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Background Conserving migratory birds is challenging due to their reliance on multiple distant sites at different stages of their annual life cycle. The concept of “flyway”, which refers to all areas covered by the breeding, nonbreeding, and migrating of birds, provides a framework for international cooperation for conservation. In the same flyway, however, the migratory activities of the same species can differ substantially between seasons and populations. Clarifying the seasonal and population differences in migration is helpful for understanding migration ecology and for identifying conservation gaps. Methods Using satellite-tracking we tracked the migration of Whimbrels (Numenius phaeopus variegatus) from nonbreeding sites at Moreton Bay (MB) and Roebuck Bay (RB) in Australia in the East Asian–Australasian Flyway. Mantel tests were used to analyze the strength of migration connectivity between the nonbreeding and breeding sites of MB and RB populations. Welch’s t test was used to compare the migration activities between the two populations and between northward and southward migration. Results During northward migration, migration distance and duration were longer for the MB population than for the RB population. The distance and duration of the first leg flight during northward migration were longer for the MB population than for the RB population, suggesting that MB individuals deposited more fuel before departing from nonbreeding sites to support their longer nonstop flight. The RB population exhibited weaker migration connectivity (breeding sites dispersing over a range of 60 longitudes) than the MB population (breeding sites concentrating in a range of 5 longitudes in Far Eastern Russia). Compared with MB population, RB population was more dependent on the stopover sites in the Yellow Sea and the coastal regions in China, where tidal habitat has suffered dramatic loss. However, RB population increased while MB population decreased over the past decades, suggesting that loss of tidal habitat at stopover sites had less impact on the Whimbrel populations, which can use diverse habitat types. Different trends between the populations might be due to the different degrees of hunting pressure in their breeding grounds. Conclusions This study highlights that conservation measures can be improved by understanding the full annual life cycle of movements of multiple populations of Whimbrels and probably other migratory birds.

Stopover sites are critical for refueling and resting by migrating birds. Clarifying the habitat requirements of migratory birds during stopover is important for understanding migration ecology and for conservation management. Habitat use by migratory birds at stopover sites, however, has been inadequately studied, and individual variation in habitat use among species is largely unexplored. We tracked the movement of migrating Whimbrels, Numenius phaeopus, using Global Positioning System–Global System for Mobile Communication tags at Chongming Dongtan, an important stopover site in the South Yellow Sea, China, in spring 2016 and in spring and autumn 2017. Multinomial logistic regression and multimodel inference were used to detect the effects of the individual bird, the diel factor (day vs. night), and tide height on the habitat use by Whimbrels during the stopover. The activity intensity of Whimbrels was lower during the night than during the day, while the maximum distance that tagged Whimbrels moved was similar between day and night. The saltmarsh and mudflat were intensively used by all of the individuals in all three seasons: > 50% and 20% of all records were obtained from the saltmarsh and mudflat, respectively. Habitat use significantly differed among individuals; the farmland and woodland were used by some individuals in spring 2016, while the restoration wetland near the intertidal area was used by some individuals in 2017. In general, the saltmarsh, farmland, and woodland were more frequently used in the daytime, while the mudflat was more frequently used at night. As tide height increased, the use of the mudflat decreased while the use of the saltmarsh increased. The results suggest that individual-based bio-tracking can provide detailed data on habitat use both during the day and at night. Differences in habitat use among individuals and periods highlight the importance of diverse habitats for bird conservation.

Additional file 2: Figure S1. Changes in the body mass of the Whimbrels at Moreton Bay (red circles) and Roebuck Bay (blue circles) during the nonbreeding period.

Additional file 1: Table S1. Stopover sites used by the Whimbrels from MB (Moreton Bay) and RB (Roebuck Bay) during northward and southward migration. Table S2. Results of linear mixed model testing for the effect of overall stopover duration (Rstopover duration) and travel speed (Rtravelled speed) on the overall migration speed (Rmigration speed) of Whimbrels. Table S3. Distance and duration of the first-leg flights during northward migration of shorebirds in Australia and New Zealand. Table S4. Migration parameters (means) of Whimbrels in the East Asian–Australasian Flyway (EAAF, nonbreeding at Moreton Bay (MB) and Roebuck Bay (RB) in Australia), the Eurasian-Africa Flyway (breeding in Iceland), and the America Flyway (breeding in Manitoba, Canada).