Temperature-associated population diversity in salmon confers benefits to mobile consumers

Habitat heterogeneity can generate intraspecific diversity through local adaptation of populations. While it is becoming increasingly clear that population diversity can increase stability in species abundance, less is known about how population diversity can benefit consumers that can integrate across population diversity in their prey. Here we demonstrate cascading effects of thermal heterogeneity on trout-salmon interactions in streams where rainbow trout rely heavily on the seasonal availability of anadromous salmon eggs. Water temperature in an Alaskan stream varied spatially from 5 degrees C to 17.5 degrees C, and spawning sockeye salmon showed population differentiation associated with this thermal heterogeneity. Individuals that spawned early in cool regions of the 5 km long stream were genetically differentiated from those spawning in warmer regions later in the season. Sockeye salmon spawning generates a pulsed resource subsidy that supports the majority of seasonal growth in stream-dwelling rainbow trout. The spatial and temporal structuring of sockeye salmon spawn timing in our focal stream extended the duration of the pulsed subsidy compared to a thermally homogeneous stream with a single population of salmon. Further, rainbow trout adopted movement strategies that exploited the multiple pulses of egg subsidies in the thermally heterogeneous stream. Fish that moved to track the resource pulse grew at rates about 2.5 times higher than those that remained stationary or trout in the reference stream with a single seasonal pulse of eggs. Our results demonstrate that habitat heterogeneity can have important effects on the population diversity of dominant species, and in turn, influence their value to species that prey upon them. Therefore, habitat homogenization may have farther-reaching ecological effects than previously considered.     

Effects of an Invasive Plant on Population Dynamics in Toads

When populations decline in response to unfavorable environmental change, the dynamics of their population growth shift. In populations that normally exhibit high levels of variation in recruitment and abundance, as do many amphibians, declines may be difficult to identify from natural fluctuations in abundance. However, the onset of declines may be evident from changes in population growth rate in sufficiently long time series of population data. With data from 23 years of study of a population of Fowler's toad (Anaxyrus [ = Bufo] fowleri) at Long Point, Ontario (1989–2011), we sought to identify such a shift in dynamics. We tested for trends in abundance to detect a change point in population dynamics and then tested among competing population models to identify associated intrinsic and extrinsic factors. The most informative models of population growth included terms for toad abundance and the extent of an invasive marsh plant, the common reed (Phragmites australis), throughout the toads’ marshland breeding areas. Our results showed density‐dependent growth in the toad population from 1989 through 2002. After 2002, however, we found progressive population decline in the toads associated with the spread of common reeds and consequent loss of toad breeding habitat. This resulted in reduced recruitment and population growth despite the lack of significant loss of adult habitat. Our results underscore the value of using long‐term time series to identify shifts in population dynamics coincident with the advent of population decline. Efectos de una Planta Invasora sobre las Dinámica Poblacional de Sapos     

A noninvasive demographic assessment of sea lions based on stage-specific abundances

A pressing need exists to develop new approaches for obtaining information on demographic rates without causing further threats to imperiled animal populations. In this paper, we illustrate and apply a data-fitting technique based on quadratic programming that uses stage-specific abundance data to estimate demographic rates and asymptotic population growth rates (lambda). We used data from seven breeding colonies of California sea lions (Zalophus californianus) in the Gulf of California, Mexico. Estimates of lambda were similar to those from previous studies relying on a diffusion approximation using trends in total abundance. On average, predicted abundances were within 24% of the observed value for the inverse estimation method and within 29% of the observed value for the diffusion approximation. Our results suggest that three of the seven populations are declining (lambda < 1), but as many as six may be at risk. Elasticity and sensitivity analyses suggest that population management in most sites should focus on the protection of adults, whose survival generally contributes the most to lambda. The quadratic programming approach is a promising noninvasive technique for estimating demographic rates and assessing the viability of populations of imperiled species.     

Population viability analysis for several populations using multivariate state-space models

The International Union for the Conservation of Nature and Natural Resources (IUCN), the world's largest and most important global conservation network, has listed approximately 16,000 species worldwide as threatened. The most important tool for recognizing and listing species as threatened is population viability analysis (PVA), which estimates the probability of extinction of a population or species over a specified time horizon. The most common PVA approach is to apply it to single time series of population abundance. This approach to population viability analysis ignores covariability of local populations. Covariability can be important because high synchrony of local populations reduces the effective number of local populations and leads to greater extinction risk. Needed is a way of extending PVA to model correlation structure among multiple local populations. Multivariate state-space modeling is applied to this problem and alternative estimation methods are compared. The multivariate state-space technique is applied to endangered populations of pacific salmon, USA. Simulations demonstrated that the correlation structure can strongly influence population viability and is best estimated using restricted maximum likelihood instead of maximum likelihood.     

Assessing conservation status with extensive but low-resolution data: Application of frequentist and Bayesian models to endangered Athabasca River rainbow trout

Use of extensive but low-resolution abundance data is common in the assessment of species at-risk status based on quantitative decline criteria under International Union for Conservation of Nature (IUCN) and national endangered species legislation. Such data can be problematic for 3 reasons. First, statistical power to reject the null hypothesis of no change is often low because of small sample size and high sampling uncertainty leading to a high frequency of type II errors. Second, range-wide assessments composed of multiple site-specific observations do not effectively weight site-specific trends into global trends. Third, uncertainty in site-specific temporal trends and relative abundance are not propagated at the appropriate spatial scale. A common result is the propensity to underestimate the magnitude of declines and therefore fail to identify the appropriate at-risk status for a species. We used 3 statistical approaches, from simple to more complex, to estimate temporal decline rates for a designatable unit (DU) of rainbow trout in the Athabasca River watershed in western Canada. This DU is considered a native species for purposes of listing because of its genetic composition characterized as >0.95 indigenous origin in the face of continuing introgressive hybridization with introduced populations in the watershed. Analysis of abundance trends from 57 time series with a fixed-effects model identified 33 sites with negative trends, but only 2 were statistically significant. By contrast, a hierarchical linear mixed model weighted by site-specific abundance provided a DU-wide decline estimate of 16.4% per year and a 3-generation decline of 93.2%. A hierarchical Bayesian mixed model yielded a similar 3-generation decline trend of 91.3% and the posterior distribution showed that the estimate had a >99% probability of exceeding thresholds for an endangered listing. We conclude that the Bayesian approach was the most useful because it provided a probabilistic statement of threshold exceedance in support of an at-risk status recommendation.     

Density dependence and density independence during the early life stages of four marine fish stocks

Recruitment variability caused by density-dependent and density-independent processes is an important area within the study of fish dynamics. These processes can exhibit nonlinearities and nonadditive properties that may have profound dynamic effects. We investigate the importance of population density (i.e., density dependence) and environmental forcing (i.e., density independence) on the age-0 and age-1 abundance of capelin (Mallotus villosus), northeast Arctic cod (Gadus morhua), northeast Arctic haddock (Melanogrammus aeglefinus), and Norwegian spring spawning herring (Clupea harengus) in the Barents Sea. We use statistical methods that explicitly account for nonlinearities and nonadditive interactions between internal and external variables in the abundance of these two pre-recruitment stages. Our results indicate that, during their first five months of life, cod, haddock, and herring experience higher density-dependent survival than capelin. The abundance of age-0 cod depends on the mean age and biomass of the spawning stock, a result which has implications for the management of the entire cod stock. Temperature is another important factor influencing the abundance at age-0 and age-1 of all four species, except herring at age-1. Between age-0 and age-1, there is an attenuation of density-dependent survival for cod and herring, while haddock and capelin experience density dependence at high and low temperatures, respectively. Predation by subadult cod is important for both capelin and cod at age-1. We found strong indications for interactions among the studied species, pointing to the importance of viewing the problem of species recruitment variability as a community, rather than as a population phenomenon.     

Parasite facilitates plant species coexistence in a coastal wetland

Outbreaks of infectious agents in natural ecosystems are on the rise. Understanding host-pathogen interactions and their impact on community composition may be central to the conservation of biological diversity. Infectious agents can convey both exploitive and facilitative effects that regulate host populations and community structure. Parasitic angiosperms are highly conspicuous in many plant communities, and they provide a tractable model for understanding parasite effects in multispecies communities. I examined host identity and variation in host infectivity of a holoparasitic vine (Cuscuta salina) within a California salt marsh. In a two-year parasite removal experiment, I measured the effect of C. salina on its most frequent host, a rare hemiparasite, and the plant community. C. salina clearly suppressed the dominant host, but rare plant fitness and plant species diversity were enhanced through indirect effects. Priority effects played a role in the strength of the outcome due to the timing of life history characteristics. The differential influence of parasites on the fecundity of multiple hosts can change population dynamics, benefit rare species, and alter community structure. The continuum of negative to positive consequences of parasitic interactions deserves more attention if we are to understand community dynamics and successfully restore tidal wetlands.     

Composite forces shape population dynamics of copepod crustaceans

Understanding the processes that control species abundance and distribution is a major challenge in ecology, yet for a large number of potentially important organisms, we know little about the biotic and abiotic factors that influence population size. One group of aquatic organisms that defies traditional demographic analyses is the Crustacea, particularly those with complex life cycles. We used likelihood techniques and information theoretics to evaluate a suite of models representing alternative hypotheses on factors controlling the abundance of two copepod crustaceans in a small, tropical floodplain lake. Quantitative zooplankton samples were collected at three stations in a Venezuelan floodplain lake from June through December 1984; the average sampling interval was two days. We constructed a series of models with stage structure that incorporated six biotic and abiotic covariates in various combinations to account for temporal changes in abundance of these target species and in their population growth rates. Our analysis produced several novel insights into copepod population dynamics. We found that multiple forces affected the abundance of particular stages, that these factors differed between species as well as among stages within each species, and that biotic processes had the largest effects on copepod population dynamics. Density dependence had a large effect on the survival of Oithona amazonica copepodites and on population growth rate of Diaptomus negrensis.     

Range-Wide Selection of Catchments for Pacific Salmon Conservation

Abstract:  Freshwater ecosystems are declining in quality globally, but a lack of data inhibits identification of areas valuable for conservation across national borders. We developed a biological measure of conservation value for six species of Pacific salmon ( Oncorhynchus spp.) in catchments of the northern Pacific across Canada, China, Japan, Russia, and the United States. We based the measure on abundance and life-history richness and a model-based method that filled data gaps. Catchments with high conservation value ranged from California to northern Russia and included catchments in regions that are strongly affected by human development (e.g., Puget Sound). Catchments with high conservation value were less affected by agriculture and dams than other catchments, although only 1% were within biodiversity reserves. Our set of high-value areas was largely insensitive to simulated error, although classification remained uncertain for 3% of catchments. Although salmon face many threats, we propose they will be most likely to exhibit resilience into the future if a complementary mosaic of conservation strategies can be proactively adopted in catchments with healthy salmon populations. Our analysis provides an initial map of where these catchments are likely to be located.     

Incorporating catastrophic risk assessments into setting conservation goals for threatened Pacific salmon

Catastrophic die-offs can have important consequences for vertebrate population growth and biodiversity, but catastrophic risks are not commonly incorporated into endangered-species recovery planning. Natural (e.g., landslides, floods) and anthropogenic (e.g., toxic leaks and spills) catastrophes pose a challenge for evolutionarily significant units (ESUs) of Pacific salmon listed under the Endangered Species Act and teetering at precariously low population levels. To spread risks among Puget Sound chinook salmon populations, recovery strategies for ESU-wide viability recommend at least two viable populations of historical life-history types in each of five geographic regions. We explored the likelihood of Puget Sound chinook salmon ESU persistence by examining spatial patterns of catastrophic risk and testing ESU viability recommendations for 22 populations of the threatened Puget Sound chinook salmon ESU. We combined geospatial information about catastrophic risks and chinook salmon distribution in Puget Sound watersheds to categorize relative catastrophic risks for each population. We then analyzed similarities in risk scores among regions and compared risk distributions among strategies: (1) population groups selected using the ESU viability recommendations of having populations spread out geographically and including historical life-history diversity, and (2) population groups selected at random. Risks from individual catastrophes varied among populations, but overall risk from catastrophes was similar within geographic regions. Recovery strategies that called for two viable populations in each of five geographic regions had lower risk than random strategies; strategies that included life-history diversity had even lower risks. Geographically distributed populations have varying catastrophic-risks profiles, thus identifying and reinforcing the spatial and life-history diversity critical for populations to respond to environmental change or needed to rescue severely depleted or extirpated populations. Recovery planning can promote viability of Pacific salmon ESUs across the landscape by incorporating catastrophic risk assessments.     

Colonization of the Southern Patagonia Ocean by Exotic Chinook Salmon

Abstract:  Anadromous salmonids have been particularly successful at establishing wild populations in southern Patagonia, in contrast to their limited success elsewhere outside their native ranges. The most recent such discovery is a spawning population of Chinook salmon in the Santa Cruz River, which flows into the Atlantic Ocean from Argentina. We used mitochondrial DNA analysis to discriminate between alternative potential sources of this population and were able to discard in situ introductions of fish imported directly from California in the early twentieth century. Our results showed that the fish most likely came from Puget Sound, Washington, imported into southern Chile for salmon-ranching experiments in the 1980s. This finding provides concrete evidence of colonization of Atlantic rivers from Pacific locations. The southern Pacific and Atlantic oceans provide a favorable marine environment for the success of invading salmon. In particular, the waters associated with fjords, southern channels, and the inshore portion of the Patagonian shelf provide a rather bounded, continuous waterway for exotic anadromous salmonids, rich in diverse forage species.     

Bayesian Decision Analysis for Evaluating Management Options to Promote Recovery of a Depleted Salmon Population

Abstract:  The endangered population of sockeye salmon (Oncorhynchus nerka) in Cultus Lake, British Columbia, Canada, migrates through commercial fishing areas along with other, much more abundant sockeye salmon populations, but it is not feasible to selectively harvest only the latter, abundant populations. This situation creates controversial trade-offs between recovery actions and economic revenue. We conducted a Bayesian decision analysis to evaluate options for recovery of Cultus Lake sockeye salmon. We used a stochastic population model that included 2 sources of uncertainty that are often omitted from such analyses: structural uncertainty in the magnitude of a potential Allee effect and implementation uncertainty (the deviation between targets and actual outcomes of management actions). Numerous state-dependent, time-independent management actions meet recovery objectives. These actions prescribe limitations on commercial harvest rates as a function of abundance of Cultus Lake sockeye salmon. We also quantified how much reduction in economic value of commercial harvests of the more abundant sockeye salmon populations would be expected for a given increase in the probability of recovery of the Cultus population. Such results illustrate how Bayesian decision analysis can rank options for dealing with conservation risks and can help inform trade-off discussions among decision makers and among groups that have competing objectives.     

Stochastic population dynamics in populations of western terrestrial garter snakes with divergent life histories

Comparative evaluations of population dynamics in species with temporal and spatial variation in life-history traits are rare because they require long-term demographic time series from multiple populations. We present such an analysis using demographic data collected during the interval 1978-1996 for six populations of western terrestrial garter snakes (Thamnophis elegans) from two evolutionarily divergent ecotypes. Three replicate populations from a slow-living ecotype, found in mountain meadows of northeastern California, were characterized by individuals that develop slowly, mature late, reproduce infrequently with small reproductive effort, and live longer than individuals of three populations of a fast-living ecotype found at lakeshore locales. We constructed matrix population models for each of the populations based on 8-13 years of data per population and analyzed both deterministic dynamics based on mean annual vital rates and stochastic dynamics incorporating annual variation in vital rates. (1) Contributions of highly variable vital rates to fitness (lambda(s)) were buffered against the negative effects of stochastic variation, and this relationship was consistent with differences between the meadow (M-slow) and lakeshore (L-fast) ecotypes. (2) Annual variation in the proportion of gravid females had the greatest negative effect among all vital rates on lambda(s). The magnitude of variation in the proportion of gravid females and its effect on lambda(s) was greater in M-slow than L-fast populations. (3) Variation in the proportion of gravid females, in turn, depended on annual variation in prey availability, and its effect on lambda(s) was 4 23 times greater in M-slow than L-fast populations. In addition to differences in stochastic dynamics between ecotypes, we also found higher mean mortality rates across all age classes in the L-fast populations. Our results suggest that both deterministic and stochastic selective forces have affected the evolution of divergent life-history traits in the two ecotypes, which, in turn, affect population dynamics. M-slow populations have evolved life-history traits that buffer fitness against direct effects of variation in reproduction and that spread lifetime reproduction across a greater number of reproductive bouts. These results highlight the importance of long-term demographic and environmental monitoring and of incorporating temporal dynamics into empirical studies of life-history evolution.     

Mapping shifts in spatial synchrony in grassland birds to inform conservation planning

Spatial synchrony, defined as the correlated fluctuations in abundance of spatially separated populations, can be caused by regional fluctuations in natural and anthropogenic environmental population drivers. Investigations into the geography of synchrony can provide useful insight to inform conservation planning efforts by revealing regions of common population drivers and metapopulation extinction vulnerability. We examined the geography of spatial synchrony and decadal changes in these patterns for grassland birds in the United States and Canada, which are experiencing widespread and persistent population declines. We used Bayesian hierarchical models and over 50 years of abundance data from the North American Breeding Bird Survey to generate population indices within a 2° latitude by 2° longitude grid. We computed and mapped mean local spatial synchrony for each cell (mean detrended correlation of the index among neighboring cells), along with associated uncertainty, for 19 species in 2, 26-year periods, 1968–1993 and 1994–2019. Grassland birds were predicted to increase in spatial synchrony where agricultural intensification, climate change, or interactions between the 2 increased. We found no evidence of an overall increase in synchrony among grassland bird species. However, based on the geography of these changes, there was considerable spatial heterogeneity within species. Averaging across species, we identified clusters of increasing spatial synchrony in the Prairie Pothole and Shortgrass Prairie regions and a region of decreasing spatial synchrony in the eastern United States. Our approach has the potential to inform continental-scale conservation planning by adding an additional layer of relevant information to species status assessments and spatial prioritization of policy and management actions. Our work adds to a growing literature suggesting that global change may result in shifting patterns of spatial synchrony in population dynamics across taxa with broad implications for biodiversity conservation.     

Taxonomic and Geographic Patterns of Decline for Threatened and Endangered Species in the United States

Abstract: Species listed under the U.S. Endangered Species Act (i.e., listed species) have declined to the point that the probability of their extinction is high. The decline of these species, however, may manifest itself in different ways, including reductions in geographic range, number of populations, or overall abundance. Understanding the pattern of decline can help managers assess extinction probability and define recovery objectives. Although quantitative data on changes in geographic range, number of populations, and abundance usually do not exist for listed species, more often qualitative data can be obtained. We used qualitative data in recovery plans for federally listed species to determine whether each listed species declined in range size, number of populations, or abundance relative to historical levels. We calculated the proportion of listed species in each state (or equivalent) that declined in each of those ways. Nearly all listed species declined in abundance, and range size or number of populations declined in approximately 80% of species for which those data were available. Patterns of decline, however, differed taxonomically and geographically. Declines in range were more common among vertebrates than plants, whereas population extirpations were more common among plants. Invertebrates had high incidence of range and population declines. Narrowly distributed plants and invertebrates may be subject to acute threats that may result in population extirpations, whereas vertebrates may be affected by chronic threats that reduce the extent and size of populations. Additionally, in the eastern United States and U.S. coastal areas, where the level of land conversion is high, a greater percentage of species’ ranges declined and more populations were extirpated than in other areas. Species in the Southwest, especially plants, had fewer range and population declines than other areas. Such relations may help in the selection of species’ recovery criteria.     

Climate correlates of 20 years of trophic changes in a high-elevation riparian system

The consequences of climate change for ecosystem structure and function remain largely unknown. Here, I examine the ability of climate variation to explain long-term changes in bird and plant populations, as well as trophic interactions in a high-elevation riparian system in central Arizona, USA, based on 20 years of study. Abundances of dominant deciduous trees have declined dramatically over the 20 years, correlated with a decline in overwinter snowfall. Snowfall can affect overwinter presence of elk, whose browsing can significantly impact deciduous tree abundance. Thus, climate may affect the plant community indirectly through effects on herbivores, but may also act directly by influencing water availability for plants. Seven species of birds were found to initiate earlier breeding associated with an increase in spring temperature across years. The advance in breeding time did not affect starvation of young or clutch size. Earlier breeding also did not increase the length of the breeding season for single-brooded species, but did for multi-brooded species. Yet, none of these phenology-related changes was associated with bird population trends. Climate had much larger consequences for these seven bird species by affecting trophic levels below (plants) and above (predators) the birds. In particular, the climate-related declines in deciduous vegetation led to decreased abundance of preferred bird habitat and increased nest predation rates. In addition, summer precipitation declined over time, and drier summers also were further associated with greater nest predation in all species. The net result was local extinction and severe population declines in some previously common bird species, whereas one species increased strongly in abundance, and two species did not show clear population changes. These data indicate that climate can alter ecosystem structure and function through complex pathways that include direct and indirect effects on abundances and interactions of multiple trophic components.     

Habitat saturation drives thresholds in stream subsidies

Understanding how abundance regulates the effects of organisms on their ecosystems remains a critical goal of ecology, especially for understanding inter-ecosystem transfers of energy and nutrients. Here we examined how territoriality and nest-digging by anadromous salmon mediate trophic subsidies to stream fishes. Salmon eggs become available for consumption primarily by the digging of salmon that superimpose their nests on previous nests. An individual-based model of spawning salmon predicted that territoriality and habitat saturation produce a nonlinear effect of salmon density on numbers of available eggs to resident predators. Field studies in Alaskan streams found that higher densities of salmon produce disproportionately more eggs in stream drift and in diets of resident fishes (Arctic grayling and rainbow trout). Bioenergetics model simulations indicated that these subsidies produce substantially enhanced growth rates of trout. These results demonstrate that small changes in salmon abundance can drive large changes in subsidies to stream food webs. Thus, the ecological consequences of population declines of keystone species, such as salmon, will be exacerbated when behavior generates nonlinear impacts.     

Directional selection by fisheries and the timing of sockeye salmon (Oncorhynchus nerka) migrations.

The timing of migration from feeding to breeding areas is a critical link between the growth and survival of adult animals, their reproduction, and the fitness of their progeny. Commercial fisheries often catch a large fraction of the migrants (e.g., salmon), and exploitation rates can vary systematically over the fishing season. We examined daily records of sockeye salmon (Oncorhynchus nerka) in the Egegik and Ugashik management districts in Bristol Bay, Alaska (USA), for evidence of such temporally selective fishing. In recent years, the early migrants have experienced lower fishing rates than later migrants, especially in the Egegik district, and the median migration date of the fish escaping the fisheries has been getting progressively earlier in both districts. Moreover, the overall runs (catch and escapement) in the Egegik district and, to a lesser extent the Ugashik district, have been getting earlier, as predicted in response to the selection on timing. The trends in timing were not correlated with sea surface temperature in the region of the North Pacific Ocean where the salmon tend to concentrate, but the trends in the two districts were correlated with each other, indicating that there may be some common environmental influence in addition to the effect of selection. Despite the selection, both groups of salmon have remained productive. We hypothesize that this resilience may result from representation of all component populations among the early and late migrants, so that the fisheries have not eliminated entire populations, and from density-dependent processes that may have helped maintain the productivity of these salmon populations.     

Effects of Urbanization on the Distribution and Abundance of Amphibians and Invasive Species in Southern California Streams

Abstract:  Urbanization negatively affects natural ecosystems in many ways, and aquatic systems in particular. Urbanization is also cited as one of the potential contributors to recent dramatic declines in amphibian populations. From 2000 to 2002 we determined the distribution and abundance of native amphibians and exotic predators and characterized stream habitat and invertebrate communities in 35 streams in an urbanized landscape north of Los Angeles (U.S.A.). We measured watershed development as the percentage of area within each watershed occupied by urban land uses. Streams in more developed watersheds often had exotic crayfish ( Procambarus clarkii ) and fish, and had fewer native species such as California newts ( Taricha torosa ) and California treefrogs ( Hyla cadaverina ). These effects seemed particularly evident above 8% development, a result coincident with other urban stream studies that show negative impacts beginning at 10–15% urbanization. For Pacific treefrogs ( H. regilla ), the most widespread native amphibian, abundance was lower in the presence of exotic crayfish, although direct urbanization effects were not found. Benthic macroinvertebrate communities were also less diverse in urban streams, especially for sensitive species. Faunal community changes in urban streams may be related to changes in physical stream habitat, such as fewer pool and more run habitats and increased water depth and flow, leading to more permanent streams. Variation in stream permanence was particularly evident in 2002, a dry year when many natural streams were dry but urban streams were relatively unchanged. Urbanization has significantly altered stream habitat in this region and may enhance invasion by exotic species and negatively affect diversity and abundance of native amphibians.