Ecology and Evolutionary Biology Commons^™

Field Evidence Challenges The Often-Presumed Relationship Between Early Male Maturation And Female-Biased Sexual Size Dimorphism, Marie Claire Chelini, Eileen Hebets

Eileen Hebets Publications

Female-biased sexual size dimorphism (SSD) is often considered an epiphenomenon of selection for the increased mating opportunities provided by early male maturation (i.e., protandry). Empirical evidence of the adaptive significance of protandry remains nonetheless fairly scarce. We use field data collected throughout the reproductive season of an SSD crab spider, Mecaphesa celer, to test two hypotheses: Protandry provides fitness benefits to males, leading to female-biased SSD, or protandry is an indirect consequence of selection for small male size/large female size. Using field-collected data, we modeled the probability of mating success for females and males according to their timing of …

Tracing The Genetic Footprints Of The Redbelly Yellowtail Fusilier, Caesio Cuning, Across Multiple Spatial And Evolutionary Scales, Amanda Susanne Ackiss

Biological Sciences Theses & Dissertations

Overfishing is one of the most pervasive threats to coral reef ecosystems, and management of these multi-species resources is hampered by limited species-specific population level information. The reefs in the western tropical Pacific Ocean, including the Coral Triangle, are the most bio-diverse in the world. Home to more than 400 million people, this region contains some of the most threatened coral reef ecosystems. Presented here is the first comprehensive analysis of the genetic structure of Caesio cuning, planktivorous fish inhabiting reefs in the Coral Triangle and western Pacific Ocean. Data from both classical Sanger and next-generation sequencing were analyzed …

Population Structure Of Lethrinus Lentjan (Lethrinidae, Percoidei) Across The South China Sea And The Philippines Is Detected With Lane-Affected Radseq Data, Ellen E. Biesack

Biological Sciences Theses & Dissertations

Southeast Asia includes the Coral Triangle, a marine biodiversity hotspot that supports important fishery resources experiencing varied threats. Patterns of speciation and population structure in the Coral Triangle have been examined to test hypotheses relating to the historical geologic processes that may have influenced this biodiversity phenomenon. This study investigates the genetic population structure of the Pink-ear Emperor Snapper, Lethrinus lentjan (Lacepède, 1802), across the Philippines and the South China Sea. The species is fished throughout the Coral Triangle by subsistence and commercial fishers and their landings have been in decline for several years, which could be indicative of depleted …

Mitochondrial Phylogenomics Of Hemiptera Reveals Adaptive Innovations Driving The Diversification Of True Bugs, Hu Li, John Moeller Leavengood Jr., Eric G. Chapman, Daniel Burkhardt, Fan Song, Pei Jiang, Jinpeng Liu, Xuguo Zhou, Wanzhi Cai

Entomology Faculty Publications

Hemiptera, the largest non-holometabolous order of insects, represents approximately 7% of metazoan diversity. With extraordinary life histories and highly specialized morphological adaptations, hemipterans have exploited diverse habitats and food sources through approximately 300 Myr of evolution. To elucidate the phylogeny and evolutionary history of Hemiptera, we carried out the most comprehensive mitogenomics analysis on the richest taxon sampling to date covering all the suborders and infraorders, including 34 newly sequenced and 94 published mitogenomes. With optimized branch length and sequence heterogeneity, Bayesian analyses using a site-heterogeneous mixture model resolved the higher-level hemipteran phylogeny as (Sternorrhyncha, (Auchenorrhyncha, (Coleorrhyncha, Heteroptera))). Ancestral character …

Comparative Phylogeographic, Population Genomic, And Selection Inference With Development Of Hierarchical Co-Demographic Models, Alexander Xue

Dissertations, Theses, and Capstone Projects

Comparing demographic histories across assemblages of populations, species, and sister pairs has been a focus in phylogeography since its inception. Initial approaches utilized organelle genetic data and involved qualitative comparisons of genetic patterns for evaluating hypotheses of shared evolutionary responses to past environmental changes. This endeavor has progressed with coalescent model-based statistical techniques and advances in next-generation sequencing, yet there remains a need for methods that can analyze aggregated genomic-scale data from non-model organisms within a unified framework that considers individual taxon uncertainty and variance. To this end, the aggregate site frequency spectrum (aSFS), an expansion of the site frequency …

Large-Scale Differences In Microbial Biodiversity Discovery Between 16s Amplicon And Shotgun Sequencing, Michael Tessler, Johannes S. Neumann, Ebrahim Afshinnekoo, Michael Pineda, Rebecca Hersch, Luiz Felipe M. Velgo, Bianca T. Segovia, Fabio A. Lansac-Toha, Michael Lemke, Rob Desalle, Christopher E. Mason, Mercer R. Brugler

Publications and Research

Modern metagenomic environmental DNA studies are almost completely reliant on next-generation sequencing, making evaluations of these methods critical. We compare two next-generation sequencing techniques – amplicon and shotgun – on water samples across four of Brazil’s major river floodplain systems (Amazon, Araguaia, Paraná, and Pantanal). Less than 50% of phyla identified via amplicon sequencing were recovered from shotgun sequencing, clearly challenging the dogma that mid-depth shotgun recovers more diversity than amplicon-based approaches. Amplicon sequencing also revealed ~27% more families. Overall the amplicon data were more robust across both biodiversity and community ecology analyses at different taxonomic scales. Our work doubles …

Draft Genome Sequence Of Bacillus Altitudinis Ynp4-Tsu, Isolated From Yellowstone National Park, Joshua A. O'Hair, Hui Li, Santosh Thapa, Matthew Scholz, Suping Zhou

Agricultural and Environmental Sciences Faculty Research

Undisturbed hot springs inside Yellowstone National Park remain a dynamic biome for novel cellulolytic thermophiles. We report here the draft genome sequence of one of these isolates, Bacillus altitudinis YNP4-TSU.

Analysis Of Population Structure In A California Newt (Taricha Torosa) Metapopulation, Jessica Vincent

Mahurin Honors College Capstone Experience/Thesis Projects

As anthropogenic influences take an ever-increasing toll on the environment, understanding how environmental change affects species is paramount. Concern regarding decline in amphibian populations has spurred research examining the effects of habitat change on the dynamics of populations at landscape levels. One important goal is to understand how gene flow among populations is affected by changes in habitat. Biologists need to consider the relationship between gene flow and habitat alterations so that movements among individual breeding ponds can be maintained over time, reducing risk of local extinction events. This study focuses on patterns of gene flow among thirteen populations of …

Naturally-Derived Molecular Ensembles In Medicine, Materials Science And Evolutionary Biology: An Interdisciplinary Study, Silvio Panettieri

Dissertations, Theses, and Capstone Projects

The first chapter will introduce the work carried out in collaboration with the Govind laboratory at CCNY. Our quest was set forth to investigate the intimate relationship lying between chronic inflammation and tumor development. For at least the last fifteen years much research has been conducted on this topic; yet, the level of complexity arising from exceedingly interwoven biochemical pathways in mammals has resulted in slow advancements in this field. This is why we resorted to a simple yet powerful immunogenetic model organism, the fruit fly Drosophila melanogaster, in combination with the administration of the most common anti-inflammatory drug, …

Lichen Conservation In Eastern North America: Population Genomics, Climate Change, And Translocations, Jessica Allen

Dissertations, Theses, and Capstone Projects

Conservation biology is a scientific discipline that draws on methods from diverse fields to address specific conservation concerns and inform conservation actions. This field is overwhelmingly focused on charismatic animals and vascular plants, often ignoring other diverse and ecologically important groups. This trend is slowly changing in some ways; for example, increasing number of fungal species are being added to the IUCN Red-List. However, a strong taxonomic bias still exists. Here I contribute four research chapters to further the conservation of lichens, one group of frequently overlooked organisms. I address specific conservation concerns in eastern North America using modern methods. …

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 …

The Santa Ana Speckled Dace (Rhinichthys Osculus): Phylogeography And Molecular Evolution Of The Mitochondrial Dna Control Region, James Jay Vanmeter

Electronic Theses, Projects, and Dissertations

The purpose of this genetic study of the Santa Ana Speckled Dace Rhinichthys osculus was three-fold. The first goal was to characterize the molecular structure of the mtDNA control region of R. osculus. An 1143 base-pair region of the mitochondrial DNA genome, which included the complete control region was sequenced for all individuals. Analysis of the sequence data revealed that the molecular structure of the speckled dace control region was similar to the molecular structure described for other vertebrate taxa. The speckled dace control region contains three major domains, which vary in base frequency as well as in the frequency …

Software Development For Genome Sequence Analysis, David Farr

Symposium Of University Research and Creative Expression (SOURCE)

The cost of genome sequencing has decreased rapidly, expanding availability for many biological applications (Muir 2016). For example, researchers can now obtain genome sequences from multiple populations under different types of selection. Comparison of these sequences allows for identification of chromosome regions and specific genes associated with adaptive evolution (Kelly 2013). As an increasing number of researchers engage in this type of inquiry, many have created in-house computer scripts to analyze the raw sequence data (e.g., Kelly 2013), creating a gap in both continuity and standardization.

Using a test dataset and preliminary results from an ongoing artificial selection experiment in …

Does Genotype Correlate With Phenotype? Evaluating Ruffed Lemur (Varecia Spp.) Color Vision Using Subject Mediated Automatic Remote Testing Apparatus (Smarta), Raymond Vagell

Theses and Dissertations

Ruffed lemur (Varecia spp.) color vision research was conducted using a multidisciplinary approach: psychophysics, genetic analysis, technology, and animal training. The behavioral manifestation of Varecia spp. trichromacy was shown using a touchscreen apparatus (SMARTA). Trichromats performed better than dichromats when discriminating red from green (G₂ = 78.10, p < 0.001).

Population Structure, Connectivity, And Phylogeography Of Two Balistidae With High Potential For Larval Dispersal: Balistes Capriscus And Balistes Vetula, Luca Antoni

Dissertations

The gray triggerfish (Balistes capriscus) and the queen triggerfish (Balistes vetula) are two exploited reef fish distributed in tropical and temperate shelf waters of the Atlantic Ocean and the Mediterranean Sea. Both species are highly sedentary as adults but disperse pelagic larvae for extended periods of time potentially allowing connectivity across long distances under the action of oceanic currents. In this work population structure, phylogeography, and migration patterns were examined in the two species and contrasted with predictions of larval transport based on surface circulation data. A total of 1,017 gray triggerfish from twelve sampling localities …

Investigating The Genetic Basis For Hominoid Taillessness, Samantha M. Tickey-Mccrane, Holly Dunsworth, Johanna E. Wegener

Senior Honors Projects

Investigating the Genetic Basis for Hominoid Taillessness:

A Comparative Genetic Approach Across Ten Catarrhine Taxa

Samantha Tickey-McCrane1,2, Johanna E. Wegener2, and Holly Dunsworth1

Honors Thesis Abstract Written by Samantha Tickey-McCrane, Departments of Anthropology & Biology

Advisor: Dr. Holly Dunsworth, Department of Anthropology

How did hominoid tail loss occur? My goals are to test phylogenetic and adaptive hypotheses for tail length variation among macaques, and use those insights to reconstruct the evolution of hominoid taillessness. Further, I aim to ultimately uncover which candidate genes or pathways may be responsible for catarrhine tail loss, and what other traits may be affected by …

Development Of Site Fidelity In The Nocturnal Amblypygid, Phrynus Marginemaculatus, Jacob M. Graving, Verner P. Bingman, Eileen Hebets, Daniel D. Wiegmann

Eileen Hebets Publications

Amblypygids are capable of navigation in the complex terrain of rainforests in near complete darkness. Path integration is unnecessary for successful homing, and the alternative mechanisms by which they navigate have yet to be elucidated. Here, our aims were to determine whether the amblypygid Phrynus marginemaculatus could be trained to reliably return to a target shelter in a laboratory arena—indicating goal recognition—and to document changes in behavior associated with the development of fidelity. We recorded nocturnal movements and space use by individuals over five nights in an arena in which subjects were provided with two shelters that differed in quality. …

Phylogenetic Studies Of The Madagascan Freshwater Crabs (Potamoidea, Potamonautidae, Deckeniinae), Rainee Stevens

All NMU Master's Theses

Relationships within the Madagascan freshwater crab fauna were examined based on unstudied specimens from all parts of Madagascar. This study allowed the examination of the validity of existing genera and species, and identified potential new taxa. The new specimens provided phylogenetic and evolutionary data, as well as new insights into the distribution patterns of the Malagasy freshwater crab fauna. In addition, the large number of new localities from previously unsurveyed areas of Madagascar allowed the construction of updated distribution maps.

The present analysis included 62 unidentified specimens plus 13 identified species of Malagasy freshwater crab taxa that had already been …

Draft Genome Sequences Of Three Cellulolytic Bacillus Licheniformis Strains Isolated From Imperial Geyser, Amphitheater Springs, And Whiterock Springs Inside Yellowstone National Park, Joshua A. O'Hair, Hui Li, Santosh Thapa, Matthew Scholz, Suping Zhou

Agricultural and Environmental Sciences Faculty Research

Novel cellulolytic microorganisms are becoming more important for rapidly growing biofuel industries. This paper reports the draft genome sequences of Bacillus licheniformis strains YNP2-TSU, YNP3-TSU, and YNP5-TSU. These cellulolytic isolates were collected from several hydrothermal features inside Yellowstone National Park.

Species Delimitation And Lineage Separation History Of A Species Complex Of Aspens In China, Honglei Zheng, Liqiang Fan, Richard I. Milne, Lei Zhang, Yaling Wang, Kangshan Mao

Aspen Bibliography

Species delimitation in tree species is notoriously challenging due to shared polymorphisms among species. An integrative survey that considers multiple operational criteria is a possible solution, and we aimed to test it in a species complex of aspens in China. Genetic [four chloroplast DNA (cpDNA) fragments and 14 nuclear microsatellite loci (nSSR)] and morphological variations were collected for 76 populations and 53 populations, respectively, covering the major geographic distribution of the Populus davidiana-rotundifoliacomplex. Bayesian clustering, analysis of molecular variance (AMOVA), Principle Coordinate Analysis (PCoA), ecological niche modeling (ENM), and gene flow (migrants per generation), were employed to …

Patterns Of Morphological And Molecular Evolution In The Antillean Tree Bat, Ardops Nichollsi (Chiroptera: Phyllostomidae), Roxanne J. Larsen, Peter A. Larsen, Caleb D. Phillips, Hugh H. Genoways, Gary G. Kwiecinski, Scott C. Pedersen, Carleton J. Phillips, Robert J. Baker

University of Nebraska State Museum: Mammalogy Papers

Species endemic to oceanic islands offer unique insights into the mechanisms underlying evolution and have served as model systems for decades. Often these species show phenotypic variation that is correlated with the ecosystems in which they occur and such correlations may be a product of genetic drift, natural selection, and/or environmental factors. We explore the morphologic and genetic variation within Ardops nichollsi, a species of phyllostomid bat endemic to the Lesser Antillean islands. Ardops nichollsi is an ideal taxon to investigate the tempo of evolution in Chiroptera, as it: is a recently derived genus in the family Phyllostomidae; contains …

Taxonomic Placement Of The Nidulariaceae Of Nebraska And Iowa Based On Molecular And Morphological Data, Goodmond H. Danielsen Iv

UNO Student Research and Creative Activity Fair

Proper taxonomic and molecular study is necessary to better organize closely related species that may not only be used for human needs, but also in the quest for knowledge of how the world around us works. Though important, the taxonomic placement of Nebraskan and Iowan bird’s nest fungi (Nidulariaceae) is not well documented. Here, phylogenetic analysis is used to place the Nidulariaceae of Nebraska and Iowa in the tree of life using molecular and morphological techniques. Based on these results and results of further work done on these specimens, it will be possible to better place the Nidulariaceae of Nebraska …

An Assessment Of Potential False Positive E.Coli Pyroprints In The Cplop Database, Skyler A. Gordon

Master's Theses

The genetic information found in each species of organism is unique, and can be used as a tool to differentiate at the molecular level. This has caused rapid genotyping methods to become the cornerstone of a new area of research dependent on reading the genome as a form of identification. One of these specific identification methods, known as pyroprinting, relies on the small variation of DNA sequences within the same species to develop a unique, reproducible fingerprint. By simultaneously pyrosequencing multiple polymorphic loci within the ribosomal operons known as the intergenic transcribed spacers, a reproducible output is obtained, known as …

The Subject Librarian Newsletter, Biology, Spring 2017, Sandy Avila

Libraries' Newsletters

No abstract provided.

Restoration Of The Iconic Pando Aspen Clone: Emerging Evidence Of Recovery, Paul C. Rogers, Jody A. Gale

Aspen Bibliography

Quaking aspen (Populus tremuloides Michx.) is being stressed across the America West from a variety of sources including drought, herbivory, fire suppression, development, and past management practices. Rich assemblages of plants and animals that utilize aspen forests, as well as economic values of tourism, grazing, hunting, and water conservation, make aspen ecosystems among the most valuable vegetation types in this region. The 43-ha Pando clone near Fish Lake, Utah, is an iconic example of an aspen community undergoing rapid decline due to overstory mortality and chronic recruitment failure. As part of a larger project to restore Pando, we fenced, …

Mrub_2642, Mrub_1054, And Mrub_1059 Genes Are Orthologs Of The Escherichia Coli Genes B2942, B0159, And B2687 Genes, Respectively, Which Code For Methionine Adenosyltransferase, Adenosylhomocysteine Nucleosidase, And S-Ribosylhomocysteine Lyase, Nicholas M. Orslini, Dr. Lori R. Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_2642, Mrub_1054, and Mrub_1059.

We predict that Mrub_2642 encodes the enzyme methionine adenosyltransferase (DNA coordinates [2677251…2678426] on the reverse strand), the first step of the methionine degradation pathway (KEGG map number 00270). Methionine adenosyltransferase catalyzes the conversion of the substrates, ATP, L-methionine, and water, to yield the products S-adenosyl-L-methionine (SAM), inorganic phosphate, and diphosphate. Mrub_1054 encodes adenosylhomocysteine nucleosidase (DNA …

Mrub_1867, Mrub_1868, And Mrub_1869 Genes Are Predicted Orthologs Of The B2279, B2280, And B2281 Genes Found In Escherichia Coli Coding For The Nadh Dehydrogenase Subunits K, J, And I Respectively, Wade Smith, Dr. Lori R. Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_1867, Mrub_1868, and Mrub_1869. We predict that Mrub_1867 (DNA coordinates 1927237..1927527 on the reverse strand), Mrub_1868 (DNA coordinates 1927524..1928123 on the reverse strand), and Mrub_1869 (DNA coordinates 1928248..1928781 on the reverse strand) are subunits of the NADH: ubiquinone oxidoreductase complex (KEGG map number 00190). This complex catalyzes the translocation of H+ across the cytoplasmic …

Fisheries Management Paper No.283 - Abalone Resource Of Western Australia Harvest Strategy 2106 - 2021, Department Of Fisheries Western Australia

Fisheries Management Papers

Harvest strategies for aquatic resources managed by the Western Australian Department of Fisheries (the Department) are formal documents prepared to support the decision-making processes required to ensure the management of these resources are consistent with the principles of Ecologically Sustainable Development (ESD). The objectives of ESD are reflected in the objects of the Fish Resources Management Act 1994 (FRMA) and Section 9 of the Aquatic Resources Management Act, which will replace the FRMA once proclaimed.

The publication of these strategies is intended to make the decision-making considerations and processes for the management of specified aquatic resources publicly transparent and provide …

Increased Insertion Number Leads To Increased Sperm Transfer And Fertilization Success In A Nursery Web Spider, Alissa G. Anderson, Eileen Hebets

Eileen Hebets Publications

Across animals, a male's fitness is largely dictated by his ability to fertilize eggs; and there exists a plethora of male adaptations associated with increasing fertilization success. In the nursery web spider, Pisaurina mira, males restrain females prior to and during copulation by wrapping them with silk. Previous research demonstrates that copulatory silk wrapping reduces a male's chance of being sexually cannibalized and increases the number of sperm transfer opportunities (termed insertions) that a male can achieve within a mating. While avoiding cannibalism provides an obvious survival benefit to males, the impact of insertion number on male fitness remains …

Importance Of The Antenniform Legs, But Not Vision, For Homing By The Neotropical Whip Spider Paraphrynus Laevifrons, Verner P. Bingman, Jacob M. Graving, Eileen Hebets, Daniel D. Wiegmann

Eileen Hebets Publications

Amblypygids, or whip spiders, are nocturnal, predatory arthropods that display a robust ability to navigate to their home refuge. Prior field observations and displacement studies in amblypygids demonstrated an ability to home from distances as far away as 10 m. In the current study, micro-transmitters were used to take morning position fixes of individual Paraphrynus laevifrons following an experimental displacement of 10 m from their home refuge. The intention was to assess the relative importance of vision compared with sensory input acquired from the antenniform legs for navigation as well as other aspects of their spatial behavior. Displaced individuals were …