Complete mitochondrial genome MK992912 of Great Knot (Calidris tenuirostris) is a chimera with DNA from Pacific Golden Plover Pluvialis fulva (Aves: Charadriiformes)

A complete mitochondrial genome of Great Knot (Calidris tenuirostris), MK992912, was published by He and colleagues in 2020. Here we show that this mitogenome is actually a chimera containing DNA fragments of both C. tenuirostris (15,567 bp, 92.8%) and Pacific Golden Plover (Pluvialis fulva, 1208 bp, 7.2%). Detecting such errors is possible before publication if each sequenced fragment is separately analyzed phylogenetically before assembling the fragments into a single mitogenome. This mitogenome has been re-used in at least four phylogenies. The error is documented to avoid the perpetuation of erroneous sequence information in the literature.

Stopover habitat selection drives variation in the gut microbiome composition and pathogen acquisition by migrating shorebirds

Long-distance host movements play a major regulatory role in shaping microbial communities of their digestive tract. Here, we studied gut microbiota composition during seasonal migration in five shorebird species (Charadrii) that use different migratory (stopover) habitats. Our analyses revealed significant interspecific variation in both composition and diversity of gut microbiome, but the effect of host identity was weak. A strong variation in gut microbiota was observed between coastal and inland (dam reservoir and river valley) stopover habitats within species. Comparisons between host age classes provided support for an increasing alpha diversity of gut microbiota during ontogeny and an age-related remodeling of microbiome composition. There was, however, no correlation between microbiome and diet composition across study species. Finally, we detected high prevalence of avian pathogens, which may cause zoonotic diseases in humans (e.g. Vibrio cholerae) and we identified stopover habitat as one of the major axes of variation in the bacterial pathogen exposure risk in shorebirds. Our study not only sheds new light on ecological processes that shape avian gut microbiota, but also has implications for our better understanding of host-pathogen interface and the role of birds in long-distance transmission of pathogens.

Environmental factors influencing red knot (Calidris canutus islandica) departure times of relocation flights within the non-breeding period

Deciding when to depart on long-distance, sometimes global, movements can be especially important for flying species. Adverse weather conditions can affect energetic flight costs and navigational ability. While departure timings and conditions have been well-studied for migratory flights to and from the breeding range, few studies have focussed on flights within the non-breeding season. Yet in some cases, overwintering ranges can be large enough that ecological barriers, and a lack of resting sites en route, may resist movement, especially in unfavorable environmental conditions. Understanding the conditions that will enable or prohibit flights within an overwintering range is particularly relevant in light of climate change, whereby increases in extreme weather events may reduce the connectivity of sites. We tracked 495 (n = 251 in 2019; n = 244 in 2020) overwintering red knots (Calidris canutus islandica) in the Dutch Wadden Sea and investigated how many departed towards the UK (on westward relocation flights), which requires flying over the North Sea. For those that departed, we used a resource selection model to determine the effect of environmental conditions on the timing of relocation flights. Specifically, we investigated the effects of wind, rain, atmospheric pressure, cloud cover, and migratory timing relative to sunset and tidal cycle, which have all been shown to be crucial to migratory departure conditions. Approximately 37% (2019) and 36% (2020) of tagged red knots departed on westward relocation flights, indicating differences between individuals' space use within the overwintering range. Red knots selected for departures between 1 and 2.5 h after sunset, approximately 4 h before high tide, with tailwinds and little cloud cover. However, rainfall and changes in atmospheric pressure appear unimportant. Our study reveals environmental conditions that are important for relocation flights across an ecological barrier, indicating potential consequences of climate change on connectivity.

Spatial synchrony cascades across ecosystem boundaries and up food webs via resource subsidies

Cross-ecosystem subsidies are critical to ecosystem structure and function, especially in recipient ecosystems where they are the primary source of organic matter to the food web. Subsidies are indicative of processes connecting ecosystems and can couple ecological dynamics across system boundaries. However, the degree to which such flows can induce cross-ecosystem cascades of spatial synchrony, the tendency for system fluctuations to be correlated across locations, is not well understood. Synchrony has destabilizing effects on ecosystems, adding to the importance of understanding spatiotemporal patterns of synchrony transmission. In order to understand whether and how spatial synchrony cascades across the marine-terrestrial boundary via resource subsidies, we studied the relationship between giant kelp forests on rocky nearshore reefs and sandy beach ecosystems that receive resource subsidies in the form of kelp wrack (detritus). We found that synchrony cascades from rocky reefs to sandy beaches, with spatiotemporal patterns mediated by fluctuations in live kelp biomass, wave action, and beach width. Moreover, wrack deposition synchronized local abundances of shorebirds that move among beaches seeking to forage on wrack-associated invertebrates, demonstrating that synchrony due to subsidies propagates across trophic levels in the recipient ecosystem. Synchronizing resource subsidies likely play an underappreciated role in the spatiotemporal structure, functioning, and stability of ecosystems.

The published complete mitochondrial genome of Spotted Greenshank (Tringa guttifer) is a chimera with DNA from Red-necked Stint (Calidris ruficollis) (Aves: Charadriiformes)

A recently published complete mitochondrial genome of Spotted Greenshank (Tringa guttifer) was the first DNA sequence of this species (GenBank accession number MK905885, RefSeq number NC_044665; Liu et al. 2019, The complete mitochondrial genome of the Spotted Greenshank Tringa guttifer (Charadriiforemes [sic]: Charadriidae), Mitochondrial DNA Part B. 4:2353-2354). Here we show that this mitogenome is actually a chimera containing DNA fragments of both a Tringa sandpiper (presumably T. guttifer) and the Red-necked Stint (Calidris ruficollis). This mitogenome has been re-used in at least three phylogenies. The error is documented to avoid the perpetuation of erroneous sequence information in the literature.

An impact evaluation of conservation investments targeting long-distance migratory species

We evaluated the impact of a philanthropic program investing in the conservation of sites along the Pacific Americas Flyway, which spans >16,000 km of coastline and is used by millions of shorebirds. Using a quasi-experimental, mixed methods approach, we estimated what would have happened to shorebird populations at 17 wintering sites without the sustained and additional investment they received. We modeled shorebird populations across the entire flyway and at sites with and without investment. Combining shorebird abundance estimates with a land-cover classification model, we used the synthetic control method to create counterfactuals for shorebird trends at the treatment sites. We found no evidence of an overall effect across three outcome variables. Species- and site-level treatment effects were heterogeneous, with a few cases showing evidence of a positive effect, including a site with a high level of overall investment. Results suggest six shorebirds declined across the entire flyway, including at many Latin American sites. However, the percentage of flyway populations present at the sites remained stable, and the percentage at the treatment sites was higher (i.e., investment sites) than at control sites. Multiple mechanisms behind our results are possible, including that investments have yet to mitigate impacts and negative impacts at other sites are driving declines at the treatment sites. A limitation of our evaluation is the sole focus on shorebird abundance and the lack of data that prohibits the inclusion of other outcome variables. Monitoring infrastructure is now in place to design a more robust and a priori shorebird evaluation framework across the entire flyway. With this framework, it will prove easier to prioritize limited dollars to result in the most positive conservation outcomes.

Arriving late and lean at a stopover site is selected against in a declining migratory bird population

Loss and/or deterioration of refuelling habitats have caused population declines in many migratory bird species but whether this results from unequal mortality among individuals varying in migration traits remains to be shown. Based on 13 years of body mass and size data of great knots (Calidris tenuirostris) at a stopover site of the Yellow Sea, combined with resightings of individuals marked at this stopover site along the East Asian-Australasian Flyway, we assessed year to year changes in annual apparent survival rates, and how apparent survival differed between migration phenotypes (i.e. migration timing and fuel stores). The measurements occurred over a period of habitat loss and/or deterioration in this flyway. We found that the annual apparent survival rates of great knots rapidly declined from 2006 to 2018, late-arriving individuals with small fuel stores exhibiting the lowest apparent survival rate. There was an advancement in mean arrival date and an increase in the mean fuel load of stopping birds over the study period. Our results suggest that late-arriving individuals with small fuel loads were selected against. Thus, habitat loss and/or deterioration at staging sites may cause changes in the composition of migratory phenotypes at the population-level.

The Effects of Climate Change on the Nesting Phenology of Three Shorebird Species in the United States

Previous research suggests that a frequent response of organisms to the ongoing climate crisis is the adjustment of their reproductive timing or breeding phenology. Shorebirds may be especially vulnerable to increasing temperatures and precipitation, as many are migratory and depend on coastal habitats for wintering and breeding. These particular habitats could be at risk due to changes in climate, and nesting times often depend on food availability, which is often directly influenced by temperature. We investigated if clutch initiation dates (CID) for three shorebird species in the United States have become earlier over time with increasing temperatures and precipitation. We used nest records from Cornell's NestWatch program and various museum databases and weather station data from the National Oceanic and Atmospheric Administration. We found evidence that CIDs have become earlier over time, though this was only a significant factor for one species. While temperature in our study areas has increased significantly over time, precipitation changes were more variable and not always significantly predicted by time. We found evidence that one species may be responding to increasing temperatures by nesting earlier, but there was no support for our hypothesis that CID has changed due to changes in precipitation for any species. Results varied for each species, indicating the importance of further studies on shorebirds as the effects of climate change on their nesting phenology may not be fully realized and will likely depend on the species' biology and distribution.

Metal Levels in Delaware Bay Horseshoe Crab Eggs from the Surface Reflect Metals in Egg Clutches Laid beneath the Sand

Understanding variations in metal levels in biota geographically and under different environmental conditions is essential to determining risk to organisms themselves and to their predators. It is often difficult to determine food chain relationships because predators may eat several different prey types. Horseshoe crab (Limulus polyphemus) eggs form the basis for a complex food web in Delaware Bay, New Jersey, USA. Female horseshoe crabs lay thumb-sized clutches of eggs, several cm below the surface, and often dislodge previously laid eggs that are brought to the surface by wave action, where they are accessible and critical food for migrant shorebirds. This paper compares metal and metalloid (chromium [Cr], cadmium [Cd], lead [Pb], mercury [Hg], arsenic [As] and selenium [Se]) concentrations in horseshoe crab eggs collected on the surface with concentrations in eggs from clutches excavated from below the sand surface, as well as examining metals in eggs from different parts of the Bay. The eggs were all collected in May 2019, corresponding to the presence of the four main species of shorebirds migrating through Delaware Bay. These migrating birds eat almost entirely horseshoe crab eggs during their stopover in Delaware Bay, and there are differences in the levels of metals in blood of different shorebirds. These differences could be due to whether they have access to egg clutches below sand (ruddy turnstones, Arenaria interpres) or only to eggs on the surface (the threatened red knot [Calidris canutus rufa] and other species of shorebirds). Correlations between metals in clutches were also examined. Except for As and Cd, there were no significant differences between the metals in crab egg clutches and eggs on the surface that shorebirds, gulls, and other predators eat. There were significant locational differences in metal levels in horseshoe crab eggs (except for Pb), with most metals being highest in the sites on the lower portion of Delaware Bay. Most metals in crab eggs have declined since studies were conducted in the mid-1990s but were similar to levels in horseshoe crab eggs in 2012. The data continue to provide important monitoring and assessment information for a keystone species in an ecosystem that supports many species, including threatened and declining shorebird species during spring migration.

Does experimental seaweed cultivation affect benthic communities and shorebirds? Applications for extensive aquaculture

Extensive seaweed aquaculture is a growing industry expected to expand globally due to its relatively low impact and benefits in the form of ecosystem services. However, seaweeds are ecosystem engineers that may alter coastal environments by creating complex habitats on previously bare mudflats. These changes may scale up to top-consumers, particularly migratory shorebirds, species of conservation concern that regulate trophic webs at these habitats. Understanding how habitats are transformed and how this affects different species is critical to direct ecological applications for commercial seaweed management. We experimentally assessed through a Before-After Control-Impact design the potential changes exerted by Gracilaria chilensis farming on bare mudflats on the abundance, biomass, and assemblage structure of benthic macroinvertebrates, and their scaled-up effects on shorebirds' habitat use and prey consumption. As predicted, experimental cultivation of G. chilensis significantly affects different components of biodiversity that scale-up from lower to upper trophic levels. The total biomass of benthic macroinvertebrates increased with seaweed cultivation and remained high for at least 2 months after harvest, boosted by an increase in the median size of polychaetes, particularly Nereids. Tactile-foraging shorebirds tracked these changes at the patch level increasing their abundance and spending more time foraging at seaweed cultivated plots. These results suggest that seaweed farming has the potential to impact shorebird populations by favoring tactile-foraging species which could lead to a competitive disadvantage to species that rely on visual cues. Therefore, the establishment of new seaweed farms in bare mudflats at key sites for shorebirds must be planned warranting habitat heterogeneity (i.e., cultivated and non-cultivated areas) at the landscape level and based on a previous experimental approach to account for local characteristics. Fostering properly designed extensive seaweed farming over other aquaculture industries with greater negative environmental impacts would provide benefits for human well-being and for ecosystem functions.

Multi-year monitoring of Piping Plovers (Charadriusmelodus) and other shorebirds in The Bahamas

Background

The Bahamas provides a wide range of crucial coastal habitats to many declining resident and migratory birds. Amongst these species is the Piping Plover (Charadriusmelodus), whose breeding populations are all listed as federally threatened or endangered in the United States and Canada. This species winters in the southern U.S. and the Caribbean, including The Bahamas, spending most of the year on the wintering grounds. Nonetheless, prior to the census data presented here, reports of Piping Plovers from The Bahamas were few and incidental. Therefore, repeated surveys are essential to increase understanding of the distribution, abundance and movement patterns of Piping Plovers and other shorebirds in the Bahamian territory. This dataset provides information on the abundance and distribution of the Piping Plover across multiple islands and much of the suitable habitat that exists in The Bahamas. It also provides some information on the variability of Piping Plover count data and presence of other shorebird species. Furthermore, these data may serve as baseline information on Piping Plover abundance and shorebird site occupancy by which to assess key candidate sites for protection and also future impacts of climate change, such as sea level rise and hurricanes.

New information

The National Audubon Society (NAS), Environment and Climate Change Canada (ECCC) and the United States Geological Survey (USGS) conducted a multi-year shorebird census in The Bahamas. Surveys initiated by ECCC and many other collaborators were also part of a multi-year survival study. Censuses were conducted across 16 different islands between the years 2006 and 2020. These surveys were performed with the cooperation of the Bahamas National Trust (BNT), volunteer biologists and scientists from the United States and Canada. Biologists working with NAS, ECCC and USGS used satellite imagery, historical records and local knowledge from Bahamian residents to identify sites with suitable habitat for Piping Plovers. Experienced researchers visited each site during winter (November-February), identified and counted Piping Plovers and, when possible, other bird species in each of the sampled locations. In total, the resulting database holds 2,684 observations of 62 bird species, of which 77% belong to 24 shorebird species. Approximately 30% of all presence records belong to the Piping Plover. It is important to emphasise that the counts reported in this dataset represent minimum estimates of local shorebird assemblages. Since abundance and distribution of birds vary with changing conditions, representative estimates are best achieved via repeated surveys that reflect a range of conditions including timing (day, year, month), weather (wind direction and speed, precipitation), tide state etc.

Curves for Curlew: Identifying Curlew breeding status from GPS tracking data

Identifying the breeding status of cryptic bird species has proved problematic without intense or inherently expensive monitoring. Most, if not all, intensive bird monitoring comes with disturbance risks and many projects now rely on tagging of individuals to provide remote information on movements. Given the importance of breeding status when targeting conservation interventions novel methods are needed. This study aimed to identify breeding status in Eurasian Curlew (Numenius arquata) from GPS tag movement patterns using the “recurse” package in R. This package identifies foci of activity (using K‐means clustering) based on revisitations. Using a training data set from an individual of known breeding status, we visually assessed the frequency of revisits to particular locations to identify prebreeding, incubation, chick guarding, and post‐breeding stages to an accuracy of a within at most half a day and thus breeding outcomes. Limited validation was provided by additional field observations. Based on our results, we estimate a low daily nest survival rate of 0.935 during incubation, that only a small proportion of individuals successfully raised young, and that there was a high proportion (26%) of non‐breeders in the population. The Eurasian Curlew is a species of high conservation concern across Europe, and our results concur with recent studies highlighting that population declines are likely to be driven by low levels of productivity. The acquisition of improved knowledge on the behaviors of individuals at each stage of breeding enables more targeted conservation efforts and reduces the need for additional monitoring visits that may cause increased disturbance and risk of nest failure. We hope that the approach outlined may be developed to provide practitioners who have detailed knowledge of the behavior of their study species with a practical means of assessing the breeding status and outcomes of their study populations.

Current breeding distributions and predicted range shifts under climate change in two subspecies of Black-tailed Godwits in Asia

Habitat loss and shifts associated with climate change threaten global biodiversity, with impacts likely to be most pronounced at high latitudes. With the disappearance of the tundra breeding habitats, migratory shorebirds that breed at these high latitudes are likely to be even more vulnerable to climate change than those in temperate regions. We examined this idea using new distributional information on two subspecies of Black-tailed Godwits Limosa limosa in Asia: the northerly, bog-breeding L. l. bohaii and the more southerly, steppe-breeding L. l. melanuroides. Based on breeding locations of tagged and molecularly assayed birds, we modelled the current breeding distributions of the two subspecies with species distribution models, tested those models for robustness and then used them to predict climatically suitable breeding ranges in 2070 according to bioclimatic variables and different climate change scenarios. Our models were robust and showed that climate change is expected to push bohaii into the northern rim of the Eurasian continent. Melanuroides is also expected to shift northward, stopping in the Yablonovyy and Stanovoy Ranges, and breeding elevation is expected to increase. Climatically suitable breeding habitat ranges would shrink to 16% and 11% of the currently estimated ranges of bohaii and melanuroides, respectively. Overall, this study provides the first predictions for the future distributions of two little-known Black-tailed Godwit subspecies and highlights the importance of factoring in shifts in bird distribution when designing climate-proof conservation strategies.

Both real-time and long-term environmental data perform well in predicting shorebird distributions in managed habitat

Highly mobile species, such as migratory birds, respond to seasonal and interannual variability in resource availability by moving to better habitats. Despite the recognized importance of resource thresholds, species-distribution models typically rely on long-term average habitat conditions, mostly because large-extent, temporally resolved, environmental data are difficult to obtain. Recent advances in remote sensing make it possible to incorporate more frequent measurements of changing landscapes; however, there is often a cost in terms of model building and processing and the added value of such efforts is unknown. Our study tests whether incorporating real-time environmental data increases the predictive ability of distribution models, relative to using long-term average data. We developed and compared distribution models for shorebirds in California's Central Valley based on high temporal resolution (every 16 days), and 17-year long-term average surface water data. Using abundance-weighted boosted regression trees, we modeled monthly shorebird occurrence as a function of surface water availability, crop type, wetland type, road density, temperature, and bird data source. Although modeling with both real-time and long-term average data provided good fit to withheld validation data (the area under the receiver operating characteristic curve, or AUC, averaged between 0.79 and 0.89 for all taxa), there were small differences in model performance. The best models incorporated long-term average conditions and spatial pattern information for real-time flooding (e.g., perimeter-area ratio of real-time water bodies). There was not a substantial difference in the performance of real-time and long-term average data models within time periods when real-time surface water differed substantially from the long-term average (specifically during drought years 2013-2016) and in intermittently flooded months or locations. Spatial predictions resulting from the models differed most in the southern region of the study area where there is lower water availability, fewer birds, and lower sampling density. Prediction uncertainty in the southern region of the study area highlights the need for increased sampling in this area. Because both sets of data performed similarly, the choice of which data to use may depend on the management context. Real-time data may ultimately be best for guiding dynamic, adaptive conservation actions, whereas models based on long-term averages may be more helpful for guiding permanent wetland protection and restoration.

Mismatch-induced growth reductions in a clade of Arctic-breeding shorebirds are rarely mitigated by increasing temperatures

In seasonal environments subject to climate change, organisms typically show phenological changes. As these changes are usually stronger in organisms at lower trophic levels than those at higher trophic levels, mismatches between consumers and their prey may occur during the consumers' reproduction period. While in some species a trophic mismatch induces reductions in offspring growth, this is not always the case. This variation may be caused by the relative strength of the mismatch, or by mitigating factors like increased temperature-reducing energetic costs. We investigated the response of chick growth rate to arthropod abundance and temperature for six populations of ecologically similar shorebirds breeding in the Arctic and sub-Arctic (four subspecies of Red Knot Calidris canutus, Great Knot C. tenuirostris and Surfbird C. virgata). In general, chicks experienced growth benefits (measured as a condition index) when hatching before the seasonal peak in arthropod abundance, and growth reductions when hatching after the peak. The moment in the season at which growth reductions occurred varied between populations, likely depending on whether food was limiting growth before or after the peak. Higher temperatures led to faster growth on average, but could only compensate for increasing trophic mismatch for the population experiencing the coldest conditions. We did not find changes in the timing of peaks in arthropod availability across the study years, possibly because our series of observations was relatively short; timing of hatching displayed no change over the years either. Our results suggest that a trend in trophic mismatches may not yet be evident; however, we show Arctic-breeding shorebirds to be vulnerable to this phenomenon and vulnerability to depend on seasonal prey dynamics.

Diel timing of nest predation changes across breeding season in a subtropical shorebird

Predation is the most common cause of nest failure in birds. While nest predation is relatively well studied in general, our knowledge is unevenly distributed across the globe and taxa, with, for example, limited information on shorebirds breeding in subtropics. Importantly, we know fairly little about the timing of predation within a day. Here, we followed 444 nests of the red-wattled lapwing (Vanellus indicus), a ground-nesting shorebird, for a sum of 7,828 days to estimate a nest predation rate, and continuously monitored 230 of these nests for a sum of 2,779 days to reveal how the timing of predation changes over the day and season in a subtropical desert. We found that 312 nests (70%) hatched, 76 nests (17%) were predated, 23 (5%) failed for other reasons, and 33 (7%) had an unknown fate. Daily predation rate was 0.95% (95%CrI: 0.76% - 1.19%), which for a 30-day long incubation period translates into ~25% (20% - 30%) chance of nest being predated. Such a predation rate is low compared to most other avian species. Predation events (N = 25) were evenly distributed across day and night, with a tendency for increased predation around sunrise, and evenly distributed also across the season, although night predation was more common later in the season, perhaps because predators reduce their activity during daylight to avoid extreme heat. Indeed, nests were never predated when midday ground temperatures exceeded 45℃. Whether the diel activity pattern of resident predators undeniably changes across the breeding season and whether the described predation patterns hold for other populations, species, and geographical regions await future investigations.

Mudflat geomorphology determines invasive macroalgal effect on invertebrate prey and shorebird predators

Impacts of invasive species are often context specific due to varying ecological interactions. Physical structure of environments hosting invaders is also potentially important but has received limited attention. An invasive macroalga, Agarophyton vermiculophyllum, has spread across the northern hemisphere with mixed positive, neutral and negative effects on resident species. Agarophyton colonizes mudflats that vary in topography due to interactions of sediments with hydrodynamic forces. We tested the hypothesis that mudflat geomorphology moderates the effect of Agarophyton on shorebirds and invertebrates. We surveyed 30 mudflats in the Virginia Coast Reserve quantifying elevation and topography. Invertebrate and bird abundances were also quantified. Mudflat geomorphology ranged from smooth to hummocky and was correlated with invertebrate and shorebird abundance and interactions based on piecewise structural equation models. After accounting for geomorphology, Agarophyton had little effect on invertebrate abundance. Shorebird numbers were differentially influenced by mudflat topography, with positive correlations to invertebrates (worms) on smooth mudflats, and to macroalgae on hummocky mudflats. These differences are likely to be due to sediment properties in interaction with structural changes induced by Agarophyton mats that affect prey accessibility for birds. Even on apparently simple mudflats, geomorphic structure emerged as important, modifying invasive species impacts and differentially influencing consumers.

Reassortment and Persistence of Influenza A Viruses from Diverse Geographic Origins within Australian Wild Birds: Evidence from a Small, Isolated Population of Ruddy Turnstones

Australian lineages of avian influenza A viruses (AIVs) are thought to be phylogenetically distinct from those circulating in Eurasia and the Americas, suggesting the circulation of endemic viruses seeded by occasional introductions from other regions. However, processes underlying the introduction, evolution and maintenance of AIVs in Australia remain poorly understood. Waders (order Charadriiformes, family Scolopacidae) may play a unique role in the ecology and evolution of AIVs, particularly in Australia, where ducks, geese, and swans (order Anseriformes, family Anatidae) rarely undertake intercontinental migrations. Across a 5-year surveillance period (2011 to 2015), ruddy turnstones (Arenaria interpres) that "overwinter" during the Austral summer in southeastern Australia showed generally low levels of AIV prevalence (0 to 2%). However, in March 2014, we detected AIVs in 32% (95% confidence interval [CI], 25 to 39%) of individuals in a small, low-density, island population 90 km from the Australian mainland. This epizootic comprised three distinct AIV genotypes, each of which represent a unique reassortment of Australian-, recently introduced Eurasian-, and recently introduced American-lineage gene segments. Strikingly, the Australian-lineage gene segments showed high similarity to those of H10N7 viruses isolated in 2010 and 2012 from poultry outbreaks 900 to 1,500 km to the north. Together with the diverse geographic origins of the American and Eurasian gene segments, these findings suggest extensive circulation and reassortment of AIVs within Australian wild birds over vast geographic distances. Our findings indicate that long-term surveillance in waders may yield unique insights into AIV gene flow, especially in geographic regions like Oceania, where Anatidae species do not display regular inter- or intracontinental migration.IMPORTANCE High prevalence of avian influenza viruses (AIVs) was detected in a small, low-density, isolated population of ruddy turnstones in Australia. Analysis of these viruses revealed relatively recent introductions of viral gene segments from both Eurasia and North America, as well as long-term persistence of introduced gene segments in Australian wild birds. These data demonstrate that the flow of viruses into Australia may be more common than initially thought and that, once introduced, these AIVs have the potential to be maintained within the continent. These findings add to a growing body of evidence suggesting that Australian wild birds are unlikely to be ecologically isolated from the highly pathogenic H5Nx viruses circulating among wild birds throughout the Northern Hemisphere.

Age- and sex-related dietary specialization facilitate seasonal resource partitioning in a migratory shorebird

Dietary specialization is common in animals and has important implications for individual fitness, inter- and intraspecific competition, and the adaptive potential of a species. Diet composition can be influenced by age- and sex-related factors including an individual's morphology, social status, and acquired skills; however, specialization may only be necessary when competition is intensified by high population densities or increased energetic demands.To better understand the role of age- and sex-related dietary specialization in facilitating seasonal resource partitioning, we inferred the contribution of biofilm, microphytobenthos, and benthic invertebrates to the diets of western sandpipers (Calidris mauri) from different demographic groups during mid-winter (January/February) and at the onset of the breeding migration (April) using stable isotope mixing models. Western sandpipers are sexually dimorphic with females having significantly greater body mass and bill length than males.Diet composition differed between seasons and among demographic groups. In winter, prey consumption was similar among demographic groups, but, in spring, diet composition differed with bill length and body mass explaining 31% of the total variation in diet composition. Epifaunal invertebrates made up a greater proportion of the diet in males which had lesser mass and shorter bills than females. Consumption of Polychaeta increased with increasing bill length and was greatest in adult females. In contrast, consumption of microphytobenthos, thought to be an important food source for migrating sandpipers, increased with decreasing bill length and was greatest in juvenile males.Our results provide the first evidence that age- and sex-related dietary specialization in western sandpipers facilitate seasonal resource partitioning that could reduce competition during spring at the onset of the breeding migration.Our study underscores the importance of examining resource partitioning throughout the annual cycle to inform fitness and demographic models and facilitate conservation efforts.

Widespread Presence of Domestic Dogs on Sandy Beaches of Southern Chile

Dogs on sandy beaches are a threat to shorebirds. Managing this problem requires understanding the factors that influence the abundance of dogs in these ecosystems. We aimed to determine the proportion of beaches used by dogs and the effects of human presence on dog abundance on sandy beaches of southern Chile. We conducted dog counts and recorded the presence of tracks on 14 beaches. We used zero-inflated generalized linear mixed models to determine if the number of people, number of households, and other covariates were associated with dog abundance. We detected dog tracks on all the beaches, and dog sightings on most of them. Dogs were frequently not supervised (45%) and only 13% of them were leashed. The number of people on the beach and the number of houses near the beach were positively associated with the number of dogs on beaches. Finally, when dogs co-occurred with whimbrels (Numenius phaeopus), the probability of dog harassment was high (59%). Our work reveals that human presence determines the abundance of dogs on sandy beaches. Therefore, our study suggests that any strategy aiming at reducing dog harassment of shorebirds requires changes in those human behaviors that favor the presence of free-ranging dogs at beaches.

Long-distance dispersal of the beach strawberry, Fragaria chiloensis, from North America to Chile and Hawaii

BACKGROUND AND AIMS

The beach strawberry, Fragaria chiloensis, is found in a narrow coastal band from the Aleutian Islands to central California and then jumps thousands of kilometres all the way to Hawaii and Chile. As it probably had a North American origin, it must have been introduced to the other locations by long-distance dispersal. The aim of this study was to determine which agent carried the beach strawberry to its Pacific and South American locations.

METHODS

A deductive framework was constructed to separate between the possible modes of long-distance dispersal involving animals, wind and ocean currents. Bird migration was subsequently identified as the most likely scenario, and then the routes, habitats, feeding preferences and flight distances of all the shorebird species were evaluated to determine the most likely carrier.

KEY RESULTS

Six species migrate between North America and Chile and feed on the beaches and rocky shores where F. chiloensis grows naturally: Black-bellied Plovers, Greater Yellowlegs, Ruddy Turnstones, Sanderlings, Whimbrels and Willets. Of these, only two eat fruit and migrate in long continuous flight: Ruddy Turnstones and Whimbrels. Two species travel between North America and Hawaii, eat fruit and forage on the beaches and rocky shores where F. chiloensis grows naturally: Pacific Golden-plovers and Ruddy Turnstones. Ruddy Turnstones eat far less fruit than Pacific Golden-plovers and Whimbrels, making them less likely to have introduced the beach strawberry to either location.

CONCLUSIONS

We provide evidence that F. chiloesis seeds were probably dispersed to Hawaii by Pacific Golden-plovers and to Chile by Whimbrels.

The mitochondrial genome of two long-distance migratory shorebirds: the Hudsonian godwit (Limosa haemastica) and the Red knot (Calidris canutus)

We report the mitochondrial genome sequences of two migratory shorebirds, the Hudsonian godwit (Limosa haemastica) and the Red knot (Calidris canutus) obtained through shotgun sequencing. The mitogenome is of 16.445 bp for the godwit and 15.609 bp for the knot containing thirteen protein-coding genes, two rRNAs, twenty-two tRNAs, and a control region. The ATP8 and tRNA-Glu were not found in the knot. Bayesian phylogenetic analysis supported the position of both species in the clade of the Scolopacidae Family.

Salmonella enterica Serovar Hvittingfoss in Bar-Tailed Godwits (Limosa lapponica) from Roebuck Bay, Northwestern Australia

Salmonella enterica serovar Hvittingfoss is an important foodborne serotype of Salmonella, being detected in many countries where surveillance is conducted. Outbreaks can occur, and there was a recent multistate foodborne outbreak in Australia. S Hvittingfoss can be found in animal populations, though a definitive animal host has not been established. Six species of birds were sampled at Roebuck Bay, a designated Ramsar site in northwestern Australia, resulting in 326 cloacal swabs for bacterial culture. Among a single flock of 63 bar-tailed godwits (Limosa lapponica menzbieri) caught at Wader Spit, Roebuck Bay, in 2018, 17 (27%) were culture positive for Salmonella All other birds were negative for Salmonella The isolates were identified as Salmonella enterica serovar Hvittingfoss. Phylogenetic analysis revealed a close relationship between isolates collected from godwits and the S Hvittingfoss strain responsible for a 2016 multistate foodborne outbreak originating from tainted cantaloupes (rock melons) in Australia. While it is not possible to determine how this strain of S Hvittingfoss was introduced into the bar-tailed godwits, these findings show that wild Australian birds are capable of carrying Salmonella strains of public health importance.IMPORTANCE Salmonella is a zoonotic pathogen that causes gastroenteritis and other disease presentations in both humans and animals. Serovars of S. enterica commonly cause foodborne disease in Australia and globally. In 2016-2017, S Hvittingfoss was responsible for an outbreak that resulted in 110 clinically confirmed human cases throughout Australia. The origin of the contamination that led to the outbreak was never definitively established. Here, we identify a migratory shorebird, the bar-tailed godwit, as an animal reservoir of S Hvittingfoss. These birds were sampled in northwestern Australia during their nonbreeding period. The presence of a genetically similar S Hvittingfoss strain circulating in a wild bird population, 2 years after the 2016-2017 outbreak and ∼1,500 km from the suspected source of the outbreak, demonstrates a potentially unidentified environmental reservoir of S Hvittingfoss. While the birds cannot be implicated in the outbreak that occurred 2 years prior, this study does demonstrate the potential role for wild birds in the transmission of this important foodborne pathogen.

Daily Rhythms of Female Self-maintenance Correlate with Predation Risk and Male Nest Attendance in a Biparental Wader

Parents make tradeoffs between care for offspring and themselves. Such a tradeoff should be reduced in biparental species, when both parents provide parental care. However, in some biparental species, the contribution of one sex varies greatly over time or between pairs. How this variation in parental care influences self-maintenance rhythms is often unclear. In this study, we used continuous video recording to investigate the daily rhythms of sleep and feather preening in incubating females of the Northern Lapwing (Vanellus vanellus), a wader with a highly variable male contribution to incubation. We found that the female's sleep frequency peaked after sunrise and before sunset but was low in the middle of the day and especially during the night. In contrast, preening frequency followed a 24-h rhythm and peaked in the middle of the day. Taken together, incubating females rarely slept or preened during the night, when the predation pressure was highest. Moreover, the sleeping and preening rhythms were modulated by the male contribution to incubation. Females that were paired with more contributing males showed a stronger sleep rhythm but also a weaker preening rhythm. If more incubating males also invest more in nest guarding and deterring daylight predators, their females may afford more sleep on the nest during the day and preen more when they are off the nest. Whether the lack of sleep in females paired with less caregiving males has fitness consequences awaits future investigation.

Serologic Evidence of Exposure to Highly Pathogenic Avian Influenza H5 Viruses in Migratory Shorebirds, Australia

Highly pathogenic avian influenza (HPAI) H5Nx viruses of the goose/Guangdong/96 lineage continue to cause outbreaks in poultry and wild birds globally. Shorebirds, known reservoirs of avian influenza viruses, migrate from Siberia to Australia along the East-Asian-Australasian Flyway. We examined whether migrating shorebirds spending nonbreeding seasons in Australia were exposed to HPAI H5 viruses. We compared those findings with those for a resident duck species. We screened >1,500 blood samples for nucleoprotein antibodies and tested positive samples for specific antibodies against 7 HPAI H5 virus antigens and 2 low pathogenicity avian influenza H5 virus antigens. We demonstrated the presence of hemagglutinin inhibitory antibodies against HPAI H5 virus clade 2.3.4.4 in the red-necked stint (Calidris ruficolis). We did not find hemagglutinin inhibitory antibodies in resident Pacific black ducks (Anas superciliosa). Our study highlights the potential role of long-distance migratory shorebirds in intercontinental spread of HPAI H5 viruses.

Does intensive goose grazing affect breeding waders?

Increasing goose population sizes gives rise to conflicts with human socioeconomic interests and in some circumstances conservation interests. Grazing by high abundances of geese in grasslands is postulated to lead to a very short and homogeneous sward height negatively affecting cover for breeding meadow birds and impacting survival of nests and chicks. We studied the effects of spring grazing barnacle geese Branta leucopsis and brent geese Branta bernicla on occupancy of extensively farmed freshwater grasslands by nesting and brood-rearing waders on the island Mandø in the Danish Wadden Sea. We hypothesized that goose grazing would lead to a shorter grass sward, negatively affecting the field occupancy by territorial/nesting and chick-rearing waders, particularly species preferring taller vegetation. Goose grazing led to a short grass sward (<5 cm height) over most of the island. To achieve a variation in sward height, we kept geese off certain fields using laser light. We analyzed effects of field size, sward height, mosaic structure of the vegetation, proximity to shrub as cover for potential predators, and elevation above ground water level as a measure of wetness on field occupancy by nesting and chick-rearing waders. The analysis indicated that the most important factor explaining field occupancy by nesting redshank Tringa totanus, black-tailed godwit Limosa limosa, oystercatcher Haematopus ostralegus and lapwing Vanellus vanellus as well as by chick-rearing black-tailed godwit and lapwing was short vegetation height. Distance to shrub cover and elevation were less important. Hence, despite very intensive goose grazing, we could not detect any negative effect on the field occupancy by nesting nor chick-rearing waders, including redshank and black-tailed godwit, which are known to favor longer vegetation to conceal their nests and hide their chicks. Possible negative effects may be buffered by mosaic structures in fields and proximity to taller vegetation along fences and ditches.

Demographic Histories and Genome-Wide Patterns of Divergence in Incipient Species of Shorebirds

Understanding how incipient species are maintained with gene flow is a fundamental question in evolutionary biology. Whole genome sequencing of multiple individuals holds great potential to illustrate patterns of genomic differentiation as well as the associated evolutionary histories. Kentish (Charadrius alexandrinus) and the white-faced (C. dealbatus) plovers, which differ in their phenotype, ecology and behavior, are two incipient species and parapatrically distributed in East Asia. Previous studies show evidence of genetic diversification with gene flow between the two plovers. Under this scenario, it is of great importance to explore the patterns of divergence at the genomic level and to determine whether specific regions are involved in reproductive isolation and local adaptation. Here we present the first population genomic analysis of the two incipient species based on the de novo Kentish plover reference genome and resequenced populations. We show that the two plover lineages are distinct in both nuclear and mitochondrial genomes. Using model-based coalescence analysis, we found that population sizes of Kentish plover increased whereas white-faced plovers declined during the Last Glaciation Period. Moreover, the two plovers diverged allopatrically, with gene flow occurring after secondary contact. This has resulted in low levels of genome-wide differentiation, although we found evidence of a few highly differentiated genomic regions in both the autosomes and the Z-chromosome. This study illustrates that incipient shorebird species with gene flow after secondary contact can exhibit discrete divergence at specific genomic regions and provides basis to further exploration on the genetic basis of relevant phenotypic traits.

Differential Change in Hippocampal Radial Astrocytes and Neurogenesis in Shorebirds With Contrasting Migratory Routes

Little is known about environmental influences on radial glia-like (RGL) α cells (radial astrocytes) and their relation to neurogenesis. Because radial glia is involved in adult neurogenesis and astrogenesis, we investigated this association in two migratory shorebird species that complete their autumnal migration using contrasting strategies. Before their flights to South America, the birds stop over at the Bay of Fundy in Canada. From there, the semipalmated sandpiper (Calidris pusilla) crosses the Atlantic Ocean in a non-stop 5-day flight, whereas the semipalmated plover (Charadrius semipalmatus) flies primarily overland with stopovers for rest and feeding. From the hierarchical cluster analysis of multimodal morphometric features, followed by the discriminant analysis, the radial astrocytes were classified into two main morphotypes, Type I and Type II. After migration, we detected differential changes in the morphology of these cells that were more intense in Type I than in Type II in both species. We also compared the number of doublecortin (DCX)-immunolabeled neurons with morphometric features of radial glial-like α cells in the hippocampal V region between C. pusilla and C. semipalmatus before and after autumn migration. Compared to migrating birds, the convex hull surface area of radial astrocytes increased significantly in wintering individuals in both C. semipalmatus and C. pusilla. Although to a different extent we found a strong correlation between the increase in the convex hull surface area and the increase in the total number of DCX immunostained neurons in both species. Despite phylogenetic differences, it is of interest to note that the increased morphological complexity of radial astrocytes in C. semipalmatus coincides with the fact that during the migratory process over the continent, the visuospatial environment changes more intensely than that associated with migration over Atlantic. The migratory flight of the semipalmated plover, with stopovers for feeding and rest, vs. the non-stop flight of the semipalmated sandpiper may differentially affect radial astrocyte morphology and neurogenesis.

Heavy Metals in Biota in Delaware Bay, NJ: Developing a Food Web Approach to Contaminants

Understanding the relationship between heavy metal and selenium levels in biota and their foods is important, but often difficult to determine because animals eat a variety of organisms. Yet such information is critical to managing species populations, ecological integrity, and risk to receptors (including humans) from consumption of certain prey. We examine levels of cadmium, lead, mercury, and selenium in biota from Delaware Bay (New Jersey, USA) to begin construction of a “springtime” food web that focuses on shorebirds. Horseshoe crab (Limulus polyphemus) eggs are one of the key components at the base of the food web, and crab spawning in spring provides a food resource supporting a massive stopover of shorebirds. Fish and other biota also forage on the crab eggs, and a complex food web leads directly to top-level predators such as bluefish (Pomatomus saltatrix) and striped bass (Morone saxatilis), both of which are consumed by egrets, eagles, ospreys (Pandion haliaetus), and humans. Metal levels in tissues were generally similar in algae, invertebrates, and small fish, and these were similar to those in blood of shorebirds (but not feathers). There was a significant direct relationship between the levels of metals in eggs of horseshoe crabs and mean metal levels in the blood of four species of shorebirds. Metal levels in shorebird feathers were higher than those in blood (except for selenium), reflecting sequestration of metals in feathers during their formation. Levels in feathers of laughing gulls (Leucophaeus atricilla) were similar to those in feathers of shorebirds (except for selenium). Selenium bears special mention as levels were significantly higher in the blood of all shorebird species than in other species in the food web, and were similar to levels in their feathers. Levels of metals in bluefish and striped bass were similar or higher than those found in the blood of shorebirds (except for selenium). The mean levels of cadmium, lead, and mercury in the blood and feathers of shorebirds were below any effect levels, but selenium levels in the blood and feathers of shorebirds were higher than the sublethal effect levels for birds. This is a cause for concern, and warrants further examination.

Phenological mismatch in Arctic-breeding shorebirds: Impact of snowmelt and unpredictable weather conditions on food availability and chick growth

The ecological consequences of climate change have been recognized in numerous species, with perhaps phenology being the most well-documented change. Phenological changes may have negative consequences when organisms within different trophic levels respond to environmental changes at different rates, potentially leading to phenological mismatches between predators and their prey. This may be especially apparent in the Arctic, which has been affected more by climate change than other regions, resulting in earlier, warmer, and longer summers. During a 7-year study near Utqiaġvik (formerly Barrow), Alaska, we estimated phenological mismatch in relation to food availability and chick growth in a community of Arctic-breeding shorebirds experiencing advancement of environmental conditions (i.e., snowmelt). Our results indicate that Arctic-breeding shorebirds have experienced increased phenological mismatch with earlier snowmelt conditions. However, the degree of phenological mismatch was not a good predictor of food availability, as weather conditions after snowmelt made invertebrate availability highly unpredictable. As a result, the food available to shorebird chicks that were 2-10 days old was highly variable among years (ranging from 6.2 to 28.8 mg trap-1 day-1 among years in eight species), and was often inadequate for average growth (only 20%-54% of Dunlin and Pectoral Sandpiper broods on average had adequate food across a 4-year period). Although weather conditions vary among years, shorebirds that nested earlier in relation to snowmelt generally had more food available during brood rearing, and thus, greater chick growth rates. Despite the strong selective pressure to nest early, advancement of nesting is likely limited by the amount of plasticity in the start and progression of migration. Therefore, long-term climatic changes resulting in earlier snowmelt have the potential to greatly affect shorebird populations, especially if shorebirds are unable to advance nest initiation sufficiently to keep pace with seasonal advancement of their invertebrate prey.

Multiple habitat use by declining migratory birds necessitates joined-up conservation

Many species depend on multiple habitats at different points in space and time. Their effective conservation requires an understanding of how and when each habitat is used, coupled with adequate protection. Migratory shorebirds use intertidal and supratidal wetlands, both of which are affected by coastal landscape change. Yet the extent to which shorebirds use artificial supratidal habitats, particularly at highly developed stopover sites, remains poorly understood leading to potential deficiencies in habitat management. We surveyed shorebirds on their southward migration in southern Jiangsu, a critical stopover region in the East Asian Australasian Flyway (EAAF), to measure their use of artificial supratidal habitats and assess linkages between intertidal and supratidal habitat use. To inform management, we examined how biophysical features influenced occupancy of supratidal habitats, and whether these habitats were used for roosting or foraging. We found that shorebirds at four of five sites were limited to artificial supratidal habitats at high tide for ~11-25 days per month because natural intertidal flats were completely covered by seawater. Within the supratidal landscape, at least 37 shorebird species aggregated on artificial wetlands, and shorebirds were more abundant on larger ponds with less water cover, less vegetation, at least one unvegetated bund, and fewer built structures nearby. Artificial supratidal habitats were rarely used for foraging and rarely occupied when intertidal flats were available, underscoring the complementarity between supratidal roosting habitat and intertidal foraging habitat. Joined-up artificial supratidal management and natural intertidal habitat conservation are clearly required at our study site given the simultaneous dependence by over 35,000 migrating shorebirds on both habitats. Guided by observed patterns of habitat use, there is a clear opportunity to improve habitat condition by working with local land custodians to consider shorebird habitat requirements when managing supratidal ponds. This approach is likely applicable to shorebird sites throughout the EAAF.

Warming springs and habitat alteration interact to impact timing of breeding and population dynamics in a migratory bird

In seasonal environments, increasing spring temperatures lead many taxa to advance the timing of reproduction. Species that do not may suffer lower fitness. We investigated why black-tailed godwits (Limosa limosa limosa), a ground-breeding agricultural grassland shorebird, have not advanced timing of reproduction during the last three decades in the face of climate change and human-induced habitat degradation. We used data from an 11-year field study to parameterize an Integral Projection Model to predict how spring temperature and habitat quality simultaneously influence the timing of reproduction and population dynamics. We found apparent selection for earlier laying, but not a correlation between the laying dates of parents and their offspring. Nevertheless, in warmer springs, laying dates of adults show a stronger positive correlation with laying date in previous springs than in cooler ones, and this leads us to predict a slight advance in the timing of reproduction if spring temperatures continue to increase. We also show that only in landscapes with low agricultural activity, the population can continue to act as a source. This study shows how climate change and declining habitat quality may enhance extinction risk.

Evaluating the effectiveness of conservation measures for European grassland-breeding waders

Farmland birds are among the most threatened bird species in Europe, largely as a result of agricultural intensification which has driven widespread biodiversity losses. Breeding waders associated with grassland and arable habitats are particularly vulnerable and a frequent focus of agri-environment schemes (AES) designed to halt and reverse population declines. We review existing literature, providing a quantitative assessment of the effectiveness of policy and management interventions used throughout Europe to improve population and demographic metrics of grassland-breeding waders. Targeted AES and site protection measures were more likely to be effective than less targeted AES and were ten times more likely to be effective than would be expected by chance, particularly for population trend and productivity metrics. Positive effects of AES and site protection did not appear synergistic. Management interventions which had the greatest chance of increasing population growth or productivity included modification of mowing regimes, increasing wet conditions, and the use of nest protection. Success rates varied according to the species and metric being evaluated. None of the policy or management interventions we evaluated were associated with a significant risk of negative impacts on breeding waders. Our findings support the use of agri-environment schemes, site protection, and management measures for grassland-breeding wader conservation in Europe. Due to publication bias, our findings are most applicable to intensively managed agricultural landscapes. More studies are needed to identify measures that increase chick survival. Despite broadly effective conservation measures already in use, grassland-breeding waders in Europe continue to decline. More research is needed to improve the likelihood and magnitude of positive outcomes, coupled with wider implementation of effective measures to substantially increase favorable land management for these species.

Body condition explains migratory performance of a long-distance migrant

Body condition (i.e. relative mass after correcting for structural size) affects the behaviour of migrating birds, but how body condition affects migratory performance, timing and fitness is still largely unknown. Here, we studied the effects of relative body condition on individual departure decisions, wind selectivity, flight speed and timing of migration for a long-distance migratory shorebird, the red knot Calidris canutus rufa. By using automated VHF telemetry on a continental scale, we studied knots' migratory movements with unprecedented temporal resolution over a 3-year period. Knots with a higher relative body condition left the staging site later than birds in lower condition, yet still arrived earlier to their Arctic breeding grounds compared to knots in lower relative body condition. They accomplished this by selecting more favourable winds at departure, thereby flying faster and making shorter stops en route. Individuals with a higher relative body condition in spring migrated south up to a month later than individuals in lower condition, suggesting that individuals in better condition were more likely to have bred successfully. Moreover, individuals with a lower relative body condition in spring had a lower probability of being detected in autumn, suggestive of increased mortality. The pressure to arrive early to the breeding grounds is considered to be an important constraint of migratory behaviour and this study highlights the important influence of body condition on migratory decisions, performance and potentially fitness of migrant birds.

Marine biorhythms: bridging chronobiology and ecology

Marine organisms adapt to complex temporal environments that include daily, tidal, semi-lunar, lunar and seasonal cycles. However, our understanding of marine biological rhythms and their underlying molecular basis is mainly confined to a few model organisms in rather simplistic laboratory settings. Here, we use new empirical data and recent examples of marine biorhythms to highlight how field ecologists and laboratory chronobiologists can complement each other's efforts. First, with continuous tracking of intertidal shorebirds in the field, we reveal individual differences in tidal and circadian foraging rhythms. Second, we demonstrate that shorebird species that spend 8–10 months in tidal environments rarely maintain such tidal or circadian rhythms during breeding, likely because of other, more pertinent, temporally structured, local ecological pressures such as predation or social environment. Finally, we use examples of initial findings from invertebrates (arthropods and polychaete worms) that are being developed as model species to study the molecular bases of lunar-related rhythms. These examples indicate that canonical circadian clock genes (i.e. the homologous clock genes identified in many higher organisms) may not be involved in lunar/tidal phenotypes. Together, our results and the examples we describe emphasize that linking field and laboratory studies is likely to generate a better ecological appreciation of lunar-related rhythms in the wild.

This article is part of the themed issue ‘Wild clocks: integrating chronobiology and ecology to understand timekeeping in free-living animals’.

Mercury, Lead, Cadmium, Cobalt, Arsenic and Selenium in the Blood of Semipalmated Sandpipers (Calidris pusilla) from Suriname, South America: Age-related Differences in Wintering Site and Comparisons with a Stopover Site in New Jersey, USA

It is essential to understand contaminant exposure and to compare levels of contaminants in organisms at different ages to determine if there is bioaccumulation, and to compare levels encountered in different geographical areas. In this paper, we report levels of mercury, lead, cadmium, cobalt, arsenic and selenium in the blood of semipalmated sandpipers (Calidris pusilla) wintering in Suriname as a function of age, and compare them to blood levels in northbound migrants at a stopover in Delaware Bay, New Jersey. We found (1) young birds had higher levels of cadmium, cobalt, and lead than adults (after second year birds); (2) there were no age-related differences for arsenic, mercury and selenium; (3) only four of the possible 16 inter-metal correlations were significant, at the 0.05 level; (4) the highest correlation was between cadmium and lead (Kendall tau = 0.37); and (5) the adult sandpipers had significantly higher levels of cadmium, mercury and selenium in Suriname than in New Jersey, while the New Jersey birds had significantly higher levels of arsenic. Suriname samples were obtained in April, after both age classes had spent the winter in Suriname, which suggests that sandpipers are accumulating higher levels of trace elements in Suriname than in Delaware Bay. The levels of selenium may be within a range of concern for adverse effects, but little is known about adverse effect levels of trace elements in the blood of wild birds.

Influenza A virus: sampling of the unique shorebird habitat at Delaware Bay, USA

Delaware (DE) Bay, in the northeastern USA, has long been recognized as a hotspot for avian influenza A virus (IAV); every spring, this coastal region serves as a brief stopover site for thousands of long-distance migrating shorebirds, en route to breeding grounds in the Arctic. During these stopovers, IAV has been consistently recovered from ruddy turnstones (Arenaria interpres) that are likely to become infected as they feed by probing sand and cobble in search of food. In May 2010-2012, we successfully isolated 19 IAV from environmental samples (sand, n = 18; horseshoe crab eggs, n = 1) obtained from DE Bay sites. Two of these viruses were subjected to laboratory conditions similar to those in the DE Bay spring-time environment, and remained infectious for 7 days. Here, through the recovery of IAV from environmental samples, temperature monitoring at and below the sand surface and simulated laboratory trials, we provide evidence that the beach environment may enable localized transmission and short-term maintenance of IAV in this unique ecosystem.

Influenza A virus: sampling of the unique shorebird habitat at Delaware Bay, USA

Delaware (DE) Bay, in the northeastern USA, has long been recognized as a hotspot for avian influenza A virus (IAV); every spring, this coastal region serves as a brief stopover site for thousands of long-distance migrating shorebirds, en route to breeding grounds in the Arctic. During these stopovers, IAV has been consistently recovered from ruddy turnstones (Arenaria interpres) that are likely to become infected as they feed by probing sand and cobble in search of food. In May 2010-2012, we successfully isolated 19 IAV from environmental samples (sand, n = 18; horseshoe crab eggs, n = 1) obtained from DE Bay sites. Two of these viruses were subjected to laboratory conditions similar to those in the DE Bay spring-time environment, and remained infectious for 7 days. Here, through the recovery of IAV from environmental samples, temperature monitoring at and below the sand surface and simulated laboratory trials, we provide evidence that the beach environment may enable localized transmission and short-term maintenance of IAV in this unique ecosystem.

Multispecies comparisons of adaptability to climate change: A role for life-history characteristics?

Phenological advancement allows individuals to adapt to climate change by timing life‐history events to the availability of key resources so that individual fitness is maximized. However, different trophic levels may respond to changes in their environment at different rates, potentially leading to a phenological mismatch. This may be especially apparent in the highly seasonal arctic environment that is experiencing the effects of climate change more so than any other region. During a 14‐year study near Utqiaġvik (formerly Barrow), Alaska, we estimated phenological advancement in egg laying in relation to snowmelt for eight arctic‐breeding shorebirds and investigated potential linkages to species‐specific life‐history characteristics. We found that snowmelt advanced 0.8 days/year—six times faster than the prior 60‐year period. During this same time, six of the eight species exhibited phenological advancement in laying dates (varying among species from 0.1 to 0.9 days earlier per year), although no species appeared capable of keeping pace with advancing snowmelt. Phenological changes were likely the result of high phenotypic plasticity, as all species investigated in this study showed high interannual variability in lay dates. Commonality among species with similar response rates to timing of snowmelt suggests that nesting later and having an opportunistic settlement strategy may increase the adaptability of some species to changing climate conditions. Other life‐history characteristics, such as migration strategy, previous site experience, and mate fidelity did not influence the ability of individuals to advance laying dates. As a failure to advance egg laying is likely to result in greater phenological mismatch, our study provides an initial assessment of the relative risk of species to long‐term climatic changes.

Genetic isolation in an endemic African habitat specialist

The Chestnut-banded Plover Charadrius pallidus is a Near-Threatened shorebird species endemic to mainland Africa. We examined levels of genetic differentiation between its two morphologically and geographically distinct subspecies, C. p. pallidus in southern Africa (population size 11 000-16 000) and C. p. venustus in eastern Africa (population size 6500). In contrast to other plover species that maintain genetic connectivity over thousands of kilometres across continental Africa, we found profound genetic differences between remote sampling sites. Phylogenetic network analysis based on four nuclear and two mitochondrial gene regions, and population genetic structure analyses based on 11 microsatellite loci, indicated strong genetic divergence, with 2.36% mitochondrial sequence divergence between individuals sampled in Namibia (southern Africa) and those of Kenya and Tanzania (eastern Africa). This distinction between southern and eastern African populations was also supported by highly distinct genetic clusters based on microsatellite markers (global F_ST  = 0.309, GST' = 0.510, D = 0.182). Behavioural factors that may promote genetic differentiation in this species include habitat specialization, monogamous mating behaviour and sedentariness. Reliance on an extremely small number of saline lakes for breeding and limited dispersal between populations are likely to promote reproductive and genetic isolation between eastern and southern Africa. We suggest that the two Chestnut-banded Plover subspecies may warrant elevation to full species status. To assess this distinction fully, additional sample collection will be needed, with analysis of genetic and phenotypic traits from across the species' entire breeding range.

Nest trampling and ground nesting birds: Quantifying temporal and spatial overlap between cattle activity and breeding redshank

Conservation grazing for breeding birds needs to balance the positive effects on vegetation structure and negative effects of nest trampling. In the UK, populations of Common redshank Tringa totanus breeding on saltmarshes declined by >50% between 1985 and 2011. These declines have been linked to changes in grazing management. The highest breeding densities of redshank on saltmarshes are found in lightly grazed areas. Conservation initiatives have encouraged low‐intensity grazing at <1 cattle/ha, but even these levels of grazing can result in high levels of nest trampling. If livestock distribution is not spatially or temporally homogenous but concentrated where and when redshank breed, rates of nest trampling may be much higher than expected based on livestock density alone. By GPS tracking cattle on saltmarshes and monitoring trampling of dummy nests, this study quantified (i) the spatial and temporal distribution of cattle in relation to the distribution of redshank nesting habitats and (ii) trampling rates of dummy nests. The distribution of livestock was highly variable depending on both time in the season and the saltmarsh under study, with cattle using between 3% and 42% of the saltmarsh extent and spending most their time on higher elevation habitat within 500 m of the sea wall, but moving further onto the saltmarsh as the season progressed. Breeding redshank also nest on these higher elevation zones, and this breeding coincides with the early period of grazing. Probability of nest trampling was correlated to livestock density and was up to six times higher in the areas where redshank breed. This overlap in both space and time of the habitat use of cattle and redshank means that the trampling probability of a nest can be much higher than would be expected based on standard measures of cattle density. Synthesis and applications: Because saltmarsh grazing is required to maintain a favorable vegetation structure for redshank breeding, grazing management should aim to keep livestock away from redshank nesting habitat between mid‐April and mid‐July when nests are active, through delaying the onset of grazing or introducing a rotational grazing system.

Restoring fire to grasslands is critical for migrating shorebird populations

Fire is a disturbance process that maintains the structure and function of grassland ecosystems while sustaining grassland biodiversity. Conversion of grasslands to other land uses coupled with altered disturbance regimes has greatly diminished the habitat available to many grassland-dependent species. These changes have been linked to declines in breeding bird populations, but may also be critical for migrating bird populations such as those shorebird species that depend on mesic grasslands during migration. We examined migratory shorebird use of burned grasslands in the southern Great Plains of North America using DISTANCE sampling to estimate and compare bird densities across recently burned and not recently burned landscapes (1-5 yr post fire). We conducted two surveys per week for 8-10 weeks along a 54-km route starting at the end of March and concluding in mid-May during 2014-2015. We encountered 2,509 total shorebirds in recently burned areas compared to 130 individuals in areas that were unburned. Fire was a major attractant for our three focal species with American Golden-plover (Pluvialis dominica), Upland Sandpiper (Bartramia longicauda), and Killdeer (Charadrius vociferus) densities of 20.48, 11.09, and 26.09 birds/km² in burned areas compared with 0.00, 1.27, and 0.92 birds/km² in unburned areas, respectively. This research illustrates the importance of burned grassland for migrating shorebirds, a phenomenon that has largely gone unreported previously. Generally, these findings add to a body of knowledge that demonstrates the value of managing grasslands with historic disturbances that vary over space and time. The application of these findings should improve decision-making for shorebird conservation and provides evidence that prescribed fire planning should include consideration for breeding, transient, and non-breeding populations that vary in their temporal use of the landscape.

Metal Levels in Blood of Three Species of Shorebirds during Stopover on Delaware Bay Reflect Levels in Their Food, Horseshoe Crab Eggs

Understanding the relationship between metal level in predators and their prey is an important issue, and is usually difficult to determine because animals eat a variety of organisms. However, shorebirds that stop over during spring migration along Delaware Bay (New Jersey) stay for only 2–3 weeks, and eat mainly horseshoe crab (Limulus polyphemus) eggs. In this paper, we examine the relationship between metal levels in horseshoe crab eggs, and blood and feather levels of metals in red knot (Calidris canutus rufa; n = 30), sanderling (Calidris alba; n = 20) and semipalmated sandpiper (Calidris pusilla; n = 38) from Delaware Bay. There is a rich literature on metal levels in feathers. For all three species, the levels of arsenic, cadmium, chromium, lead and mercury in blood were highly correlated with the levels of metals in the eggs of horseshoe crab (17 pooled samples). This indicates that the levels in the blood of these shorebirds quickly reflect levels in their prey (horseshoe crab eggs), while metals in the feathers were not correlated with the levels in eggs. Semipalmated sandpipers had the lowest levels of arsenic in blood and the highest levels of arsenic in feathers, compared to the other species. At Delaware Bay, semipalmated sandpipers have a diet higher in marsh invertebrates than the other species, which may account for the differences. The levels of cadmium and chromium in blood were significantly higher in knots than other species; knots only ate horseshoe crab eggs. For all of the metals except arsenic, the ratio of levels in blood/feathers was similar among species. For arsenic, the ratio of levels in blood/feathers were significantly lower in semipalmated sandpipers than in the other species, by an order of magnitude.

Ecology of Avian Influenza Virus in Wild Birds in Tropical Africa

Several ecologic factors have been proposed to describe the mechanisms whereby host ecology and the environment influence the transmission of avian influenza viruses (AIVs) in wild birds, including bird's foraging behavior, migratory pattern, seasonal congregation, the rate of recruitment of juvenile birds, and abiotic factors. However, these ecologic factors are derived from studies that have been conducted in temperate or boreal regions of the Northern Hemisphere. These factors cannot be directly translated to tropical regions, where differences in host ecology and seasonality may produce different ecologic interactions between wild birds and AIV. An extensive dataset of AIV detection in wildfowl and shorebirds sampled across tropical Africa was used to analyze how the distinctive ecologic features of Afrotropical regions may influence the dynamics of AIV transmission in wild birds. The strong seasonality of rainfall and surface area of wetlands allows testing of how the seasonality of wildfowl ecology (reproduction phenology and congregation) is related to AIV seasonal dynamics. The diversity of the African wildfowl community provides the opportunity to investigate the respective influence of migratory behavior, foraging behavior, and phylogeny on species variation in infection rate. Large aggregation sites of shorebirds in Africa allow testing for the existence of AIV infection hot spots. We found that the processes whereby host ecology influence AIV transmission in wild birds in the Afrotropical context operate through ecologic factors (seasonal drying of wetlands and extended and nonsynchronized breeding periods) that are different than the one described in temperate regions, hence, resulting in different patterns of AIV infection dynamics.

Setting conservation priorities for migratory networks under uncertainty

Conserving migratory species requires protecting connected habitat along the pathways they travel. Despite recent improvements in tracking animal movements, migratory connectivity remains poorly resolved at a population level for the vast majority of species, thus conservation prioritization is hampered. To address this data limitation, we developed a novel approach to spatial prioritization based on a model of potential connectivity derived from empirical data on species abundance and distance traveled between sites during migration. We applied the approach to migratory shorebirds of the East Asian-Australasian Flyway. Conservation strategies that prioritized sites based on connectivity and abundance metrics together maintained larger populations of birds than strategies that prioritized sites based only on abundance metrics. The conservation value of a site therefore depended on both its capacity to support migratory animals and its position within the migratory pathway; the loss of crucial sites led to partial or total population collapse. We suggest that conservation approaches that prioritize sites supporting large populations of migrants should, where possible, also include data on the spatial arrangement of sites.

HISTORICAL EXAMINATION OF DELAYED PLUMAGE MATURATION IN THE SHOREBIRDS (AVES: CHARADRIIFORMES)

Delayed plumage maturation refers to the presence of nonadultlike immature plumages (juvenal plumage excluded). It is usually considered the result of selection for distinctive first-winter or first-summer appearance. In the present study, evolution of delayed plumage maturation is examined in the shorebirds: the sandpipers, plovers, gulls, and their allies. Nine plumage-maturation characters were identified, and their states were superimposed onto topologies generated during two recent investigations of shorebird relationships (Sibley and Ahlquist; revised Strauch). The characters were then optimized so as to assign character states to interior nodes of the trees in the most parsimonious way. Reconstructions of character evolution on six of the shortest revised Strauch trees were ambiguous with respect to delayed plumage maturation in the hypothetical ancestral shorebird. If plumage maturation was not delayed in the shorebird ancestor, optimization indicated that delay appeared when nonadultlike juvenal feathers were acquired. In contrast, on the single Sibley and Ahlquist tree, absence of delayed plumage maturation in the shorebird ancestor was indicated unambiguously, with three evolutionary novelties (nonadultlike juvenal feathers, seasonal plumage change, and a reduced first-spring molt) implicated in its acquisition. Optimization indicated that delayed plumage maturation in shorebirds can be explained plausibly without invoking selection for distinctive first-winter or first-summer appearance. Two of the novel conditions generating delayed plumage maturation (modified juvenal feathers and seasonal plumage change) did so only because they were acquired in a taxon possessing restricted first-year molts, which are primitive. Given these observations, it seems simplest to explain the delay in plumage maturation as an incidental consequence of the phylogenetic inertia of shorebird molts. The third novelty that generates delayed plumage maturation, a reduced first-spring molt, may have been acquired to reduce molt-associated energetic demands in young birds.

Rapid climate-driven loss of breeding habitat for Arctic migratory birds

Millions of birds migrate to and from the Arctic each year, but rapid climate change in the High North could strongly affect where species are able to breed, disrupting migratory connections globally. We modelled the climatically suitable breeding conditions of 24 Arctic specialist shorebirds and projected them to 2070 and to the mid-Holocene climatic optimum, the world's last major warming event ~6000 years ago. We show that climatically suitable breeding conditions could shift, contract and decline over the next 70 years, with 66-83% of species losing the majority of currently suitable area. This exceeds, in rate and magnitude, the impact of the mid-Holocene climatic optimum. Suitable climatic conditions are predicted to decline acutely in the most species rich region, Beringia (western Alaska and eastern Russia), and become concentrated in the Eurasian and Canadian Arctic islands. These predicted spatial shifts of breeding grounds could affect the species composition of the world's major flyways. Encouragingly, protected area coverage of current and future climatically suitable breeding conditions generally meets target levels; however, there is a lack of protected areas within the Canadian Arctic where resource exploitation is a growing threat. Given that already there are rapid declines of many populations of Arctic migratory birds, our results emphasize the urgency of mitigating climate change and protecting Arctic biodiversity.

Building a database for long-term monitoring of benthic macrofauna in the Pertuis-Charentais (2004-2014)

Background

Long-term benthic monitoring is rewarding in terms of science, but labour-intensive, whether in the field, the laboratory, or behind the computer. Building and managing databases require multiple skills, including consistency over time as well as organisation via a systematic approach. Here, we introduce and share our spatially explicit benthic database, comprising 11 years of benthic data. It is the result of intensive benthic sampling that has been conducted on a regular grid (259 stations) covering the intertidal mudflats of the Pertuis-Charentais (Marennes-Oléron Bay and Aiguillon Bay). Samples were taken by foot or by boats during winter depending on tidal height, from December 2003 to February 2014. The present dataset includes abundances and biomass densities of all mollusc species of the study regions and principal polychaetes as well as their length, accessibility to shorebirds, energy content and shell mass when appropriate and available. This database has supported many studies dealing with the spatial distribution of benthic invertebrates and temporal variations in food resources for shorebird species as well as latitudinal comparisons with other databases. In this paper, we introduce our benthos monitoring, share our data, and present a "guide of good practices" for building, cleaning and using it efficiently, providing examples of results with associated R code.

New information

The dataset has been formatted into a geo-referenced relational database, using PostgreSQL open-source DBMS. We provide density information, measurements, energy content and accessibility of thirteen bivalve, nine gastropod and two polychaete taxa (a total of 66,620 individuals)​ for 11 consecutive winters. Figures and maps are provided to describe how the dataset was built, cleaned, and how it can be used. This dataset can again support studies concerning spatial and temporal variations in species abundance, interspecific interactions as well as evaluations of the availability of food resources for small- and medium size shorebirds and, potentially, conservation and impact assessment studies.

Diet preferences as the cause of individual differences rather than the consequence

Behavioural variation within a species is usually explained as the consequence of individual variation in physiology. However, new evidence suggests that the arrow of causality may well be in the reverse direction: behaviours such as diet preferences cause the differences in physiological and morphological traits. Recently, diet preferences were proposed to underlie consistent differences in digestive organ mass and movement patterns (patch residence times) in red knots (Calidris canutus islandica). Red knots are molluscivorous and migrant shorebirds for which the size of the muscular stomach (gizzard) is critical for the food processing rate. In this study, red knots (C. c. canutus, n = 46) were caught at Banc d'Arguin, an intertidal flat ecosystem in Mauritania, and released with radio-tags after the measurement of gizzard mass. Using a novel tracking system (time-of-arrival), patch residence times were measured over a period of three weeks. Whether or not gizzard mass determined patch residence times was tested experimentally by offering 12 of the 46 tagged red knots soft diets prior to release; this reduced an individual's gizzard mass by 20-60%. To validate whether the observed range of patch residence times would be expected from individual diet preferences, we simulated patch residence times as a function of diet preferences via a simple departure rule. Consistent with previous empirical studies, patch residence times in the field were positively correlated with gizzard mass. The slope of this correlation, as well as the observed range of patch residence times, was in accordance with the simulated values. The 12 birds with reduced gizzard masses did not decrease patch residence times in response to the reduction in gizzard mass. These findings suggest that diet preferences can indeed cause the observed among-individual variation in gizzard mass and patch residence times. We discuss how early diet experiences can have cascading effects on the individual expression of both behavioural and physiomorphic traits. This emphasizes that to understand the ecological consequences of individual differences, knowledge of the environment during development is required.