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

The evolutionary history and genomics of European blackcap migration

Seasonal migration is a taxonomically widespread behaviour that integrates across many traits. The European blackcap exhibits enormous variation in migration and is renowned for research on its evolution and genetic basis. We assembled a reference genome for blackcaps and obtained whole genome resequencing data from individuals across its breeding range. Analyses of population structure and demography suggested divergence began ~30,000 ya, with evidence for one admixture event between migrant and resident continent birds ~5000 ya. The propensity to migrate, orientation and distance of migration all map to a small number of genomic regions that do not overlap with results from other species, suggesting that there are multiple ways to generate variation in migration. Strongly associated single nucleotide polymorphisms (SNPs) were located in regulatory regions of candidate genes that may serve as major regulators of the migratory syndrome. Evidence for selection on shared variation was documented, providing a mechanism by which rapid changes may evolve

Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

Abstract: Background: Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly. Results: As part of the Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (> 10 kbp, PacBio or Nanopore) and short (100–300 bp, Illumina) reads. Our pipeline leads to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We observe that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we identify errors, missing sequences, and incomplete genes in those references, particularly in repetitive regions. Our assemblies also identify novel gene region duplications. The presence of repeats and duplications in over half of the species herein assembled indicates that their occurrence is a principle of mitochondrial structure rather than an exception, shedding new light on mitochondrial genome evolution and organization. Conclusions: Our results indicate that even in the “simple” case of vertebrate mitogenomes the completeness of many currently available reference sequences can be further improved, and caution should be exercised before claiming the complete assembly of a mitogenome, particularly from short reads alone

Migratory divides and the genetic basis of reproductive isolation

Differences in seasonal migratory behaviour could be an important driver of ecological speciation. Many divergent groups form migratory divides on their breeding grounds; they breed adjacent to one another but use different routes to navigate around unsuitable areas on migration. Hybrids in divides are predicted to employ intermediate and inferior routes. I used light-level geolocators to track birds from the edges and center of a hybrid zone between inland and coastal Swainson’s thrushes (Catharus ustulatus) in western Canada. These data provided the first direct identification of a migratory divide (Chapter 2) and support for the prediction that hybrids in divides take intermediate routes (Chapter 3). Hybrid routes crossed arid and mountainous regions, further suggesting that these routes are inferior. I extended this work to examine the genetic basis of reproductive isolation between thrushes, assembling a reference genome and generating whole-genome sequence data for populations adjacent to the hybrid zone between these groups (Chapter 4). I documented genome-wide heterogeneity in genetic differentiation and uncovered patterns suggesting selective sweeps and variation in recombination generated this heterogeneity; within-population variation and absolute genetic differentiation were lower in regions of high relative differentiation and these reductions often coincided with centromeres and the Z chromosome. Genes associated with migration were concentrated in highly differentiated areas, further supporting migration’s role in reproductive isolation between thrushes. I complimented this work using a comparative approach to determine if patterns in the Swainson’s thrush could be extended to other species (Chapter 5). Specifically, I compared rates of phenotypic divergence between sister pairs that form divides and those that do not. I considered phenotypic divergence a proxy for reproductive isolation and contrary to expectations, found divergence was greater among taxa that do not form divides. This pattern could be explained by differential fusion, with sister pairs that do not form divides fusing into a single unit during periods of secondary contact unless they were sufficiently diverged phenotypically. Differences in migration would have permitted the persistence of pairs that form divides even without phenotypic differentiation. Under this scenario, migration serves as one of the major sources of speciation in North American birds.Science, Faculty ofZoology, Department ofGraduat

Maintenance of stability in the andrigitra brown lemur hybrid zone

Bibliography: p. 124-138Some pages are in colour

sites.156.N.W.distr.mtdata

Mitochondrial DNA mean hybrid index of each site along with distr (Km away from the isocline) and distr.corrected (distr+1200Km) for 2015-16 sampling

TOWAHEWA_pres_hist.ageParentalcorrectedHI.sitemean.distr

Plumage mean hybrid index of each site along with distr (Km away from the isocline) and distr.corrected (distr+1200Km) for 1980s and 2015-16 sampling

HZ.stable.MS.July2019.genomicEV.80s

Genomic hybrid index of each site along with the distance (Km) from isocline (distr) and corrected distr (distr.corrected=distr+1200) for 1987-94 sampling