Combining demographic and genetic factors to assess population vulnerability in stream species

Erin L. Landguth; Clint C. Muhlfeld; Leslie W. Jones; Robin S. Waples; Diane Whited; Winsor H. Lowe; John Lucotch; Helen Neville; Gordon Luikart

doi:10.1890/13-0499.1

USGS · 70132321

Combining demographic and genetic factors to assess population vulnerability in stream species

Erin L. Landguth·Clint C. Muhlfeld·Leslie W. Jones·Robin S. Waples·Diane Whited·Winsor H. Lowe·John Lucotch·Helen Neville·Gordon Luikart

View original source ↗Export metadata ↓

Abstract

Accelerating climate change and other cumulative stressors create an urgent need to understand the influence of environmental variation and landscape features on the connectivity and vulnerability of freshwater species. Here, we introduce a novel modeling framework for aquatic systems that integrates spatially explicit, individual‐based, demographic and genetic (demogenetic) assessments with environmental variables. To show its potential utility, we simulated a hypothetical network of 19 migratory riverine populations (e.g., salmonids) using a riverscape connectivity and demogenetic model (CDFISH). We assessed how stream resistance to movement (a function of water temperature, fluvial distance, and physical barriers) might influence demogenetic connectivity, and hence, population vulnerability. We present demographic metrics (abundance, immigration, and change in abundance) and genetic metrics (diversity, differentiation, and change in differentiation), and combine them into a single vulnerability index for identifying populations at risk of extirpation. We considered four realistic scenarios that illustrate the relative sensitivity of these metrics for early detection of reduced connectivity: (1) maximum resistance due to high water temperatures throughout the network, (2) minimum resistance due to low water temperatures throughout the network, (3) increased resistance at a tributary junction caused by a partial barrier, and (4) complete isolation of a tributary, leaving resident individuals only. We then applied this demogenetic framework using empirical data for a bull trout ( Salvelinus confluentus ) metapopulation in the upper Flathead River system, Canada and USA, to assess how current and predicted future stream warming may influence population vulnerability. Results suggest that warmer water temperatures and associated barriers to movement (e.g., low flows, dewatering) are predicted to fragment suitable habitat for migratory salmonids, resulting in the loss of genetic diversity and reduced numbers in certain vulnerable populations. This demogenetic simulation framework, which is illustrated in a web‐based interactive mapping prototype, should be useful for evaluating population vulnerability in a wide variety of dendritic and fragmented riverscapes, helping to guide conservation and management efforts for freshwater species.

Explore related subjects

Ecological Applications Article

Source-reported bounding extent: 47.63763431783611° to 49.33228198473771° latitude; -114.7906494140625° to -113.44482421875° longitude. This indicates report coverage, not an exact sampling location. View area on OpenStreetMap.

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Erin L. Landguth, Clint C. Muhlfeld, Leslie W. Jones, Robin S. Waples, Diane Whited, Winsor H. Lowe, John Lucotch, Helen Neville, Gordon Luikart. 2014. Combining demographic and genetic factors to assess population vulnerability in stream species. https://doi.org/10.1890/13-0499.1

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related USGS reports

USGS2026

Improving predictions of insect harassment for barren-ground caribou in the Arctic

Many populations of barren-ground caribou ( Rangifer tarandus ) have declined or are declining, which is concerning given their ecological role in Arctic ecosystems and their societal role in northern communities. Insect harassment is an important driver of the behavior, energetics, and demographic rates of caribou, and yet, due to challenges in predicting harassment, there is limited understanding of how it is responding to changing Arctic conditions. We investigated environmental correlates of mosquito (Culicidae) and oestrid fly (Oestridae) harassment for the Porcupine caribou herd, with the aim of improving our ability to predict harassment. We collected field observations of mosquito activity and used video collars to detect oestrid fly activity across the summer range, which spans the Alaska–Yukon border. Additionally, we documented the composition of harassing insects collected in malaise traps using DNA metabarcoding. We developed predictive mosquito and oestrid fly harassment models using remotely sensed variables relevant to the insects' biology within a nonlinear modeling framework. We then used the top mosquito and oestrid fly models to hindcast predictions of harassment during 1950–2024 and investigate long-term changes in severity and phenology. The top mosquito harassment model included wind speed, temperature, days since snowmelt, precipitation, topographic position, and soil moisture. The top oestrid fly harassment model included temperature, cumulative growing degree days, and time of day. Harassment of both insects was limited at low temperatures (<10°C), with mosquitoes being additionally limited at high temperatures (>22°C) and wind speeds (>7 m/s). The phenology of mosquito and oestrid fly harassment exhibited curvilinear trends across the summer, peaking in midsummer based on the number of days since snowmelt and cumulative growing degree days, respectively. Mosquito harassment also increased with greater soil moisture, precipitation, and at lower relative elevations. Hindcasting indicated that insect harassment notably intensified and advanced over time. Intensifying harassment could decrease caribou foraging opportunities and body condition, and advancing harassment is likely to increasingly overlap with the calving season when calves are most vulnerable. Our results highlight climate-driven changes in insect harassment and provide improved indices for predicting harassment in the Arctic for future applications.

Alaska↗

USGS2026

Application of close-kin mark–recapture to an American black bear population using harvest samples

Close-kin mark–recapture (CKMR) offers a promising alternative to traditional mark–recapture methods for estimating wildlife population parameters. CKMR estimates demographic parameters by identifying genetic relationships between individuals, effectively “recapturing” parental genotypes through their offspring's genetic profiles. One key advantage of CKMR over traditional methods is the ability to estimate abundance without recapture, facilitating the use of lethally collected biological samples. Here, we present an application of CKMR to a terrestrial species using samples collected from harvested individuals. We analyzed genetic data from 1767 American black bears ( Ursus americanus ) harvested over two consecutive years in Michigan's Upper Peninsula. Using Genotyping-in-Thousands by sequencing (GT-seq), we identified parent-offspring pairs and developed sex-specific models tailored to black bear reproductive biology and management strategies. Female population estimates aligned with our expectations, based on prior knowledge of the population. In contrast, male population estimates deviated from expectations, potentially due to an unmodeled combination of factors pertaining to male reproductive biology and sampling bias. Our study not only demonstrates the viability of using harvest-based CKMR for monitoring of terrestrial wildlife populations, but also highlights the need for careful model specification. By providing a novel method to estimate demographic parameters and population size, CKMR using harvest samples can inform management decisions and harvest quotas. This approach leverages existing management practices involving collection of genetic samples, such as mandatory harvest registrations and health monitoring programs. Our findings contribute to the growing body of CKMR applications and expand its use to terrestrial species management.

Michigan↗

USGS2026

Listening for extinction: Range-wide occupancy highlights critical risks and priorities for northern spotted owls

The northern spotted owl ( Strix occidentalis caurina ) continues to decline across its range, threatened by habitat disturbances and invasive barred owls ( Strix varia ). We conducted a range-wide spotted owl occupancy assessment using 2.1 million h of passive acoustic recordings from 4081 survey stations within 1027 randomly selected 5-km 2 hexagons across six physiographic regions. Applying multistate occupancy models, we estimated probabilities of landscape use (by at least one northern spotted owl) and pair occupancy (occupied by both a male and a female), while accounting for imperfect and sex-biased detection probability. Detection probability of pairs was low in most regions, primarily due to undetected females, but increased with survey effort. If management decisions can only be made when there is a high probability of detecting both sexes when they are present, then longer surveys are one approach to support the decisions. Landscape use and pair occupancy were positively associated with old-growth forest structure and topographic diversity. We also found a pronounced latitudinal gradient in spotted owl landscape use rates with estimated mean landscape use of 0.17 (SE = 0.03) and 0.16 (SE = 0.02) in the two most northern regions, and 0.54 (SE = 0.04) and 0.52 (SE = 0.05) in the two most southern regions. Pair occupancy rates were higher in southern regions (0.29, SE = 0.03, 0.43, SE = 0.05) and very low in northern regions (0.04, SE = 0.01, 0.03, SE = 0.01). In contrast to spotted owls, barred owls were detected in 90% of northern hexagons and 50% of southern hexagons, and barred owl calling intensity was over eight times higher than spotted owls. These results highlight extinction risks in several regions and suggest that management actions, such as spatially targeted barred owl control and protection of structurally complex habitats, have a narrow temporal window in which they can be effective in lowering the probability of regional extirpations. We generated predictive maps of landscape use and pair occupancy, which could help guide regional conservation strategies. This study demonstrates how passive acoustic monitoring and machine learning can be used for broad-scale ecological monitoring, identifying extinction risk thresholds, supporting adaptive management, and improving conservation outcomes for wide-ranging and elusive species that can reliably be detected through unique vocalizations.

California, Oregon, Washington↗