Ornithology Commons^™

Exploring The Role Of Ecological Traits In Shaping Spatial Patterns Of Genetic Diversity, Rilquer Mascarenhas Da Silva

Dissertations, Theses, and Capstone Projects

The field of comparative phylogeography aims at uncovering common underlying causes for shared patterns of diversity and diversification at the population level. However, it is now widely accepted that intraspecific genetic diversity patterns can differ considerably across co-occurring taxa due to ecological processes acting at the population level (and influencing individual movement and abundance). To model the processes underlying lineage diversification and demographic shifts in response to environmental changes, phylogeographers and population geneticists are now faced with the challenge of incorporating measurements of species ecological traits into their molecular studies. This dissertation aimed at investigating how different types of ecological …

The Role Of Elevation In The Migration, Physiology, And Genomic Diversification Of Birds, Jessie L. Williamson

Biology ETDs

Elevational gradients cause profound eco-climatic variation across short distances. Partial pressure of oxygen (PO₂) is a severe challenge that organisms face at high elevations; due partly to specialization on PO₂, most Neotropical bird species have narrow elevational ranges. However, a small fraction are elevational generalists that span sea level to high elevations, and a subset undertake extreme migratory journeys from low to high elevations biannually. My dissertation combines diverse approaches across levels of biological organization to understand how elevation impacts the ecology, evolution, physiology, and migration of montane birds. I examined ‘extreme’ elevational …

Hybridization Between The Rare Gray-Headed Chickadee And The Abundant Boreal Chickadee In The Midst Of Shifting Climate, Matthew R. Armstrong

School of Natural Resources: Dissertations, Theses, and Student Research

As species respond to changing climate, distributions and abundances may shift and alter species interactions. Hybridization, a relatively widespread phenomenon becoming more common with climate change, can have beneficial and detrimental effects on population growth rates and genetic integrity. Beneficial effects due to the introduction of advantageous alleles and increased genetic diversity may result from hybridization. Species may also accrue fitness costs associated with changing climates if mismatches occur between environmental variables and phenotypes. The gray-headed chickadee, Poecile cinctus lathami, is an extremely rare songbird that has experienced marked declines in recent decades within its restricted distribution in Alaska …

Crossing The Ocean: The Importance Of Gene Flow In Island Evolution, Ethan F. Gyllenhaal

Biology ETDs

Islands have long been a critical arena for the development of ecological and evolutionary theory, particular due to persistent open-water gaps between them. In this dissertation I demonstrates how these caps are permeable, which can be leveraged to understand evolution on islands and more broadly. The first chapter develops this connection between ongoing, overwater gene flow and island biogeographic theory, and tests it on an archipelago species. The second take a three-pronged approach in demonstrating how over-water gene flow can bias phylogenetic inference, and how many phylogeographic metrics in islands are likely shaped by long-term gene flow. The final two …

Avian Symbionts Of Sulawesi: Identifying And Correlating Malaria Parasites And The Microbiome In Communities Of Endemic Avian Hosts, Rachael Joakim

Dissertations, Theses, and Capstone Projects

Since the evolution of complex organisms, there have been communities of symbionts inhabiting them. Thanks to the development of parallel sequencing techniques, DNA of entire microbial communities can be sequenced from a single sample. Some microbes can be parasitic in nature, such as Haemosporida, an order of eukaryotes causing malaria. While most symbionts form a more commensal host relationship in wild systems, host-symbiont dynamics can vary in pathogenicity based on biotic and abiotic factors. In vertebrates, microbial communities in the gut play a major role in host function, including immune responses to Haemosporida. Though this relationship is most commonly explored …

The Influence Of Genes On The Migratory Timing Of Great Reed Warblers, Emily Fackler

Honors Undergraduate Theses

Many organisms migrate; however, there is a lack of knowledge on the mechanisms that drive migration timing, including which genes play a role. The great reed warbler (Acrocephalus arundinaceus), a migratory bird that breeds in Eurasia and overwinters in sub-Saharan Africa, is an excellent model to study the genetics of migration. Each season, some individuals migrate early, whereas others migrate later in the season. In other words, they exhibit differences in their migratory chronotypes. Past research has identified three candidate genes (TOP1, PEAK1, and CPNE4) that influence the migratory chronotypes of another avian species, …

Investigating Birds As Dispersal Vectors Of Litylenchus Crenatae Subsp. Mccannii (Anguinidae), The Nematode Associated With Beech Leaf Disease, Spencer Rock Parkinson

Graduate Theses, Dissertations, and Problem Reports (ETD)

Beech leaf disease (BLD) is an emerging forest pathogen primarily affecting American beech (Fagus grandifolia, Ehrh.) in North America and has been attributed to tree mortality of sapling sized trees within five to seven years of infection. Symptoms typically occur in regenerating American beech thickets sprouting from roots of trees killed by beech bark disease. Scientists first observed BLD in Ohio in 2012 and currently has spread to 15 states in the USA and one Canadian province. The nematode Litylenchus crenatae subsp. mccannii (Lcm) is highly associated with BLD symptoms, interveinal chlorosis and defoliation of leaves, and is currently …

Characterization Of Antimicrobial Properties Of Excrement And Functional Microbiome Of Black Vultures (Coragyps Atratus), Bridgette Gray

Theses

Black vultures, Coragyps atratus, are obligate scavenging birds that consume and dispose of decaying carcasses and carrion. They fulfill a key ecological niche in the environments in which they live. It has been observed that these vultures sometimes excrete bodily waste onto their legs. This adaptive behavior could help aid them in controlling bacteria and other microbes they encounter while stepping into a carcass to eat. This study directly examined the antimicrobial properties of the excrement of black vultures across various bacterial species utilizing a zone of inhibition test and a nematode species utilizing a survival assay. The black vulture …

Advancing Methods Of Diet Analysis: A Case Study Using Degraded Merlin (Falco Columbarius) Prey Remains, Taylor A. Coon

Undergraduate Theses, Professional Papers, and Capstone Artifacts

Prey remains have long been used as a mechanism to approach diet analyses. As understanding diet is key to comprehending ecosystem dynamics, prey remains identification requires a unique methodological approach to determine diversity within a sample. With the advancement of technology, molecular protocols designed for species-specific identification have improved to incredible accuracy and precision. Yet, the visual identification method has remained a predominant technique within diet studies. With entry-level observers, we matched visual identifications with molecular-based methods to quantify the accuracy of the visual identification method. This study determined what fraction of visually identified prey remains could be correctly identified …

The Effect Of Infection Risk On Female Blood Transcriptomics, Brenna M. G. Gormally, Patricia C. Lopes

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Defenses against pathogens can take on many forms. For instance, behavioral avoidance of diseased conspecifics is widely documented. Interactions with these infectious conspecifics can also, however, lead to physiological changes in uninfected animals, an effect that is much less well understood. These changes in behavior and physiology are particularly important to study in a reproductive context, where they can impact reproductive decisions and offspring quality. Here, we studied how an acute (3 h) exposure to an immune-challenged male affected female blood transcriptomics and behavior. We predicted that females paired with immune-challenged males would reduce eating and drinking behaviors (as avoidance …

Insights Into The Speciation Process From Genomic And Phenotypic Analysis Of An Avian Hybrid Zone In Amazonia, Glaucia Christina Del-Rio

LSU Doctoral Dissertations

Understanding the outcome of secondary contact is essential to shed light on the mechanisms governing species formation and maintenance. In Amazonia, closely related bird taxa with limited dispersal abilities are often separated by rivers, which presumably act as dispersal barriers. However, at the headwaters, rivers cease to be dispersal barriers, and this generates opportunities for secondary contact. In my dissertation, I studied genomic mechanisms associated with phenotypic differences, mitochondrial DNA structure, and putative reproductive barriers between two hybridizing Amazonian bird species in the genus Rhegmatorhina, a group of antbirds that find their arthropod prey exclusively by following army-ant swarms. …

A Review Of Current Methods In Avian Dietary Analysis And Their Integrated Application To Characterize The Trophic Niche Of Louisiana Waterthrush (Parkesia Motacilla)., Brandon Hoenig

Electronic Theses and Dissertations

Characterizing a species’ dietary composition presents an avenue to understand many facets of its ecological niche and can provide essential information for the species’ long-term conservation. To date, the vast majority of diet studies have relied on direct identification of prey during foraging observations or from diet samples to characterize the dietary habits of birds. However, advancements in laboratory-based approaches have revolutionized the field of trophic ecology by allowing researchers to indirectly infer dietary habits with higher resolution across greater time scales. Here, I apply two of these laboratory-based techniques, namely DNA metabarcoding and stable isotope analysis, to characterize the …

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 …

Molecular Taxonomy And Phylogenetic Analysis Of Dove And Pigeon Species (Aves: Columbidae) Of Pakistan, Based On Coi Region Of Mitochondrial Dna, Hina Rafiq, Fakhar -I-Abbas, Fakhra Nazir, Fida Muhammad Khan

Journal of Bioresource Management

Doves and Pigeons are the members of living family Columbidae (Order: Columbiformes) having a wide range of taxonomic diversity and geographic distribution. Seven species with one sample each of family Columbidae were collected via random sampling from different districts of Pakistan to carry out this study. The targeted gene region was sequenced and identified by using BLAST tool at National Center for Biotechnology Information (NCBI). CLUSTALW was used for sequence alignment and MEGA6 for reconstruction of phylogenetic trees to predict the effective ancestry of different Columbidae species. The following phylogenetic trees were obtained i.e. Maximum Likelihood tree, Neighborhood joining tree, …

Knemidokoptes Mites And Their Effects On The Gripping Position Of Steller’S Jay Feet, Wade M. Burris

Cal Poly Humboldt theses and projects

Steller’s jays (Cyanocitta stelleri) with swollen legs and feet resembling the signs of scaly leg have been commonly seen around Arcata, California, USA. These signs are thought to be caused by knemidokoptic mites, a group of parasites specialized at exploiting a range of avian hosts. I compared the gripping position in the feet of jays with variable signs of this condition as an index of their ability to perch, confirmed the presence of mites and identified them to the nearest species using genetic analysis, and compared the relatedness of the cytochrome oxidase subunit I (COI) gene between mites …

Blood Parasites Infecting The Hoatzin (Opisthocomus Hoazin), A Unique Neotropical Folivorous Bird, M. Andreína Pacheco, M. Alexandra García-Amado, Jaime Manzano, Nubia E. Matta, Ananias A. Escalante

Harold W. Manter Laboratory of Parasitology: Library Materials

The Hoatzin (Opisthocomus hoazin) is the only extant member of the order Opisthocomiformes. This unique South American bird lives in the riparian lowland vegetation characteristic of the Amazon and Orinoco basins. Hoatzins nest in communal social units close to water bodies; they are strictly folivores being the only bird with pregastric fermentation in the crop. Because of the complex logistics involved in capturing this bird, there is a knowledge gap on its parasites. This study documents two distant lineages of haemosporidian parasites (Plasmodium spp.) in a juvenile and two adults sampled in the Cojedes state, Venezuela. Although …

The Evaluation Of Genetic And Phenotypic Differences Associated With Short Term Selection Of Four Different Feed Efficiency Strategies In Japanese Quail, Alex David Gilley

Graduate Theses and Dissertations

The concept of feed efficiency (FE), one unit of feed required to improve one unit of desired output, is relatively simple. However multiple outputs are desired in a commercial poultry breeding program, resulting in the need for nutrients to be partitioned in a particular manner. At the broadest level, nutrients are partitioned between production and maintenance requirements. The requirements for production and maintenance varies between birds. It is the poultry breeder’s responsibility to select individuals most aligned with the breeding objective. Irrespective of the breeding objective, various related and non-related traits influence a bird’s FE. To effectively improve FE, the …

Transcriptomic Response To Immune Challenge In Zebra Finch (Taeniopygia Guttata) Using Rna-Seq, Cassandra Scalf

Masters Theses & Specialist Projects

Despite the convergence of rapid technological advances in genomics and the maturing field of ecoimmunology, our understanding of the genes that regulate immunity in wild populations is still nascent. Previous work to assess immune function has relied upon relatively crude measures of immunocompetence. However, with next-generation RNA-sequencing, it is now possible to create a profile of gene expression in response to an immune challenge. In this study, captive zebra finch (Taeniopygia guttata; adult males) were challenged with bacterial lipopolysaccharide (2 mg/Kg BW; dissolved in 0.9% saline) or vehicle (0.9% saline) to stimulate the immune system. Two hours after injection, birds …

The Effects Of Forest Degradation On Dna Methylation In Central African Songbirds, Andrew K. Wiegardt

Cal Poly Humboldt theses and projects

Environmentally-induced stress can initiate a molecular response through DNA methylation, which can alter gene expression, thereby serving as a mechanism allowing individuals to acclimate to a changing environment within their lifetime. In addition to DNA methylation, the production and release of corticosterone is a physiological mechanism by which birds can cope with acute environmental stressors. To assess how environmental stress impacted DNA methylation and corticosterone, I collected blood and feather samples from three understory avian species (Alethe castanea, Bleda notatus and Pseudalethe poliocephala), along a disturbance gradient in the lowland Guinean rainforest adjacent to the village of …

Genomic Data Reveal A Loss Of Diversity In Two Species Of Tuco-Tucos (Genus Ctenomys) Following A Volcanic Eruption, Jeremy L. Hsu, Jeremy Chase Crawford, Mauro N. Tammone, Uma Ramakrishnan, Eileen A. Lacey, Elizabeth A. Hadly

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Marked reductions in population size can trigger corresponding declines in genetic variation. Understanding the precise genetic consequences of such reductions, however, is often challenging due to the absence of robust pre- and post-reduction datasets. Here, we use heterochronous genomic data from samples obtained before and immediately after the 2011 eruption of the Puyehue-Cordón Caulle volcanic complex in Patagonia to explore the genetic impacts of this event on two parapatric species of rodents, the colonial tuco-tuco (Ctenomys sociabilis) and the Patagonian tuco-tuco (C. haigi). Previous analyses using microsatellites revealed no post-eruption changes in genetic variation in C. …

Dna Markers Identify Genetic Heritage Between Chickadees Near A Contact Zone In Illinois, Fahad M. Alshammari

Masters Theses

I studied the genetic interactions of Black-capped (Poecile atricapilus) (BCCH) and Carolina (P. carolinensis) (CACH) Chickadees in and near the largest hybrid contact zone in Illinois. Biologists have assumed Carolina and Black-capped Chickadees hybridize in their large contact zone in Bond and Fayette Counties, based on intermediate morphological measurements, plumage characteristics and the production of aberrant vocalizations. In determining hybridization, however, diagnostic genetics may be more useful than any other criterion. The genetic and environmental factors that have contributed to the survival of this chickadees hybrid zone have underscored the genetic integrity of both species. We …

The Maintenance Of Phenotypic Divergence Through Sexual Selection: An Experimental Study In Barn Swallows Hirundo Rustica, Rebecca Safran, Yoni Vortman, Brittany R. Jenkins, Joanna K. Hubbard, Matt Wilkins, Rachel J. Bradley, Arnon Lotem

School of Biological Sciences: Faculty Publications

Previous studies have shown that sexual signals can rapidly diverge among closely related species. However, we lack experimental studies to demonstrate that differences in trait-associated reproductive performance maintain sexual trait differences between closely related populations, in support for a role of sexual selection in speciation. Populations of Northern Hemisphere distributed barn swallows Hirundo rustica are closely related, yet differ in two plumage-based traits: ventral color and length of the outermost tail feathers (streamers). Here we provide experimental evidence that manipulations of these traits result in different reproductive consequences in two subspecies of barn swallow: (H. r. erythrogaster in North …

Analysis Of Standard Dna Procedures On Feathers Of Late 19th To Late 20th Century Osprey (Pandion Haliaetus), Alia A. Hamdan, Catherine B. Viverette, Rodney J. Dyer

Rice Rivers Center Research Symposium

Species with well-documented demographic histories and well known perturbations to gene flow provide good models for understanding how historic events impact contemporary population genetic structure1,2. Osprey (Pandion haliaetus), a marine bird-of-prey, experienced steep declines after widespread organochloride pesticide (e.g. DDT) use in the mid-twentieth century 3, however, population genetic consequences remain unknown. Use of historic specimens can aid population genetic studies4,5, however, these samples can degrade over time impacting quantity and quality of extracted DNA5. We compared the concentrations of extracted DNA of Osprey feathers from museum and research collections to those of contemporary samples collected according to standard field …

Comparative Genomics Reveals Insights Into Avian Genome Evolution And Adaptation, Guojie Zhang, Cai Li, Qiye Li, Bo Li, Dennis M. Larkin, Chul Lee, Jay F. Storz, Agostinho Antunes, Matthew J. Greenwold, Robert W. Meredith, Anders Ödeen, Jie Cui, Qi Zhou, Luohao Xu, Hailin Pan, Zongji Wang, Lijun Jin, Pei Zhang, Haofu Hu, Wei Yang, Jiang Hu, Jin Xiao, Zhikai Yang, Yang Liu, Qiaolin Xie, Hao Yu, Jinmin Lian, Ping Wen, Fang Zhang, Hui Li, Yongli Zeng, Zijun Xiong, Shiping Liu, Long Zhou, Zhiyong Huang, Na An, Jie Wang, Quimei Zheng, Yingqi Xiong, Guangbiao Wang, Bo Wang, Jingjing Wang, Yu Fan, Rute R. Da Fonseca, Alonzo Alfaro-Núñez, Mikkel Schubert, Ludovic Orlando, Tobias Mourier, Jason T. Howard, Ganeshkumar Ganapathy, Andreas Pfenning, Osceola Whitney, Miriam V. Rivas, Erina Hara, Julia Smith, Marta Farré, Jitendra Narayan, Gancho Slavov, Michael N. Romanov, Rui Borges, João Paulo Machado, Imran Khan, Mark S. Springer, John Gatesy, Federico G. Hoffmann, Juan C. Opazo, Olle Håstad, Roger H. Sawyer, Heebal Kim, Kyu-Won Kim, Hyeon Jeong Kim, Seoae Cho, Ning Li, Yinhua Huang, Michael W. Bruford, Xiangjiang Zhan, Andrew Dixon, Mads F. Bertelsen, Elizabeth Derryberry, Wesley Warren, Richard K. Wilson, Shengbin Li, David A. Ray, Richard E. Green, Stephen J. O'Brien, Darren Griffin, Warren E. Johnson, David Haussler, Oliver A. Ryder, Eske Willerslev, Gary R. Graves, Per Alström, Jon Fjeldså, David P. Mindell, Scott V. Edwards, Edward L. Braun, Carsten Rahbek, David W. Burt, Peter Houde, Yong Zhang, Huanming Yang, Jian Wang, Avian Genome Consortium, Erich D. Jarvis, M. Thomas P. Gilbert, Jun Wang

Jay F. Storz Publications

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses …

The Causes And Consequences Of Individual Variation In Parental Care Behavior, Daniel P. Wetzel

Theses and Dissertations--Biology

Behavioral traits can be remarkably flexible depending on the conditions in which they are expressed, yet, in spite of this flexibility, persistent differences between individuals appear to limit the potential expression of behaviors. For example, despite evidence that parents provide variable amounts of parental care in response to changing environmental conditions, they also differ in the overall level of care they provide. I used a behavioral reaction norm approach to study individual variation in parental care behavior in free-living house sparrows (Passer domesticus). I investigated the nature of this variation by studying the relationship between different forms of …

The Role Of Historical And Contemporary Processes On Phylogeographic Structure And Genetic Diversity In The Northern Cardinal, Cardinalis Cardinalis, Brian T. Smith, Patricia Escalante, Blanca E. Hernandez-Banos, Adolfo G. Navarro-Siguenza, Sievert Rohwer, John Klicka

Ornithology Program (HRC)

Background

Earth history events such as climate change are believed to have played a major role in shaping patterns of genetic structure and diversity in species. However, there is a lag between the time of historical events and the collection of present-day samples that are used to infer contemporary population structure. During this lag phase contemporary processes such as dispersal or non-random mating can erase or reinforce population differences generated by historical events. In this study we evaluate the role of both historical and contemporary processes on the phylogeography of a widespread North American songbird, the Northern Cardinal, Cardinalis cardinalis …

Isolation By Distance Explains Genetic Structure Of Buggy Creek Virus, A Bird-Associated Arbovirus, Abinash Padhi, Amy T. Moore, Mary Bomberger Brown, Jerome E. Foster, Martin Pfeffer, Charles R. Brown

School of Natural Resources: Faculty Publications

Many of the arthropod-borne viruses (arboviruses) show extensive genetic variability and are widely distributed over large geographic areas. Understanding how virus genetic structure varies in space may yield insight into how these pathogens are adapted to and dispersed by different hosts or vectors, the relative importance of mutation, drift, or selection in generating genetic variability, and where and when epidemics or epizootics are most likely to occur. However, because most arboviruses tend to be sampled opportunistically and often cannot be isolated in large numbers at a given locale, surprisingly little is known about their spatial genetic structure on the local …

It's Not Too Late For The Harpy Eagle (Harpia Harpyja): High Levels Of Genetic Diversity And Differentiation Can Fuel Conservation Programs, Heather R. Lerner, Jeff A. Johnson, Alec R. Lindsay Ph. D., Lloyd F. Kiff, David P. Mindell

Faculty Works

Background: The harpy eagle (Harpia harpyja) is the largest Neotropical bird of prey and is threatened by human persecution and habitat loss and fragmentation. Current conservation strategies include local education, captive rearing and reintroduction, and protection or creation of trans-national habitat blocks and corridors. Baseline genetic data prior to reintroduction of captive-bred stock is essential for guiding such efforts but has not been gathered previously.

Methodology/Findings: We assessed levels of genetic diversity, population structure and demographic history for harpy eagles using samples collected throughout a large portion of their geographic distribution in Central America (n = 32) and South America …

Geographic Variation In Malarial Parasite Lineages In The Common Yellowthroat (Geothlypis Trichas), K. M. Pagenkopp, John Klicka, K. L. Durrant, J. C. Garvin, R. C. Fleischer

Ornithology Program (HRC)

Our current understanding of migration routes of many birds is limited and researchers have employed various methods to determine migratory patterns. Recently, parasites have been used to track migratory birds. The objective of this study was to determine whether haemosporidian parasite lineages detect significant geographic structure in common yellowthroats (Geothlypis trichas). We examined liver tissue or blood from 552 birds sampled from multiple locations throughout the continental United States, southern Canada, and the Bahamas. We found a 52.7% overall prevalence of haematozoan infection. We identified 86.1% of these infections to genus: 81% were Plasmodium; 5% were Haemoproteus …

Historic Genetic Structuring And Paraphyly Within The Great-Tailed Grackle, Jeffrey M. Dacosta, Walter Wehtje, John Klicka

Ornithology Program (HRC)

The Great-tailed Grackle (Quiscalus mexicanus) and Boat-tailed Grackle (Q. major) are sister species that have expanded their ranges during historical times. This expansion has created an area of sympatry between these species in Texas and Louisiana, and between distinctive Great-tailed Grackle subspecies in the southwestern United States and northern Mexico. We investigated the evolutionary histories of both species using mitochondrial DNA sequence data and modern phylogenetic methods. Our results reveal genetic structure within Great-tailed, but not Boat-tailed Grackles. Great-tailed Grackles are separated into two clades, but range expansion in the north has led to secondary contact …