Biology Commons^™

Illuminating The Drivers Of Genomic Diversification In Lamprologine Cichlids Of The Lower Congo River, Naoko P. Kurata

Dissertations, Theses, and Capstone Projects

Freshwater fishes are extraordinarily diverse, considering their available habitats represent a tiny proportion of the earth’s surface. Rivers connect heterogeneous habitats in a linear form and provide excellent simplified models to understand how aquatic biodiversity evolves. In particular, the lower Congo River (LCR) in west Central Africa consists of a dynamic hydroscape exhibiting extraordinary aquatic biodiversity, endemicity, and morphological and ecological specialization. This system is thus an excellent natural laboratory for understanding complex speciation and population diversification processes. In my research, I explore various drivers of diversification, and adaptive evolution in rheophilic lamprologine cichlids endemic to the LCR, including Lamprologus …

Hybrid Sterility, Genetic Conflict And Complex Speciation: Lessons From The Drosophila Simulans Clade Species, Daven C. Presgraves, Colin D. Meiklejohn

School of Biological Sciences: Faculty Publications

The three fruit fly species of the Drosophila simulans clade— D. simulans, D. mauritiana, and D. sechellia— have served as important models in speciation genetics for over 40 years. These species are reproductively isolated by geography, ecology, sexual signals, postmating-prezygotic interactions, and postzygotic genetic incompatibilities. All pairwise crosses between these species conform to Haldane’s rule, producing fertile F1 hybrid females and sterile F1 hybrid males. The close phylogenetic proximity of the D. simulans clade species to the model organism, D. melanogaster, has empowered genetic analyses of their species differences, including reproductive incompatibilities. But perhaps no phenotype has been subject to …

The Effect Of Sampling Density And Study Area Size On Landscape Genetics Inferences For The Mississippi Slimy Salamander (Plethodon Mississippi), Stephanie M. Burgess, Ryan C. Garrick

Faculty and Student Publications

In landscape genetics, it is largely unknown how choices regarding sampling density and study area size impact inferences upon which habitat features impede vs. facilitate gene flow. While it is recommended that sampling locations be spaced no further apart than the average individual's dispersal distance, for low-mobility species, this could lead to a challenging number of sampling locations, or an unrepresentative study area. We assessed the effects of sampling density and study area size on landscape genetic inferences for a dispersal-limited amphibian, Plethodon mississippi, via analysis of nested datasets. Microsatellite-based genetic distances among individuals were divided into three datasets representing …

Small-Scale Population Connectivity And Genetic Structure In Canada Thistle (Cirsium Arvense), Mahboubeh Hosseinalizadeh Nobarinezhad, Lavanya Challagundla, Lisa E. Wallace

Biological Sciences Faculty Publications

Premise of research. Population connectivity, the exchange of genes among geographically separated subpopulations, is thought to be a key process for the maintenance of genetic diversity and the survival of invasive species in newly colonized areas. Plant populations' degree of genetic connectivity, which occurs via pollen and seed dispersal, leads to different degrees of genetic admixture and genetic structure. Environmental barriers and differential selection pressures that are variable across time and space tend to alter genetic structure within and among populations via restriction or facilitation of gene flow. Canada thistle, an invasive species of the United States and Canada, is …

Do Genetic Structure And Landscape Heterogeneity Impact Color Morph Frequency In A Polymorphic Salamander?, Maggie M. Hantak, Robert B. Page, Paul E. Converse, Carl D. Anthony, Shawn R. Kuchta

2019 Faculty Bibliography

Landscape heterogeneity plays an important role in population structure and divergence, particularly for species with limited vagility. Here, we used a landscape genetic approach to identify how landscape and environmental variables affect genetic structure and color morph frequency in a polymorphic salamander. The eastern red- backed salamander, Plethodon cinereus, is widely distributed in northeastern North America and contains two common color morphs, striped and unstriped, that are divergent in ecology, behavior, and physiology. To quantify population structure, rates of gene flow, and genetic drift, we amplified 10 microsatellite loci from 648 individuals across 28 sampling localities. This study was conducted …

Impact Of Suburban Landscape Features On Gene Flow Of The Model Invasive Grass, Brachypodium Sylvaticum, Tina Marie Arredondo

Dissertations and Theses

Rapid range expansion of newly invasive species provides a unique opportunity for studying patterns of dispersal and gene flow. In this thesis, I examined the effect of landscape features on gene flow in the invasive grass Brachypodium sylvaticum at the edge of its expanding range. I used genome-wide Single Nucleotide Polymorphism (SNP) surveys of individuals from 22 locations in the Clackamas Watershed in the Portland, Oregon metropolitan region to assess genetic diversity and structure, to identify putative source populations, and to conduct landscape genetic analyses. Resistance surfaces were created for each landscape feature, using ResistanceGA to optimize resistance parameters. My …

Sympatric Serpentine Endemic Monardella (Lamiaceae) Species Maintain Habitat Differences Despite Hybridization, Kathleen M. Kay, Suzie Woolhouse, Brett A. Smith, Nathaniel S. Pope, Nishanta Rajakaruna

Biological Sciences

Ecological differentiation and genetic isolation are thought to be critical in facilitating coexistence between related species, but the relative importance of these phenomena and the interactions between them are not well understood. Here, we examine divergence in abiotic habitat affinity and the extent of hybridization and introgression between two rare species of Monardella (Lamiaceae) that are both restricted to the same serpentine soil exposure in California. Although broadly sympatric, they are found in microhabitats that differ consistently in soil chemistry, slope, rockiness and vegetation. We identify one active hybrid zone at a site with intermediate soil and above-ground characteristics, and …

The Population Genetics Of Morro Bay Eelgrass (Zostera Marina), Julia Gardner Harencar

Master's Theses

Seagrass populations are in decline worldwide. Zostera marina (eelgrass), one of California’s native seagrasses, is no exception to this trend. In the last 8 years, Morro Bay, California has lost 95% of its eelgrass. Eelgrass is an ecosystem engineer, providing important ecosystem services such as sediment stabilization, nutrient cycling, and nursery habitats for fish. The failure of recent restoration efforts necessitates a better understanding of the causes of eelgrass decline in this estuary. Previous research on eelgrass in California has demonstrated a link between population genetic diversity and eelgrass bed health, ecosystem functioning, and resilience to disturbance and extreme climatic …

A Longitudinal Cline Characterizes The Genetic Structure Of Human Populations In The Tibetan Plateau, Choongwon Jeong, Benjamin M. Peter, Buddha Basnyat, Maniraj Neupane, Geoff Childs, Sienna Craig, John Novembre, Anna Di Rienzo

Dartmouth Scholarship

Indigenous populations of the Tibetan plateau have attracted much attention for their good performance at extreme high altitude. Most genetic studies of Tibetan adaptations have used genetic variation data at the genome scale, while genetic inferences about their de- mography and population structure are largely based on uniparental markers. To provide genome-wide information on population structure, we analyzed new and published data of 338 individuals from indigenous populations across the plateau in conjunction with world- wide genetic variation data. We found a clear signal of genetic stratification across the east- west axis within Tibetan samples. Samples from more eastern locations …

A Comparative Study Of Isolation In Headwater Fishes, Bjorn Victor Schmidt

Dissertations

Headwater resident fishes may be prone to a high rate of population fragmentation within river networks because large streams have habitat conditions outside of their preferred ecological niche and may limit gene flow in the dendritic ecological network. To investigate patterns of population structure, asymmetrical gene flow, and influences on genetic distance and isolation from connecting habitat pathways, species specific ecological traits, and basin scale characteristics, a multi-species, multi-regional study was performed. Six headwater species of fish from four taxonomic groupings were sampled for genetic material in three regions of paired neighbor drainages and then genotyped for eight microsatellite loci. …

What, If Anything, Are Hybrids: Enduring Truths And Challenges Associated With Population Structure And Gene Flow, Zachariah Gompert, C. Alex Buerkle

Biology Faculty Publications

Hybridization is a potent evolutionary process that can affect the origin, maintenance, and loss of biodiversity. Because of its ecological and evolutionary consequences, an understanding of hybridization is important for basic and applied sciences, including conservation biology and agriculture. Herein, we review and discuss ideas that are relevant to the recognition of hybrids and hybridization. We supplement this discussion with simulations. The ideas we present have a long history, particularly in botany, and clarifying them should have practical consequences for managing hybridization and gene flow in plants. One of our primary goals is to illustrate what we can and cannot …

The Relative Influence Of Habitat Amount And Configuration On Genetic Structure Across Multiple Spatial Scales, Katie L Millette, Nusha Keyghobadi

Biology Publications

Despite strong interest in understanding how habitat spatial structure shapes the genetics of populations, the relative importance of habitat amount and configuration for patterns of genetic differentiation remains largely unexplored in empirical systems. In this study, we evaluate the relative influence of, and interactions among, the amount of habitat and aspects of its spatial configuration on genetic differentiation in the pitcher plant midge, Metriocnemus knabi. Larvae of this species are found exclusively within the water-filled leaves of pitcher plants (Sarracenia purpurea) in a system that is naturally patchy at multiple spatial scales (i.e., leaf, plant, cluster, peatland). Using generalized linear …

Landscape Genetics Of The Endangered California Tiger Salamander (Ambystoma Californiense) In The Los Vaqueros Watershed, Ryan Neal Vincent

Mahurin Honors College Capstone Experience/Thesis Projects

Genetic diversity is essential for maintaining healthy biological systems, and dispersal-mediated gene flow increases genetic diversity by introducing new alleles to a gene pool. Populations that frequently experience gene flow will show characteristic similarities in allele frequencies. Measuring genetic diversity among many populations across a landscape has proven to be a powerful approach for assessing the ways that habitat discontinuities may affect patterns of gene flow, and in turn, influence allele frequencies and population dynamics. This study examines the landscape-level population genetic structure of the California tiger salamander, Ambystoma californiense, within the Los Vaqueros Watershed of Contra Costa County, …

Combining Demographic And Genetic Factors To Assess Population Vulnerability In Stream Species, Erin Landguth, C. C. Muhlfeld, R. S. Waples, L. Jones, Winsor H. Lowe, Diane C. Whited, J. Lucotch, H. Neville, Gordon Luikart

Biological Sciences Faculty Publications

Accelerating climate change and other cumulative stressors create an urgent need to understand the influence of environmental variation and landscape features on the connectivity and vulnerability of freshwater species. Here, we introduce a novel modeling framework for aquatic systems that integrates spatially explicit, individual-based, demographic and genetic (demogenetic) assessments with environmental variables. To show its potential utility, we simulated a hypothetical network of 19 migratory riverine populations (e.g., salmonids) using a riverscape connectivity and demogenetic model (CDFISH). We assessed how stream resistance to movement (a function of water temperature, fluvial distance, and physical barriers) might influence demogenetic connectivity, and hence, …

Population Genetics Of The Western Toad (Bufo Boreas) In The Central Valley Of California, Morgan Murrell

Mahurin Honors College Capstone Experience/Thesis Projects

A worldwide decline in amphibian populations has intensified the need for data comparing the influence of habitats on population dynamics and the potential for local extinction. From a conservation perspective it is important to understand the connections between ecology, geography, and genetics across landscapes that are increasingly affected by human influences and other uncontrollable environmental events such as climate change. The purpose of this study is to examine the landscape-level genetic patterns of Western toads, Bufo (Anaxyrus) boreas, and to conclude if gene flow is occurring between ponds. This will allow conservation practitioners to understand geographic features that might impede …

Pronounced Genetic Structure In A Highly Mobile Coral Reef Fish, Caesio Cuning, In The Coral Triangle, Amanda S. Ackiss, Shinta Pardede, Eric D. Crandall, Ma Carmen A. Ablan-Lagman, Ambariyanto, November Romena, Paul H. Barber, Kent E. Carpenter

Biological Sciences Faculty Publications

The redbelly yellowtail fusilier Caesio cuning has a tropical Indo-West Pacific range that straddles the Coral Triangle, a region of dynamic geological history and the highest marine biodiversity on the planet. Previous genetic studies in the Coral Triangle indicate the presence of multiple limits to connectivity. However, these studies have focused almost exclusively on benthic, reef-dwelling species. Schooling, reef-associated fusiliers (Perciformes: Caesionidae) account for a sizable portion of the annual reef catch in the Coral Triangle, yet to date, there have been no indepth studies on the population structure of fusiliers or other mid-water, reef-associated planktivores across this region. We …

Population Structure And Conservation Genetics Of The Oregon Spotted Frog, Rana Pretiosa, Michael S. Blouin, Ivan C. Phillipsen, Kirsten Monsen

Department of Biology Faculty Scholarship and Creative Works

The Oregon spotted frog (Rana pretiosa) is one of the most threatened amphibians in the Pacific Northwest. Here we analyzed data from 13 microsatellite loci and 298 bp of mitochondrial DNA in frogs collected from 23 of the remaining R. pretiosa populations in order to (1) assess levels of genetic diversity within populations of R. pretiosa, (2) identify the major genetic groups in the species, (3) estimate levels of genetic differentiation and gene flow among populations within each major group, and (4) compare the pattern of differentiation among R. pretiosa populations with that among populations of R. cascadae, a non-endangered …

Microsatellite Development, Population Structure And Demographic Histories For Two Species Of Amazonian Peacock Bass Cichla Temensis And Cichla Monoculus (Perciformes: Cichlidae)., Jason C. Macrander

School of Biological Sciences: Dissertations, Theses, and Student Research

The Neotropics of South America represent one of the most diverse assemblages of freshwater organisms in the world. The geologic and ecological changes that have occurred throughout the Amazon and Orinoco River basins have resulted in the two most diverse rivers in the world producing very heterogeneous environments potentially influencing current population structure of Neotropical species. To investigate specific ecological and geological events influencing populations in these regions, I explore population structure and demographic histories of two species from the genus Cichla with wide distributions among the Amazon and Orinoco. First, I describe the methods used to isolate and characterize …

Evolution And Maintenance Of Plumage Polymorphism: The Case Of The Red-Footed Booby (Sula Sula), Patricia Carvalho Baiao

Dissertations

The red-footed booby (Sula sula) is considered one of the most polymorphic seabirds, with three recognized major adult plumage types: (1) white; (2) white-tailed brown; and (3) brown, and several degrees of intermediates. The ratio of these color morphs varies among populations, with the white morph typically predominating. However, there are a few populations that present an inversed ratio of color morphs, such as Isla Europa in the Indian Ocean and the Galapagos archipelago, with the white-tailed brown or brown morphs predominating. I studied natural populations of red-footed boobies from three geographic locations, namely, the Galapagos archipelago, Johnston Atoll in …

Genetic And Phenotypic Evolution In The Ornate Chorus Frog (Pseudacris Ornata): Testing The Relative Roles Of Natural Selection,, Jacob Degner

Electronic Theses and Dissertations

Understanding how migration, genetic drift, and natural selection interact to maintain the genetic and phenotypic variation we observe in natural populations is a central goal of population genetics. Amphibians provide excellent model organisms for investigating the interplay between these evolutionary forces because amphibians are generally characterized by limited dispersal abilities, high philopatry, and are obligately associated with the areas around suitable habitats (e.g. breeding ponds). Thus, on relatively small geographic scales, the relative effects of all of these evolutionary forces can be studied together. Here, we study the interaction of migration, genetic drift, natural selection, and historical process in the …

Linking Direct And Indirect Data On Dispersal: Isolation By Slope In A Headwater Stream Salamander, Winsor H. Lowe, Gene E. Likens, Mark A. Mcpeek, Don C. Buso

Dartmouth Scholarship

There is growing recognition of the need to incorporate information on movement behavior in landscape-scale studies of dispersal. One way to do this is by using indirect indices of dispersal (e.g., genetic differentiation) to test predictions derived from direct data on movement behavior. Mark–recapture studies documented upstream-biased movement in the salamander Gyrinophilus porphyriticus (Plethodontidae). Based on this information, we hypothesized that gene flow in G. porphyriticus is affected by the slope of the stream. Specifically, because the energy required for upstream dispersal is positively related to slope, we predicted gene flow to be negatively related to change in elevation between …

Molecular Population Genetics Of The Atlantic Sand Fiddler Crab, Uca Pugilator, Along The Atlantic Coast, David A. Weese

Electronic Theses and Dissertations

Author's abstract: The Atlantic sand fiddler crab, Uca pugilator, is an extremely abundant fiddler crab found along the eastern and Gulf coast of the United States. Fiddler crabs have a life cycle with an obligatory planktonic larval phase of 30-90 days, which might be expected to lead to widespread larval dispersal and consequent genetic homogeneity over considerable distances. However a large amount of morphological and behavioral variation is found between northern and southern populations along the eastern coast. This study was undertaken to determine the population genetic structure of U. pugilator and to determine whether these differences may have a …

Gene Flow Among Habitat Patches On A Fragmented Landscape In The Spider Argiope Trifasciata (Araneae: Araneidae), Martina G. Ramirez, Kirsten E. Haakonsen

Biology Faculty Works

The banded garden spider (Argiope trifasciata) is a common orb weaver of old field habitats in the United States. In this study, we determined levels of genetic variability and gene flow among seven populations in central Pennsylvania, based on variation at eight allozyme loci. Mean heterozygosity (observed) per population was 7.5% and mean polymorphism was 39.3%, consistent with levels of variability in other arthropods. Values of GST for the four polymorphic loci (mean G_ST=0.011) suggest that gene flow prevents the genetic differentiation of these populations. The average number of migrants per generation (Nm) among …

The Influence Of Dispersal And Diet Breadth On Patterns Of Genetic Isolation By Distance In Phytophagous Insects, Merrill A. Peterson

Biology Faculty and Staff Publications

To determine the effects of dispersal ability and diet breadth on population-genetic structure, we reviewed the allozyme literature and estimated genetic isolation by distance (IBD) for 43 species/host races of phytophagous insects. Subsequently, we tested two opposing hypotheses regarding the influence of dispersal ability on IBD: that IBD slopes do not vary with mobility, but that intercepts increase with mobility, and, alternatively, that IBD slopes vary with dispersal ability. We found that from tens of kilometers to more than 1,000 km, IBD is weak in sedentary and highly mobile species but pronounced in moderately mobile species. We attribute the weak …

Genetic Variation Within And Among Populations Of Florida Burrowing Owls (Athene Cunicularia Floridana), Wendy T. Denton

Legacy ETDs

This study employed DNA Polymerase Chain Reaction (PGR) and Single-Stranded Conformation Polymorphisms (SSCP) on a mitochondrial control region target to assess population structure and possible gene flow in the Florida Burrowing Owl (Athene cunicularia floridana), a Florida Species of Special Concern. Although widespread in Florida, Burrowing Owls occur at low densities in semi-isolated populations that are susceptible to extirpation from human development and the demographic consequences of small population size. To better manage these populations, there is a need for data on the population genetic structure of the Florida Burrowing Owl. Therefore, I acquired DNA from Burrowing Owls …

The Use Of Banding Recovery Data To Estimate Dispersal Rates And Gene Flow In Avian Species: Case Studies In The Red-Winged Blackbird And Common Grackle, William S. Moore, Richard A. Dolbeer

Biological Sciences Faculty Research Publications

Dispersal resulting in gene flow strongly affects the evolution of genetic structure in populations. This report describes statistical estimators of dispersal parameters based on USFWS banding recovery records. Finite-area studies of avian species yield estimates of root-mean-square (RMS) dispersal along a transect of about 1 km per generation. In contrast, estimates of RMS dispersal for the Red-winged Blackbird (Agelaius phoeniceus) and Common Grackle (Quiscalus quiscula), based on USFWS banding recovery records, are 94.6 and 111.4 km per generation, respectively. Distributions for both species are extremely leptokurtic, and confidence intervals based on jackknife statistics are large because the estimators are sensitive …

Amount And Distribution Of Isozyme Variation In Ponderosa Pine From Eastern Montana, John Herbert Woods, G. M. Blake, Fred W. Allendorf

Biological Sciences Faculty Publications

Pinus ponderosa seeds from 50 trees in each of six small isolated stands located within a nine kilometer radius of Colstrip, Montana, were examined at 23 isozyme loci. Megagametophyte and embryo tissue from each seed were screened separately. Measures of genetic diversity showed no significant differences between male and female components within or between stands. The average proportion of heterozygous loci per embryo (H_e) was not significantly different between stands. For all stands combined, H_e was 0.012. Genotype proportions did not deviate from expected Hardy-Weinberg proportions.

Nearly 99 % of the genetic diversity resided within individual stands, …

The Columbia River As A Barrier To Gene Flow In The Vagrant Shrew, Sorex Vagrans Vagrans Baird, James J. Kirk

Dissertations and Theses

Twenty-one morphological characters were measured in shrews from four islands in the Columbia River and from the adjacent Oregon and Washington shores. Information on the history and characteristics of the river islands was gathered to facilitate interpretation of the shrew’s morphology data. Significant differences between character means of different populations were detected and average taxonomic distances between pairs of populations were calculated. The Columbia River is an incomplete barrier to gene flow, but its influence has been sufficient to allow divergence of island populations. Natural selection on the small gene pools of island populations has probably contributed to the divergence. …