The application of predictive modelling for determining bio-environmental factors affecting the distribution of blackflies (Diptera: Simuliidae) in the Gilgel Gibe watershed in Southwest Ethiopia

Blackflies are important macroinvertebrate groups from a public health as well as ecological point of view. Determining the biological and environmental factors favouring or inhibiting the existence of blackflies could facilitate biomonitoring of rivers as well as control of disease vectors. The combined use of different predictive modelling techniques is known to improve identification of presence/absence and abundance of taxa in a given habitat. This approach enables better identification of the suitable habitat conditions or environmental constraints of a given taxon. Simuliidae larvae are important biological indicators as they are abundant in tropical aquatic ecosystems. Some of the blackfly groups are also important disease vectors in poor tropical countries. Our investigations aim to establish a combination of models able to identify the environmental factors and macroinvertebrate organisms that are favourable or inhibiting blackfly larvae existence in aquatic ecosystems. The models developed using macroinvertebrate predictors showed better performance than those based on environmental predictors. The identified environmental and macroinvertebrate parameters can be used to determine the distribution of blackflies, which in turn can help control river blindness in endemic tropical places. Through a combination of modelling techniques, a reliable method has been developed that explains environmental and biological relationships with the target organism, and, thus, can serve as a decision support tool for ecological management strategies

Simulations and Modelling for Biological Invasions

Biological invasions are characterized by the movement of organisms from their native geographic region to new, distinct regions in which they may have significant impacts. Biological invasions pose one of the most serious threats to global biodiversity, and hence significant resources are invested in predicting, preventing, and managing them. Biological systems and processes are typically large, complex, and inherently difficult to study naturally because of their immense scale and complexity. Hence, computational modelling and simulation approaches can be taken to study them. In this dissertation, I applied computer simulations to address two important problems in invasion biology. First, in invasion biology, the impact of genetic diversity of introduced populations on their establishment success is unknown. We took an individual-based modelling approach to explore this, leveraging an ecosystem simulation called EcoSim to simulate biological invasions. We conducted reciprocal transplants of prey individuals across two simulated environments, over a gradient of genetic diversity. Our simulation results demonstrated that a harsh environment with low and spatially-varying resource abundance mediated a relationship between genetic diversity and short-term establishment success of introduced populations rather than the degree of difference between native and introduced ranges. We also found that reducing Allee effects by maintaining compactness, a measure of spatial density, was key to the establishment success of prey individuals in EcoSim, which were sexually reproducing. Further, we found evidence of a more complex relationship between genetic diversity and long-term establishment success, assuming multiple introductions were occurring. Low-diversity populations seemed to benefit more strongly from multiple introductions than high-diversity populations. Our results also corroborated the evolutionary imbalance hypothesis: the environment that yielded greater diversity produced better invaders and itself was less invasible. Finally, our study corroborated a mechanical explanation for the evolutionary imbalance hypothesis – the populations evolved in a more intense competitive environment produced better invaders. Secondly, an important advancement in invasion biology is the use of genetic barcoding or metabarcoding, in conjunction with next-generation sequencing, as a potential means of early detection of aquatic introduced species. Barcoding and metabarcoding invariably requires some amount of computational DNA sequence processing. Unfortunately, optimal processing parameters are not known in advance and the consequences of suboptimal parameter selection are poorly understood. We aimed to determine the optimal parameterization of a common sequence processing pipeline for both early detection of aquatic nonindigenous species and conducting species richness assessments. We then aimed to determine the performance of optimized pipelines in a simulated inoculation of sequences into community samples. We found that early detection requires relatively lenient processing parameters. Further, optimality depended on the research goal – what was optimal for early detection was suboptimal for estimating species richness and vice-versa. Finally, with optimal parameter selection, fewer than 11 target sequences were required in order to detect 90% of nonindigenous species

Evolutionary Inference from Admixed Genomes: Implications of Hybridization for Biodiversity Dynamics and Conservation

Hybridization as a macroevolutionary mechanism has been historically underappreciated among vertebrate biologists. Yet, the advent and subsequent proliferation of next-generation sequencing methods has increasingly shown hybridization to be a pervasive agent influencing evolution in many branches of the Tree of Life (to include ancestral hominids). Despite this, the dynamics of hybridization with regards to speciation and extinction remain poorly understood. To this end, I here examine the role of hybridization in the context of historical divergence and contemporary decline of several threatened and endangered North American taxa, with the goal to illuminate implications of hybridization for promoting—or impeding—population persistence in a shifting adaptive landscape. Chapter I employed population genomic approaches to examine potential effects of habitat modification on species boundary stability in co-occurring endemic fishes of the Colorado River basin (Gila robusta and G. cypha). Results showed how one potential outcome of hybridization might drive species decline: via a breakdown in selection against interspecific heterozygotes and subsequent genetic erosion of parental species. Chapter II explored long-term contributions of hybridization in an evolutionarily recent species complex (Gila) using a combination of phylogenomic and phylogeographic modelling approaches. Massively parallel computational methods were developed (and so deployed) to categorize sources of phylogenetic discordance as drivers of systematic bias among a panel of species tree inference algorithms. Contrary to past evidence, we found that hypotheses of hybrid origin (excluding one notable example) were instead explained by gene-tree discordance driven by a rapid radiation. Chapter III examined patterns of local ancestry in the endangered red wolf genome (Canis rufus) – a controversial taxon of a long-standing debate about the origin of the species. Analyses show how pervasive autosomal introgression served to mask signatures of prior isolation—in turn misleading analyses that led the species to be interpreted as of recent hybrid origin. Analyses also showed how recombination interacts with selection to create a non-random, structured genomic landscape of ancestries with, in the case of the red wolf, the ‘original’ species tree being retained only in low-recombination ‘refugia’ of the X chromosome. The final three chapters present bioinformatic software that I developed for my dissertation research to facilitate molecular approaches and analyses presented in Chapters I–III. Chapter IV details an in-silico method for optimizing similar genomic methods as used herein (RADseq of reduced representation libraries) for other non-model organisms. Chapter V describes a method for parsing genomic datasets for elements of interest, either as a filtering mechanism for downstream analysis, or as a precursor to targeted-enrichment reduced-representation genomic sequencing. Chapter VI presents a rapid algorithm for the definition of a ‘most parsimonious’ set of recombinational breakpoints in genomic datasets, as a method promoting local ancestry analyses as utilized in Chapter III. My three case studies and accompanying software promote three trajectories in modern hybridization research: How does hybridization impact short-term population persistence? How does hybridization drive macroevolutionary trends? and How do outcomes of hybridization vary in the genome? In so doing, my research promotes a deeper understanding of the role that hybridization has and will continue to play in governing the evolutionary fates of lineages at both contemporary and historic timescales

The genomic basis of adaptation in threespine stickleback fish

Evolutionary biology consists in the study of the evolutionary processes responsible of the diversification and adaptation of life forms over time. When adapting to a new environment (or changes in their local environment), populations have to adapt through natural selection. Until recently, the study of adaptation was focusing on fathoming the consequences of natural selection at the phenotypic level and how phenotypic evolution is linked to genetic changes. The development of new genetic and genomic tools in the last 20 years, like high-throughput sequencing technologies, now allows the construction of reference genomes in a variety of non-model organisms and the investigation of the genomic basis of adaptation. In my thesis, I investigated the genomic basis of adaptation by exploring the consequences of natural selection at the molecular level using the threespine stickleback fish (Gasterosteus acualeatus) as a model. In more detail, my work focused on three main topics: the genomic basis of parallel adaptation to acidic versus basic lochs of North Uist (Outer Hebrides, Scotland); the maintenance of standing genetic variation in Atlantic stickleback fish, and the characterization of reproductive isolation at the genomic level between parapatric stickleback populations of the Misty watershed (Vancouver Island, British Columbia, Canada)

Population genomics as a tool for management and conservation of brown trout (Salmo trutta) in the Iberian Peninsula

Brown trout (Salmo trutta) is a cold-water salmonid with ecological, commercial and recreational importance. Previous genetic studies highlighted a notable genetic structure in natural populations, which is a fundamental biological feature for the conservation of the species. Nevertheless, many factors threaten this genetic richness. One of the most important is genetic introgression, that originated from the introduction of aquaculture individuals in the wild environment in the last decades. This genetic erosion can have adverse consequences in brown trout adaptation capacity, especially in the context of a reduction of available habitats driven, among other causes, by global warming. This doctoral thesis had two main strands: (1) A bioinformatic benchmark to evaluate the biological conclusion robustness drawn from diverse SNP panels derived from different building-loci pipelines. For this strand, a broad of five aquatic species representing different genomic and/or population structure scenarios was used. This strand was performed in a context in which, due to the irruption of new techniques as RAD-seq (Restricion site-associated DNA sequencing) for the library preparation and Next Generation DNA Sequencing (NGS), the volume of data generated has grown exponentially in the last decade, promoting the development of new bioinformatics tools to process it. On the other side, (2) a genomic approach was used for the first time on brown trout populations from the Iberian Peninsula, to evaluate genetic diversity levels, population structure, natural hybridization patterns, evaluation of population introgression with aquaculture individuals of the same species and the detection of candidate genomic regions under selection pressure. The information obtained will allow the improvement of current management and conservation strategies of wild brown trout genetic resources

Identifying the Genetic Population Structure Knowledge Gaps Hindering an Improved Management of the Spurdog (Squalus acanthias) stock in the Northeast Atlantic: A Systematic Review

Despite its long history of exploitation, there is limited information about the spurdog. Therefore, it is important to identify which general and genetic information is available for the species and what is missing to resolve stock structure and advice future management schemes. The goal of this study was to identify the knowledge gaps, in terms of genetic population structure and diversity, which could inform an improved fisheries management for the spurdog in the Northeast Atlantic Ocean and Mediterranean Sea. To achieve this, a systematic review and a series of phylogenetic analyses using the NADH2 marker were done. Results from the review showed there is very limited general information about the species in the study regions, with only 38 documents found out of over 6000 hits. Only 3 studies were found concerning its genetic structure and diversity, with high diversity found for all studies but no genetic differentiation, except for the subpopulation in the Adriatic Sea. No genetic structure was found for the species in the Northeast Atlantic, but fine structuring was found for the Mediterranean Sea, indicating different stocks. The phylogenetic trees showed complex taxonomical relationships within the Squalus genus and no clear formation of monophyletic clades according to the location in which the samples were taken for sequences of S. acanthias. Major conclusions indicate the need for collecting more information, particularly with less invasive methods, given the zero TAC in the areas and the limitations of fisheries surveys, as well as more sampling efforts in regions different from Norway, the United Kingdom, and the Adriatic Sea. Furthermore, given that the phylogenetic analysis of the species with the NADH2 marker was inconclusive, the use of more efficient genetic markers, such as microsatellites or single nucleotide polymorphisms, is recommended for identifying fine genetic structuring in the populations

2016 Conference Abstracts: Annual Undergraduate Research Conference at the Interface of Biology and Mathematics

Schedule and abstract book for the Eighth Annual Undergraduate Research Conference at the Interface of Biology and Mathematics Date: October 8-9, 2016Location: UT Conference Center, KnoxvillePlenary Speaker: Jorge X. Velasco Hernández, Universidad Nacional Autónoma de MéxicoFeatured Speaker: Judy Day, University of Tennessee, Knoxvill