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BackgroundRapid adaptation to new environments can facilitate species invasions and range expansions. Understanding the mechanisms of adaptation used by invasive disease vectors in new regions has key implications for mitigating the prevalence and spread of vector-borne disease, although they remain relatively unexplored.ResultsHere, we use whole-genome sequencing data from 103Aedes aegyptimosquitoes collected from various sites in southern and central California to infer the genetic structure of invasive populations. We integrate genome data with 25 topo-climate variables to investigate genome-wide signals of local adaptation among populations. Patterns of population structure, as inferred using principle components and admixture analysis, were consistent with three genetic clusters, likely resulting from multiple independent introductions. Using various landscape genomics approaches, which all remove the confounding effects of shared ancestry on correlations between genetic and environmental variation, we identified 112 genes showing strong signals of local environmental adaptation associated with one or more topo-climate factors. Some of them have known effects in climate adaptation, such as heat-shock proteins, which shows selective sweep and recent positive selection acting on these genomic regions.ConclusionsOur results provide a genome wide perspective on the distribution of adaptive loci and lay the foundation for future work to understand how environmental adaptation inAe. aegyptiimpacts the arboviral disease landscape and how such adaptation could help or hinder efforts at population control.

Despite efforts to minimize the impacts of malaria and reduce the number of primary vectors, malaria has yet to be eliminated in Zambia. Understudied vector species may perpetuate malaria transmission in pre-elimination settings. Anopheles squamosus is one of the most abundantly caught mosquito species in southern Zambia and has previously been found with Plasmodium falciparum sporozoites, a causal agent of human malaria. This species may be a critical vector of malaria transmission, however, there is a lack of genetic information available for An. squamosus. We report the first genome data and the first complete mitogenome (Mt) sequence of An. squamosus. The sequence was extracted from one individual mosquito from the Chidakwa area in Macha, Zambia. The raw reads were obtained using Illumina Novaseq 6000 and assembled through NOVOplasty alignment with related species. The length of the An. squamosus Mt was 15,351 bp, with 77.9 % AT content. The closest match to the whole mitochondrial genome in the phylogenetic tree is the African malaria mosquito, Anopheles gambiae. Its genome data is available through National Center for Biotechnology Information (NCBI) Sequencing Reads Archive (SRA) with accession number SRR22114392. The mitochondrial genome was deposited in NCBI GenBank with the accession number OP776919. The ITS2 containing contig sequence was deposited in GenBank with the accession number OQ241725. Mitogenome annotation and a phylogenetic tree with related Anopheles mosquito species are provided.

CLIMEX and MED-FOES models integrate climate and data on Mediterranean fruit fly (medfly), Ceratitis capitata (Wiedemann), biology and use it to define the environmental suitability for the pest at specific geographical locations. CLIMEX calculates growth indices as indicators of conditions that are suitable for medfly population growth. MED-FOES incorporates additional information on pest management interventions to simulate the process and timing of medfly eradication. CLIMEX simulations of climatic suitability in California and Florida indicated that the most favorable periods for medfly population growth are March through May and October through November, whereas the environment would be especially stressful during the summer months, except when irrigation is applied. With irrigation, California is highly suitable for medfly population growth during the summer months. Due to cool temperatures, medfly populations are likely to decline significantly in January through February in Los Angeles, Tampa, and Miami, and probably not survive in San Francisco. According to MED-FOES simulations, it possibly would take longer to eradicate medfly from California than Florida, particularly if the incursions are initiated in the summer months. Medfly annual growth indices for the ENSO La Niña years are relatively low for San Francisco and Los Angeles but above neutral for Tampa and very high for Miami. During the El Niño phase, the growth index remains unchanged for San Francisco, increases for Los Angeles, and decreases for Tampa and Miami. CLIMEX and MED-FOES models are useful for informing plans to manage invasion threats from medfly and other invasive insects.

New or improved technologies can enable entomologists to address previously intractable questions, especially in the area of insect behavior. In this review, we describe the basic elements of applied computer vision for entomologists: image capture, data extraction, and analysis. We describe some of the currently available options in imaging hardware and cameras, lighting, software, as well as some basic data collection scenarios, and give detailed examples from our own experience. We suggest that the study of insect behavior is increasingly based on quantification of behavioral phenomena, that use of computer vision techniques for quantification will increase, and that the application of these tools and approaches will bring new insight and answers to questions in entomology. We hope this review can serve as a starting point for those interested in delving deeper into how computer vision can be applied to their research.

Areas of the world that do not have established populations of the Mediterranean fruit fly Ceratitis capitata (Wiedemann) and other invasive pestivorous Tephritidae are sometimes subject to incursions due to increasing travel and trade. When these occur, control programmes are put in place often including quarantine and additional measures until eradication of the outbreak is declared. A critical practical question that arises is how long to maintain the eradication programme and associated area-wide measures after the last sampling of the invading Mediterranean fruit fly. Current practice is usually to maintain measures and increased monitoring until enough time has passed for three generations of flies without another fly catch; generation times are calculated via thermal unit accumulation (“Degree Day”). A recent alternative or complementary approach is to model the invading population using an Agent-Based Simulation (ABS). This chapter outlines the use of MEDiterranean fruit Fly Outbreak and Eradication Simulation (MED-FOES), an ABS implementation aimed at modelling invading Mediterranean fruit fly populations to determine effective duration of quarantine and other eradication measures following the last detection of an incursion. Basic concepts are described, together with a description of major functions and use of thousands of individual simulations to encompass the range of demographic possibilities. Finally, specific examples from Santiago, Chile and California, USA are offered to show how the ABS can provide useful information for programme managers setting eradication programme durations.

Anopheles coluzzii is a major malaria vector throughout its distribution in west-central Africa. Here we present a whole-genome study of 142 specimens from nine countries in continental Africa and three islands in the Gulf of Guinea. This sample set covers a large part of this species’ geographic range. Our population genomic analyses included a description of the structure of mainland populations, island populations, and connectivity between them. Three genetic clusters are identified among mainland populations and genetic distances (FST) fits an isolation-by-distance model. Genomic analyses are applied to estimate the demographic history and ancestry for each island. Taken together with the unique biogeography and history of human occupation for each island, they present a coherent explanation underlying levels of genetic isolation between mainland and island populations. We discuss the relationship of our findings to the suitability of São Tomé and Príncipe islands as candidate sites for potential field trials of genetic-based malaria control strategies., Campos, Lanzaro and colleagues use whole-genome sequencing and population genomic analyses to infer connectivity between mainland and island mosquito populations in West Africa. The unique biogeographic history for each island population is reported, and the findings highlight potential candidate sites for genetic-based malaria control strategies.

During their life cycles, microbes infecting mosquitoes encounter components of the mosquito anti-microbial innate immune defenses. Many of these immune responses also mediate susceptibility to malaria parasite infection. In West Africa, the primary malaria vectors are Anopheles coluzzii and A. gambiae sensu stricto, which is subdivided into the Bamako and Savanna sub-taxa. Here, we performed whole genome comparisons of the three taxa as well as genotyping of 333 putatively functional SNPs located in 58 immune signaling genes. Genome data support significantly higher differentiation in immune genes compared with a randomly selected set of non-immune genes among the three taxa (permutation test p &lt, 0.001). Among the 58 genes studied, the majority had one or more segregating mutations (72.9%) that were significantly diverged among the three taxa. Genes detected to be under selection include MAP2K4 and Raf. Despite the genome-wide distribution of immune genes, a high level of linkage disequilibrium (r2 &gt, 0.8) was detected in over 27% of SNP pairs. We discuss the potential role of immune gene divergence as adaptations to the different larval habitats associated with A. gambiae taxa and as a potential force driving ecological speciation in this group of mosquitoes.

Simple Summary A comparison of the genomes of the African malaria vectors, Anopheles gambiae and A. coluzzii, revealed that immune genes are highly diverged. Although these two species frequently co-occur within a single site, they occur in distinct larval habitats. Our results taken in the context of known differences in the larval habitats occupied by these taxa support the hypothesis that observed genetic divergence may be driven by immune response to microbial agents specific to these habitats. Strict within species mating may have subsequently evolved in part to maintain immunocompetence which might be compromised by dysregulation of immune pathways in hybrids. We conclude that the evolution of immune gene divergence among this important group of species may serve as a useful model to explore ecological speciation in general. Abstract During their life cycles, microbes infecting mosquitoes encounter components of the mosquito anti-microbial innate immune defenses. Many of these immune responses also mediate susceptibility to malaria parasite infection. In West Africa, the primary malaria vectors are Anopheles coluzzii and A. gambiae sensu stricto, which is subdivided into the Bamako and Savanna sub-taxa. Here, we performed whole genome comparisons of the three taxa as well as genotyping of 333 putatively functional SNPs located in 58 immune signaling genes. Genome data support significantly higher differentiation in immune genes compared with a randomly selected set of non-immune genes among the three taxa (permutation test p < 0.001). Among the 58 genes studied, the majority had one or more segregating mutations (72.9%) that were significantly diverged among the three taxa. Genes detected to be under selection include MAP2K4 and Raf. Despite the genome-wide distribution of immune genes, a high level of linkage disequilibrium (r2 > 0.8) was detected in over 27% of SNP pairs. We discuss the potential role of immune gene divergence as adaptations to the different larval habitats associated with A. gambiae taxa and as a potential force driving ecological speciation in this group of mosquitoes.

Anopheles coluzzii is a major malaria vector throughout its distribution in west-central Africa. Here we present a whole-genome resequencing study of 77 specimens from eight localities, that covers a large part of this species’ range, including three islands in the Gulf of Guinea: Bioko, Sao Tome and Principe. Population genomic analyses encompassed structure of mainland populations, of island populations and connectivity between island and mainland populations. Three genetic clusters were found among mainland populations and genetic distances among all populations fit an isolation-by-distance model. Genomic analyses were applied to estimating the demographic history and ancestry (cross-coalescence) for each island. Taken together with the unique biogeography and history of human occupation for each island they present a coherent explanation underlying contemporary levels of genetic isolation between mainland and island populations and among island populations. We discuss the relation of our findings to the suitability of Sao Tome and Principe islands as candidate sites for potential field trials of genetic-based malaria control strategies.

A number of recent papers report that standing genetic variation in natural populations includes ubiquitous polymorphisms within target sites for Cas9-based gene drive (CGD) and that these “drive resistant alleles” (DRA) preclude the successful application of CGD for managing these populations. Here we report the results of a survey of 1280 genomes of the mosquitoes Anopheles gambiae, An. coluzzii, and Aedes aegypti in which we determine that ~90% of all protein-encoding CGD target genes in natural populations include at least one target site with no DRAs at a frequency of ≥1.0%. We conclude that the abundance of conserved target sites in mosquito genomes and the inherent flexibility in CGD design obviates the concern that DRAs present in the standing genetic variation of mosquito populations will be detrimental to the deployment of this technology for population modification strategies., Genetic variation in natural populations could represent gene drive resistant alleles, preventing successful application for population management. Here the authors survey 1280 genomes from three mosquito species and concludes natural variation will not be detrimental to deploying gene drive technology.

Cas9/guide RNA (gRNA)-based gene drive systems are expected to play a transformative role in malaria elimination efforts., whether through population modification, in which the drive system contains parasite-refractory genes, or population suppression, in which the drive system induces a severe fitness load resulting in population decline or extinction. DNA sequence polymorphisms representing alternate alleles at gRNA target sites may confer a drive-resistant phenotype in individuals carrying them. Modeling predicts that, for observed levels of SGV at potential target sites and observed rates of de novo DRA formation, population modification strategies are uniquely resilient to DRAs. We conclude that gene drives can succeed when fitness costs incurred by drive-carrying mosquitoes are low enough to prevent strong positive selection for DRAs produced de novo or as part of the SGV and that population modification strategies are less prone to failure due to drive resistance.

We report the complete mitogenome (Mt) sequences of Aedes (Howardina) busckii and Aedes (Ochlerotatus) taeniorhynchus. The sequences were extracted from one individual per species from the Dutch Le...

The mosquito Anopheles gambiae s.s. is distributed across most of sub-Saharan Africa and is of major scientific and public health interest for being an African malaria vector. Here we present population genomic analyses of 111 specimens sampled from west to east Africa, including the first whole genome sequences from oceanic islands, the Comoros. Genetic distances between populations of A. gambiae are discordant with geographic distances but are consistent with a stepwise migration scenario in which the species increases its range from west to east Africa through consecutive founder events over the last ~200,000 years. Geological barriers like the Congo River basin and the East African rift seem to play an important role in shaping this process. Moreover, we find a high degree of genetic isolation of populations on the Comoros, confirming the potential of these islands as candidate sites for potential field trials of genetically engineered mosquitoes for malaria control., Schmidt et al. present population genomic analyses of 111 mosquito Anopheles gambiae specimens sampled from west to east Africa. This study suggests a high degree of genetic isolation of populations on the Comoros, highlighting the importance of physical barriers to gene flow in this African malaria vector species.

Background In the summer of 2013, Aedes aegypti Linnaeus was first detected in three cities in central California (Clovis, Madera and Menlo Park). It has now been detected in multiple locations in central and southern CA as far south as San Diego and Imperial Counties. A number of published reports suggest that CA populations have been established from multiple independent introductions. Results Here we report the first population genomics analyses of Ae. aegypti based on individual, field collected whole genome sequences. We analyzed 46 Ae. aegypti genomes to establish genetic relationships among populations from sites in California, Florida and South Africa. Based on 4.65 million high quality biallelic SNPs, we identified 3 major genetic clusters within California; one that includes all sample sites in the southern part of the state (South of Tehachapi mountain range) plus the town of Exeter in central California and two additional clusters in central California. Conclusions A lack of concordance between mitochondrial and nuclear genealogies suggests that the three founding populations were polymorphic for two main mitochondrial haplotypes prior to being introduced to California. One of these has been lost in the Clovis populations, possibly by a founder effect. Genome-wide comparisons indicate extensive differentiation between genetic clusters. Our observations support recent introductions of Ae. aegypti into California from multiple, genetically diverged source populations. Our data reveal signs of hybridization among diverged populations within CA. Genetic markers identified in this study will be of great value in pursuing classical population genetic studies which require larger sample sizes. Electronic supplementary material The online version of this article (10.1186/s12864-019-5586-4) contains supplementary material, which is available to authorized users.

Whole mitogenome sequences (mtDNA) have been exploited for insect ecology studies, using them as molecular markers to reconstruct phylogenies, or to infer phylogeographic relationships and gene flow. Recent Anopheles phylogenomic studies have provided information regarding the time of deep lineage divergences within the genus. Here we report the complete 15,393 bp mtDNA sequences of Anopheles aquasalis, a Neotropical human malaria vector. When comparing its structure and base composition with other relevant and available anopheline mitogenomes, high similarity and conserved genomic features were observed. Furthermore, 22 mtDNA sequences comprising anopheline and Dipteran sibling species were analyzed to reconstruct phylogenies and estimate dates of divergence between taxa. Phylogenetic analysis using complete mtDNA sequences suggests that A. aquasalis diverged from the Anopheles albitarsis complex ~28 million years ago (MYA), and ~38 MYA from Anopheles darlingi. Bayesian analysis suggests that the most recent ancestor of Nyssorhynchus and Anopheles + Cellia was extant ~83 MYA, corroborating current estimates of ~79-100 MYA. Additional sampling and publication of African, Asian, and North American anopheline mitogenomes would improve the resolution of the Anopheles phylogeny and clarify early continental dispersal routes.

Animal species are able to acquire new genetic material via hybridization and subsequent introgression. However, little is known about how foreign genomic material is incorporated into a population over time and what genes are susceptible to introgression. Here, we follow the closely related mosquito sister species Anopheles coluzzii and Anopheles gambiae in a sympatric natural population in Mali at multiple time points spanning a period of 25 years. During this period, we observed the temporary breakdown of mating barriers, which allowed us to explore the fate of alleles that crossed the species boundary in a natural population. Whole genome sequencing of 74 individuals revealed introgression within only 34 genes (0.26% of total genes) from A. gambiae to A. coluzzii, the majority contained within a 4 Mb region on the 2L chromosome which includes the insecticide resistance gene (AGAP004707). We designed a genotyping assay to follow 25 of the 34 introgressed alleles over time and found that all A. gambiae alleles, except four, reached a frequency of 50% in the A. coluzzii population within 4 years (~50 generations) and increased to ~80% within 6 years (~75 generations). However, the frequency of all introgressed alleles, except three, decreased to ~60% in 2016. This suggests an ongoing process of purifying selection in the population against DNA of foreign ancestry, except for alleles that are under positive selection, resulting in a complex genomic landscape. This study shows that stable introgression is limited to only specific genes even within closely related species.

Here we report the complete mitochondrial sequences of 70 individual field collected mosquito specimens from throughout Sub-Saharan Africa. We generated this dataset to identify species specific markers for the followingAnophelesspecies and chromosomal forms:An. arabiensis,An. coluzzii(TheForestandMoptichromosomal forms) andAn. gambiae(TheBamakoandSavannahchromosomal forms). The raw Illumina sequencing reads were mapped to the NC_002084 reference mitogenome sequence. A total of 783 single nucleotide polymorphisms (SNPs) were detected on the mitochondrial genome, of which 460 are singletons (58.7%). None of these SNPs are suitable as molecular markers to distinguish amongAn. arabiensis,An. coluzziiandAn. gambiaeor any of the chromosomal forms. The lack of species or chromosomal form specific markers is also reflected in the constructed phylogenetic tree, which shows no clear division among the operational taxonomic units considered here.

Alarm calling is common in many species. A prevalent assumption is that calling puts the vocalizing individual at increased risk of predation. If calling is indeed costly, we need special explanations for its evolution and maintenance. In some, but not all species, callers vocalize away from safety and thus may be exposed to an increased risk of predation. However, for species that emit bouts with one or a few calls, it is often difficult to identify the caller and find the precise location where a call was produced. We analyzed the spatial dynamics of yellow-bellied marmot (Marmota flaviventris) alarm calling using an acoustic localization system to determine the location from where calls were emitted. Marmots almost always called from positions close to the safety of their burrows, and, if they produced more than one alarm call, tended to end their calling bouts closer to safety than they started them. These results suggest that for this species, potential increased predation risk from alarm calling is greatly mitigated and indeed calling may have limited predation costs.

Field biologists use animal sounds to discover the presence of individuals and to study their behavior. Collecting bio-acoustic data has traditionally been a difficult and time-consuming process in which researchers use portable microphones to record sounds while taking notes of their own detailed observations. The recent development of new deployable acoustic sensor platforms presents opportunities to develop automated tools for bio-acoustic field research. In this work, we implement both two-dimensional (2D) and three-dimensional (3D) AML-based source localization algorithms. The 2D algorithm is used to localize marmot alarm-calls of marmots on the meadow ground. The 3D algorithm is used to localize the song of Acorn Woodpecker and Mexican Antthrush birds situated above the ground. We assess the performance of these techniques based on the results from four field experiments: two controlled test of direction-of-arrival (DOA) accuracy using a pre-recorded source signal for 2D and 3D analysis, an experiment to detect and localize actual animals in their habitat, with a comparison to ground truth gathered from human observations, and a controlled test of localization experiment using pre-recorded source to enable careful ground truth measurements. Although small arrays yield ambiguities from spatial aliasing of high frequency signals, we show that these ambiguities are readily eliminated by proper bearing crossings of the DOAs from several arrays. These results show that the AML source localization algorithm can be used to localize actual animals in their natural habitat using a platform that is practical to deploy.

In certain cases, a species may have access to important genetic variation present in a related species via adaptive introgression. These novel alleles may interact with their new genetic background, resulting in unexpected phenotypes. In this study, we describe a selective sweep on standing variation on the X chromosome in the mosquito Anopheles coluzzii, a principal malaria vector in West Africa. This event may have been influenced by the recent adaptive introgression of the insecticide resistance gene known as kdr from the sister species Anopheles gambiae. Individuals carrying both kdr and a nearly fixed X‐linked haplotype, encompassing at least four genes including the P450 gene CYP9K1 and the cuticular protein CPR125, have rapidly increased in relative frequency. In parallel, a reproductively isolated insecticide‐susceptible A. gambiae population (Bamako form) has been driven to local extinction, likely due to strong selection from increased insecticide‐treated bed net usage.

The Psorophora confinnis complex is currently composed of three species--Psorophora confinnis sensu stricto (Lynch Arribalzaga) in South America, Psorophora columbiae (Dyar and Knab) in North America, and Psorophora jamaicensis (Theobald) in the Caribbean. Members of the complex are of considerable importance as vectors of arboviruses, for example, Venezuelan equine encephalitis virus, and are significant biting pests throughout their range. The biological and geographic boundaries of Ps. confinnis and Ps. columbiae are unclear. In fact, the name Ps. columbiae is presently designated as "provisional." In this article, we aim to clarify the taxonomy and geographic distributions of species within the Ps. confinnis complex. A population genetics approach was employed using gene and genotypic frequency data at 26 isozyme loci. The results suggest that the Ps. confinnis complex in North and South America is composed of four species. Ps. confinnis s.s. and Ps. columbiae are distinct species in South and North America, respectively. Populations in Colombia, South America, formally designated as Ps. funiculus (Dyar) and populations in the southwestern United States and western Mexico, formally designated Ps. toltecum (Dyar and Knab), are distinct species. Psorophora toltecum and Psorophora funiculus species names should be resurrected from synonymy. In addition we identified a Ps. columbiae and Ps. toltecum hybrid zone in central Texas in a region described as being one of 13 North American suture zones, being geographical areas in which closely related species occur in sympatry and frequently hybridize.

Communication among adaptive agents can be framed as language acquisition and broken down into three problems; symbol grounding, language learning, and language evolution. We propose that this view clarifies many of the difficulties framing issues of collaboration and self-organization. Additionally, we demonstrate simple classification systems that can provide the first step in grounding real-world data and provide general schema for constructing other such systems. The first system classifies auditory input from frog calls and is presented as a model of grounding objects. The second system uses the minimum description length framework to distinguish patterns of robot movement as a model of grounding actions.

In an effort to better guide research into self-confguring wireless sensor networks, we discuss a technical defnition of the term self-organization. We define a self-organizing system as one where a collection of units coordinate with each other to form a system that adapts to achieve a goal more efficiently. We then lay out some conditions that must hold for a system to meet this definition and discuss some examples of self-organizing systems. Finally, we explore some of the ways this definition applies to wireless sensor networks.

We describe the evolution of macromolecules as an information transmission process and apply tools from Shannon information theory to it. This allows us to isolate three independent, competing selective pressures that we term compression, transmission, and neutrality selection. The first two affect genome length: the pressure to conserve resources by compressing the code, and the pressure to acquire additional information that improves the channel, increasing the rate of information transmission into each offspring. Noisy transmission channels (replication with mutations) gives rise to a third pressure that acts on the actual encoding of information; it maximizes the fraction of mutations that are neutral with respect to the phenotype. This neutrality selection has important implications for the evolution of evolvability. We demonstrate each selective pressure in experiments with digital organisms., 16 pages, 3 figures, to be published in J. theor. Biology

We investigate common design decisions for constructing a computational genetic language in an autoadaptive system. Such languages must support self-replication and are typically Turing-complete so as not to limit the types of computations they can perform. We examine the importance of using templates to denote locations in the genome, the methods by which those templates are located (direct-matching versus complement-matching), methods used in the calculation of genome length and the size and complexity of the language. For each test, we examine the effects on the rate of evolution of the populations and isolate those factors that contribute to it, most notably the organisms' ability to withstand mutations.

Digital organisms are computer programs that self-replicate, mutate and adapt by natural selection. They offer an opportunity to test generalizations about living systems that may extend beyond the organic life that biologists usually study. Here we have generated two classes of digital organism: simple programs selected solely for rapid replication, and complex programs selected to perform mathematical operations that accelerate replication through a set of defined 'metabolic' rewards. To examine the differences in their genetic architecture, we introduced millions of single and multiple mutations into each organism and measured the effects on the organism's fitness. The complex organisms are more robust than the simple ones with respect to the average effects of single mutations. Interactions among mutations are common and usually yield higher fitness than predicted from the component mutations assuming multiplicative effects; such interactions are especially important in the complex organisms. Frequent interactions among mutations have also been seen in bacteria, fungi and fruitflies. Our findings support the view that interactions are a general feature of genetic systems.

Acoustic sensor arrays are recognized as an important development for field studies of animal behavior and ecology. While birds live in a 3D world and all dimensions seem important for most birds, use of these arrays has been limited almost entirely to 2D. A notable exception was the development by S. Asgari of Approximate Maximum Likelihood methods for 3D, tested with recorded sounds. Here we describe experiments with a time-of-arrival method for 3D localization of calls from Shrike-tanagers and Wood Wrens in a Mexican rain forest, using an acoustic sensor array we have used in past. Sub-meter accuracy was obtained in all of the x, y, z directions. It appears that the acoustic sensor arrays may prove very helpful for studying the behavior of birds in 3D.

In this paper, we present simulation and experimental studies of localization and source separation for a bio-complexity bird study based on a new wireless acoustic array node named Voxnet. The Approximate Maximum Likelihood (AML) method is used to estimate blindly the direction-of-arrivals (DOAs) of sources which can be used to both locate the sources using a DOA-based localization method and generate the steering vectors in order to separate the sources via beamforming. Simulation and measured data confirmed the proper operations of the AML-based 2-D/3-D localization and 2-D source separation, as well as the Voxnet hardware nodes.

In this paper, we present simulation and experimental studies of multiple bird source separation based on the Voxnet acoustic array node. The Approximate Maximum Likelihood (AML) method is used to estimate blindly the direction-of-arrivals(DOAs) of the sources to generate the steering vectors in order to separate the sources via beamforming. Simulation and measured data confirmed the proper operations of the AML beamforming algorithm and the Voxnet hardware node.

Malaria transmission is dependent on the propensity of Anopheles mosquitoes to bite humans (anthropophily) instead of other dead end hosts. Recent increases in the usage of Long Lasting Insecticide Treated Nets (LLINs) in Africa have been associated with reductions in highly anthropophilic and endophilic vectors such as Anopheles gambiae s.s., leaving species with a broader host range, such as Anopheles arabiensis, as the most prominent remaining source of transmission in many settings. An. arabiensis appears to be more of a generalist in terms of its host choice and resting behavior, which may be due to phenotypic plasticity and/or segregating allelic variation. To investigate the genetic basis of host choice and resting behavior in An. arabiensis we sequenced the genomes of 23 human-fed and 25 cattle-fed mosquitoes collected both in-doors and out-doors in the Kilombero Valley, Tanzania. We identified a total of 4,820,851 SNPs, which were used to conduct the first genome-wide estimates of “SNP heritability” for host choice and resting behavior in this species. A genetic component was detected for host choice (human vs cow fed; permuted P = 0.002), but there was no evidence of a genetic component for resting behavior (indoors versus outside; permuted P = 0.465). A principal component analysis (PCA) segregated individuals based on genomic variation into three groups which were characterized by differences at the 2Rb and/or 3Ra paracentromeric chromosome inversions. There was a non-random distribution of cattle-fed mosquitoes between the PCA clusters, suggesting that alleles linked to the 2Rb and/or 3Ra inversions may influence host choice. Using a novel inversion genotyping assay, we detected a significant enrichment of the standard arrangement (non-inverted) of 3Ra among cattle-fed mosquitoes (N = 129) versus all non-cattle-fed individuals (N = 234; χ2, p = 0.007). Thus, tracking the frequency of the 3Ra in An. arabiensis populations may be of use to infer selection on host choice behavior within these vector populations; possibly in response to vector control. Controlled host-choice assays are needed to discern whether the observed genetic component has a direct relationship with innate host preference. A better understanding of the genetic basis for host feeding behavior in An. arabiensis may also open avenues for novel vector control strategies based on driving genes for zoophily into wild mosquito populations., Author Summary Malaria transmission is driven by the propensity for mosquito vectors to bite people, while its control depends on the tendency of mosquitoes to bite and rest in places where they will come into contact with insecticides. In many parts of Africa, where coverage with Long Lasting Insecticide Treated Nets is high, Anopheles arabiensis is the only remaing malaria vector. We sought to assess the potential for An. arabiensis to adapt its behavior to avoid control measures by investigating the genetic basis for its host choice and resting behavior. Blood fed An. arabiensis were collected resting indoors and outdoors in the Kilombero Valley, Tanzania. We sequenced a total of 48 genomes representing 4 phenotypes (human or cow fed, resting in or outdoors) and tested for genetic associations with each phenotype. Genomic analysis followed up by application of a novel molecular karyotyping assay revealed a relationship between An. arabiensis that fed on cattle and the standard arrangement of the 3Ra inversion. This is strong support that An. arabiensis blood-feeding behavior has a substantial genetic component. Controlled host choice assays are needed to confirm a direct link between allelic variation within the 3Ra inversion and host preference.

In this abstract, we present a beamforming method for estimating the directions and locations of multiple sources and separating each source's spectrum from field data collected by a wireless acoustic sensor network. Each acoustic sensor is equipped with four microphones that receive acoustic signals in a time-synchronized manner. The difference in time-of-arrival of proximal signals depends on the source direction with respect to the geometry of the microphone array. We show that by using beamforming in the frequency domain, the locations and Direction-Of-Arrivals (DOAs) of multiple 3D sources may be estimated, and the source spectrum may be separated from the audio data spectra.

In this abstract, we present a beamforming method for estimating the directions and locations of multiple sources and separating each source's spectrum from field data collected by a wireless acoustic sensor network. Each acoustic sensor is equipped with four microphones that receive acoustic signals in a time-synchronized manner. The difference in time-of-arrival of proximal signals depends on the source direction with respect to the geometry of the microphone array. We show that by using beamforming in the frequency domain, the locations and Direction-Of-Arrivals (DOAs) of multiple 3D sources may be estimated, and the source spectrum may be separated from the audio data spectra.

The long term goal of our research is to produce a collection of heterogeneous agents that learn about their environment, communicate with one another about it, affect the environment in ways that take advantage of one another’s special abilities and circumstances, and report to human observers. A principal challenge of this research is to define the cognitive and linguistic features that allow agents to develop a high-level language among themselves. For most purposes we would like all agents to agree on a common language so that each can communicate with all others. This is in some ways analogous to wishing convergent control of distributed adaptive agents. There are several reasons why it is desirable for autonomous agents to acquire their own language [5, 17]. First, an acquired language can evolve over time to adopt its structure to various types of noise and different types of information to be transmitted, thus providing a truly flexible communication channel. Second, agents with heterogeneous sensors can map the same symbol to an environmental stimulus despite having very different internal representations. This feature also allows agents to express observations that were not anticipated by the designer of the system. Third, with a learned high-level language, agents

The focus of most direction-of-arrival (DOA) estimation problems has been based mainly on a two-dimensional (2D) scenario where we only need to estimate the azimuth angle. But in various practical situations we have to deal with a three-dimensional scenario. The importance of being able to estimate both azimuth and elevation angles with high accuracy and low complexity is of interest. We present the theoretical and the practical issues of DOA estimation using the Approximate-Maximum-Likelihood (AML) algorithm in a 3D scenario. We show that the performance of the proposed 3D AML algorithm converges to the Cramer-Rao Bound. We use the concept of an isotropic array to reduce the complexity of the proposed algorithm by advocating a decoupled 3D version. We also explore a modified version of the decoupled 3D AML algorithm which can be used for DOA estimation with non-isotropic arrays. Various numerical results are presented. We use two acoustic arrays each consisting of 8 microphones to do some field measurements. The processing of the measured data from the acoustic arrays for different azimuth and elevation angles confirms the effectiveness of the proposed methods.

Field biologists use animal sounds to discover the presence of individuals and to study their behavior. The recent development of new deployable acoustic sensor platforms presents opportunities to develop automated tools for bio-acoustic field research. In this work, we demonstrate a real-time wireless sensor system that implements an AML-based source localization algorithm. We will demonstrate a system that is easy to set up and that can localize a whistle in the demonstration area in real time. This demonstration will use the techniques we described in our corresponding paper [1].

Field biologists use animal sounds to discover the presence of individuals and to study their behavior. Collecting bio- acoustic data has traditionally been a difficult and time- consuming process in which researchers use portable microphones to record sounds while taking notes of their own detailed observations. The recent development of new deploy- able acoustic sensor platforms presents opportunities to develop automated tools for bio-acoustic field research. In this work, we implement an AML-based source localization algorithm, and use it to localize marmot alarm-calls. We assess the performance of these techniques based on results from two field experiments: (1) a controlled test of direction-of- arrival (DOA) accuracy using a pre-recorded source signal, and (2) an experiment to detect and localize actual animals in their habitat, with a comparison to ground truth gathered from human observations. Although small arrays yield ambiguities from spatial aliasing of high frequency signals, we show that these ambiguities are readily eliminated by proper bearing crossings of the DOAs from several arrays. These results show that the AML source localization algorithm can be used to localize actual animals in their natural habitat, using a platform that is practical to deploy.

The complexity, variation, and change of languages make evident the importance of representation and learning in the acquisition and evolution of language. For example, analytic studies of simple language in unstructured populations have shown complex dynamics, depending on the fidelity of language transmission. In this study we extend these analysis of evolutionary dynamics to include grammars inspired by the principles and parameters paradigm. In particular, the space of languages is structured so that some pairs of languages are more similar than others, and mutations tend to change languages to nearby variants. We found that coherence emerges with lower learning fidelity than predicted by earlier work with an unstructured language space.

We investigate the evolutionary processes behind the development and optimization of multiple threads of execution in digital organisms using the avida platform, a softwcire package that implements Darwinian evolution on populations of self-replicating computer programs. The system is seeded with a linearly executed ancestor capable only of reproducing its own genome, whereas its underlying language has the capacity for multiple threads of execution (i.e., simultaneous expression of sections of the genome.) We witness the evolution to multithreaded organisms and track the development of distinct expression patterns. Additionally, we examine both the evolvability of multithreaded organisms and the level of thread differentiation as a function of environmental complexity, and find that differentiation is more pronounced in complex environments.

The African malaria vector, Anopheles gambiae, is characterized by multiple polymorphic chromosomal inversions and has become widely studied as a system for exploring models of speciation. Near complete reproductive isolation between different inversion types, known as chromosomal forms, has led to the suggestion that A. gambiae is in early stages of speciation, with divergence evolving in the face of considerable gene flow. We compared the standard chromosomal arrangement (Savanna form) with genomes homozygous for j, b, c, and u inversions (Bamako form) in order to identify regions of genomic divergence with respect to inversion polymorphism. We found levels of divergence between the two sub-taxa within some of these inversions (2Rj and 2Rb), but at a level lower than expected and confined near the inversion breakpoints, consistent with a gene flux model. Unexpectedly, we found that the majority of diverged regions were located on the X chromosome, which contained half of all significantly diverged regions, with much of this divergence located within exons. This is surprising given that the Bamako and Savanna chromosomal forms are both within the S molecular form that is defined by a locus near centromere of X chromosome. Two X-linked genes (a heat shock protein and P450 encoding genes) involved in reproductive isolation between the M and S molecular forms of A. gambiae were also significantly diverged between the two chromosomal forms. These results suggest that genes mediating reproductive isolation are likely located on the X chromosome, as is thought to be the case for the M and S molecular forms. We conclude that genes located on the sex chromosome may be the major force driving speciation between these chromosomal forms of A. gambiae.

Terrestrial bioacoustic census is a difficult problem because of propagation characteristics, obstructions, the diversity of bioacoustic sources, and the impact of noise. To address this problem we have developed VoxNet, a complete hardware and software platform for distributed acoustic monitoring applications. Each VoxNet node is a portable, self‐contained processor with a small four‐channel acoustic array. Using a distributed set of VoxNet nodes, a forested habitat can be monitored and the behavior of animals can be recorded and analyzed acoustically. In this work we present our experiences applying VoxNet to bioacoustic census. This work is based on data collected using the system during a deployment in Chiapas, Mexico at the Chajul Biological Field Station. The Chajul station is located in a region of dense rain forest and is home to Mexico's most diverse ecosystem. Using VoxNet in this harsh environment, we obtained census estimates based on observation of bird calls.

Tropical rainforests contain diverse avian communities incorporating species that compete vocally to propagate their signals to intended receivers. In order to effectively communicate with birds of the same species, birds need to organize their song performance temporally and spatially. An automated identification and localization system can provide information on the spatial and temporal arrangement of songs. Acoustic sensor arrays were tested for the ability to localize the source of songs of antbirds recorded in a Mexican rainforest. Pilot studies with a five‐node array arranged in a rough circle with a 20‐m diameter located the song of Dusky Antbird (Cercomacra tyrannina) with an error of 73 cm and Mexican Antthrush (Formicarius moniliger) with an error of 65 cm from the location of a source loudspeaker within the array. An additional source 21 m outside was also localized. Results will be presented for experiments and recordings of individuals at the Mexican rainforest site in October 2006. Locations...