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USGS2012

Biodiversity loss and its impact on humanity

The most unique feature of Earth is the existence of life, and the most extraordinary feature of life is its diversity. Approximately 9 million types of plants, animals, protists and fungi inhabit the Earth. So, too, do 7 billion people. Two decades ago, at the first Earth Summit, the vast majority of the world's nations declared that human actions were dismantling the Earth's ecosystems, eliminating genes, species and biological traits at an alarming rate. This observation led to the question of how such loss of biological diversity will alter the functioning of ecosystems and their ability to provide society with the goods and services needed to prosper.

Nature↗

USGS2014

Rate of tree carbon accumulation increases continuously with tree size

Forests are major components of the global carbon cycle, providing substantial feedback to atmospheric greenhouse gas concentrations. Our ability to understand and predict changes in the forest carbon cycle—particularly net primary productivity and carbon storage - increasingly relies on models that represent biological processes across several scales of biological organization, from tree leaves to forest stands. Yet, despite advances in our understanding of productivity at the scales of leaves and stands, no consensus exists about the nature of productivity at the scale of the individual tree, in part because we lack a broad empirical assessment of whether rates of absolute tree mass growth (and thus carbon accumulation) decrease, remain constant, or increase as trees increase in size and age. Here we present a global analysis of 403 tropical and temperate tree species, showing that for most species mass growth rate increases continuously with tree size. Thus, large, old trees do not act simply as senescent carbon reservoirs but actively fix large amounts of carbon compared to smaller trees; at the extreme, a single big tree can add the same amount of carbon to the forest within a year as is contained in an entire mid-sized tree. The apparent paradoxes of individual tree growth increasing with tree size despite declining leaf-level and stand-level productivity can be explained, respectively, by increases in a tree’s total leaf area that outpace declines in productivity per unit of leaf area and, among other factors, age-related reductions in population density. Our results resolve conflicting assumptions about the nature of tree growth, inform efforts to understand and model forest carbon dynamics, and have additional implications for theories of resource allocation and plant senescence.

Nature↗

USGS2021

Solutions in microbiome engineering: Prioritizing barriers to organism establishment

Microbiome engineering is increasingly being employed as a solution to challenges in health, agriculture, and climate. Often manipulation involves inoculation of new microbes designed to improve function into a preexisting microbial community. Despite, increased efforts in microbiome engineering inoculants frequently fail to establish and/or confer long-lasting modifications on ecosystem function. We posit that one underlying cause of these shortfalls is the failure to consider barriers to organism establishment. This is a key challenge and focus of macroecology research, specifically invasion biology and restoration ecology. We adopt a framework from invasion biology that summarizes establishment barriers in three categories: (1) propagule pressure, (2) environmental filtering, and (3) biotic interactions factors. We suggest that biotic interactions is the most neglected factor in microbiome engineering research, and we recommend a number of actions to accelerate engineering solutions.

The ISME Journal: Multidisciplinary Journal of Mic↗

USGS2021

Comparison of sample types from white-tailed deer (Odocoileus virginianus) for DNA extraction and analyses

Collection of biological samples for DNA is necessary in a variety of disciplines including disease epidemiology, landscape genetics, and forensics. Quantity and quality of DNA varies depending on the method of collection or media available for collection (e.g., blood, tissue, fecal). Blood is the most common sample collected in vials or on Whatman Flinders Technology Associates (FTA) cards with short- and long-term storage providing adequate DNA for study objectives. The focus of this study was to determine if biological samples stored on Whatman FTA Elute cards were a reasonable alternative to traditional DNA sample collection, storage, and extraction. Tissue, nasal swabs, and ocular fluid were collected from white-tailed deer ( Odocoileus virginianus ). Tissue samples and nasal swabs acted as a control to compare extraction and DNA suitability for microsatellite analysis for nasal swabs and ocular fluid extracted from FTA Elute cards. We determined that FTA Elute cards improved the extraction time and storage of samples and that nasal swabs and ocular fluid containing pigmented fluid were reasonable alternatives to traditional tissue DNA extractions.

Pennsylvania↗

USGS2025

A molecular specimen bank for contemporary and future study captures landscape-scale biodiversity baselines before Klamath River dam removal

Global restoration and conservation of freshwater biodiversity are represented in practice by works such as the Klamath River Renewal Project (KRRP), the largest dam removal and river restoration in the United States, which has reconnected 640 river kilometers. With dam removals, many biological outcomes remain understudied due to a lack of pre-impact data and complex ecosystem recovery timeframes. To avoid this, we created the KRRP molecular library, an environmental specimen bank, for long-term curation of environmental nucleic acids collected from the restoration project. We used these initial samples, environmental DNA metabarcoding, and generalized linear mixed-effects models to evaluate patterns of pre-dam removal fish richness and diversity. Demonstrating the suitability to resolve biological differences, the baseline shows that tributary and mainstem streams had greater native fish diversity and 2.3–10.7 times greater native fish species richness than reservoirs. These and future sampling efforts should, at a minimum, allow tracking of fish community response to ecosystem restoration. Anticipating the acceleration of omics innovation, we preserved samples for long-term storage and identified requisite phases for sustained function and adaptation of the molecular library: securing a physical storage facility for genetic material, establishing a governance structure, and confirming support for archive management.

California, Oregon↗

USGS2002

Variation in survivorship of a migratory songbird throughout its annual cycle

1. Demographic data from both breeding and non-breeding periods are needed to manage populations of migratory birds, many of which are declining in abundance and are of conservation concern. Although habitat associations, and to a lesser extent, reproductive biology, are known for many migratory species, few studies have measured survival rates of these birds at different parts of their annual cycle. 2. Cormack–Jolly–Seber models and Akaike’s information criterion model selection were used to investigate seasonal variation in survival of a Nearctic – Neotropical migrant songbird, the black-throated blue warbler, Dendroica caerulescens . Seasonal and annual survival were estimated from resightings of colour-ringed individuals on breeding grounds in New Hampshire, USA from 1986 to 2000 and on winter quarters in Jamaica, West Indies from 1986 to 1999. Warblers were studied each year during the May–August breeding period in New Hampshire and during the October–March overwinter period in Jamaica. 3. In New Hampshire, males had higher annual survival (0·51 ± 0·03) and recapture probabilities (0·93 ± 0·03) than did females (survival: 0·40 ± 0·04; recapture: 0·87 ± 0·06). In Jamaica, annual survival (0·43 ± 0·03) and recapture (0·95 ± 0·04) probabilities did not differ between sexes. Annual survival and recapture probabilities of young birds (i.e. yearlings in New Hampshire and hatch-year birds in Jamaica) did not differ from adults, indicating that from the time hatch-year individuals acquire territories on winter quarters in mid-October, they survive as well as adults within the same habitat. 4. Monthly survival probabilities during the summer (May–August) and winter (October–March) stationary periods were high: 1·0 for males in New Hampshire, and 0·99 ± 0·01 for males in Jamaica and for females in both locations. 5. These annual and seasonal survival estimates were used to calculate warbler survival for the migratory periods. Monthly survival probability during migration ranged from 0·77 to 0·81 ± 0·02. Thus, apparent mortality rates were at least 15 times higher during migration compared to that in the stationary periods, and more than 85% of apparent annual mortality of D. caerulescens occurred during migration. 6. Additional data from multiple species, especially measures of habitat-specific demography and dispersal, will improve our understanding of the relative impacts of the breeding, migratory, and winter periods on population dynamics of migratory birds and thus enhance future conservation efforts.

Journal of Animal Ecology↗

USGS2012

Facilitating fish passage at ultra low head dams: An alternative to dam removal

Ecosystem sustainability and returning the biological integrity to rivers continue to change the landscape of fish passage technology. Installing a conventional fishways has a limited degree of success in accommodating fish passage needs. Recently, the option of total dam removal has been gaining momentum among resource managers, conservationists, and even engineers. Certain dams, however, cannot be removed, and conventional fishways are either too expensive to build or the real estate is simply not available; yet freedom of passage must be attained. At the Little Falls Dam on the Potomac River a notch in the crest of the dam was installed to accommodate passage of fish. The notch has three labyrinth weirs used for energy dissipation. Water velocities are maintained at less than about 4 m/s anywhere within the passage structure during migratory season of the target species (American shad). Construction of this novel design was recently completed (March 2000) and future biological evaluations are ongoing. Copyright ASCE 2004.

Conference Paper↗

USGS2012

Competing risks and the development of adaptive management plans for water resources: Field reconnaissance investigation of risks to fishes and other aquatic biota exposed to endocrine disrupting chemicals (edcs) in lake mead, Nevada USA

The analysis and characterization of competing risks for water resources rely on a wide spectrum of tools to evaluate hazards and risks associated with their management. For example, waters of the lower Colorado River stored in reservoirs such as Lake Mead present a wide range of competing risks related to water quantity and water quality. These risks are often interdependent and complicated by competing uses of source waters for sustaining biological resources and for supporting a range of agricultural, municipal, recreational, and industrial uses. USGS is currently conducting a series of interdisciplinary case-studies on water quality of Lake Mead and its source waters. In this case-study we examine selected constituents potentially entering the Lake Mead system, particularly endocrine disrupting chemicals (EDCs). Worldwide, a number of environmental EDCs have been identified that affect reproduction, development, and adaptive behaviors in a wide range of organisms. Many EDCs are minimally affected by current treatment technologies and occur in treated sewage effluents. Several EDCs have been detected in Lake Mead, and several substances have been identified that are of concern because of potential impacts to the aquatic biota, including the sport fishery of Lake Mead and endangered razorback suckers (Xyrauchen texanus) that occur in the Colorado River system. For example, altered biomarkers relevant to reproduction and thyroid function in fishes have been observed and may be predictive of impaired metabolism and development. Few studies, however, have addressed whether such EDC-induced responses observed in the field have an ecologically significant effect on the reproductive success of fishes. To identify potential linkages between EDCs and species of management concern, the risk analysis and characterization in this reconnaissance study focused on effects (and attendant uncertainties) that might be expressed by exposed populations. In addition, risk reduction measures that may be of interest to resource managers are considered relative to emerging contaminants in treated effluents, interdependencies among biological resources at risk, and uses of reservoir waters derived from multiple inflows of widely varying qualities. ??2009 ASCE.

Nevada↗

USGS2007

A cold phase of the East Pacific triggers new phytoplankton blooms in San Francisco Bay

Ecological observations sustained over decades often reveal abrupt changes in biological communities that signal altered ecosystem states. We report a large shift in the biological communities of San Francisco Bay, first detected as increasing phytoplankton biomass and occurrences of new seasonal blooms that began in 1999. This phytoplankton increase is paradoxical because it occurred in an era of decreasing wastewater nutrient inputs and reduced nitrogen and phosphorus concentrations, contrary to the guiding paradigm that algal biomass in estuaries increases in proportion to nutrient inputs from their watersheds. Coincidental changes included sharp declines in the abundance of bivalve mollusks, the key phytoplankton consumers in this estuary, and record high abundances of several bivalve predators: Bay shrimp, English sole, and Dungeness crab. The phytoplankton increase is consistent with a trophic cascade resulting from heightened predation on bivalves and suppression of their filtration control on phytoplankton growth. These community changes in San Francisco Bay across three trophic levels followed a state change in the California Current System characterized by increased upwelling intensity, amplified primary production, and strengthened southerly flows. These diagnostic features of the East Pacific "cold phase" lead to strong recruitment and immigration of juvenile flatfish and crustaceans into estuaries where they feed and develop. This study, built from three decades of observation, reveals a previously unrecognized mechanism of ocean-estuary connectivity. Interdecadal oceanic regime changes can propagate into estuaries, altering their community structure and efficiency of transforming land-derived nutrients into algal biomass.

California↗

USGS2011

Social network models predict movement and connectivity in ecological landscapes

Network analysis is on the rise across scientific disciplines because of its ability to reveal complex, and often emergent, patterns and dynamics. Nonetheless, a growing concern in network analysis is the use of limited data for constructing networks. This concern is strikingly relevant to ecology and conservation biology, where network analysis is used to infer connectivity across landscapes. In this context, movement among patches is the crucial parameter for interpreting connectivity but because of the difficulty of collecting reliable movement data, most network analysis proceeds with only indirect information on movement across landscapes rather than using observed movement to construct networks. Statistical models developed for social networks provide promising alternatives for landscape network construction because they can leverage limited movement information to predict linkages. Using two mark-recapture datasets on individual movement and connectivity across landscapes, we test whether commonly used network constructions for interpreting connectivity can predict actual linkages and network structure, and we contrast these approaches to social network models. We find that currently applied network constructions for assessing connectivity consistently, and substantially, overpredict actual connectivity, resulting in considerable overestimation of metapopulation lifetime. Furthermore, social network models provide accurate predictions of network structure, and can do so with remarkably limited data on movement. Social network models offer a flexible and powerful way for not only understanding the factors influencing connectivity but also for providing more reliable estimates of connectivity and metapopulation persistence in the face of limited data.

Proceedings of the National Academy of Sciences of↗

USGS2015

Biodiversity influences plant productivity through niche–efficiency

The loss of biodiversity is threatening ecosystem productivity and services worldwide, spurring efforts to quantify its effects on the functioning of natural ecosystems. Previous research has focused on the positive role of biodiversity on resource acquisition (i.e., niche complementarity), but a lack of study on resource utilization efficiency, a link between resource and productivity, has rendered it difficult to quantify the biodiversity–ecosystem functioning relationship. Here we demonstrate that biodiversity loss reduces plant productivity, other things held constant, through theory, empirical evidence, and simulations under gradually relaxed assumptions. We developed a theoretical model named niche–efficiency to integrate niche complementarity and a heretofore-ignored mechanism of diminishing marginal productivity in quantifying the effects of biodiversity loss on plant productivity. Based on niche–efficiency, we created a relative productivity metric and a productivity impact index (PII) to assist in biological conservation and resource management. Relative productivity provides a standardized measure of the influence of biodiversity on individual productivity, and PII is a functionally based taxonomic index to assess individual species’ inherent value in maintaining current ecosystem productivity. Empirical evidence from the Alaska boreal forest suggests that every 1% reduction in overall plant diversity could render an average of 0.23% decline in individual tree productivity. Out of the 283 plant species of the region, we found that large woody plants generally have greater PII values than other species. This theoretical model would facilitate the integration of biological conservation in the international campaign against several pressing global issues involving energy use, climate change, and poverty.

Proceedings of the National Academy of Sciences of↗

USGS2020

Specialized meltwater biodiversity persists despite widespread deglaciation

Glaciers are important drivers of environmental heterogeneity and biological diversity across mountain landscapes. Worldwide, glaciers are receding rapidly due to climate change, with important consequences for biodiversity in mountain ecosystems. However, the effects of glacier loss on biodiversity have never been quantified across a mountainous region, primarily due to a lack of adequate data at large spatial and temporal scales. Here, we combine high-resolution biological and glacier change (ca. 1850–2015) datasets for Glacier National Park, USA, to test the prediction that glacier retreat reduces biodiversity in mountain ecosystems through the loss of uniquely adapted meltwater stream species. We identified a specialized cold-water invertebrate community restricted to the highest elevation streams primarily below glaciers, but also snowfields and groundwater springs. We show that this community and endemic species have unexpectedly persisted in cold, high-elevation sites, even in catchments that have not been glaciated in ∼170 y. Future projections suggest substantial declines in suitable habitat, but not necessarily loss of this community with the complete disappearance of glaciers. Our findings demonstrate that high-elevation streams fed by snow and other cold-water sources continue to serve as critical climate refugia for mountain biodiversity even after glaciers disappear.

Montana↗

USGS2004

Monitoring programs need to take into account imperfect species detectability

Biodiversiry monitoring is important to identify biological units in need of conservation and to check the effectiveness of conservation actions. Programs generally monitor species richness and its changes (trend). Usually, no correction is made for imperfect species detectability. Instead, it is assumed that each species present has the same probability of being recorded and that there is no difference in this detectability across space and time, e.g. among observers and habitats. Consequently, species richness is determined by enumeration as the sum of species recorded. In Switzerland, the federal government has recently launched a comprehensive program that aims at detecting changes in biodiversity at all levels of biological integration. Birds are an important part of that program. Since 1999, 23 visits per breeding season are made to each of >250 1 km2 squares to map the territories of all detected breeding bird species. Here, we analyse data from three squares to illustrate the use of capture-recapture models in monitoring to obtain detectability-corrected estimates of species richness and trend. Species detectability averaged only 85%. Hence an estimated 15% of species present remained overlooked even after three visits. Within a square, changes in detectability for different years were of the same magnitude when surveys were conducted by the same observer as when they were by different observers. Estimates of trend were usually biased and community turnover was overestimated when based on enumeration. Here we use bird data as an illustration of methods. However, species detectability for any taxon is unlikely ever to be perfect or even constant across categories to be compared. Therefore, monitoring programs should correct for species detectability.

Basic and Applied Ecology↗

USGS2012

Evidence of recent climate change within the historic range of Rio Grande cutthroat trout: implications for management and future persistence

Evidence of anthropogenically influenced climate change has motivated natural resource managers to incorporate adaptive measures to minimize risks to sensitive and threatened species. Detecting trends in climate variables (i.e., air temperature and hydrology) can serve as a valuable management tool for protecting vulnerable species by increasing our understanding of localized conditions and trends. The Rio Grande cutthroat trout Oncorhynchus clarkii virginalis has suffered a severe decline in its historical distribution, with the majority of current populations persisting in isolated headwater streams. To evaluate recent climate change within the subspecies' historical range, we examined trends in average air temperatures, biologically important hydrological variables (timing of snowmelt and seasonal flows), and the April 1 snow water equivalent over the last 45 years (1963–2007). While rates of change in all three metrics were variable across sites, rangewide patterns were evident. Across the subspecies' historical range, average annual air temperatures increased (0.29°C per decade) and the timing of snowmelt shifted 10.6 d earlier in the year (2.3 d/decade). Flows increased during biologically important periods, including winter (January 1–March 31; 6.6% increase per decade), prespawning (April 1–May 14; 6.9% increase per decade), and spawning (May 15–June 15; 4.2% increase per decade) and decreased in summer (June 16–September 15; 1.9% decrease per decade). Evidence of decreasing April 1 snow water equivalent (5.3% per decade) was also observed. While the impacts of these changes at the population level are equivocal, it is likely that negative effects would influence the subspecies by altering its distribution, decreasing available habitat, and altering the timing of important life history components. Continued monitoring and proactive management will be required to increase the resiliency of remaining populations to ensure long-term persistence and protection in a changing climate.

Colorado;New Mexico↗

USGS2013

Book review: Conservation, ecology, and management of catfish: The second international symposium

This is the second publication in a series published by the American Fisheries Society devoted to catfish research, biology, and management, which was organized as a symposium held in St. Louis Missouri, in 2010 and builds upon the first symposium that was held in Davenport, Iowa, in 1998 (Irwin et al. 1999). The organizations of the second symposium stated that this was to "serve as an addendum to Catfish 2000" and "to cover the four corners of catfish science: catfish biology, ecology, management, and conservation" (p. xi). The book meets this standard easily. With 64 pages organized into nine sections (plenary, catfishes as sport fish, non-game catfishes, nonnative catfishes, movement and habitat use, sampling and population assessment, age and growth, behavior, and future directions), this publication covers these four corners and more. Review info: Conservation, Ecology, and Management of Catfish: The Second International Symposium. Edited by P. H. Michaletz and V. H. Travnichek, 2011. ISBN: 978-1934874257, 800 pp.

Fisheries↗

USGS2016

Anticipated water quality changes in response to climate change and potential consequences for inland fishes

Healthy freshwater ecosystems are a critical component of the world's economy, with a critical role in maintaining public health, inland biological diversity, and overall quality of life. Globally, our climate is changing, with air temperature and precipitation regimes deviating significantly from historical patterns. Healthy freshwater ecosystems are a critical component of the world's economy, with a critical role in maintaining public health, inland biological diversity, and overall quality of life. Globally, our climate is changing, with air temperature and precipitation regimes deviating significantly from historical patterns. Changes anticipated with climate change in the future are likely to have a profound effect on inland aquatic ecosystems through diverse pathways, including changes in water quality. In this brief article, we present an initial discussion of several of the water quality responses that can be anticipated to occur within inland water bodies with climate change and how those changes are likely to impact fishes.

Fisheries↗

USGS2010

North American osprey populations and contaminants: Historic and contemporary perspectives

Osprey ( Pandion haliaetus ) populations were adversely affected by DDT and perhaps other contaminants in the United States and elsewhere. Reduced productivity, eggshell thinning, and high DDE concentrations in eggs were the signs associated with declining osprey populations in the 1950s, 1960s, and 1970s. The species was one of the first studied on a large scale to bring contaminant issues into focus. Although few quantitative population data were available prior to the 1960s, many osprey populations in North America were studied during the 1960s and 1970s with much learned about basic life history and biology. This article reviews the historical and current effects of contaminants on regional osprey populations. Breeding populations in many regions of North America showed post-DDT-era (1972) population increases of varying magnitudes, with many populations now appearing to stabilize at much higher numbers than initially reported in the 1970s and 1980s. However, the magnitude of regional population increases in the United States between 1981 (first Nationwide Survey, ∼8,000 pairs), when some recovery had already occurred, 1994 (second survey, ∼14,200), and 2001 (third survey, ∼16,000–19,000), or any other years, is likely not a simple response to the release from earlier contaminant effects, but a response to multi-factorial effects. This indirect “contaminant effects” measurement comparing changes (i.e., recovery) in post-DDT-era population numbers over time is probably confounded by changing human attitudes toward birds of prey (shooting, destroying nests, etc.), changing habitats, changing fish populations, and perhaps competition from other species. The species' adaptation to newly created reservoirs and its increasing use of artificial nesting structures (power poles, nesting platforms, cell towers, channel markers, offshore duck blinds, etc.) are two important factors. The timing of the initial use of artificial nesting structures, which replaced declining numbers of suitable trees at many locations, varied regionally (much later in the western United States and Mexico). Because of the increasing use of artificial nesting structures, there may be more ospreys nesting in North America now than ever before. Now, with the impact of most legacy organic contaminants (DDT, other organochlorine [OC] pesticides, polychlorinated biphenyls [PCB], polychlorinated dibenzo- p -dioxins [PCDD], polychlorinated dibenzofurans (PCDF]) greatly reduced or eliminated, and some osprey populations showing evidence of stabilizing, the species was proposed as a Worldwide Sentinel Species for evaluating emerging contaminants. Several emerging contaminants are already being studied, such as polybrominated diphenyl ethers (PBDE) and perfluorinated acids and sulfonate compounds (PFC). The many advantages for continued contaminant investigations using the osprey include a good understanding of its biology and ecology, its known distribution and abundance, and its ability to habituate to humans and their activities, which permits nesting in some of the potentially most contaminated environments. It is a top predator in most ecosystems, and its nests are relatively easy to locate and study with little researcher impact on reproductive success.

Journal of Toxicology and Environmental Health, Pa↗

USGS2001

The status of the macroinvertebrate community in the St. Croix River, Minnesota and Wisconsin: An examination of ecological health using techniques of multivariate analysis

A statistical procedure that integrates physical, chemical and biological data is used to operationally define and analyze ecological health. Benthic macroinvertebrates collected from May through September from eight locations along the St. Croix River in Minnesota and Wisconsin were analyzed by canonical correspondence analyses. A sequential multivariate analysis procedure was developed that included: 1) determining which environmental variables explained the most variation in the taxonomic data, individually and collectively, 2) running canonical correspondence analyses on the taxonomic data along with environmental variables chosen from a stepwise forward selection procedure, 3) performing a cluster analysis of the taxonomic data in sampling times to determine artificial biological seasons, and 4) analyzing the seasonal data (three time intervals) separately, as in steps 1 and 2. Changes in community structure were significantly associated with changes in environmental factors (physical and chemical) that varied in time and space. The variables found to be significant were largely those expected to be associated with the variations in the structure of benthic macroinvertebrate community in an unimpacted river. A slight influence of nitrogen could be detected in agricultural areas.

Minnesota, Wisconsin↗