider a more holistic, interdisciplinary perspective on the genomic evolution of multi-species communities in complex environments.

Trends in Ecology and Evolution↗

USGS2015

Climate-induced range contraction of a rare alpine aquatic invertebrate

Climate warming poses a serious threat to alpine-restricted species worldwide, yet few studies have empirically documented climate-induced changes in distributions. The rare stonefly, Zapada glacier (Baumann and Gaufin), endemic to alpine streams of Glacier National Park (GNP), Montana, was recently petitioned for listing under the US Endangered Species Act because of climate-change-induced glacier loss, yet little was known about its current status and distribution. We resampled streams throughout the historical distribution of Z. glacier to investigate trends in occurrence associated with changes in temperature and glacial extent. The current geographic distribution of the species was assessed using morphological characteristics of adults and DNA barcoding of nymphs. Bayesian phylogenetic analysis of mtDNA data revealed 8 distinct clades of the genus corresponding with 7 known species from GNP, and one potentially cryptic species. Climate model simulations indicate that average summer air temperature increased (0.67–1.00°C) during the study period (1960–2012), and glacial surface area decreased by &sim;35% from 1966 to 2005. We detected Z. glacier in only 1 of the 6 historically occupied streams and at 2 new locations in GNP. These results suggest that an extremely restricted historical distribution of Z. glacier in GNP has been further reduced over the past several decades by an upstream retreat to higher, cooler sites as water temperatures increased and glacial masses decreased. More research is urgently needed to determine the status, distribution, and vulnerability of Z. glacier and other alpine stream invertebrates threatened by climate change in mountainous ecosystems.

Montana↗

USGS2015

Estimating bighorn sheep (Ovis canadensis) abundance using noninvasive sampling at a mineral lick within a National Park Wilderness Area

Conservation of species requires accurate population estimates. We used genetic markers from feces to determine bighorn sheep abundance for a herd that was hypothesized to be declining and in need of population status monitoring. We sampled from a small but accessible portion of the population's range where animals naturally congregate at a natural mineral lick to test whether we could accurately estimate population size by sampling from an area where animals concentrate. We used mark-recapture analysis to derive population estimates, and compared estimates from this smaller spatial sampling to estimates from sampling of the entire bighorn sheep range. We found that estimates were somewhat comparable; in 2009, the mineral lick sample and entire range sample differed by 20 individuals, and in 2010 they differed by only one individual. However, we captured 13 individuals in the entire range sample that were not captured at the mineral lick, and thus violated a model assumption that all individuals had an equal opportunity of being captured. This eliminated the possibility of inferring a total population estimate from just animals visiting the mineral lick, but because estimates were relatively similar, monitoring at the mineral lick can provide a useful index for management and conservation. We compared our results to a radio-collar study conducted in 2003–2004 and confirmed that the population remained stable since 2004. Our population estimates were 78 (CI 62–114) in 2009 and 95 (CI 77–131) in 2010. Between 7 and 11 sampling dates were needed to achieve a CV of 20% for population estimates, assuming a capture probability between 0.09 and 0.13. We relied on citizen science volunteers to maximize data collection and reduce costs; 71% of all fecal samples were collected by volunteers, compared to 29% collected by paid staff. We conclude that our technique provides a useful monitoring tool for managers. The technique could be tested and applied in similar populations where animals congregate with high fidelity at a mineral lick or other area.

Colorado↗