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Wolbachia pipientis, a bacterial symbiont infecting arthropods and nematodes, is vertically transmitted through the female germline and manipulates its host’s reproduction to favor infected females. Wolbachia also infects somatic tissues where it can cause nonreproductive phenotypes in its host, including resistance to viral pathogens. Wolbachia-mediated phenotypes are strongly associated with the density of Wolbachia in host tissues. Little is known, however, about how Wolbachia density is regulated in native or heterologous hosts. Here, we measure the broad-sense heritability of Wolbachia density among families in field populations of the mosquito Culex pipiens, and show that densities in ovary and nongonadal tissues of females in the same family are not correlated, suggesting that Wolbachia density is determined by distinct mechanisms in the two tissues. Using introgression analysis between two different strains of the closely related species C. quinquefasciatus, we show that Wolbachia densities in ovary tissues are determined primarily by cytoplasmic genotype, while densities in nongonadal tissues are determined by both cytoplasmic and nuclear genotypes and their epistatic interactions. Quantitative-trait-locus mapping identified two major-effect quantitative-trait loci in the C. quinquefasciatus genome explaining a combined 23% of variance in Wolbachia density, specifically in nongonadal tissues. A better understanding of how Wolbachia density is regulated will provide insights into how Wolbachia density can vary spatiotemporally in insect populations, leading to changes in Wolbachia-mediated phenotypes such as viral pathogen resistance.

Made available in DSpace on 2019-10-06T17:09:58Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-05-17 Background: In the Amazon Basin, Nyssorhynchus (Anopheles) darlingi is the most aggressive and effective malaria vector. In endemic areas, behavioral aspects of anopheline vectors such as host preference, biting time and resting location post blood meal have a key impact on malaria transmission dynamics and vector control interventions. Nyssorhynchus darlingi presents a range of feeding and resting behaviors throughout its broad distribution. Methods: To investigate the genetic diversity related to biting behavior, we collected host-seeking Ny. darlingi in two settlement types in Acre, Brazil: Granada (~ 20-year-old, more established, better access by road, few malaria cases) and Remansinho (~ 8-year-old, active logging, poor road access, high numbers malaria cases). Mosquitoes were classified by the location of collection (indoors or outdoors) and time (dusk or dawn). Results: Genome-wide SNPs, used to assess the degree of genetic divergence and population structure, identified non-random distributions of individuals in the PCA for both location and time analyses. Although genetic diversity related to behavior was confirmed by non-model-based analyses and F ST values, model-based STRUCTURE detected considerable admixture of these populations. Conclusions: To our knowledge, this is the first study to detect genetic markers associated with biting behavior in Ny. darlingi. Additional ecological and genomic studies may help to understand the genetic basis of mosquito behavior and address appropriate surveillance and vector control. Biotechnology Institute (IBTEC) Biosciences Institute at Botucatu (IBB) Sao Paulo State University (UNESP) Department of Biomedical Sciences School of Public Health University at Albany (State University of New York) Wadsworth Center New York State Department of Health Division of Infectious Diseases Department of Medicine University of California San Diego Laboratorio de Investigación y Desarrollo Departamento de Ciencias Celulares y Moleculares Instituto de Medicina Tropical Alexander von Humboldt Universidad Peruana Cayetano Heredia Biology Department St. Mary's College of Maryland Biotechnology Institute (IBTEC) Biosciences Institute at Botucatu (IBB) Sao Paulo State University (UNESP)

The relationship between deforestation and malaria in Amazonian Brazil is complex, and a deeper understanding of this relationship is required to inform effective control measures in this region. Here, we are particularly interested in characterizing the impact of land use and land cover change on the genetics of the major regional vector of malaria, Nyssorhynchus darlingi (Root). We used nextera-tagmented, Reductively Amplified DNA (nextRAD) genotyping-by-sequencing to genotype 164 Ny. darlingi collected from 16 collection sites with divergent forest cover levels in seven municipalities in four municipality groups that span the state of Amazonas in northwestern Amazonian Brazil: Sao Gabriel da Cachoeira, Presidente Figueiredo, four municipalities in the area around Cruzeiro do Sul, and Labrea. Using a dataset of 5,561 Single Nucleotide Polymorphisms (SNPs), we investigated the genetic structure of these Ny. darlingi populations with a combination of model- and non-model-based analyses. We identified weak to moderate genetic differentiation among the four municipality groups. There was no evidence for microgeographic genetic structure of Ny. darlingi among forest cover levels within the municipality groups, indicating that there may be gene flow across areas of these municipalities with different degrees of deforestation. Additionally, we conducted an environmental association analysis using two outlier detection methods to determine whether individual SNPs were associated with forest cover level without affecting overall population genetic structure. We identified 14 outlier SNPs, and investigated functions associated with their proximal genes, which could be further characterized in future studies.

In the Amazon Basin, Anopheles (Nyssorhynchus) darlingi is the most aggressive and effective malaria vector. In endemic areas, behavioral aspects of anopheline species such as host preference, biting time and resting location after a blood meal have a key impact on malaria transmission dynamics and transmission control strategies. An. darlingi present a variety in behavior throughout its broad distribution including blood feeding related. To investigate the genetic basis of its biting behaviors, host-seeking An. darlingi were collected in two settlements (Granada and Remansinho) in Acre, Brazil. Mosquitoes were classified by captured location (indoors or outdoors) and time (dusk or dawn). Genome-wide SNPs were used to assess the degree of genetic diversity and structure in these groups. There was evidence of genetic component of biting behavior regarding both location and time in this species. This study supports that An. darlingi blood-feeding behavior has a genetic component. Additional ecological and genomic studies may help to understand the genetic basis of mosquito behavior and address appropriate surveillance and vector control.Author SummaryMalaria is a disease caused by parasite of the genus Plasmodium and is transmitted by mosquitoes of the genus Anopheles. In the Amazon Basin, the main malaria vector is Anopheles darlingi, which is present in high densities in this region. Egg development requires that females of this mosquito seek hosts for blood meals. Anopheles females blood feeding may occur indoor or outdoor the houses and typically from the sunset to dawn. Anopheles darlingi in particular present great variability regarding its behaviour, presenting variety of peak biting times and patterns. This work shows that there is a genetic component that partially explains these two behaviors: location of the blood meal (inside or outside the houses) and time of feeding. Single nucleotide polymorphisms (SNPs) scattered throughout the genome of Anopheles darlingi showed genetic diversity and structure in these groups. A comprehensive understanding of the genetic basis for mosquito behaviour may support innovative vector surveillance and control strategies.

Population structure inference using the software STRUCTURE has become an integral part of population genetic studies covering a broad spectrum of taxa including humans. The ever-expanding size of genetic data sets poses computational challenges for this analysis. Although at least one tool currently implements parallel computing to reduce computational overload of this analysis, it does not fully automate the use of replicate STRUCTURE analysis runs required for downstream inference of optimal K. There is pressing need for a tool that can deploy population structure analysis on high performance computing clusters. We present an updated version of the popular Python program StrAuto, to streamline population structure analysis using parallel computing. StrAuto implements a pipeline that combines STRUCTURE analysis with the Evanno Δ K analysis and visualization of results using STRUCTURE HARVESTER. Using benchmarking tests, we demonstrate that StrAuto significantly reduces the computational time needed to perform iterative STRUCTURE analysis by distributing runs over two or more processors. StrAuto is the first tool to integrate STRUCTURE analysis with post-processing using a pipeline approach in addition to implementing parallel computation – a set up ideal for deployment on computing clusters. StrAuto is distributed under the GNU GPL (General Public License) and available to download from http://strauto.popgen.org .

Made available in DSpace on 2018-12-11T17:31:27Z (GMT). No. of bitstreams: 0 Previous issue date: 2017-02-13 Background: In recent decades, throughout the Amazon Basin, landscape modification contributing to profound ecological change has proceeded at an unprecedented rate. Deforestation that accompanies human activities can significantly change aspects of anopheline biology, though this may be site-specific. Such local changes in anopheline biology could have a great impact on malaria transmission. The aim of this study was to investigate population genetics of the main malaria vector in Brazil, Anopheles darlingi, from a microgeographical perspective. Methods: Microsatellites and ddRADseq-derived single nucleotide polymorphisms (SNPs) were used to assess levels of population genetic structuring among mosquito populations from two ecologically distinctive agricultural settlements (~60 km apart) and a population from a distant (~700 km) urban setting in the western Amazon region of Brazil. Results: Significant microgeographical population differentiation was observed among Anopheles darlingi populations via both model- and non-model-based analysis only with the SNP dataset. Microsatellites detected moderate differentiation at the greatest distances, but were unable to differentiate populations from the two agricultural settlements. Both markers showed low polymorphism levels in the most human impacted sites. Conclusions: At a microgeographical scale, signatures of genetic heterogeneity and population divergence were evident in Anopheles darlingi, possibly related to local environmental anthropic modification. This divergence was observed only when using high coverage SNP markers. Biotechnology Institute (IBTEC) and Biosciences Institute at Botucatu (IBB) Sao Paulo State University (UNESP) Department of Biomedical Sciences School of Public Health University at Albany State University of New York New York State Department of Health Wadsworth Center Division of Infectious Diseases Department of Medicine University of California San Diego Instituto de Medicina Tropical Alexander von Humboldt, Departamento de Ciencias Celulares y Moleculares Laboratorio de Investigación y Desarrollo Universidad Peruana Cayetano Heredia Biology Department St. Mary's College of Maryland Biotechnology Institute (IBTEC) and Biosciences Institute at Botucatu (IBB) Sao Paulo State University (UNESP)

The ubiquity of endogenous, circadian (daily) clocks among eukaryotes has long been held as evidence that they serve an adaptive function, usually cited as the ability to properly time biological events in concordance with the daily cycling of the environment. Herein we test directly whether fitness is a function of the matching of the period of an organism's circadian clock with that of its environment. We find that fitness, measured as the per capita expectation of future offspring, a composite measure of fitness incorporating both survivorship and reproduction, is maximized in environments that are integral multiples of the period of the organism's circadian clock. Hence, we show that organisms require temporal concordance between their internal circadian clocks and their external environment to maximize fitness and thus the long-held assumption is true that, having evolved in a 24-h world, circadian clocks are adaptive.

The subgenus Melanoconion is the second largest subgenus within the genus Culex, with 160 described species. Several of the species are proven vectors of arboviruses, including West Nile virus, Venezuelan equine encephalitis virus complex and Eastern equine encephalomyelitis virus. Species of Melanoconion are well distributed from southern North America to most countries of South America and display the highest species diversity in tropical regions. Taxonomical identification within this group has been primarily based on morphological characters, with the male genitalia as the source of the most solid diagnostic features. The difficulty in reaching accurate species determinations when studying specimens of Culex (Melanoconion) has been extensively documented as a real limitation to expand knowledge of these insects. We tested the utility of the mitochondrial gene COI as a complementary tool in the taxonomy of Melanoconion. Using a data set of 120 COI sequences from Culex specimen captured in several localities in Brazil, the utility of COI barcodes for species delimitation is discussed through the evaluation of genetic divergences among specimens and the clustering patterns of species in three topologies obtained with Neighbor Joining, Maximum Likelihood and Bayesian phylogenetic inference. For all specimens included in this study a previous morphological examination was performed, and most of the taxonomical determinations were corroborated using the COI barcode. We generated COI sequences that belong to 48 species of Melanoconion, with a mean intraspecific K2P genetic divergence of 3%; and all interspecific divergence values higher than the intraspecific divergence values. This is the first comprehensive study of subgenus Melanoconion, with evidence of COI as a useful and accessible DNA barcode.

Dominance and epistatic effects are predicted to be larger in life-history than in morphological traits. We test these predictions using published results from line cross analyses. We find that dominance is found in more than 95% of traits, regardless of the type of trait, but that the magnitude of the effect in relation to the additive effect is much greater in life-history than in morphological traits. Epistatic effects were detected more often in life-history than in morphological traits (79% and 67%, respectively). We also test for a difference in the magnitude of the effects by comparing the ratio of the nonadditive components separately to the additive component. For both dominance and epistatic components, the ratio of the nonadditive component to additive effects in life-history traits is approximately twice as large as that for morphological traits.

Herein we tested the repeatability of phylogenetic inference based on high throughput sequencing by increased taxon sampling using our previously published techniques in the pitcher-plant mosquito, Wyeomyia smithii in North America. We sampled 25 natural populations drawn from different localities nearby 21 previous collection localities and used these new data to construct a second, independent phylogeny, expressly to test the reproducibility of phylogenetic patterns. Comparison of trees between the two data sets based on both maximum parsimony and maximum likelihood with Bayesian posterior probabilities showed close correspondence in the grouping of the most southern populations into clear clades. However, discrepancies emerged, particularly in the middle of W. smithii's current range near the previous maximum extent of the Laurentide Ice Sheet, especially concerning the most recent common ancestor to mountain and northern populations. Combining all 46 populations from both studies into a single maximum parsimony tree and taking into account the post-glacial historical biogeography of associated flora provided an improved picture of W. smithii's range expansion in North America. In a more general sense, we propose that extensive taxon sampling, especially in areas of known geological disruption is key to a comprehensive approach to phylogenetics that leads to biologically meaningful phylogenetic inference.

Identifying regions of the genome contributing to phenotypic evolution often involves genetic mapping of quantitative traits. The focus then turns to identifying regions of ‘major’ effect, overlooking the observation that traits of ecological or evolutionary relevance usually involve many genes whose individual effects are small but whose cumulative effect is large. Herein, we use the power of fully interfertile natural populations of a single species of mosquito to develop three quantitative trait loci (QTL) maps: one between two post-glacially diverged populations and two between a more ancient and a post-glacial population. All demonstrate that photoperiodic response is genetically a highly complex trait. Furthermore, we show that marker regressions identify apparently ‘non-significant’ regions of the genome not identified by composite interval mapping, that the perception of the genetic basis of adaptive evolution is crucially dependent upon genetic background and that the genetic basis for adaptive evolution of photoperiodic response is highly variable within contemporary populations as well as between anciently diverged populations.

The genetic relationship between the daily circadian clock and the seasonal photoperiodic timer remains a subject of intense controversy. In Wyeomyia smithii, the critical photoperiod (an overt expression of the photoperiodic timer) evolves independently of the rhythmic response to the Nanda–Hamner protocol (an overt expression of the daily circadian clock) over a wide geographical range in North America. Herein, we focus on these two processes within a single local population in which there is a negative genetic correlation between them. We show that antagonistic selection against this genetic correlation rapidly breaks it down and, in fact, reverses its sign, showing that the genetic correlation is due primarily to linkage and not to pleiotropy. This rapid reversal of the genetic correlation within a small, single population means that it is difficult to argue that circadian rhythmicity forms the necessary, causal basis for the adaptive divergence of photoperiodic time measurement within populations or for the evolution of photoperiodic time measurement among populations over a broad geographical gradient of seasonal selection.

The distinction between model and nonmodel organisms is becoming increasingly blurred. High-throughput, second-generation sequencing approaches are being applied to organisms based on their interesting ecological, physiological, developmental, or evolutionary properties and not on the depth of genetic information available for them. Here, we illustrate this point using a low-cost, efficient technique to determine the fine-scale phylogenetic relationships among recently diverged populations in a species. This application of restriction site-associated DNA tags (RAD tags) reveals previously unresolved genetic structure and direction of evolution in the pitcher plant mosquito, Wyeomyia smithii , from a southern Appalachian Mountain refugium following recession of the Laurentide Ice Sheet at 22,000–19,000 B.P. The RAD tag method can be used to identify detailed patterns of phylogeography in any organism regardless of existing genomic data, and, more broadly, to identify incipient speciation and genome-wide variation in natural populations in general.

Background The mosquito Wyeomyia smithii overwinters in a larval diapause that is initiated, maintained and terminated by day length (photoperiod). We use a forward genetic approach to investigate transcriptional events involved in the termination of diapause following exposure to long-days. Methods/Principal Findings We incorporate a novel approach that compares two populations that differentially respond to a single day length. We identify 30 transcripts associated with differential response to day length. Most genes with a previously annotated function are consistent with their playing a role in the termination of diapause, in downstream developmental events, or in the transition from potentially oxygen-poor to oxygen-rich environments. One gene emerges from three separate forward genetic screens as a leading candidate for a gene contributing to the photoperiodic timing mechanism itself (photoperiodic switch). We name this gene photoperiodic response gene 1 (ppdrg1). WsPpdrg1 is up-regulated under long-day response conditions, is located under a QTL for critical photoperiod and is associated with critical photoperiod after 25 generations of recombination from a cross between extreme phenotypes. Conclusions Three independent forward genetic approaches identify WsPpdrg1 as a gene either involved in the photoperiodic switch mechanism or very tightly linked to a gene that is. We conclude that continued forward genetic approaches will be central to understanding not only the molecular basis of photoperiodism and diapause, but also the evolutionary potential of temperate and polar animal populations when confronted with rapid climate change.

For over 70 years, researchers have debated whether the ability to use day length as a cue for the timing of seasonal events (photoperiodism) is related to the endogenous circadian clock that regulates the timing of daily events. Models of photoperiodism include two components: (1) a photoperiodic timer that measures the length of the day, and (2) a photoperiodic counter that elicits the downstream photoperiodic response after a threshold number of days has been counted. Herein, we show that there is no geographical pattern of genetic association between the expression of the circadian clock and the photoperiodic timer or counter. We conclude that the photoperiodic timer and counter have evolved independently of the circadian clock in the pitcher-plant mosquito Wyeomyia smithii and hence, the evolutionary modification of photoperiodism throughout the range of W. smithii has not been causally mediated by a corresponding evolution of the circadian clock.

A wide diversity of organisms use photoperiod (daylength) as an environmental cue to anticipate the changing seasons and to time various life-history events such as dormancy and migration. Photoperiodic time measurement consists of two main components, (1) the photoperiodic timer that discriminates between long and short days, and (2) the photoperiodic counter that accumulates and stores information from the timer and then induces the phenotypic output. Herein, we use extended night treatments to show that light is necessary to accumulate photoperiodic information across the geographic range of the mosquito, Wyeomyia smithii and that the photoperiodic counter counts extrinsic (external) light:dark cycles and not endogenous (internal) circadian cycles.

The major drivers of the extensive biodiversity of the Neotropics are proposed to be geological and tectonic events together with Pliocene and Pleistocene environmental and climatic change. Geographical barriers represented by the rivers Amazonas/Solimões, the Andes and the coastal mountain ranges in eastern Brazil have been hypothesized to lead to diversification within the primary malaria vector, Anopheles (Nyssorhynchus) darlingi Root, which primarily inhabits rainforest. To test this biogeographical hypothesis, we analyzed 786 single nucleotide polymorphisms (SNPs) in 12 populations of An. darlingi from across the complex Brazilian landscape. Both model-based (STRUCTURE) and non-model-based (Principal Components and Discriminant Analysis) analysis of population structure detected three major genetic clusters that correspond with newly described Neotropical biogeographical regions: 1) Atlantic Forest province (= southeast population); 2) Parana Forest province (= West Atlantic forest population, with one Chacoan population - SP); and 3) Brazilian dominion population (= Amazonian population with one Chacoan population - TO). Significant levels of pairwise genetic divergences were found among the three clusters, allele sharing among clusters was negligible, and geographical distance did not contribute to differentiation. We infer that the Atlantic forest coastal mountain range limited dispersal between the Atlantic Forest province and the Parana Forest province populations, and that the large, diagonal open vegetation region of the Chacoan dominion dramatically reduced dispersal between the Parana and Brazilian dominion populations. We hypothesize that the three genetic clusters may represent three putative species.