Evolution Commons^™

Pickleweed In The Disappearing Marsh: Population Genetics & Metal Accumulation In Salicornia Depressa, Alice Kaisla

Graduate Doctoral Dissertations

Salicornia is a genus of succulent halophytes found in salt marshes around the world. Salicornia species have a remarkably high tolerance for heavy metal pollution and have been shown to accumulate high concentrations of heavy metals in their tissue under experimental conditions. As a result, they are both a useful system for studying evolution in polluted coastlines and a potential candidate for use in phytoremediation. My research focuses on Salicornia depressa, known as pickleweed, a species commonly found in marshes along the heavily urbanized and industrialized New England coast. I investigate genetic diversity and population structure in S. depressa populations …

Investigating Cryptic Diversity In The Hawaiian Endemic Plant, Psychotria Mariniana (Rubiaceae), Uyen Thi Hoang Nguyen

Master's Theses

Islands, with their isolation and steep environmental gradients, serve as natural laboratories for studying speciation. Molecular phylogenetic and population genetic methods utilizing Next-Generation Sequencing (NGS) have revolutionized our ability to document patterns of genetic divergence and diversity. Cryptic diversity, genetically distinct populations that were previously unrecognized as unique, and cryptic speciation, where divergent genetic populations may be deserving of status as unique species, have been observed in many taxa. The Hawaiian Islands provide an ideal setting for studying divergence and speciation due to their extreme isolation, known ages, and volcanic origin. Previous work has investigated the evolutionary relationships of the …

Exploring Factors Mediating White-Nose Syndrome In Little Brown Bats, Carly R. Trujillo

Graduate Theses/Dissertations

The little brown bat (Myotis lucifugus) has experienced drastic population declines across North America due to the recent disease white-nose syndrome (WNS). Previous studies have identified putatively adaptive alleles (PAAs) that may give individuals a greater likelihood of survival. However, there could be geographic-specific adaptation, creating different adaptive landscapes. Additionally, there may be energetic trade-offs between disease survival and reproductive output, and it is not clear what the long-term survival outcomes for the species may be as a result. Long-term evolutionary outcomes are unclear because this species has a lifespan exceeding the arrival of WNS and is difficult …

Population Structure Analysis Of Four Basal Higher-Attines Using Bioinformatic Approaches, Gabriel Mcdanield

Biology Theses

Metapopulations within the family Formicidae are unique among other animals due to the large colonies they build, and the mating strategies required to fertilize a specialized reproductive caste that will often produce young for the life of the colony. One group of ants, the fungus-gardeners (tribe Attini). The population structure of North American non-leafcutting, fungus-gardening ants has been understudied, especially in the southwest of the United States. Additionally, not much is known about their dispersal biology, so the dynamics of dispersal of these species and how they affect population structure is likewise not well known. To shed light on the …

Hidden Markov Model For Identifying Local Variants In Human Genomes Using Simulated Data, Scott Mccallum

Electronic Theses and Dissertations

Identifying adaptive mutations in genetic data is challenging due to the low frequency of occurrence of such events, and because signatures of selection are intertwined with the footprints of various other evolutionary forces that shape our genomes. Even when a larger region appears to be under selection, genomic sites that are linked to adaptive mutations have similar statistical signals, and thus can obfuscate the identification of the actual adaptive mutation. The new method described here uses a Hidden Markov Model that allows for classification of neutral, linked, and sweep (adaptive mutation) genomic sites. This model is general and can be …

The Influence Of Environmental Change On Genetic Diversity Across Spatial And Taxonomic Scales, Connor M. French

Dissertations, Theses, and Capstone Projects

The spatial distribution of genetic diversity is of interest to biodiversity scientists and conservationists and is a fundamental metric of biodiversity. Genetic diversity patterns across spatial and taxonomic scales contain information about population and assemblage dynamics that can convey their resilience to environmental change. Ectotherms are especially linked to their environments and may be especially sensitive to fluctuations in the environment over time. Herein, I investigate global and regional patterns of genetic diversity in two groups of ectotherms, insects and lizards, to understand the relationship between environmental change and genetic diversity, from populations to assemblages. Overall, my research aims to …

Omani Camels From A Cultural And Genomics Perspective, Al Muatasim Al Zadjali

Electronic Theses and Dissertations

The Dromedarian camel, Camelus dromedarius, is native to the Arabian Peninsula, including the Sultanate of Oman. These camels are used for food, milk, as well as show and racing competitions. Despite their economic and cultural importance research on camels in Oman is limited. The goal of this study was to examine their genomic variation, relationship with camels in other parts of the Arabian Peninsula, and to determine if selective breeding has led to the establishment of distinct breeds in Oman. Information was compiled from multiple sources to produce a comprehensive review on the breeding, management, economic and cultural use, …

Evolution Of Forest Bitis (Macrocerastes) In Africa: Phylogeography, Population Genetics, And Potential As A Model For Batesian Mimicry, Eugene Richard Vaughan

Open Access Theses & Dissertations

The major biogeographical patterns characterizing the diversification of widely distributed species in the African rainforest remain poorly understood because of the low number of well-sampled studies that are focused on this region. I examine the phylogeography and population genetics of two broadly sympatric sister lineages of large African forest vipers (genus Bitis, subgenus Macrocerastes), the rhinoceros viper (B. nasicornis) and the Gaboon vipers (B. gabonica and B. rhinoceros). Despite their close relationship, these two lineages have notably different patterns of divergence in time and space. A time-calibrated phylogeny with sequence data from five genes, and population structure and PCA analyses …

A Comparison Of Microsatellites And Single Nucleotide Polymorphisms For The Assessment Of Population Structure In The Amblyomma Maculatum Koch, 1844 Species Complex, Henrey A. Deese

Electronic Theses and Dissertations

The Gulf Coast tick, Amblyomma maculatum Koch, 1844 is widespread throughout North and Central America and is the primary vector for the emerging pathogen Rickettsia parkeri. In the U.S., the population in the Southwest (A. maculatum morphotype III) is morphologically different from the population east of the Rocky Mountains (A. maculatum morphotype II). This research tests the hypothesis that A. maculatum morphotype II and morphotype III represent distinct species through the analysis and comparison of 6 microsatellite loci and suite of 135,221 Single nucleotide polymorphisms (SNPs) generated from ddRADseq. Population genetic analysis of both microsatellites and SNPs …

Plastic And Evolved Responses In The Eastern Oyster, Crassostrea Virginica, To Environmental Variation In The Northern Gulf Of Mexico, Kyle Sirovy

LSU Doctoral Dissertations

Climate change and other anthropogenic impacts are causing rapid alterations to many of the world’s most productive coastal ecosystems and there is an urgent need to understand how species will respond to these environmental changes. Organisms may respond through plasticity, evolution, or the evolution of plasticity. In this dissertation, I evaluate the role of plastic and evolved responses in the eastern oyster, Crassostrea virginica, to environmental variation in the northern Gulf of Mexico. I use comparative transcriptomics, physiology, and morphology to examine the relative contribution of plastic and evolved responses for oysters exposed to low salinity and outplant sites …

Evaluating Population Genetic Structure And Potential Genomic Signals Of Natural Selection In A Migratory Songbird (Protonotaria Citrea), Tyler A. Hohenstein

Theses and Dissertations

In this study I attempted to further resolve the population genetic structure in the Prothonotary Warbler (Protonotaria citrea), and conducted an outlier SNP analysis and exploratory gene ontology analysis to investigate potential ongoing natural selection in the species. This analysis of population structure confirms previous work by DeSaix et al. (2019), where weak population structure was observed between eastern sites along the Atlantic Coastal Plain, and western sites in the Mississippi Alluvial Valley, possibly due to a genetic discontinuity across the Appalachian Mountains. I conducted two forms of outlier SNP analyses, a principal component analysis (PCA)-based approach to identify SNPs …

Population Genomics Of Redbreast Sunfish (Lepomis Auritus): Exploring Gene Flow And Local Adaptation In A Widely Distributed Freshwater Fish, Garret J. Strickland

College of Graduate Studies: Theses & Dissertations

Little information is available concerning the distribution of genetic diversity in non-salmonid, non-imperiled, freshwater fish. In order to fill in this knowledge gap, I conducted a population genomics survey in Redbreast Sunfish (Lepomis auritus; RBS), a widespread, generalist species distributed along the Atlantic slope rivers of eastern North America. I sampled four basins (ACF, Savannah, Roanoke, and James) at eight sites each with a factorial experimental design. Sites were distributed among coastal plain, Piedmont, or mountain ecoregions in order to capture the greatest range of environmental states experienced by RBS, with the intention of finding evidence for local adaptation to …

An Analysis Of The Spatial Genetic Structure Of A Hybrid Zone Between Two Species Of Killifish, Fundulus Heteroclitus And F. Grandis, Andrew Lee Hardy

UNF Graduate Theses and Dissertations

Hybridization offers unique insight into the evolutionary process of speciation and the forces that maintain barriers to reproduction. In northeast Florida, a hybrid zone between two species of killifish, Fundulus heteroclitus and F. grandis, has been identified near Flagler Beach, FL, although the exact boundaries of the hybrid zone remain unknown (Gonzalez et al. 2009). This study aims to determine the fine-scale spatial genetic patterns of the hybrid zone and test the hypothesis that species ranges are influenced by changes in dominant vegetation. Results from an ADMIXTURE analysis and F_ST data indicated the boundary of the area of …

Comparative Conservation Genomics Of A Suite Of Imperiled Freshwater Mussels, Scott C. Meyer

College of Graduate Studies: Theses & Dissertations

Maintenance of genetic diversity is a critical component to the management and recovery of imperiled species. By ensuring that a species’ genetic diversity is maintained, issues like inbreeding depression and loss of local adaptation can be prevented. However, the genetic diversity of many species are not well-characterized, and the factors that influence a species’ genetic diversity are often not well understood. In the case of imperiled unionid freshwater mussels, it is important to conduct conservation genetic assessments to aid in their management and preserve genetic diversity. This is the first study to conduct a comparative conservation genomic assessment for eight …

Lepidopteran Granivory Reduces Seed Counts In A Rare Species Of Riparian Scour Prairies, Cheyenne Moore, Angela J. Mcdonnell, Scott Schuette, Christopher T. Martine

Faculty Journal Articles

In Pennsylvania Baptisia australis var. australis is found along only four waterways: the Allegheny River, Youghiogheny River, Clarion River, and Red Bank Creek. Because of its limited distribution and small number of extant populations, the species is considered state-threatened in Pennsylvania. In addition, the riparian prairie habitat that Pennsylvania Baptisia australis var. australis is restricted to is also in decline and considered vulnerable. Because of these conservation concerns, insights into the natural history of the taxon in the state is valuable and will inform conservation efforts. Field surveys and fruit collections along the Allegheny River and herbarium collections were used …

Evolutionary Inference From Admixed Genomes: Implications Of Hybridization For Biodiversity Dynamics And Conservation, Tyler Chafin

Graduate Theses and Dissertations

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 …

Spatial Genetic Structure And Local Adaptation Within And Among Foxtail Pine (Pinus Balfouriana Subsp. Balfouriana) Populations Located In The Klamath Mountains, California, Rebecca D. Piri

Theses and Dissertations

Foxtail pine (Pinus balfouriana) is a subalpine conifer endemic to California, notably separated into two disjunct subspecies. Previous studies have described the northern subspecies,Pinus balfouriana subsp. balfouriana,as having an uncommonly high level of genetic differentiation and no discernible spatial patterns in phenotypic variation. This study seeks to characterize the spatial genetic structure and patterns of selection of the northern subspecies (Pinus balfouriana subsp. balfouriana) using genome-wide data and to identify the influence of ecology and environment on the unique genetic patterns. I show that genetic differentiation among populations is much less than previously estimated …

The Evolutionary History Of Nebraska Deer Mice: Local Adaptation In The Face Of Strong Gene Flow, Susanne P Pfeifer, Stefan Laurent, Vitor C. Sousa, Catherine R. Linnen, Matthieu Foll, Laurent Excoffier, Hopi E. Hoekstra, Jeffrey D. Jensen

Biology Faculty Publications

The interplay of gene flow, genetic drift, and local selective pressure is a dynamic process that has been well studied from a theoretical perspective over the last century. Wright and Haldane laid the foundation for expectations under an island-continent model, demonstrating that an island-specific beneficial allele may be maintained locally if the selection coefficient is larger than the rate of migration of the ancestral allele from the continent. Subsequent extensions of this model have provided considerably more insight. Yet, connecting theoretical results with empirical data has proven challenging, owing to a lack of information on the relationship between genotype, phenotype, …

Dna Extraction And Microsatellite Amplification Of Daphnia Pulicaria Resting Eggs: Analysis Of Allele Frequencies Through Time, Anna Ries

Departmental Honors Projects

A paleoecological approach allows for the study of genetic change in populations over longer periods of time than would be possible if one were sampling populations from year to year. Daphnia and other cladoceran zooplankton are amenable to this type of study because they produce diapausing embryos (ephippial eggs) when they sexually reproduce, and these resting eggs can remain viable for decades to centuries in lake sediments. This study uses paleoecological methods as well as a new methodology for ephippial DNA extraction and amplification to assay for genetic variation in ephippial eggs obtained from sediments of varying ages from Square …

Climate-Driven Habitat Shifts In South America: Biogeography, Historical Demography, And Population Genomics Of Anole Lizards, Ivan Prates

Dissertations, Theses, and Capstone Projects

Shifts in the geographic distribution of habitats over time can promote dispersal and vicariance, thereby influencing large-scale biogeographic patterns and ecological processes. The establishment of corridors of suitable habitat across previously disjunct yet ecologically similar regions has been widely linked to climate change over time. Such climate-mediated habitat changes may have played a key role in the assembly of tropical biotas, including those of Amazonia and the coastal Atlantic Forest in South America, two of the most diverse ecosystems on Earth. The history of biogeographic associations between tropical rainforest habitats in response to former climatic shifts, as well as their …

Evolutionary Linkage Of Mimetic And Non-Mimetic Color Traits In A Coral Snake Mimicry Complex, John D. Curlis Jr

College of Graduate Studies: Theses & Dissertations

Color polymorphism in aposematic mimicry systems is a perplexing phenomenon for evolutionary biologists, as theoretically the benefits of converging on a model phenotype should constrain the evolution of phenotypic diversity in these systems (i.e., color polymorphism should not occur). Nevertheless, color polymorphism in mimicry systems is prevalent throughout many taxa. In some of these systems, the evolution of color polymorphism results in the existence of non-mimetic morphs, such as those that are cryptic. The case of ground snakes (Sonora semiannulata) is unique in that color polymorphism encompasses both mimetic and cryptic morphs, as well as individual mimetic and …

Genetic Perspectives On Biodiversity In Rocky Mountain Alpine Streams, Scott Hotaling

Theses and Dissertations--Biology

In alpine regions worldwide, climate change is dramatically altering ecosystems, affecting biodiversity across habitats and taxonomic scales. For streams, the associated recession of mountain glaciers and snowfields, paired with altered precipitation regimes, are driving shifts in hydrology, species distributions, and basal resources – often threatening the very existence of some habitats and biota. Globally, alpine streams harbor particularly substantial species and genetic diversity due to significant habitat insularity and environmental heterogeneity: however, anthropogenic warming threatens to homogenize habitats through the reduction of the cryosphere, thereby reducing biodiversity from micro- to macroscopic organisms and genes to communities. Still, alpine stream biodiversity, …

Evolution In The Deep Sea: Scales And Mechanisms Of Population Divergence, Amanda E. Glazier

Graduate Doctoral Dissertations

The deep sea is the Earth’s largest ecosystem and harbors a unique and largely endemic fauna. Although most research has focused on the ecological mechanisms that allow coexistence, recent studies have begun to investigate how this remarkable fauna evolved.. My work quantifies geographic patterns of genetic variation and investigates potential mechanisms that shape evolution in the deep ocean.

Bathymetric genetic divergence is common in the deep sea with population structure typically decreasing with depth. The evolutionary mechanisms that underlie these patterns are poorly understood. Geographic patterns of genetic variation indicated that the protobranch bivalve Neilonella salicensis was composed of two …

The Effect Of Population History On Hominoid Intraspecific Cranial Shape Diversity: Combining Population Genetic And 3d Geometric Morphometric Data, Julia Marie Zichello

Dissertations, Theses, and Capstone Projects

Cranial shape diversity within hominoids has been previously studied with the aim of understanding how levels of diversity in extant species compare with extinct hominin specimens. This dissertation addresses the question of why cranial shape diversity differs among extant hominoids. Levels of intraspecific cranial shape diversity are highly varied among hominoids. For example, Sumatran orangutan cranial shape diversity is more than twice that of all living humans. Here, the population history of each species, or sub-species, is considered as a force potentially structuring phenotypic variation. It is already well established that population history has shaped patterns of modern human cranial …

Inter-And Intra-Population Variability Across The Transcriptome Of Lake Baikal’S Endemic Copepod With Ramifications For Adapting To Climate Change, Larry L. Bowman Jr

Electronic Theses and Dissertations

The future of Lake Baikal’s biodiversity is uncertain in response to climate change. Unlike its diverse benthos, Lake Baikal’s zooplankton is species poor, with up to 96% of its biomass being composed of a single Calanoid copepod species, Epischura baikalensis. This study characterizes the genetic differentiation and differential gene expression of E. baikalensis. Using partial-transcriptome sequences obtained by 454 Rosche and Illumina sequencing technologies, the genetic differentiation at inferred single nucleotide polymorphism (SNP) sites and differential gene expression in populations sampled from various parts of the lake were analyzed. The functional genomics of genes showed significant differential …

Assessing Genetic Differentiation Among Populations Of The Invasive Plant Impatiens Glandulifera In Maine, Jordan R. Schoonover

Honors Theses

The annual herbaceous plant Impatiens glandulifera Royle is native to the Himalayas and is a significant invasive species in Europe. In the past century, it was introduced to the United States, where it has become established in 12 states. This study evaluated genetic differentiation among four Maine populations, to address a theory that posits hybridization of distinct lineages as a trigger for invasiveness. Regions of microsatellite repeats were evaluated at two polymorphic loci for 41 plants sampled from the four populations. A striking finding was that the observed heterozygosity was substantially higher than the heterozygosity expected from random combination of …