Digital fragment analysis of short tandem repeats by high‐throughput amplicon sequencing

High‐throughput sequencing has been proposed as a method to genotype microsatellites and overcome the four main technical drawbacks of capillary electrophoresis: amplification artifacts, imprecise sizing, length homoplasy, and limited multiplex capability. The objective of this project was to test a high‐throughput amplicon sequencing approach to fragment analysis of short tandem repeats and characterize its advantages and disadvantages against traditional capillary electrophoresis. We amplified and sequenced 12 muskrat microsatellite loci from 180 muskrat specimens and analyzed the sequencing data for precision of allele calling, propensity for amplification or sequencing artifacts, and for evidence of length homoplasy. Of the 294 total alleles, we detected by sequencing, only 164 alleles would have been detected by capillary electrophoresis as the remaining 130 alleles (44%) would have been hidden by length homoplasy. The ability to detect a greater number of unique alleles resulted in the ability to resolve greater population genetic structure. The primary advantages of fragment analysis by sequencing are the ability to precisely size fragments, resolve length homoplasy, multiplex many individuals and many loci into a single high‐throughput run, and compare data across projects and across laboratories (present and future) with minimal technical calibration. A significant disadvantage of fragment analysis by sequencing is that the method is only practical and cost‐effective when performed on batches of several hundred samples with multiple loci. Future work is needed to optimize throughput while minimizing costs and to update existing microsatellite allele calling and analysis programs to accommodate sequence‐aware microsatellite data

Evaluating behavioral responses of nesting lesser snow geese to unmanned aircraft surveys

Unmanned aircraft systems (UAS) are relatively new technologies gaining popularity among wildlife biologists. As with any new tool in wildlife science, operating protocols must be developed through rigorous protocol testing. Few studies have been conducted that quantify the impacts UAS may have on unhabituated individuals in the wild using standard aerial survey protocols. We evaluated impacts of unmanned surveys by measuring UAS-induced behavioral responses during the nesting phase of lesser snow geese (Anser caerulescens caerulescens) in Wapusk National Park, Manitoba, Canada. We conducted surveys with a fixed-wing Trimble UX5 and monitored behavioral changes via discreet surveillance cameras at 25 nests. Days with UAS surveys resulted in decreased resting and increased nest maintenance, low scanning, high scanning, head-cocking and off-nest behaviors when compared to days without UAS surveys. In the group of birds flown over, head-cocking for overhead vigilance was rarely seen prior to launch or after landing (mean estimates 0.03% and 0.02%, respectively) but increased to 0.56% of the time when the aircraft was flying overhead suggesting that birds were able to detect the aircraft during flight. Neither UAS survey altitude nor launch distance alone in this study was strong predictors of nesting behaviors, although our flight altitudes (≥75 m above ground level) were much higher than previously published behavioral studies. Synthesis and applications: The diversity of UAS models makes generalizations on behavioral impacts difficult, and we caution that researchers should design UAS studies with knowledge that some minimal disturbance is likely to occur. We recommend flight designs take potential behavioral impacts into account by increasing survey altitude where data quality requirements permit. Such flight designs should consider a priori knowledge of focal species’ behavioral characteristics. Research is needed to determine whether any such disturbance is a result of visual or auditory stimuli

“Working the System”—British American Tobacco's Influence on the European Union Treaty and Its Implications for Policy: An Analysis of Internal Tobacco Industry Documents

Katherine Smith and colleagues investigate the ways in which British American Tobacco influenced the European Union Treaty so that new EU policies advance the interests of major corporations, including those that produce products damaging to health

The James Webb Space Telescope Mission

Twenty-six years ago a small committee report, building on earlier studies, expounded a compelling and poetic vision for the future of astronomy, calling for an infrared-optimized space telescope with an aperture of at least $4m$. With the support of their governments in the US, Europe, and Canada, 20,000 people realized that vision as the $6.5m$ James Webb Space Telescope. A generation of astronomers will celebrate their accomplishments for the life of the mission, potentially as long as 20 years, and beyond. This report and the scientific discoveries that follow are extended thank-you notes to the 20,000 team members. The telescope is working perfectly, with much better image quality than expected. In this and accompanying papers, we give a brief history, describe the observatory, outline its objectives and current observing program, and discuss the inventions and people who made it possible. We cite detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space Telescope Overview, 29 pages, 4 figure

Data from: Digital fragment analysis of short tandem repeats by high-throughput amplicon sequencing

High-throughput sequencing has been proposed as a method to genotype microsatellites and overcome the four main technical drawbacks of capillary electrophoresis: amplification artifacts, imprecise sizing, length homoplasy, and limited multiplex capability. The objective of this project was to test a high-throughput amplicon sequencing approach to fragment analysis of short tandem repeats and characterize its advantages and disadvantages against traditional capillary electrophoresis. We amplified and sequenced 12 muskrat microsatellite loci from 180 muskrat specimens and analyzed the sequencing data for precision of allele calling, propensity for amplification or sequencing artifacts, and for evidence of length homoplasy. Of the 294 total alleles, we detected by sequencing, only 164 alleles would have been detected by capillary electrophoresis as the remaining 130 alleles (44%) would have been hidden by length homoplasy. The ability to detect a greater number of unique alleles resulted in the ability to resolve greater population genetic structure. The primary advantages of fragment analysis by sequencing are the ability to precisely size fragments, resolve length homoplasy, multiplex many individuals and many loci into a single high-throughput run, and compare data across projects and across laboratories (present and future) with minimal technical calibration. A significant disadvantage of fragment analysis by sequencing is that the method is only practical and cost-effective when performed on batches of several hundred samples with multiple loci. Future work is needed to optimize throughput while minimizing costs and to update existing microsatellite allele calling and analysis programs to accommodate sequence-aware microsatellite data

digital Fragment Analysis Histograms

Histograms (in text files) of each microsatellite locus from Ondatra zibethicus (muskrat). These histograms were created with a custom Python script from Illumina MiSeq paired-end sequencing reads that were merged, quality filtered, and de-replicated. A file to map the sample to the specimen ID (and its sampling population) is in the ReadMe file

digital Fragment Analysis Final Genotypes

Final microsatellite genotypes for each muskrat specimen, including muskrat ID, location, allele (0,1), and eleven micorsatellite loci. A text file that maps alleles to their sequence is in the ReadMe file

Data from: Evaluating behavioral responses of nesting lesser snow geese to unmanned aircraft surveys

Unmanned aircraft systems (UAS) are relatively new technologies gaining popularity among wildlife biologists. As with any new tool in wildlife science, operating protocols must be developed through rigorous protocol testing. Few studies have been conducted that quantify the impacts UAS may have on unhabituated individuals in the wild using standard aerial survey protocols. We evaluated impacts of unmanned surveys by measuring UAS-induced behavioral responses during the nesting phase of lesser snow geese (Anser caerulescens caerulescens) in Wapusk National Park, Manitoba, Canada. We conducted surveys with a fixed-wing Trimble UX5 and monitored behavioral changes via discreet surveillance cameras at 25 nests. Days with UAS surveys resulted in decreased resting and increased nest maintenance, low scanning, high scanning, head-cocking and off-nest behaviors when compared to days without UAS surveys. In the group of birds flown over, head-cocking for overhead vigilance was rarely seen prior to launch or after landing (mean estimates 0.03% and 0.02%, respectively) but increased to 0.56% of the time when the aircraft was flying overhead suggesting that birds were able to detect the aircraft during flight. Neither UAS survey altitude nor launch distance alone in this study was strong predictors of nesting behaviors, although our flight altitudes (≥75 m above ground level) were much higher than previously published behavioral studies. Synthesis and applications: The diversity of UAS models makes generalizations on behavioral impacts difficult, and we caution that researchers should design UAS studies with knowledge that some minimal disturbance is likely to occur. We recommend flight designs take potential behavioral impacts into account by increasing survey altitude where data quality requirements permit. Such flight designs should consider a priori knowledge of focal species’ behavioral characteristics. Research is needed to determine whether any such disturbance is a result of visual or auditory stimuli

A first genetic assessment of the newly introduced Isle Royale gray wolves (Canis lupus)

The gray wolf (Canis lupus) population of Isle Royale National Park suffered an extreme population decline where by 2017 only two wolves that were both half-siblings and a father-daughter pair remained with low probability of producing viable young. This precipitous decline was in part due to the negative fitness consequences associated with inbreeding. To restore the Isle Royale ecosystem 19 gray wolves were translocated in 2018 and 2019. The founders were translocated from Grand Portage, MN (n = 4), western Upper Peninsula, MI (n = 4), Jostle Lake, ON (n = 3), and Michipicoten Island, ON (n = 8), and genotyped using 18 microsatellite loci. Allelic richness and heterozygosity of translocated Isle Royale founders was similar to reference populations. Population structure assigned the Isle Royale founders to gray wolves with little evidence of admixture from eastern wolves (Canis lycaon cf). In addition, we confirmed wolves translocated from Michipicoten Island were a single family-group. Through simulation and empirical analysis of the new Isle Royale founders we projected a loss in genetic variation over the next 50 years and an increase in inbreeding. However, varying levels of immigration may allow the retention of some genetic variation. Our findings indicate Isle Royale founders are genetically diverse and representative of the Great Lakes region, but the numerical dominance of a single family group may have negative implications for retaining genetic diversity and success of establishment for specific wolves, reinforcing the importance of continued monitoring of genetic fitness

Snow_goose_behaviours

Spreadsheet of proportion time spent on six (6) observed behaviours in lesser snow gees