Low-coverage whole genome sequencing for highly accurate population assignment: Mapping migratory connectivity in the American Redstart (Setophaga ruticilla)

Understanding the geographic linkages among populations across the annual cycle is an essential component for understanding the ecology and evolution of migratory species and for facilitating their effective conservation. While genetic markers have been widely applied to describe migratory connections, the rapid development of new sequencing methods, such as low-coverage whole genome sequencing (lcWGS), provides new opportunities for improved estimates of migratory connectivity. Here, we use lcWGS to identify fine-scale population structure in a widespread songbird, the American Redstart (Setophaga ruticilla), and accurately assign individuals to genetically distinct breeding populations. Assignment of individuals from the nonbreeding range reveals population-specific patterns of varying migratory connectivity. By combining migratory connectivity results with demographic analysis of population abundance and trends, we consider full annual cycle conservation strategies for preserving numbers of individuals and genetic diversity. Notably, we highlight the importance of the Northern Temperate-Greater Antilles migratory population as containing the largest proportion of individuals in the species. Finally, we highlight valuable considerations for other population assignment studies aimed at using lcWGS. Our results have broad implications for improving our understanding of the ecology and evolution of migratory species through conservation genomics approaches.

Demographic consequences of phenological asynchrony for North American songbirds

Changes in phenology in response to ongoing climate change have been observed in numerous taxa around the world. Differing rates of phenological shifts across trophic levels have led to concerns that ecological interactions may become increasingly decoupled in time, with potential negative consequences for populations. Despite widespread evidence of phenological change and a broad body of supporting theory, large-scale multitaxa evidence for demographic consequences of phenological asynchrony remains elusive. Using data from a continental-scale bird-banding program, we assess the impact of phenological dynamics on avian breeding productivity in 41 species of migratory and resident North American birds breeding in and around forested areas. We find strong evidence for a phenological optimum where breeding productivity decreases in years with both particularly early or late phenology and when breeding occurs early or late relative to local vegetation phenology. Moreover, we demonstrate that landbird breeding phenology did not keep pace with shifts in the timing of vegetation green-up over a recent 18-y period, even though avian breeding phenology has tracked green-up with greater sensitivity than arrival for migratory species. Species whose breeding phenology more closely tracked green-up tend to migrate shorter distances (or are resident over the entire year) and breed earlier in the season. These results showcase the broadest-scale evidence yet of the demographic impacts of phenological change. Future climate change-associated phenological shifts will likely result in a decrease in breeding productivity for most species, given that bird breeding phenology is failing to keep pace with climate change.

Abiotic conditions shape spatial and temporal morphological variation in North American birds

Quantifying environment-morphology relationships is important not only for understanding the fundamental processes driving phenotypic diversity within and among species but also for predicting how species will respond to ongoing global change. Despite a clear set of expectations motivated by ecological theory, broad evidence in support of generalizable effects of abiotic conditions on spatial and temporal intraspecific morphological variation has been limited. Using standardized data from >250,000 captures of 105 landbird species, we assessed intraspecific shifts in the morphology of adult male birds since 1989 while simultaneously measuring spatial morphological gradients across the North American continent. We found strong spatial and temporal trends in average body size, with warmer temperatures associated with smaller body sizes both at more equatorial latitudes and in more recent years. The magnitude of these thermal effects varied both across and within species, with results suggesting it is the warmest, rather than the coldest, temperatures that drive both spatial and temporal trends. Stronger responses to spatial-rather than temporal-variation in temperature suggest that morphological change may not be keeping up with the pace of climate change. Additionally, as elevation increases, we found that body size declines as relative wing length increases, probably due to the benefits that longer wings confer for flight in thin air environments. Our results provide support for both existing and new large-scale ecomorphological 'rules' and highlight how the response of functional trade-offs to abiotic variation drives morphological change.

Demographic responses to climate-driven variation in habitat quality across the annual cycle of a migratory bird species

The demography and dynamics of migratory bird populations depend on patterns of movement and habitat quality across the annual cycle. We leveraged archival GPS‐tagging data, climate data, remote‐sensed vegetation data, and bird‐banding data to better understand the dynamics of black‐headed grosbeak (Pheucticus melanocephalus) populations in two breeding regions, the coast and Central Valley of California (Coastal California) and the Sierra Nevada mountain range (Sierra Nevada), over 28 years (1992–2019). Drought conditions across the annual cycle and rainfall timing on the molting grounds influenced seasonal habitat characteristics, including vegetation greenness and phenology (maturity dates). We developed a novel integrated population model with population state informed by adult capture data, recruitment rates informed by age‐specific capture data and climate covariates, and survival rates informed by adult capture–mark–recapture data and climate covariates. Population size was relatively variable among years for Coastal California, where numbers of recruits and survivors were positively correlated, and years of population increase were largely driven by recruitment. In the Sierra Nevada, population size was more consistent and showed stronger evidence of population regulation (numbers of recruits and survivors negatively correlated). Neither region showed evidence of long‐term population trend. We found only weak support for most climate–demographic rate relationships. However, recruitment rates for the Coastal California region were higher when rainfall was relatively early on the molting grounds and when wintering grounds were relatively cool and wet. We suggest that our approach of integrating movement, climate, and demographic data within a novel modeling framework can provide a useful method for better understanding the dynamics of broadly distributed migratory species.

Genetic variation reveals individual-level climate tracking across the annual cycle of a migratory bird

For migratory species, seasonal movements complicate local climate adaptation, as it is unclear whether individuals track climate niches across the annual cycle. In the migratory songbird yellow warbler (Setophaga petechia), we find a correlation between individual-level wintering and breeding precipitation, but not temperature. Birds wintering in the driest regions of the Neotropics breed in the driest regions of North America. Individuals from drier regions also possess distinct morphologies and population responses to varying rainfall. We find a positive association between bill size and breeding season precipitation which, given documented climate-associated genomic variation, might reflect adaptation to local precipitation regimes. Relative abundance in the breeding range is linked to interannual fluctuations in precipitation, but the directionality of this response varies across geography. Together, our results suggest that variation in climate optima may exist across the breeding range of yellow warblers and provide a mechanism for selection across the annual cycle.

A genoscape-network model for conservation prioritization in a migratory bird

Migratory animals are declining worldwide and coordinated conservation efforts are needed to reverse current trends. We devised a novel genoscape-network model that combines genetic analyses with species distribution modeling and demographic data to overcome challenges with conceptualizing alternative risk factors in migratory species across their full annual cycle. We applied our method to the long distance, Neotropical migratory bird, Wilson's Warbler (Cardellina pusilla). Despite a lack of data from some wintering locations, we demonstrated how the results can be used to help prioritize conservation of breeding and wintering areas. For example, we showed that when genetic, demographic, and network modeling results were considered together it became clear that conservation recommendations will differ depending on whether the goal is to preserve unique genetic lineages or the largest number of birds per unit area. More specifically, if preservation of genetic lineages is the goal, then limited resources should be focused on preserving habitat in the California Sierra, Basin Rockies, or Coastal California, where the 3 most vulnerable genetic lineages breed, or in western Mexico, where 2 of the 3 most vulnerable lineages overwinter. Alternatively, if preservation of the largest number of individuals per unit area is the goal, then limited conservation dollars should be placed in the Pacific Northwest or Central America, where densities are estimated to be the highest. Overall, our results demonstrated the utility of adopting a genetically based network model for integrating multiple types of data across vast geographic scales and better inform conservation decision-making for migratory animals.

Yearling proportion correlates with habitat structure in a boreal forest landbird community

Landbird vital rates, such as productivity and adult survivorship, can be estimated by modeling mist-netting capture data. The proportion in which an adult breeding bird is 1 year of age (a “yearling”), however, has been studied only minimally in a few landbird species. Here we relate yearling proportion to habitat-structure covariates, including reclamation age, in a boreal forest landbird community. Data were collected at 35 constant-effort mist-netting stations over a 6-year period, and consisted of 12,714 captures of adults, of 29 landbird species, including 4,943 captures of yearlings. Accuracy of age determination (yearling or older) was assessed based on recapture data and error rates were estimated at a mean of 8.1% (range 0.0–19.4%) among the 29 species, with 20 species showing age-error rates <10%. The estimated mean yearling proportion was 0.407, ranging from 0.178 to 0.613 among species. Remote-sensed Enhanced Vegetation Index (EVI), a measure of habitat greenness, was positively correlated with age since reclamation up to 20 years, at which time it became comparable to that of natural stations. The probability of capturing a yearling for species associated with mature forest was lower at stations with higher EVI and the opposite was the case for species favoring successional habitats. These results suggest that yearling birds are being excluded from preferred breeding habitats by older birds through despotism and/or that yearlings are simply selecting poorer habitat due to lack of breeding experience or other factors. This dynamic appears to be operating in multiple species within this forest landbird community. Captured yearlings may also be “floaters”, or non-breeding individuals not holding territories. However, presuming that yearlings show lower reproductive success whether floating or not, our results suggest that stations with high yearling proportions could be located within sink as opposed to source habitats. Overall, we infer that yearling proportion may become an important vital-rate measure of habitat quality and reclamation efforts, when combined with indices of population size, productivity, reproductive condition and survivorship.

Integrating broad-scale data to assess demographic and climatic contributions to population change in a declining songbird

Climate variation and trends affect species distribution and abundance across large spatial extents. However, most studies that predict species response to climate are implemented at small spatial scales or are based on occurrence-environment relationships that lack mechanistic detail. Here, we develop an integrated population model (IPM) for multi-site count and capture-recapture data for a declining migratory songbird, Wilson's warbler (Cardellina pusilla), in three genetically distinct breeding populations in western North America. We include climate covariates of vital rates, including spring temperatures on the breeding grounds, drought on the wintering range in northwest Mexico, and wind conditions during spring migration. Spring temperatures were positively related to productivity in Sierra Nevada and Pacific Northwest genetic groups, and annual changes in productivity were important predictors of changes in growth rate in these populations. Drought condition on the wintering grounds was a strong predictor of adult survival for coastal California and Sierra Nevada populations; however, adult survival played a relatively minor role in explaining annual variation in population change. A latent parameter representing a mixture of first-year survival and immigration was the largest contributor to variation in population change; however, this parameter was estimated imprecisely, and its importance likely reflects, in part, differences in spatio-temporal distribution of samples between count and capture-recapture data sets. Our modeling approach represents a novel and flexible framework for linking broad-scale multi-site monitoring data sets. Our results highlight both the potential of the approach for extension to additional species and systems, as well as needs for additional data and/or model development.

Phenology and productivity in a montane bird assemblage: Trends and responses to elevation and climate variation

Climate variation has been linked to historical and predicted future distributions and dynamics of wildlife populations. However, demographic mechanisms underlying these changes remain poorly understood. Here, we assessed variation and trends in climate (annual snowfall and spring temperature anomalies) and avian demographic variables from mist-netting data (breeding phenology and productivity) at six sites along an elevation gradient spanning the montane zone of Yosemite National Park between 1993 and 2017. We implemented multi-species hierarchical models to relate demographic responses to elevation and climate covariates. Annual variation in climate and avian demographic variables was high. Snowfall declined (10 mm/year at the highest site, 2 mm at the lowest site), while spring temperature increased (0.045°C/year) over the study period. Breeding phenology (mean first capture date of juvenile birds) advanced by 0.2 day/year (5 days); and productivity (probability of capturing a juvenile bird) increased by 0.8%/year. Breeding phenology was 12 days earlier at the lowest compared to highest site, 18 days earlier in years with lowest compared to highest snowfall anomalies, and 6 d earlier in relatively warm springs (after controlling for snowfall effects). Productivity was positively related to elevation. However, elevation-productivity responses varied among species; species with higher productivity at higher compared to lower elevations tended to be species with documented range retractions during the past century. Productivity tended to be negatively related to snowfall and was positively related to spring temperature. Overall, our results suggest that birds have tracked the variable climatic conditions in this system and have benefited from a trend toward warmer, drier springs. However, we caution that continued warming and multi-year drought or extreme weather years may alter these relationships in the future. Multi-species demographic modeling, such as implemented here, can provide an important tool for guiding conservation of species assemblages under global change.

Avian demographic responses to drought and fire: a community-level perspective

Drought stress is an important consideration for wildlife in arid and semiarid regions under climate change. Drought can impact plant and animal populations directly, through effects on their physiology, as well as indirectly through effects on vegetation productivity and resource availability, and by creating conditions conducive to secondary disturbance, such as wildfire. We implemented a novel approach to understanding community-level demographic responses of birds and their habitats to these stressors in the context of climate change at 14 study sites in the Four Corners region of the southwestern United States. A large wildfire affecting three of the sites provided a natural experiment for also examining fire effects on vegetation and the bird community. We assessed (1) trends in drought and end-of-century (2071-2100) predicted average drought conditions under mid-range and high greenhouse gas concentration trajectory scenarios; (2) effects of drought and fire on habitat (vegetation greenness); and (3) effects of drought and fire on community-level avian productivity and adult apparent survival rates. Drought has increased and is expected to increase further at our study sites under climate change. Under spring drought conditions, vegetation greenness and avian productivity declined, while summer drought appeared to negatively affect adult apparent survival rates. Response to fire was mixed; in the year of the fire, avian productivity declined, but was higher than normal for several years post-fire. Our results highlight important links between environmental stressors and avian vital rates that will likely affect population trajectories in this region under climate change. We suggest that the use and continued development of community-level demographic models will provide useful tool for leveraging sparse species-level data to provide multi-species inferences and inform conservation.

Drivers of demographic decline across the annual cycle of a threatened migratory bird

Migratory species are rapidly declining but we rarely know which periods of the annual cycle are limiting for most species. This knowledge is needed to effectively allocate conservation resources to the periods of the annual cycle that best promote species recovery. We examined demographic trends and response to human footprint for Canada warblers (Cardellina canadensis), a threatened Neotropical migrant, using range-wide data (1993–2016) from the Monitoring Avian Productivity and Survivorship (MAPS) program on the breeding grounds. Declines in abundance were steepest in the eastern breeding region, followed by the western region. Breeding productivity did not decline in any region. In contrast, we observed declining recruitment in all regions, low apparent survival in the east and west, and a decline in apparent survival in the east. Abundance declined with increasing disturbance around MAPS stations. Between 1993 and 2009, the human footprint index on the breeding range increased by 0.11% in contrast to a 14% increase on the wintering range. Landscape-scale disturbance on the breeding grounds may influence abundance in some regions; however, the observed trends in demography and footprint suggests limitation during the non-breeding period as the likely driver of overall declines, particularly for eastern populations.

An integrated population model for bird monitoring in North America

Integrated population models (IPMs) provide a unified framework for simultaneously analyzing data sets of different types to estimate vital rates, population size, and dynamics; assess contributions of demographic parameters to population changes; and assess population viability. Strengths of an IPM include the ability to estimate latent parameters and improve the precision of parameter estimates. We present a hierarchical IPM that combines two broad-scale avian monitoring data sets: count data from the North American Breeding Bird Survey (BBS) and capture-recapture data from the Monitoring Avian Productivity and Survivorship (MAPS) program. These data sets are characterized by large numbers of sample sites and observers, factors capable of inducing error in the sampling and observation processes. The IPM integrates the data sets by modeling the population abundance as a first-order autoregressive function of the previous year's population abundance and vital rates. BBS counts were modeled as a log-linear function of the annual index of population abundance, observation effects (observer identity and first survey year), and overdispersion. Vital rates modeled included adult apparent survival, estimated from a transient Cormack-Jolly-Seber model using MAPS data, and recruitment (surviving hatched birds from the previous season + dispersing adults) estimated as a latent parameter. An assessment of the IPM demonstrated it could recover true parameter values from 200 simulated data sets. The IPM was applied to data sets (1992-2008) of two bird species, Gray Catbird (Dumetella carolinensis) and Wood Thrush (Hylocichla mustelina) in the New England/Mid-Atlantic coastal Bird Conservation Region of the United States. The Gray Catbird population was relatively stable (trend +0.4% per yr), while the Wood Thrush population nearly halved (trend -4.5% per yr) over the 17-yr study period. IPM estimates of population growth rates, adult survival, and detection and residency probabilities were similar and as precise as estimates from the stand-alone BBS and CJS models. A benefit of using the IPM was its ability to estimate the latent recruitment parameter. Annual growth rates for both species correlated more with recruitment than survival, and the relationship for Wood Thrush was stronger than for Gray Catbird. The IPM's unified modeling framework facilitates integration of these important data sets.

Persistent impacts of West Nile virus on North American bird populations

Since its introduction to North America in 1999, West Nile virus (WNV) has had devastating impacts on native host populations, but to date these impacts have been difficult to measure. Using a continental-scale dataset comprised of a quarter-million birds captured over nearly two decades and a recently developed model of WNV risk, we estimated the impact of this emergent disease on the survival of avian populations. We find that populations were negatively affected by WNV in 23 of the 49 species studied (47%). We distinguished two groups of species: those for which WNV negatively impacted survival only during initial spread of the disease (n = 11), and those that show no signs of recovery since disease introduction (n = 12). Results provide a novel example of the taxonomic breadth and persistent impacts of this wildlife disease on a continental scale. Phylogenetic analyses further identify groups (New World sparrows, finches, and vireos) disproportionally affected by temporary or persistent WNV effects, suggesting an evolutionary dimension of disease risk. Identifying the factors affecting the persistence of a disease across host species is critical to mitigating its effects, particularly in a world marked by rapid anthropogenic change.

Assessing migratory connectivity for a long-distance migratory bird using multiple intrinsic markers

Patterns of migratory connectivity are a vital yet poorly understood component of the ecology and evolution of migratory birds. Our ability to accurately characterize patterns of migratory connectivity is often limited by the spatial resolution of the data, but recent advances in probabilistic assignment approaches have begun pairing stable isotopes with other sources of data (e.g., genetic and mark-recapture) to improve the accuracy and precision of inferences based on a single marker. Here, we combine stable isotopes and geographic variation in morphology (wing length) to probabilistically assign Wood Thrush (Hylocichla mustilena) captured on the wintering grounds to breeding locations. In addition, we use known-origin samples to validate our model and assess potentially important impacts of isotopic and morphological covariates (age, sex, and breeding location). Our results show that despite relatively high levels of mixing across their breeding and nonbreeding ranges, moderate levels of migratory connectivity exist along an east-west gradient. In addition, combining stable isotopes with geographic variation in wing length improved the precision of breeding assignments by 10% and 37% compared to assignments based on isotopes alone or wing length alone, respectively. These results demonstrate that geographical variation in morphological traits can greatly improve estimates of migratory connectivity when combined with other intrinsic markers (e.g., stable isotopes or genetic data). The wealth of morphological data available from museum specimens across the world represents a tremendously valuable, but largely untapped, resource that is widely applicable for quantifying patterns of migratory connectivity.

Mapping the risk of avian influenza in wild birds in the US

BACKGROUND

Avian influenza virus (AIV) is an important public health issue because pandemic influenza viruses in people have contained genes from viruses that infect birds. The H5 and H7 AIV subtypes have periodically mutated from low pathogenicity to high pathogenicity form. Analysis of the geographic distribution of AIV can identify areas where reassortment events might occur and how high pathogenicity influenza might travel if it enters wild bird populations in the US. Modelling the number of AIV cases is important because the rate of co-infection with multiple AIV subtypes increases with the number of cases and co-infection is the source of reassortment events that give rise to new strains of influenza, which occurred before the 1968 pandemic. Aquatic birds in the orders Anseriformes and Charadriiformes have been recognized as reservoirs of AIV since the 1970s. However, little is known about influenza prevalence in terrestrial birds in the order Passeriformes. Since passerines share the same habitat as poultry, they may be more effective transmitters of the disease to humans than aquatic birds. We analyze 152 passerine species including the American Robin (Turdus migratorius) and Swainson's Thrush (Catharus ustulatus).

METHODS

We formulate a regression model to predict AIV cases throughout the US at the county scale as a function of 12 environmental variables, sampling effort, and proximity to other counties with influenza outbreaks. Our analysis did not distinguish between types of influenza, including low or highly pathogenic forms.

RESULTS

Analysis of 13,046 cloacal samples collected from 225 bird species in 41 US states between 2005 and 2008 indicates that the average prevalence of influenza in passerines is greater than the prevalence in eight other avian orders. Our regression model identifies the Great Plains and the Pacific Northwest as high-risk areas for AIV. Highly significant predictors of AIV include the amount of harvested cropland and the first day of the year when a county is snow free.

CONCLUSIONS

Although the prevalence of influenza in waterfowl has long been appreciated, we show that 22 species of song birds and perching birds (order Passeriformes) are influenza reservoirs in the contiguous US.

How do frugivores track resources? Insights from spatial analyses of bird foraging in a tropical forest

Frugivores often track ripe fruit abundance closely across local areas despite the ephemeral and typically patchy distributions of this resource. We use spatial auto- and cross-correlation analyses to quantify spatial patterns of fruit abundance and avian frugivory across a 4-month period within a forested 4.05-ha study grid in Puerto Rico. Analyses focused on two tanager species, Spindalis portoricensis and Nesospingus speculiferus, and their principal food plants. Three broad questions are addressed: (1). at what spatial scales is fruit abundance and frugivory patchy; (2). at what spatial scales do frugivores respond to fruit abundance; and (3). to what extent do spatial patterns of frugivory overlap between bird species? Fruit patch size, species composition, and heterogeneity was variable among months, despite fruit patch locations remaining relatively consistent between months. Positive correlations between frugivory and fruit abundance suggested tanagers successfully tracked fruit abundance. Frugivory was, however, more localized than fruit abundance. Scales of spatial overlap in frugivory and monthly variation in the foraging locations of the two tanager species suggested that interspecific facilitation may have been important in determining bird foraging locations. In particular, S. portoricensis, a specialist frugivore, may have relied on the loud calls of the gregarious generalist, N. speculiferus, to find new foraging areas. Such a mechanism could help explain the formation of mixed species feeding flocks and highlights the potential importance of facilitation between species that share resources.