Neural divergence and hybrid disruption between ecologically isolated Heliconius butterflies

The importance of behavioral evolution during speciation is well established, but we know little about how this is manifest in sensory and neural systems. A handful of studies have linked specific neural changes to divergence in host or mate preferences associated with speciation. However, the degree to which brains are adapted to local environmental conditions, and whether this contributes to reproductive isolation between close relatives that have diverged in ecology, remains unknown. Here, we examine divergence in brain morphology and neural gene expression between closely related, but ecologically distinct, Heliconius butterflies. Despite ongoing gene flow, sympatric species pairs within the melpomene–cydno complex are consistently separated across a gradient of open to closed forest and decreasing light intensity. By generating quantitative neuroanatomical data for 107 butterflies, we show that Heliconius melpomene and Heliconius cydno clades have substantial shifts in brain morphology across their geographic range, with divergent structures clustered in the visual system. These neuroanatomical differences are mirrored by extensive divergence in neural gene expression. Differences in both neural morphology and gene expression are heritable, exceed expected rates of neutral divergence, and result in intermediate traits in first-generation hybrid offspring. Strong evidence of divergent selection implies local adaptation to distinct selective optima in each parental microhabitat, suggesting the intermediate traits of hybrids are poorly matched to either condition. Neural traits may therefore contribute to coincident barriers to gene flow, thereby helping to facilitate speciation

The molecular basis of high duty-cycle echolocation in bats, and its role in the divergence of populations and species

PhD thesisHow populations diverge and form new species in the face of gene flow is a key question in evolutionary biology. Recent research suggests this may be possible where the same traits affect the ecological niche and are involved in assortative mating, and that a small number of genes could be involved in driving speciation in these cases. Echolocation call frequency in bats has roles in ecology and social communication. Bats using HDC echolocation have hearing tuned to specific frequencies, with frequency shifts impacting ecological niche and mate recognition, meaning this is a good candidate trait to drive speciation. HDC echolocation has evolved independently in two highly divergent groups of bats, providing a unique opportunity to study the molecular basis of a trait potentially driving speciation. I have combined selection testing of specific loci with genomewide divergence scans to test hypotheses concerning the evolution of HDC echolocation. Members of the yangochiropteran genus Pteronotus use low duty-cycle echolocation, except for the subgenus Phyllodia. Selection tests on coding sequence data revealed loci associated with hearing under positive selection in Phyllodia and in Pteronotus, including eleven shared with a yinpterochiropteran HDC echolocator, Rhinolophus sinicus. Three size and acoustic morphs of Rhinolophus philippinensis exist in sympatry on Buton Island. Phylogenetic reconstructions revealed population structure between the morphs, though with conflicting topologies based on mitochondrial and nuclear data. Species delimitation identified at least two separate taxa. Genomewide scans of divergence indicated low background FST between the morphs, punctuated with highly diverged islands featuring an overrepresentation of genes associated with body size and hearing. 3 This thesis represents the first genome-wide investigation of HDC echolocation, highlighting candidate genes related to this trait. It additionally describes a rarely observed mammalian ecological speciation, providing support for the claim that species designated R. philippinensis represent a complex across their range

GEOGRAPHIC VARIATION OF DESICCATION RESISTANCE IN RHAGOLETIS ZEPHYRIA (DIPTERA: TEPHRITIDAE) IN THE PACIFIC NORTHWEST: AN ADAPTIVE RESPONSE TO LOCAL BIOCLIMATE

Species with broad distributions exist in heterogenous landscapes and therefore must be able to maintain key physiological processes under a variety of abiotic conditions. This can lead to localized variation in phenotypes associated with environmental cues. Atmospheric water loss is a major source of physiological stress for terrestrial insects and one which is predicted to have major implications for biodiversity under future climate scenarios. Understanding which species exhibit adaptive variation can provide crucial insights into how individual species and thus ecological communities have evolved to cope with changing climate conditions as well as inform predictions as to how they may adapt to future climates. These adaptions can also introgress into non-native congeners via hybridization and allow introduced species to become increasingly invasive. In this study I investigate variation in desiccation resistance of larval and early pupal Rhagoletis zephyria, a widespread endemic species within the Pacific Northwest. The region is characterized by mesic coastal conditions west of the Cascade Range and xeric steppe and pine forests to the east, of which both eastern and western biomes are home to R. zephyria and its obligate plant host, Symphoricarpos albus. Wild-collected larvae from across the region were subjected to desiccation treatment during the early pupal life stage, with desiccation resistance assessed via weight retention following exposure. Modeling with machine learning algorithms and regional bioclimate variables demonstrated that most of the regional variation in desiccation response could be predicted by regional bioclimate, with increased weight retention in areas with increased evapotranspiration and decreased winter precipitation. This prediction was constrained to areas deemed suitable to the host plant via species distribution modeling in MaxEnt. The modeling identified likely regions of dramatic variation in desiccation resistance along localized bioclimate gradients, suggesting that the localized selection pressure on this response is very strong and/or that the response is plastic. While this study design does not allow distinction to be made between these two forms of variation in response to climate cues, the presence of adaptive variation in response to localized desiccation stress in the evolutionarily and economically important Rhagoletis genus is shown here for the first time

Tuning Hyperparameters in Supervised Learning Models and Applications of Statistical Learning in Genome-Wide Association Studies with Emphasis on Heritability

Machine learning is a buzz word that has inundated popular culture in the last few years. This is a term for a computer method that can automatically learn and improve from data instead of being explicitly programmed at every step. Investigations regarding the best way to create and use these methods are prevalent in research. Machine learning models can be difficult to create because models need to be tuned. This dissertation explores the characteristics of tuning three popular machine learning models and finds a way to automatically select a set of tuning parameters. This information was used to create an R software package called EZtune that can be used to automatically tune three widely used machine learning algorithms: support vector machines, gradient boosting machines, and adaboost. The second portion of this dissertation investigates the implementation of machine learning methods in finding locations along a genome that are associated with a trait. The performance of methods that have been commonly used for these types of studies, and some that have not been commonly used, are assessed using simulated data. The affect of the strength of the relationship between the genetic code and the trait is of particular interest. It was found that the strength of this relationship was the most important characteristic in the efficacy of each method

Gene discovery in the horned beetle Onthophagus taurus

<p>Abstract</p> <p>Background</p> <p>Horned beetles, in particular in the genus <it>Onthophagus</it>, are important models for studies on sexual selection, biological radiations, the origin of novel traits, developmental plasticity, biocontrol, conservation, and forensic biology. Despite their growing prominence as models for studying both basic and applied questions in biology, little genomic or transcriptomic data are available for this genus. We used massively parallel pyrosequencing (Roche 454-FLX platform) to produce a comprehensive EST dataset for the horned beetle <it>Onthophagus taurus</it>. To maximize sequence diversity, we pooled RNA extracted from a normalized library encompassing diverse developmental stages and both sexes.</p> <p>Results</p> <p>We used 454 pyrosequencing to sequence ESTs from all post-embryonic stages of <it>O. taurus. </it>Approximately 1.36 million reads assembled into 50,080 non-redundant sequences encompassing a total of 26.5 Mbp. The non-redundant sequences match over half of the genes in <it>Tribolium castaneum</it>, the most closely related species with a sequenced genome. Analyses of Gene Ontology annotations and biochemical pathways indicate that the <it>O. taurus </it>sequences reflect a wide and representative sampling of biological functions and biochemical processes. An analysis of sequence polymorphisms revealed that SNP frequency was negatively related to overall expression level and the number of tissue types in which a given gene is expressed. The most variable genes were enriched for a limited number of GO annotations whereas the least variable genes were enriched for a wide range of GO terms directly related to fitness.</p> <p>Conclusions</p> <p>This study provides the first large-scale EST database for horned beetles, a much-needed resource for advancing the study of these organisms. Furthermore, we identified instances of gene duplications and alternative splicing, useful for future study of gene regulation, and a large number of SNP markers that could be used in population-genetic studies of <it>O. taurus </it>and possibly other horned beetles.</p

Nondestructive Multivariate Classification of Codling Moth Infested Apples Using Machine Learning and Sensor Fusion

Apple is the number one on the list of the most consumed fruits in the United States. The increasing market demand for high quality apples and the need for fast, and effective quality evaluation techniques have prompted research into the development of nondestructive evaluation methods. Codling moth (CM), Cydia pomonella L. (Lepidoptera: Tortricidae), is the most devastating pest of apples. Therefore, this dissertation is focused on the development of nondestructive methods for the detection and classification of CM-infested apples. The objective one in this study was aimed to identify and characterize the source of detectable vibro-acoustic signals coming from CM-infested apples. A novel approach was developed to correlate the larval activities to low-frequency vibro-acoustic signals, by capturing the larval activities using a digital camera while simultaneously registering the signal patterns observed in the contact piezoelectric sensors on apple surface. While the larva crawling was characterized by the low amplitude and higher frequency (around 4 Hz) signals, the chewing signals had greater amplitude and lower frequency (around 1 Hz). In objective two and three, vibro-acoustic and acoustic impulse methods were developed to classify CM-infested and healthy apples. In the first approach, the identified vibro-acoustic patterns from the infested apples were used for the classification of the CM-infested and healthy signal data. The classification accuracy was as high as 95.94% for 5 s signaling time. For the acoustic impulse method, a knocking test was performed to measure the vibration/acoustic response of the infested apple fruit to a pre-defined impulse in comparison to that of a healthy sample. The classification rate obtained was 99% for a short signaling time of 60-80 ms. In objective four, shortwave near infrared hyperspectral imaging (SWNIR HSI) in the wavelength range of 900-1700 nm was applied to detect CM infestation at the pixel level for the three apple cultivars reaching an accuracy of up to 97.4%. In objective five, the physicochemical characteristics of apples were predicted using HSI method. The results showed the correlation coefficients of prediction (Rp) up to 0.90, 0.93, 0.97, and 0.91 for SSC, firmness, pH and moisture content, respectively. Furthermore, the effect of long-term storage (20 weeks) at three different storage conditions (0 °C, 4 °C, and 10 °C) on CM infestation and the detectability of the infested apples was studied. At a constant storage temperature the detectability of infested samples remained the same for the first three months then improved in the fourth month followed by a decrease until the end of the storage. Finally, a sensor data fusion method was developed which showed an improvement in the classification performance compared to the individual methods. These findings indicated there is a high potential of acoustic and NIR HSI methods for detecting and classifying CM infestation in different apple cultivars

Encoding of fruit odours by the peripheral olfactory system in Drosophila suzukii: Fruitprints for host selection and prospects for sustainable management

The fly Drosophila suzukii is an invasive pest responsible for major economic losses in fruit industries. Females lay eggs through a punctured hole in the skin of ripening fruits which otherwise would be available for retail. Since 2010 the fly is included in the World Invasive Species Compendium, developed by CAB international (CABI) and on the Pest Alert List of the European Plant Protection Organization (EPPO) as an invasive agricultural pest threatening fruit production. Intensive research has been carried out to improve current management methods and develop Integrated Pest Management (IPM) techniques. One of the challenges is to develop species specific tools which require fundamental research on species-specific host selection processes. D. suzukii is also valuable to study host selection and the mechanisms of host detection in a polyphagous pest insect. It has a fascinating ecology and its close relatedness to one of the most intensively studied biological research models Drosophila melanogaster facilitates its study. Using a highly sensitive sensory system, females detect and select host plants to lay eggs in the ripening fruits. Semiochemicals released by these fruits may be used to lure them to traps or disrupt host detection. The aim of the research presented in this thesis was to determine how host fruit odours are encoded by the peripheral olfactory system in D. suzukii to enable host fruit detection and discrimination. The results provide a model of olfactory detection of hosts for polyphagous insects. The key result is that the peripheral olfactory system encodes ripe fruit odours via combinations of only a few classes of olfactory receptor neurons (ORNs). The combinatorial activation of the fruit specific ORNs guides host selection behaviour and enables the flies to discriminate among oviposition substrates. This model offers a novel approach for identifying semiochemicals to use in pest management. It enables a rapid screen of chemicals for potential attraction to oviposition sites by determining if the responses they elicit are part of the fruitprint: the pattern of neuron activity induced by host-fruit odours in the peripheral olfactory system

In search of a better fly trap: chemical and visual ecology of Drosophila suzukii

Drosophila suzukii is an invasive species of concern to fruit growers throughout temperate regions worldwide. Unlike most Drosophila species, D. suzukii has an enlarged and heavily sclerotized ovipositor that allows female flies to lay eggs in fruits before they are fully ripened and, in most cases, before fruits are harvestable. Initial efforts at mitigating damage have relied on chemical pesticides to reduce D. suzukii populations in crop areas; however, on-going research efforts have focused on more environmentally sustainable integrated pest management alternatives. This thesis investigates aspects of D. suzukii behaviour and physiology that promoted its successful global invasion. Chapter one discusses the role of behavioural and physiological plasticity in giving D. suzukii an ecological edge during introduction and successful invasion. Chapter two investigates D. suzukii host selection behaviour and preference among commercial fruits and novel native fruits in a boreal environment. I investigated the fruit characters thought to play a role in host choice, including fruit sweetness (brix), fruit acidity (pH), and fruit firmness (penetration force [gfmm2]). Based on D. suzukii behaviour observed in field settings, the investigation was expanded to include the role of fruit and foliage colour in host selection. Additionally, we beta-tested a citizen science initiative to identify native fruit species at risk and to confirm the range limits of D. suzukii in Atlantic Canada. Chapter three further explores colour preference and use of colour by D. suzukii as attraction cues, first as cues to differentiate among fruits of different ripeness stages, and second as visual targets for potential use in monitoring traps. Chapter four investigates D. suzukii physiological sensitivity and behavioural activity to odorants associated with fruits and foliage, and odorants known to be important to other Drosophila species. An iterative process of laboratory and field trials was used to test individual odorant compounds and odorant blends in combination with results of colour preference testing to improve trapping efficacy. Given the behavioural and physiological plasticity of D. suzukii, trials were conducted among different fruit crops and growing environments. Chapter five synthesizes lessons learned about D. suzukii behaviour and preferences to make recommendations for effective monitoring traps for blueberry and raspberry crop systems

Olfactory preferences of gravid femaile stable flies Stomoxys calcitrans L. (Diptera : muscidae) and their fitness consequences

Oviposition decisions are a prominent example of behaviour directly affecting the fitness, abundance, distribution, and population dynamics of holometabolous insects. Due to eggs being immobile and adult insects often not practicing biparental and/or maternal care, gravid females, when ovipositing, should select substrate(s) that maximise fitness of their offspring. Studies have revealed that this selection is influenced by biotic (intra and interspecific competition, parasitism, larval experience, etc…) and abiotic (olfactory cues, visuals cues, substrate physiochemical properties, etc…) factors. However, in the stable fly, Stomoxys calcitrans L. (Diptera: Muscidae), a cosmopolitan blood-feeder that transmits several pathogens to animals, the influence of these factors in gravid female oviposition decisions is still unknown. Therefore, in this thesis, I examined oviposition decisions by S. calcitrans, associated fitness consequences for offspring, the olfactory cue(s) involved, and the influence of biotic factors in egg-laying decisions. I demonstrated (Chapter 2) that S. calcitrans prefer to lay on donkey and sheep dung over camel, cow, elephant, giraffe, and zebra dung or grass. I showed that this preference was related to the good nutritional value of these substrates that consequently led to the best performance of S. calcitrans offspring. Furthermore, I identified β-citronellene and (R)-(-)- carvone, from donkey and sheep dung, respectively, as the olfactory cues responsible for observed preference-performance behaviour. In the laboratory, β-citronellene and carvone elicited the strongest oviposition behaviour in S. calcitrans. I confirmed this in the field by showing that traps baited with these compounds also caught more gravid S. calcitrans. To develop a better understanding of oviposition site selection in S. calcitrans, I went on to show (Chapter 3) that S. calcitrans avoided substrates with conspecific larvae, heterospecific (Musca domestica) larvae, or the mite, Macrocheles muscaedomesticae. This avoidance behaviour was associated with fitness costs to offspring incurred in the presence of competition and parasitism. Competition with conspecific larvae led to significant changes in wing morphology (Chapter 4), with flies reared in a group of 5 having larger wing centroid size, wing length, wing width, wing area and wing loading compared with those reared in a group of 25. Also, these parameters were higher in flies developed in donkey and sheep dung in comparison with those grown in camel and cow dung. Preferred dung may lead to adults with better dispersal capabilities. Larval experience does not affect oviposition decisions by female S. calcitrans because they did not prefer to oviposit on their developmental substrate. This ruled out the Hopkins’ host selection principle in S. calcitrans and verifies the importance of innate rather than learned oviposition preferences in this species. Overall, the results reported in this thesis have enabled me to generate a fundamental knowledge of S. calcitrans oviposition decisions. Also, I have identified novel candidate attractants that could enhance trap catch of S. calcitrans to improve surveillance and limit transmission of pathogens. Furthermore, this thesis opens new research avenues in identifying repellents from conspecific and heterospecific larvae, which if packaged with the identified attractants could be used in a push-pull control system against S. calcitrans.Thesis (PhD)--University of Pretoria, 2019.Zoology and EntomologyPhDUnrestricte