Genes and gene networks underlying spatial cognition in food-caching chickadees.

Substantial progress has been made in understanding the genetic architecture of phenotypes involved in a variety of evolutionary processes. Behavioral genetics remains, however, among the least understood. We explore the genetic architecture of spatial cognitive abilities in a wild passerine bird, the mountain chickadee (Poecile gambeli). Mountain chickadees cache thousands of seeds in the fall and require specialized spatial memory to recover these caches throughout the winter. We previously showed that variation in spatial cognition has a direct effect on fitness and has a genetic basis. It remains unknown which specific genes and developmental pathways are particularly important for shaping spatial cognition. To further dissect the genetic basis of spatial cognitive abilities, we combine experimental quantification of spatial cognition in wild chickadees with whole-genome sequencing of 162 individuals, a new chromosome-scale reference genome, and species-specific gene annotation. We have identified a set of genes and developmental pathways that play a key role in creating variation in spatial cognition and found that the mechanism shaping cognitive variation is consistent with selection against mildly deleterious non-coding mutations. Although some candidate genes were organized into connected gene networks, about half do not have shared regulation, highlighting that multiple independent developmental or physiological mechanisms contribute to variation in spatial cognitive abilities. A large proportion of the candidate genes we found are associated with synaptic plasticity, an intriguing result that leads to the hypothesis that certain genetic variants create antagonism between behavioral plasticity and long-term memory, each providing distinct benefits depending on ecological context.

What's in a mate? Social pairing decisions and spatial cognitive ability in food-caching mountain chickadees.

While researchers have investigated mating decisions for decades, gaps remain in our understanding of how behaviour influences social mate choice. We compared spatial cognitive performance and food caching propensity within social pairs of mountain chickadees inhabiting differentially harsh winter climates to understand how these measures contribute to social mate choice. Chickadees rely on specialized spatial cognitive abilities to recover food stores and survive harsh winters, and females can discriminate among males with varying spatial cognition. Because spatial cognition and caching propensity are critical for survival and likely heritable, pairing with a mate with such enhanced traits may provide indirect benefits to offspring. Comparing the behaviour of social mates, we found that spatial cognitive performance approached a significant correlation within pairs at low, but not at high elevation. We found no correlation within pairs in spatial reversal cognitive performance at either elevation; however, females at high elevation tended to perform better than their social mates. Finally, we found that caching propensity correlated within pairs at low, while males cached significantly more food than their social mates at high elevations. These results suggest that cognition and caching propensity may influence social mating decisions, but only in certain environments and for some aspects of cognition.

A multi-sensor array for detecting and analyzing nocturnal avian migration.

Avian migration has fascinated humans for centuries. Insights into the lives of migrant birds are often elusive; however, recent, standalone technological innovations have revolutionized our understanding of this complex biological phenomenon. A future challenge for following these highly mobile animals is the necessity of bringing multiple technologies together to capture a more complete understanding of their movements. Here, we designed a proof-of-concept multi-sensor array consisting of two weather surveillance radars (WSRs), one local and one regional, an autonomous moon-watching sensor capable of detecting birds flying in front of the moon, and an autonomous recording unit (ARU) capable of recording avian nocturnal flight calls. We deployed this array at a field site in central Oklahoma on select nights in March, April, and May of 2021 and integrated data from this array with wind data corresponding to this site to examine the influence of wind on the movements of spring migrants aloft across these spring nights. We found that regional avian migration intensity is statistically significantly negatively correlated with wind velocity, in line with previous research. Furthermore, we found evidence suggesting that when faced with strong, southerly winds, migrants take advantage of these conditions by adjusting their flight direction by drifting. Importantly, we found that most of the migration intensities detected by the sensors were intercorrelated, except when this correlation could not be ascertained because we lacked the sample size to do so. This study demonstrates the potential for multi-sensor arrays to reveal the detailed ways in which avian migrants move in response to changing atmospheric conditions while in flight.

Food-caching chickadees with specialized spatial cognition do not use scrounging as a stable strategy when learning a spatial task.

Social animals may use alternative strategies when foraging, with producer-scrounger being one stable dichotomy of strategies. While 'producers' search and discover new food sources, 'scroungers' obtain food discovered by producers. Previous work suggests that differences in cognitive abilities may influence tendencies toward being either a producer or a scrounger, but scrounging behaviour in the context of specialized cognitive abilities is less understood. We investigated whether food-caching mountain chickadees, which rely on spatial cognition to retrieve food caches, engage in scrounging when learning a spatial task. We analysed data from seven seasons of spatial cognition testing, using arrays of radio frequency identification-enabled bird feeders, to identify and quantify potential scrounging behaviour. Chickadees rarely engaged in scrounging, scrounging was not repeatable within individuals and nearly all scrounging events occurred before the bird learned the 'producer' strategy. Scrounging was less frequent in harsher winters, but adults scrounged more than juveniles, and birds at higher elevations scrounged more than chickadees at lower elevations. There was no clear association between spatial cognitive abilities and scrounging frequency. Overall, our study suggests that food-caching species with specialized spatial cognition do not use scrounging as a stable strategy when learning a spatial task, instead relying on learning abilities.

Food-caching mountain chickadees can learn abstract rules to solve a complex spatial-temporal pattern.

The use of abstract rules in behavioral decisions is considered evidence of executive functions associated with higher-level cognition. Laboratory studies across taxa have shown that animals may be capable of learning abstract concepts, such as the relationships between items, but often use simpler cognitive abilities to solve tasks. Little is known about whether or how animals learn and use abstract rules in natural environments. Here, we tested whether wild, food-caching mountain chickadees (Poecile gambeli) could learn an abstract rule in a spatial-temporal task in which the location of a food reward rotated daily around an 8-feeder square spatial array for up to 34 days. Chickadees initially searched for the daily food reward by visiting the most recently rewarding locations and then moving backward to visit previously rewarding feeders, using memory of previous locations. But by the end of the task, chickadees were more likely to search forward in the correct direction of rotation, moving away from the previously rewarding feeders. These results suggest that chickadees learned the direction rule for daily feeder rotation and used this to guide their decisions while searching for a food reward. Thus, chickadees appear to use an executive function to make decisions on a foraging-based task in the wild. VIDEO ABSTRACT.

Environmental conditions lead to shifts in individual communication, which can cause cascading effects on soundscape composition.

Climate change is increasing aridity in grassland and desert habitats across the southwestern United States, reducing available resources and drastically changing the breeding habitat of many bird species. Increases in aridity reduce sound propagation distances, potentially impacting habitat soundscapes, and could lead to a breakdown of the avian soundscapes in the form of loss of vocal culture, reduced mating opportunities, and local population extinctions. We developed an agent-based model to examine how changes in aridity will affect both sound propagation and the ability of territorial birds to audibly contact their neighbors. We simulated vocal signal attenuation under a variety of environmental scenarios for the south, central semi-arid prairies of the United States, ranging from contemporary weather conditions to predicted droughts under climate change. We also simulated how changes in physiological conditions, mainly evaporative water loss (EWL), would affect singing behavior. Under contemporary and climate change-induced drought conditions, we found that significantly fewer individuals successfully contacted all adjacent neighbors than did individuals in either the contemporary or predicted climate change conditions. We also found that at higher sound frequencies and higher EWL, fewer individuals were able to successfully contact all their neighbors, particularly in drought and climate change drought conditions. These results indicate that climate change-mediated aridification may alter the avian soundscape, such that vocal communication no longer effectively functions for mate attraction or territorial defense. As climate change progresses, increased aridity in current grasslands may favor shifts toward low-frequency songs, colonial resource use, and altered songbird community compositions.

Natural variation in developmental condition has limited effect on spatial cognition in a wild food-caching bird.

Laboratory studies show that increased physiological burden during development results in cognitive impairment. In the wild, animals experience a wide range of developmental conditions, and it is critical to understand how variation in such conditions affects cognitive abilities later in life, especially in species that strongly depend on such abilities for survival. We tested whether variation in developmental condition is associated with differences in spatial cognitive abilities in wild food-caching mountain chickadees. Using tail feathers grown during development in juvenile birds, we measured feather corticosterone (Cortf) levels and growth rates and tested these birds during their first winter on two spatial learning tasks. In only 1 of the 3 years, higher feather Cortf was negatively associated with memory acquisition. No significant associations between feather Cortf and any other measurement of spatial cognition were detected in the other 2 years of the study or between feather growth rate and any measurement of cognition during the entire study. Our results suggest that in the wild, naturally existing variation in developmental condition has only a limited effect on spatial cognitive abilities, at least in a food-caching species. This suggests that there may be compensatory mechanisms to buffer specialized cognitive abilities against developmental perturbations.

Environmental, individual and social traits of free-ranging raccoons influence performance in cognitive testing.

Cognitive abilities, such as learning and flexibility, are hypothesized to aid behavioral adaptation to urbanization. Although growing evidence suggests that cognition may indeed facilitate persistence in urban environments, we currently lack knowledge of the cognitive abilities of many urban taxa. Recent methodological advances, including radio frequency identification (RFID), have extended automated cognitive testing into the field but have yet to be applied to a diversity of taxa. Here, we used an RFID-enabled operant conditioning device to assess the habituation, learning and cognitive flexibility of a wild population of raccoons (Procyon lotor). We examined how several biological and behavioral traits influenced participation and performance in testing. We then compared the cognitive performance of wild raccoons tested in natural conditions with that of wild-caught raccoons tested in captivity from a previous study. In natural conditions, juvenile raccoons were more likely to habituate to the testing device, but performed worse in serial reversal learning, compared with adults. We also found that docile raccoons were more likely to learn how to operate the device in natural conditions, which suggests a relationship between emotional reactivity and cognitive ability in raccoons. Although raccoons in both captive and natural conditions demonstrated rapid associative learning and flexibility, raccoons in captive conditions generally performed better, likely owing to the heightened vigilance and social interference experienced by raccoons in natural conditions. Our results have important implications for future research on urban carnivores and cognition in field settings, as well as our understanding of behavioral adaptation to urbanization and coexistence with urban wildlife.

Use of the LunAero Open-Source Hardware Platform to Enhance the Accuracy and Precision of Traditional Nocturnal Migration Bird Counts.

Quantification of nocturnal migration of birds through moon watching is a technique ripe for modernization with superior computational power. In this paper, collected by a motorized telescope mount was data analyzed using both video observations by trained observers and modernized approaches using computer vision. The more advanced data extraction used the OpenCV library of computer vision tools to identify bird silhouettes by means of image stabilization and background subtraction. The silhouettes were sanitized and analyzed in sequence to produce stacked relationships between temporally close contours, discriminating birds from noise based on the assumption that birds migrate in stable paths. The flight ceiling of the birds was determined by extracting relevant correlation coefficient data from doppler radar co-located with the LunAero instrument in Norman, OK, USA using a method with low-computational overhead. The bird paths and flight ceiling were combined with lunar ephemera to provide input for the original method used for nocturnal migration quantification as well as an enhanced version of the same method with more advanced computational tools. We found that the manual quantification of migration activity detected 16,300 birds/km•h heading northwest from 110°, whereas the automated analysis reported a density of 43,794 birds/km•h heading northwest from 106.67°. Hence, there was agreement with regard to flight direction, but the automated method overestimated migration density by approximately three times. The reasons for the discrepancy between flight path detection appeared to be due to a substantial amount of noise in the video data as well as a tendency for the computer vision analysis to split single flight paths into two or more segments. The authors discuss ongoing innovations aimed at addressing these methodological challenges.

The genetic basis of spatial cognitive variation in a food-caching bird.

Spatial cognition is used by most organisms to navigate their environment. Some species rely particularly heavily on specialized spatial cognition to survive, suggesting that a heritable component of cognition may be under natural selection. This idea remains largely untested outside of humans, perhaps because cognition in general is known to be strongly affected by learning and experience.1-4 We investigated the genetic basis of individual variation in spatial cognition used by non-migratory food-caching birds to recover food stores and survive harsh montane winters. Comparing the genomes of wild, free-living birds ranging from best to worst in their performance on a spatial cognitive task revealed significant associations with genes involved in neuron growth and development and hippocampal function. These results identify candidate genes associated with differences in spatial cognition and provide a critical link connecting individual variation in spatial cognition with natural selection. VIDEO ABSTRACT.

Social dominance has limited effects on spatial cognition in a wild food-caching bird.

Social dominance has long been used as a model to investigate social stress. However, many studies using such comparisons have been performed in captive environments. These environments may produce unnaturally high antagonistic interactions, exaggerating the stress of social subordination and any associated adverse consequences. One such adverse effect concerns impaired cognitive ability, often thought to be associated with social subordination. Here, we tested whether social dominance rank is associated with differences in spatial learning and memory, and in reversal spatial learning (flexibility) abilities in wild food-caching mountain chickadees at different montane elevations. Higher dominance rank was associated with higher spatial cognitive flexibility in harsh environments at higher elevations, but not at lower, milder elevations. By contrast, there were no consistent differences in spatial learning and memory ability associated with dominance rank. Our results suggest that spatial learning and memory ability in specialized food-caching species is a stable trait resilient to social influences. Spatial cognitive flexibility, on the other hand, appears to be more sensitive to environmental influences, including social dominance. These findings contradict those from laboratory studies and suggest that it is critical to investigate the biological consequences of social dominance under natural conditions.

UnCanny: Exploiting Reversed Edge Detection as a Basis for Object Tracking in Video.

Few object detection methods exist which can resolve small objects (<20 pixels) from complex static backgrounds without significant computational expense. A framework capable of meeting these needs which reverses the steps in classic edge detection methods using the Canny filter for edge detection is presented here. Sample images taken from sequential frames of video footage were processed by subtraction, thresholding, Sobel edge detection, Gaussian blurring, and Zhang-Suen edge thinning to identify objects which have moved between the two frames. The results of this method show distinct contours applicable to object tracking algorithms with minimal "false positive" noise. This framework may be used with other edge detection methods to produce robust, low-overhead object tracking methods.

Food discovery is associated with different reliance on social learning and lower cognitive flexibility across environments in a food-caching bird.

Social learning is a primary mechanism for information acquisition in social species. Despite many benefits, social learning may be disadvantageous when independent learning is more efficient. For example, searching independently may be more advantageous when food sources are ephemeral and unpredictable. Individual differences in cognitive abilities can also be expected to influence social information use. Specifically, better spatial memory can make a given environment more predictable for an individual by allowing it to better track food sources. We investigated how resident food-caching chickadees discovered multiple novel food sources in both harsher, less predictable high elevation and milder, more predictable low elevation winter environments. Chickadees at high elevation were faster at discovering multiple novel food sources and discovered more food sources than birds at low elevation. While birds at both elevations used social information, the contribution of social learning to food discovery was significantly lower at high elevation. At both elevations, chickadees with better spatial cognitive flexibility were slower at discovering food sources, likely because birds with lower spatial cognitive flexibility are worse at tracking natural resources and therefore spend more time exploring. Overall, our study supported the prediction that harsh environments should favour less reliance on social learning.

Rapid adjustments of migration and life history in hemisphere-switching cliff swallows.

Many aspects of bird migration are necessarily innate.1 However, the extent of deterministic genetic control, environmental influence, and individual decision making in the control of migration remains unclear.2-8 Globally, few cases of rapid and dramatic life-history changes resulting in novel migration strategies are known. An example is latitudinal trans-hemispheric breeding colonization, whereby a subpopulation suddenly begins breeding on its non-breeding range.9-13 These life-history reversals demand concomitant changes in the timing of migration, feather molt, and breeding if the population is to remain viable.13 Cliff swallows, Petrochelidon pyrrhonota, are long-distance migrants that breed in North America and spend the non-breeding season mostly in South America.14 However, in 2015, a small population switched hemispheres by breeding successfully in Argentina,9 over 8,000 km from the nearest potential source, after presumably failed attempts.15,16 This provided a unique chance to characterize the early mechanisms of change in migratory behavior and phenology and to assess the possibility of double breeding. We tracked cliff swallows with geolocators following their second and fourth breeding seasons in Argentina, documenting inverted seasonality, three new migratory patterns and non-breeding areas (North America, Mesoamerica, and South America), and a shift of molt phenology by approximately 6 months, all possibly arising within a single generation. These birds did not practice migratory double breeding, although some spent the boreal summer in the traditional breeding range. Our data show that fundamental phenological changes occurred very rapidly during colonization and that phenotypic plasticity can underlie profound changes in the life histories of migratory birds.

Specialized spatial cognition is associated with reduced cognitive senescence in a food-caching bird.

Senescence, the gradual reduction and loss of function as organisms age, is a widespread process that is especially pronounced in cognitive abilities. Senescence appears to have a genetic basis and can be affected by evolutionary processes. If cognitive senescence is shaped by natural selection, it may be linked with selection on cognitive abilities needed for survival and reproduction, such that species where fitness is directly related to cognitive abilities should evolve delayed cognitive senescence likely resulting in higher lifetime fitness. We used wild food-caching mountain chickadees, which rely on specialized spatial cognition to recover thousands of food caches annually, to test for cognitive senescence in spatial learning and memory and reversal spatial learning and memory abilities. We detected no signs of age-related senescence in spatial cognitive performance on either task in birds ranging from 1 to 6 years old; older birds actually performed better on spatial learning and memory tasks. Our results therefore suggest that cognitive senescence may be either delayed (potentially appearing after 6 years) or negligible in species with strong selection on cognitive abilities and that food-caching species may present a useful model to investigate mechanisms associated with cognitive senescence.

Variation in reversal learning by three generalist mesocarnivores.

Urbanization imposes novel challenges for wildlife, but also provides new opportunities for exploitation. Generalist species are commonly found in urban habitats, but the cognitive mechanisms facilitating their successful behavioral adaptations and exploitations are largely under-investigated. Cognitive flexibility is thought to enable generalists to be more plastic in their behavior, thereby increasing their adaptability to a variety of environments, including urban habitats. Yet direct measures of cognitive flexibility across urban wildlife are lacking. We used a classic reversal-learning paradigm to investigate the cognitive flexibility of three generalist mesocarnivores commonly found in urban habitats: striped skunks (Mephitis mephitis), raccoons (Procyon lotor), and coyotes (Canis latrans). We developed an automated device and testing protocol that allowed us to administer tests of reversal learning in captivity without extensive training or experimenter involvement. Although most subjects were able to rapidly form and reverse learned associations, we found moderate variation in performance and behavior during trials. Most notably, we observed heightened neophobia and a lack of habituation expressed by coyotes. We discuss the implications of such differences among generalists with regard to urban adaptation and we identify goals for future research. This study is an important step in investigating the relationships between cognition, generalism, and urban adaptation.

Testing the greater male variability phenomenon: male mountain chickadees exhibit larger variation in reversal learning performance compared with females.

The greater male variability phenomenon predicts that males exhibit larger ranges of variation in cognitive performance compared with females; however, support for this pattern has come exclusively from studies of humans and lacks mechanistic explanation. Furthermore, the vast majority of the literature assessing sex differences in cognition is based on studies of humans and a few other mammals. In order to elucidate the underpinnings of cognitive variation and the potential for fitness consequences, we must investigate sex differences in cognition in non-mammalian systems as well. Here, we assess the performance of male and female food-caching birds on a spatial learning and memory task and a reversal spatial task to address whether there are sex differences in mean cognitive performance or in the range of variation in performance. For both tasks, male and female mean performance was similar across four years of testing; however, males did exhibit a wider range of variation in performance on the reversal spatial task compared with females. The implications for mate choice and sexual selection of cognitive abilities are discussed and future directions are suggested to aid in the understanding of sex-related cognitive variation.

LunAero: Automated "smart" hardware for recording video of nocturnal migration.

Moon watching is a method of quantifying nocturnal bird migration by focusing a telescope on the moon and recording observations of flying birds silhouetted against the lunar surface. Although simple and well-established, researchers use moon watching infrequently due in part to the hours of late night observation it requires. To reduce the labor entailed in moon watching, we designed a low-cost system called LunAero that can track and record video of the moon at night. Here we present a proof-of-concept prototype that can serve as a platform for citizen scientists interested in observing nocturnal bird migration. We tested the video recording on clear nights from February 2018 to May 2019 when the moon was full or nearly full. Manual analysis of a 1.5 h sample of video revealed a total of 450 birds, which is a much higher detection rate than previous moon watching efforts have yielded. The hardware described here is part of a larger effort involving software development (currently underway) to automate recorded video analysis. We argue that LunAero can reduce the labor involved in moon watching, offer improved data quality over traditional moon watching, and provide insights into social behavior and wind-drift compensation in migrating birds.

Light-level geolocator analyses: A user's guide.

Light-level geolocator tags use ambient light recordings to estimate the whereabouts of an individual over the time it carried the device. Over the past decade, these tags have emerged as an important tool and have been used extensively for tracking animal migrations, most commonly small birds. Analysing geolocator data can be daunting to new and experienced scientists alike. Over the past decades, several methods with fundamental differences in the analytical approach have been developed to cope with the various caveats and the often complicated data. Here, we explain the concepts behind the analyses of geolocator data and provide a practical guide for the common steps encompassing most analyses - annotation of twilights, calibration, estimating and refining locations, and extraction of movement patterns - describing good practices and common pitfalls for each step. We discuss criteria for deciding whether or not geolocators can answer proposed research questions, provide guidance in choosing an appropriate analysis method and introduce key features of the newest open-source analysis tools. We provide advice for how to interpret and report results, highlighting parameters that should be reported in publications and included in data archiving. Finally, we introduce a comprehensive supplementary online manual that applies the concepts to several datasets, demonstrates the use of open-source analysis tools with step-by-step instructions and code and details our recommendations for interpreting, reporting and archiving.

Assessing Behavioral Associations in a Hybrid Zone through Social Network Analysis: Complex Assortative Behaviors Structure Associations in a Hybrid Quail Population.

Behavior can strongly influence rates and patterns of hybridization between animal populations and species. Yet few studies have examined reproductive behaviors in natural hybrid zones within the fine-scale social context in which they naturally occur. We use radio-frequency identification tags with social network analyses to test whether phenotypic similarity in plumage and mass correlate with social behavior throughout a breeding season in a California and Gambel's quail hybrid zone. We use a novel approach to partition phenotypic variation in a way that does not confound differences between sexes and species, and we illustrate the complex ways that phenotype and behavior structure the social environment, mating opportunities, and male-male associations. Associations within the admixed population were random with respect to species-specific plumage but showed strong patterns of assortment based on sexually dimorphic plumage, monomorphic plumage, and mass. Weak behavioral reproductive isolation in this admixed population may be the result of complex patterns of phenotypic assortment based on multiple traits rather than a lack of phenotypic discrimination. More generally, our results support the utility of social network analyses for analyzing behavioral factors affecting genetic exchange between populations and species.