Andrew Farnsworth

Use of a Bacteriophage Lysin to Identify a Novel Target for Antimicrobial Development

We identified an essential cell wall biosynthetic enzyme in Bacillus anthracis and an inhibitor thereof to which the organism did not spontaneously evolve measurable resistance. This work is based on the exquisite binding specificity of bacteriophage-encoded cell wall-hydrolytic lysins, which have evolved to recognize critical receptors within the bacterial cell wall. Focusing on the B. anthracis-specific PlyG lysin, we first identified its unique cell wall receptor and cognate biosynthetic pathway. Within this pathway, one biosynthetic enzyme, 2-epimerase, was required for both PlyG receptor expression and bacterial growth. The 2-epimerase was used to design a small-molecule inhibitor, epimerox. Epimerox prevented growth of several Gram-positive pathogens and rescued mice challenged with lethal doses of B. anthracis. Importantly, resistance to epimerox was not detected (<10−11 frequency) in B. anthracis and S. aureus. These results describe the use of phage lysins to identify promising lead molecules with reduced resistance potential for antimicrobial development.

Nocturnally migrating songbirds drift when they can and compensate when they must

The shortest possible migratory route for birds is not always the best route to travel. Substantial research effort has established that birds in captivity are capable of orienting toward the direction of an intended goal, but efforts to examine how free-living birds use navigational information under conditions that potentially make direct flight toward that goal inefficient have been limited in spatiotemporal scales and in the number of individuals observed because of logistical and technological limitations. Using novel and recently developed techniques for analysis of Doppler polarimetric weather surveillance radar data, we examined two impediments for nocturnally migrating songbirds in eastern North America following shortest-distance routes: crosswinds and oceans. We found that migrants in flight often drifted sideways on crosswinds, but most strongly compensated for drift when near the Atlantic coast. Coastal migrants’ tendency to compensate for wind drift also increased through the night, while no strong temporal differences were observed at inland sites. Such behaviors suggest that birds migrate in an adaptive way to conserve energy by assessing while airborne the degree to which they must compensate for wind drift.

A comparison of similarity-based approaches in the classification of flight calls of four species of North American wood-warblers (Parulidae)

Abstract Numerous methods are available for analysis of avian vocalizations, but few research efforts have compared recent methods for calculating and evaluating similarity among calls, particularly those collected in the field. This manuscript compares a suite of methodologies for analyzing flight calls of New World warblers, investigating the effectiveness of four techniques for calculating call similarity: (1) spectrographic cross-correlation, (2) dynamic time warping, (3) Euclidean distance between spectrogram-based feature measurements, and (4) random forest distance between spectrogram-based feature measurements. We tested these methods on flight calls, which are short, structurally simple vocalizations typically used during nocturnal migration, as these signals may contain important ecological or demographic information. Using the four techniques listed above, we classified flight calls from three datasets, one collected from captive birds and two collected from wild birds in the field. Each dataset contained an equal number of calls from four warbler species commonly recorded during acoustic monitoring: American Redstart, Chestnut-sided Warbler, Hooded Warbler, and Ovenbird. Using captive recordings to train the classification models, we created four similarity-based classifiers which were then tested on the captive and field datasets. We show that these classification methods are limited in their ability to successfully classify the calls of these warbler species, and that classification accuracy was lower on field recordings than captive recordings for each of the tested methods. Of the four methods we compared, the random forest technique had the highest classification accuracy, enabling correct classification of 67.6% of field recordings. To compare the performance of the automated techniques to manual classification, the most common method used in flight call research, human experts were also asked to classify calls from each dataset. The experts correctly classified approximately 90% of field recordings, indicating that although the automated techniques are faster, they remain less accurate than manual classification. However, because of the challenges inherent to these data, such as the structural similarity among the flight calls of focal species and the presence of environmental noise in the field recordings, some of the tested automated classification techniques may be acceptable for real-world applications. We believe that this comparison of broadly applicable methodologies provides information that will prove to be useful for analysis, detection and classification of short duration signals. Based on our results, we recommend that a combination of feature measurements and random forest classification can be used to assign flight calls to species, while human experts oversee the process.

Migration timing and its determinants for nocturnal migratory birds during autumn migration

1. Migration is a common strategy used by birds that breed in seasonal environments, and multiple environmental and biological factors determine the timing of migration. How these factors operate in combination during autumn migration, which is considered to be under weaker time constraints relative to spring migration, is not clear. 2. Here, we examine the patterns and determinants of migration timing for nocturnal migrants during autumn migration in the north-eastern USA using nocturnal reflectivity data from 12 weather surveillance radar stations and modelled diurnal probability of occurrence for 142 species of nocturnal migrants. We first model the capacity of seasonal atmospheric conditions (wind and precipitation) and ecological productivity (vegetation greenness) to predict autumn migration intensity. We then test predictions, formulated under optimal migration theory, on how migration timing should be related to assemblage-level estimates of body size and total migration distance within the context of dietary guild (insectivore and omnivore) and level of dietary plasticity during autumn migration. 3. Our results indicate seasonal declines in ecological productivity delineate the beginning and end of peak migration, whose intensity is best predicted by the velocity of winds at migration altitudes. Insectivorous migrants departed earlier in the season and, consistent with our predictions, large-bodied and long-distance insectivorous migrants departed the earliest. Contrary to our predictions, large-bodied and some long-distance omnivorous migrants departed later in the season, patterns that were replicated in part by insectivorous migrants that displayed dietary plasticity during autumn migration. 4. Our findings indicate migration timing in the region is dictated by optimality strategies, modified based on the breadth and flexibility of migrants foraging diets, with declining ecological productivity defining possible resource thresholds during which migration occurs when winds at migration altitudes are mild. These observations provide the basis to assess how avian migration strategies may be affected by adjustments in seasonal patterns of atmospheric circulation and ecological productivity that may occur under global climate change.

Bayesian Classification of Flight Calls with a Novel Dynamic Time Warping Kernel

In this paper we propose a probabilistic classification algorithm with a novel Dynamic Time Warping (DTW) kernel to automatically recognize flight calls of different species of birds. The performance of the method on a real world dataset of warbler (Parulidae) flight calls is competitive to human expert recognition levels and outperforms other classifiers trained on a variety of feature extraction approaches. In addition we offer a novel and intuitive DTW kernel formulation which is positive semi-definite in contrast with previous work. Finally we obtain promising results with a larger dataset of multiple species that we can handle efficiently due to the explicit multiclass probit likelihood of the proposed approach.

Autumn morning flights of migrant songbirds in the northeastern United States are linked to nocturnal migration and winds aloft

ABSTRACT Many passerines that typically migrate at night also engage in migratory flights just after sunrise. These widely observed “morning flights” often involve birds flying in directions other than those aimed toward their ultimate destinations, especially in coastal areas. Morning flights have received little formal investigation, and their study may improve our understanding of how birds orient themselves during and after nocturnal movements and how they use stopover habitat. We studied autumn morning flights in the northeastern United States to identify associations between the number of birds undertaking morning flights and the magnitude of nocturnal migratory movements, nocturnal winds, and local topography. Our analyses included observations of more than 15,000 passerines at 7 locations. We found positive relationships between morning flight size and nocturnal migration density and winds aloft: Significantly more birds flew following larger nocturnal movements, quantified from weather surveillance radar and recordings of nocturnal flight calls, and after stronger nocturnal crosswinds. We also found consistent differences in morning flight size and direction among sites. These patterns are consistent with migrants engaging in morning flight as a corrective measure following displacement by nocturnal winds and to search for suitable stopover habitat.

High-intensity urban light installation dramatically alters nocturnal bird migration

Significance Artificial light at night is a novel stimulus in the evolutionary history of nocturnal animals. Light pollution can significantly alter these organisms’ behaviors, from migration to foraging to vocal communication. Nocturnally migrating birds are particularly susceptible to artificial light because of adaptations and requirements for navigating and orienting in darkness. However, light’s effects on in-flight behaviors have not been well quantified, especially in urbanized environments. Here we report that an iconic urban light installation dramatically altered multiple behaviors of nocturnally migrating birds—but these effects disappeared when lights were extinguished. We recommend selective removal of light pollution during nights with substantial bird migration to mitigate negative effects on birds, in particular collisions with lighted structures. Billions of nocturnally migrating birds move through increasingly photopolluted skies, relying on cues for navigation and orientation that artificial light at night (ALAN) can impair. However, no studies have quantified avian responses to powerful ground-based light sources in urban areas. We studied effects of ALAN on migrating birds by monitoring the beams of the National September 11 Memorial & Museums “Tribute in Light” in New York, quantifying behavioral responses with radar and acoustic sensors and modeling disorientation and attraction with simulations. This single light source induced significant behavioral alterations in birds, even in good visibility conditions, in this heavily photopolluted environment, and to altitudes up to 4 km. We estimate that the installation influenced ≈1.1 million birds during our study period of 7 d over 7 y. When the installation was illuminated, birds aggregated in high densities, decreased flight speeds, followed circular flight paths, and vocalized frequently. Simulations revealed a high probability of disorientation and subsequent attraction for nearby birds, and bird densities near the installation exceeded magnitudes 20 times greater than surrounding baseline densities during each year’s observations. However, behavioral disruptions disappeared when lights were extinguished, suggesting that selective removal of light during nights with substantial bird migration is a viable strategy for minimizing potentially fatal interactions among ALAN, structures, and birds. Our results also highlight the value of additional studies describing behavioral patterns of nocturnally migrating birds in powerful lights in urban areas as well as conservation implications for such lighting installations.

Seasonal differences in landbird migration strategies

ABSTRACT Migrating birds make strategic decisions at multiple temporal and spatial scales. They must select flight altitudes, speeds, and orientations in order to maintain preferred directions of movement and to minimize energy expenditure and risk. Spring flights follow a rapid phenology, but how this rapid transit translates to in-flight decisions is not clear. We described flight strategies of nocturnally migrating landbirds using 6 weather surveillance radars during spring (2013–2015) and fall (2013–2014) migratory periods in the eastern United States to investigate seasonal decision-making patterns and how climate change may influence these trends. During spring, we found groundspeed and airspeed of migrants to be significantly higher than those of fall migrants; compensation for wind drift was also significantly greater during spring. Our results indicate that birds make more rapid and precise flights in spring that are only partially explained by meteorological phenomena. Future applications at greater spatial scales will allow direct comparisons of in-flight behaviors with predictions from migration theory.

Seasonal changes in the altitudinal distribution of nocturnally migrating birds during autumn migration

Wind plays a significant role in the flight altitudes selected by nocturnally migrating birds. At mid-latitudes in the Northern Hemisphere, atmospheric conditions are dictated by the polar-front jet stream, whose amplitude increases in the autumn. One consequence for migratory birds is that the region’s prevailing westerly winds become progressively stronger at higher migration altitudes. We expect this seasonality in wind speed to result in migrants occupying progressively lower flight altitudes, which we test using density estimates of nocturnal migrants at 100 m altitudinal intervals from 12 weather surveillance radar stations located in the northeastern USA. Contrary to our expectations, median migration altitudes deviated little across the season, and the variance was lower during the middle of the season and higher during the beginning and especially the end of the season. Early-season migrants included small- to intermediate-sized long-distance migrants in the orders Charadriiformes and Passeriformes, and late-season migrants included large-bodied and intermediate-distance migrants in the order Anseriformes. Therefore, seasonality in the composition of migratory species, and related variation in migration strategies and behaviours, resulted in a convex–concave bounded distribution of migration altitudes. Our results provide a basis for assessing the implications for migratory bird populations of changes in mid-latitude atmospheric conditions probably occurring under global climate change.

Documenting stewardship responsibilities across the annual cycle for birds on U.S. public lands.

In the face of global environmental change, the importance of protected areas in biological management and conservation is expected to grow. Birds have played an important role as biological indicators of the effectiveness of protected areas, but with little consideration given to where species occur outside the breeding season. We estimated weekly probability of occurrence for 308 bird species throughout the year within protected areas in the western contiguous USA using eBird occurrence data for the combined period 2004 to 2011. We classified species based on their annual patterns of occurrence on lands having intermediate conservation mandates (GAP status 2 and 3) administered by the Bureau of Land Management (BLM) and the United States Forest Service (USFS). We identified species having consistent annual association with one agency, and species whose associations across the annual cycle switched between agencies. BLM and USFS GAP status 2 and 3 lands contained low to moderate proportions of species occurrences, with proportions highest for species that occurred year-round or only during the summer. We identified two groups of species whose annual movements resulted in changes in stewardship responsibilities: (1) year-round species that occurred on USFS lands during the breeding season and BLM lands during the nonbreeding season; and (2) summer species that occurred on USFS lands during the breeding season and BLM lands during spring and autumn migration. Species that switched agencies had broad distributions, bred on high-elevation USFS lands, were not more likely to be identified as species of special management concern, and migrated short (year-round species) to long distances (summer species). Our findings suggest cooperative efforts that address the requirements of short-distance migratory species on GAP status 2 lands (n = 20 species) and GAP status 3 lands (n = 24) and long-distance migratory species on GAP status 2 lands (n = 9) would likely benefit their populations. Such efforts may prove especially relevant for species whose seasonal movements result in associations with different environments containing contrasting global change processes and management mandates.