Endotherms, unlike ectotherms, generate metabolic heat to meet their thermoregulatory demands. As homeotherms their body temperature stays within a certain range of body temperature, often higher than the environment. This ability to maintain a biochemically optimal body temperature bestows protection against unfavourable thermal conditions for endotherms. The energetic costs associated with thermoregulatory metabolism and the limits for thermoregulatory capacity will, however, still set a boundary upon the range and duration of conditions that are tolerated by an endotherm. Especially within the context of global climate change, the effect of ahistorically high ambient temperatures on endotherms will depend heavily on the cost the new conditions will impose upon them. Despite various statistical and mechanistic evaluations of endotherm energy metabolism and heat exchange, these costs and limits are poorly known on the interspecific level. In the first chapter, we review and summarise current understanding of endotherm thermal physiology, identify the unresolved questions and examine the conceptual and methodological challenges to a consensus.

The field metabolic rate (FMR) of an endothermic animal represents its energy expenditure in a natural environment, or its energy budget, and the field water flux of an animal reflects the animal’s water requirements. In the second chapter, we examined FMR of 97 avian species and field water flux of 76 species for adults from direct field measurements by the doubly-labelled water (DLW) method, and conducted a phylogenetically informed, comprehensive analysis of the relationship between FMR and field wtaer flux, and multiple environmental and biological variables. FMR was strongly associated with body mass with an allometric exponent of 0.6, and seabirds had lower FMR than terrestrial birds. Birds consuming plant matter had lower FMR compared to omnivores, carnivores or nectarivores, and low ambient temperature was associated with higher FMR. Unlike for BMR, there was scarce evidence for phylogenetic covariance in FMR. Life history traits such as fecundity and migration were also not strongly associated with FMR. Field water flux was strongly associated with body mass with an allometric exponent of 0.6, and seabirds, breeding birds and birds from relatively humid habitats had higher field water flux. There was considerable evidence for phylogenetic covariance, but granivory and mean temperature were not associated with field water flux.

Endotherms maintain a stable body temperature at high ambient temperatures by continuous dissipation of metabolic heat to the environment. This requires endotherms to maintain a balance between heat dissipation and water conservation at multiple temperatures. Birds are relatively small, contain a large amount of metabolically expensive tissue, and are mostly diurnal. As a result, they are severely affected by physiological challenges. In the third chapter, we compiled evaporative water loss measurements for birds exposed to different temperatures and examined their relationships with ambient temperature, precipitation, diet and circadian cycles. While evaporative water loss at normothermic conditions was associated with precipitation and water content in diet, ambient temperature in their natural habitat was important when birds were exposed to heat stress. Additionally, the circadian cycle had an effect on water evaporation. Activephase birds that had higher resting metabolic rates lost more water through evaporation than resting-phase birds. The direction and magnitude of relationship between ambient temperature and evaporative water loss at a high temperature also differed between active- and resting-phase birds. These results suggest that birds do not experience a tradeoff between water conservation at lower temperatures and efficient heat dissipation under heat stress, and that the activity level of a bird may affect the ability to dissipate heat through water evaporation.

The upper critical temperature (UCT) of an endotherm represents the temperature that requires it to actively dissipate mettabolic heat through increased energy consumption. Endotherms have relatively low variation in UCT compared to the variation in the lower critical temperature (LCT), but environmental conditions are also linked to intraspecific and interspecific variation in UCT. Difficulty in estimating UCT and differences in data quality complicate the comparative analysis of this variation in UCT. In the fourth chapter, we compiled estimates of UCT for 210 bird species, categorised the information by data quality, and evaluated the relationship between UCT and ambient temperature, precipitation, seasonality, migration and circadian cycle. UCT was positively correlated with maximum temperature in the natural range and negatively correlated with body mass, long-distance migration and summer precipitation. Birds in the resting phase of the circadian cycle had lower UCT compared to birds in the active phase. Including the studies that did not include temperatures well above UCT resulted in slightly reduced coefficient estimates for UCT and thus lower accuracy. However, data quality did not severely impact the precision of estimates.

Anthropogenic climate and land-use change are widely considered to be the two greatest threats to global biodiversity and ecosystem functioning. Although species may respond to changing environments in a variety of ways, the majority of species are expected to shift their distributions to track ecologically favorable habitats. The extent of these shifts may be heterogenous across species or even within a species occupying different regions, but our knowledge of what drives this heterogeneity is still sorely lacking. In particular, the effects of climate and land-use change on shifting species distributions have largely been studied independently. In more realistic scenarios, most species will experience both drivers simultaneously, creating the potential for heterogeneous changes in species composition across regions with different histories of climate and land-use change, as well as species with different sensitivities to that change.

To investigate the combined effects of climate and land-use change on species occupancy and community composition, I surveyed avian diversity at 71 sites in the California Central Valley and Los Angeles. These sites were originally surveyed in the early 1900s by Joseph Grinnell and colleagues from the Museum of Vertebrate Zoology, providing a unique opportunity to directly compare bird occupancy and its relation to site-specific climate and land-use covariates across a century of change. Historic surveys paired with modern resurveys documented changing distributions by 148 bird species across two regions with similar initial species and habitat composition but differing patterns of climate and land-use change.

Our knowledge of species’ ecological and life history traits as predictors of sensitivity to land-use change is well developed, but the same cannot be said for traits as predictors of climate-induced range shifts. There is strong theoretical support that range shifts under climate change may be mediated by traits that facilitate dispersal and population establishment, but empirical evidence for this relationship has been mixed. In my first chapter, I conducted a meta-analysis of studies that analyzed climate-induced range shifts as a function of species’ traits, with the goal of identifying which traits have provided the strongest results. I show that the majority of traits failed to predict range shifts consistently across studies, while a much smaller number of traits, particularly habitat breadth, had strong empirical support. In subsequent chapters, I use the most informative species’ traits revealed by this meta-analysis to explore differences in species-specific occupancy change across my Central Valley and Los Angeles survey sites.

Both climate and land-use change are expected to favor exotic and generalist species over specialists, resulting in declining occupancy and diversity. Using occurrence data for 122 bird species from 41 resurvey sites in the California Central Valley, my second chapter examined how occupancy and diversity changed over the past 100 years in this predominantly agricultural region, as well as the relative influence of climate versus land-use covariates to occupancy within each survey period. In contrast to expectations that occupancy and diversity would decline, both remained stable: species that increased in occupancy (predominantly habitat generalists or human adapters) roughly balanced species that decreased in occupancy (predominantly open-habitat species), resulting in no significant change in average species richness or between-site diversity. Equally surprising was the far greater importance of water availability (precipitation and water cover) to occupancy within each survey period as compared to urbanization or agricultural cover.

The relative importance of climate versus land-use change to changes in species occupancy is poorly known and may result in heterogeneous patterns of diversity change across regions with different climate and land-use change histories. In my third chapter, I used occurrence data for 148 bird species across the full set of 42 Central Valley sites and 29 Los Angeles sites. I directly assessed the relative importance of climate and land-use covariates to probabilities of occupancy, persistence, and colonization, as well as compared patterns of occupancy and diversity change between the two regions. Climate and land-use covariates were both important, but to different aspects of occupancy and turnover, with climate driving initial occupancy, climate and land-use both having similar influence on colonization, and urban cover emerging as the biggest driver of local persistence. In contrast to stability in occupancy and diversity in the Central Valley, both declined in Los Angeles. This diversity loss resulted from a greater amount of urban development in Los Angeles and larger species-specific occupancy decreases in particularly forest and open-habitat species.

Overall, my dissertation provides a detailed picture of how bird species have responded to over a century of climate and land-use change. These changes were highly heterogeneous across species – driven by traits, namely habitat preference – and across very similar ecological regions – driven by divergent patterns in both climate change and urbanization. As we continue to create range projections and plans to conserve future diversity, it will be important to utilize knowledge generated by long-term historical datasets and to incorporate multiple drivers of heterogeneity in species’ responses to global change.

Dispersal and gene flow connect habitat patches, linking demographic and genetic processes within metapopulations. Demographic connectivity can prevent local extinctions and increase species persistence. It allows species to colonize new areas, making it possible for them to shift their ranges in response to changes in the environment. Genetic connectivity may impede local adaptation, but is often advantageous because it minimizes the negative effects of habitat loss and fragmentation, such as inbreeding.

This research explored different methodologies for estimating dispersal and gene flow, and estimated connectivity for two species of secretive wetland birds, the California black rail (Laterallus jamaicensis coturniculus) and the Virginia rail (Rallus limicola), from an inland metapopulation in the Sierra Nevada foothills and a coastal metapopulation in the San Francisco Bay Area, California. The research presented includes: (1) a synthesis of landscape genetics methods used to examine spatial patterns of genetic variation, (2) a validation of dispersal distances estimated from occupancy models using dispersal distances estimated from genetic parentage assignments within the inland metapopulation, (3) an estimate of the frequency and distance of long-distance dispersal events between the inland and coastal metapopulations, and (4) an assessment of the effects of habitat loss and fragmentation on gene flow within the coastal metapopulation.

Despite its importance in ecology and evolution, dispersal distances are poorly understood for many species, especially those that are secretive and rare, such as rails. For these species, indirect methods, including the use of occupancy models, genetics, and isotopic markers, may be optimal for estimating dispersal. In the Sierra Nevada foothills, Black and Virginia rails exhibited contrasting relationships between connectivity metrics and patch colonization. For black rails, model-averaged dispersal distances from occupancy models (Buffer Radius Metric = 3.46 km; Incidence Function Metric = 3.70 km) showed good agreement with the mean dispersal distance from genetic parentage assignments (5.58 ± 1.92 km). For Virginia rails, however, it was difficult to identify a spatial scale with the best fit in occupancy models, and the sample size for estimating dispersal distance from parentage assignments was limited. Combined inference from genetic and isotopic population assignments suggested that long-distance dispersal of black rails between the Sierra Nevada foothills and the San Francisco Bay Area occurred infrequently, but, somewhat surprisingly, three dispersal events greater than 100 km were recorded during the study. The first was recorded from a band return for a black rail that traveled 128 km. Two other long-distance dispersal estimates were obtained using isotopic and genetic population assignments. Within the San Francisco Bay Area, estimates of gene flow for black rails among 11 wetlands (FST range: 0.014 to 0.067) indicated rails dispersed frequently between wetlands at shorter spatial scales (tens of kilometers), but that gene flow at a larger spatial scale (greater than 50 km) between the North Bay and South Bay (FST = 0.018) was limited. Although previously thought to be dispersal-limited, black rails appear to be capable of dispersing and maintaining some level of gene flow at spatial scales less than 50 km. Therefore, wetland mitigation and restoration efforts for rails should focus on protecting and creating habitat at smaller spatial scales (tens of kilometers) to maintain demographic and genetic connectivity and metapopulation viability.

Species extinctions and population declines have accelerated over recent decades due to habitat destruction, overexploitation, and invasive species, with cascading effects on ecosystem functions and services as well as human well-being. Climate change has emerged as another powerful driver of species decline, one whose effects are beginning to intensify. It should lead to shifts in species distributions and rearranged communities, unless climatic disruption acts as a systemic threat leading to a community collapse. Desert birds comprise a species-rich, easily detectable assemblage, and are closely coupled to their physical environment, which makes them suitable indicators of climatic change. I assessed how desert bird populations have been impacted over the past century by resurveying 106 sites throughout the Mojave and Great Basin deserts that were originally surveyed for avian diversity in the early 20th century by Joseph Grinnell and colleagues from the Museum of Vertebrate Zoology at University of California, Berkeley.

Multispecies occupancy models were employed throughout this research to capture the dynamics of the entire avian community. In my first chapter, I review the impacts of imperfect detection on the estimation of community diversity and how the application of multispecies occupancy models to estimate these measures can alleviate this source of error. The hierarchical structure of the model allows data from the entire sample to inform the estimation of occupancy, colonization, survival, and detection probabilities, despite encounter histories being stratified by historic and modern surveys, species, site, and visit. Data from all species’ informs the estimation of community-level values, and the structure of the model itself facilitates the modeling of all species, including rare ones. Correcting for detection is particularly important when using historic data, because differences in methodology and changes in technology that can alter the detectability of species through time can also influence the conclusions drawn from the comparison.

Deserts, already defined by climatic extremes, have warmed and dried more than other regions in the contiguous United States due to climate change. In my second chapter, I assessed how climate change and habitat disturbance have impacted bird populations of the Mojave Deserts. The resurveys of sites originally visited in the early 20th century found Mojave Desert birds strongly declined in occupancy and sites lost nearly half of their species. Declines were associated with climate change, particularly decreased precipitation. The magnitude of the decline in the avian community and the absence of species that were local climatological “winners” is exceptional. Our results provide evidence that bird communities in the Mojave Desert have collapsed to a new, lower baseline. Declines could accelerate with future climate change, as this region is predicted to become drier and hotter by the end of the century.

Where the Mojave and Great Basin meet is a juncture of two distinct avifauna. My third chapter uses a dynamic multispecies occupancy model to evaluate the cumulative effects of the redistribution of all 162 observed breeding species across space, time, and biomes. Cross-system comparisons can verify that trends are more than just regional in nature, which legitimizes their application to the development of broad-scale predictive models or management recommendations. The Mojave, a warm desert, and the Great Basin, a cold desert, are two very different systems with distinct vegetation and animal assemblages. The contiguity of the deserts creates an ideal place to study how 20th century climate change is differentially impacting communities across biomes. A transition zone can persist through a changing climate if biotic factors lag behind climate, such as the leading and trailing-edge range disequilibria in vegetation response, and inherent abiotic factors, such as topography and edaphic factors that contribute to the Mojave-Great Basin transition. Barriers to northward expansion for birds could result in range collapse if the southern limits of warm desert species are also contracting. I evaluated whether species of the warmer Mojave, which continues to warm, are expanding into the colder Great Basin Desert, which has incurred less warming, or whether the transition zone behaves as a barrier to northward expansion. Individual species experienced occupancy changes in consistent directions in both deserts. A substantial proportion of species were in decline in one or both deserts (39.5%), while relatively few species were increasing (6.2%). Most species (n = 80) shifted one or both of their latitudinal range limits. Range shifts were highly idiosyncratic in nature, causing the avifaunas of the two deserts to be less strongly structured than they were in the past. The redistribution of species is driving the genesis of novel communities which may have ecological consequences that are yet to be realized.

This dissertation presents a detailed picture of how desert avifauna has change over the past century. The unique ecology of the deserts means that can serve as bellwethers of climate change. Community collapse of the Mojave avifauna and the redistribution of species across both deserts would have been overlooked without the original faunal surveys of Joseph Grinnell and colleagues from the early 20th century. Although similar changes may be occurring in other ecoregions that lack comparable historical data, the harsh nature of desert environments makes them more likely to become less suitable for life and offers a prescient warning for biodiversity loss as future climates are pushed further toward extremes.

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.

In working landscapes where natural resource extraction co-occurs with habitat conservation, species are often structured as a metapopulation occupying fragmented patches of habitat. Because patches change due to human management decisions, understanding how metapopulations persist in working landscapes requires assessing both how the species’ intrinsic factors drive turnover and how the behaviors of key actors drive patch changes. Coupled human and natural systems (CHANS) research uses a multidisciplinary approach to identify the key actors, processes, and feedbacks that drive the dynamics of a region. This dissertation integrates five diverse datasets—wildlife occupancy surveys, land-use change mapping, a survey of landowner decision-making, hydrological databases, and disease vector trapping—to assess how wetlands, irrigation, and two avian metapopulations function as a CHANS in the rangelands of the foothills of the California Sierra Nevada. The threatened, dispersal-limited black rail (Laterallus jamaicensis) and widespread, vagile Virginia rail (Rallus limicola) inhabit patchy wetlands throughout the foothills. The black rail has declined over the past decade, with drought and the arrival of West Nile virus potential causes. The first chapter assesses how the human-induced diversity of hydrological processes altered the CHANS’ resilience to an exceptional disturbance, a historically severe drought from 2012–2015. The second chapter tests if the “rescue effect” (dispersing individuals preventing local extinctions) actually occurs as predicted by theory and occupancy models. The third chapter integrates these interdisciplinary datasets into a simulation model that combines agent-based models of land-use change with stochastic patch occupancy models of metapopulations, in order to (1) quantify the relative importance of different drivers of metapopulation dynamics, (2) test predictions of the behavior of metapopulations in dynamic landscapes, and (3) evaluate the potential impacts of mandated irrigation cutbacks during drought and wetland incentive policies on metapopulation persistence.

Complex metapopulation dynamics emerged from the CHANS, and irrigation water was critical for black rail persistence. Wetlands were primarily fed by “waste” from the irrigation system. Landowners and water sources showed response diversity to drought, increasing the resilience of the wetland landscape and maintaining the black rail metapopulation through the 2012–2015 drought. The rescue effect was operating for both rail metapopulations during this period, providing one of the first empirical validations of this process, and occurred at notably higher rates during the lowest precipitation year. However, inferences from occupancy models were unreliable and underestimated the rescue effect (1) when using autoregressive measures that incorporated patch area, (2) when the species was not dispersal-limited, and (3) during a period of nonequilibrium metapopulation dynamics. Simulations showed rail metapopulations were strongly top-down regulated by precipitation, with synergistic negative impacts because droughts affected multiple system processes at the same time. The black rail decline was caused by the combination of West Nile virus and drought. Two key theoretical predictions were not borne out due to the CHANS’ complexity. First, dispersal limitations of black rails did not result in greater sensitivity to patch change rates compared to Virginia rails, because patch heterogeneity affected patch change rates and the two species’ colonization and extinction rates in different ways. Second, because incentive programs were coupled to CHANS dynamics they made the black rail metapopulation more sensitive to other parameters, not less. Drought irrigation cutbacks posed a substantial extinction risk that incentive policies were unable to reduce. Integrating “waste” water into regional wetland management may thus offer more cost-effective conservation than attempting to restore a lost “natural” state. These results highlight that conserving metapopulations in working landscapes requires assessing how human transformation of CHANS may create new diversity in system processes that benefits wildlife.