Avian population genomics taking off: latest findings and future prospects

Birds are one of the most recognizable and diverse groups of organisms on earth. This group has played animportant role in many fields, including the development of methods in behavioral ecology and evolution-ary theory. The use of population genomics took off following the advent of high-throughput sequencingin various taxa. Several features of avian genomes make them particularly amenable for work in this field,including their nucleated red blood cells permitting easy DNA extraction and small, compact genomes. Wereview the latest findings in the population genomics of birds here, emphasizing questions related tobehavior, ecology, evolution, and conservation. Additionally, we include insights in trait mapping and theability to obtain accurate estimates of important summary statistics for conservation (e.g., genetic diversityand inbreeding). We highlight roadblocks that will need to be overcome in order to advance work on thepopulation genomics of birds and prospects for future work. Roadblocks include the assembly of morecontiguous reference genomes using long-reads and optical mapping. Prospects include the integration ofpopulation genomics with additional fields (e.g., landscape genetics, phylogeography, and genomicmapping) along with studies beyond genetic variants (e.g., epigenetics)

Determining Reactor Flux from Xenon-136 and Cesium-135 in Spent Fuel

The ability to infer the reactor flux from spent fuel or seized fissile material would enhance the tools of nuclear forensics and nuclear nonproliferation significantly. We show that reactor flux can be inferred from the ratios of xenon-136 to xenon-134 and cesium-135 to cesium-137. If the average flux of a reactor is known, the flux inferred from measurements of spent fuel could help determine whether that spent fuel was loaded as a blanket or close to the mid-plane of the reactor. The cesium ratio also provides information on reactor shutdowns during the irradiation of fuel, which could prove valuable for identifying the reactor in question through comparisons with satellite reactor heat monitoring data. We derive analytic expressions for these correlations and compare them to experimental data and to detailed reactor burn simulations. The enrichment of the original uranium fuel affects the correlations by up to 3 percent, but only at high flux.Comment: 10 pages, 9 figure

Micro Ion Source Program NA22 Plutonium Detection Portfolio Final Report

The purpose of the micro ion source program was to enhance the performance of thermal ionization mass spectrometry (TIMS) for various actinides and fission products. The proposal hypothesized that when ions are created at the ion optic center of the mass spectrometer, ion transmission is significantly increased and the resulting ion beam is more sharply focused. Computer modeling demonstrated this logic. In order to prove this hypothesis it was first necessary to understand the chemistry and physics governing the particular ion production process that concentrates the emission of ions into a small area. This has been achieved for uranium and technetium, as was shown in the original proposal and the improvement of both the beam transmission and sharpness of focus were proven. Significantly improved analytical methods have been developed for these two elements based upon this research. The iodine portion of the proposal turned out to be impractical due to volatility of iodine and its compounds. We knew this was a possibility prior to research and we proceeded anyway but did not succeed. Plutonium is a potential option, but is not quite up to the performance level of resin beads. Now, we more clearly understand the chemical and physical issues for plutonium, but have not yet translated this knowledge into improved analytical processes. The problems are that plutonium is considerably more difficult to convert to the required intermediate species, plutonium carbide, and the chemical method we developed that works with uranium functions only moderately well with plutonium. We are of the opinion that, with this knowledge, similar progress can be made with plutonium

High Temperature Condensed Phase Mass Spectrometric Analysis

This program (in the 20th month as of this writing) was initiated with the goal of designing, constructing and operating a materials analysis instrument capable of obtaining a wide variety of chemical measurements on a material at high temperature. This instrument is being built around a quadrupole mass spectrometer. There are three main modes of obtaining spectra from the high temperature condensed phase material; surface ionization from the condensed phase, secondary ion mass spectrometry (SIMS, both static and dynamic modes) of the condensed phase, and electron impact ionization of vapor phase neutral species. The combination of the data from these three modes will allow the gleaning of chemical information concerning the nature of the chemical species present in both the condensed phase (solid or molten) and the vapor phase. The intended application is the identification of the chemical species present in materials at high temperatures

High Temperature Condensed Phase Mass Spectrometric Analysis

The EMSP Program ''High Temperature Condensed Phase Mass Spectrometric Analysis'' was funded in Sep. 1997 for 36 months. The purpose of this program is to address the issues associated with understanding properties and reactions when materials such as glasses and ceramics are heated to high temperatures in a variety of processes. The reason this is important to DOE EM is the fact that many processes are either in operation or are planned that entail the processing of waste materials at high temperatures. These systems have been engineered, but in many cases the actual scientific details of what goes on in these processes are poorly understood. This program was funded to build a high temperature mass spectrometric analysis instrument designed specifically to analyze materials heated to high temperatures that allows the study of materials both held at these temperatures and undergoing chemical reactions at these temperatures. This program is now at the 30 month point, and the end product of this program, a mass spectrometer system with multiple ionization and analysis modes for high temperature samples, is now operational. The instrument is built around a high temperature ''Langmuir evaporation source,'' and has the following ionization modes: (a) Static SIMS for cations and anions. (b) Dynamic SIMS for cations and anions. (c) Surface ionization for cations and anions. (d) Electron impact ionization (EI) for cations. These ionization modes are all designed into a single ion source housing interfaced to a high sensitivity quadrupole mass spectrometer

High Temperature Condensed Phase Mass Spectrometric Analysis Program

This program (EMSP Project No.60424) was funded by the EM Science Program for the development of an integrated mass spectrometric analysis system (see Figure 1.) capable of analyzing materials from room up to high temperatures, with the practical upper temperature limit to be experimentally determined. A primary objective of the program was the development of techniques to analyze waste materials during vitrification processing to produce waste forms. The sample is heated in the ion formation region of the mass spectrometer. This instrument geometry allows the atoms and molecules that volatilize from the sample as neutrals to be ionized before they have a chance to condense on surfaces that generally are cooler that the sample. In addition, this geometry facilitates more efficient focusing of SIMS and thermal ions into the quadrupole mass analyzer. Instrumental capabilities include the detection of volatilizing neutral species by electron bombardment, ions forming on the surface by surface ionization, and surface species by static SIMS. In addition, the instrument has elemental analysis capability (by dynamic SIMS)

(Micro)evolutionary changes and the evolutionary potential of bird migration

Seasonal migration is the yearly long-distance movement of individuals between their breeding and wintering grounds. Individuals from nearly every animal group exhibit this behavior, but probably the most iconic migration is carried out by birds, from the classic V-shape formation of geese on migration to the amazing nonstop long-distance flights undertaken by Arctic Terns Sterna paradisaea. In this chapter, we discuss how seasonal migration has shaped the field of evolution. First, this behavior is known to turn on and off quite rapidly, but controversy remains concerning where this behavior first evolved geographically and whether the ancestral state was sedentary or migratory (Fig. 7.1d, e). We review recent work using new analytical techniques to provide insight into this topic. Second, it is widely accepted that there is a large genetic basis to this trait, especially in groups like songbirds that migrate alone and at night precluding any opportunity for learning. Key hypotheses on this topic include shared genetic variation used by different populations to migrate and only few genes being involved in its control. We summarize recent work using new techniques for both phenotype and genotype characterization to evaluate and challenge these hypotheses. Finally, one topic that has received less attention is the role these differences in migratory phenotype could play in the process of speciation. Specifically, many populations breed next to one another but take drastically different routes on migration (Fig. 7.2). This difference could play an important role in reducing gene flow between populations, but our inability to track most birds on migration has so far precluded evaluations of this hypothesis. The advent of new tracking techniques means we can track many more birds with increasing accuracy on migration, and this work has provided important insight into migration's role in speciation that we will review here

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