Feather corticosterone is lower in translocated and historical populations of the endangered Laysan duck (Anas laysanensis).

Identifying reliable bioindicators of population status is a central goal of conservation physiology. Physiological stress measures are often used as metrics of individual health and can assist in managing endangered species if linked to fitness traits. We analysed feather corticosterone, a cumulative physiological stress metric, of individuals from historical, translocated, and source populations of an endangered endemic Hawaiian bird, the Laysan duck (Anas laysanensis). We hypothesized that feather corticosterone would reflect the improved reproduction and survival rates observed in populations translocated to Midway and Kure Atolls from Laysan Island. We also predicted less physiological stress in historical Laysan birds collected before ecological conditions deteriorated and the population bottleneck. All hypotheses were supported: we found lower feather corticosterone in the translocated populations and historical samples than in those from recent Laysan samples. This suggests that current Laysan birds are experiencing greater physiological stress than historical Laysan and recently translocated birds. Our initial analysis suggests that feather corticosterone may be an indicator of population status and could be used as a non-invasive physiological monitoring tool for this species with further validation. Furthermore, these preliminary results, combined with published demographic data, suggest that current Laysan conditions may not be optimal for this species.

Biased assessment of thermal properties of birds from estimated body density.

Parameter approximation is often necessary when calculating species thermal properties, and researchers historically have assumed animals are spherical when estimating volume and density. We hypothesized that a spherical model would result in significantly biased measures of density for birds, which are generally longer than they are tall or wide, and that these inaccuracies would significantly alter the outputs of thermal models. We calculated the densities of 154 bird species using sphere and ellipsoid volume equations and compared these estimates to one another and to published bird densities measured using more exact volume displacement methods. We also calculated evaporative water loss as a percentage of body mass per hour, a variable known to be critical for bird survival, twice for each species, once with the sphere-based density and once with the ellipsoid-based density. We found that volume and density estimates were statistically similar between published densities and those estimated using the ellipsoid volume equation, suggesting that this method is suitable for approximating bird volume and calculating density. In contrast, the spherical model overestimated body volume and therefore underestimated body densities. This resulted in the spherical approach consistently overestimating evaporative water loss as a percent of mass lost per hour than the ellipsoid approach. This outcome would result in mischaracterizing thermal conditions as lethal for a given species, including overestimating vulnerability to increased temperatures due to climate change.

Phylogenomics clarifies biogeographic and evolutionary history, and conservation status of West Indian tremblers and thrashers (Aves: Mimidae).

The West Indian avifauna has provided fundamental insights into island biogeography, taxon cycles, and the evolution of avian behavior. Our interpretations, however, should rely on robust hypotheses of evolutionary relationships and consistent conclusions about taxonomic status in groups with many endemic island populations. Here we present a phylogenetic study of the West Indian thrashers, tremblers, and allies, an assemblage of at least 5 species found on 29 islands, including what is considered the Lesser Antilles' only avian radiation. We improve on previous phylogenetic studies of this group by using double-digest restriction site-associated DNA sequencing (ddRAD-seq) to broadly sample loci scattered across the nuclear genome. A variety of analyses, based on either nucleotide variation in 2223 loci recovered in all samples or at 13,282 loci confidently scored as present or absent in all samples, converged on a single well-supported phylogenetic hypothesis. Results indicate that the resident West Indian taxa form a monophyletic group, exclusive of the Neotropical-Nearctic migratory Gray Catbird Dumetella carolinensis, which breeds in North America; this outcome differs from earlier studies suggesting that Gray Catbird was nested within a clade of island resident species. Thus, our findings imply a single colonization of the West Indies without the need to invoke a subsequent 'reverse colonization' of the mainland by West Indian taxa. Additionally, our study is the first to sample both endemic subspecies of the endangered White-breasted Thrasher Ramphocinclus brachyurus. We find that these subspecies have a long history of evolutionary independence with no evidence of gene flow, and are as genetically divergent from each other as other genera in the group. These findings support recognition of R. brachyurus (restricted to Martinique) and the Saint Lucia Thrasher R. sanctaeluciae as two distinct, single-island endemic species, and indicate the need to re-evaluate conservation plans for these taxa. Our results demonstrate the utility of phylogenomic datasets for generating robust systematic hypotheses.

Profile repeatability: A new method for evaluating repeatability of individual hormone response profiles.

There is broad interest in determining repeatability of individual responses. Current methods calculate repeatability of individual points (initial and/or peak), time to peak value, or a single measure of the integrated total response (area under the curve), rather than the shape of the response profile. Repeatability estimates of response profiles using linear mixed models (LMM) generate an average repeatability for an aggregate of individuals, rather than an estimate of individual repeatability. Here we use a novel ad hoc method to calculate repeatability of individual response profiles and demonstrate the need for a more rigorous assessment protocol. Response profile repeatability has not been defined at the individual level. We do this using a new metric, Profile Repeatability (PR), which incorporates components of variance and the degree to which response profiles cross each other in a time series. Values range from 0 (no repeatability) to 1 (complete repeatability). We created synthetic data to represent a range of apparent time series repeatability, and 20 independent observers visually ranked those data sets by degree of repeatability. We also applied the method to real data on stress responses of European starlings Sturnus vulgaris. We then computed PR scores for the synthetic data and for real data from European starling corticosterone responses over time, and contrast the results to those from LMM. Finally, we assessed the sensitivity of PR to reductions in the number of time points in the corticosterone response, as well as reductions in the number of replicates per individual. We found the average PR scores for a group of individuals to be somewhat robust to reductions in points in the time series; however, the ranks of individuals (PR values relative to one another) could change substantially with reduction in the number of values in a time series. PR showed threshold sensitivity to losing replicate time series between 6 and 4 replicates. Surprisingly, human observers fell into two disparate groups when ranking repeatability of the synthetic data, and the PR score indicated that human observers may underestimate repeatability of data where replicates cross each other. In contrast to the average profile repeatability estimated using LMMs, our approach calculates individual repeatability. From our perspective, LMM does not provide a definitive idea of repeatability at the individual level; in essence, it concludes that suites of time series with low within-individual variance has high repeatability, regardless of replicate trajectories. LMM and PR have non-linear relationships between 0 and 1, but PR has greater discrimination for mid-values of repeatability. Consistent average group repeatability can be associated with substantial differences in individual ranks suggests that estimating individual repeatability is critical. The PR score should be useful in comparing repeatability of any type of nonlinear, including non-monotonic, response profiles over time, which are common in both physiology and behavior, and it demonstrates the specific needs for future improvements of a profile repeatability metric.

Evaluating an icon of population persistence: the Devil's Hole pupfish.

The Devil's Hole pupfish Cyprinodon diabolis has iconic status among conservation biologists because it is one of the World's most vulnerable species. Furthermore, C. diabolis is the most widely cited example of a persistent, small, isolated vertebrate population; a chronic exception to the rule that small populations do not persist long in isolation. It is widely asserted that this species has persisted in small numbers (less than 400 adults) for 10 000-20 000 years, but this assertion has never been evaluated. Here, we analyse the time series of count data for this species, and we estimate time to coalescence from microsatellite data to evaluate this hypothesis. We conclude that mean time to extinction is approximately 360-2900 years (median 410-1800), with less than a 2.1% probability of persisting 10 000 years. Median times to coalescence varied from 217 to 2530 years, but all five approximations had wide credible intervals. Our analyses suggest that Devil's Hole pupfish colonized this pool well after the Pleistocene Lakes receded, probably within the last few hundred to few thousand years; this could have occurred through human intervention.

Potential extinction cascades in a desert ecosystem: Linking food web interactions to community viability.

Desert communities are threatened with species loss due to climate change, and their resistance to such losses is unknown. We constructed a food web of the Mojave Desert terrestrial community (300 nodes, 4080 edges) to empirically examine the potential cascading effects of bird extinctions on this desert network, compared to losses of mammals and lizards. We focused on birds because they are already disappearing from the Mojave, and their relative thermal vulnerabilities are known. We quantified bottom-up secondary extinctions and evaluated the relative resistance of the community to losses of each vertebrate group. The impact of random bird species loss was relatively low compared to the consequences of mammal (causing the greatest number of cascading losses) or reptile loss, and birds were relatively less likely to be in trophic positions that could drive top-down effects in apparent competition and tri-tropic cascade motifs. An avian extinction cascade with year-long resident birds caused more secondary extinctions than the cascade involving all bird species for randomized ordered extinctions. Notably, we also found that relatively high interconnectivity among avian species has formed a subweb, enhancing network resistance to bird losses.

Is resilience a unifying concept for the biological sciences?

There is increasing interest in applying resilience concepts at different scales of biological organization to address major interdisciplinary challenges from cancer to climate change. It is unclear, however, whether resilience can be a unifying concept consistently applied across the breadth of the biological sciences, or whether there is limited capacity for integration. In this review, we draw on literature from molecular biology to community ecology to ascertain commonalities and shortcomings in how resilience is measured and interpreted. Resilience is studied at all levels of biological organization, although the term is often not used. There is a suite of resilience mechanisms conserved across biological scales, and there are tradeoffs that affect resilience. Resilience is conceptually useful to help diverse researchers think about how biological systems respond to perturbations, but we need a richer lexicon to describe the diversity of perturbations, and we lack widely applicable metrics of resilience.

Investigating the effects of acute and chronic stress on DNA damage.

A hallmark of the vertebrate stress response is a rapid increase in glucocorticoids and catecholamines; however, this does not mean that these mediators are the best, or should be the only, metric measured when studying stress. Instead, it is becoming increasingly clear that assaying a suite of downstream metrics is necessary in stress physiology. One component of this suite could be assessing double-stranded DNA damage (dsDNA damage), which has recently been shown to increase in blood with both acute and chronic stress in house sparrows (Passer domesticus). To further understand the relationship between stress and dsDNA damage, we designed two experiments to address the following questions: (1) how does dsDNA damage with chronic stress vary across tissues? (2) does the increase in dsDNA damage during acute stress come from one arm of the stress response or both? We found that (1) dsDNA damage affects tissues differently during chronic stress and (2) the hypothalamic-pituitary-adrenal axis influences dsDNA damage with acute stress, but the sympathetic-adreno-medullary system does not. Surprisingly, our data are not explained by studies on changes in hormone receptor levels with chronic stress, so the underlying mechanism remains unclear.

Quantifying phenological landmarks of migration shows nonuniform use of the Caribbean by shorebirds.

Of the boreal- and Arctic-breeding North American shorebirds that migrate south through the Caribbean, most individuals continue farther south. However, for many species, some individuals remain beyond the southbound migration period (i.e., throughout the temperate winter and/or summer). This variation among individuals adds complexity to observation data, obscures migration patterns, and could prevent the examination of the use of different Caribbean regions by various shorebird species during migration and in the nonmigratory seasons. Here, we present a novel method that leverages a well-established statistical approach (generalized additive models) to systematically identify migration phenology even for complex passage migrant species with individuals that remain beyond migration. Our method identifies the active migration period using derivatives of a fitted GAM and then calculates phenology metrics based on quantiles of that migration period. We also developed indices to quantify oversummering and overwintering patterns with respect to migration. We analyzed eBird data for 16 North American shorebird species as they traveled South through the insular Caribbean, identifying separate migratory patterns for Cuba, Puerto Rico, Guadeloupe, Aruba, Bonaire, Curaçao, and Trinidad and Tobago. Our results confirm past reports and provide additional detail on shorebird migration in the Caribbean, and identify several previously unpublished regional patterns. Despite Puerto Rico being farther north and closer to continental North America, most species reached Puerto Rico later than other regions, supporting a long-standing hypothesis that migration strategy (transcontinental vs. transoceanic) leads to geographic differences in migration timing. We also found distinct patterns of migration curves, with some regions and species consistently having either symmetrical or skewed curves; these differences in migration curve shape reflect different migration processes. Our novel method proved reliable and adaptable for most species and serves as a valuable tool for identifying phenological patterns in complex migration data, potentially unlocking previously intractable data.

A New Paradigm for Pandemic Preparedness.

Purpose of Review: Preparing for pandemics requires a degree of interdisciplinary work that is challenging under the current paradigm. This review summarizes the challenges faced by the field of pandemic science and proposes how to address them. Recent Findings: The structure of current siloed systems of research organizations hinders effective interdisciplinary pandemic research. Moreover, effective pandemic preparedness requires stakeholders in public policy and health to interact and integrate new findings rapidly, relying on a robust, responsive, and productive research domain. Neither of these requirements are well supported under the current system. Summary: We propose a new paradigm for pandemic preparedness wherein interdisciplinary research and close collaboration with public policy and health practitioners can improve our ability to prevent, detect, and treat pandemics through tighter integration among domains, rapid and accurate integration, and translation of science to public policy, outreach and education, and improved venues and incentives for sustainable and robust interdisciplinary work.

Testing the role of patch openness as a causal mechanism for apparent area sensitivity in a grassland specialist.

Area sensitivity, species being disproportionately present on larger habitat patches, has been identified in many taxa. We propose that some apparently area-sensitive species are actually responding to how open a habitat patch is, rather than to patch size. We tested this hypothesis for Bobolinks (Dolichonyx oryzivorus) by comparing density and occupancy to a novel openness index, patch area, and edge effects. Bobolink density and occupancy showed significant relationships with openness, but logistic models based on an openness occupancy threshold had greater explanatory power. Thresholds remained approximately consistent from June through August, and shifted to be more open in September. Variance partitioning supported the openness index as unique and relevant. We found no relationships between measures of body condition (body mass, body size, circulating corticosterone levels) and either openness or area. Our findings have implications for studies of area sensitivity, especially with regards to inconsistencies reported within species: specifically, (1) whether or not a study finds a species to be area sensitive may depend on whether small, open sites were sampled, and (2) area regressions were sensitive to observed densities at the largest sites, suggesting that variation in these fields could lead to inconsistent area sensitivity responses. Responses to openness may be a consequence of habitat selection mediated by predator effects. Finally, openness measures may have applications for predicting effects of habitat management or development, such as adding wind turbines, in open habitat.

Identifying anomalous reports of putatively extinct species and why it matters.

As species become very rare and approach extinction, purported sightings can stir controversy, especially when scarce management resources are at stake. We used quantitative methods to identify reports that do not fit prior sighting patterns. We also examined the effects of including records that meet different evidentiary standards on quantitative extinction assessments for four charismatic bird species that might be extinct: Eskimo Curlew (Numenius borealis), Ivory-billed Woodpecker (Campephilus principalis), Nukupu'u (Hemignathus lucidus), and O'ahu 'Alauahio (Paroreomyza maculata). For all four species the probability of there being a valid sighting today, given the past pattern of verified sightings, was estimated to be very low. The estimates of extinction dates and the chance of new sightings, however, differed considerably depending on the criteria used for data inclusion. When a historical sighting record lacked long periods without sightings, the likelihood of new sightings declined quickly with time since the last confirmed sighting. For species with this type of historical record, therefore, new reports should meet an especially high burden of proof to be acceptable. Such quantitative models could be incorporated into the International Union for Conservation of Nature's Red List criteria to set evidentiary standards required for unconfirmed sightings of "possibly extinct" species and to standardize extinction assessments across species.

Identification of priority shorebird conservation areas in the Caribbean.

Despite being geographically central to the Atlantic Americas Flyway for migratory birds, the Caribbean is often overlooked or underappreciated when addressing the conservation of North American shorebirds. To our knowledge, this is the first Caribbean-wide assessment of shorebird use in the region. We analyzed 211,013 shorebird species observations in the insular Caribbean from 2010-2019, representing 78,794 eBird checklists and cumulative total of 2.1 million shorebirds of 45 species. We conclude that priority areas for shorebird conservation include Humedal Sur de Pinar del Río (Humedal Sur de Los Palacios) in Cuba, and Monte Cristi in the Dominican Republic as they each likely support more than 20,000 shorebirds annually, and they host large abundances of geographic populations for particular taxa. Specifically, the former site hosts >10% of Short-billed Dowitchers (Limnodromus griseus griseus/hendersoni), and >1% of Black-bellied Plovers (Pluvialis squatarola cynosurae) and Wilson's Plovers (Charadrius wilsonia wilsonia), while the latter site supports large numbers of Black-necked Stilts (Himantopus mexicanus). We also identified at least 15 additional sites that likely cross the 1% population threshold for one or more shorebird taxa. These sites may qualify for special international designations such as Important Bird and Biodiversity Areas or as part of the Western Hemisphere Shorebird Reserve Network; 11 of the 17 sites we identified do not hold either of these titles. Data on subspecific or geographic distributions of three species, Snowy Plover (C. nivosus), Black-necked Stilt, and Killdeer (C. vociferous), are insufficient to reveal if the sites with the highest abundances were mostly comprised of Caribbean populations or migrants, but the limited information suggests that they also likely exceed 1% thresholds on several islands. Based on our results, we recommend more extensive systematic surveys of shorebirds in the Caribbean, including research on turnover rates and movements between islands, as well as assimilation of shorebird survey data not yet included in the eBird portal.

Non-parallel changes in songbird migration timing are not explained by changes in stopover duration.

Shifts in the timing of animal migration are widespread and well-documented; however, the mechanism underlying these changes is largely unknown. In this study, we test the hypothesis that systematic changes in stopover duration-the time that individuals spend resting and refueling at a site-are driving shifts in songbird migration timing. Specifically, we predicted that increases in stopover duration at our study site could generate increases in passage duration-the number of days that a study site is occupied by a particular species-by changing the temporal breadth of observations and vise versa. We analyzed an uninterrupted 46-year bird banding dataset from Massachusetts, USA using quantile regression, which allowed us to detect changes in early-and late-arriving birds, as well as changes in passage duration. We found that median spring migration had advanced by 1.04 days per decade; that these advances had strengthened over the last 13 years; and that early-and late-arriving birds were advancing in parallel, leading to negligible changes in the duration of spring passage at our site (+0.07 days per decade). In contrast, changes in fall migration were less consistent. Across species, we found that median fall migration had delayed by 0.80 days per decade, and that changes were stronger in late-arriving birds, leading to an average increase in passage duration of 0.45 days per decade. Trends in stopover duration, however, were weak and negative and, as a result, could not explain any changes in passage duration. We discuss, and provide some evidence, that changes in population age-structure, cryptic geographic variation, or shifts in resource availability are consistent with increases in fall passage duration. Moreover, we demonstrate the importance of evaluating changes across the entire phenological distribution, rather than just the mean, and stress this as an important consideration for future studies.

Feather corticosterone does not correlate with environmental stressors or body condition in an endangered waterbird.

Physiological metrics are becoming popular tools for assessing individual condition and population health to inform wildlife management and conservation decisions. Corticosterone assays can provide information on how animals cope with individual and habitat-level stressors, and the recent development of feather assays is an exciting innovation that could yield important insights for conservation of wild birds. Due to the widespread enthusiasm for feather corticosterone as a potential bioindicator, studies are needed to assess the ability of this technique to detect meaningful differences in physiological stress across a variety of stressor types and intensities. We examined feather corticosterone from 144 individuals among the 13 known breeding populations of Hawaiian gallinule (Gallinula galeata sandvicensis), an endangered waterbird, on the island of O'ahu. These ecologically independent subpopulations are known to have low genetic connectivity and movement rates and differ largely across a number of important conditions, including level of predator management, human disturbance, proximity to urban development and conspecific population density. This system is well suited for assessing the performance of feather corticosterone as a bioindicator of different known habitat-level threats common to this and many other conservation-reliant species. We found no statistically significant relationship between feather corticosterone and level of predator control, level of human disturbance, gallinule population density, percent urban cover or body condition across all sites despite the substantial difference in stressor magnitude in our dataset. We did find that gallinules in habitats with larger population densities were in worse body condition. These findings suggest that feather corticosterone is not a consistent indicator of anthropogenic impacts on populations. Furthermore, they suggest that feather corticosterone may be a poor bioindicator of known habitat-level threats for Hawaiian gallinules and that it should be used with caution in other avian taxa of conservation concern.

Goodness of fit of probability distributions for sightings as species approach extinction.

Estimating the probability that a species is extinct and the timing of extinctions is useful in biological fields ranging from paleoecology to conservation biology. Various statistical methods have been introduced to infer the time of extinction and extinction probability from a series of individual sightings. There is little evidence, however, as to which of these models provide adequate fit to actual sighting records. We use L-moment diagrams and probability plot correlation coefficient (PPCC) hypothesis tests to evaluate the goodness of fit of various probabilistic models to sighting data collected for a set of North American and Hawaiian bird populations that have either gone extinct, or are suspected of having gone extinct, during the past 150 years. For our data, the uniform, truncated exponential, and generalized Pareto models performed moderately well, but the Weibull model performed poorly. Of the acceptable models, the uniform distribution performed best based on PPCC goodness of fit comparisons and sequential Bonferroni-type tests. Further analyses using field significance tests suggest that although the uniform distribution is the best of those considered, additional work remains to evaluate the truncated exponential model more fully. The methods we present here provide a framework for evaluating subsequent models.

Exogenous and endogenous corticosterone alter feather quality.

We investigated how exogenous and endogenous glucocorticoids affect feather replacement in European starlings (Sturnus vulgaris) after approximately 56% of flight feathers were removed. We hypothesized that corticosterone would retard feather regrowth and decrease feather quality. After feather regrowth began, birds were treated with exogenous corticosterone or sham implants, or endogenous corticosterone by applying psychological or physical (food restriction) stressors. Exogenous corticosterone had no impact on feather length and vane area, but rectrices were lighter than controls. Exogenous corticosterone also decreased inter-barb distance for all feathers and increased barbule number for secondaries and rectrices. Although exogenous corticosterone had no affect on rachis tensile strength and stiffness, barbicel hooking strength was reduced. Finally, exogenous corticosterone did not alter the ability of Bacillus licheniformis to degrade feathers or affect the number of feathers that failed to regrow. In contrast, endogenous corticosterone via food restriction resulted in greater inter-barb distances in primaries and secondaries, and acute and chronic stress resulted in greater inter-barb distances in rectrices. Food-restricted birds had significantly fewer barbules in primaries than chronic stress birds and weaker feathers compared to controls. We conclude that, although exogenous and endogenous corticosterone had slightly different effects, some flight feathers grown in the presence of high circulating corticosterone are lighter, potentially weaker, and with altered feather micro-structure.

The corticosterone stress response and mercury contamination in free-living tree swallows, Tachycineta bicolor.

We determined mercury concentrations in tree swallows, Tachycineta bicolor, from Massachusetts and Maine with different levels of contamination. Baseline and stress-induced plasma corticosterone concentrations from adults and nestlings (Massachusetts only) were compared with mercury concentrations. In Massachusetts, adult baseline corticosterone was negatively correlated with blood mercury, but showed a nearly-significant positive correlation with feather mercury. There was a negative relationship between baseline corticosterone and blood mercury in nestlings and between baseline corticosterone and egg mercury. There was no relationship between mercury and stress-induced corticosterone in any of the groups, or with baseline corticosterone in Maine sites where mercury levels were lower. The findings suggest blood and egg mercury may be a better indicator of current condition than feather mercury. Further, mercury contamination may not alter stress-induced corticosterone concentrations in tree swallows but appears to have a significant impact on baseline circulating corticosterone.

A half-century of changes in migratory landbird numbers along coastal Massachusetts.

We analyzed data from across five decades of passerine bird banding at Manomet in Plymouth, Massachusetts, USA. This included 172,609 captures during spring migration and 253,265 during fall migration, from 1969 to 2015. Migration counts are prone to large interannual variation and trends are often difficult to interpret, but have the advantage of sampling many breeding populations in a single locale. We employed a Bayesian state-space modeling approach to estimate patterns in abundance over time while accounting for observation error, and a hierarchical clustering method to identify species groups with similar trends over time. Although continent-wide there has been an overall decrease in landbird populations over the past 40 years, we found a variety of patterns in abundance over time. Consistent with other studies, we found an overall decline in numbers of birds in the aggregate, with most species showing significant net declines in migratory cohort size in spring, fall, or both (49/73 species evaluated). Other species, however, exhibited different patterns, including abundance increases (10 species). Even among increasing and declining species, the specific trends varied in shape over time, forming seven distinct clusters in fall and ten in spring. The remaining species followed largely independent and irregular pathways. Overall, life-history traits (dependence on open habitat, nesting on or near the ground, migratory strategy, human commensal, spruce budworm specialists) did a poor job of predicting species groupings of abundance patterns in both spring and fall, but median date of passage was a good predictor of abundance trends during spring (but not fall) migration. This suggests that some species with very similar patterns of abundance were unlikely to be responding to the same environmental forces. Changes in abundance at this banding station were generally consistent with BBS trend data for the same geographic region.