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Status and opportunities for genomics research with rainbow trout

The rainbow trout (Oncorhynchus mykiss) is one of the most widely studied of model fish species. Extensive basic biological information has been collected for this species, which because of their large size relative to other model fish species are particularly suitable for studies requiring ample quantities of specific cells and tissue types. Rainbow trout have been widely utilized for research in carcinogenesis, toxicology, comparative immunology, disease ecology, physiology and nutrition. They are distinctive in having evolved from a relatively recent tetraploid event, resulting in a high incidence of duplicated genes. Natural populations are available and have been well characterized for chromosomal, protein, molecular and quantitative genetic variation. Their ease of culture, and experimental and aquacultural significance has led to the development of clonal lines and the widespread application of transgenic technology to this species. Numerous microsatellites have been isolated and two relatively detailed genetic maps have been developed. Extensive sequencing of expressed sequence tags has begun and four BAC libraries have been developed. The development and analysis of additional genomic sequence data will provide distinctive opportunities to address problems in areas such as evolution of the immune system and duplicate genes. ?? 2002 Elsevier Science Inc. All rights reserved.

Conference Paper

The role of ecology in allopatric speciation of darters in the Central Highlands, USA

Allopatric speciation is the predominant mode of speciation in riverine fishes. However, the relative importance of genetic drift versus natural selection in the allopatric speciation of these fishes remain uncertain. Here, we present a case study that demonstrates the role of ecology in the diversification of a group of imperiled freshwater fishes from the central United States. We integrate a phylogenomic dataset with analyses of streamwise distance, environmental variables, meristic and morphological traits, and diet to investigate the ecological context and outcomes of allopatric speciation within a species complex comprising the Slenderhead Darter Percina phoxocephala (Nelson), Ouachita Darter Percina brucethompsoni (Robison, Cashner, and Near), and Longnose Darter Percina nasuta (Bailey). We find that two of the species traditionally delimited based on disparity in snout length, P. phoxocephala and P. nasuta , are polyphyletic, revealing three instances of the parallel evolution of snout length disparity. We propose a revised taxonomy including the delimitation of six new species based on disparity in phenotypic traits and phylogenomic analyses. We find that morphological differences are not correlated with genetic divergence but are congruent with variations in diet and environmental niches, suggesting a role for ecological factors in allopatric speciation of riverine fishes.

Arkansas, Kansas, Missouri, Oklahoma

Wildlife associates of nine-banded armadillo (Dasypus novemcinctus) burrows in Arkansas

The Nine-banded Armadillo ( Dasypus novemcinctus ) is a widespread burrowing species with an expanding geographic range across the southeastern and midwestern United States. Armadillos dig numerous, large burrows within their home ranges and these burrows are likely used by a diverse suite of wildlife species as has been reported for other burrowing ecosystem engineers such as Gopher Tortoises ( Gopherus polyphemus ), Desert Tortoises ( Gopherus agassizi ), and Black-tailed Prairie Dogs ( Cynomys ludovicianus ). We used motion-triggered game cameras at 35 armadillo burrows in 4 ecoregions of Arkansas and documented 19 species of mammals, 4 species of reptile, 1 species of amphibian, and 40 species of bird interacting with burrows. Bobcat ( Lynx rufus ), Coyote ( Canis latrans ), Eastern Cottontail ( Sylvilagus floridanus ), Gray Fox ( Urocyon cinereoargenteus ), Gray Squirrel ( Sciurus carolinensis ), Northern Raccoon ( Procyon lotor ), Virginia Opossum ( Didelphis virginiana ), and unidentified rodents (mice and rats) were documented using burrows in all four ecoregions. We documented wildlife hunting, seeking shelter, rearing young in, and taking over and modifying armadillo burrows. The rate of use was highest in the Mississippi Alluvial Valley, a landscape dominated by agriculture, where natural refugia may be limited and rodents are abundant. Armadillo burrows are clearly visited and used by numerous wildlife species to fulfill various life stage requirements, and this list will likely expand if more attention is devoted to understanding the role of armadillos burrows. Armadillos are important ecosystem engineers, and their ecological role warrants more investigation and attention as opposed to only being viewed and managed as agricultural and garden pests.

Arkansas

Introduction to the special issue on “Understanding and predicting change in the coastal ecosystems of the northern Gulf of Mexico”

The coastal region of the northern Gulf of Mexico owes its current landscape structure to an array of tectonic, erosional and depositional, climatic, geochemical, hydrological, ecological, and human processes that have resulted in some of the world's most complex, dynamic, productive, and threatened ecosystems. Catastrophic hurricane landfalls, ongoing subsidence and erosion exacerbated by sea-level rise, disintegration of barrier island chains, and high rates of wetland loss have called attention to the vulnerability of northern Gulf coast ecosystems, habitats, built infrastructure, and economy to natural and anthropogenic threats. The devastating hurricanes of 2005 (Katrina and Rita) motivated the U.S. Geological Survey Coastal and Marine Geology Program and partnering researchers to pursue studies aimed at understanding and predicting landscape change and the associated storm hazard vulnerability of northern Gulf coast region ecosystems and human communities. Attaining this science goal requires increased knowledge of landscape evolution on geologic, historical, and human time scales, and analysis of the implications of such changes in the natural and built components of the landscape for hurricane impact susceptibility. This Special Issue of the Journal of Coastal Research communicates northern Gulf of Mexico research results that (1) improve knowledge of prior climates and depositional environments, (2) assess broad regional ecosystem structure and change over Holocene to human time scales, (3) undertake process studies and change analyses of dynamic landscape components, and (4) integrate framework, climate, variable time and spatial scale mapping, monitoring, and discipline-specific process investigations within interdisciplinary studies.

Journal of Coastal Research

Population and genetic outcomes 20 years after reintroducing bobcats ( Lynx rufus ) to Cumberland Island, Georgia USA

In 1988–1989, 32 bobcats Lynx rufus were reintroduced to Cumberland Island (CUIS), Georgia, USA, from which they had previously been extirpated. They were monitored intensively for 3 years immediately post-reintroduction, but no estimation of the size or genetic diversity of the population had been conducted in over 20 years since reintroduction. We returned to CUIS in 2012 to estimate abundance and effective population size of the present-day population, as well as to quantify genetic diversity and inbreeding. We amplified 12 nuclear microsatellite loci from DNA isolated from scats to establish genetic profiles to identify individuals. We used spatially explicit capture–recapture population estimation to estimate abundance. From nine unique genetic profiles, we estimate a population size of 14.4 (SE = 3.052) bobcats, with an effective population size ( N e ) of 5–8 breeding individuals. This is consistent with predictions of a population viability analysis conducted at the time of reintroduction, which estimated the population would average 12–13 bobcats after 10 years. We identified several pairs of related bobcats (parent-offspring and full siblings), but ~75% of the pairwise comparisons were typical of unrelated individuals, and only one individual appeared inbred. Despite the small population size and other indications that it has likely experienced a genetic bottleneck, levels of genetic diversity in the CUIS bobcat population remain high compared to other mammalian carnivores. The reintroduction of bobcats to CUIS provides an opportunity to study changes in genetic diversity in an insular population without risk to this common species. Opportunities for natural immigration to the island are limited; therefore, continued monitoring and supplemental bobcat reintroductions could be used to evaluate the effect of different management strategies to maintain genetic diversity and population viability. The successful reintroduction and maintenance of a bobcat population on CUIS illustrates the suitability of translocation as a management tool for re-establishing felid populations.

Georgia

Effects of environment and metacommunity delineation on multiple dimensions of stream fish beta diversity

Introduction: Beta diversity represents changes in community composition among locations across a landscape. While the effects of human activities on beta diversity are becoming clearer, few studies have considered human effects on the three dimensions of beta diversity: taxonomic, functional, and phylogenetic. Including anthropogenic factors and multiple dimensions of biodiversity may explain additional variation in stream fish beta diversity, providing new insight into how metacommunities are structured within different spatial delineations. Methods: In this study, we used a 350 site stream fish abundance dataset from South Carolina, United States to quantify beta diversity explainable by spatial, natural environmental, and anthropogenic variables. We investigated three spatial delineations: (1) a single whole-state metacommunity delineated by political boundaries, (2) two metacommunities delineated by a natural geomorphic break separating uplands from lowlands, and (3) four metacommunities delineated by natural watershed boundaries. Within each metacommunity we calculated taxonomic, functional, and phylogenetic beta diversity and used variation partitioning to quantify spatial, natural environmental, and anthropogenic contributions to variations in beta diversity. Results: We explained 25–81% of the variation in stream fish beta diversity. The importance of these three factors in structuring metacommunities differed among the diversity dimensions, providing complementary perspectives on the processes shaping beta diversity in fish communities. The effect of spatial, natural environmental, and anthropogenic factors varied among the spatial delineations, which indicate conclusions drawn from variation partitioning may depend on the spatial delineation chosen by researchers. Discussion: Our study highlights the importance of considering human effects on metacommunity structure, quantifying multiple dimensions of beta diversity, and careful consideration of user-defined metacommunity boundaries in beta diversity analyses.

South Carolina

Reviews and syntheses: Variable inundation across Earth's terrestrial ecosystems

The structure, function, and dynamics of Earth's terrestrial ecosystems are profoundly influenced by how often (frequency) and how long (duration) they are inundated with water. A diverse array of natural and human-engineered systems experience temporally variable inundation whereby they fluctuate between inundated and non-inundated states. Variable inundation spans extreme events to predictable sub-daily cycles. Variably inundated ecosystems (VIEs) include hillslopes, non-perennial streams, wetlands, floodplains, temporary ponds, tidal systems, storm-impacted coastal zones, and human-engineered systems. VIEs are diverse in terms of inundation regimes, water chemistry and flow velocity, soil and sediment properties, vegetation, and many other properties. The spatial and temporal scales of variable inundation are vast, ranging from sub-meter to whole landscapes and from sub-hourly to multi-decadal. The broad range of system types and scales makes it challenging to predict the hydrology, biogeochemistry, ecology, and physical evolution of VIEs. Despite all experiencing the loss and gain of an overlying water column, VIEs are rarely considered together in conceptual, theoretical, modeling, or measurement frameworks and approaches. Studying VIEs together has the potential to generate mechanistic understanding that is transferable across a much broader range of environmental conditions, relative to knowledge generated by studying any one VIE type. We postulate that enhanced transferability will be important for predicting changes in VIE function in response to global change. Here we aim to catalyze cross-VIE science that studies drivers and impacts of variable inundation across Earth's VIEs. To this end, we complement expert mini-reviews of eight major VIE systems with overviews of VIE-relevant methods and challenges associated with scale. We conclude with perspectives on how cross-VIE science can derive transferable understanding via unifying conceptual models in which the impacts of variable inundation are studied across multi-dimensional environmental space.

Biogeosciences

Restricted gene flow between resident Oncorhynchus mykiss and an admixed population of anadromous steelhead

The species Oncorhynchus mykiss is characterized by a complex life history that presents a significant challenge for population monitoring and conservation management. Many factors contribute to genetic variation in O. mykiss populations, including sympatry among migratory phenotypes, habitat heterogeneity, hatchery introgression, and immigration (stray) rates. The relative influences of these and other factors are contingent on characteristics of the local environment. The Rock Creek subbasin in the middle Columbia River has no history of hatchery supplementation and no dams or artificial barriers. Limited intervention and minimal management have led to a dearth of information regarding the genetic distinctiveness of the extant O. mykiss population in Rock Creek and its tributaries. We used 192 SNP markers and collections sampled over a 5‐year period to evaluate the temporal and spatial genetic structures of O. mykiss between upper and lower watersheds of the Rock Creek subbasin. We investigated potential limits to gene flow within the lower watershed where the stream is fragmented by seasonally dry stretches of streambed, and between upper and lower watershed regions. We found minor genetic differentiation within the lower watershed occupied by anadromous steelhead ( F ST = 0.004), and evidence that immigrant influences were prevalent and ubiquitous. Populations in the upper watershed above partial natural barriers were highly distinct ( F ST = 0.093) and minimally impacted by apparent introgression. Genetic structure between watersheds paralleled differences in local demographics (e.g., variation in size), migratory restrictions, and habitat discontinuity. The evidence of restricted gene flow between putative remnant resident populations in the upper watershed and the admixed anadromous population in the lower watershed has implications for local steelhead productivity and regional conservation.

Washington

How does pedogenesis drive plant diversity?

Some of the most species-rich plant communities occur on ancient, strongly weathered soils, whereas those on recently developed soils tend to be less diverse. Mechanisms underlying this well-known pattern, however, remain unresolved. Here, we present a conceptual model describing alternative mechanisms by which pedogenesis (the process of soil formation) might drive plant diversity. We suggest that long-term soil chronosequences offer great, yet largely untapped, potential as 'natural experiments' to determine edaphic controls over plant diversity. Finally, we discuss how our conceptual model can be evaluated quantitatively using structural equation modeling to advance multivariate theories about the determinants of local plant diversity. This should help us to understand broader-scale diversity patterns, such as the latitudinal gradient of plant diversity.

Trends in Ecology and Evolution

The role of paleoecology in restoration and resource management—The past as a guide to future decision-making: Review and example from the Greater Everglades Ecosystem, U.S.A

Resource managers around the world are challenged to develop feasible plans for sustainable conservation and/or restoration of the lands, waters, and wildlife they administer—a challenge made greater by anticipated climate change and associated effects over the next century. Increasingly, paleoecologic and geologic archives are being used to extend the period of record of observed data and provide information on centennial to millennial scale responses to long-term drivers of ecosystem change. The development of paleoecology from an emerging field investigating past environments to a highly relevant applied science is reviewed and general examples of the application of paleoecologic research to resource management questions in diverse habitats and regions are provided. Specific examples of the application of paleoecologic research to the restoration of the Greater Everglades Ecosystem of south Florida (U.S.A) are presented. Conducting valuable scientific research that would benefit resource management decisions, however, is not enough. Scientists and resource managers need to be engaged in collaborative discussions from the beginning of the research process to ensure that management questions are being addressed and that the science reaches the people who will benefit from the information. Paleoecology and related disciplines provide an understanding of how ecosystems and individual species function and change over time in response to both natural and anthropogenic drivers. Information on pre-anthropogenic baseline conditions is provided by paleoecologic research, but it is the detection of long-term trends and cycles that allow resource managers to set realistic goals and targets by moving away from the fixed-point baseline concept to one of dynamic landscapes that anticipates and incorporates an expectation of change into decision-making.

Florida

Urban landscapes can change virus gene flow and evolution in a fragmentation-sensitive carnivore

Urban expansion has widespread impacts on wildlife species globally, including the transmission and emergence of infectious diseases. However, there is almost no information about how urban landscapes shape transmission dynamics in wildlife. Using an innovative phylodynamic approach combining host and pathogen molecular data with landscape characteristics and host traits, we untangle the complex factors that drive transmission networks of Feline Immunodeficiency Virus (FIV) in bobcats ( Lynx rufus ). We found that the urban landscape played a significant role in shaping FIV transmission. Even though bobcats were often trapped within the urban matrix, FIV transmission events were more likely to occur in areas with more natural habitat elements. Urban fragmentation also resulted in lower rates of pathogen evolution, possibly owing to a narrower range of host genotypes in the fragmented area. Combined, our findings show that urban landscapes can have impacts on a pathogen and its evolution in a carnivore living in one of the most fragmented and urban systems in North America. The analytical approach used here can be broadly applied to other host-pathogen systems, including humans.

Molecular Ecology

Moose habitat selection and fitness consequences during two critical winter tick life stages in Vermont, United States

The moose ( Alces alces ) is a charismatic species in decline across much of their southern distribution in North America. In the northeastern United States, much of the reduction has been attributed to winter tick ( Dermacentor albipictus ) infestations. Winter ticks are fairly immobile throughout all life stages, and therefore their distribution patterns at any given time are shaped largely by the occurrence of moose across the landscape during the peak of two critical time periods: fall questing (when ticks latch onto moose) and spring drop-off (when engorged female ticks detach from moose). We used recent land cover and lidar data within a dynamic occupancy modeling framework to estimate first-order habitat selection (use vs. non-use) of female moose ( n = 74) during the tick questing and drop-off periods. Patch extinction and colonization rates between the fall questing and spring drop-off periods were strongly influenced by habitat and elevation, but these effects were diminished during the fall questing period when moose were more active across the landscape. From the fall questing period to the spring drop-off period, patches where colonization was high and extinction was low had higher proportions of young (shrub/forage) mixed forest at higher elevations. Further, we evaluated the fitness consequences of habitat selection by adult females during the fall questing period, when females and their calves acquire ticks. We compared Resource Selection Functions (RSF) for five females that successfully reared a calf to age 1 with five females whose calves perished due to ticks. Adult female moose whose offspring perished selected habitats in the fall that spatially coincided with areas of high occupancy probability during the spring tick drop-off period. In contrast, adult female moose whose offspring survived selected areas where the probability of occupancy during the spring drop-off was low; at present, natural selection may favor female adults who do not select the same habitats in fall as in spring. Our model coefficients and mapped results define “hotspots” that are likely encouraging the deleterious effects of the tick-moose cycle. These findings fill knowledge gaps about moose habitat selection that may improve the effectiveness of management aimed at reversing declining population trends.

Vermont

The evolution of different maternal investment strategies in two closely related desert vertebrates

We compared egg size phenotypes and tested several predictions from the optimal egg size (OES) and bet-hedging theories in two North American desert-dwelling sister tortoise taxa, Gopherus agassizii and G. morafkai , that inhabit different climate spaces: relatively unpredictable and more predictable climate spaces, respectively. Observed patterns in both species differed from the predictions of OES in several ways. Mean egg size increased with maternal body size in both species. Mean egg size was inversely related to clutch order in G. agassizii , a strategy more consistent with the within-generation hypothesis arising out of bet-hedging theory or a constraint in egg investment due to resource availability, and contrary to theories of density dependence, which posit that increasing hatchling competition from later season clutches should drive selection for larger eggs. We provide empirical evidence that one species, G. agassizii , employs a bet-hedging strategy that is a combination of two different bet-hedging hypotheses. Additionally, we found some evidence for G. morafkai employing a conservative bet-hedging strategy. (e.g., lack of intra- and interclutch variation in egg size relative to body size). Our novel adaptive hypothesis suggests the possibility that natural selection favors smaller offspring in late-season clutches because they experience a more benign environment or less energetically challenging environmental conditions (i.e., winter) than early clutch progeny, that emerge under harsher and more energetically challenging environmental conditions (i.e., summer). We also discuss alternative hypotheses of sexually antagonistic selection, which arise from the trade-offs of son versus daughter production that might have different optima depending on clutch order and variation in temperature-dependent sex determination (TSD) among clutches. Resolution of these hypotheses will require long-term data on fitness of sons versus daughters as a function of incubation environment, data as yet unavailable for any species with TSD.

Arizona, California

U.S. Geological Survey science strategy to address highly pathogenic avian influenza and its effects on wildlife health 2025–29

Executive Summary Highly pathogenic avian influenza (HPAI) is an ecologically and economically important animal disease that can also directly affect humans (a “zoonotic” disease). HPAI was once limited almost exclusively to domestic poultry but has rapidly adapted to diverse animal hosts. Viruses causing HPAI now appear to be maintained and dispersed by wild birds largely independent of poultry, though HPAI continues to cause considerable economic losses and supply chain disruptions in the domestic poultry trade. Coincident with the adaptation of HPAI viruses to wild birds, particularly waterfowl and gulls, increasingly diverse wild bird hosts are becoming exposed to HPAI, often resulting in disease and death. More sporadically, HPAI has caused mass mortality events, particularly among seabirds. Furthermore, viral spillover to wild and domestic mammals has become more common. Spillover to wild mammals has resulted in mortality among diverse terrestrial and marine taxa, including episodic losses of such scale as to represent potential conservation challenges. Since approximately March 2024, HPAI has also affected dairy cows, which represents a new threat to the agricultural economy. Lastly, HPAI has increasingly affected humans through domestic animal exposures, exemplifying the considerable implications of this disease beyond animal health. Rapid changes in the ecology of HPAI are currently outpacing research efforts. For example, it is not entirely clear which newly established hosts may become reservoirs for HPAI viruses (in other words, capable of maintaining HPAI viruses within a broad population indefinitely) and how this may influence viral evolution and dissemination. As a result, there are considerable information gaps regarding HPAI in wildlife that, if filled, would improve the ability of scientists, managers, agricultural industry representatives, and healthcare professionals to understand and to anticipate the effects of HPAI on wild animal, domestic animal, environmental, and human health (“One Health”). The U.S. Geological Survey (USGS) is the lead Federal agency providing scientific research on avian influenza viruses (AIVs), including HPAI viruses, that affect wildlife for which the Department of the Interior (DOI) has management authority. States have jurisdiction over wildlife on Federal lands within their borders (43 CFR § 24.3), so the USGS Ecosystems Mission Area (EMA) coordinates with State natural resource management agencies. The EMA focuses its research on HPAI through priorities identified by the USGS Avian Influenza Science Team ( app. 1 ). Priorities identified by the USGS Avian Influenza Science Team are based on Administration priorities, Congressional direction, and discussions with State, Federal, and Tribal natural resource management agencies that identify specific scientific gaps that need to be filled to inform sound wildlife management decisions. Notable non-DOI Federal partners include the U.S. Department of Agriculture, the lead for the HPAI regulatory response in poultry and livestock, and the Centers for Disease Control and Prevention (CDC), the lead agency for the HPAI response pertaining to human health. The USGS offers unique expertise and capacity pertaining to research on diseases affecting free-ranging wildlife populations. This expertise has been critical to interjurisdictional surveillance and capacity-building efforts, including programs administered by the U.S. Department of Agriculture and the CDC. The USGS also provides resources, guidance, and tools to inform surveillance and interventions conducted by natural resource management agencies. More specifically, the USGS EMA provides objective and rigorous scientific data for inferring (1) the utility of new methods to detect and characterize AIVs, including those maintained in wildlife and the environment; (2) effects of HPAI on wildlife; (3) spatiotemporal patterns of wildlife host and AIV dispersal; (4) the presence and persistence of AIVs in the environment; (5) how HPAI in wildlife influences consumptive and nonconsumptive utilization of wildlife; (6) how new tools and scientific methods may promote sound management decisions for HPAI-affected wildlife, particularly species of conservation concern; and (7) the combined effects of HPAI and other stressors on ecosystem health and resiliency. This science strategy builds upon research outlined in a previous USGS science strategy for HPAI (2016–20) by Harris and others (2016) . This strategy also details research priorities identified by the Administration (for example, U.S. Department of Agriculture, 2025 ) and others based on USGS Avian Influenza Science Team discussions with natural resource management agencies to address HPAI and wildlife health over the next 5 years (2025–29). This strategy presents 7 goals and 26 objectives that focus USGS and partner efforts on priorities that will fill data gaps regarding the effects of HPAI on wildlife managed by or co-managed with the U.S. Department of the Interior such that agencies and partners might anticipate or limit adverse effects on public resources. This strategy also identifies research priorities intended to address HPAI in wildlife and wildlife habitat that are anticipated to support interjurisdictional One Health efforts.

Circular

Unbiased survival estimates and evidence for skipped breeding opportunities in females

1.  Estimates of demographic parameters for females, in many organisms, are sparse. This is particularly worrisome as more and more species are faced with high extinction probabilities and conservation increasingly depends on actions dictated by complex predictive models that require accurate estimates of demographic parameters for each sex and species. 2.  This study assesses demographic parameters, specifically temporary emigration and survival, for females, a class that has been difficult to investigate historically because of lack of data. Amphibians provide a particularly good example because there is global concern about amphibian decline; yet most demographic parameter estimates are based on data from males, which we show can lead to erroneous conclusions. 3.  We use 10 years of capture–recapture data from boreal toads ( Bufo boreas ) and the multi-state open robust design model to provide evidence for the occurrence of skipped breeding opportunities (i.e. temporary emigration) in females. This is the first time that the open robust design model has been applied to an analysis of an amphibian population that we are aware of. 4.  We determined that the transition from breeder to non-breeder is obligate and the probability of a non-breeder remaining a non-breeder is 64%; thus, temporary emigration is first-order Markovian in nature, where breeding probability is dependent on the previous year’s activity, i.e. if a female did not breed in year one, there is a 36% chance that she will breed in year two. With temporary emigration accounted for, we estimated between-year female survival at 87%. 5.  Establishing the occurrence of temporary emigration not only reduces bias in estimates of survival probabilities but also provides information about expected breeding attempts by females, a critical element in understanding the ecology of an organism and the impacts of outside stressors and conservation actions.

Methods in Ecology and Evolution

Estimating occupancy dynamics for large-scale monitoring networks: amphibian breeding occupancy across protected areas in the northeast United States

Regional monitoring strategies frequently employ a nested sampling design where a finite set of study areas from throughout a region are selected within which intensive sub-sampling occurs. This sampling protocol naturally lends itself to a hierarchical analysis to account for dependence among sub-samples. Implementing such an analysis within a classic likelihood framework is computationally prohibitive with species occurrence data when accounting for detection probabilities. Bayesian methods offer an alternative framework to make this analysis feasible. We demonstrate a general approach for estimating occupancy when data come from a nested sampling design. Using data from a regional monitoring program of wood frogs (Lithobates sylvaticus) and spotted salamanders (Ambystoma maculatum) in vernal pools, we analyzed data using static and dynamic occupancy frameworks. We analyzed observations from 2004-2013collected within 14 protected areas located throughout the northeast United States . We use the data set to estimate trends in occupancy at both the regional and individual protected area level. We show that occupancy at the regional level was relatively stable for both species. Much more variation occurred within individual study areas, with some populations declining and some increasing for both species. We found some evidence for a latitudinal gradient in trends among protected areas. However, support for this pattern is overestimated when the hierarchical nature of the data collection is not controlled for in the analysis. For both species, occupancy appeared to be declining in the most southern areas, while occupancy was stable or increasing in more northern areas. These results shed light on the range-level population status of these pond-breeding amphibians and our approach provides a framework that can be used to examine drivers of change including among-year and among-site variation in occurrence dynamics, while properly accounting for nested structure of data collection.

Ecology and Evolution

Mediterranean-type ecosystems: the influence of biodiversity on their functioning

Ecosystems in the Mediterranean-climate regions of the world have served as a unit for comparative ecological studies for over two decades. The cohesiveness of research in this set of widely distributed regions rests on the similarity of the climates where they occur, and the identifiable convergence in elements of their vegetation structure (Di Castri and Mooney 1973). In this chapter we review functional aspects of what have come to be known as Mediterranean-type ecosystems (METs) in the context of a concerned global interest in the sustainability of the human environment and its dependence on biological diversity. The approach we adopt here is to look for evidence that this biodiversity, for which some MTEs are renowned (Cowling, 1992; Hobbs, 1992), has an influence on processes which are important both for the maintenance of natural systems, and for providing "ecosystem services" with human utility. Almost a century ago, Schimper (1903) recognized the biological similarities between five widely separated regions characterized by Mediterranean-type climates, and much comparative work has been done on that basis since. These regions comprise the Mediterranean basin itself, a major portion of California, central Chile, the southwestern and southern extremities of South Africa, and parts of southwestern and southern Australia (Figure 7.1). The first attention paid to MTEs in terms of quantitative ecological research arose out of the International Biological Programme (IBP) of the 1960s and 1970s. Those efforts focused on comparisons between the Chilean and Californian systems (Mooney 1977), and dealt with parallel models of ecosystem processes, especially water flux (Fuentes et al 1995). Because of the already perceived similarities between vegetation in these and the other three regions, the project was soon extended to include all five regions. The first broad comparative overview was published as an anthology which considered the origins and the convergent evolution of MTE components (Di Castri and Mooney 1973). Although the currently accepted classifications of the MTEs is to some extent artificial, it does provide a basis for comparative work, as well as placing mild, temperate winter rainfall regions in perspective with other system types, such as forests, arid lands and even savannas. It is against this backdrop that the MTE research collegium has grown, giving rise to the organizational structure known as ISOMED (the International Society of Mediterranean Ecologists), which has convened regular conferences under the label MEDECOS, plus a number of extra meetings on specific topics (Table 7.1). One of the more recent in this series of MTE meetings was convened under the auspices of ICSU's Scientific Committee on Problems of the Environment (SCOPE) (see Table 7.1), and dealt with the questions about the functional value of biodiversity. This chapter is based on that meeting and its proceedings (Richardson and Cowling 1993); David and Richardson 1995), and is a distillation of input by teams of ecologists from each of the five regions.

Book chapter

The cost of self-defense: Browsing effects in the rare plant species Salix arizonica

Coevolution between plants and their animal predators has led to diverse defensive adaptations. Multiple theories of defense propose that there are resource allocation costs associated with producing chemical defenses. One leading hypothesis, optimal defense theory (ODT), suggests that natural selection will result in the allocation of resources to defenses that optimize the cost-to-benefit ratio between defense and other functional processes. The population decline of the rare subalpine wetland species, Arizona willow ( Salix arizonica ), has been attributed to various biotic and abiotic factors, with browsing from wild and domestic ungulates as a significant concern for at least three decades. In a field experiment using natural populations, we compare the relationship between phytochemical defense and height in Arizona willows with and without long-term protection from browsing via browse exclosures. Consistent with the predictions of ODT, individuals with physical protection from ungulate browsing for multiple years had significantly lower phenolic glycoside (PG) concentrations and increased plant height compared to unprotected individuals. A similar pattern was found across all individuals, whereby total PG concentration and height were negatively correlated. In a short-term experiment in natural populations, changes in levels of defense were not observed when plants received protection for only one growing season. The contrasting pattern of defense plasticity in response to long-term versus short-term physical protection suggests a differential plastic response in this long-lived species. Delayed reduction in PG concentration may serve as a benefit to avoid mismatches between environmental cues and responses. Our research sheds light on the intricate dynamics between plant-defense strategies, environmental pressures, and evolutionary adaptations in shaping plant–browser interactions.

Arizona, Colorado, New Mexico, Utah