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Spatiotemporal patterns in biological communities are typically driven by environmental factors and species interactions. Spatial data from communities are naturally described by stacking models for all species in the community. Two important considerations in such multispecies or joint species distribution models (JSDMs) are measurement errors and correlations between species. Up to now, virtually all JSDMs have included either one or the other, but not both features simultaneously, even though both measurement errors and species correlations may be essential for achieving unbiased inferences about the distribution of communities and species co-occurrence patterns. We developed two presence–absence JSDMs for modeling pairwise species correlations while accommodating imperfect detection: one using a latent variable and the other using a multivariate probit approach. We conducted three simulation studies to assess the performance of our new models and to compare them to earlier latent variable JSDMs that did not consider imperfect detection. We illustrate our models with a large Atlas data set of 62 passerine bird species in Switzerland. Under a wide range of conditions, our new latent variable JSDM with imperfect detection and species correlations yielded estimates with little or no bias for occupancy, occupancy regression coefficients, and the species correlation matrix. In contrast, with the multivariate probit model we saw convergence issues with large data sets (many species and sites) resulting in very long run times and larger errors. A latent variable model that ignores imperfect detection produced correlation estimates that were consistently negatively biased, that is, underestimated. We found that the number of latent variables required to represent the species correlation matrix adequately may be much greater than previously suggested, namely around n/2, where n is community size. The analysis of the Swiss passerine data set exemplifies how not accounting for imperfect detection will lead to negative bias in occupancy estimates and to attenuation in the estimated covariate coefficients in a JSDM. Furthermore, spatial heterogeneity in detection may cause spurious patterns in the estimated species correlation matrix if not accounted for. Our new JSDMs represent an important extension of current approaches to community modeling to the common case where species presence–absence cannot be detected with certainty.

Provision of supplementary food for wild birds at garden feeding stations is a common, large-scale and year-round practice in multiple countries including Great Britain (GB). While these additional dietary resources can benefit wildlife, there is a concomitant risk of disease transmission, particularly when birds repeatedly congregate in the same place at high densities and through interactions of species that would not normally associate in close proximity. Citizen science schemes recording garden birds are popular and can integrate disease surveillance with population monitoring, offering a unique opportunity to explore inter-relationships between supplementary feeding, disease epidemiology and population dynamics. Here, we present findings from a national surveillance programme in GB and note the dynamism of endemic and emerging diseases over a 25-year period, focusing on protozoal (finch trichomonosis), viral (Paridae pox) and bacterial (passerine salmonellosis) diseases with contrasting modes of transmission. We also examine the occurrence of mycotoxin contamination of food residues in bird feeders, which present both a direct and indirect (though immunosuppression) risk to wild bird health. Our results inform evidence-based mitigation strategies to minimize anthropogenically mediated health hazards, while maintaining the benefits of providing supplementary food for wild birds. This article is part of the theme issue ‘Anthropogenic resource subsidies and host–parasite dynamics in wildlife’.

In Himalayan songbirds, the speciation rate is ultimately set by ecological competition, rather than by the rate of acquisition of reproductive isolation. New species need new niches The beginnings of adaptive radiation and speciation have been widely studied — in Darwin's finches, sticklebacks and cichlid fish, for example — but relatively little is known about what happens next. Specifically, what is the rate-limiting step for the establishment of new species? This seven-year study of the 358 songbird species found on the Himalayan slopes suggests that it is the rates at which new niches are created and occupied that limits diversification, not the rate at which new species form through reproductive isolation. Speciation generally involves a three-step process—range expansion, range fragmentation and the development of reproductive isolation between spatially separated populations 1 , 2 . Speciation relies on cycling through these three steps and each may limit the rate at which new species form 1 , 3 . We estimate phylogenetic relationships among all Himalayan songbirds to ask whether the development of reproductive isolation and ecological competition, both factors that limit range expansions 4 , set an ultimate limit on speciation. Based on a phylogeny for all 358 species distributed along the eastern elevational gradient, here we show that body size and shape differences evolved early in the radiation, with the elevational band occupied by a species evolving later. These results are consistent with competition for niche space limiting species accumulation 5 . Even the elevation dimension seems to be approaching ecological saturation, because the closest relatives both inside the assemblage and elsewhere in the Himalayas are on average separated by more than five million years, which is longer than it generally takes for reproductive isolation to be completed 2 , 3 , 6 ; also, elevational distributions are well explained by resource availability, notably the abundance of arthropods, and not by differences in diversification rates in different elevational zones. Our results imply that speciation rate is ultimately set by niche filling (that is, ecological competition for resources), rather than by the rate of acquisition of reproductive isolation.

Animals living in temporally dynamic environments experience variation in resource availability, climate and threat of infection over the course of the year. Thus, to survive and reproduce successfully, these organisms must allocate resources among competing physiological systems in such a way as to maximize fitness in changing environments. Here, we review evidence supporting the hypothesis that physiological trade-offs, particularly those between the reproductive and immune systems, mediate part of the seasonal changes detected in the immune defences of many vertebrates. Abundant recent work has detected significant energetic and nutritional costs of immune defence. Sometimes these physiological costs are sufficiently large to affect fitness (e.g. reproductive output, growth or survival), indicating that selection for appropriate allocation strategies probably occurred in the past. Because hormones often orchestrate allocations among physiological systems, the endocrine mediators of seasonal changes in immune activity are discussed. Many hormones, including melatonin, glucocorticoids and androgens have extensive and consistent effects on the immune system, and they change in systematic fashions over the year. Finally, a modified framework within which to conduct future studies in ecological immunology is proposed, viz. a heightened appreciation of the complex but intelligible nature of the vertebrate immune system. Although other factors besides trade-offs undoubtedly influence seasonal variation in immune defence in animals, a growing literature supports a role for physiological trade-offs and the fitness consequences they sometimes produce.

The small size of the billions of migrating songbirds commuting between temperate breeding sites and the tropics has long prevented the study of the largest part of their annual cycle outside the breeding grounds. Using light-level loggers (geolocators), we recorded the entire annual migratory cycle of the red-backed shrike Lanius collurio, a trans-equatorial Eurasian-African passerine migrant. We tested differences between autumn and spring migration for nine individuals. Duration of migration between breeding and winter sites was significantly longer in autumn (average 96 days) when compared with spring (63 days). This difference was explained by much longer staging periods during autumn (71 days) than spring (9 days). Between staging periods, the birds travelled faster during autumn (356 km d–1) than during spring (233 km d–1). All birds made a protracted stop (53 days) in Sahelian sub-Sahara on southbound migration. The birds performed a distinct loop migration (22 000 km) where spring distance, including a detour across the Arabian Peninsula, exceeded the autumn distance by 22 per cent. Geographical scatter between routes was particularly narrow in spring, with navigational convergence towards the crossing point from Africa to the Arabian Peninsula. Temporal variation between individuals was relatively constant, while different individuals tended to be consistently early or late at different departure/arrival occasions during the annual cycle. These results demonstrate the existence of fundamentally different spatio-temporal migration strategies used by the birds during autumn and spring migration, and that songbirds may rely on distinct staging areas for completion of their annual cycle, suggesting more sophisticated endogenous control mechanisms than merely clock-and-compass guidance among terrestrial solitary migrants. After a century with metal-ringing, year-round tracking of long-distance migratory songbirds promises further insights into bird migration.

Costly interactions between species that arise as a by-product of ancestral similarities in communication signals are expected to persist only under specific evolutionary circumstances. Territorial aggression between species, for instance, is widely assumed to persist only when extrinsic barriers prevent niche divergence or selection in sympatry is too weak to overcome gene flow from allopatry. However, recent theoretical and comparative studies have challenged this view. Here we present a large-scale, phylogenetic analysis of the distribution and determinants of interspecific territoriality. We find that interspecific territoriality is widespread in birds and strongly associated with hybridization and resource overlap during the breeding season. Contrary to the view that territoriality only persists between species that rarely breed in the same areas or where niche divergence is constrained by habitat structure, we find that interspecific territoriality is positively associated with breeding habitat overlap and unrelated to habitat structure. Furthermore, our results provide compelling evidence that ancestral similarities in territorial signals are maintained and reinforced by selection when interspecific territoriality is adaptive. The territorial signals linked to interspecific territoriality in birds depend on the evolutionary age of interacting species, plumage at shallow (within-family) timescales, and song at deeper (between-family) timescales. Evidently, territorial interactions between species have persisted and shaped phenotypic diversity on a macroevolutionary timescale.

1. Properly timed spring migration enhances reproduction and survival. Climate change requires organisms to respond to changes such as advanced spring phenology. Pied flycatchers Ficedula hypoleuca have become a model species to study such phenological adaptations of long-distance migratory songbirds to climate change, but data on individuals' time schedules outside the breeding season are still lacking. 2. Using light-level geolocators, we studied variation in migration schedules across the year in a pied flycatcher population in the Netherlands, which sheds light on the ability for individual adjustments in spring arrival timing to track environmental changes at their breeding grounds. 3. We show that variation in arrival dates to breeding sites in 2014 was caused by variation in departure date from sub-Saharan Africa and not by environmental conditions encountered en route. Spring migration duration was short for all individuals, on average 2 weeks. Males migrated ahead of females in spring, while migration schedules in autumn were flexibly adjusted according to breeding duties. Individuals were therefore not consistently early or late throughout the year. 4. In fast migrants like our Dutch pied flycatchers, advancement of arrival to climate change likely requires changes in spring departure dates. Adaptation for earlier arrival may be slowed down by harsh circumstances in winter, or years with high costs associated with early migration.

Behavioral interference between species can influence a wide range of ecological and evolutionary processes. Here, we test foundational hypotheses regarding the origins and maintenance of interspecific territoriality, and evaluate the role of interspecific territoriality and hybridization in shaping species distributions and transitions from parapatry to sympatry in sister species of North American perching birds (Passeriformes). We find that interspecific territoriality is pervasive among sympatric sister species pairs, and that interspecifically territorial species pairs have diverged more recently than sympatric noninterspecifically territorial pairs. None of the foundational hypotheses alone explains the observed patterns of interspecific territoriality, but our results support the idea that some cases of interspecific territoriality arise from misdirected intraspecific aggression while others are evolved responses to resource competition. The combination of interspecific territoriality and hybridization appears to be an unstable state associated with parapatry, whereas species that are interspecifically territorial and do not hybridize are able to achieve extensive fine- and coarse-scale breeding range overlap. In sum, these results suggest that interspecific territoriality has multiple origins and impacts coexistence at multiple spatial scales.

Lunar cycle and moonlight exposure have significant impacts on animal behaviour and physiology. The presence or absence of moonlight, along with predictable changes in brightness throughout the lunar cycle, can shape reproduction, foraging, communication, and other aspects of an animal’s world. While it has been shown that invertebrates use the moonlight for orientation, little is known on the effect of the lunar cycle on migratory birds. We found that the lunar cycle affected the nocturnal migration activity of a diurnal songbird species, the Eurasian Skylark Alauda arvensis. The occurrence of birds increased with moon fraction, moonlight intensity and duration, while abundance correlated positively with increasing moonlight intensity. Our findings of increased migration activity in bright nights around full moon contradict previous assumptions that small bird migrants would avoid such nights due to increased predation pressure and decreased visibility of stars for orientation. We argue that migrants relying on visual cues for orientation might favour moonlit nights, while future studies should also test whether the position of the moon can be used for navigation by birds.

Avian influenza A viruses (IAV) have received significant attention due to the threat they pose to human, livestock, and wildlife health. In this review, we focus on what is known about IAV dynamics in less common avian species that may play a role in trafficking IAVs to poultry operations. Specifically, we focus on synanthropic bird species. Synanthropic species, otherwise known as peridomestic, are species that are ecologically associated with humans and anthropogenically modified landscapes, such as agricultural and urban areas. Aquatic birds such as waterfowl and shorebirds are the species most commonly associated with avian IAVs, and are generally considered the reservoir or maintenance hosts in the natural ecology of these viruses. Waterfowl and shorebirds are occasionally associated with poultry facilities, but are uncommon or absent in many areas, especially large commercial operations. In these cases, spillover hosts that share resources with both maintenance hosts and target hosts such as poultry may play an important role in introducing wild bird viruses onto farms. Consequently, our focus here is on what is known about IAV dynamics in synanthropic hosts that are commonly found on both farms and in nearby habitats, such as fields, lakes, wetlands, or riparian areas occupied by waterfowl or shorebirds.