Modeling effects of nonbreeders on population growth estimates

Acknowledgements We thank the Beissinger lab and reviewers for helpful comments on manuscript drafts. This research was funded by a Marie Curie International Outgoing Fellowship within the 7th European Community Framework Programme (project NON- BREEDERS). The contents of this paper reflect the views of the researchers, not the views of the European Commission. Data Accessibility R-code available from the Dryad Digital Repository: http://dx.doi.org/10.5061/dryad.t56cn (Lee, Reid & Beissinger, 2016).Peer reviewedPostprin

Selection for Silage Yield and Composition Did Not Affect Genomic Diversity Within the Wisconsin Quality Synthetic Maize Population

Maize silage is forage of high quality and yield, and represents the second most important use of maize in the United States. The Wisconsin Quality Synthetic (WQS) maize population has undergone five cycles of recurrent selection for silage yield and composition, resulting in a genetically improved population. The application of high-density molecular markers allows breeders and geneticists to identify important loci through association analysis and selection mapping, as well as to monitor changes in the distribution of genetic diversity across the genome. The objectives of this study were to identify loci controlling variation for maize silage traits through association analysis and the assessment of selection signatures and to describe changes in the genomic distribution of gene diversity through selection and genetic drift in theWQS recurrent selection program. We failed to find any significant marker-trait associations using the historical phenotypic data from WQS breeding trials combined with 17,719 high-quality, informative single nucleotide polymorphisms. Likewise, no strong genomic signatures were left by selection on silage yield and quality in the WQS despite genetic gain for these traits. These results could be due to the genetic complexity underlying these traits, or the role of selection on standing genetic variation. Variation in loss of diversity through drift was observed across the genome. Some large regions experienced much greater loss in diversity than what is expected, suggesting limited recombination combined with small populations in recurrent selection programs could easily lead to fixation of large swaths of the genome

Large fluctuations in stochastic population dynamics: momentum space calculations

Momentum-space representation renders an interesting perspective to theory of large fluctuations in populations undergoing Markovian stochastic gain-loss processes. This representation is obtained when the master equation for the probability distribution of the population size is transformed into an evolution equation for the probability generating function. Spectral decomposition then brings about an eigenvalue problem for a non-Hermitian linear differential operator. The ground-state eigenmode encodes the stationary distribution of the population size. For long-lived metastable populations which exhibit extinction or escape to another metastable state, the quasi-stationary distribution and the mean time to extinction or escape are encoded by the eigenmode and eigenvalue of the lowest excited state. If the average population size in the stationary or quasi-stationary state is large, the corresponding eigenvalue problem can be solved via WKB approximation amended by other asymptotic methods. We illustrate these ideas in several model examples.Comment: 20 pages, 9 figures, to appear in JSTA

An R Framework for the Partitioning of Linkage Disequilibrium between and Within Populations

Patterns of linkage disequilibrium (LD) across the genome result from a myriad of contributing factors including selection and genetic drift. Natural selection can increase LD near individually selected loci, or it can influence LD between epistatically selected groups of loci. Statistics have previously been derived which compare levels of linkage disequilibrium in subpopulations relative to the total population. These statistics may be leveraged to identify loci that may be under selection or epistatic selection. This is a powerful approach, but to date no framework exists to support its use on a genome-wide scale. We present ohtadstats, an R package designed to facilitate the implementation of Ohta’s D statistics in a variety of use cases. Statistics calculated by this package can be used to determine whether a locus is under selection or not, and can provide insight into the nature of the selection that is taking place (hard sweep or epistatic selection). This package is available on the Comprehensive R Archive Network (CRAN).   Funding statement: This research was supported by funding from the USDA Agricultural Research Service. PFP is funded by the University of Missouri Life Sciences Fellowship and a training grant from the National Institute of Health (T32GM008396)

Predation and infanticide influence ideal free choice by a parrot occupying heterogeneous tropical habitats

The ideal free distribution (IFD) predicts that organisms will disperse to sites that maximize their fitness based on availability of resources. Habitat heterogeneity underlies resource variation and influences spatial variation in demography and the distribution of populations. We relate nest site productivity at multiple scales measured over a decade to habitat quality in a box-nesting population of Forpus passerinus (green-rumped parrotlets) in Venezuela to examine critical IFD assumptions. Variation in reproductive success at the local population and neighborhood scales had a much larger influence on productivity (fledglings per nest box per year) than nest site or female identity. Habitat features were reliable cues of nest site quality. Nest sites with less vegetative cover produced greater numbers of fledglings than sites with more cover. However, there was also a competitive cost to nesting in high-quality, low-vegetative cover nest boxes, as these sites experienced the most infanticide events. In the lowland local population, water depth and cover surrounding nest sites were related with F. passerinus productivity. Low vegetative cover and deeper water were associated with lower predation rates, suggesting that predation could be a primary factor driving habitat selection patterns. Parrotlets also demonstrated directional dispersal. Pairs that changed nest sites were more likely to disperse from poor-quality nest sites to high-quality nest sites rather than vice versa, and juveniles were more likely to disperse to, or remain in, the more productive of the two local populations. Parrotlets exhibited three characteristics fundamental to the IFD: habitat heterogeneity within and between local populations, reliable habitat cues to productivity, and active dispersal to sites of higher fitness

MSMC and MSMC2: the multiple sequentially markovian coalescent

The Multiple Sequentially Markovian Coalescent (MSMC) is a population genetic method and software for inferring demographic history and population structure through time from genome sequences. Here we describe the main program MSMC and its successor MSMC2. We go through all the necessary steps of processing genomic data from BAM files all the way to generating plots of inferred population size and separation histories. Some background on the methodology itself is provided, as well as bash scripts and python source code to run the necessary programs. The reader is also referred to community resources such as a mailing list and github repositories for further advice

A Primer on High-Throughput Computing for Genomic Selection

High-throughput computing (HTC) uses computer clusters to solve advanced computational problems, with the goal of accomplishing high-throughput over relatively long periods of time. In genomic selection, for example, a set of markers covering the entire genome is used to train a model based on known data, and the resulting model is used to predict the genetic merit of selection candidates. Sophisticated models are very computationally demanding and, with several traits to be evaluated sequentially, computing time is long, and output is low. In this paper, we present scenarios and basic principles of how HTC can be used in genomic selection, implemented using various techniques from simple batch processing to pipelining in distributed computer clusters. Various scripting languages, such as shell scripting, Perl, and R, are also very useful to devise pipelines. By pipelining, we can reduce total computing time and consequently increase throughput. In comparison to the traditional data processing pipeline residing on the central processors, performing general-purpose computation on a graphics processing unit provide a new-generation approach to massive parallel computing in genomic selection. While the concept of HTC may still be new to many researchers in animal breeding, plant breeding, and genetics, HTC infrastructures have already been built in many institutions, such as the University of Wisconsin–Madison, which can be leveraged for genomic selection, in terms of central processing unit capacity, network connectivity, storage availability, and middleware connectivity. Exploring existing HTC infrastructures as well as general-purpose computing environments will further expand our capability to meet increasing computing demands posed by unprecedented genomic data that we have today. We anticipate that HTC will impact genomic selection via better statistical models, faster solutions, and more competitive products (e.g., from design of marker panels to realized genetic gain). Eventually, HTC may change our view of data analysis as well as decision-making in the post-genomic era of selection programs in animals and plants, or in the study of complex diseases in humans

Are Newspapers’ Online Discussion Boards Democratic Tools or Conspiracy Theories’ Engines? A Case Study on an Eastern European “Media War”

This article analyzes quantitatively and qualitatively 1,583 comments by national newspapers’ online readers in Bulgaria. It investigates readers’ reactions to articles discussing the media war between the biggest press groups—one owned by a Member of Parliament known as “the Murdoch of the East.” The study explores how these stories influence the relationship between newspapers and their readers, and whether they enhance the democratic potential of online discussion. The results show a higher level of reader engagement than in established democracies or nondemocracies. The online space provides an arena for democratic conversations and it is also used as an engine for conspiracy theories

National protest agenda and the dimensionality of party politics: Evidence from four East-Central European democracies

Contemporary democracies show considerable differences in the issue composition of their protest politics, which tends to remain relatively stable over time. In countries like Germany or the Czech Republic, the vast majority of protests have been mobilised around sociocultural issues, such as human rights, peace, nuclear power or the environment, and only a tiny portion of protest has focused on economic issues. At the opposite extreme, protest in France or Poland usually has a strongly economic character and voices demands relating to material redistribution and social policy. What lies behind the cross-country differences in national protest agendas? In this article, the national protest agenda depends on what issues mainstream political parties are contesting: the content and strength of the master-issue dimension. In reference to the literature on the multidimensional political space and niche political parties, one should expect that there is a substitutive effect; where the stronger a specific master-issue dimension is in party politics, the less salient that issue dimension is in protest politics. This substitutive effect results from the tendency of electoral politics to reduce political conflict to a single-dimension equilibrium, which decreases the importance of other issues and relegates the contest over secondary, niche issues to the realm of policy-seeking strategies, with protest being a common type of this political strategy. In party systems where single-dimension equilibrium does not exist and the master-issue dimension is weaker, the same dynamics result in a more convergent relationship between party and protest politics and a greater similarity between the protest- and party-system agendas. To investigate this theory, the national protest agendas in four countries are examined. The Czech Republic, Hungary, Poland and Slovakia show four combinations of two crucial factors that are not available in the old Western democracies: the content and the strength of the master-issue dimension. The study draws on an original dataset of protest events organised in the four countries between 1993 and 2010, and on qualitative and quantitative data on issue dimensions of party politics obtained from studies on party politics and expert surveys. The results show that in the Czech Republic, where the master-issue dimension has remained strongly economic, protest has been predominantly sociocultural. In Poland between 1993 and 2001 and Hungary between 1993 and 2006, the master-issue dimensions are strongly sociocultural, while protest is predominantly economic. There is no single-dimension equilibrium in party politics in Slovakia or in post-2001 Poland and mainstream parties compete on both economic and sociocultural issues. Consequently, the substitutive dynamics between party and protest politics is weaker and the issue agendas in party and protest arenas are here more alike. <br/