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Opportunities and challenges of macrogenetic studies

The rapidly emerging field of macrogenetics focuses on analysing publicly accessible genetic datasets from thousands of species to explore large-scale patterns and predictors of intraspecific genetic variation. Facilitated by advances in evolutionary biology, technology, data infrastructure, statistics and open science, macrogenetics addresses core evolutionary hypotheses (such as disentangling environmental and life-history effects on genetic variation) with a global focus. Yet, there are important, often overlooked, limitations to this approach and best practices need to be considered and adopted if macrogenetics is to continue its exciting trajectory and reach its full potential in fields such as biodiversity monitoring and conservation. Here, we review the history of this rapidly growing field, highlight knowledge gaps and future directions, and provide guidelines for further research.

Nature Reviews Genetics↗

Persistence of coral reef structures into the twenty-first century

Coral reefs provide important socioecological services but are vulnerable to climate change, which shifts the balance between the production and erosion of calcium carbonate (CaCO 3 ). In this Review, we summarize understanding of reef accretion, describe the mechanisms of carbonate production and erosion, and consider the effects of future ocean warming and acidification on key reef-building and eroding taxa. The combined stressors of climate change substantially reduce net carbonate production, with a more pronounced effect on calcifying algae than corals. However, declining coral cover driven by marine heatwaves and mass bleaching will probably be the dominant determinant of future reef carbonate budgets, and thus only reefs with thermally adapted populations are predicted to maintain the ability to sustain positive CaCO 3 production under climate change, even if calcareous algal cover increases. As carbonate budgets become net negative in the future, the longevity of pre-existing reef frameworks remains unknown and understudied owing to the timescales required to meaningfully assess framework removal rates. Improving estimates of the rates of biologically driven framework loss and chemical dissolution will also be important in better predicting future reef persistence. Key knowledge gaps exist in understanding the effects of deoxygenation on coral reefs, as well as the influence of climate change on understudied sediment-producing taxa such as foraminifera and tropical molluscs.

Nature Reviews Earth & Environment↗

Size, growth, and density data for shallow-water sea urchins from Mexico to the Aleutian Islands, Alaska, 1956–2016

Size, growth, and density have been studied for North American Pacific coast sea urchins Strongylocentrotus purpuratus , S. droebachiensis, S. polyacanthus , Mesocentrotus (Strongylocentrotus) franciscanus , Lytechinus pictus , Centrostephanus coronatus , and Arbacia stellata by various workers at diverse sites and for varying lengths of time from 1956 to present. Numerous peer-reviewed publications have used some of these data but some data have appeared only in graduate theses or the gray literature. There also are data that have never appeared outside original data sheets. Motivation for studies has included fisheries management and environmental monitoring of sewer and power plant outfalls as well as changes associated with disease epidemics. Studies also have focused on kelp restoration, community effects of sea otters, basic sea urchin biology, and monitoring. The data sets presented here are a historical record of size, density, and growth for a common group of marine invertebrates in intertidal and nearshore environments that can be used to test hypotheses concerning future changes associated with fisheries practices, shifts of predator distributions, climate and ecosystem changes, and ocean acidification along the Pacific Coast of North America and islands of the north Pacific.

Pacific Coast↗

Designing ecological climate change impact assessments to reflect key climatic drivers

Identifying the climatic drivers of an ecological system is a key step in assessing its vulnerability to climate change. The climatic dimensions to which a species or system is most sensitive – such as means or extremes – can guide methodological decisions for projections of ecological impacts and vulnerabilities. However, scientific workflows for combining climate projections with ecological models have received little explicit attention. We review Global Climate Model (GCM) performance along different dimensions of change and compare frameworks for integrating GCM output into ecological models. In systems sensitive to climatological means, it is straightforward to base ecological impact assessments on mean projected changes from several GCMs. Ecological systems sensitive to climatic extremes may benefit from what we term the ‘model space’ approach: a comparison of ecological projections based on simulated climate from historical and future time periods. This approach leverages the experimental framework used in climate modeling, in which historical climate simulations serve as controls for future projections. Moreover, it can capture projected changes in the intensity and frequency of climatic extremes, rather than assuming that future means will determine future extremes. Given the recent emphasis on the ecological impacts of climatic extremes, the strategies we describe will be applicable across species and systems. We also highlight practical considerations for the selection of climate models and data products, emphasizing that the spatial resolution of the climate change signal is generally coarser than the grid cell size of downscaled climate model output. Our review illustrates how an understanding of how climate model outputs are derived and downscaled can improve the selection and application of climatic data used in ecological modeling.

Global Change Biology↗

Applications of spatial statistical network models to stream data

Streams and rivers host a significant portion of Earth's biodiversity and provide important ecosystem services for human populations. Accurate information regarding the status and trends of stream resources is vital for their effective conservation and management. Most statistical techniques applied to data measured on stream networks were developed for terrestrial applications and are not optimized for streams. A new class of spatial statistical model, based on valid covariance structures for stream networks, can be used with many common types of stream data (e.g., water quality attributes, habitat conditions, biological surveys) through application of appropriate distributions (e.g., Gaussian, binomial, Poisson). The spatial statistical network models account for spatial autocorrelation (i.e., nonindependence) among measurements, which allows their application to databases with clustered measurement locations. Large amounts of stream data exist in many areas where spatial statistical analyses could be used to develop novel insights, improve predictions at unsampled sites, and aid in the design of efficient monitoring strategies at relatively low cost. We review the topic of spatial autocorrelation and its effects on statistical inference, demonstrate the use of spatial statistics with stream datasets relevant to common research and management questions, and discuss additional applications and development potential for spatial statistics on stream networks. Free software for implementing the spatial statistical network models has been developed that enables custom applications with many stream databases.

WIREs Water↗

Life history with emphasis on geographic variation

Every organism is defined by a set of vital rates that evolve to enhance lifetime reproductive fitness and survival of individuals and their progeny. These traits vary due to the complex but sometimes predictable interactions between individuals, populations and their environments. Collectively, these attributes are referred to as life history traits and include age and size of maturity, longevity, clutch size, clutch frequency, and survivorship during all phases of an organism’s life cycle. A significant body of literature has been devoted to life history theory and our intent is not to plow that ground again since it is beyond the scope of this chapter. Instead, the reader is referred to seminal papers on the topic including the works of authors such as Bernardo, Cole, Congdon, Stearns, and others. Our objective in this chapter is to review the life history traits of diamond-backed terrapins (DBTs) across all subspecies (SEE TAXONOMY CHAPTER) to better understand both their unique adaptations and their vulnerabilities in the modern world. In addition, we provide analyses of geographic variation in demography and body size among DBT populations. The latter is important since some reproductive traits in turtles are strongly influenced by body size (e.g., Ryan and Lindeman 2007). A recent summary of terrapin biology is contained in Ernst and Lovich (2009) and the reader is referred there to avoid duplication and for additional information.

Book chapter↗

Vascular Plant and Vertebrate Inventory of Chiricahua National Monument

This report summarizes the results of the first comprehensive inventory of vascular plants and vertebrates at Chiricahua National Monument (NM) in Arizona. This project was part of a larger effort to inventory vascular plants and vertebrates in eight National Park Service units in the Sonoran Desert Network of parks in Arizona and New Mexico. In 2002, 2003, and 2004 we surveyed for plants and vertebrates (amphibians, reptiles, birds, and mammals) at Chiricahua NM to document the presence of species within the boundaries of the monument. Because we used repeatable study designs and standardized field methods, these inventories can serve as the first step in a biological monitoring program for the monument. This report is also the first summary of previous research from the monument and therefore it provides an important overview of survey efforts to date. We used data from our inventory and previous research to compile complete species lists for the monument and to assess inventory completeness. We recorded a total of 424 species, including 37 not previously found at the monument (Table 1). We found 10 species of non-native plants and one non-native mammal. Most non-native plants were found along the western boundary of the monument. Based on a review of our inventory and past research at the monument, there have been a total of 1,137 species of plants and vertebrates found at the monument. We believe the inventories of vascular plants and vertebrates are nearly complete and that the monument has one of the most complete inventories of any unit in the Sonoran Desert Network. The mammal community at the monument had the highest species richness (69 species) and the amphibian and reptile community was among the lowest species richness (33 species) of any park in the Sonoran Desert Network. Species richness of the plant and bird communities was intermediate. Among the important determinants of species richness for all groups is the geographic location of the monument at the intergrades between the Chihuahuan and Sonoran deserts with influences from the Great Plains and Madrean ecological provinces. The diversity of plants results from a wide variety of soil types and aspects (from cool, moist canyons to semi-desert grasslands to pine forests). In turn, the vertebrate communities respond to this diversity of vegetation, topography, and microsites. For example, for each taxonomic group we found that some species were only associated with a single community type, most often the riparian areas or semi-desert grasslands. The area of highest species richness for most groups was the western-most portion of Bonita Canyon. The low species richness observed in the amphibian and reptile community was likely because the monument is at the elevational edge of the more species-rich semi-desert grasslands. This report includes management implications from our work and suggestions for how the monument staff might better maintain or enhance the unique biological resources of the monument. We suggest additional inventory, monitoring, and research studies and we identify components of our effort that could be improved upon, either through the application of new techniques (e.g., establishment of vegetation monitoring plots) or by extending the temporal and/or spatial scope of our work.

Open-File Report↗

Sandrewia, n. gen., a problematical plant from the Lower Permian of Texas and Kansas

Sandrewia , n. gen., monotypified by S. texana , n. sp., is a plant from Lower Permian beds of north-central Texas and east-central Kansas. It is characterized by stout axes with spirally disposed, laxly inserted, petiolate leaves; the laminae are broadly flabelliform with coarse, open venation. The leaves are reminiscent of the vojnovskyalean Nephropsis , of the Permian Petchora Basin, U.S.S.R., but biologic relationships are only speculative because of limited material. However, leaf characteristics render Sandrewia easily identifiable. Its presently limited stratigraphic range, along with floristic associations, indicates it may be a useful guide fossil and supports the author's beliefs regarding important times and places in Paleozoic plant evolution.

Kansas, Texas↗

Quantitative tools for implementing the new definition of significant portion of the range in the U.S. Endangered Species Act

In 2014, the Fish and Wildlife Service (FWS) and National Marine Fisheries Service announced a new policy interpretation for the U.S. Endangered Species Act (ESA). According to the act, a species must be listed as threatened or endangered if it is determined to be threatened or endangered in a significant portion of its range (SPR). The 2014 policy seeks to provide consistency by establishing that a portion of the range should be considered significant if the associated individuals’ “removal would cause the entire species to become endangered or threatened.” We reviewed 20 quantitative techniques used to assess whether a portion of a species’ range is significant according to the new guidance. Our assessments are based on the 3R criteria—redundancy (i.e., buffering from catastrophe), resiliency (i.e., ability to withstand stochasticity), and representation (i.e., ability to evolve)—that the FWS uses to determine if a species merits listing. We identified data needs for each quantitative technique and considered which methods could be implemented given the data limitations typical of rare species. We also identified proxies for the 3Rs that may be used with limited data. To assess potential data availability, we evaluated 7 example species by accessing data in their species status assessments, which document all the information used during a listing decision. In all species, an SPR could be evaluated with at least one metric for each of the 3Rs robustly or with substantial assumptions. Resiliency assessments appeared most constrained by limited data, and many species lacked information on connectivity between subpopulations, genetic variation, and spatial variability in vital rates. These data gaps will likely make SPR assessments for species with complex life histories or that cross national boundaries difficult. Although we reviewed techniques for the ESA, other countries require identification of significant areas and could benefit from this research.

Conservation Biology↗

Toward immunogenetic studies of amphibian chytridiomycosis: Linking innate and acquired immunity

Recent declines in amphibian diversity and abundance have contributed significantly to the global loss of biodiversity. The fungal disease chytridiomycosis is widely considered to be a primary cause of these declines, yet the critical question of why amphibian species differ in susceptibility remains unanswered. Considerable evidence links environmental conditions and interspecific variability of the innate immune system to differential infection responses, but other sources of individual, population, or species-typical variation may also be important. In this article we review the preliminary evidence supporting a role for acquired immune defenses against chytridiomycosis, and advocate for targeted investigation of genes controlling acquired responses, as well as those that functionally bridge the innate and acquired immune systems. Immunogenetic data promise to answer key questions about chytridiomycosis susceptibility and host-pathogen coevolution, and will draw much needed attention to the importance of considering evolutionary processes in amphibian conservation management and practice. ?? 2009 by American Institute of Biological Sciences.

BioScience↗

Development and application of methods used to source prehistoric Southwestern maize: a review

Archaeological cobs free of mineral contaminants should be used to source the soils in which they were grown. Mineral contaminants often contain much higher concentrations of metals than vegetal materials and can alter a cob’s apparent metal and heavy-isotope content. Cleaning a cob via immersion in an acid solution for more than a few minutes will result in the incongruent and sometimes complete leaching of metals, including strontium (Sr), from the cob. When using 87 Sr/ Sr to determine the location of potential agriculture fields, it is best to either integrate several depth-integrated soil samples or to integrate several vegetation samples from individual fields. Biologically labile Sr in semi-arid Southwestern soils largely originates from eolian source or sources and usually is not derived from underlying bedrock. Existing Sr-isotope data indicate that archaeological cobs from Aztec Ruins came from either the Mesa Verde-McElmo Dome or Totah areas, that Pueblo Bonito and Chetro Ketl cobs, from Chaco Canyon that predate A.D. 1130, probably came from the Rio Chaco corridor, and that cobs from Chaco Canyon, that postdate A.D. 1130, probably came from either the Totah or Zuni areas.

Journal of Archaeological Science↗

Sources, fate, and effects of PAHs in shallow water environments: a review with special reference to small watercraft

Polycyclic aromatic hydrocarbons (PAHs) are aromatic hydrocarbons with two to seven fused carbon (benzene) rings that can have substituted groups attached. Shallow coastal, estuarine, lake, and river environments receive PAHs from treated wastewater, stormwater runoff, petroleum spills and natural seeps, recreational and commercial boats, natural fires, volcanoes, and atmospheric deposition of combustion products. Abiotic degradation of PAHs is caused by photooxidation, photolysis in water, and chemical oxidation. Many aquatic microbes, plants, and animals can metabolize and excrete ingested PAHs; accumulation is associated with poor metabolic capabilities, high lipid content, and activity patterns or distributions that coincide with high concentrations of PAHs. Resistance to biological transformation increases with increasing number of carbon rings. Four- to seven-ring PAHs are the most difficult to metabolize and the most likely to accumulate in sediments. Disturbance by boating activity of sediments, shorelines, and the surface microlayer of water causes water column re-entry of recently deposited or concentrated PAHs. Residence time for PAHs in undisturbed sediment exceeds several decades. Toxicity of PAHs causes lethal and sublethal effects in plants and animals, whereas some substituted PAHs and metabolites of some PAHs cause mutations, developmental malformations, tumors, and cancer. Environmental concentrations of PAHs in water are usually several orders of magnitude below levels that are acutely toxic, but concentrations can be much higher in sediment. The best evidence for a link between environmental PAHs and induction of cancerous neoplasms is for demersal fish in areas with high concentrations of PAHs in the sediment.

Book chapter↗

A review of fire effects on vegetation and soils in the Great Basin region: response and ecological site characteristics

This review synthesizes the state of knowledge on fire effects on vegetation and soils in semi-arid ecosystems in the Great Basin Region, including the central and northern Great Basin and Range, Columbia River Basin, and the Snake River Plain. We summarize available literature related to: (1) the effects of environmental gradients, ecological site, and vegetation characteristics on resilience to disturbance and resistance to invasive species; (2) the effects of fire on individual plant species and communities, biological soil crusts, seed banks, soil nutrients, and hydrology; and (3) the role of fire severity, fire versus fire surrogate treatments, and post-fire grazing in determining ecosystem response. From this, we identify knowledge gaps and present a framework for predicting plant successional trajectories following wild and prescribed fires and fire surrogate treatments. Possibly the three most important ecological site characteristics that influence a site’s resilience (ability of the ecological site to recover from disturbance) and resistance to invasive species are soil temperature/moisture regimes and the composition and structure of vegetation on the ecological site just prior to the disturbance event.

Columbia River Basin;Great Basin↗

Biology and impacts of Pacific island invasive species 9. Capra hircus , the feral goat, (Mammalia: Bovidae)

Domestic goats, Capra hircus , were intentionally introduced to numerous oceanic islands beginning in the sixteenth century. The remarkable ability of C. hircus to survive in a variety of conditions has enabled this animal to become feral and impact native ecosystems on islands throughout the world. Direct ecological impacts include consumption and trampling of native plants, leading to plant community modification and transformation of ecosystem structure. While the negative impacts of feral goats are well-known and effective management strategies have been developed to control this invasive species, large populations persist on many islands. This review summarizes the impacts of feral goats on Pacific island ecosystems, and the management strategies available to control this invasive species.

Pacific Science↗

Detecting temporal change in freshwater fisheries surveys: statistical power and the important linkages between management questions and monitoring objectives

Monitoring to detect temporal trends in biological and habitat indices is a critical component of fisheries management. Thus, it is important that management objectives are linked to monitoring objectives. This linkage requires a definition of what constitutes a management-relevant “temporal trend.” It is also important to develop expectations for the amount of time required to detect a trend (i.e., statistical power) and for choosing an appropriate statistical model for analysis. We provide an overview of temporal trends commonly encountered in fisheries management, review published studies that evaluated statistical power of long-term trend detection, and illustrate dynamic linear models in a Bayesian context, as an additional analytical approach focused on shorter term change. We show that monitoring programs generally have low statistical power for detecting linear temporal trends and argue that often management should be focused on different definitions of trends, some of which can be better addressed by alternative analytical approaches.

Fisheries↗

Agricultural drainwater effects on wildlife in central California

In California's San Joaquin Valley and in numerous other agricultural areas in the western U.S., irrigation wastewater may accumulate in confined shallow aquifers, eventually rising to levels that adversely affect crops. To sustain long-term agricultural productivity in these regions, systems for the drainage and disposal of this subsurface wastewater must be installed. 1,2 the drained water may contain an array of soluble chemicals that have been applied to the crops, as well as those that have been leached from native soils. Agricultural drainwater is frequently disposed of by discharging it to surface aquatic systems where these constituents may be directly toxic to aquatic organisms, or they may bioaccumulate through the aquatic food webs upon which birds and other wildlife feed. The focus of this chapter is research conducted since 1983 to assess the effects of wildlife exposure to subsurface agricultural drainwater in the San Joaquin Valley. Agricultural drainwater is discharged primarily to tributaries and wetlands of the San Joaquin River system or, especially in the southern San Joaquin Valley, to evaporation ponds. 3 Because of high nutrient content in the drainwater, evaporation ponds have high levels of biological productivity and provide an abundant food supply for aquatic birds. Aquatic birds (primarily waterfowl and shorebirds) have been the main focus of wildlife research at the evaporation ponds, and at managed wetlands (primarily hunting clubs) within the San Joaquin River system, but mammals, snakes, and frogs have also been studied. Findings of those studies are summarized in this chapter. Other studies have been conducted on fish and aquatic invertebrates in areas receiving agricultural drainwater, but in this review those findings are described only as they relate to dietary exposure of wildlife.

Book chapter↗

The Partners in Flight handbook on species assessment Version 2017

Partners in Flight (PIF) is a cooperative venture of federal, state, provincial, and territorial agencies, industry, non-governmental organizations, researchers, and many others whose common goal is the conservation of North American birds (www.partnersinflight.org). While PIF has focused primarily on landbirds, it works in conjunction with other bird partners to promote coordinated conservation of all birds. PIF follows an iterative, adaptive planning approach that develops a sound scientific basis for decision-making and a logical process for setting, implementing, and evaluating conservation objectives (Pashley et al. 2000, Rich et al. 2004, Berlanga et al. 2010). The steps include: 1. Assessing conservation vulnerability of all bird species; 2. Identifying species most in need of conservation attention at continental and regional scales; 3. Setting of numerical population objectives for species of continental and regional importance; 4. Identifying conservation needs and recommended actions for species and habitats of importance; 5. Implementing strategies for meeting species and habitat objectives at continental and regional scales; 6. Evaluating success, making revisions, and setting new objectives for the future. The 2017 PIF Handbook on Species Assessment (2017 PIF Handbook) documents assessment rules and scores used in the Partners in Flight Landbird Conservation Plan: 2016 Revision for Canada and Continental United States (Rosenberg et al. 2016) and The State of North America’s Birds 2016 (NABCI 2016). It updates previous versions of the handbook (Panjabi et al. 2012, 2005, 2001) developed to accompany other PIF applications including Saving Our Shared Birds: Partners in Flight Tri-National Vision for Landbird Conservation (Berlanga et al. 2010) and the North American Landbird Conservation Plan (Rich et al. 2004). All current and past scores, data sources, and other related information are contained in databases hosted by the Bird Conservancy of the Rockies. Scores can be viewed online and downloaded as excel files, including archived versions (http://pif.birdconservancy.org/acad). The current accompanying Avian Conservation Assessment Database (ACAD) holds assessment scores and data for all 1585 native and 18 well-established non-native bird species found in mainland North America south to Panama plus adjacent islands and oceans. The taxonomy follows the American Ornithological Society’s 7th Edition Checklist of North and Middle American Birds, including updates though the 57th supplement, published in 2016 (http://checklist.aou.org/). The ACAD builds on archived PIF databases that hosted only data on the 882 landbirds native to Canada, USA and Mexico. This handbook is presented in two principal sections. Part I details the factors and scoring used by PIF to assess the vulnerability of species at continental and regional scales (i.e. step 1 of the planning approach above). Each assessment factor is based on biological criteria that evaluate distinct components of vulnerability throughout the life cycle of each species across its range. Part II describes the process of how the factors and the corresponding scores can be combined to highlight conservation needs (i.e. step 2 of the planning approach above). Both the scores and the process have evolved over time (Hunter et al. 1992, Carter et al. 2000, Panjabi et al. 2001, 2005, 2012) and continue to be updated in response to external review (Beissinger et al. 2000), broad partner expertise, and the emergence of new data and analytical tools.

Report↗

Biological soil crusts: An organizing principle in dryland ecosystems (aka: the role of biocrusts in arid land hydrology)

Biocrusts exert a strong influence on hydrological processes in drylands by modifying numerous soil properties that affect water retention and movement in soils. Yet, their role in these processes is not clearly understood due to the large number of factors that act simultaneously and can mask the biocrust effect. The influence of biocrusts on soil hydrology depends on biocrust intrinsic characteristics such as cover, composition, and external morphology, which differ greatly among climate regimes, but also on external factors as soil type, topography and vegetation distribution patterns, as well as interactions among these factors. This chapter reviews the most recent literature published on the role of biocrusts in infiltration and runoff, soil moisture, evaporation and non-rainfall water inputs (fog, dew, water absorption), in an attempt to elucidate the key factors that explain how biocrusts affect land hydrology. In addition to the crust type and site characteristics, recent studies point to the crucial importance of the type of rainfall and the spatial scale at which biocrust effects are analyzed to understand their role in hydrological processes. Future studies need to consider the temporal and spatial scale investigated to obtain more accurate generalizations on the role of biocrusts in land hydrology.

Book chapter↗