A Zugunruhe Data Collection System Using Passive Infrared Sensors

When engineers and biologists work together, there is a lot to learn on both sides. For instance, our work introduced us to zugunruhe, which is a German word that means “unrest”. It is used in the context of migratory birds, as they become restless at night, inside their cages, during their migratory period. When does zugunruhe start? It usually starts when the weather becomes cold and the days shorter, but it varies for different bird species. Moreover, global warming has caused changes in zungunruhe’s timing, which made it even harder to predict. Another question is about genetics: is there a specific gene or a group of genes that cause birds to migrate? To help scientists answer questions related to zugunruhe and the genes underlying migratory behavior, this paper presents the design and implementation of a zugunruhe data collection system to study the Swainson’s thrush, a migratory songbird that breeds in North America. Our goal is to share how custom-off-the-shelf (COTS) devices and existing technologies were used in this project, such as passive infrared motion sensors, telecom cables, custom printed circuit boards (PCB) and a data acquisition system using LabView software. All these were combined to monitor bird movements. We also discuss how the learned lessons from our first winter of data collection, in which we monitored 30 bird cages, led to improvements to scale the system to support the monitoring of 60 birds in the second year. Samples of the collected data are presented to show that the system works, which was validated by comparing our data with the images obtained using an infrared camera. Some of the challenges on maintaining the system are also discussed. Moreover, this paper provides an example of an interdisciplinary, applied research project that is still on-going, and it was created by a group of undergraduate students. We hope it can inspire other researchers and undergraduate students to get involved in interdisciplinary research

Shared patterns of genome-wide differentiation are more strongly predicted by geography than by ecology

Closely related populations often display similar patternsof genomic differentiation, yet it remains an open question which ecological and evolutionary forces generate these patterns. The leading hypothesis is that this similarity in divergence is driven by parallel natural selection. However, several recent studies have suggested that these patterns may instead be a product of the depletion of genetic variation that occurs as result of background selection (i.e., linked negative selection). To date, there have been few direct tests of these competing hypotheses. To determine the relative contributions of background selection and parallel selection to patterns of repeated differentiation, we examined 24 independently derived populations of freshwater stickleback occupying a variety of niches and estimated genomic patterns of differentiation in each relative to their common marine ancestor. Patterns of genetic differentiation were strongly correlated across pairs of freshwater populations adapting to the same ecological niche, supporting a role for parallel natural selection. In contrast to other recent work, our study comparing populations adapting to the same niche produced no evidence signifying that similar patterns of genomic differentiation are generated by background selection. We also found that overall patterns of genetic differentiation were considerably more similar for populations found in closer geographic proximity. In fact, the effect of geography on the repeatability of differentiation was greater than that of parallel selection. Our results suggest that shared selective landscapes and ancestral variation are the key drivers of repeated patterns of differentiation in systems that have recently colonized novel environments

Data from: Habitat preference facilitates successful early breeding in an open-cup nesting songbird

Selecting breeding habitats that ameliorate environmental limits on fitness and facilitate successful reproduction should benefit individual animals. This is particularly true in the temperate zone, where breeding early in a season presents a unique series of environmental challenges that can limit an individual's fitness. While many studies document links between habitat quality and reproductive success, few identify the cues used to assess habitat quality or the components of reproduction most influenced by occupying higher quality habitat, particularly during the early breeding season. We used detailed spatial maps and observations of all early season nesting attempts in an insular song sparrow (Melospiza melodia) population over 38 years to estimate the influence of nest-site preference on reproductive success and to test whether relative microclimate or food availability may act as cues for early season site selection. Female sparrows in preferred early season nest sites had earlier laying dates, exhibited more energetically efficient incubation behaviour and produced more offspring that recruited to the population than those nesting in less-preferred sites. Preference for potential nesting sites was positively related to leaf damage by Lepidopteran larvae, an indicator of food abundance, negatively related to early season microclimate, likely due to greater vegetation cover, and unrelated to site-specific plant phenology. Our findings show that breeding in preferred, high-quality habitat may offer females a fitness advantage by facilitating early laying and the production of offspring more likely to recruit to the population at a lower potential reproductive cost to the parent. We provide a clear demonstration of potential links between habitat preference and quality and their contributions to the ecology and life history of animals in seasonal environments

Data from: Recurrent selection explains parallel evolution of genomic regions of high relative but low absolute differentiation in a ring species

Recent technological developments allow investigation of the repeatability of evolution at the genomic level. Such investigation is particularly powerful when applied to a ring species, in which spatial variation represents changes during the evolution of two species from one. We examined genomic variation among three subspecies of the greenish warbler ring species, using genotypes at 13 013 950 nucleotide sites along a new greenish warbler consensus genome assembly. Genomic regions of low within-group variation are remarkably consistent between the three populations. These regions show high relative differentiation but low absolute differentiation between populations. Comparisons with outgroup species show the locations of these peaks of relative differentiation are not well explained by phylogenetically conserved variation in recombination rates or selection. These patterns are consistent with a model in which selection in an ancestral form has reduced variation at some parts of the genome, and those same regions experience recurrent selection that subsequently reduces variation within each subspecies. The degree of heterogeneity in nucleotide diversity is greater than explained by models of background selection, but is consistent with selective sweeps. Given the evidence that greenish warblers have had both population differentiation for a long period of time and periods of gene flow between those populations, we propose that some genomic regions underwent selective sweeps over a broad geographic area followed by within-population selection-induced reductions in variation. An important implication of this ‘sweep-before-differentiation’ model is that genomic regions of high relative differentiation may have moved among populations more recently than other genomic regions

Genomic architecture of migration timing in a long-distance migratory songbird

The impact of climate change on spring phenology poses risks to migratory birds, as migration timing is controlled predominantly by endogenous mechanisms. Despite recent advances in our understanding of the underlying genetic basis of migration timing, the ways that migration timing phenotypes in wild individuals may map to specific genomic regions requires further investigation. We examined the genetic architecture of migration timing in a long-distance migratory songbird (purple martin, Progne subis subis) by integrating genomic data with an extensive dataset of direct migratory tracks. A moderate to large amount of variance in spring migration arrival timing was explained by genomics (proportion of phenotypic variation explained by genomics = 0.74; polygenic score R-2 = 0.24). On chromosome 1, a region that was differentiated between migration timing phenotypes contained genes that could facilitate nocturnal flights and act as epigenetic modifiers. Overall, these results advance our understanding of the genomic underpinnings of migration timing