GBS and a newly developed mRNA-GBS approach to link population genetic and transcriptome analyses reveal pattern differences between sites and treatments in red clover (Trifolium pratense L.)

The important worldwide forage crop red clover (Trifolium pratense L.) is widely cultivated as cattle feed and for soil improvement. Wild populations and landraces have great natural diversity that could be used to improve cultivated red clover. However, to date, there is still insufficient knowledge about the natural genetic and phenotypic diversity of the species. Here, we developed a low-cost transcriptome analysis (mRNA-GBS) with reduced complexity and compared the results with population genetic (GBS) and previously published mRNA-Seq data, to assess whether analysis of intraspecific variation within and between populations and transcriptome responses is possible simultaneously. The mRNA-GBS approach was successful. SNP analyses from the mRNA-GBS approach revealed comparable patterns to the GBS results, but it was not possible to link transcriptome analyses with reduced complexity and sequencing depth to previously published greenhouse and field expression studies. The use of short sequences upstream of the poly(A) tail of mRNA to reduce complexity are promising approaches that combine population genetics and expression profiling to analyze many individuals with trait differences simultaneously and cost-effectively, even in non-model species. Our mRNA-GBS approach revealed too many additional short mRNA sequences, hampering sequence alignment depth and SNP recovery. Optimizations are being discussed. Nevertheless, our study design across different regions in Germany was also challenging as the use of differential expression analyses with reduced complexity, in which mRNA is fragmented at specific sites rather than randomly, is most likely counteracted under natural conditions by highly complex plant reactions at low sequencing depth.

Scenarios for urban drainage on a Legal Amazon planned city: a case study in Palmas, Brazil

ABSTRACT The significant urbanization of Brazil in the last decades has pushed cities to combine population growth with protection and harmonic living with their natural resources. The city of Palmas, a planned city in the Legal Amazon, is inserted in this context. In this sense, this study sought to analyze the hydrological and hydraulic responses to different scenarios of land use and occupation in one of its watersheds. Scenarios modeled with SWMM software were current, critical and compensatory techniques. The results showed that the conveyance system, including the main stream, are fully capable of conveying the affluent flow, even in the scenarios with greater impermeability of the watershed. The peak flow of the critical scenario is up to 11.12% higher than the current scenario. However, with compensatory techniques, it is possible to have a peak flow up to 25.76% smaller than the critical scenario.

Looking for ‘Voice’ in Business and Citizen Groups: Who’s Being Heard?

Why do some associations provide members with an effective voice whereas others appear to have internal democracy in name only? We theoretically combine population ecology with Hirschman’s strategic response model. This leads us to hypothesize that in dense, competitive organizational environments, the effective alternatives available make it likely that dissatisfied members respond with exit rather than voice. However, in low-dense, monopoly-like situations dissatisfied members demand and receive effective voice options. We further hypothesize that the particular sets of incentives of firms and individuals as members moderates this effect. We assess our argument on the basis of the Comparative Interest Group elite survey among interest group leaders in five European countries and at the EU level. We control for the level of professionalization and use country dummies to identify country-level differences. We find strong empirical support for our theoretical argument. The contribution of this article is to theoretically connect macro-level population-level factors to micro-level intra-organizational processes and specifies the nature of the organizational link between interests in society and those represented in the interest group system.

cchsflow: an open science approach to transform and combine population health surveys

Setting The Canadian Community Health Survey (CCHS) is one of the world’s largest ongoing cross-sectional population health surveys, with over 130,000 respondents every two years or over 1.1 million respondents since its inception in 2001. While the survey remains relatively consistent over the years, there are differences between cycles that pose a challenge to analyze the survey over time. Intervention A program package called cchsflow was developed to transform and harmonize CCHS variables to consistent formats across multiple survey cycles. An open science approach was used to maintain transparency, reproducibility and collaboration. Outcomes The cchsflow R package uses CCHS survey data between 2001 and 2014. Worksheets were created that identify variables, their names in previous cycles, their category structure, and their final variable names. These worksheets were then used to recode variables in each CCHS cycle into consistently named and labelled variables. Following, survey cycles can be combined. The package was then added as a GitHub repository to encourage collaboration with other researchers. Implication The cchsflow package has been added to the Comprehensive R Archive Network (CRAN) and contains support for over 160 CCHS variables, generating a combined data set of over 1 million respondents. By implementing open science practices, cchsflow aims to minimize the amount of time needed to clean and prepare data for the many CCHS users across Canada.

Soft Selective Sweep on Chemosensory Genes Correlates with Ancestral Preference for Toxic Noni in a Specialist Drosophila Population

Understanding how organisms adapt to environmental changes is a major question in evolution and ecology. In particular, the role of ancestral variation in rapid adaptation remains unclear because its trace on genetic variation, known as soft selective sweep, is often hardly recognizable from genome-wide selection scans. Here, we investigate the evolution of chemosensory genes in Drosophila yakuba mayottensis, a specialist subspecies on toxic noni (Morinda citrifolia) fruits on the island of Mayotte. We combine population genomics analyses and behavioral assays to evaluate the level of divergence in chemosensory genes and perception of noni chemicals between specialist and generalist subspecies of D. yakuba. We identify a signal of soft selective sweep on a handful of genes, with the most diverging ones involving a cluster of gustatory receptors expressed in bitter-sensing neurons. Our results highlight the potential role of ancestral genetic variation in promoting host plant specialization in herbivorous insects and identify a number of candidate genes underlying behavioral adaptation.

Population Genetic Divergence and Environment Influence the Gut Microbiome in Oregon Threespine Stickleback

Much of animal-associated microbiome research has been conducted in species for which little is known of their natural ecology and evolution. Microbiome studies that combine population genetic, environment, and geographic data for wild organisms can be very informative, especially in situations where host genetic variation and the environment both influence microbiome variation. The few studies that have related population genetic and microbiome variation in wild populations have been constrained by observation-based kinship data or incomplete genomic information. Here we integrate population genomic and microbiome analyses in wild threespine stickleback fish distributed throughout western Oregon, USA. We found that gut microbiome diversity and composition partitioned more among than within wild host populations and was better explained by host population genetic divergence than by environment and geography. We also identified gut microbial taxa that were most differentially abundant across environments and across genetically divergent populations. Our findings highlight the benefits of studies that investigate host-associated microbiomes in wild organisms.

Selection, linkage, and population structure interact to shape genetic variation among threespine stickleback genomes

The outcome of selection on genetic variation depends on the geographic organization of individuals and populations as well as the syntenic organization of loci within the genome. Spatially variable selection between marine and freshwater habitats has had a significant and heterogeneous impact on patterns of genetic variation across the genome of threespine stickleback fish. When marine stickleback invade freshwater habitats, more than a quarter of the genome can respond to divergent selection, even in as little as 50 years. This process largely uses standing genetic variation that can be found ubiquitously at low frequency in marine populations, can be millions of years old, and is likely maintained by significant bidirectional gene flow. Here, we combine population genomic data of marine and freshwater stickleback from Cook Inlet, Alaska, with genetic maps of stickleback fish derived from those same populations to examine how linkage to loci under selection affects genetic variation across the stickleback genome. Divergent selection has had opposing effects on linked genetic variation on chromosomes from marine and freshwater stickleback populations: near loci under selection, marine chromosomes are depauperate of variation while these same regions among freshwater genomes are the most genetically diverse. Forward genetic simulations recapitulate this pattern when different selective environments also differ in population structure. Lastly, dense genetic maps demonstrate that the interaction between selection and population structure may impact large stretches of the stickleback genome. These findings advance our understanding of how the structuring of populations across geography influences the outcomes of selection, and how the recombination landscape broadens the genomic reach of selection.

A Model for Perceptual Averaging and Stochastic Bistable Behavior and the Role of Voluntary Control

We combine population coding, winner-take-all competition, and differentiated inhibitory feedback to model the process by which information from different, continuously variable signals is integrated for perceptual awareness. We focus on “slant rivalry,” where binocular disparity is in conflict with monocular perspective in specifying surface slant. Using a robust single parameter set, our model successfully replicates three key experimental results: (1) transition from signal averaging to bistability with increasing signal conflict, (2) change in perceptual reversal rates as a function of signal conflict, and (3) a shift in the distribution of percept durations through voluntary control exertion. Voluntary control is implemented through the use of a single top-down bias input. The transition from signal averaging to bistability arises as a natural consequence of combining population coding and wide receptive fields, common to higher cortical areas. The model architecture does not contain any assumption that would limit it to this particular example of stimulus rivalry. An emergent physiological interpretation is that differentiated inhibitory feedback may play an important role for increasing percept stability without reducing sensitivity to large stimulus changes, which for bistable conditions leads to increased alternation rate as a function of signal conflict.