Species' traits as predictors of range shifts under contemporary climate change: A review and meta-analysis

A growing body of literature seeks to explain variation in range shifts using species' ecological and life-history traits, with expectations that shifts should be greater in species with greater dispersal ability, reproductive potential, and ecological generalization. Despite strong theoretical support for species' traits as predictors of range shifts, empirical evidence from contemporary range shift studies remains limited in extent and consensus. We conducted the first comprehensive review of species' traits as predictors of range shifts, collecting results from 51 studies across multiple taxa encompassing over 11,000 species' responses for 54 assemblages of taxonomically related species occurring together in space. We used studies of assemblages that directly compared geographic distributions sampled in the 20th century prior to climate change with resurveys of distributions after contemporary climate change and then tested whether species traits accounted for heterogeneity in range shifts. We performed a formal meta-analysis on study-level effects of body size, fecundity, diet breadth, habitat breadth, and historic range limit as predictors of range shifts for a subset of 21 studies of 26 assemblages with sufficient data. Range shifts were consistent with predictions based on habitat breadth and historic range limit. However, body size, fecundity, and diet breadth showed no significant effect on range shifts across studies, and multiple studies reported significant relationships that contradicted predictions. Current understanding of species' traits as predictors of range shifts is limited, and standardized study is needed for traits to be valid indicators of vulnerability in assessments of climate change impacts.

Inferring the timing of long-distance dispersal between Rail metapopulations using genetic and isotopic assignments

The stochastic and infrequent nature of long-distance dispersal often makes it difficult to detect. We quantified the frequency, distance, and timing of long-distance dispersal in a nonmigratory, secretive wetland bird, the California Black Rail (Laterallus jamaicensis coturniculus), between an inland and a coastal metapopulation separated by greater than 100 km. Using 15 microsatellites in conjunction with stable carbon, nitrogen, and sulfur isotopes, we classified Rails as residents of their capture population, recent migrants that dispersed to their capture population less than one year before capture, established migrants that dispersed to their capture population more than one year before capture, and seasonal migrants that dispersed away from their capture population to forage, but returned the next season. Most Rails (195 of 204, or 95.6%) were classified as residents, but we detected two established migrants that had moved >100 km more than a year before capture. Seven Rails appeared to be seasonal migrants, but comparisons of feather isotope values with isotope values from wetland soils indicated that the isotope values in the feathers of these Rails likely resulted from natural environmental variation (e.g., source element effects) rather than long-distance dispersal of individuals. Thus, these seven Rails were most likely misassigned by isotopic population assignments due to small-scale variation in the isoscape. Using genetic data in conjunction with isotopic data allowed us to not only infer the timing of long-distance dispersal events, but to successfully track long-distance movements of nonmigratory Rails between metapopulations even when environmental variation of isotopes occurred across small spatial scales.

Modelling effects of nonbreeders on population growth estimates

Adult individuals that do not breed in a given year occur in a wide range of natural populations. However, such nonbreeders are often ignored in theoretical and empirical population studies, limiting our knowledge of how nonbreeders affect realized and estimated population dynamics and potentially impeding projection of deterministic and stochastic population growth rates. We present and analyse a general modelling framework for systems where breeders and nonbreeders differ in key demographic rates, incorporating different forms of nonbreeding, different life histories and frequency-dependent effects of nonbreeders on demographic rates of breeders. Comparisons of estimates of deterministic population growth rate, λ, and demographic variance, σd2, from models with and without distinct nonbreeder classes show that models that do not explicitly incorporate nonbreeders give upwardly biased estimates of σd2, particularly when the equilibrium ratio of nonbreeders to breeders, Nnb∗/Nb∗, is high. Estimates of λ from empirical observations of breeders only are substantially inflated when individuals frequently re-enter the breeding population after periods of nonbreeding. Sensitivity analyses of diverse parameterizations of our model framework, with and without negative frequency-dependent effects of nonbreeders on breeder demographic rates, show how changes in demographic rates of breeders vs. nonbreeders differentially affect λ. In particular, λ is most sensitive to nonbreeder parameters in long-lived species, when Nnb∗/Nb∗>0, and when individuals are unlikely to breed at several consecutive time steps. Our results demonstrate that failing to account for nonbreeders in population studies can obscure low population growth rates that should cause management concern. Quantifying the size and demography of the nonbreeding section of populations and modelling appropriate demographic structuring is therefore essential to evaluate nonbreeders' influence on deterministic and stochastic population dynamics.

Managing Climate Change Refugia for Climate Adaptation

Refugia have long been studied from paleontological and biogeographical perspectives to understand how populations persisted during past periods of unfavorable climate. Recently, researchers have applied the idea to contemporary landscapes to identify climate change refugia, here defined as areas relatively buffered from contemporary climate change over time that enable persistence of valued physical, ecological, and socio-cultural resources. We differentiate historical and contemporary views, and characterize physical and ecological processes that create and maintain climate change refugia. We then delineate how refugia can fit into existing decision support frameworks for climate adaptation and describe seven steps for managing them. Finally, we identify challenges and opportunities for operationalizing the concept of climate change refugia. Managing climate change refugia can be an important option for conservation in the face of ongoing climate change.

Spatially heterogeneous impact of climate change on small mammals of montane California

Resurveys of historical collecting localities have revealed range shifts, primarily leading edge expansions, which have been attributed to global warming. However, there have been few spatially replicated community-scale resurveys testing whether species' responses are spatially consistent. Here we repeated early twentieth century surveys of small mammals along elevational gradients in northern, central and southern regions of montane California. Of the 34 species we analysed, 25 shifted their ranges upslope or downslope in at least one region. However, two-thirds of ranges in the three regions remained stable at one or both elevational limits and none of the 22 species found in all three regions shifted both their upper and lower limits in the same direction in all regions. When shifts occurred, high-elevation species typically contracted their lower limits upslope, whereas low-elevation species had heterogeneous responses. For high-elevation species, site-specific change in temperature better predicted the direction of shifts than change in precipitation, whereas the direction of shifts by low-elevation species was unpredictable by temperature or precipitation. While our results support previous findings of primarily upslope shifts in montane species, they also highlight the degree to which the responses of individual species vary across geographically replicated landscapes.

Incorporating evolutionary processes into population viability models

We examined how ecological and evolutionary (eco-evo) processes in population dynamics could be better integrated into population viability analysis (PVA). Complementary advances in computation and population genomics can be combined into an eco-evo PVA to offer powerful new approaches to understand the influence of evolutionary processes on population persistence. We developed the mechanistic basis of an eco-evo PVA using individual-based models with individual-level genotype tracking and dynamic genotype-phenotype mapping to model emergent population-level effects, such as local adaptation and genetic rescue. We then outline how genomics can allow or improve parameter estimation for PVA models by providing genotypic information at large numbers of loci for neutral and functional genome regions. As climate change and other threatening processes increase in rate and scale, eco-evo PVAs will become essential research tools to evaluate the effects of adaptive potential, evolutionary rescue, and locally adapted traits on persistence.

Digging the pupfish out of its hole: risk analyses to guide harvest of Devils Hole pupfish for captive breeding

The Devils Hole pupfish is restricted to one wild population in a single aquifer-fed thermal pool in the Desert National Wildlife Refuge Complex. Since 1995 the pupfish has been in a nearly steady decline, where it was perched on the brink of extinction at 35-68 fish in 2013. A major strategy for conserving the pupfish has been the establishment of additional captive or "refuge" populations, but all ended in failure. In 2013 a new captive propagation facility designed specifically to breed pupfish was opened. I examine how a captive population can be initiated by removing fish from the wild without unduly accelerating extinction risk for the pupfish in Devils Hole. I construct a count-based PVA model, parameterized from estimates of the intrinsic rate of increase and its variance using counts in spring and fall from 1995-2013, to produce the first risk assessment for the pupfish. Median time to extinction was 26 and 27 years from spring and fall counts, respectively, and the probability of extinction in 20 years was 26-33%. Removing individuals in the fall had less risk to the wild population than harvest in spring. For both spring and fall harvest, risk increased rapidly when levels exceeded six adult pupfish per year for three years. Extinction risk was unaffected by the apportionment of total harvest among years. A demographic model was used to examine how removal of different stage classes affects the dynamics of the wild population based on reproductive value (RV) and elasticity. Removing eggs had the least impact on the pupfish in Devils Hole; RV of an adult was roughly 25 times that of an egg. To evaluate when it might be prudent to remove all pupfish from Devils Hole for captive breeding, I used the count-based model to examine how extinction risk related to pupfish population size. Risk accelerated when initial populations were less than 30 individuals. Results are discussed in relation to the challenges facing pupfish recovery compared to management of other highly endangered species.

Beyond a warming fingerprint: individualistic biogeographic responses to heterogeneous climate change in California

Understanding recent biogeographic responses to climate change is fundamental for improving our predictions of likely future responses and guiding conservation planning at both local and global scales. Studies of observed biogeographic responses to 20th century climate change have principally examined effects related to ubiquitous increases in temperature - collectively termed a warming fingerprint. Although the importance of changes in other aspects of climate - particularly precipitation and water availability - is widely acknowledged from a theoretical standpoint and supported by paleontological evidence, we lack a practical understanding of how these changes interact with temperature to drive biogeographic responses. Further complicating matters, differences in life history and ecological attributes may lead species to respond differently to the same changes in climate. Here, we examine whether recent biogeographic patterns across California are consistent with a warming fingerprint. We describe how various components of climate have changed regionally in California during the 20th century and review empirical evidence of biogeographic responses to these changes, particularly elevational range shifts. Many responses to climate change do not appear to be consistent with a warming fingerprint, with downslope shifts in elevation being as common as upslope shifts across a number of taxa and many demographic and community responses being inconsistent with upslope shifts. We identify a number of potential direct and indirect mechanisms for these responses, including the influence of aspects of climate change other than temperature (e.g., the shifting seasonal balance of energy and water availability), differences in each taxon's sensitivity to climate change, trophic interactions, and land-use change. Finally, we highlight the need to move beyond a warming fingerprint in studies of biogeographic responses by considering a more multifaceted view of climate, emphasizing local-scale effects, and including a priori knowledge of relevant natural history for the taxa and regions under study.

Inferring recent historic abundance from current genetic diversity

Recent historic abundance is an elusive parameter of great importance for conserving endangered species and understanding the pre-anthropogenic state of the biosphere. The number of studies that have used population genetic theory to estimate recent historic abundance from contemporary levels of genetic diversity has grown rapidly over the last two decades. Such assessments often yield unexpectedly large estimates of historic abundance. We review the underlying theory and common practices of estimating recent historic abundance from contemporary genetic diversity, and critically evaluate the potential issues at various estimation steps. A general issue of mismatched spatio-temporal scales between the estimation itself and the objective of the estimation emerged from our assessment; genetic diversity-based estimates of recent historic abundance represent long-term averages, whereas the objective typically is an estimate of recent abundance for a specific population. Currently, the most promising approach to estimate the difference between recent historic and contemporary abundance requires that genetic data be collected from samples of similar spatial and temporal duration. Novel genome-enabled inference methods may be able to utilize additional information of dense genome-wide distributions of markers, such as of identity-by-descent tracts, to infer recent historic abundance from contemporary samples only.

Anthropogenic refugia ameliorate the severe climate-related decline of a montane mammal along its trailing edge

We conducted detailed resurveys of a montane mammal, Urocitellus beldingi, to examine the effects of climate change on persistence along the trailing edge of its range. Of 74 California sites where U. beldingi were historically recorded (1902–1966), 42 per cent were extirpated, with no evidence for colonization of previously unoccupied sites. Increases in both precipitation and temperature predicted site extirpations, potentially owing to snowcover loss. Surprisingly, human land-use change buffered climate change impacts, leading to increased persistence and abundance. Excluding human-modified sites, U. beldingi has shown an upslope range retraction of 255 m. Generalized additive models of past distribution were predictive of modern range contractions (AUC = 0.76) and projected extreme reductions (52% and 99%, respectively) of U. beldingi's southwestern range to 2080 climates (Hadley and CCCMA A2). Our study suggests the strong impacts of climate change on montane species at their trailing edge and how anthropogenic refugia may mitigate these effects.

Impact of cattle grazing on the occupancy of a cryptic, threatened rail

Impacts of livestock grazing in arid and semiarid environments are often concentrated in and around wetlands where animals congregate for water, cooler temperatures, and green forage. We assessed the impacts of winter-spring (November-May) cattle grazing on marsh vegetation cover and occupancy of a highly secretive marsh bird that relies on dense vegetation cover, the California Black Rail (Laterallus jamaicensis coturniculus), in the northern Sierra Nevada foothills of California, U.S.A. Using detection-nondetection data collected during repeated call playback surveys at grazed vs. ungrazed marshes and a "random changes in occupancy" parameterization of a multi-season occupancy model, we examined relationships between occupancy and habitat covariates, while accounting for imperfect detection. Marsh vegetation cover was significantly lower at grazed marshes than at ungrazed marshes during the grazing season in 2007 but not in 2008. Winter-spring grazing had little effect on Black Rail occupancy at irrigated marshes. However, at nonirrigated marshes fed by natural springs and streams, grazed sites had lower occupancy than ungrazed sites. Black Rail occupancy was positively associated with marsh area, irrigation as a water source, and summer vegetation cover, and negatively associated with marsh isolation. Residual dry matter (RDM), a commonly used metric of grazing intensity, was significantly associated with summer marsh vegetation cover at grazed sites but not spring cover. Direct monitoring of marsh vegetation cover, particularly at natural spring- or stream-fed marshes, is recommended to prevent negative impacts to rails from overgrazing.

Vertical transmission of learned signatures in a wild parrot

Learned birdsong is a widely used animal model for understanding the acquisition of human speech. Male songbirds often learn songs from adult males during sensitive periods early in life, and sing to attract mates and defend territories. In presumably all of the 350+ parrot species, individuals of both sexes commonly learn vocal signals throughout life to satisfy a wide variety of social functions. Despite intriguing parallels with humans, there have been no experimental studies demonstrating learned vocal production in wild parrots. We studied contact call learning in video-rigged nests of a well-known marked population of green-rumped parrotlets (Forpus passerinus) in Venezuela. Both sexes of naive nestlings developed individually unique contact calls in the nest, and we demonstrate experimentally that signature attributes are learned from both primary care-givers. This represents the first experimental evidence for the mechanisms underlying the transmission of a socially acquired trait in a wild parrot population.

Factors shaping the ontogeny of vocal signals in a wild parrot

Parrots rely heavily on vocal signals to maintain their social and mobile lifestyles. We studied vocal ontogeny in nests of wild green-rumped parrotlets (Forpus passerinus) in Venezuela. We identified three successive phases of vocal signaling that corresponded closely to three independently derived phases of physiological development. For each ontogenetic phase, we characterized the relative importance of anatomical constraints, motor skills necessary for responding to specific contexts of the immediate environment, and the learning of signals that are necessary for adult forms of communication. We observed shifts in the relative importance of these three factors as individuals progressed from one stage to the next; there was no single fixed ratio of factors that applied across the entire ontogenetic sequence. The earliest vocalizations were short in duration as predicted from physical constraints and under-developed motor control. Calls became longer and frequency modulated during intermediate nestling ages in line with motor skills required for competitive begging. In the week before fledging, calls drastically shortened in accordance with the flight-constrained short durations of adult contact calls. The latter constraints were made evident by the demonstrated links between wing-assisted incline running, a widespread prelude to avian flight, just before the shift from long duration begging calls to short duration contact calls. At least in this species, the shifting emphases of factors at different ontogenetic stages precluded the morphing of the intermediate stage begging calls into adult contact calls; as shown in a prior study (Berg et al. 2012), the latter are influenced by sample templates provided by parents.

Microbial and environmental effects on avian egg viability: do tropical mechanisms act in a temperate environment?

The viability of freshly laid avian eggs declines after several days of exposure to ambient temperatures above physiological zero, and declines occur faster in tropical than temperate ecosystems. Microbial infection during preincubation exposure has recently been shown as a second cause of egg viability decline in the tropics, but whether microbial processes influence the viability of wild bird eggs in temperate ecosystems is unknown. We determined the microbial load on eggshells, the incidence of microbial penetration of egg contents, and changes in the viability of wild bird eggs (Sialia mexicana, Tachycineta bicolor, Tachycineta thalassina) experimentally exposed to temperate-zone ambient conditions in situ in a mediterranean climate in northern California. Initial microbial loads on eggshells were generally low, although they were significantly higher on eggs laid in old boxes than in new boxes. Eggshell microbial loads did not increase with exposure to ambient conditions, were not reduced by twice-daily disinfection with alcohol, and were unaffected by parental incubation. The rate of microbial penetration into egg contents was low and unaffected by the duration of exposure. Nevertheless, egg viability declined very gradually and significantly with exposure duration, and the rate of decline differed among species. In contrast to studies performed in the tropics, we found little evidence that temperature or microbial mechanisms of egg viability decline were important at our temperate-zone site; neither temperatures above physiological zero nor alcohol disinfection was significantly related to hatching success. Delaying the onset of incubation until the penultimate or last egg of a clutch at our study site may maintain hatching synchrony without a large trade-off in egg viability. These results provide insight into the environmental mechanisms that may be responsible for large-scale latitudinal patterns in avian clutch size and hatching asynchrony.