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The large uncertainty surrounding the future effects of sea-level rise and other aspects of climate change on tidal marsh ecosystems exacerbates the difficulty in planning effective conservation and restoration actions. We addressed these difficulties in the context of large-scale wetland restoration activities underway in the San Francisco Estuary (Suisun, San Pablo and San Francisco Bays). We used a boosted regression tree approach to project the future distribution and abundance of five marsh bird species (through 2110) in response to changes in habitat availability and suitability as a result of projected sea-level rise, salinity, and sediment availability in the Estuary. To bracket the uncertainty, we considered four future scenarios based on two sediment availability scenarios (high or low), which varied regionally, and two rates of sea-level rise (0.52 or 1.65 m/100 yr). We evaluated three approaches for using model results to inform the selection of potential restoration projects: (1) Use current conditions only to prioritize restoration. (2) Use a single future scenario (among the four referred to above) in combination with current conditions to select priority restoration projects. (3) Combine current conditions with all four future scenarios, while incorporating uncertainty among future scenarios into the selection of restoration projects. We found that simply using current conditions resulted in the poorest performing restoration projects selected in terms of providing habitat for tidal marsh birds in light of possible future scenarios. The most robust method for selecting restoration projects, the \"combined\" strategy, used projections from all future scenarios with a discounting of areas with high levels of variability among future scenarios. We show that uncertainty about future conditions can be incorporated in site prioritization algorithms and should motivate the selection of adaptation measures that are robust to uncertain future conditions. These results and data have been made available via an interactive decision support tool at www.prbo.org/sfbayslr .

Eastern equine encephalitis virus (EEEV; family Togaviridae, genus Alphavirus) is a mosquito-borne pathogen found in eastern North America that causes severe disease in humans and horses. The mosquito Culiseta melanura (Coquillett) (Diptera: Culicidae) is the primary enzootic vector of EEEV throughout eastern North America while several mosquito species belonging to diverse genera serve as bridge vectors. The ecology of EEEV differs between northern and southern foci, with respect to phenology of outbreaks, important vertebrate hosts, and bridge vector species. Active transmission is limited to roughly half of the year in northern foci (New York, New Hampshire, Massachusetts, Connecticut), while year-round transmission occurs in the southeastern region (particularly Florida). Multiple phylogenetic analyses indicate that EEEV strains circulating in northern foci are likely transported from southern foci by migrating birds. Bird species that overwinter or migrate through Florida, are bitten by Cs. melanura in late spring, and arrive at northern breeding grounds in May are the most likely candidates to disperse EEEV northward. Available data indicate that common yellowthroat and green heron satisfy these criteria and could serve as virus dispersers. Understanding the factors that drive the phenology of Cs. melanura reproduction in the south and the timing of avian migration from southern foci could provide insight into how confluence of these biological phenomena shapes outbreaks of EEE throughout its range. This information could be used to develop models predicting the likelihood of outbreaks in a given year, allowing vector control districts to more efficiently marshal resources necessary to protect their stakeholders.

Seasonal migration has fascinated scientists and natural historians for centuries. While the genetic basis of migration has been widely studied across different taxa, there is little consensus regarding which genomic regions play a role in the ability to migrate and whether they are similar across species. Here, we examine the genetic basis of intraspecific variation within and between distinct migratory phenotypes in a songbird. We focus on the Common Yellowthroat (Geothlypis trichas) as a model system because the polyphyletic origin of eastern and western clades across North America provides a strong framework for understanding the extent to which there has been parallel or convergent evolution in the genes associated with migratory behavior. First, we investigate genome-wide population genetic structure in the Common Yellowthroat in 196 individuals collected from 22 locations across breeding range. Then, to identify candidate genes involved in seasonal migration, we identify signals of putative selection in replicate comparisons between resident and migratory phenotypes within and between eastern and western clades. Overall, we find wide-spread support for parallel evolution at the genic level, particularly in genes that mediate biological timekeeping. However, we find little evidence of parallelism at the individual SNP level, supporting the idea that there are multiple genetic pathways involved in the modulation of migration.

Ornaments are thought to honestly signal individual quality to potential mates. Individual quality may include the ability to cope with stress through the production of glucocorticoids (GCs), such as corticosterone (CORT), which help to redirect resources from growth or reproduction to survival during an acute stress response. However, elevated levels of CORT may also increase oxidative stress and reduce immune function. Thus, an important question is whether high‐quality individuals, with more elaborate ornaments, signal their ability to produce a strong stress response and mitigate some of the negative effects of doing so through higher resistance to oxidative stress. We tested whether ornamentation and resistance to oxidative stress were related to the increase in CORT during an acute stress response in a warbler, the common yellowthroat (Geothlypis trichas). Males in this species have two plumage ornaments, a black (eumelanin‐based) facial mask and a yellow (carotenoid‐based) bib. We measured the increase in CORT in response to the stress of capture and handling. Males with more elaborate ornaments (larger masks and more colourful bibs) had a greater increase in CORT during an acute stress response. However, the increase in CORT was not related to resistance to oxidative stress. These results suggest that both melanin‐ and carotenoid‐based plumage ornaments can signal the ability of a male to cope with stressors through a greater increase in CORT. Thus, the association between ornamentation and stress‐induced CORT is not likely due to a mechanism specific to a particular colour (melanin or carotenoid), but instead may result from more general interactions between CORT and health or condition. A plain language summary is available for this article. Plain Language Summary

Declines in populations of birds that breed in disturbance-dependent early-successional forest have largely been ascribed to habitat loss. Clearcutting is an efficient and effective means for creating early-successional vegetation; however, negative public perceptions of clearcutting and the small parcel size typical of private forested land in much of the eastern United States make this practice impractical in many situations. Group selection harvests, where groups of adjacent trees are removed from a mature forest matrix, may be more acceptable to the public and could provide habitat for shrubland birds. Although some shrubland bird species that occupy clearcuts are scarce or absent from smaller patches created by group selection, some of these smaller patches support shrubland species of conservation concern. The specific factors affecting shrubland bird occupancy of these smaller patches, such as habitat structure, patch area, and landscape context, are poorly understood. We sampled birds in forest openings ranging 0.02–1.29 ha to identify species-specific minimum-area habitat requirements and other factors affecting shrubland birds. We modeled bird occurrence in relation to microhabitat-, patch-, and landscape-level variables using occupancy models. The minimum-area requirements for black-and-white warblers (Mniotilta varia), common yellowthroats (Geothlypis trichas), chestnut-sided warblers (Setophaga pensylvanica), eastern towhees (Pipilo erythrophthalmus), and gray catbirds (Dumetella carolinensis) were ≤0.23 ha, whereas indigo buntings (Passerina cyanea) and prairie warblers (S. discolor) required openings of 0.56 ha and 1.11 ha, respectively. Notably, prairie warblers were more likely to occur in openings closer to large patches of habitat such as powerline corridors, even if those openings were small in size. We concluded that, despite their inability to support the entire suite of shrubland species, small forest openings can provide habitat for several species of conservation concern if proper attention is given to promoting suitable microhabitat, patch, and landscape characteristics.

Cross‐ecosystem subsidies move substantial amounts of nutrients between ecosystems. Emergent aquatic insects are a particularly important prey source for riparian songbirds but may also move aquatic contaminants, such as mercury (Hg), to riparian food webs. While many studies focus on species that eat primarily emergent aquatic insects, we instead study riparian songbirds with flexible foraging strategies, exploiting both aquatic and terrestrial prey sources. The goal in this study is to trace reliance on aquatic prey sources and correlate it to Hg concentrations in common riparian arachnids (Families Tetragnathidae, Opiliones, and Salticidae) and songbirds (Common Yellowthroat Geothlypis trichas, Spotted Towhee Pipilo maculatus, Swainson's Thrush Catharus ustulatus, Song Sparrow Melospiza melodia, and Yellow Warbler Setophaga petechia). We used stable isotopes of δ13C and δ15N and Bayesian mixing models in MixSIAR to determine the reliance of riparian predators on aquatic prey sources. Using mixed effects models, we found that arachnid families varied in their reliance on aquatic prey sources. While songbird species varied in their reliance on aquatic prey sources, songbirds sampled earlier in the season consistently relied more on aquatic prey sources than those sampled later in the season. For both arachnids and songbirds, we found a positive correlation between the amount of the aquatic prey source in their diet and their Hg concentrations. While the seasonal pulse of aquatic prey to terrestrial ecosystems is an important source of nutrients to riparian species, our results show that aquatic prey sources are linked with higher Hg exposure. For songbirds, reliance on aquatic prey sources early in the breeding season (and subsequent higher Hg exposure) coincides with timing of egg laying and development, both of which may be impacted by Hg exposure. To understand how exploiting emergent aquatic prey sources could also expose the riparian community to aquatic‐based contaminants, we used stable isotopes of δ13C and δ15N in a MixSIAR Bayesian mixing model to trace emergent aquatic prey in riparian predators (songbirds and arachnids). We determined that individual reliance on aquatic prey was positively correlated with mercury exposure, with songbirds relying more in aquatic prey early in the season. Our results show the seasonal pulse of aquatic prey to terrestrial ecosystems is likely an important source of nutrients to riparian species but may also drive season‐dependent exposure to aquatic contaminants.

In many species, both males and females possess sexual signals, but most research focuses on understanding signal expression in males. Females are often assumed to possess signals as a non-functional by-product of selection on males, but increasing evidence demonstrates functional explanations for variation in female signals. Theory suggests that—for many bird species—differences in long-term fitness associated with female signaling are more likely to be driven by variation in offspring quality than quantity, but research paradigms developed for studying male signals have primarily focused on counting offspring produced. Here, we tested the hypothesis that female ornamentation reliably signals the ability to incubate effectively. We used temperature loggers placed in the nest of common yellowthroat warblers (Geothlypis trichas) to record incubation behavior across multiple breeding attempts. Incubation bout length and the onset of daily activity were highly variable between females, but repeatable within females across multiple nesting attempts. Females with longer bouts and later onset of activity had higher hatching success. Wing length and plumage coloration were not related to incubation length or onset of activity, but were correlated with the total percentage of time spent on the nest each day. However, there was only a trend for repeatability in percentage of time spent on the nest and this measure was not correlated with any metrics of offspring quality or hatching success that we recorded. Therefore, we did not find any single aspect of incubation behavior that was (i) consistent, (ii) related to nestling quality or success, and (iii) signaled by ornamentation. Our results demonstrate the importance of variation in incubation behavior, but also suggest that ornaments are of limited utility as a signal of incubation ability in this species. Nevertheless, our study highlights the need to explore alternative fitness proxies in order to understand variation in female ornamentation.

Summary Male ornaments are hypothesized to signal the ability of males to produce an effective immune response without extensive oxidative stress and damage to DNA. We examined this hypothesis in male common yellowthroats (Geothlypis trichas), which have two ornaments, a black (eumelanin‐based) facial mask and a yellow (carotenoid‐based) bib. In our study population, only the black mask is sexually selected. As predicted by the oxidative stress hypothesis, males with larger black masks were more resistant to oxidative stress, as measured by an in vitro assay of the resistance of erythrocytes to haemolysis by free radicals. Furthermore, males with larger masks also tended to have lower levels of glutathione, which was predicted because glutathione inhibits eumelanin production. In contrast, mask size was not related to absolute levels of oxidative stress measured in the plasma. Although the yellow bib is not under sexual selection in our population, males with larger bibs and feathers with greater carotenoid chroma had lower levels of oxidative stress. The oxidative stress hypothesis was first proposed for carotenoid‐based ornaments. However, our results suggest that, even in the same individuals, carotenoid and eumelanin‐based plumage ornaments may both signal the ability of males to resist or manage oxidative stress. Lay Summary

The Hamilton–Zuk hypothesis predicts that ornament expression is a signal of the ability of individuals to resist parasite infection. Thus, across a population (i.e. between-individuals) more ornamented individuals should have lower levels of parasitism. Numerous studies have tested this prediction and the results are mixed. One reason for these conflicting results may be that many studies have examined this relationship at the between-individual level, which may be affected by confounding factors such as selective mortality. Using within-subject centering we examined the relationship between male ornamentation and avian blood parasites at both the between- and within-individual levels. These relationships focus on differences in genetically-based resistance to parasites and the trade-off in resource allocation between parasite resistance and ornament expression within an individual, respectively. We studied male common yellowthroats Geothlypis trichas, which have two plumage ornaments, a yellow, carotenoid-based bib (throat and chest) and a black, melanin-based facial mask. Surprisingly, within-individuals, an increase in parasitism between years was associated with an increase in mask size and, potentially, greater concentration of carotenoids in the yellow feathers. This suggests that males may be able to tolerate an increase in parasitism and still increase ornament expression. In contrast, ornamentation was not related to parasitism at the between-individual level. Thus, our study revealed relationships between ornaments and parasitism at the withinindividual level that were not present at the between-individual level. Our results highlight the importance of examining both within- and between-individual relationships as correlations between variables, such as ornaments and parasites, may depend on the level of analysis (i.e. within- or between-individuals).

Female preference for older or more disease-resistant males are both possible outcomes of parasite-mediated sexual selection, but the extent to which infection alters the development of ornaments to yield signals of male age and health has rarely been explored. In a longitudinal study of 61 male common yellowthroats (Geothlypis trichas), age-related increases in the size of the melanin-based mask and carotenoid-based bib were not correlated among young males, likely owing to differences in how blood parasites affect ornament development. Infection with trypanosomes and hemosporidians in a male’s first breeding season was associated with slower growth of the mask; uninfected males attained large masks in their second breeding season, while infected males attained large masks in their third breeding season. In contrast, the bib size of males increased every year regardless of infection. As a consequence, different populations of males are identified by the largest ornaments—older males in the case of bib and a combination of older males and young, uninfected males in the case of mask. Although mask is thus the more informative trait with respect to male health, females prefer large bibs in our population. If infection is opportunistic, young, uninfected males may not possess good genes for parasite resistance but simply good luck, and it may benefit females to prefer older males who are more likely to have withstood prior episodes of selection. A “pure” signal of age may be a more reliable signal of resistance to parasites than an ornament whose expression is modulated by infection.