Biology Commons^™

Reef Fish Biodiversity In The Florida Keys National Marine Sanctuary, Megan E. Hepner

USF Tampa Graduate Theses and Dissertations

The biological diversity of reef-fish in the Florida Keys National Marine Sanctuary (FKNMS) from 1999 – 2016 was evaluated in terms of abundance, biomass, species richness, evenness, Shannon diversity, Simpson diversity, and functional diversity, using observations collected by multiple agencies and institutions under the Reef Visual Census (RVC) program. To compare the different diversity indices species richness, Shannon diversity, Simpson diversity, and functional diversity were converted into effective number of species. I examined the seven indices by no-take marine zones, in seven benthic habitat strata, and across the three-distinct geographic subregions in the Florida Keys domain (Upper, Middle, and Lower …

The Parasite Extinction Assessment & Red List: An Open-Source, Online Biodiversity Database For Neglected Symbionts, Colin J. Carlson, Oliver C. Muellerklein, Anna J. Phillips, Kevin R. Burgio, Giovanni Castaldo, Carrie A. Cizauskas, Graeme S. Cumming, Tad Dallas, Jorge Doña, Nyeema Harris, Roger Jovani, Zhongqi Miao, Heather Proctor, Hyun Seok Yoon, Wayne M. Getz

Faculty Publications

Parasite conservation is a rapidly growing field at the intersection of ecology, epidemiology, parasitology, and public health. The overwhelming diversity of parasitic life on earth, and recent work showing that parasites and other symbionts face severe extinction risk, necessitates infrastructure for parasite conservation assessments. Here, we describe the release of the Parasite Extinction Assessment & Red List (PEARL) version 1.0, an open-access database of conservation assessments and distributional data for almost 500 macroparasitic invertebrates. The current approach to vulnerability assessment is based on range shifts and loss from climate change, and will be expanded as additional data (e.g., host-parasite associations …

Negative Density Dependence Mediates Biodiversity–Productivity Relationships Across Scales, Joseph A. Lamanna, R Travis Belote, Laura A. Burkle, Christopher P. Catano, Jonathan A. Myers

Biology Faculty Research

Regional species diversity generally increases with primary productivity whereas local diversity–productivity relationships are highly variable. This scale-dependence of the biodiversity–productivity relationship highlights the importance of understanding the mechanisms that govern variation in species composition among local communities, which is known as β-diversity. Hypotheses to explain changes in β-diversity with productivity invoke multiple mechanisms operating at local and regional scales, but the relative importance of these mechanisms is unknown. Here we show that changes in the strength of local density-dependent interactions within and among tree species explain changes in β-diversity across a subcontinental-productivity gradient. Stronger conspecific relative to …

Using Maximum Entropy Species Distribution Modeling For Long-Term Conservation Planning Of Three Federally Listed Bats In North America, Mitchell L. Meyer

Master's Theses or Doctor of Nursing Practice

We are currently in a sixth mass extinction event in which the extinction rate is higher than it has ever been. This mass extinction event is caused by human influence on the environment. Biodiversity is worth conserving because of its many uses to humans. Bats are a diverse group of mammals that humans rely on for pest control services. The gray bat, northern long-eared bat, and Indiana bat are on the Threatened and Endangered Species List and are in need of conservation. I built species distribution models using occurrence records, climate data, and Maximum entropy (MaxEnt) modeling technique. I predicted …

Vegetation Community Changes In Two National Forests In The Pineywoods, East Texas, Trisha L. Williams

Electronic Theses and Dissertations

Despite extensive research into forest succession, little research has been directed to long-term studies. The fundamental properties of succession remain unclear and further research into terrestrial vegetation and an accounting of drivers in specific ecosystem types is required. This study addresses change in plant communities from five ecosystem types in two east Texas National Forests over a 20-year period. An analysis of 30 sample stands yields results due to various ecosystem drivers of vegetation change and uncovers plant community responses in multiple ecosystem types over this period. This research provided three key results: 1) that vegetation composition change occurs more …

Presence/Absence And Density Data For Epipelagic Tows From 48 Stations In The Northern Gulf Of Mexico From R/V Blazing Seven Cruises Lf2015a And Lf2015b June 2015 And July 2015, Jay R. Rooker, R.J. David Wells

DEEPEND Datasets

Larval catch data after the oil spill is being used to improve our understanding of the causes of temporal variability as it relates to the Deep Water Horizon oil spill (DWHOS). Bongo and neuston net tows were conducted at 48 stations in both June and July, 2015 in the northern Gulf of Mexico. Cruise data collected at each site included latitude/longitude, date, time and environmental data (temperature, salinity, dissolved oxygen). The occurrence and density of selected epipelagic (e.g., billfishes, tunas, dolphinfishes, flyingfishes) and deep pelagic (e.g., lanternfishes, bristlemouths, marine hatchetfishes) fish larvae were quantified and are being used to extend …

Do The Shuffle: Changes In Symbiodinium Consortia Throughout Juvenile Coral Development, Hannah G. Reich, Deborah L. Robertson, Gretchen Goodbody-Gringley

Biology

Previous studies of symbiotic associations between scleractinians corals and Symbiodinium have demonstrated that the consortium of symbionts can change in response to environmental conditions. However, less is known about symbiont shuffling during early coral development, particularly in brooding species. This study examined whether Symbiodinium consortia (1) varied in Porites astreoides on shallow (10m) and upper mesophotic (30m) reefs, (2) changed during coral development, and (3) influenced growth of juveniles in different environments. Symbiodinium ITS2 sequences were amplified using universal primers and analyzed using phylotype-specific primers designed for phylotypes A, B, and C. Adults from both depths were found to host …

An On-Campus Botanical Tour To Promote Student Satisfaction And Learning In A University Level Biodiversity Or General Biology Course, Harish H. Ratnayaka

Faculty and Staff Publications

Outdoor, hands-on and experiential learning, as opposed to instruction-based learning in classroom, increases student satisfaction and motivation leading to a deeper understanding of the subject. However, the use of outdoor exercises in undergraduate biology courses is declining due to a variety of constraints. Thus, the goal of this paper is to describe a convenient, no-cost and flexible exercise using an on-campus botanical tour for strengthening specific knowledge areas of major plant groups. Its assessment on conduct and coverage, and student-perceived and actual knowledge gain is also described. Data presented derived from traditional biology undergraduates in sophomore year over nine fall …

Komarekiella Atlantica Gen. Et Sp. Nov. (Nostocaceae, Cyanobacteria): A New Subaerial Taxon From The Atlantic Rainforest And Kauai, Hawaii, Jeffrey R. Johansen, Guilherme Scotta Hentschke, Nicole Pietrasiak, Janaina Rigonato, Marli F. Fiore, Célia Leite Sant’Anna

2017 Faculty Bibliography

Six strains of Cyanobacteria sampled in the Brazilian Atlantic rainforest and one strain from Kauai, Hawaii, were studied using morphological and molecular approaches, including 16S rRNA gene phylogenies and 16S–23S ITS secondary structures, and are herein described as Komarekilla atlantica gen. et sp. nov.. Morphologically they are similar to Nostoc, Desmonostoc, Halotia, and Mojavia and indistinguishable from Chlorogloeopsis. The parsimony and Bayesian phylogenies of the 16S rDNA show that these strains are close to nostocacean strains, in strongly supported clades and separated from all other genera. The secondary structures of the 16S–23S ITS were very consistent between strains of K. …

Diversity And Evolution Of Fruits In Cuscuta (Dodders; Convolvulaceae), Anna Ho

Theses and Dissertations (Comprehensive)

Cuscuta (dodder) is a genus of roughly 200 species of obligate stem parasites with sub-cosmopolitan distribution. The fruit, generally regarded as a capsule, has a thin pericarp containing one to four seeds and opening at the base (circumscissile dehiscence; DE), or remaining closed (indehiscent; IN). IN has evolved multiple times in Cuscuta from DE, and is most common in the North American clades of subgenus Grammica. In addition, some species produce fruits that open irregularly. Characteristics pertaining to the fruits of Cuscuta are important as their seeds contribute most to their distribution and prevalence across the globe, and their reduced …

Mitigating The Impacts Of Human Land-Use Change On Biodiversity: With A Focus On Large Migratory Herbivores, Kina Rebekah Murphy

Biology ETDs

Land-use change, commercial over-harvesting of species, and climate change are recognized as the main drivers of biodiversity loss. As a result, it is estimated that 30% of the planet’s biodiversity may go extinct by 2050. This dissertation focuses on how to mitigate the impacts of land-use change on biodiversity. I focus on large migratory herbivores because they are among the most heavily impacted by global change due to their large home range requirements. Habitat fragmentation, illegal hunting, and human-wildlife conflicts are among the biggest threats to large herbivores and result from land-use change. For this reason, my first chapter focuses …

Phylogeography Of The American Green Treefrog Species Group, Paul Nathaniel Pasichnyk

Biology Dissertations - Archive

The southeastern United States is an important temperate biodiversity hotspot, housing a multitude of endemic species and multiple large rivers fragmenting their ranges. To determine if the Riverine Barriers Hypothesis explains population divergence in this region, this study utilizes of a combination of phylogeographic methods and ecological niche modeling to investigate the role of rivers in genetic dispersal. Intra-and interspecific phylogenies for the hylid treefrogs Dryophytes cinereus, D. gratiosus and D. squirellus were estimated using nuclear and mitochondrial DNA sequences to identify relationships and genetic variation within these species and test for population structure, especially with respect to potential riverine …

Reintroducing Environmental Change Drivers In Biodiversity-Ecosystem Functioning Research., Frederik De Laender, Jason R. Rohr, Roman Ashauer, Donald J Baird, Uta Berger, Nico Eisenhauer, Volker Grimm, Udo Hommen, Lorraine Maltby, Carlos J Meliàn

Integrative Biology Faculty and Staff Publications

For the past 20 years, research on biodiversity and ecosystem functioning (B-EF) has only implicitly considered the underlying role of environmental change. We illustrate that explicitly reintroducing environmental change drivers in B-EF research is needed to predict the functioning of ecosystems facing changes in biodiversity. Next we show how this reintroduction improves experimental control over community composition and structure, which helps to provide mechanistic insight on how multiple aspects of biodiversity relate to function and how biodiversity and function relate in food webs. We also highlight challenges for the proposed reintroduction and suggest analyses and experiments to better understand how …

The Biodiversity Of Gastrointestinal Nematodes In South African Wildlife, Chalis J. Bird

Theses, Dissertations, and Projects

In this study, I investigated the diversity of parasites found in cheetah and wild ungulates in South Africa in collaboration with the Samara Private Game Reserve in Graaff Reinet, South Africa. Scat samples were collected over a period of two months, from September November, 2014, and DNA was extracted on the preserve for gastrointestinal nematode analysis. Wildlife was tracked using radio telemetry, tracks, and sign, while habitat and host distribution were documented. The aim was to determine the community composition of gastrointestinal nematodes in the wildlife hosts through molecular identification and to examine the role of host habitat preference, geographical …

Human Observers Differ In Ability To Perceive Insect Diversity, Joseph S. Wilson, Joshua P. Jahner, Matthew L. Forister

Biology Faculty Publications

Human perception of biological variation is an important and understudied issue in the conservation and management of natural resources. Here, we took a novel approach by asking 1152 participants, primarily college biology students, to score examples of insect mimicry by the number of distinct kinds of animals they saw. Latent class analysis successfully separated participants based on their accuracy of perception as well as demographic information and opinions about biodiversity. Contrary to expectations, factors such as childhood experience (growing up in urban, suburban or rural areas) did not affect the ability to see biodiversity as much as political views (location …

A New Method For Ecoacoustics? Toward The Extraction And Evaluation Of Ecologically-Meaningful Soundscape Components Using Sparse Coding Methods, Alice Eldridge, Michael Casey, Paola Moscoso, Mika Peck

Dartmouth Scholarship

Passive acoustic monitoring is emerging as a promising non-invasive proxy for ecological complexity with potential as a tool for remote assessment and monitoring (Sueur & Farina, 2015). Rather than attempting to recognise species-specific calls, either manually or automatically, there is a growing interest in evaluating the global acoustic environment. Positioned within the conceptual framework of ecoacoustics, a growing number of indices have been proposed which aim to capture community- level dynamics by (e.g., Pieretti, Farina & Morri, 2011; Farina, 2014; Sueur et al.,2008b) by providing statistical summaries of the frequency or time domain signal. Although promising, the ecological relevance and …

Transforming Ecosystems: When, Where, And How To Restore Contaminated Sites, Jason R. Rohr, Aïda M. Farag, Marc W. Cadotte, William H. Clements, James R. Smith, Cheryl P. Ulrich, Richard Woods

Integrative Biology Faculty and Staff Publications

Chemical contamination has impaired ecosystems, reducing biodiversity and the provisioning of functions and services. This has spurred a movement to restore contaminated ecosystems and develop and implement national and international regulations that require it. Nevertheless, ecological restoration remains a young and rapidly growing discipline and its intersection with toxicology is even more nascent and underdeveloped. Consequently, we provide guidance to scientists and practitioners on when, where, and how to restore contaminated ecosystems. Although restoration has many benefits, it also can be expensive, and in many cases systems can recover without human intervention. Hence, the first question we address is: "When …

Assessment Of Biodiversity On Mount Timpanogos With A Focus On Flies, Diptera: Agromyzidae, Samantha Smith, Dr. Riley Nelson

Journal of Undergraduate Research

Mount Timpanogos, with an elevation of 3,582 meters, is home to an amazing array of insect species. Through much previous effort, many have studied the insects found in American Fork Canyon leading up to Mount Timpanogos. They have still barely scratched the surface of the abundant biodiversity on the mountain. Varied temperature regimes can cause changes in insects’ life cycle and the length of their feeding period, making the collections at different elevations of Mount Timpanogos during different years of particularly great value (Petitt et al 1991). Thus the value of collections along Mount Timpanogos is two-fold; both to study …

Zootaxa: Guide To The Parasites Of Fishes Of Canada Part V: Nematoda, Hisao P. Arai, John W. Smith

Biology Faculty Publications

Keys are provided for the identification of the nematode species known to be parasites of Canadian fishes. The nematodes are described and illustrated, with a note of the site(s) they occupy in named fish host(s) and their geographical distribution. Parasite records are given by author and date, full details of which can be found in a bibliography of over 800 references. Diagnoses and keys for 22 Families, 47 genera and 88 species of nematodes are also given, together with a glossary of terms, a host-parasite list, and indices to both nematode parasites and hosts

Are We Missing Important Areas In Pelagic Marine Conservation? Redefining Conservation Hotspots In The Ocean, Dana K. Briscoe, Sara M. Maxwell, Raphael Kudela, Larry B. Crowder

Biological Sciences Faculty Publications

The protection of biodiversity is one of the most important goals in terrestrial and marine conservation. Marine conservation approaches have traditionally followed the example of terrestrial initiatives. However, patterns, processes, habitats, and threats differ greatly between the 2 systems - and even within the marine environment. As a result, there is still a lack of congruence as to how to best identify and prioritize conservation approaches moving from the static terrestrial and nearshore realm into a more fluid, 3-dimensional pelagic realm. To address this problem, we investigate how the conservation science literature has been used to inform and guide management …

Parasitoid Communities Of Remnant And Constructed Prairie Fragments In Western Ohio, Michael Drew Sheaffer

Browse all Theses and Dissertations

The ability of organisms to disperse to, utilize, and persist in novel habitats in a fragmented landscape is vital to the success of many ecosystem restoration and construction efforts. With less than four percent of original tallgrass prairie persisting across its range, conservationists have made efforts to both protect and restore remnant prairies as well as to plant new prairies. Previous studies suggest that restored ecosystems do not support the same levels of biodiversity and ecosystems services as their remnant counterparts. In this study I measured tachinid fly diversity and orthopteran parasitism rates in order to assess ecological similarity of …

Phylogeography Of The Natal Puddle Frog Phrynobatrachus Natalensis (Anura: Phrynobatrachidae) In Sub-Saharan Africa, Joshua Adan Lara

Open Access Theses & Dissertations

The Family Phrynobatrachidae (Laurent, 1941) has one genus (Phrynobatrachus, Günther, 1862) containing 89 species. Commonly known as puddle frogs, they comprise one of the most species rich sub-Saharan amphibian groups. The objective of this study was to investigate P. natalensis from the Albertine Rift (AR) with systematic and phylogeographic methods. One mitochondrial DNA gene (16S = 555 base pairs [bp]) and one nuclear gene (RAG1 = 774 bp) were analyzed for 61 representatives of P. natalensis. Nine cryptic lineages were identified from Angola, Burundi, Côte d’Ivoire, Democratic Republic of the Congo, Ethiopia, Ghana, Mozambique, Namibia, Tanzania, Rwanda, and Uganda. Several …

Synthesis Of Phylogeny And Taxonomy Into A Comprehensive Tree Of Life, Cody E. Hinchliff, Stephen A. Smith, James F. Allman, J. Gordon Burleigh, Ruchi Chaudhary, Lyndon M. Coghill, Keith A. Crandall, Jiabin Deng, Bryan T. Drew, Romina Gazis, Karl Gude, David S. Hibbett, Laura A. Katz, H. Dail Laughinghouse Iv, Emily Jane Mctavish, Peter E. Midford, Christopher L. Owen, Richard H. Ree, Jonathan A. Rees, Douglas E. Soltis, Tiffani Williams, Karen A. Cranston

Biological Sciences: Faculty Publications

Reconstructing the phylogenetic relationships that unite all line- ages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips— the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. …

Environmental And Adaptive Buffers That Mediate The Response Of Subalpine Ecosystems To Environmental Change, Lafe G. Conner

Student Works

This document reports the results of 4 studies of subalpine ecosystem ecology, describing ways that spatial heterogeneity in soils and plant communities mediate ecosystem responses to environmental change. Ecosystem responses to environmental change are also mediated by regional climate patterns and interannual variability in weather. In the first chapter we report the results of an experiment to test for the mediating effects of associational resistance in a forest community that experienced wide-spread beetle kill. We found that Engelmann spruce were more likely to survive a beetle outbreak when growing in low densities (host dilution) and not through other types of …

Environmental And Adaptive Buffers That Mediate The Response Of Subalpine Ecosystems To Environmental Change, Lafe G. Conner

Theses and Dissertations

This document reports the results of 4 studies of subalpine ecosystem ecology, describing ways that spatial heterogeneity in soils and plant communities mediate ecosystem responses to environmental change. Ecosystem responses to environmental change are also mediated by regional climate patterns and interannual variability in weather. In the first chapter we report the results of an experiment to test for the mediating effects of associational resistance in a forest community that experienced wide-spread beetle kill. We found that Engelmann spruce were more likely to survive a beetle outbreak when growing in low densities (host dilution) and not through other types of …

Evolution And Biodiversity, Timothy Henkel, Emily Croteau, Matthew Waters

Biological Sciences Grants Collections

This Grants Collection for Evolution and Biodiversity was created under a Round Four ALG Textbook Transformation Grant.

Affordable Learning Georgia Grants Collections are intended to provide faculty with the frameworks to quickly implement or revise the same materials as a Textbook Transformation Grants team, along with the aims and lessons learned from project teams during the implementation process.

Documents are in .pdf format, with a separate .docx (Word) version available for download. Each collection contains the following materials:

• Linked Syllabus
• Initial Proposal
• Final Report

Subsistence Strategies In Traditional Societies Distinguish Gut Microbiomes, Alexandra J. Obregon-Tito, Raul Y. Tito, Jessica Metcalf, Krithivasan Sankaranarayanan, Jose C. Clemente, Luke K. Ursell, Zhenjiang Zech Xu, Will Van Treuren, Rob Knight, Patrick M. Gaffney, Paul Spicer, Paul Lawson, Luis Marin-Reyes, Omar Trujillo-Villarroel, Morris Foster, Emilio Guija-Poma, Luzmila Troncoso-Corzo, Christina Warinner, Andrew T. Ozga, Cecil M. Lewis Jr.

Biology Faculty Articles

Recent studies suggest that gut microbiomes of urban-industrialized societies are different from those of traditional peoples. Here we examine the relationship between lifeways and gut microbiota through taxonomic and functional potential characterization of faecal samples from hunter-gatherer and traditional agriculturalist communities in Peru and an urban-industrialized community from the US. We find that in addition to taxonomic and metabolic differences between urban and traditional lifestyles, hunter-gatherers form a distinct sub-group among traditional peoples. As observed in previous studies, we find that Treponema are characteristic of traditional gut microbiomes. Moreover, through genome reconstruction (2.2–2.5 MB, coverage depth × 26–513) and functional …

Systematics Of The African River Frog Genus Amietia (Anura: Pyxicephalidae) From Eastern Democratic Republic Of The Congo, Thornton Robert Larson

Open Access Theses & Dissertations

The African river frog genus Amietia is found near rivers and other lentic water sources throughout central, eastern and southern Africa. Because the genus includes multiple morphologically conservative species, taxonomic studies of river frogs have been limited. We sampled 49 individuals of Amietia from multiple localities in and near the Albertine Rift (AR) of Burundi, Democratic Republic of the Congo and Uganda. We utilized single-gene (16S) and concatenated (12S, 16S, cytochrome b and RAG1) gene-tree analyses and coalescent species-tree analyses to construct phylogenetic trees. Two divergence dating approaches were used in BEAST, including secondary calibration points with 12S, 16S and …

Human Appropriation Of Net Primary Production (Hanpp) In An Agriculturally-Dominated Watershed, Southeastern Usa, C. Brannon Andersen, R. Kyle Donovan, John Quinn

Biology Publications

Human appropriation of net primary production (HANPP) quantifies alteration of the biosphere caused by land use change and biomass harvest. In global and regional scale assessments, the majority of HANPP is associated with agricultural biomass harvest. We adapted these methods to the watershed scale and calculated land cover change and HANPP in an agricultural watershed in 1968 and 2011. Between 1968 and 2011, forest cover remained near 50% of the watershed, but row crop decreased from 26% to 0.4%, pasture increased from 19% to 32%, and residential area increased from 2% to 10%. Total HANPP decreased from 35% of potential …

Predictive Modeling Of Floral Species Richness In Michigan Prairie Fen Communities, Nichole R. Mason

Masters Theses

Prairie fens contain high levels of floral biodiversity, including 19 state threatened or endangered plant species, and are classified as rare and vulnerable communities by the Michigan Natural Features Inventory. The objective of this thesis was to develop multiple-regression (MR) models that reliably predict total, native, and invasive floral species richness for use by conservation organizations. Floral biodiversity surveys were conducted in eight southern Michigan prairie fens during the 2012 growing season. Simple linear regressions between fen size and biodiversity were used to optimize sampling strategy and effort (i.e., number of transects and plots per transect) in surveys conducted in …