Genetics of adaptation

The rediscovery of Mendel’s work showing that the heredity of phenotypes is controlled by discrete genes was followed by the reconciliation of Mendelian genetics with evolution by natural selection in the middle of the last century with the Modern Synthesis. In the past two decades, dramatic advances in genomic methods have facilitated the identification of the loci, genes, and even individual mutations that underlie phenotypic variants that are the putative targets of natural selection. Moreover, these methods have also changed how we can study adaptation by flipping the problem around, allowing us to first examine what loci show evidence of having been under selection, and then connecting these genetic variants to phenotypic variation. As a result, we now have an expanding list of actual genetic changes that underlie potentially adaptive phenotypic variation. Here, we synthesize how considering the effects of these adaptive loci in the context of cellular environments, genomes, organisms, and populations has provided new insights to the genetic architecture of adaptation

The 100 kDa F-actin capping protein of Dictyostelium amoebae is a villin prototype (‘protovillin’)

AbstractThe 100 kDa actin-binding protein from Dictyostelium amoebae is an F-actin capping protein that displays neither severing nor crosslinking nor nucleating activities [Hofmann et al. (1992) Cell Motil. Cytoskel. 23,133-144]. Cloning and sequencing of the gene revealed that the protein is highly homologous to vertebrate villin, a unique component of brush border microvilli and contains six domains fused to a villin-like headpiece domain via a threonine/proline rich neck region. The functional differences and similarities between the 100 kDa protein and villin are reflected in the amino acid sequences. We draw from the data the following conclusions, (i) The presence of a six domain protein in Dictyostelium suggests that in contrast to the current view gene duplications must have happened before Dictyostelium branched off during evolution, (ii) The villin-like molecule in Dictyostelium appears to be a premature villin (‘protovillin’) which is able to cap actin filaments but still lacks the other villin-type actin-binding activities. This renders capping of actin filaments as the evolutionarily oldest function of an F-actin binding protein

Evaluation of daily precipitation from the era5 global reanalysis against ghcn observations in the northeastern united states

Licensee MDPI, Basel, Switzerland. Precipitation is a primary input for hydrologic, agricultural, and engineering models, so making accurate estimates of it across the landscape is critically important. While the distribution of in-situ measurements of precipitation can lead to challenges in spatial interpolation, gridded precipitation information is designed to produce a full coverage product. In this study, we compare daily precipitation accumulations from the ERA5 Global Reanalysis (hereafter ERA5) and the US Global Historical Climate Network (hereafter GHCN) across the northeastern United States. We find that both the distance from the Atlantic Coast and elevation difference between ERA5 estimates and GHCN observations affect precipitation relationships between the two datasets. ERA5 has less precipitation along the coast than GHCN observations but more precipitation inland. Elevation differences between ERA5 and GHCN observations are positively correlated with precipitation differences. Isolated GHCN stations on mountain peaks, with elevations well above the ERA5 model grid elevation, have much higher precipitation. Summer months (June, July, and August) have slightly less precipitation in ERA5 than GHCN observations, perhaps due to the ERA5 convective parameterization scheme. The heavy precipitation accumulation above the 90th, 95th, and 99th percentile thresholds are very similar for ERA5 and the GHCN. We find that daily precipitation in the ERA5 dataset is comparable to GHCN observations in the northeastern United States and its gridded spatial continuity has advantages over in-situ point precipitation measurements for regional modeling applications

Balancing Selection at the Tomato RCR3 Guardee Gene Family Maintains Variation in Strength of Pathogen Defense

Coevolution between hosts and pathogens is thought to occur between interacting molecules of both species. This results in the maintenance of genetic diversity at pathogen antigens (or so-called effectors) and host resistance genes such as the major histocompatibility complex (MHC) in mammals or resistance (R) genes in plants. In plant-pathogen interactions, the current paradigm posits that a specific defense response is activated upon recognition of pathogen effectors via interaction with their corresponding R proteins. According to the''Guard-Hypothesis,'' R proteins (the ``guards'') can sense modification of target molecules in the host (the ``guardees'') by pathogen effectors and subsequently trigger the defense response. Multiple studies have reported high genetic diversity at R genes maintained by balancing selection. In contrast, little is known about the evolutionary mechanisms shaping the guardee, which may be subject to contrasting evolutionary forces. Here we show that the evolution of the guardee RCR3 is characterized by gene duplication, frequent gene conversion, and balancing selection in the wild tomato species Solanum peruvianum. Investigating the functional characteristics of 54 natural variants through in vitro and in planta assays, we detected differences in recognition of the pathogen effector through interaction with the guardee, as well as substantial variation in the strength of the defense response. This variation is maintained by balancing selection at each copy of the RCR3 gene. Our analyses pinpoint three amino acid polymorphisms with key functional consequences for the coevolution between the guardee (RCR3) and its guard (Cf-2). We conclude that, in addition to coevolution at the ``guardee-effector'' interface for pathogen recognition, natural selection acts on the ``guard-guardee'' interface. Guardee evolution may be governed by a counterbalance between improved activation in the presence and prevention of auto-immune responses in the absence of the corresponding pathogen

Autoimmune Response as a Mechanism for a Dobzhansky-Muller-Type Incompatibility Syndrome in Plants

Epistatic interactions between genes are a major factor in evolution. Hybrid necrosis is an example of a deleterious phenotype caused by epistatic interactions that is observed in many intra- and interspecific plant hybrids. A large number of hybrid necrosis cases share phenotypic similarities, suggesting a common underlying mechanism across a wide range of plant species. Here, we report that approximately 2% of intraspecific crosses in Arabidopsis thaliana yield F1 progeny that express necrosis when grown under conditions typical of their natural habitats. We show that several independent cases result from epistatic interactions that trigger autoimmune-like responses. In at least one case, an allele of an NB-LRR disease resistance gene homolog is both necessary and sufficient for the induction of hybrid necrosis, when combined with a specific allele at a second locus. The A. thaliana cases provide insights into the molecular causes of hybrid necrosis, and serve as a model for further investigation of intra- and interspecific incompatibilities caused by a simple epistatic interaction. Moreover, our finding that plant immune-system genes are involved in hybrid necrosis suggests that selective pressures related to host–pathogen conflict might cause the evolution of gene flow barriers in plants

Coupled impacts of climate and land use change across a river-lake continuum: Insights from an integrated assessment model of Lake Champlain\u27s Missisquoi Basin, 2000-2040

Global climate change (GCC) is projected to bring higher-intensity precipitation and higher-variability temperature regimes to the Northeastern United States. The interactive effects of GCC with anthropogenic land use and land cover changes (LULCCs) are unknown for watershed level hydrological dynamics and nutrient fluxes to freshwater lakes. Increased nutrient fluxes can promote harmful algal blooms, also exacerbated by warmer water temperatures due to GCC. To address the complex interactions of climate, land and humans, we developed a cascading integrated assessment model to test the impacts of GCC and LULCC on the hydrological regime, water temperature, water quality, bloom duration and severity through 2040 in transnational Lake Champlain\u27s Missisquoi Bay. Temperature and precipitation inputs were statistically downscaled from four global circulation models (GCMs) for three Representative Concentration Pathways. An agent-based model was used to generate four LULCC scenarios. Combined climate and LULCC scenarios drove a distributed hydrological model to estimate river discharge and nutrient input to the lake. Lake nutrient dynamics were simulated with a 3D hydrodynamic-biogeochemical model. We find accelerated GCC could drastically limit land management options to maintain water quality, but the nature and severity of this impact varies dramatically by GCM and GCC scenario

Seasonality of Plasmodium falciparum transmission: a systematic review

This article is fully open access and the published version is available free of charge from the jounal website.http://www.malariajournal.com/content/14/1/343Background Although Plasmodium falciparum transmission frequently exhibits seasonal patterns, the drivers of malaria seasonality are often unclear. Given the massive variation in the landscape upon which transmission acts, intra-annual fluctuations are likely influenced by different factors in different settings. Further, the presence of potentially substantial inter-annual variation can mask seasonal patterns; it may be that a location has “strongly seasonal” transmission and yet no single season ever matches the mean, or synoptic, curve. Accurate accounting of seasonality can inform efficient malaria control and treatment strategies. In spite of the demonstrable importance of accurately capturing the seasonality of malaria, data required to describe these patterns is not universally accessible and as such localized and regional efforts at quantifying malaria seasonality are disjointed and not easily generalized. Methods The purpose of this review was to audit the literature on seasonality of P. falciparum and quantitatively summarize the collective findings. Six search terms were selected to systematically compile a list of papers relevant to the seasonality of P. falciparum transmission, and a questionnaire was developed to catalogue the manuscripts. Results and discussion 152 manuscripts were identified as relating to the seasonality of malaria transmission, deaths due to malaria or the population dynamics of mosquito vectors of malaria. Among these, there were 126 statistical analyses and 31 mechanistic analyses (some manuscripts did both). Discussion Identified relationships between temporal patterns in malaria and climatological drivers of malaria varied greatly across the globe, with different drivers appearing important in different locations. Although commonly studied drivers of malaria such as temperature and rainfall were often found to significantly influence transmission, the lags between a weather event and a resulting change in malaria transmission also varied greatly by location. Conclusions The contradicting results of studies using similar data and modelling approaches from similar locations as well as the confounding nature of climatological covariates underlines the importance of a multi-faceted modelling approach that attempts to capture seasonal patterns at both small and large spatial scales. Keywords: Plasmodium falciparum ; Seasonality; Climatic driversAcknowledgements This work was supported by the Research and Policy for Infectious Disease Dynamics (RAPIDD) program of the Science and Technology Directory, Department of Homeland Security, and Fogarty International Center, National Institutes of Health. DLS is funded by a grant from the Bill & Melinda Gates Foundation (OPP1110495), which also supports RCR. PMA is grateful to the University of Utrecht for supporting him with The Belle van Zuylen Chair. PWG is a Career Development Fellow (K00669X) jointly funded by the UK Medical Research Council (MRC) and the UK Department for International Development (DFID) under the MRC/DFID Concordat agreement and receives support from the Bill and Melinda Gates Foundation (OPP1068048, OPP1106023)

Chromosome and DNA methylation dynamics during meiosis in autotetraploid Arabidopsis arenosa

Variation in chromosome number due to polyploidy can seriously compromise meiotic stability. In autopolyploids, the presence of more than two homologous chromosomes may result in complex pairing patterns and subsequent anomalous chromosome segregation. In this context, chromocenter, centromeric, telomeric and ribosomal DNA locus topology and DNA methylation patterns were investigated in the natural autotetraploid, Arabidopsis arenosa. The data show that homologous chromosome recognition and association initiates at telomeric domains in premeiotic interphase, followed by quadrivalent pairing of ribosomal 45S RNA gene loci (known as NORs) at leptotene. On the other hand, centromeric regions at early leptotene show pairwise associations rather than associations in fours. These pairwise associations are maintained throughout prophase I, and therefore likely to be related to the diploid-like behavior of A. arenosa chromosomes at metaphase I, where only bivalents are observed. In anthers, both cells at somatic interphase as well as at premeiotic interphase show 5-methylcytosine (5-mC) dispersed throughout the nucleus, contrasting with a preferential co-localization with chromocenters observed in vegetative nuclei. These results show for the first time that nuclear distribution patterns of 5-mC are simultaneously reshuffled in meiocytes and anther somatic cells. During prophase I, 5-mC is detected in extended chromatin fibers and chromocenters but interestingly is excluded from the NORs what correlates with the pairing patter