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Estimating abundance and population size is essential for many ecological and conservation studies of parrots. Achieving these goals requires methods that yield reliable estimates, but parrot traits can make them difficult to detect, count, and capture. We review established and emergent sampling and analytical methods used to estimate parrot abundance and population size, focusing on their assumptions, requirements, and limitations. Roost surveys are cost-effective if all roost locations in a region are known and stable, which is uncommon. Capture-recapture methods incorporate detection probability, but capturing, marking and resighting parrots can be difficult. Distance sampling estimates detection probability and surveys multiple species simultaneously, but is sensitive to the spatial distribution of individuals and excludes birds in flight. Roadside transects can cover large areas and survey multiple species, but habitats near roads may differ from the surrounding areas, biasing abundance estimates. Occupancy surveys and hierarchical models usually require spatially and temporally replicated datasets. Both allow estimation of detection probability; the former dispenses with count data, while the latter is a versatile set of methods that can incorporate multiple processes influencing detection and abundance. Finally, passive acoustic surveys can sample multiple species simultaneously, but identification of vocalisations can be difficult and time-consuming.

Species distribution models (SDMs) are commonly applied to predict species' responses to anticipated global change, but lack of data from future time periods precludes assessment of their reliability. Instead, performance against test data in the same era is assumed to correlate with accuracy in the future. Moreover, high-confidence absence data is required for testing model accuracy but is often unavailable since a species may be present when undetected. Here we evaluate the performance of eight SDMs trained with historic (1900-1939) or modern (1970-2009) climate data and occurrence records for 18 mammalian species. Models were projected to the same or the opposing time period and evaluated with data obtained from surveys conducted by Joseph Grinnell and his colleagues in the Sierra Nevada of California from 1900 to 1939 and modern resurveys from 2003 to 2011. Occupancy modeling was used to confidently assign absences at test sites where species were undetected. SDMs were evaluated using species' presences combined with this high-confidence absence (HCA) set, a low-confidence set in which non-detections were assumed to indicate absence (LCA), and randomly located 'pseudoabsences' (PSA). Model performance increased significantly with the quality of absences (mean AUC ± SE: 0.76 ± 0.01 for PSA, 0.79 ± 0.01 for LCA, and 0.81 ± 0.01 for HCA), and apparent differences between SDMs declined as the quality of test absences increased. Models projecting across time performed as well as when projecting within the same time period when assessed with threshold-independent metrics. However, accuracy of presence and absence predictions sometimes declined in cross-era projections. Although most variation in performance occurred among species, autecological traits were only weakly correlated with model accuracy. Our study indicates that a) the quality of evaluation data affects assessments of model performance; b) within-era performance correlates positively but unreliably with cross-era performance; and c) SDMs can be reliably but cautiously projected across time. © 2013 The Author. Ecography © 2013 Nordic Society Oikos.

Infanticide and adoption have been attributed to sexual selection, where an individual later reproduces with the parent whose offspring it killed or adopted. While sexually selected infanticide is well known, evidence for sexually selected adoption is anecdotal. We report on both behaviors at 346 nests over 27 y in green-rumped parrotlets ( Forpus passerinus ) in Venezuela. Parrotlets are monogamous with long-term pair bonds, exhibit a strongly male-biased adult sex ratio, and nest in cavities that are in short supply, creating intense competition for nest sites and mates. Infanticide attacks occurred at 256 nests in two distinct contexts: 1) Attacks were primarily committed by nonbreeding pairs (69%) attempting to evict parents from the cavity. Infanticide attacks per nest were positively correlated with population size and evicting pairs never adopted abandoned offspring. Competition for limited nest sites was a primary cause of eviction-driven infanticide, and 2) attacks occurred less frequently at nests where one mate died (31%), was perpetrated primarily by stepparents of both sexes, and was independent of population size. Thus, within a single species and mating system, infanticide occurred in multiple contexts due to multiple drivers. Nevertheless, 48% of stepparents of both sexes adopted offspring, and another 23% of stepfathers exhibited both infanticide and long-term care. Stepfathers were often young males who subsequently nested with widows, reaching earlier ages of first breeding than competitors and demonstrating sexually selected adoption. Adoption and infanticide conferred similar fitness benefits to stepfathers and appeared to be equivalent strategies driven by limited breeding opportunities, male-biased sex ratios, and long-term monogamy., Competing Interests: Competing interests statement:The authors declare no competing interest.

Correlative species distribution models are widely used to quantify past shifts in ranges or communities, and to predict future outcomes under ongoing global change. Practitioners confront a wide range of potentially plausible models for ecological dynamics, but most specific applications only consider a narrow set. Here, we clarify that certain model structures can embed restrictive assumptions about key sources of forecast uncertainty into an analysis. To evaluate forecast uncertainties and our ability to explain community change, we fit and compared 39 candidate multi- or joint species occupancy models to avian incidence data collected at 320 sites across California during the early 20th century and resurveyed a century later. We found massive (>20,000 LOOIC) differences in within-time information criterion across models. Poorer fitting models omitting multivariate random effects predicted less variation in species richness changes and smaller contemporary communities, with considerable variation in predicted spatial patterns in richness changes across models. The top models suggested avian environmental associations changed across time, contemporary avian occupancy was influenced by previous site-specific occupancy states, and that both latent site variables and species associations with these variables also varied over time. Collectively, our results recapitulate that simplified model assumptions not only impact predictive fit but may mask important sources of forecast uncertainty and mischaracterize the current state of system understanding when seeking to describe or project community responses to global change. We recommend that researchers seeking to make long-term forecasts prioritize characterizing forecast uncertainty over seeking to present a single best guess. To do so reliably, we urge practitioners to employ models capable of characterizing the key sources of forecast uncertainty, where predictors, parameters and random effects may vary over time or further interact with previous occurrence states., (© 2023 The Authors. Global Change Biology published by John Wiley & Sons Ltd.)

The Virginia rail, Rallus limicola, is a member of the family Rallidae, which also includes many other species of secretive and poorly studied wetland birds. It is recognized as a single species throughout its broad distribution in North America where it is exploited as a game bird, often with generous harvest limits, despite a lack of systematic population surveys and evidence of declines in many areas due to wetland loss and degradation. To help advance understanding of the phylogeography, biology, and ecology of this elusive species, we report the first reference genome assembly for the Virginia rail, produced as part of the California Conservation Genomics Project (CCGP). We produced a de novo genome assembly using Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology with an estimated sequencing error rate of 0.191%. The assembly consists of 1,102 scaffolds spanning 1.39 Gb, with a contig N50 of 11.0 Mb, scaffold N50 of 25.3 Mb, largest contig of 45 Mb, and largest scaffold of 128.4 Mb. It has a high BUSCO completeness score of 96.9% and represents the first genome assembly available for the genus Rallus. This genome assembly will help resolve questions about the complex evolutionary history of rails and evaluate the potential of rails for adaptive evolution in the face of growing threats from climate change and habitat loss and fragmentation. It will also provide a valuable resource for rail conservation efforts by quantifying Virginia rail vagility, population connectivity, and effective population sizes., (© The American Genetic Association. 2023.)

The black rail, Laterallus jamaicensis, is one of the most secretive and poorly understood birds in the Americas. Two of its five subspecies breed in North America: the Eastern black rail (L. j. jamaicensis), found primarily in the southern and mid-Atlantic states, and the California black rail (L. j. coturniculus), inhabiting California and Arizona, are recognized across the highly disjunct distribution. Population declines, due primarily to wetland loss and degradation, have resulted in conservation status listings for both subspecies. To help advance understanding of the phylogeography, biology, and ecology of this elusive species, we report the first reference genome assembly for the black rail, produced as part of the California Conservation Genomics Project (CCGP). We produced a de novo genome assembly using Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology with an estimated sequencing error rate of 0.182%. The assembly consists of 964 scaffolds spanning 1.39 Gb, with a contig N50 of 7.4 Mb, scaffold N50 of 21.4 Mb, largest contig of 44.8 Mb, and largest scaffold of 101.2 Mb. The assembly has a high BUSCO completeness score of 96.8% and represents the first genome assembly available for the genus Laterallus. This genome assembly can help resolve questions about the complex evolutionary history of rails, assess black rail vagility and population connectivity, estimate effective population sizes, and evaluate the potential of rails for adaptive evolution in the face of growing threats from climate change, habitat loss and fragmentation, and disease., (© The American Genetic Association. 2023.)

Climate and land-use change could exhibit concordant effects that favor or disfavor the same species, which would amplify their impacts, or species may respond to each threat in a divergent manner, causing opposing effects that moderate their impacts in isolation. We used early 20th century surveys of birds conducted by Joseph Grinnell paired with modern resurveys and land-use change reconstructed from historic maps to examine avian change in Los Angeles and California's Central Valley (and their surrounding foothills). Occupancy and species richness declined greatly in Los Angeles from urbanization, strong warming (+1.8°C), and drying (-77.2 millimeters) but remained stable in the Central Valley, despite large-scale agricultural development, average warming (+0.9°C), and increased precipitation (+11.2 millimeters). While climate was the main driver of species distributions a century ago, the combined impacts of land-use and climate change drove temporal changes in occupancy, with similar numbers of species experiencing concordant and opposing effects.

Phenotypic convergence across distantly related taxa can be driven by similar selective pressures from the environment or intrinsic constraints. The roles of these processes on physiological strategies, such as homeothermy, are poorly understood. We studied the evolution of thermal properties of mammalian pelage in a diverse community of rodents inhabiting the Mojave Desert, USA. We used a heat flux device to measure the thermal insulation of museum specimens and determined whether thermal properties were associated with habitat preferences while assessing phylogenetic dependence. Species that prefer arid habitats exhibited lower conductivity and thinner pelage relative to species with other habitat preferences. Despite being thinner, the pelage of arid species exhibited comparable insulation to the pelage of the other species due to its lower conductivity. Thus, arid species have insulative pelage while simultaneously benefitting from thin pelage that promotes convective cooling. We found no evidence of intrinsic constraints or phylogenetic dependence, indicating pelage readily evolves to environmental pressures. Thermoregulatory simulations demonstrated that arid specialists reduced energetic costs required for homeothermy by 14.5% by evolving lower conductivity, providing support for adaptive evolution of pelage. Our study indicates that selection for lower energetic requirements of homeothermy has shaped evolution of pelage thermal properties., (© 2022 The Authors. Evolution published by Wiley Periodicals LLC on behalf of The Society for the Study of Evolution.)

Converging lines of inquiry from across the social and biological sciences target the adult sex ratio (ASR; the proportion of males in the adult population) as a fundamental population-level determinant of behavior. The ASR, which indicates the relative number of potential mates to competitors in a population, frames the selective arena for competition, mate choice, and social interactions. Here we review a growing literature, focusing on methodological developments that sharpen knowledge of the demographic variables underlying ASR variation, experiments that enhance understanding of the consequences of ASR imbalance across societies, and phylogenetic analyses that provide novel insights into social evolution. We additionally highlight areas where research advances are expected to make accelerating contributions across the social sciences, evolutionary biology, and biodiversity conservation., (© 2022. The Author(s).)

Climate change is increasing the frequency of extreme events, such as droughts or hurricanes, with substantial impacts on human and wildlife communities. Extreme events can affect individuals through two pathways: by altering the fitness of adults encountering a current extreme, and by affecting the development of individuals born during a natal extreme, a largely overlooked process. Here, we show that the impact of natal drought on an avian predator overrode the effect of current drought for decades, so that individuals born during drought were disadvantaged throughout life. Incorporation of natal effects caused a 40% decline in forecasted population size and a 21% shortening of time to extinction. These results imply that climate change may erode populations more quickly and severely than currently appreciated, suggesting the urgency to incorporate "penalties" for natal legacies in the analytical toolkit of impact forecasts. Similar double impacts may apply to other drivers of global change., (© 2022. The Author(s).)

Prelinguistic babbling is a critical phase in infant language development and is best understood in temperate songbirds where it occurs primarily in males at reproductive maturity and is modulated by sex steroids. Parrots of both sexes are icons of tropical vocal plasticity, but vocal babbling is unreported in this group and whether the endocrine system is involved is unknown. Here we show that vocal babbling is widespread in a wild parrot population in Venezuela, ensues in both sexes during the nestling stage, occurs amidst a captive audience of mixed-aged siblings, and is modulated by corticosteroids. Spectrographic analysis and machine learning found phoneme diversity and combinatorial capacity increased precipitously for the first week, thereafter, crystalizing into a smaller repertoire, consistent with the selective attrition model of language development. Corticosterone-treated nestlings differed from unmanipulated birds and sham controls in several acoustic properties and crystallized a larger repertoire post-treatment. Our findings indicate babbling occurs during an early life-history stage in which corticosteroids help catalyse the transition from a universal learning programme to one finely tuned for the prevailing ecological environment, a potentially convergent scenario in human prelinguistic development.

Small mammals in hot deserts often avoid heat via nocturnality and fossoriality, and are thought to have a limited capacity to dissipate heat using evaporative cooling. Research to date has focused on thermoregulatory responses to air temperatures (Ta) below body temperature (Tb). Consequently, the thermoregulatory performance of small mammals exposed to high Ta is poorly understood, particularly responses across geographic and seasonal scales. We quantified the seasonal thermoregulatory performance of four cricetid rodents (Neotoma albigula, Neotoma lepida, Peromyscus eremicus, Peromyscus crinitus) exposed to high Ta, at four sites in the Mojave Desert. We measured metabolism, evaporative water loss and Tb using flow-through respirometry. When exposed to Ta≥Tb, rodents showed steep increases in Tb, copious salivation and limited evaporative heat dissipation. Most individuals were only capable of maintaining Ta-Tb gradients of ∼1°, resulting in heat tolerance limits (HTLs) in the range Ta=43-45°C. All species exhibited a thermoneutral Tb of ∼35-36°C, and Tb increased to maximal levels of ∼43°C. Metabolic rates and rates of evaporative water loss increased steeply in all species as Ta approached Tb. We also observed significant increases in resting metabolism and evaporative water loss from summer to winter at Ta within and above the thermoneutral zone. In contrast, we found few differences in the thermoregulatory performance within species across sites. Our results suggest that cricetid rodents have a limited physiological capacity to cope with environmental temperatures that exceed Tb and that a rapidly warming environment may increasingly constrain their nocturnal activity., Competing Interests: Competing interests The authors declare no competing or financial interests., (© 2022. Published by The Company of Biologists Ltd.)

High exposure to warming from climate change is expected to threaten biodiversity by pushing many species toward extinction. Such exposure is often assessed for all taxa at a location from climate projections, yet species have diverse strategies for buffering against temperature extremes. We compared changes in species occupancy and site-level richness of small mammal and bird communities in protected areas of the Mojave Desert using surveys spanning a century. Small mammal communities remained remarkably stable, whereas birds declined markedly in response to warming and drying. Simulations of heat flux identified different exposure to warming for birds and mammals, which we attribute to microhabitat use. Estimates from climate projections are unlikely to accurately reflect species' exposure without accounting for the effects of microhabitat buffering on heat flux., (Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

Transition zones between biomes, also known as ecotones, are areas of pronounced ecological change. They are primarily maintained by abiotic factors and disturbance regimes that could hinder or promote species range shifts in response to climate change. We evaluated how climate change has affected metacommunity dynamics in two adjacent biomes and across their ecotone by resurveying 106 sites that were originally surveyed for avian diversity in the early 20th century by Joseph Grinnell and colleagues. The Mojave, a warm desert, and the Great Basin, a cold desert, have distinct assemblages and meet along a contiguous, east-west boundary. Both deserts substantially warmed over the past century, but the Mojave dried while the Great Basin became wetter. We examined whether the distinctiveness and composition of desert avifaunas have changed, if species distributions shifted, and how the transition zone impacted turnover patterns. Avifauna change was characterized by (a) reduced occupancy, range contractions, and idiosyncratic species redistributions; (b) degradation of historic community structure, and increased taxonomic and climatic differentiation of the species inhabiting the two deserts; and (c) high levels of turnover at the transition zone but little range expansion of species from the warm, dry Mojave into the cooler, wetter Great Basin. Although both deserts now support more drier and warmer tolerant species, their bird communities still occupy distinct climatological space and differ significantly in climatic composition. Our results suggest a persistent transition zone between biomes contributes to limiting the redistribution of birds, and highlight the importance of understanding how transition zone dynamics impact responses to climate change., (© 2020 John Wiley & Sons Ltd.)

Life history theory predicts that physiological and behavioral responsiveness to stress should be delayed in development until the benefits of heightened reactivity outweigh the costs of potentially chronic glucocorticoid levels. Birds often acquire stress-responsiveness at locomotor independence, however, both stress-responsiveness and locomotor ability are delayed in birds with altricial developmental strategies. Parrots (Psittacidae) are extremely altricial, but it is not known whether they also postpone physiological responsiveness to stress until locomotor independence. We quantified individual variation in baseline and stress-induced plasma corticosterone (CORT) concentrations, the main avian glucocorticoid, in wild green-rumped parrotlets (Forpus passerinus) of Venezuela at four stages of nestling development. Parrotlet neonates are very underdeveloped and compete for parental care among extreme sibling size hierarchies, a competitive scenario that might benefit from early hypothalamic-pituitary-adrenal (HPA) functionality. Nestlings that underwent a standardized restraint stress-treatment showed higher average CORT concentrations compared to baseline in all age groups sampled, and exhibited no evidence of age-related changes in the stress response. This is 2 weeks before locomotor independence and earlier than previously documented for altricial species. Results suggest that precocity of HPA function may be advantageous to growth and survivorship in extremely altricial birds., (© 2019 Wiley Periodicals, Inc.)

Climate change threatens global biodiversity by increasing extinction risk, yet few studies have uncovered a physiological basis of climate-driven species declines. Maintaining a stable body temperature is a fundamental requirement for homeothermic animals, and water is a vital resource that facilitates thermoregulation through evaporative cooling, especially in hot environments. Here, we explore the potential for thermoregulatory costs to underlie the community collapse of birds in the Mojave Desert over the past century in response to climate change. The probability of persistence was lowest for species occupying the warmest and driest sites, which imposed the greatest cooling costs. We developed a general model of heat flux to evaluate whether water requirements for evaporative cooling contributed to species' declines by simulating thermoregulatory costs in the Mojave Desert for 50 bird species representing the range of observed declines. Bird species' declines were positively associated with climate-driven increases in water requirements for evaporative cooling and exacerbated by large body size, especially for species with animal-based diets. Species exhibiting reductions in body size across their range saved up to 14% in cooling costs and experienced less decline than species without size reductions, suggesting total cooling costs as a mechanism underlying Bergmann's rule. Reductions in body size, however, are unlikely to offset the 50 to 78% increase in cooling costs threatening desert birds from future climate change. As climate change spreads warm, dry conditions across the planet, water requirements are increasingly likely to drive population declines, providing a physiological basis for climate-driven extinctions., Competing Interests: The authors declare no conflict of interest., (Copyright © 2019 the Author(s). Published by PNAS.)

Biological responses to climate change have been widely documented across taxa and regions, but it remains unclear whether species are maintaining a good match between phenotype and environment, i.e. whether observed trait changes are adaptive. Here we reviewed 10,090 abstracts and extracted data from 71 studies reported in 58 relevant publications, to assess quantitatively whether phenotypic trait changes associated with climate change are adaptive in animals. A meta-analysis focussing on birds, the taxon best represented in our dataset, suggests that global warming has not systematically affected morphological traits, but has advanced phenological traits. We demonstrate that these advances are adaptive for some species, but imperfect as evidenced by the observed consistent selection for earlier timing. Application of a theoretical model indicates that the evolutionary load imposed by incomplete adaptive responses to ongoing climate change may already be threatening the persistence of species.

Understanding how metapopulations persist in dynamic working landscapes requires assessing the behaviors of key actors that change patches as well as intrinsic factors driving turnover. Coupled human and natural systems (CHANS) research uses a multidisciplinary approach to identify the key actors, processes, and feedbacks that drive metapopulation and landscape dynamics. We describe a framework for modeling metapopulations in CHANS that integrates ecological and social data by coupling stochastic patch occupancy models of metapopulation dynamics with agent-based models of land-use change. We then apply this framework to metapopulations of the threatened black rail (Laterallus jamaicensis) and widespread Virginia rail (Rallus limicola) that inhabit patchy, irrigation-fed wetlands in the rangelands of the California Sierra Nevada foothills. We collected data from five diverse sources (rail occupancy surveys, land-use change mapping, a survey of landowner decision making, climate and reservoir databases, and mosquito trapping and West Nile virus testing) and integrated them into an agent-based stochastic patch occupancy model. We used the model to (1) quantify the drivers of metapopulation dynamics, and the potential interactions and feedbacks among them; (2) test predictions of the behavior of metapopulations in dynamic working landscapes; and (3) evaluate the impact of three policy options on metapopulation persistence (irrigation district water cutbacks during drought, incentives for landowners to create wetlands, and incentives for landowners to protect wetlands). Complex metapopulation dynamics emerged when landscapes functioned as CHANS, highlighting the importance of integrating human activities and other ecological processes into metapopulation models. Rail metapopulations were strongly top-down regulated by precipitation, and the black rail's decade-long decline was caused by the combination of West Nile virus and drought. Theoretical predictions of the two metapopulations' responses to dynamic landscapes and incentive programs were complicated by heterogeneity in patch quality and CHANS couplings, respectively. Irrigation cutbacks during drought posed a serious extinction risk that neither incentive policy effectively ameliorated., (© 2019 by the Ecological Society of America.)

Climate and land-use changes are thought to be the greatest threats to biodiversity, but few studies have directly measured their simultaneous impacts on species distributions. We used a unique historic resource-early 20th-century bird surveys conducted by Joseph Grinnell and colleagues-paired with contemporary resurveys a century later to examine changes in bird distributions in California's Central Valley, one of the most intensively modified agricultural zones in the world and a region of heterogeneous climate change. We analyzed species- and community-level occupancy using multispecies occupancy models that explicitly accounted for imperfect detection probability, and developed a novel, simulation-based method to compare the relative influences of climate and land-use covariates on site-level species richness and beta diversity (measured by Jaccard similarity). Surprisingly, we show that mean occupancy, species richness and between-site similarity have remained remarkably stable over the past century. Stability in community-level metrics masked substantial changes in species composition; occupancy declines of some species were equally matched by increases in others, predominantly species with generalist or human-associated habitat preferences. Bird occupancy, richness and diversity within each era were driven most strongly by water availability (precipitation and percent water cover), indicating that both climate and land-use are important drivers of species distributions. Water availability had much stronger effects than temperature, urbanization and agricultural cover, which are typically thought to drive biodiversity decline., (© 2018 John Wiley & Sons Ltd.)

Climate change has caused deserts, already defined by climatic extremes, to warm and dry more rapidly than other ecoregions in the contiguous United States over the last 50 years. Desert birds persist near the edge of their physiological limits, and climate change could cause lethal dehydration and hyperthermia, leading to decline or extirpation of some species. We evaluated how desert birds have responded to climate and habitat change by resurveying historic sites throughout the Mojave Desert that were originally surveyed for avian diversity during the early 20th century by Joseph Grinnell and colleagues. We found strong evidence of an avian community in collapse. Sites lost on average 43% of their species, and occupancy probability declined significantly for 39 of 135 breeding birds. The common raven was the only native species to substantially increase across survey sites. Climate change, particularly decline in precipitation, was the most important driver of site-level persistence, while habitat change had a secondary influence. Habitat preference and diet were the two most important species traits associated with occupancy change. The presence of surface water reduced the loss of site-level richness, creating refugia. The collapse of the avian community over the past century may indicate a larger imbalance in the Mojave and provide an early warning of future ecosystem disintegration, given climate models unanimously predict an increasingly dry and hot future., Competing Interests: The authors declare no conflict of interest., (Copyright © 2018 the Author(s). Published by PNAS.)

Dispersal distances are commonly inferred from occupancy data but have rarely been validated. Estimating dispersal from occupancy data is further complicated by imperfect detection and the presence of unsurveyed patches. We compared dispersal distances inferred from seven years of occupancy data for 212 wetlands in a metapopulation of the secretive and threatened California black rail (Laterallus jamaicensis coturniculus) to distances between parent-offspring dyads identified with 16 microsatellites. We used a novel autoregressive multi-season occupancy model that accounted for both unsurveyed patches and imperfect detection to quantify patch isolation using buffer radius (BRM) and incidence function (IFM) connectivity measures at 15 scales (1-10, 15, 20, 25, and 30 km). Connectivity measures were then fit as colonization covariates in occupancy models to estimate a model-averaged dispersal distance. As predicted, colonization was more strongly related to connectivity at small spatial scales (<10 km). AIC weights were greatest at 7 km for BRM and at 4 km for IFM. Model-averaged dispersal distances (BRM = 7.46 km; IFM = 5.48 km) showed good agreement with the mean M(±SE) dispersal distance from 23 parent-offspring dyads (5.58 ± 1.92 km), indicating reasonably accurate mean dispersal distances can be inferred from occupancy data when isolation strongly affects colonization., (© 2018 The Authors. Journal of Animal Ecology © 2018 British Ecological Society.)

Species respond to climate change in two dominant ways: range shifts in latitude or elevation and phenological shifts of life-history events. Range shifts are widely viewed as the principal mechanism for thermal niche tracking, and phenological shifts in birds and other consumers are widely understood as the principal mechanism for tracking temporal peaks in biotic resources. However, phenological and range shifts each present simultaneous opportunities for temperature and resource tracking, although the possible role for phenological shifts in thermal niche tracking has been widely overlooked. Using a canonical dataset of Californian bird surveys and a detectability-based approach for quantifying phenological signal, we show that Californian bird communities advanced their breeding phenology by 5-12 d over the last century. This phenological shift might track shifting resource peaks, but it also reduces average temperatures during nesting by over 1 °C, approximately the same magnitude that average temperatures have warmed over the same period. We further show that early-summer temperature anomalies are correlated with nest success in a continental-scale database of bird nests, suggesting avian thermal niches might be broadly limited by temperatures during nesting. These findings outline an adaptation surface where geographic range and breeding phenology respond jointly to constraints imposed by temperature and resource phenology. By stabilizing temperatures during nesting, phenological shifts might mitigate the need for range shifts. Global change ecology will benefit from further exploring phenological adjustment as a potential mechanism for thermal niche tracking and vice versa., Competing Interests: The authors declare no conflict of interest.

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., (© 2017 John Wiley & Sons Ltd.)

Adult sex ratio (ASR, the proportion of males in the adult population) is a central concept in population and evolutionary biology, and is also emerging as a major factor influencing mate choice, pair bonding and parental cooperation in both human and non-human societies. However, estimating ASR is fraught with difficulties stemming from the effects of spatial and temporal variation in the numbers of males and females, and detection/capture probabilities that differ between the sexes. Here, we critically evaluate methods for estimating ASR in wild animal populations, reviewing how recent statistical advances can be applied to handle some of these challenges. We review methods that directly account for detection differences between the sexes using counts of unmarked individuals (observed, trapped or killed) and counts of marked individuals using mark-recapture models. We review a third class of methods that do not directly sample the number of males and females, but instead estimate the sex ratio indirectly using relationships that emerge from demographic measures, such as survival, age structure, reproduction and assumed dynamics. We recommend that detection-based methods be used for estimating ASR in most situations, and point out that studies are needed that compare different ASR estimation methods and control for sex differences in dispersal.This article is part of the themed issue 'Adult sex ratios and reproductive decisions: a critical re-examination of sex differences in human and animal societies'., (© 2017 The Author(s).)

Jennions et al. introduce the different kinds of sex ratio and their biology., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

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., (© 2016 by the Ecological Society of America.)

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., (© 2016 The Authors. Journal of Animal Ecology © 2016 British Ecological Society.)

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.

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., (© 2014 Society for Conservation Biology.)

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.

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.

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., (© 2014 The Authors. Global Change Biology Published by John Wiley & Sons Ltd.)

Estimates of species richness and diversity are central to community and macroecology and are frequently used in conservation planning. Commonly used diversity metrics account for undetected species primarily by controlling for sampling effort. Yet the probability of detecting an individual can vary among species, observers, survey methods, and sites. We review emerging methods to estimate alpha, beta, gamma, and metacommunity diversity through hierarchical multispecies occupancy models (MSOMs) and multispecies abundance models (MSAMs) that explicitly incorporate observation error in the detection process for species or individuals. We examine advantages, limitations, and assumptions of these detection-based hierarchical models for estimating species diversity. Accounting for imperfect detection using these approaches has influenced conclusions of comparative community studies and creates new opportunities for testing theory., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

Studies of evolution in wild populations often find that the heritable phenotypic traits of individuals producing the most offspring do not increase proportionally in the population. This paradox may arise when phenotypic traits influence both fecundity and viability and when there is a tradeoff between these fitness components, leading to opposing selection. Such tradeoffs are the foundation of life history theory, but they are rarely investigated in selection studies. Timing of breeding is a classic example of a heritable trait under directional selection that does not result in an evolutionary response. Using a 22-y study of a tropical parrot, we show that opposing viability and fecundity selection on the timing of breeding is common and affects optimal breeding date, defined by maximization of fitness. After accounting for sampling error, the directions of viability (positive) and fecundity (negative) selection were consistent, but the magnitude of selection fluctuated among years. Environmental conditions (rainfall and breeding density) primarily and breeding experience secondarily modified selection, shifting optimal timing among individuals and years. In contrast to other studies, viability selection was as strong as fecundity selection, late-born juveniles had greater survival than early-born juveniles, and breeding later in the year increased fitness under opposing selection. Our findings provide support for life history tradeoffs influencing selection on phenotypic traits, highlight the need to unify selection and life history theory, and illustrate the importance of monitoring survival as well as reproduction for understanding phenological responses to climate change.

Although there are numerous examples of individual species moving up in elevation and poleward in latitude in response to 20th century climate change, how communities have responded is less well understood and requires fully accounting for changes in species-specific detectability over time, which has been neglected in past studies. We use a hierarchical Bayesian occupancy model to examine bird species richness change and turnover along three elevation gradients surveyed 80-100 years apart in the Sierra Nevada of California, USA. Richness declined over the 20th century across all elevations. Turnover was greatest at the highest and the lowest elevations. These findings were only apparent, however, after species' detectability was incorporated into measures of species richness. Further partitioning of species richness changes by elevational life zone showed that numbers of low- and high-elevation species declined, without a concurrent expansion by mid-elevation species. Our results provide empirical evidence for biodiversity loss in protected montane areas during the 20th century and highlight the importance of accounting for detectability in comparisons of species richness over time.

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 intermediate-stage begging calls into adult contact calls; as shown previously, the latter are influenced by sample templates provided by parents.

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., (© 2012 Blackwell Publishing Ltd.)

We examined how interactions between an individual's phenotype and its environment affect natal dispersal at multiple scales and the effects on lifetime reproductive success using a 22-year study of green-rumped parrotlets (Forpus passerinus). Dispersal increased or decreased lifetime reproductive success depending upon an individual's natal environment and phenotype. Many of the phenotypic traits and environmental conditions that influenced lifetime reproductive success also influenced dispersal, such as clutch size and competition, and this differed with scale. By examining phenotype-environment interactions, we observed both positive and negative effects of rainfall, habitat quality and competition on dispersal depending upon phenotype. The dispersal behaviours of juveniles typically resulted in higher lifetime reproductive success. Thus, individuals commonly exhibit ideal free behaviour and results provide support for the occurrence and maintenance of dispersal polymorphisms. This study highlights the long-term, carry-over effects of natal environment, natal phenotype and dispersal tactic on lifetime reproductive success., (© 2012 Blackwell Publishing Ltd/CNRS.)

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.

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.