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USGS2023

Lessons learned from community and citizen science monitoring projects on the Elwha River Restoration Project

Community and citizen science (CCS) projects – initiatives that involve public participation in scientific research – can both sustain and expand long-term monitoring of large dam removal projects. In this article, we discuss our perspectives on CCS associated with the Elwha River dam removals. We summarize how the public has been or could be involved in monitoring and distill lessons learned for other large dam removal projects. Much of the Elwha monitoring involved technical field work requiring training and incurring potential liability risks, guiding projects towards smaller-scale public involvement. Partnering with organizations that have capacity for volunteer management expanded CCS opportunities and provided logistical support to project managers committed to public engagement. We found that many projects engaged with students and/or with paid or unpaid interns; compensating participants in various ways can help to create reciprocal relationships that support long-term monitoring. In the future, other large dam removals could consider planning ahead for community involvement in dam removal monitoring to accommodate the technical and potentially hazardous nature of the work – broadening who may be able to participate. In addition, involving community members in setting research agendas could be an important first step in engaging them in long-term monitoring, in turn facilitating multi-generational research at the timescale of landscape-level changes. Finally, explicit relationship-building with Indigenous communities can enhance the benefits of community engagement in dam removal science for all involved.

Washington↗

USGS2025

Sampling mass mortality events to enable diagnoses: A protocol using freshwater mussels

Many taxa around the globe are threatened by often unexplained mass mortality events (MMEs), which can decimate populations and compromise key ecosystem functions. One example of a highly threatened taxon facing frequent MMEs is freshwater mussels (Unionida). There has been a recent increase in interest in understanding the causes of freshwater mussel MMEs, but standardised methodologies for how best to respond to them to facilitate diagnoses are unavailable. When an MME is observed, swift and appropriate sample collection is imperative owing to the transient nature of these phenomena. Here we provide structured guidance that will facilitate rapid and appropriate sampling of MMEs, using freshwater mussels as an example. We set out standardised procedures for sample collection, preparation and preservation. The procedures we outline will improve our capacity for diagnostic investigations of MMEs and other mortality events, not only in freshwater mussels but also across many other taxa. This, in turn, can inform appropriate management responses.

Methods in Ecology and Evolution↗

USGS2007

Proceedings of the Fourth Glacier Bay Science Symposium

Foreword Glacier Bay was established as a National Monument in 1925, in part to protect its unique character and natural beauty, but also to create a natural laboratory to examine evolution of the glacial landscape. Today, Glacier Bay National Park and Preserve is still a place of profound natural beauty and dynamic landscapes. It also remains a focal point for scientific research and includes continuing observations begun decades ago of glacial processes and terrestrial ecosystems. In recent years, research has focused on glacial-marine interactions and ecosystem processes that occur below the surface of the bay. In October 2004, Glacier Bay National Park convened the fourth in a series of science symposiums to provide an opportunity for researchers, managers, interpreters, educators, students and the general public to share knowledge about Glacier Bay. The Fourth Glacier Bay Science Symposium was held in Juneau, Alaska, rather than at the Park, reflecting a desire to maximize attendance and communication among a growing and diverse number of stakeholders interested in science in the park. More than 400 people attended the symposium. Participants provided 46 oral presentations and 41 posters covering a wide array of disciplines including geology, glaciology, oceanography, wildlife and fisheries biology, terrestrial and marine ecology, socio-cultural research and management issues. A panel discussion focused on the importance of connectivity in Glacier Bay research, and keynote speakers (Gary Davis and Terry Chapin) spoke of long-term monitoring and ecological processes. These proceedings include 56 papers from the symposium. A summary of the Glacier Bay Science Plan-itself a subject of a meeting during the symposium and the result of ongoing discussions between scientists and resource managers-also is provided. We hope these proceedings illustrate the diversity of completed and ongoing scientific studies, conducted within the Park. To this end, we invited all presenters to submit brief technical summaries of their work, to capture the gist of their study and its main findings without an overload of details and methodology. We also asked authors to include a few words on the management implications of their work to help bridge the gap between scientists and managers in understanding how specific research questions may translate to management practice. Papers in this volume are laid out by subject matter, from terrestrial and freshwater subjects to glacial-marine geology, to the ecology of marine animals and ending with risk assessment, human impacts and science-management considerations. In summary, we hope the proceedings will serve as a useful reference to completed and ongoing studies in Glacier Bay National Park, and thereby provide park enthusiasts, scientists, and managers with a road map of scientific progress.

Scientific Investigations Report↗

USGS2010

Grain-size evolution in suspended sediment and deposits from the 2004 and 2008 controlled-flood experiments in Marble and Grand Canyons, Arizona

Since the closure of Glen Canyon Dam in 1963, the hydrology, sediment supply, and distribution and size of modern alluvial deposits in the Colorado River through Grand Canyon have changed substantially (e.g., Howard and Dolan, 1981; Johnson and Carothers, 1987; Webb et al., 1999; Rubin et al., 2002; Topping et al., 2000, 2003; Wright et al., 2005; Hazel et al., 2006). The dam has reduced the fluvial sediment supply at the upstream boundary of Grand Canyon National Park by about 95 percent. Regulation of river discharge by dam operations has important implications for the storage and redistribution of sediment in the Colorado River corridor. In the absence of natural floods, sediment is not deposited at elevations that regularly received sediment before dam closure. There has been a systemwide decrease in the size and number of subaerially exposed fluvial sand deposits since the 1960s, punctuated by episodic aggradation during the exceptional high-flow intervals in the early 1980s and by sediment input from occasional tributary floods (Beus and others, 1985; Schmidt and Graf, 1990; Kearsley et al., 1994; Schmidt et al., 2004; Wright et al., 2005; Hazel et al., 2006). Fluvial sandbars are an important component of riparian ecology that, among other functions, enclose eddy backwaters that form native-fish habitat, provide a source for eolian sand that protects some archaeological sites, and are used as campsites by thousands of river-runners annually (Rubin et al., 1990; Kearsley et al., 1994; Neal et al., 2000; Wright et al., 2005; Draut and Rubin, 2008).

Arizona↗

USGS2024

A meta-analysis highlights the idiosyncratic nature of tradeoffs in laboratory models of virus evolution

Different theoretical frameworks have been invoked to guide the study of virus evolution. Three of the more prominent ones are (i) the evolution of virulence, (ii) life history theory, and (iii) the generalism–specialism dichotomy. All involve purported tradeoffs between traits that define the evolvability and constraint of virus-associated phenotypes. However, as popular as these frameworks are, there is a surprising paucity of direct laboratory tests of the frameworks that support their utility as broadly applicable theoretical pillars that can guide our understanding of disease evolution. In this study, we conduct a meta-analysis of direct experimental evidence for these three frameworks across several widely studied virus–host systems: plant viruses, fungal viruses, animal viruses, and bacteriophages. We extracted 60 datasets from 28 studies and found a range of relationships between traits in different analysis categories (e.g., frameworks, virus–host systems). Our work demonstrates that direct evidence for relationships between traits is highly idiosyncratic and specific to the host–virus system and theoretical framework. Consequently, scientists researching viral pathogens from different taxonomic groups might reconsider their allegiance to these canons as the basis for expectation, explanation, or prediction. Future efforts could benefit from consistent definitions, and from developing frameworks that are compatible with the evidence and apply to particular biological and ecological contexts.

Virus Evolution↗

USGS2022

Classifying behavior from short-interval biologging data: An example with GPS tracking of birds

Recent advances in digital data collection have spurred accumulation of immense quantities of data that have potential to lead to remarkable ecological insight, but that also present analytic challenges. In the case of biologging data from birds, common analytical approaches to classifying movement behaviors are largely inappropriate for these massive data sets. We apply a framework for using K -means clustering to classify bird behavior using points from short time interval GPS tracks. K -means clustering is a well-known and computationally efficient statistical tool that has been used in animal movement studies primarily for clustering segments of consecutive points. To illustrate the utility of our approach, we apply K -means clustering to six focal variables derived from GPS data collected at 1–11 s intervals from free-flying bald eagles ( Haliaeetus leucocephalus ) throughout the state of Iowa, USA. We illustrate how these data can be used to identify behaviors and life-stage- and age-related variation in behavior. After filtering for data quality, the K -means algorithm identified four clusters in >2 million GPS telemetry data points. These four clusters corresponded to three movement states: ascending, flapping, and gliding flight; and one non-moving state: perching. Mapping these states illustrated how they corresponded tightly to expectations derived from natural history observations; for example, long periods of ascending flight were often followed by long gliding descents, birds alternated between flapping and gliding flight. The K -means clustering approach we applied is both an efficient and effective mechanism to classify and interpret short-interval biologging data to understand movement behaviors. Furthermore, because it can apply to an abundance of very short, irregular, and high-dimensional movement data, it provides insight into small-scale variation in behavior that would not be possible with many other analytical approaches.

Ecology and Evolution↗

USGS2026

An energetic tradeoff best explains parturition timing in grizzly bears

Timing of grizzly bear ( Ursus arctos ) parturition during hibernation has been explained by ancestral traits (delayed implantation, altricial young, obligate maternal denning), but the ultimate driver underlying precise timing has not been fully explored. Capitalizing on an observed latitudinal increase in denning duration among four populations in interior North America, we tested two alternative hypotheses. First, that birth timing results from a physiological cue that synchronizes implantation with the onset of hibernation, allowing females to forgo reproduction should they lack adequate fat stores. Alternatively, that parturition is optimally timed relative to den exit to balance an energetic tradeoff between minimizing lactation time to protect the mother and maximizing developmental time to increase cub survival. Using parturition dates previously predicted from accelerometer data (27 Dec–28 Feb), we classified 115 females according to apparent litter survival when first visually observed after den exit: 57% successful (with cubs), 22% unsuccessful (alone), and 21% unknown (not observed). The number of days between birth and den exit showed no association with latitude ( p = 0.29). It averaged 103 days among successful females but only 77 days among unsuccessful females ( p < 0.001) owing to later births and earlier exit. With each increasing degree of latitude, birth date increased by 1.0 and number of days between den entry and birth increased by 2.5 ( p < 0.001). Implantation dates were not centered on den entry dates ( p < 0.001). These results supported the energetic tradeoff hypothesis and suggested natural selection has favored a consistent number of days between parturition and den exit under average body conditions and shifts toward later or earlier births for females with lower or higher levels of bodily stored energy, respectively. This flexible tradeoff may support resilience to climate change and present a possible mechanism explaining reduced natality and cub survival in high-density populations.

Alaska, British Columbia, Idaho, Montana, Wyoming↗

USGS2008

Coastal Louisiana ecosystem assessment and restoration program: The role of ecosystem forecasting in evaluating restoration planning in the Mississippi River Deltaic Plain

The development of ecosystem management plans to restore and rehabilitate natural resources requires an understanding of how specific ecological mechanisms regulate the structure and function of ecosystems. To achieve restoration goals, comprehensive plans and engineering designs must effectively change environmental drivers at the regional level to reduce stress conditions at the local environment that are responsible for ecosystem degradation. This document focuses on the Coastal Louisiana Ecosystem Assessment and Restoration (CLEAR) ecosystem forecasting framework and how it can be used to support the analysis of Louisiana’s coastal restoration plans. Specifically, the framework is designed to (1) develop and incorporate conceptual ecological models that can be used to integrate ecological needs and opportunities with engineering designs, (2) utilize wetland loss rates to describe the most likely “future without” scenario for a variety of ecosystem attributes, (3) estimate broad ecosystem responses to restoration alternatives based on processes associated with succession of geomorphic and ecological systems, and (4) calculate ecological benefits for incorporation into decision support tools associated with large-scale geomorphic and hydrologic processes. This paper provides a brief overview of the spatial framework and modular design of the CLEAR ecosystem forecasting framework and describes in greater detail the evolution of the landscape change module, concepts for its refinement, and how it was utilized in evaluating a coastal restoration alternative proposed in the Coastal Protection and Restoration Authority Preliminary Draft Master Plan. Such projections by the CLEAR forecasting framework can evaluate processes and conditions that result in sustainable coastal ecosystems with habitat functions that support higher trophic levels.

Louisiana↗

USGS2014

Microbial aggregates within tissues infect a diversity of corals throughout the Indo-Pacific

Coral reefs are highly diverse ecosystems where symbioses play a pivotal role. Corals contain cell-associated microbial aggregates (CAMA), yet little is known about how widespread they are among coral species or the nature of the symbiotic relationship. Using histology, we found CAMA within 24 species of corals from 6 genera from Hawaii, American Samoa, Palmyra, Johnston Atoll, Guam, and Australia. Prevalence (%) of infection varied among coral genera: Acropora, Porites, and Pocillopora were commonly infected whereas Montipora were not. Acropora from the Western Pacific were significantly more likely to be infected with CAMA than those from the Central Pacific, whereas the reverse was true for Porites. Compared with apparently healthy colonies, tissues from diseased colonies were significantly more likely to have both surface and basal body walls infected. The close association of CAMA with host cells in numerous species of apparently healthy corals and lack of associated cell pathology reveals an intimate agent-host association. Furthermore, CAMA are Gram negative and in some corals may be related to chlamydia or rickettsia. We propose that CAMA in adult corals are facultative secondary symbionts that could play an important ecological role in some dominant coral genera in the Indo-Pacific. CAMA are important in the life histories of other animals, and more work is needed to understand their role in the distribution, evolution, physiology, and immunology of reef corals.

Marine Ecology Progress Series↗

USGS2013

Disease in a dynamic landscape: host behavior and wildfire reduce amphibian chytrid infection

Disturbances are often expected to magnify effects of disease, but these effects may depend on the ecology, behavior, and life history of both hosts and pathogens. In many ecosystems, wildfire is the dominant natural disturbance and thus could directly or indirectly affect dynamics of many diseases. To determine how probability of infection by the aquatic fungus Batrachochytrium dendrobatidis (Bd) varies relative to habitat use by individuals, wildfire, and host characteristics, we sampled 404 boreal toads ( Anaxyrus boreas boreas ) across Glacier National Park, Montana (USA). Bd causes chytridiomycosis, an emerging infectious disease linked with widespread amphibian declines, including the boreal toad. Probability of infection was similar for females and the combined group of males and juveniles. However, only 9% of terrestrial toads were infected compared to >30% of aquatic toads, and toads captured in recently burned areas were half as likely to be infected as toads in unburned areas. We suspect these large differences in infection reflect habitat choices by individuals that affect pathogen exposure and persistence, especially in burned forests where warm, arid conditions could limit Bd growth. Our results show that natural disturbances such as wildfire and the resulting diverse habitats can influence infection across large landscapes, potentially maintaining local refuges and host behaviors that facilitate evolution of disease resistance.

Montana↗

USGS2007

Recommendations for a barrier island breach management plan for Fire Island National Seashore, including the Otis Pike High Dune Wilderness Area, Long Island, New York

The U.S Army Corps of Engineers, New York District is developing engineering plans, including economic costs and benefits, for storm damage reduction along an 83 mile stretch of the coastal barrier islands and beaches on the south shore of Long Island, NY from Fire Island Inlet east to the Montauk Point headland. The plan, expected to include various alternatives for storm protection and erosion mitigation, is referred to as the Fire Island to Montauk Point Reformulation Plan (FIMP). These plans are expected to follow the Corps of Engineers’ Environmental Operating Principles striving for long term environmental sustainability and balance between environmental protection and protection of human health and property. Fire Island National Seashore (FIIS), a 19,579 acre unit of the National Park System includes a 32 mile long coastal barrier island located within the FIMP project area. A seven-mile section of the park, Otis Pike Fire Island High Dune Wilderness Area, is also a designated Federal Wilderness Area. The FIIS includes not only the barrier island and sand dunes, but also several islands, sand flats and wetlands landward of the barrier, submerged parts of Great South Bay shoreface, extending approximately 4,000 feet into the bay with the inner shelf region extending approximately 1,000 feet seaward of the Fire Island shoreline. The Fire Island barrier islands, a sand-starved system dominated by highly dynamic processes, are struggling to maintain their integrity in the face of sea-level rise and storms. Adding to the dilemma is that development on the barriers and the mainland has increased greatly during the past 50 years. As such, managers and decision makers in federal agencies, state agencies and local governments are challenged to balance tradeoffs between protection of lives and property, public access and long term conservation of natural habitats and processes and the plants and animals that depend on these habitats. National Park Service (NPS) policy stipulates that natural coastal processes be maintained to the greatest extent possible and not be impeded so as to conserve landforms, habitats and natural ecosystem resources that reply on the landforms and processes for long-term sustainability of the national park. Storms and associated processes such as waves, tides, currents and relative sea-level change are critical elements for the formation and evolution of these barrier islands, sand dunes, back-barrier sand flats and lagoons and vegetated wetlands. Processes such as wave run-up, overwash and barrier beaching, which occur during elevated storm surge are all necessary processes in enabling the efficient transfer of sediments, nutrients and marine water from the Atlantic Ocean across barriers and into Great South Bay. A large body of scientific data and information published over the past 50 years shows that such transfers of sediment and water from the ocean to the bays are essential for the long-term maintenance of the barrier island and back-bay systems and their biologically diverse habitats an d ecosystems. Current relative sea-level rise (~12 in/century) is chronic and pervasive in driving Long Island coastal change and with the likelihood of accelerating sea level rise in the near future, coastal hazards such as erosion, inundation, and storm surge flooding will increase, with corresponding increased risk to life and property on both Fire Island and on the mainland. In addition, the cumulative effects over the past century and more, both direct and indirect, of human impacts on the Long Island coast have altered the barrier beach and dunes and sediment transport processes. These impacts have likely increased the potential for breaching and increased risk to life and property on the coast and the mainland. Examples of direct impacts are: the stone jetties at Moriches, Shinnecock, and Fire Island tidal inlets and groin field structures at Westhampton that alter littoral processes, armoring and erosion-control stabilization of the headlandds such as the Montauk Point headlands, and deepening of navigation channels by dredging through the tidal inlets and in the bays. Indirect impacts that have a bearing on decisions to deal with breaching are: high-risk development of the barrier islands and low-lying areas of the mainland vulnerable to flooding, and the dredging of nearshore sand shoals for beach nourishment. The NPS strives to employ a coastal management framework for decision making that is based on assessment of the physical and ecological properties of the shoreline as well as human welfare and property. In order to protect developed areas of Fire Island and the mainland from loss of life, flooding, and other economic and physical damage, the NPS will likely need to consider allowing artificial closure of some breaches within the FIIS under certain circumstances. The decision by the NPS to allow breaches to evolve naturally and possibly close or to allow artificially closing breaches is based on four criteria: 1. Volumes of sediment transported landward and exchange of water and nutrients; 2. Elevated water levels and flooding risk to mainland life and property; 3. Engineering processes of artificial closure; and 4. Economic costs and benefits of artificial closure. This report for breach management presents protocols which specify when breach closures within the FIIS might be desirable and necessary, as well as provides recommendations for structural breach closure engineering operations which are indented to minimize negative impacts to the natural wilderness values and cultural resources within the FIIS, particularly the Otis Pike Wilderness Area. The goal of the plan is to strike a balance between protecting natural resources and allowing natural processes to operate and avoiding loss of life and excessive property damage.

New York↗

USGS2009

Selected achievements, science directions, and new opportunities for the WEBB small watershed research program

Over nearly two decades, the Water, Energy, and Biogeochemical Budgets (WEBB) small watershed research program of the U.S. Geological Survey (USGS) has documented how water and solute fluxes, nutrient, carbon, and mercury dynamics, and weathering and sediment transport respond to natural and humancaused drivers, including climate, climate change, and atmospheric deposition. Together with a continued and increasing focus on the effects of climate change, more investigations are needed that examine ecological effects (e.g., evapotranspiration, nutrient uptake) and responses (e.g., species abundances, biodiversity) that are coupled with the physical and chemical processes historically observed in the WEBB program. Greater use of remote sensing, geographic modeling, and habitat/watershed modeling tools is needed, as is closer integration with the USGS-led National Phenology Network. Better understanding of process and system response times is needed. The analysis and observation of land-use and climate change effects over time should be improved by pooling data obtained by the WEBB program during the last two decades with data obtained earlier and (or) concurrently from other research and monitoring studies conducted at or near the five WEBB watershed sites. These data can be supplemented with historical and paleo-environmental information, such as could be obtained from tree rings and lake cores. Because of the relatively pristine nature and small size of its watersheds, the WEBB program could provide process understanding and basic data to better characterize and quantify ecosystem services and to develop and apply indicators of ecosystem health. In collaboration with other Federal and State watershed research programs, the WEBB program has an opportunity to contribute to tracking the short-term dynamics and long-term evolution of ecosystem services and health indicators at a multiplicity of scales across the landscape.

Conference Paper↗

USGS2020

Spatial capture–recapture with random thinning for unidentified encounters

Spatial capture–recapture (SCR) models have increasingly been used as a basis for combining capture–recapture data types with variable levels of individual identity information to estimate population density and other demographic parameters. Recent examples are the unmarked SCR (or spatial count model), where no individual identities are available and spatial mark–resight (SMR) where individual identities are available for only a marked subset of the population. Currently lacking, though, is a model that allows unidentified samples to be combined with identified samples when there are no separate classes of “marked” and “unmarked” individuals and when the two sample types cannot be considered as arising from two independent observation models. This is a common scenario when using noninvasive sampling methods, for example, when analyzing data on identified and unidentified photographs or scats from the same sites. Here we describe a “random thinning” SCR model that utilizes encounters of both known and unknown identity samples using a natural mechanistic dependence between samples arising from a single observation model. Our model was fitted in a Bayesian framework using NIMBLE. We investigate the improvement in parameter estimates by including the unknown identity samples, which was notable (up to 79% more precise) in low‐density populations with a low rate of identified encounters. We then applied the random thinning SCR model to a noninvasive genetic sampling study of brown bear ( Ursus arctos ) density in Oriental Cantabrian Mountains (North Spain). Our model can improve density estimation for noninvasive sampling studies for low‐density populations with low rates of individual identification, by making use of available data that might otherwise be discarded.

Ecology & Evolution↗

USGS2024

Implications for the resilience of modern coastal systems derived from mesoscale barrier dynamics at Fire Island, New York

Understanding the response of coastal barriers to future changes in rates of sea level rise, sediment availability, and storm intensity/frequency is essential for coastal planning, including socioeconomic and ecological management. Identifying drivers of past changes in barrier morphology, as well as barrier sensitivity to these forces, is necessary to accomplish this. Using remote sensing, field, and laboratory analyses, we reconstruct the mesoscale (decades–centuries) evolution of central Fire Island, a portion of a 50 km barrier island fronting Long Island, New York, USA. We find that the configuration of the modern beach and foredune at Fire Island is radically different from the system's relict morphostratigraphy. Central Fire Island is comprised of at least three formerly inlet-divided rotational barriers with distinct subaerial beach and dune–ridge systems that were active prior to the mid-19th century. Varying morphologic states reflected in the relict barriers (e.g., progradational and transgressive) contrast with the modern barrier, which is dominated by a tall and nearly continuous foredune and is relatively static, except for erosion and drowning of its fringing marsh. We suggest that this state shift indicates a transition from a regime dominated by inlet-mediated gradients in alongshore sediment availability to one where human impacts exerted greater influence on island evolution from the late 19th century onward. The retention of some geomorphic capital in Fire Island's relict subaerial features combined with its static nature renders the barrier increasingly susceptible to narrowing and passive submergence. This may lead to an abrupt geomorphic state shift in the future, a veiled vulnerability that may also exist in other stabilized barriers.

New York↗

USGS2013

Network modularity reveals critical scales for connectivity in ecology and evolution

For nearly a century, biologists have emphasized the profound importance of spatial scale for ecology, evolution and conservation. Nonetheless, objectively identifying critical scales has proven incredibly challenging. Here we extend new techniques from physics and social sciences that estimate modularity on networks to identify critical scales for movement and gene flow in animals. Using four species that vary widely in dispersal ability and include both mark-recapture and population genetic data, we identify significant modularity in three species, two of which cannot be explained by geographic distance alone. Importantly, the inclusion of modularity in connectivity and population viability assessments alters conclusions regarding patch importance to connectivity and suggests higher metapopulation viability than when ignoring this hidden spatial scale. We argue that network modularity reveals critical meso-scales that are probably common in populations, providing a powerful means of identifying fundamental scales for biology and for conservation strategies aimed at recovering imperilled species.

Nature Communications↗

USGS2015

Testing taxon tenacity of tortoises: evidence for a geographical selection gradient at a secondary contact zone

We examined a secondary contact zone between two species of desert tortoise, Gopherus agassizii and G. morafkai . The taxa were isolated from a common ancestor during the formation of the Colorado River (4-8 mya) and are a classic example of allopatric speciation. However, an anomalous population of G. agassizii comes into secondary contact with G. morafkai east of the Colorado River in the Black Mountains of Arizona and provides an opportunity to examine reinforcement of species' boundaries under natural conditions. We sampled 234 tortoises representing G. agassizii in California ( n = 103), G. morafkai in Arizona ( n = 78), and 53 individuals of undetermined assignment in the contact zone including and surrounding the Black Mountains. We genotyped individuals for 25 STR loci and determined maternal lineage using mtDNA sequence data. We performed multilocus genetic clustering analyses and used multiple statistical methods to detect levels of hybridization. We tested hypotheses about habitat use between G. agassizii and G. morafkai in the region where they co-occur using habitat suitability models. Gopherus agassizii and G. morafkai maintain independent taxonomic identities likely due to ecological niche partitioning, and the maintenance of the hybrid zone is best described by a geographical selection gradient model.

Ecology and Evolution↗

USGS2021

Gulf of Mexico blue hole harbors high levels of novel microbial lineages

Exploration of oxygen-depleted marine environments has consistently revealed novel microbial taxa and metabolic capabilities that expand our understanding of microbial evolution and ecology. Marine blue holes are shallow karst formations characterized by low oxygen and high organic matter content. They are logistically challenging to sample, and thus our understanding of their biogeochemistry and microbial ecology is limited. We present a metagenomic and geochemical characterization of Amberjack Hole on the Florida continental shelf (Gulf of Mexico). Dissolved oxygen became depleted at the hole’s rim (32 m water depth), remained low but detectable in an intermediate hypoxic zone (40–75 m), and then increased to a secondary peak before falling below detection in the bottom layer (80–110 m), concomitant with increases in nutrients, dissolved iron, and a series of sequentially more reduced sulfur species. Microbial communities in the bottom layer contained heretofore undocumented levels of the recently discovered phylum Woesearchaeota (up to 58% of the community), along with lineages in the bacterial Candidate Phyla Radiation (CPR). Thirty-one high-quality metagenome-assembled genomes (MAGs) showed extensive biochemical capabilities for sulfur and nitrogen cycling, as well as for resisting and respiring arsenic. One uncharacterized gene associated with a CPR lineage differentiated hypoxic from anoxic zone communities. Overall, microbial communities and geochemical profiles were stable across two sampling dates in the spring and fall of 2019. The blue hole habitat is a natural marine laboratory that provides opportunities for sampling taxa with under-characterized but potentially important roles in redox-stratified microbial processes.

Interational Society of Microbial Ecology (ISME) J↗

USGS2016

Chaparral

One of the most dynamic California ecosystems is chaparral. Dominated by evergreen, sclerophyllous shrubs and small trees, chaparral is the most extensive vegetation type in the state (Figure 1). The nearly impenetrable tangle of stiff branches of this unusual vegetation inhibits exploration, and as a consequence the public know little about its natural history and unique characteristics. This under-valued ecosystem is recognized instead by the threat of its extensive, high-intensity canopy-burning wildfires that characterize the dry summer and fall seasons of the state. Because urban areas frequently share borders or intermix with chaparral, societal interests often conflict with conservation of this ecosystem, and understanding its history and dynamics are a key to appreciating its importance. In this chapter we emphasize the principal structure and dynamics of this important ecosystem. The long summer rainless period has strong impacts on all organisms and, importantly, the droughts influence the fire regime that characterizes chaparral. An ecosystem currently characterized by a specific drought and wildfire regime can expect significant impacts from climate change. Because of its dominance at lower elevations, chaparral also is frequently found at or near the boundaries of urban developments and metropolitan centers. Attempts to suppress fire also affect chaparral dynamics in the long absence of fire. The conflicts between the impacts of chaparral wildfire and human life and structures has been an aspect of California’s history since the beginning, but as development encroaches ever more into chaparral regions, the conflicts have increased. Consequently, understanding this vegetation is important not only because of its significance in understanding ecological evolution and the ecological services provided by chaparral, but also because of its direct impacts on human settlements.

Book chapter↗