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Background: West Nile virus (WNV) outbreaks in birds, humans, and livestock have occurred in multiple areas in Europe and have had a significant impact on animal and human health. The patterns of emergence and spread of WNV in Europe are very different from those in the US and understanding these are important for guiding preparedness activities. Methods: We mapped the evolution and spread history of WNV in Europe by incorporating viral genome sequences and epidemiological data into phylodynamic models. Spatially explicit phylogeographic models were developed to explore the possible contribution of different drivers to viral dispersal direction and velocity. A "skygrid-GLM" approach was used to identify how changes in environments would predict viral genetic diversity variations over time. Findings: Among the six lineages found in Europe, WNV-2a (a sub-lineage of WNV-2) has been predominant (accounting for 73% of all sequences obtained in Europe that have been shared in the public domain) and has spread to at least 14 countries. In the past two decades, WNV-2a has evolved into two major co-circulating clusters, both originating from Central Europe, but with distinct dynamic history and transmission patterns. WNV-2a spreads at a high dispersal velocity (88km/yr–215 km/yr) which is correlated to bird movements. Notably, amongst multiple drivers that could affect the spread of WNV, factors related to land use were found to strongly influence the spread of WNV. Specifically, the intensity of agricultural activities (defined by factors related to crops and livestock production, such as coverage of cropland, pasture, cultivated and managed vegetation, livestock density) were positively associated with both spread direction and velocity. In addition, WNV spread direction was associated with high coverage of wetlands and migratory bird flyways. Conclusion: Our results suggest that—in addition to ecological conditions favouring bird- and mosquito- presence—agricultural land use may be a significant driver of WNV emergence and spread. Our study also identified significant gaps in data and the need to strengthen virological surveillance in countries of Central Europe from where WNV outbreaks are likely seeded. Enhanced monitoring for early detection of further dispersal could be targeted to areas with high agricultural activities and habitats of migratory birds. Author summary: Evidence for the drivers for West Nile virus (WNV) dispersal has been not clear in Europe. Here, we have comprehensively described the dispersal history of the currently predominant WNV lineage in Europe and estimated the contribution of key drivers of spread between and within countries. By fitting several phylodynamic and phylogeographic models, we found that 1) WNV in Europe has a greater lineage diversity than in other regions of the world. 2) Agricultural intensity had the greatest impact on both WNV spread direction and velocity. 3) WNV spread direction was specifically associated with urbanization and bird habitats. 4) Climate change and bio-diversity changes predicted viral genetic diversity over time. Our study revealed that to enhance preparedness for potential outbreaks, it is important to further define these drivers, and increase sampling for WNV in areas that appear to be a source of WNV in other countries in Europe, as well as in regions with known risk factors but where WNV has not yet been detected. [ABSTRACT FROM AUTHOR]

Recent avian influenza infection outbreaks have resulted in global biosecurity and economic concerns. Mallards are asymptomatic for the disease and can potentially spread AI along migratory bird flyways. In a previous study, trained mice correctly discriminated the health status of individual ducks on the basis of fecal odors when feces from post-infection periods were paired with feces from pre-infection periods. Chemical analyses indicated that avian influenza infection was associated with a marked increase of acetoin (3-hydroxy-2-butanone) in feces. In the current study, domesticated male ferrets (Mustela putorius furo) were trained to display a specific conditioned response (i.e. active scratch alert) in response to a marked increase of acetoin in a presentation of an acetoin:1-octen-3-ol solution. Ferrets rapidly generalized this learned response to the odor of irradiated feces from avian influenza infected mallards. These results suggest that a trained mammalian biosensor could be employed in an avian influenza surveillance program. [ABSTRACT FROM AUTHOR]

Land reclamation projects and the installation of drainage infrastructure has impacted coastal wetlands worldwide. By altering water levels and inundation extent, these activities have changed the viable ecosystems onsite and resulted in the proliferation of freshwater species. As more than 50% of tidal wetlands have been degraded globally over the last 100 years, the importance of this issue is increasingly being recognised and tidal wetland restoration projects are underway worldwide. However, there are currently limited sites where large-scale reintroduction of tidal flushing has been implemented with the explicit aim to foster the growth of a threatened ecosystem. In this study, the tidal restoration of an internationally recognised Ramsar listed wetland in eastern Australia is described to highlight how coastal saltmarsh can be targeted by mimicking inundation depths and hydroperiod across the 410-ha site. Coastal saltmarsh is particularly important to this site as it is part of the east Australasian flyway for migratory birds and the minimum saltmarsh extent, as listed within the Ramsar's limits of acceptable change, have been breached. To recreate coastal saltmarsh habitat onsite, water level and hydroperiod criteria were established based on similar vegetation patterns within the adjacent estuary. A calibrated 2D hydrodynamic model of the site was then used to test how the preferred inundation criteria could be applied to the largest possible restored wetland area. Once optimised, a synthetic tidal signal was implemented onsite via automated hydraulic controls. The onsite vegetation response over an 8-year period was assessed to highlight the ecosystem response to controlled tidal inundation and denoted substantial saltmarsh expansion during the period. The techniques applied onsite have successfully met the restoration targets and can be applied at similar sites worldwide, offsetting sea level rise impacts to natural inundation hydroperiod. [ABSTRACT FROM AUTHOR]

West Nile virus is a widely spread arthropod-born virus, which has mosquitoes as vectors and birds as reservoirs. Humans, as dead-end hosts of the virus, may suffer West Nile Fever (WNF), which sometimes leads to death. In Europe, the first large-scale epidemic of WNF occurred in 1996 in Romania. Since then, human cases have increased in the continent, where the highest number of cases occurred in 2018. Using the location of WNF cases in 2017 and favorability models, we developed two risk models, one environmental and the other spatio-environmental, and tested their capacity to predict in 2018: 1) the location of WNF; 2) the intensity of the outbreaks (i.e. the number of confirmed human cases); and 3) the imminence of the cases (i.e. the Julian week in which the first case occurred). We found that climatic variables (the maximum temperature of the warmest month and the annual temperature range), human-related variables (rain-fed agriculture, the density of poultry and horses), and topo-hydrographic variables (the presence of rivers and altitude) were the best environmental predictors of WNF outbreaks in Europe. The spatio-environmental model was the most useful in predicting the location of WNF outbreaks, which suggests that a spatial structure, probably related to bird migration routes, has a role in the geographical pattern of WNF in Europe. Both the intensity of cases and their imminence were best predicted using the environmental model, suggesting that these features of the disease are linked to the environmental characteristics of the areas. We highlight the relevance of river basins in the propagation dynamics of the disease, as outbreaks started in the lower parts of the river basins, from where WNF spread towards the upper parts. Therefore, river basins should be considered as operational geographic units for the public health management of the disease. Author summary: West Nile virus is a widely spread flavivirus, which is transmitted from birds to humans by mosquitoes. In humans, the virus can cause West Nile Fever (WNF) and in some cases, it affects the nervous system leading to severe symptoms that may result in death. Human cases have increased in Europe since the large-scale epidemic in 1996, being 2018 the year with the highest number of cases registered to date. We developed risk models based on 2017 cases, and predicted in 2018: 1) the occurrence of the disease; 2) the intensity of the outbreaks; and 3) the imminence of the cases. We identified favorable areas for the incidence of the virus in which environmental and human-related variables had an important role. The outbreaks began in the lower areas of large river basins and spread to higher areas, which highlights the importance of river basins in the propagation of outbreaks. Consequently, the early warning should be based on a basin scale. [ABSTRACT FROM AUTHOR]

Genetically related highly pathogenic avian influenza viruses (HPAIVs) of H5N6 subtype caused outbreaks simultaneously in East Asia and Europe—geographically distinct regions—during winter 2017–2018. This situation prompted us to consider whether the application of phylogeographic analysis to a particular gene segment of AIVs could provide clues for understanding how AIV had been disseminated across the continent. Here, the N6 NA genes of influenza viruses isolated across the world were subjected to phylogeographic analysis to illustrate the inter- and intracontinental dissemination of AIVs. Those isolated in East Asia during winter and in Mongolia/Siberia during summer were comingled within particular clades of the phylogeographic tree. For AIVs in one clade, their dissemination in eastern Eurasia extended from Yakutia, Russia, in the north to East Asia in the south. AIVs in western Asia, Europe, and Mongolia were also comingled within other clades, indicating that Mongolia/Siberia plays an important role in the dissemination of AIVs across the Eurasian continent. Mongolia/Siberia may therefore have played a role in the simultaneous outbreaks of H5N6 HPAIVs in Europe and East Asia during the winter of 2017–2018. In addition to the long-distance intracontinental disseminations described above, intercontinental disseminations of AIVs between Eurasia and Africa and between Eurasia and North America were also observed. Integrating these results and known migration flyways suggested that the migration of wild birds and the overlap of flyways, such as that observed in Mongolia/Siberia and along the Alaskan Peninsula, contributed to the long-distance intra- and intercontinental dissemination of AIVs. These findings highlight the importance of understanding the movement of migratory birds and the dynamics of AIVs in breeding areas—especially where several migration flyways overlap—in forecasting outbreaks caused by HPAIVs. [ABSTRACT FROM AUTHOR]

Biogeography, systematics and taxonomy are complementary scientific disciplines. To understand a species’ origin, migration routes, distribution and evolutionary history, it is first necessary to establish its taxonomic boundaries. Here, we use an integrative approach that takes advantage of complementary disciplines to resolve an intriguing scientific question. Populations of an unknown moss found in the Canary Islands (Tenerife Island) resembled two different Californian endemic species: Orthotrichum shevockii and O. kellmanii. To determine whether this moss belongs to either of these species and, if so, to explain its presence on this distant oceanic island, we combined the evaluation of morphological qualitative characters, statistical morphometric analyses of quantitative traits, and molecular phylogenetic inferences. Our results suggest that the two Californian mosses are conspecific, and that the Canarian populations belong to this putative species, with only one taxon thus involved. Orthotrichum shevockii (the priority name) is therefore recognized as a morphologically variable species that exhibits a transcontinental disjunction between western North America and the Canary Islands. Within its distribution range, the area of occupancy is limited, a notable feature among bryophytes at the intraspecific level. To explain this disjunction, divergence time and ancestral area estimation analyses are carried out and further support the hypothesis of a long-distance dispersal event from California to Tenerife Island. [ABSTRACT FROM AUTHOR]

Defining and identifying changes to seasonal ranges of migratory species is required for effective conservation. Historic sightings of migrating whooping cranes (Grus americana) have served as sole source of information to define a migration corridor in the Great Plains of North America (i.e., Canadian Prairies and United States Great Plains) for this endangered species. We updated this effort using past opportunistic sightings from 1942–2016 (n = 5,055) and more recent (2010–2016) location data from 58 telemetered birds (n = 4,423) to delineate migration corridors that included 50%, 75%, and 95% core areas. All migration corridors were well defined and relatively compact, with the 95% core corridor averaging 294 km wide, although it varied approximately ±40% in width from 170 km in central Texas to 407 km at the international border of the United States and Canada. Based on historic sightings and telemetry locations, we detected easterly movements in locations over time, primarily due to locations west of the median shifting east. This shift occurred from northern Oklahoma to central Saskatchewan at an average rate of 1.2 km/year (0.3–2.8 km/year). Associated with this directional shift was a decrease in distance of locations from the median in the same region averaging -0.7 km/year (-0.3–-1.3 km/year), suggesting a modest narrowing of the migration corridor. Changes in the corridor over the past 8 decades suggest that agencies and organizations interested in recovery of this species may need to modify where conservation and recovery actions occur. Whooping cranes showed apparent plasticity in their migratory behavior, which likely has been necessary for persistence of a wetland-dependent species migrating through the drought-prone Great Plains. Behavioral flexibility will be useful for whooping cranes to continue recovery in a future of uncertain climate and land use changes throughout their annual range. [ABSTRACT FROM AUTHOR]

Bird-window collisions are a major and poorly-understood generator of bird mortality. In North America, studies of this topic tend to be focused east of the Mississippi River, resulting in a paucity of data from the Western flyways. Additionally, few available data can critically evaluate factors such as time of day, sex and age bias, and effect of window pane size on collisions. We collected and analyzed 5 years of window strike data from a 3-story building in a large urban park in San Francisco, California. To evaluate our window collision data in context, we collected weekly data on local bird abundance in the adjacent parkland. Our study asks two overarching questions: first–what aspects of a bird’s biology might make them more likely to fatally strike windows; and second, what characteristics of a building’s design contribute to bird-window collisions. We used a dataset of 308 fatal bird strikes to examine the relationships of strikes relative to age, sex, time of day, time of year, and a variety of other factors, including mitigation efforts. We found that actively migrating birds may not be major contributors to collisions as has been found elsewhere. We found that males and young birds were both significantly overrepresented relative to their abundance in the habitat surrounding the building. We also analyzed the effect of external window shades as mitigation, finding that an overall reduction in large panes, whether covered or in some way broken up with mullions, effectively reduced window collisions. We conclude that effective mitigation or design will be required in all seasons, but that breeding seasons and migratory seasons are most critical, especially for low-rise buildings and other sites away from urban migrant traps. Finally, strikes occur throughout the day, but mitigation may be most effective in the morning and midday. [ABSTRACT FROM AUTHOR]

Birds of the order Anseriformes, commonly referred to as waterfowl, are frequently infected by Haemosporidia of the genera Haemoproteus, Plasmodium, and Leucocytozoon via dipteran vectors. We analyzed nucleotide sequences of the Cytochrome b (Cytb) gene from parasites of these genera detected in six species of ducks from Alaska and California, USA to characterize the genetic diversity of Haemosporidia infecting waterfowl at two ends of the Pacific Americas Flyway. In addition, parasite Cytb sequences were compared to those available on a public database to investigate specificity of genetic lineages to hosts of the order Anseriformes. Haplotype and nucleotide diversity of Haemoproteus Cytb sequences was lower than was detected for Plasmodium and Leucocytozoon parasites. Although waterfowl are presumed to be infected by only a single species of Leucocytozoon, L. simondi, diversity indices were highest for haplotypes from this genus and sequences formed five distinct clades separated by genetic distances of 4.9%–7.6%, suggesting potential cryptic speciation. All Haemoproteus and Leucocytozoon haplotypes derived from waterfowl samples formed monophyletic clades in phylogenetic analyses and were unique to the order Anseriformes with few exceptions. In contrast, waterfowl-origin Plasmodium haplotypes were identical or closely related to lineages found in other avian orders. Our results suggest a more generalist strategy for Plasmodium parasites infecting North American waterfowl as compared to those of the genera Haemoproteus and Leucocytozoon. [ABSTRACT FROM AUTHOR]

Avian influenza virus (AIV) in wild birds has been of increasing interest over the last decade due to the emergence of AIVs that cause significant disease and mortality in both poultry and humans. While research clearly demonstrates that AIVs can move across the Pacific or Atlantic Ocean, there has been no data to support the mechanism of how this occurs. In spring and autumn of 2010 and autumn of 2011 we obtained cloacal swab samples from 1078 waterfowl, gulls, and shorebirds of various species in southwest and west Iceland and tested them for AIV. From these, we isolated and fully sequenced the genomes of 29 AIVs from wild caught gulls (Charadriiformes) and waterfowl (Anseriformes) in Iceland. We detected viruses that were entirely (8 of 8 genomic segments) of American lineage, viruses that were entirely of Eurasian lineage, and viruses with mixed American-Eurasian lineage. Prior to this work only 2 AIVs had been reported from wild birds in Iceland and only the sequence from one segment was available in GenBank. This is the first report of finding AIVs of entirely American lineage and Eurasian lineage, as well as reassortant viruses, together in the same geographic location. Our study demonstrates the importance of the North Atlantic as a corridor for the movement of AIVs between Europe and North America. [ABSTRACT FROM AUTHOR]

Three H14 influenza A virus (IAV) isolates recovered in 2010 during routine virus surveillance along the Mississippi Migratory Bird Flyway in Wisconsin, U.S.A. raised questions about the natural history of these rare viruses. These were the first H14 IAV isolates recovered in the Western Hemisphere and the only H14 IAV isolates recovered since the original four isolates in 1982 in Asia. Full length genomic sequencing of the 2010 H14 isolates demonstrated the hemagglutinin (HA) gene from the 1982 and 2010 H14 isolates showed 89.6% nucleotide and 95.6% amino acid similarity and phylogenetic analysis of these viruses placed them with strong support within the H14 subtype lineage. The level of genomic divergence observed between the 1982 and 2010 viruses provides evidence that the H14 HA segment was circulating undetected in hosts and was not maintained in environmental stasis. Further, the evolutionary relationship observed between 1982 H14 and the closely related H4 subtype HA segments were similar to contemporary comparisons suggesting limited adaptive divergence between these sister subtypes. The nonstructural (NS) segment of one 2010 isolate was placed in a NS clade isolated infrequently over the last several decades that includes the NS segment from a previously reported 1982 H14 isolate indicating the existence of an unidentified pool of genomic diversity. An additional neuraminidase reassortment event indicated a recent inter-hemispheric gene flow from Asia into the center of North America. These results demonstrate temporal and spatial gaps in the understanding of IAV natural history. Additionally, the reassortment history of these viruses raises concern for the inter-continental spread of IAVs and the efficacy of current IAV surveillance efforts in detecting genomic diversity of viruses circulating in wild birds. [ABSTRACT FROM AUTHOR]

At temperate latitudes the synoptic patterns of bird migration are strongly structured by the presence of cyclones and anticyclones, both in the horizontal and altitudinal dimensions. In certain synoptic conditions, birds may efficiently cross regions with opposing surface wind by choosing a higher flight altitude with more favourable wind. We observed migratory passerines at mid-latitudes that selected high altitude wind optima on particular nights, leading to the formation of structured migration layers at varying altitude up to 3 km. Using long-term vertical profiling of bird migration by C-band Doppler radar in the Netherlands, we find that such migration layers occur nearly exclusively during spring migration in the presence of a high-pressure system. A conceptual analytic framework providing insight into the synoptic patterns of wind assistance for migrants that includes the altitudinal dimension has so far been lacking. We present a simple model for a baroclinic atmosphere that relates vertical profiles of wind assistance to the pressure and temperature patterns occurring at temperate latitudes. We show how the magnitude and direction of the large scale horizontal temperature gradient affects the relative gain in wind assistance that migrants obtain through ascending. Temperature gradients typical for northerly high-pressure systems in spring are shown to cause high altitude wind optima in the easterly sectors of anticyclones, thereby explaining the frequent observations of high altitude migration in these synoptic conditions. Given the recurring synoptic arrangements of pressure systems across temperate continents, the opportunities for exploiting high altitude wind will differ between flyways, for example between easterly and westerly oceanic coasts. [ABSTRACT FROM AUTHOR]

Tracking repeat migratory journeys of individual animals is required to assess phenotypic plasticity of individual migration behaviour in space and time. We used light-level geolocators to track the long-distance journeys of migratory songbirds (wood thrush, Hylocichla mustelina), and, for the first time, repeat journeys of individuals. We compare between- and within-individual variation in migration to examine flexibility of timing and route in spring and autumn. Date of departure from wintering sites in Central America, along with sex and age factors, explained most of the variation (71%) in arrival date at North American breeding sites. Spring migration showed high within-individual repeatability in timing, but not in route. In particular, spring departure dates of individuals were highly repeatable, with a mean difference between years of just 3 days. Autumn migration timing and routes were not repeatable. Our results provide novel evidence of low phenotypic plasticity in timing of spring migration, which may limit the ability of individuals to adjust migration schedules in response to climate change. [ABSTRACT FROM AUTHOR]

Many species of birds and bats undertake seasonal migrations between breeding and over-wintering sites. En-route, migrants alternate periods of flight with time spent at stopover - the time and space where individuals rest and refuel for subsequent flights. We assessed the spatial scale of movements made by migrants during stopover by using an array of automated telemetry receivers with multiple antennae to track the daily location of individuals over a geographic area ~20x40 km. We tracked the movements of 322 individuals of seven migratory vertebrate species (5 passerines, 1 owl and 1 bat) during spring and fall migratory stopover on and adjacent to a large lake peninsula. Our results show that many individuals leaving their capture site relocate within the same landscape at some point during stopover, moving as much as 30 km distant from their site of initial capture. We show that many apparent nocturnal departures from stopover sites are not a resumption of migration in the strictest sense, but are instead relocations that represent continued stopover at a broader spatial scale. [ABSTRACT FROM AUTHOR]

Background: Our ability to monitor populations or species that were once threatened or endangered and in the process of recovery is enhanced by using genetic methods to assess overall population stability and size over time. This can be accomplished most directly by obtaining genetic measures from temporally-spaced samples that reflect the overall stability of the population as given by changes in genetic diversity levels (allelic richness and heterozygosity), degree of population differentiation (FST and DEST), and effective population size (Ne). The primary goal of any recovery effort is to produce a longterm self-sustaining population, and these genetic measures provide a metric by which we can gauge our progress and help make important management decisions. Methodology/Principal Findings: The peregrine falcon in North America (Falco peregrinus tundrius and anatum) was delisted in 1994 and 1999, respectively, and its abundance will be monitored by the species Recovery Team every three years until 2015. Although the United States Fish and Wildlife Service makes a distinction between tundrius and anatum subspecies, our genetic results based on eleven microsatellite loci suggest limited differentiation that can be attributed to an isolation by distance relationship and warrant no delineation of these two subspecies in its northern latitudinal distribution from Alaska through Canada into Greenland. Using temporal samples collected at Padre Island, Texas during migration (seven temporal time periods between 1985-2007), no significant differences in genetic diversity or significant population differentiation in allele frequencies between time periods were observed and were indistinguishable from those obtained from tundrius/anatum breeding locations throughout their northern distribution. Estimates of harmonic mean Ne were variable and imprecise, but always greater than 500 when employing multiple temporal genetic methods. Conclusions/Significance: These results, including those from simulations to assess the power of each method to estimate Ne, suggest a stable or growing population, which is consistent with ongoing field-based monitoring surveys. Therefore, historic and continuing efforts to prevent the extinction of the peregrine falcon in North America appear successful with no indication of recent decline, at least from the northern latitude range-wide perspective. The results also further highlight the importance of archiving samples and their use for continual assessment of population recovery and long-term viability. [ABSTRACT FROM AUTHOR]