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Water crises and endangered salmon are pressing environmental concerns influencing restoration decisions in the western United States. When instream restoration necessitates initial loss of riparian cover to restore floodplain function, a short-term goal to minimize harm to riparian-associated wildlife is a worthwhile benchmark. From 2012 to 2015, we examined short-term restoration success, as measured by territory characteristics and reproductive success in restored and reference sites, for 3 riparian bird species (Song Sparrow [Melospiza melodia], Yellow-breasted Chat [Icteria virens], and Yellow Warbler [Setophaga petechia]) along a 64 km stretch of the Trinity River, California. Territory size had the highest relative variable importance in sets of candidate models explaining territory density for all 3 species, and was inversely related to territory density for each. The effect of site type (i.e. restored vs. reference) in explaining territory density was least for Song Sparrow, greater for Yellow Warbler (for which density was 1.4 times greater on reference sites), and greatest for Yellow-breasted Chat (which were more than twice as dense on reference sites). While territory density and mean territory size were inversely related, we found no relationship between territory density or site type and mean productivity per nest, and nest success did not differ between restored and reference sites for any species. In combination, these results suggest that restoration has achieved short-term success as measured by reproductive success, but has not yet been fully successful in supporting similar territory densities as reference sites. In order to determine whether long-term restoration goals are fully achieved, future research should continue to measure density of the 3 focal species as vegetation on the replanted floodplains matures.

Male song sparrows (Melospiza melodia) are territorial year-round; however, neuroendocrine responses to simulated territorial intrusion (STI) differ between breeding (spring) and non-breeding seasons (autumn). In spring, exposure to STI leads to increases in luteinizing hormone and testosterone, but not in autumn. These observations suggest that there are fundamental differences in the mechanisms driving neuroendocrine responses to STI between seasons. Microarrays, spotted with EST cDNA clones of zebra finch, were used to explore gene expression profiles in the hypothalamus after territorial aggression in two different seasons. Free-living territorial male song sparrows were exposed to either conspecific or heterospecific (control) males in an STI in spring and autumn. Behavioral data were recorded, whole hypothalami were collected, and microarray hybridizations were performed. Quantitative PCR was performed for validation. Our results show 262 cDNAs were differentially expressed between spring and autumn in the control birds. There were 173 cDNAs significantly affected by STI in autumn; however, only 67 were significantly affected by STI in spring. There were 88 cDNAs that showed significant interactions in both season and STI. Results suggest that STI drives differential genomic responses in the hypothalamus in the spring vs. autumn. The number of cDNAs differentially expressed in relation to season was greater than in relation to social interactions, suggesting major underlying seasonal effects in the hypothalamus which may determine the differential response upon social interaction. Functional pathway analyses implicated genes that regulate thyroid hormone action and neuroplasticity as targets of this neuroendocrine regulation.

Understanding the evolutionary dynamics of inbreeding and inbreeding depression requires unbiased estimation of inbreeding depression across diverse mating systems. However, studies estimating inbreeding depression often measure inbreeding with error, for example, based on pedigree data derived from observed parental behavior that ignore paternity error stemming from multiple mating. Such paternity error causes error in estimated coefficients of inbreeding (f) and reproductive success and could bias estimates of inbreeding depression. We used complete \"apparent\" pedigree data compiled from observed parental behavior and analogous \"actual\" pedigree data comprising genetic parentage to quantify effects of paternity error stemming from extra-pair reproduction on estimates of f, reproductive success, and inbreeding depression in free-living song sparrows (Melospiza melodia). Paternity error caused widespread error in estimates of f and male reproductive success, causing inbreeding depression in male and female annual and lifetime reproductive success and juvenile male survival to be substantially underestimated. Conversely, inbreeding depression in adult male survival tended to be overestimated when paternity error was ignored. Pedigree error stemming from extra-pair reproduction therefore caused substantial and divergent bias in estimates of inbreeding depression that could bias tests of evolutionary theories regarding inbreeding and inbreeding depression and their links to variation in mating system.

In many songbirds, individuals have repertoires of multiple song types, some of which may be shared with others in the local area. Hypotheses about the evolution of song repertoires differ as to whether selection acts primarily on repertoire size itself or the ability to match songs of neighbours. We used a 16-channel acoustic location system to record neighbourhoods of song sparrows (Melospiza melodía melodía) during the dawn chorus. We asked whether males sing all songs with similar frequency as predicted by the Repertoire Size Hypothesis, whether males preferentially sing highly shared songs as predicted by the General Sharing Hypothesis, or whether use of highly shared songs is associated with phenotype as predicted by the Conditional Sharing Hypothesis. Contrary to the Repertoire Size Hypothesis, most males did not sing all songs equally often. Contrary to the General Sharing Hypothesis, we found no general tendency to overproduce highly shared songs. The degree to which males overproduced highly shared songs was repeatable across days, indicating consistent individual differences, and varied across neighbourhoods. Moreover, and consistent with the Conditional Sharing Hypothesis, older males were more likely to overproduce highly shared songs. If highly shared song is a conventional signal of aggression, with the threat of receiver retaliation maintaining honesty, older males may be more willing or able to risk conflict. Alternatively, males may learn which songs are effective signals for an area. Finally, age-related variation in vocal performance may shape the adaptive value of highly shared song.

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 .

Many invading species impact native species through predation, parasitism or competition, while others affect natives indirectly by restructuring their habitat. How invasive plants affect native animals, and to what extent native animals respond to changes in their habitat and the novel selection pressures that follow, is not well known. We investigated the impacts of a habitat-altering invader, the Atlantic cordgrass Spartina alterniflora, on the nesting success of Alameda song sparrows (Melospiza melodia pusillula), a California Species of Special Concern, in tidal marshes in three sites in San Francisco Bay. Date of laying was the most influential factor in determining daily survival rate of nests, but whether the nest was placed in exotic Spartina was the most important ecological variable. Nests placed in exotic Spartina had a success rate that was 30% lower than those placed in native vegetation. Nests in exotic Spartina were significantly more likely to fail due to tidal flooding than were nests placed in native vegetation, because the densest stands of exotic Spartina occurred at significantly lower elevations relative to the tides. Our results suggest that exotic Spartina may be an ecological trap for song sparrows in San Francisco Bay, attracting birds to nest sites that are often destroyed by tidal flooding.

Predator effects on prey demography have traditionally been ascribed solely to direct killing in studies of population ecology and wildlife management. Predators also affect the prey's perception of predation risk, but this has not been thought to meaningfully affect prey demography. We isolated the effects of perceived prédation risk in a free-living population of song sparrows by actively eliminating direct predation and used playbacks of predator calls and sounds to manipulate perceived risk. We found that the perception of predation risk alone reduced the number of offspring produced per year by 40%. Our results suggest that the perception of predation risk is itself powerful enough to affect wildlife population dynamics, and should thus be given greater consideration in vertebrate conservation and management.

We investigated the division of parental care to nestlings in Melospiza melodia melodia (an eastern subspecies of Song Sparrow) by examining parental provisioning rates (number of trips/nestling/h) over two consecutive broods. Song Sparrows are a territorial, socially monogamous passerine with pairs raising up to three broods together over the breeding season. We obtained provisioning rate data for nine pairs over a total of 12 broods (7 first broods, 5 second broods) on at least some of days (stages) 2-3, 5-6, and 8-9 of the nestling period. Of these, we obtained provisioning data over all three nestling stages for six different pairs (five first broods, one second brood). Males and females provisioned young at similar rates throughout the nestling period. Provisioning rates did not differ significantly between first and second broods, but increased significantly as the nestlings aged, reflecting the increased offspring feeding demands. Offspring provisioning does appear to be truly biparental in this eastern subspecies of Song Sparrow.

In jawed vertebrates, genes of the major histocompatibility complex (MHC) play a key role in immunity by encoding cell-surface proteins that recognize and bind non-self antigens. High variability at MHC suggests that these loci may also function in social signalling such as mate choice and kin recognition. This requires that MHC genotype covaries with some perceptible phenotypic trait. In mammals and fish, MHC is signalled chemically through volatile and non-volatile peptide odour cues, facilitating MHC-dependent mate choice and other behaviours. In birds, despite evidence for MHC-dependent mating, candidate mechanisms for MHC signalling remain largely unexplored. However, feather preen wax has recently been implicated as a potential source of odour cues. We examined whether the chemical composition of preen wax correlates with MHC class IIβ genotypes of wild song sparrows (Melospiza melodia). Pairwise chemical distance reflected amino acid distance at MHC for male–female dyads, although not for same-sex dyads. Chemical diversity did not reflect MHC diversity. We used gas chromatography–mass spectrometry (GC-MS) to characterize preen wax compounds, and identified four wax esters that best reflect MHC similarity. Provided songbirds can detect variation in preen wax composition, this cue may allow individuals to assess MHC compatibility of potential mates.

Urbanization reflects a major form of environmental change impacting wild birds globally. Whereas urban habitats may provide increased availability of water, some food items, and reduced predation levels compared to rural, they can also present novel stressors including increased light at night, ambient noise, and reduced nutrient availability. Urbanization can also alter levels of brood parasitism, with some host species experiencing elevated levels of brood parasitism in urban areas compared to rural areas. Though the demographic and behavioral consequences of urbanization and brood parasitism have received considerable attention, their consequences for cellular‐level processes are less understood. Telomeres provide an opportunity to understand the cellular consequences of different environments as they are a well‐established metric of biological state that can be associated with residual lifespan, disease risk, and behavior, and are known to be sensitive to environmental conditions. Here we examine the relationships between urbanization, brood parasitism, and blood telomere lengths in adult and nestling song sparrows Melospiza melodia. Song sparrows are a North American songbird found in both urban and rural habitats that experience high rates of brood parasitism by brown‐headed cowbirds Molothrus ater in the urban, but not the rural, sites in our study system. Among adults and nestlings from non‐parasitized nests, we found no differences in relative telomere lengths between urban and rural habitats. However, among urban nestlings, the presence of a brood parasite in the nest was associated with significantly shorter relative telomere lengths compared to when a brood parasite was absent. Our results suggest a novel, indirect, impact of urbanization on nestling songbirds through the physiological impacts of brood parasitism.