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USGS2010

A rapid, strong, and convergent genetic response to urban habitat fragmentation in four divergent and widespread vertebrates

Background: Urbanization is a major cause of habitat fragmentation worldwide. Ecological and conservation theory predicts many potential impacts of habitat fragmentation on natural populations, including genetic impacts. Habitat fragmentation by urbanization causes populations of animals and plants to be isolated in patches of suitable habitat that are surrounded by non-native vegetation or severely altered vegetation, asphalt, concrete, and human structures. This can lead to genetic divergence between patches and in turn to decreased genetic diversity within patches through genetic drift and inbreeding. Methodology/Principal Findings: We examined population genetic patterns using microsatellites in four common vertebrate species, three lizards and one bird, in highly fragmented urban southern California. Despite significant phylogenetic, ecological, and mobility differences between these species, all four showed similar and significant reductions in gene flow over relatively short geographic and temporal scales. For all four species, the greatest genetic divergence was found where development was oldest and most intensive. All four animals also showed significant reduction in gene flow associated with intervening roads and freeways, the degree of patch isolation, and the time since isolation. Conclusions/Significance: Despite wide acceptance of the idea in principle, evidence of significant population genetic changes associated with fragmentation at small spatial and temporal scales has been rare, even in smaller terrestrial vertebrates, and especially for birds. Given the striking pattern of similar and rapid effects across four common and widespread species, including a volant bird, intense urbanization may represent the most severe form of fragmentation, with minimal effective movement through the urban matrix.

California↗

USGS2018

Reexamining the frequency range of hearing in silver (Hypophthalmichthys molitrix) and bighead (H. nobilis) carp

Silver ( Hypophthalmichthys molitrix ) and bighead ( H . nobilis ) carp (collectively bigheaded carp) are invasive fish that threaten aquatic ecosystems in the upper Midwest United States and the Laurentian Great Lakes. Controlling bigheaded carp is a priority of fisheries managers and one area of focus involves developing acoustic deterrents to prevent upstream migration. For an acoustic deterrent to be effective however, the hearing ability of bigheaded carp must be characterized. A previous study showed that bigheaded carp detected sound up to 3 kHz but this range is narrower than what has been reported for other ostariophysans. Therefore, silver and bighead carp frequency detection was evaluated in response to 100 Hz to 9 kHz using auditory evoked potentials (AEPs). AEPs were recorded from 100 Hz to 5 kHz. The lowest thresholds were at 500 Hz for both species (silver carp threshold: 80.6 ± 3.29 dB re 1 μPa SPL rms , bighead carp threshold: 90.5 ± 5.75 dB re 1 μPa SPL rms ; mean ± SD). These results provide fisheries managers with better insight on effective acoustic stimuli for deterrent systems, however, to fully determine bigheaded carp hearing abilities, these results need to be compared with behavioral assessments.

PLoS ONE↗

USGS2014

Influence of climate change on productivity of American White Pelicans, Pelecanus erythrorhynchos

In the past decade, severe weather and West Nile virus were major causes of chick mortality at American white pelican (Pelecanus erythrorhynchos) colonies in the northern plains of North America. At one of these colonies, Chase Lake National Wildlife Refuge in North Dakota, spring arrival by pelicans has advanced approximately 16 days over a period of 44 years (1965–2008). We examined phenology patterns of pelicans and timing of inclement weather through the 44-year period, and evaluated the consequence of earlier breeding relative to weather-related chick mortality. We found severe weather patterns to be random through time, rather than concurrently shifting with the advanced arrival of pelicans. In recent years, if nest initiations had followed the phenology patterns of 1965 (i.e., nesting initiated 16 days later), fewer chicks likely would have died from weather-related causes. That is, there would be fewer chicks exposed to severe weather during a vulnerable transition period that occurs between the stage when chicks are being brooded by adults and the stage when chicks from multiple nests become part of a thermally protective crèche.

North Dakota↗

USGS2017

A new mechanistic approach for the further development of a population with established size bimodality

Usually, the origin of a within-cohort bimodal size distribution is assumed to be caused by initial size differences or by one discrete period of accelerated growth for one part of the population. The aim of this study was to determine if more continuous pathways exist allowing shifts from the small to the large fraction within a bimodal age-cohort. Therefore, a Eurasian perch population, which had already developed a bimodal size-distribution and had differential resource use of the two size-cohorts, was examined. Results revealed that formation of a bimodal size-distribution can be a continuous process. Perch from the small size-cohort were able to grow into the large size-cohort by feeding on macroinvertebrates not used by their conspecifics. The diet shifts were accompanied by morphological shape changes. Intra-specific competition seemed to trigger the development towards an increasing number of large individuals. A stage-structured matrix model confirmed these assumptions. The fact that bimodality can be a continuous process is important to consider for the understanding of ecological processes and links within ecosystems.

PLoS ONE↗

USGS2024

Detection and transport of environmental DNA from two federally endangered mussels

Environmental DNA (eDNA) offers a novel approach to supplement traditional surveys and provide increased spatial and temporal information on species detection, and it can be especially beneficial for detecting at risk or threatened species with minimal impact on the target species. The transport of eDNA in lotic environments is an important component in providing more informed descriptions of where and when a species is present, but eDNA transport phenomena are not well understood. In this study, we used species-specific assays to detect eDNA from two federally endangered mussels in two geographically distinct rivers. Using the eDNA concentrations measured from field samples, we developed a one-dimensional (1D) hydrodynamic transport model to predict the downstream fate and transport of eDNA. We detected eDNA from both federally endangered mussels across several seasons and flow rates and up to 3.5 km downstream from the source populations, but the detection rates and eDNA concentrations were highly variable across and within rivers and study reaches. Our 1D transport models successfully integrated the variability of the eDNA field samples into the model predictions and overall model results were generally within ±1 standard error of the eDNA field concentration values. Overall, the results of this study demonstrate the importance of optimizing the spatial locations from where eDNA is collected downstream from a source population, and it highlights the need to improve understanding on the shedding mechanisms and magnitude of eDNA from source populations and biogeomorphic processes that influence eDNA transport.

Missouri, Tennessee↗

USGS2020

The geometry of reaction norms yields insights on classical fitness functions for Great Lakes salmon

Life history theory examines how characteristics of organisms, such as age and size at maturity, may vary through natural selection as evolutionary responses that optimize fitness. Here we ask how predictions of age and size at maturity differ for the three classical fitness functions–intrinsic rate of natural increase r , net reproductive rate R 0 , and reproductive value V x −for semelparous species. We show that different choices of fitness functions can lead to very different predictions of species behavior. In one’s efforts to understand an organism’s behavior and to develop effective conservation and management policies, the choice of fitness function matters. The central ingredient of our approach is the maturation reaction norm (MRN), which describes how optimal age and size at maturation vary with growth rate or mortality rate. We develop a practical geometric construction of MRNs that allows us to include different growth functions (linear growth and nonlinear von Bertalanffy growth in length) and develop two-dimensional MRNs useful for quantifying growth-mortality trade-offs. We relate our approach to Beverton-Holt life history invariants and to the Stearns-Koella categorization of MRNs. We conclude with a detailed discussion of life history parameters for Great Lakes Chinook Salmon and demonstrate that age and size at maturity are consistent with predictions using R 0 (but not r or V x ) as the underlying fitness function.

Great Lakes↗

USGS2018

Weather and landscape factors affect white-tailed deer neonate survival at ecologically important life stages in the Northern Great Plains

Offspring survival is generally more variable than adult survival and may limit population growth. Although white-tailed deer neonate survival has been intensively investigated, recent work has emphasized how specific cover types influence neonate survival at local scales (single study area). These localized investigations have often led to inconsistences within the literature. Developing specific hypotheses describing the relationships among environmental, habitat, and landscape factors influencing white-tailed deer neonate survival at regional scales may allow for detection of generalized patterns. Therefore, we developed 11 hypotheses representing the various effects of environmental (e.g., winter and spring weather), habitat (e.g., hiding and escape cover types), and landscape factors (e.g., landscape configuration regardless of specific cover type available) on white-tailed deer neonate survival up to one-month and from one- to three-months of age. At one-month, surviving fawns experienced a warmer lowest recorded June temperature and more June precipitation than those that perished. At three-months, patch connectance (percent of patches of the corresponding patch type that are connected within a predefined distance) positively influenced survival. Our results are consistent with white-tailed deer neonate ecology: increased spring temperature and precipitation are likely associated with a flush of nutritional resources available to the mother, promoting increased lactation efficiency and neonate growth early in life. In contrast, reduced spring temperature with increased precipitation place neonates at risk to hypothermia. Increased patch connectance likely reflects increased escape cover available within a neonate’s home range after they are able to flee from predators. If suitable escape cover is available on the landscape, then managers could focus efforts towards manipulating landscape configuration (patch connectance) to promote increased neonate survival while monitoring spring weather to assess potential influences on current year survival.

Minnesota, North Dakota, South Dakota↗

USGS2015

Estimating population size for Capercaillie ( Tetrao urogallus L.) with spatial capture-recapture models based on genotypes from one field sample

We conducted a survey of an endangered and cryptic forest grouse, the capercaillie Tetrao urogallus , based on droppings collected on two sampling occasions in eight forest fragments in central Switzerland in early spring 2009. We used genetic analyses to sex and individually identify birds. We estimated sex-dependent detection probabilities and population size using a modern spatial capture-recapture (SCR) model for the data from pooled surveys. A total of 127 capercaillie genotypes were identified (77 males, 46 females, and 4 of unknown sex). The SCR model yielded atotal population size estimate (posterior mean) of 137.3 capercaillies (posterior sd 4.2, 95% CRI 130–147). The observed sex ratio was skewed towards males (0.63). The posterior mean of the sex ratio under the SCR model was 0.58 (posterior sd 0.02, 95% CRI 0.54–0.61), suggesting a male-biased sex ratio in our study area. A subsampling simulation study indicated that a reduced sampling effort representing 75% of the actual detections would still yield practically acceptable estimates of total size and sex ratio in our population. Hence, field work and financial effort could be reduced without compromising accuracy when the SCR model is used to estimate key population parameters of cryptic species.

PLoS ONE↗

USGS2013

Representation of ecological systems within the protected areas network of the continental United States

If conservation of biodiversity is the goal, then the protected areas network of the continental US may be one of our best conservation tools for safeguarding ecological systems (i.e., vegetation communities). We evaluated representation of ecological systems in the current protected areas network and found insufficient representation at three vegetation community levels within lower elevations and moderate to high productivity soils. We used national-level data for ecological systems and a protected areas database to explore alternative ways we might be able to increase representation of ecological systems within the continental US. By following one or more of these alternatives it may be possible to increase the representation of ecological systems in the protected areas network both quantitatively (from 10% up to 39%) and geographically and come closer to meeting the suggested Convention on Biological Diversity target of 17% for terrestrial areas. We used the Landscape Conservation Cooperative framework for regional analysis and found that increased conservation on some private and public lands may be important to the conservation of ecological systems in Western US, while increased public-private partnerships may be important in the conservation of ecological systems in Eastern US. We have not assessed the pros and cons of following the national or regional alternatives, but rather present them as possibilities that may be considered and evaluated as decisions are made to increase the representation of ecological systems in the protected areas network across their range of ecological, geographical, and geophysical occurrence in the continental US into the future.

PLoS ONE↗

USGS2013

Aspects of embryonic and larval development in bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix

As bighead carp Hypophthalmichthys nobilis and silver carp H. molitrix (the bigheaded carps) are poised to enter the Laurentian Great Lakes and potentially damage the region’s economically important fishery, information on developmental rates and behaviors of carps is critical to assessing their ability to establish sustainable populations within the Great Lakes basin. In laboratory experiments, the embryonic and larval developmental rates, size, and behaviors of bigheaded carp were tracked at two temperature treatments, one “cold” and one “warm”. Developmental rates were computed using previously described stages of development and the cumulative thermal unit method. Both species have similar thermal requirements, with a minimum developmental temperature for embryonic stages of 12.1° C for silver carp and 12.9° C for bighead carp, and 13.3° C for silver carp larval stages and 13.4° C for bighead carp larval stages. Egg size differed among species and temperature treatments, as egg size was larger in bighead carp, and “warm" temperature treatments. The larvae started robust upwards vertical swimming immediately after hatching, interspersed with intervals of sinking. Vertical swimming tubes were used to measure water column distribution, and ascent and descent rates of vertically swimming fish. Water column distribution and ascent and descent rates changed with ontogeny. Water column distribution also showed some diel periodicity. Developmental rates, size, and behaviors contribute to the drift distance needed to fulfill the early life history requirements of bigheaded carps and can be used in conjunction with transport information to assess invasibility of a river.

PLoS ONE↗

USGS2017

Quantifying the demographic cost of human-related mortality to a raptor population

Raptors are exposed to a wide variety of human-related mortality agents, and yet population-level effects are rarely quantified. Doing so requires modeling vital rates in the context of species life-history, behavior, and population dynamics theory. In this paper, we explore the details of such an analysis by focusing on the demography of a resident, tree-nesting population of golden eagles ( Aquila chrysaetos ) in the vicinity of an extensive (142 km 2 ) windfarm in California. During 1994–2000, we tracked the fates of >250 radio-marked individuals of four life-stages and conducted five annual surveys of territory occupancy and reproduction. Collisions with wind turbines accounted for 41% of 88 uncensored fatalities, most of which were subadults and nonbreeding adults (floaters). A consistent overall male preponderance in the population meant that females were the limiting sex in this territorial, monogamous species. Estimates of potential population growth rate and associated variance indicated a stable breeding population, but one for which any further decrease in vital rates would require immigrant floaters to fill territory vacancies. Occupancy surveys 5 and 13 years later (2005 and 2013) showed that the nesting population remained intact, and no upward trend was apparent in the proportion of subadult eagles as pair members, a condition that would have suggested a deficit of adult replacements. However, the number of golden eagle pairs required to support windfarm mortality was large. We estimated that the entire annual reproductive output of 216–255 breeding pairs would have been necessary to support published estimates of 55–65 turbine blade-strike fatalities per year. Although the vital rates forming the basis for these calculations may have changed since the data were collected, our approach should be useful for gaining a clearer understanding of how anthropogenic mortality affects the health of raptor populations, particularly those species with delayed maturity and naturally low reproductive rates.

PLoS ONE↗

USGS2012

A plant distribution shift: temperature, drought or past disturbance?

Simple models of plant response to warming climates predict vegetation moving to cooler and/or wetter locations: in mountainous regions shifting upslope. However, species-specific responses to climate change are likely to be much more complex. We re-examined a recently reported vegetation shift in the Santa Rosa Mountains, California, to better understand the mechanisms behind the reported shift of a plant distribution upslope. We focused on five elevational zones near the center of the gradient that captured many of the reported shifts and which are dominated by fire-prone chaparral. Using growth rings, we determined that a major assumption of the previous work was wrong: past fire histories differed among elevations. To examine the potential effect that this difference might have on the reported upward shift, we focused on one species, Ceanothus greggii : a shrub that only recruits post-fire from a soil stored seedbank. For five elevations used in the prior study, we calculated time series of past per-capita mortality rates by counting growth rings on live and dead individuals. We tested three alternative hypotheses explaining the past patterns of mortality: 1) mortality increased over time consistent with climate warming, 2) mortality was correlated with drought indices, and 3) mortality peaked 40–50 years post fire at each site, consistent with self-thinning. We found that the sites were different ages since the last fire, and that the reported increase in the mean elevation of C. greggii was due to higher recent mortality at the lower elevations, which were younger sites. The time-series pattern of mortality was best explained by the self-thinning hypothesis and poorly explained by gradual warming or drought. At least for this species, the reported distribution shift appears to be an artifact of disturbance history and is not evidence of a climate warming effect.

California↗

USGS2022

Human populations in the world’s mountains: Spatio-temporal patterns and potential controls

Changing climate and human demographics in the world's mountains will have increasingly profound environmental and societal consequences across all elevations. Quantifying current human populations in and near mountains is crucial to ensure that any interventions in these complex social-ecological systems are appropriately resourced, and that valuable ecosystems are effectively protected. However, comprehensive and reproducible analyses on this subject are lacking. Here, we develop and implement an open workflow to quantify the sensitivity of mountain population estimates over recent decades, both globally and for several sets of relevant reporting regions, to alternative input dataset combinations. Relationships between mean population density and several potential environmental covariates are also explored across elevational bands within individual mountain regions (i.e. sub-mountain range scale). Globally, mountain population estimates vary greatly from 0.344 billion (<5% of the corresponding global total) to 2.289 billion (>31%) in 2015. A more detailed analysis using one of the population datasets (GHS-POP) revealed that in 35% of mountain sub-regions, population increased at least twofold over the 40-year period 19752015. The urban proportion of the total mountain population in 2015 ranged from 6% to 39%, depending on the combination of population and urban extent datasets used. At sub-mountain range scale, population density was found to be more strongly associated with climatic than with topographic and protected-area variables, and these relationships appear to have strengthened slightly over time. Such insights may contribute to improved predictions of future mountain population distributions under scenarios of future climatic and demographic change. Overall, our work emphasizes that irrespective of data choices, substantial human populations are likely to be directly affected by and themselves affect mountainous environmental and ecological change. It thereby further underlines the urgency with which the multitudinous challenges concerning the interactions between mountain climate and human societies under change must be tackled.

PLoS ONE↗

USGS2023

Migration, breeding location, and seascape shape seabird assemblages in the northern Gulf of Mexico

The Gulf of Mexico supports many seabird species, yet data gaps describing species composition and habitat use are prevalent. We used vessel-based observations from the Gulf of Mexico Marine Assessment Program for Protected Species to identify and characterize distinct seabird assemblages in the northern Gulf of Mexico (within the U.S. Exclusive Economic Zone; nGoM). Using cluster analysis of 17 seabird species, we identified assemblages based on seabird relative density. Vessel-based surveys documented the location, species, and number of seabirds across the nGoM between 2017–2019. For each assemblage, we identified the (co-)dominant species, spatial distribution, and areas of greater relative density. We also assessed the relationship of the total relative density within each assemblage with environmental, spatial, and temporal covariates. Of the species assessed, 76% (n = 13) breed predominantly outside the nGoM basin. We identified four seabird assemblages. Two assemblages, one dominated by black tern and the other co-dominated by northern gannet/laughing gull, occurred on the continental shelf. An assemblage dominated by sooty tern occurred along the continental slope into pelagic waters. The fourth assemblage had no dominant species, was broadly distributed, and was composed of observations with low relative density (‘singles’ assemblage). Differentiation of assemblages was linked to migratory patterns, residency, and breeding location. The spatial distributions and relationships of the black tern and northern gannet/laughing gull assemblages with environmental covariates indicate associations with river outflows and ports. The sooty tern assemblage overlapped an area prone to mesoscale feature formation. The singles assemblage may reflect commuting and dispersive behaviors. These findings highlight the importance of seasonal migrations and dynamic features across the seascape, shaping seabird assemblages. Considering the potential far-ranging effects of interactions with seabirds in the nGoM, awareness of these unique patterns and potential links with other fauna could inform future monitoring, research, restoration, offshore energy, and aquaculture development in this highly industrialized sea.

Gulf of Mexico↗

USGS2013

Of travertine and time: otolith chemistry and microstructure detect provenance and demography of endangered humpback chub in Grand Canyon, USA

We developed a geochemical atlas of the Colorado River in Grand Canyon and in its tributary, the Little Colorado River, and used it to identify provenance and habitat use by Federally Endangered humpback chub, Gila cypha. Carbon stable isotope ratios (δ 13 C) discriminate best between the two rivers, but fine scale analysis in otoliths requires rare, expensive instrumentation. We therefore correlated other tracers (SrSr, Ba, and Se in ratio to Ca) to δ 13 C that are easier to quantify in otoliths with other microchemical techniques. Although the Little Colorado River’s water chemistry varies with major storm events, at base flow or near base flow (conditions occurring 84% of the time in our study) its chemistry differs sufficiently from the mainstem to discriminate one from the other. Additionally, when fish egress from the natal Little Colorado River to the mainstem, they encounter cold water which causes the otolith daily growth increments to decrease in size markedly. Combining otolith growth increment analysis and microchemistry permitted estimation of size and age at first egress; size at first birthday was also estimated. Emigrants < 1 year old averaged 51.2 ± 4.4 (SE) days and 35.5 ± 3.6 mm at egress; older fish that had recruited to the population averaged 100 ± 7.8 days old and 51.0 ± 2.2 mm at egress, suggesting that larger, older emigrants recruit better. Back-calculated size at age 1 was unimodal and large (78.2 ± 3.3 mm) in Little Colorado caught fish but was bimodally distributed in Colorado mainstem caught fish (49.9 ± 3.6 and 79 ± 4.9 mm) suggesting that humpback chub can also rear in the mainstem. The study demonstrates the coupled usage of the two rivers by this fish and highlights the need to consider both rivers when making management decisions for humpback chub recovery.

Arizona↗

USGS2014

Influence of fuels, weather and the built environment on the exposure of property to wildfire

Wildfires can pose a significant risk to people and property. Billions of dollars are spent investing in fire management actions in an attempt to reduce the risk of loss. One of the key areas where money is spent is through fuel treatment – either fuel reduction (prescribed fire) or fuel removal (fuel breaks). Individual treatments can influence fire size and the maximum distance travelled from the ignition and presumably risk, but few studies have examined the landscape level effectiveness of these treatments. Here we use a Bayesian Network model to examine the relative influence of the built and natural environment, weather, fuel and fuel treatments in determining the risk posed from wildfire to the wildland-urban interface. Fire size and distance travelled was influenced most strongly by weather, with exposure to fires most sensitive to changes in the built environment and fire parameters. Natural environment variables and fuel load all had minor influences on fire size, distance travelled and exposure of assets. These results suggest that management of fuels provided minimal reductions in risk to assets and adequate planning of the changes in the built environment to cope with the expansion of human populations is going to be vital for managing risk from fire under future climates.

PLoS ONE↗

USGS2016

Inter-annual variability of area-scaled gaseous carbon emissions from wetland soils in the Liaohe Delta, China

Global management of wetlands to suppress greenhouse gas (GHG) emissions, facilitate carbon (C) sequestration, and reduce atmospheric CO 2 concentrations while simultaneously promoting agricultural gains is paramount. However, studies that relate variability in CO 2 and CH 4 emissions at large spatial scales are limited. We investigated three-year emissions of soil CO 2 and CH 4 from the primary wetland types of the Liaohe Delta, China, by focusing on a total wetland area of 3287 km 2 . One percent is Suaeda salsa , 24% is Phragmites australis , and 75% is rice. While S . salsa wetlands are under somewhat natural tidal influence, P . australis and rice are managed hydrologically for paper and food, respectively. Total C emissions from CO 2 and CH 4 from these wetland soils were 2.9 Tg C/year, ranging from 2.5 to 3.3 Tg C/year depending on the year assessed. Primary emissions were from CO 2 (~98%). Photosynthetic uptake of CO 2 would mitigate most of the soil CO 2 emissions, but CH 4 emissions would persist. Overall, CH 4 fluxes were high when soil temperatures were >18°C and pore water salinity <18 PSU. CH 4 emissions from rice habitat alone in the Liaohe Delta represent 0.2% of CH 4 carbon emissions globally from rice. With such a large area and interannual sensitivity in soil GHG fluxes, management practices in the Delta and similar wetlands around the world have the potential not only to influence local C budgeting, but also to influence global biogeochemical cycling.

Liaohe Delta↗

USGS2021

Joint species distribution models of Everglades wading birds to inform restoration planning

Restoration of the Florida Everglades, a substantial wetland ecosystem within the United States, is one of the largest ongoing restoration projects in the world. Decision-makers and managers within the Everglades ecosystem rely on ecological models forecasting indicator wildlife response to changes in the management of water flows within the system. One such indicator of ecosystem health, the presence of wading bird communities on the landscape, is currently assessed using three species distribution models that assume perfect detection and report output on different scales that are challenging to compare against one another. We sought to use current advancements in species distribution modeling to improve models of Everglades wading bird distribution. Using a joint species distribution model that accounted for imperfect detection, we modeled the presence of nine species of wading bird simultaneously in response to annual hydrologic conditions and landscape characteristics within the Everglades system. Our resulting model improved upon the previous model in three key ways: 1) the model predicts probability of occupancy for the nine species on a scale of 0–1, making the output more intuitive and easily comparable for managers and decision-makers that must consider the responses of several species simultaneously; 2) through joint species modeling, we were able to consider rarer species within the modeling that otherwise are detected in too few numbers to fit as individual models; and 3) the model explicitly allows detection probability of species to be less than 1 which can reduce bias in the site occupancy estimates. These improvements are essential as Everglades restoration continues and managers require models that consider the impacts of water management on key indicator wildlife such as the wading bird community.

Florida↗