At present, species are faced with a host of human-induced impacts that have already led to a loss of biodiversity and shifts in species’ ranges. Knowledge of the ecological and evolutionary processes of dynamic species’ ranges, that are either shifting or expanding, will be key to understanding the ability of species to persist and adapt during periods of environmental change. The aim of this thesis is to investigate the effects of range expansion on the genetics and evolution of species, and understand the processes that facilitate the spatial spread of populations. Using individual-based simulation models, this work demonstrates that the unique selective environment of range expansion can have a significant effect on spatial genetics and the evolution of life-history traits. It is found that the survival and spread of mutations, of various fitness effects, is influenced substantially by landscape features encountered by the expanding range. The incorporation of more specific genetic architecture shows that a substantially increased frequency of fitness peak shifts may occur on the edge of an expanding range than would arise within a stationary population. Range expansion is shown to select for increased dispersal and reproduction at the expense of competitive ability on the front of the expanding wave which results in an accelerating spread rate. The survival and spread of a population during range expansion is also affected substantially by the specific movement behaviour of individuals. The exact nature of suitable habitat, in terms of the number of suitable habitat patches and level of fragmentation, will also greatly affect the ability of a population to survive and spread during a period of environmental change. These findings are synthesised within a conceptual framework that is proposed for the evolution of populations during range expansion, where a flattening of the fitness landscape leads to adaptive revolutions.

Microtine rodents are a key component in the boreal ecosystem. Due to unique yearly fluctuation in population numbers, in addition to their central placement within boreal foodwebs, microtine rodent population dynamics control a wide variety of predator populations. Despite their grouping as microtine rodents, many individual species exhibit very different cycles, such as voles and lemmings. As such, the identification of species composition and ratio in each given habitat is of utmost importance. The purpose of this study was to compare the composition of species of small rodents between four different habitats (grassland, wetland, spruce dominated forest and pine dominated forest) and to statistically analyze if the different biotopes hosted significant differences in species composition. The project also aimed to examine differences in weight and numbers between populations of the same species in the different biotopes. To accomplish this, rodents were captured using non-lethal traps, and the resulting data was analyzed using RxC tables and ANOVA. The species captured were A. sylvaticus, C. glareolus and M. agrestis. The result of the analysis showed that the only difference in species composition existed between the grassland habitat and the rest. In addition, there existed no difference between different populations of A. sylvaticus in regards to weight. However, a difference was found between the populations of C.glareolus, with the individuals inhabiting spruce dominated forest being larger than those found in other habitats.

The species of two genera in Insecta: Hemiptera: Adelgidae were investigated through the lenses of genetics, morphology, life cycle and host species. The systematics are unclear due to complex life cycles, including multigenerational polymorphism, host switching and cyclical parthenogenesis. I studied the hemlock adelgids, including the nonnative invasive hemlock woolly adelgid on the east coast of the United States, that are currently viewed as a single species. I used multivariate morphometric analyses to identify morphological differences among hemlock adelgid lineages. With principal component analyses and MANOVA, the six lineages that were used in this study were found to be significantly different from each other. The findings of this project provide evidence for taxonomic designation of different hemlock adelgid lineages, which will hopefully inform regulation of these distinct lineages, as these distinctions between the lineages of hemlock adelgids could equate to other biological differences, ex. cold tolerance, host specialization, fecundity and dispersal ability. I also investigated the relationship between species Pineus similis, Pineus abietinus through phylogeny, genetic distances, life cycle and host species. This was done through using three mitochondrial (COI, COII, cytB) and one nuclear (EF1a) gene, in Maximum Parsimony, Maximum Likelihood and Bayesian analyses, along with genetic distance measurements. The P. similis and P. abietinus on Pinus could not be separated within the Bayesian analyses, and P. similis and P. abietinus on Abies had low calculated distance measurements (2.98%) compared to the average distance between species within the genus (28.07%). These two studies emphasize the current confusion within the Adelgidae family, and the results presented in this thesis stress the importance of using components of multiple species concepts to better understand the systematics of these lineages.

Background: Genetic recombination is a driving force in genome evolution. Among viruses it has a dual role. For genomes with higher fitness, it maintains genome integrity in the face of high mutation rates. Conversely, for genomes with lower fitness, it provides immediate access to sequence space that cannot be reached by mutation alone. Understanding how recombination impacts the cohesion and dissolution of individual whole genomes within viral sequence space is poorly understood across double-stranded DNA bacteriophages (a.k.a phages) due to the challenges of obtaining appropriately scaled genomic datasets. Results: Here we explore the role of recombination in both maintaining and differentiating whole genomes of 142 wild double-stranded DNA marine cyanophages. Phylogenomic analysis across the 51 core genes revealed ten lineages, six of which were well represented. These phylogenomic lineages represent discrete genotypic populations based on comparisons of intra-and inter-lineage shared gene content, genome-wide average nucleotide identity, as well as detected gaps in the distribution of pairwise differences between genomes. McDonald-Kreitman selection tests identified putative niche-differentiating genes under positive selection that differed across the six well-represented genotypic populations and that may have driven initial divergence. Concurrent with patterns of recombination of discrete populations, recombination analyses of both genic and intergenic regions largely revealed decreased genetic exchange across individual genomes between relative to within populations. Conclusions: These findings suggest that discrete double-stranded DNA marine cyanophage populations occur in nature and are maintained by patterns of recombination akin to those observed in bacteria, archaea and in sexual eukaryotes.

There are around 10,426 bird species around the world. Recognizing the bird species for an untrained person is almost impossible either by watching or listening them. In order to identify the bird species from their sounds, there is a need for an application that can detect the bird species from its sound. Time-frequency domain analysis techniques are used to implement the application. We implemented two time-frequency domain feature extraction methods. In feature extraction, a signature matrix which consist of extracted features is created for bird sound signals. A database of signature matrix is created with bird chirps extracted features. We implemented two feature classification methods. They are auto-correlation feature classification method and reference difference feature classification method. An unknown bird chirp is compared with the database to detect the species name. The main aim of the research is to implement the time-frequency domain feature extraction method, create a signature matrix database, implement two feature classification methods and compare them. At last, bird species were identified in the research and the auto-correlation classification method detects the bird species better than the reference difference classification method.

Shorebirds are increasingly threatened by introduced predators, invasive grasses, and human disturbance. Matrix models can be used to predict population growth and assess management options. The Pacific coast population of the western snowy plover, Charadrius alexandrinus nivosus, is listed as threatened under the Endangered Species Act, largely due to high rates of nest predation. A matrix model for the entire Pacific coast metapopulation of western snowy plovers was published in 1999 by Nur et al., but population growth has not been comprehensively reassessed since, even after development of a recovery plan (USFWS 2007) and extensive management intervention. I built and analyzed a matrix model for one subpopulation of western snowy plovers previously considered a sink habitat—Recovery Unit 2 in northern California, comprising Humboldt, Mendocino, and Del Norte counties. Based on my model, growth rate (lambda) is 1.05—countering a previous finding that Recovery Unit 2 is a sink—compared to 1.036 for the Nur et al. (1999) metapopulation model. I found that sensitivities and elasticities for each vital rate were similar between the two models; adult survival had the greatest effect on lambda, followed by juvenile survival, and fecundity had the least effect. Even though fecundity was lower for my model than Nur et al.’s (1999), adult survival was higher, which had a larger impact on population growth. In terms of management strategies, predator control, habitat restoration, and restriction of human activity should continue as outlined in the recovery plan, so as to continue the trend of positive growth for the coastal breeding population. Future directions involve performing population viability analyses for other recovery units to reassess the state of western snowy plovers compared to 1999.

Throughout human history man has utilized the environment to varying degrees, depending on technology and population. These ¨ecosystem services¨ have suffered sustained degradation over the centuries, resulting in large investments having to be made to prevent and reverse further changes to the environment. Few studies have attempted to quantitatively compare how these changes, occurring long before modern environmental monitoring programs started, affected important ecosystem services such as species diversity, water quality, carbon burial and soil stability. The aims of this study were to i) assess whether human impact on ecosystem services have varied over time in perspective of relative change, and ii) to assess the individual (per capita) contributions. I used multiple sediment proxies from a 6 m C¹⁴-dated core collected from lake Ekoln, South-Central Sweden, to reconstruct environmental changes while tracking the population growth in the city of Uppsala during the last ten centuries. Through the use of pollen and diatom assemblages I reconstructed the changing terrestrial and aquatic diversities over time, while sediment accumulation rates and the X-ray fluorescence spectroscopy of the sediment was used to reconstruct soil stability, carbon burial and water quality, respectively. In the latter case, sediment phosphorus concentrations were used as a proxy for freshwater eutrophication while metals (mercury and lead) were used to infer inputs of toxic pollutants. Finally, I normalized (z) all data to create meta-data. The z-values and reconstructed population for Uppsala made it possible to differentiate 5 unique time periods based on anthropogenic induced change, which were not previously visible in the data, and all of which have been linked to the most likely historical causes, including the Black Death. The results show that the most significant anthropogenic impacts in terms of pollution volume occurred in the 1960s, while the period from 1200-1500 AD saw the most significant environmental change in terms per head of capita, most likely caused by the shift from woodland to open landscape through twiddening, a process of burning forest to create agricultural land, prior to 1500 AD. Moreover, rapid recovery is visible after the implementation of environmental policies from the 1970s onwards. / <p>Full surname: Kilpatrick van Houte</p>

This investigation studies effects of environmental factors on growth and carotenogenesis in Corynebacterium strain 7ElC. Changes in pH were found to effect growth more than carotenogenesis. However, certain nutrients or long incubation periods stimulated carotenoid formation more than growth. Dark conditions in a mineral salts-glucose medium stimulated growth, but minimized carotenogenesis. Tryptic soy broth or yeast extract elicited carotenogenesis in darkness. Although brief light exposure during inoculation was photoinductive, continuous exposure to light following inoculation was required for maximum pigment synthesis. Dark grown stationary phase cells required 24-hours of light for maximum pigment synthesis. Chloramphenicol inhibition of carotenogenesis in dark grown cells exposed to light showed that enzymes needed for carotenoid synthesis were absent from dark grown cultures.

Invasive woody shrubs are a problem when they displace native species and threaten habitats, especially those that harbor rare or endangered species. They not only compete with native plants, but also alter habitat and food that many organisms depend upon. Invasive plants undergo a release from their specialist predators in the nonnative range, providing them advantages over native species. Because modes and pathways of how invasive species spread are not fully understood, predicting spread and implementing restoration ecological controls remain inexact. Due to the lack of comparative studies on woody shrubs, especially invasive privets, we understand very little about conditions affecting their invasiveness. A study was conducted near Dallas, Texas to determine if privet has allelopathic properties that influences growth of native plants. Soil nutrients and other analyses were made and compared between field plots supporting privet, plots in which privet has been removed, and plots where privet has not been observed. In some field plots, natives were planted under the three previously mentioned conditions, and their survival and condition were monitored to evaluate effects of privet on their establishment and growth. It was found that Chinese privet did hinder seed germination in red mulberry, soapberry and beautyberry and root formation in beautyberry cuttings. The soil in the sites were found to be normal for bottomland forests that endured two flooding events within one year.

Alcohol use disorders (AUDs) are major health issues with few known genetic explanations. This project used the fruit fly (Drosophila melanogaster) model to identify genes and gene networks that influence alcohol intoxication, a phenotype related to alcohol abuse in humans. We used bioinformatic tools to build gene networks based on 24 published Drosophila ethanol-responsive genes with human orthologs. We then assessed the role of these networks in ethanol sedation by testing two of the networks seeded on IP3K2, a gene that regulates calcium signaling, and CG14630, a gene involved in carnitine biosynthesis. We knocked down several genes in each of the networks using RNAi and tested the knockdown flies in a behavioral assay for ethanol sedation. Nervous system RNAi expression against 7 of 20 genes in the IP3K2 network and 4 of 30 genes in the CG14630 network significantly affected the sensitivity of flies to ethanol. To determine whether the hit rates in these two networks were greater than would be expected by random chance alone, we also assessed the effects of nervous system RNAi targeting a random set of fly genes. Unexpectedly, the fraction of randomly selected genes that affected ethanol sensitivity in a primary screen was comparable to or even larger than that from bioinformatically-derived gene networks. Our data are consistent with two possibilities that are not mutually exclusive. One possibility is that there are a very large number of genes that impact ethanol sedation and our bioinformatic analyses did not substantially enrich for these genes. A second possibility is that expression of RNAi could influence ethanol sedation independent of target gene knock-down. These two possibilities will be examined in future experiments.