Genetics and Genomics Commons^™

Gibsonville Healthy Forest Restoration Project: Silviculture Report, Dan Roskopf

Aspen Bibliography

The Forest Service proposes to reduce the risk of wildfire, to protect, restore, and enhance forest ecosystem components (i.e., streams, meadows, aspen areas) in the vicinity of Gibsonville, California. A combination of hazard tree removal, forest health, and fuels reduction treatments are proposed on 1,200 acres of Forest Service system lands. These actions are proposed to be implemented on the Feather River Ranger District of the Plumas National Forest.

Molecular Analysis Confirming The Introduction Of Nile Crocodiles, Crocodylus Niloticus Laurenti 1768 (Crocodylidae), In Southern Florida, With An Assessment Of Potential For Establishment, Spread, And Impacts., Michael R. Rochford, Kenneth L. Krysko, Frank J. Mazzotti, Matthew W. Shirley, Mark W. Parry, Joseph A. Wasilewski, Jeffrey S. Beauchamp, Christpher R. Gillette, Edward F. Metzger Iii, Michiko A. Squires, Louis A. Somma

Papers in Herpetology

The state of Florida, USA, has more introduced herpetofauna than any other governmental region on Earth. Four species of nonnative crocodilians have been introduced to Florida (all since 1960), one of which is established. Between 2000–2014 we field-collected three nonnative crocodilians in Miami-Dade County, Florida, and one in Hendry County, Florida. We used DNA barcoding and molecular phylogenetics to determine species identification and native range origin. Also, we described diet, movement, and growth for one crocodile. Our molecular analyses illustrated that two of the crocodiles we collected are most closely related to Nile Crocodiles (Crocodylus niloticus) from South Africa, suggesting …

Diversity-Dependent Cladogenesis Throughout Western Mexico: Evolutionary Biogeography Of Rattlesnakes (Viperidae: Crotalinae: Crotalus And Sistrurus), Christopher Blair, Santiago Sánchez-Ramírez

Publications and Research

Rattlesnakes (Crotalus and Sistrurus) represent a radiation of approximately 42 species distributed throughout the New World from southern Canada to Argentina. Interest in this enigmatic group of snakes continues to accrue due, in part, to their ecomorphological diversity, contributions to global envenomations, and potential medicinal importance. Although the group has garnered substantial attention from systematists and evolutionary biologists for decades, little is still known regarding patterns of lineage diversification. In addition, few studies have statistically quantified broad-scale biogeographic patterns in rattlesnakes to ascertain how dispersal occurred throughout the New World, particularly among the different major biomes of the …

Population Genetic Divergence Of Isle Royale Pearl Dace, Margarita Margariscus (Cyprinidae)., John F. Elder Jr., Jack R. Martin, Isaac J. Schlosser, Larry Kallemeyn

Georgia Journal of Science

In 1949, Hubbs and Lagler described morphological variation among pearl dace (Margariscus margarita) of inland lakes on Isle Royale, Michigan. For Harvey Lake, Hubbs and Lagler, proposed that pearl dace were sufficiently morphologically distinct to warrant subspecific status. They argued that divergence of the Harvey Lake pearl dace was due to allopatric differentiation in isolation from lower elevation lakes. Harvey Lake has been isolated by elevation from lower elevation lakes for approximately 10 to 15 thousand years. No genetic studies have been done on Isle Royale pearl dace to evaluate this hypothesis to date. Here we report the analysis of …

Molecular Evolution And Functional Divergence Of Trace Amine–Associated Receptors, Seong-Il Eyun, Hideaki Moriyama, Federico G. Hoffmann, Etsuko N. Moriyama

School of Biological Sciences: Faculty Publications

Trace amine-associated receptors (TAARs) are a member of the G-protein-coupled receptor superfamily and are known to be expressed in olfactory sensory neurons. A limited number of molecular evolutionary studies have been done for TAARs so far. To elucidate how lineage-specific evolution contributed to their functional divergence, we examined 30 metazoan genomes. In total, 493 TAAR gene candidates (including 84 pseudogenes) were identified from 26 vertebrate genomes. TAARs were not identified from non-vertebrate genomes. An ancestral-type TAAR-like gene appeared to have emerged in lamprey.We found four therian-specific TAAR subfamilies (one eutherian-specific and three metatherian- specific) in addition to previously known nine …

Session D-1: Science And Spaghetti Monsters: Addressing The Ethical Issues And Controversy Related To Genomics And Evolution In The Biology Classroom, Sarah O'Leary-Driscoll

Professional Learning Day

As science teachers, we may shy away from addressing the controversy surrounding particular topics in our classrooms in order to maintain focus on content. However, the real world context of knowledge is essential, and the performance expectations in the life sciences as outlined in the NGSS state that students should be able to discuss the ethical issues related to genetic modifications and the nature of science. We will discuss ideas for how to address these topics effectively and help our students understand their importance beyond academics in our global community.

The Evolution Of The Viral Rna Sensor Oas1 In Old World Monkeys And Cetartiodactyls, Ian Fish

Dissertations, Theses, and Capstone Projects

Animals produce an array of sensors patrolling the intracellular environment poised to detect and respond to viral infection. The oligoadenylate synthetase family of enzymes comprises a crucial part of this innate immune response, directly signaling endonuclease activity responsible for inhibiting viral replication. Oligoadenylate synthetase 1 plays a vital role in animal susceptibility to pathogens including flaviviruses such as dengue, West Nile, and hepatitis c virus. This thesis includes a population level analysis of OAS1 diversity within macaque and baboon species followed by a broader survey of the gene in nineteen Old World monkeys. My research found that at the species …

Comparative Population Genomics Of Latitudinal Variation In Drosophila Simulans And Drosophila Melanogaster, Heather E. Machado, Alan O. Bergland, Katherine R. O'Brien, Emily L. Behrman, Paul S. Schmidt, Dmitri A. Petrov

School of Biological Sciences: Faculty Publications

Examples of clinal variation in phenotypes and genotypes across latitudinal transects have served as important models for understanding how spatially varying selection and demographic forces shape variation within species. Here, we examine the selective and demographic contributions to latitudinal variation through the largest comparative genomic study to date of Drosophila simulans and Drosophila melanogaster, with genomic sequence data from 382 individual fruit flies, collected across a spatial transect of 19 degrees latitude and at multiple time points over 2 years. Consistent with phenotypic studies, we find less clinal variation in D. simulans than D. melanogaster, particularly for the autosomes. Moreover, …

Bigtooth And Quaking Aspen Propagation From Roots Versus Seed, Joseph M. Vande Hey

Aspen Bibliography

No abstract provided.

Absence Of Mate Choice And Postcopulatory Benefits In A Species With Extreme Sexual Size Dimorphism, Marie-Claire Chelini, Eileen A. Hebets

Eileen Hebets Publications

Most hypotheses related to the evolution of female-biased extreme sexual size dimorphism (SSD) attribute the differences in the size of each sex to selection for reproduction, either through selection for increased female fecundity or selection for male increased mobility and faster development. Very few studies, however, have tested for direct fitness benefits associated with the latter – small male size. Mecaphesa celer is a crab spider with extreme SSD, whose males are less than half the size of females and often weigh 10 times less. Here, we test the hypotheses that larger size in females and smaller size in males …

Genetic And Genomic Basis Of Antibody Response To Porcine Reproductive And Respiratory Syndrome (Prrs) In Gilts And Sows, Nick V. Serão, Robert A. Kemp, Benny Mote, Philip Willson, John C.S. Harding, Stephen C. Bishop, Graham S. Plastow, Jack C.M. Dekkers

Department of Animal Science: Faculty Publications

Background: Our recent research showed that antibody response to porcine reproductive and respiratory syndrome (PRRS), measured as sample-to-positive (S/P) ratio, is highly heritable and has a high genetic correlation with reproductive performance during a PRRS outbreak. Two major quantitative trait loci (QTL) on Sus scrofa chromosome 7 (SSC7; QTL_MHC and QTL₁₃₀) accounted for ~40 % of the genetic variance for S/P. Objectives of this study were to estimate genetic parameters for PRRS S/P in gilts during acclimation, identify regions associated with S/P, and evaluate the accuracy of genomic prediction of S/P across populations with different prevalences of …

Biogeographical Patterns In The Hard-Tick Genus Amblyomma Koch 1844 (Acari: Ixodidae), Matthew H. Seabolt

College of Graduate Studies: Theses & Dissertations

Amblyomma Koch is a genus of hard-ticks with approximately 130 species. Its geographical range is typical for organisms with a Gondwanan origin. A majority of these species are endemic to the Neo- and Afrotropical regions, with the remaining taxa dispersed throughout Southeast Asia, Australia and the Pacific islands. Based on this distribution, we hypothesize that the genus dispersal patterns will mirror the fragmentation and continental drift of the Gondwanan supercontinent. Maximum parsimony, maximum likelihood, Bayesian inference and node-dating analyses of nuclear 18S rDNA gene sequences reveal a more recent origin and radiation patterns within the genus and suggest that Amblyomma …

High And Dry: Post-Fire Tree Seedlingestablishment In Subalpine Forestsdecreases With Post-Fire Drought Andlarge Stand-Replacing Burn Patches, Brian J. Harvey, Daniel C. Donato, Monica G. Turner

Aspen Bibliography

Aim: Climate warming and increased wildfire activity are hypothesized to catalyse biogeographical shifts, reducing the resilience of fire-prone forests world-wide. Two key mechanisms underpinning hypotheses are: (1) reduced seed availability in large stand-replacing burn patches, and (2) reduced seedling establishment/survival after post-fire drought. We tested for regional evidence consistent with these mechanisms in an extensive fire-prone forest biome by assessing post-fire tree seedling establishment, a key indicator of forest resilience.

Location: Subalpine forests, US Rocky Mountains.

Methods: We analysed post-fire tree seedling establishment from 184 field plots where stand-replacing forest fires were followed by varying post-fire climate conditions. Generalized linear …

Causes And Consequences Of Variation In Female Mate Choice And Its Relation To Sexual Conflict In Drosophila Melanogaster, David Cs Filice

Theses and Dissertations (Comprehensive)

Female mate choice is a significant driving force of evolutionary change and can explain the evolution of exaggerated male traits and/or displays, and dimorphism between the sexes. Females are thought to choose mates based on the greatest provision of direct or indirect benefits. Despite this, we often still see substantial individual variation in female mate choice behaviours both within and across populations. Recent studies suggest that female mate choice is a complex decision-making process that involves many context-dependent factors. However, the precise sources of this variation, such as previous mating experience, are not completely understood. In Drosophila melanogaster, mating …

Ecology Of Two Reintroduced Black Bear Populations In The Central Appalachians, Sean Mccarthy Murphy

Theses and Dissertations--Animal and Food Sciences

Reintroduced populations are vulnerable to demographic and environmental stochasticity, deleterious genetic effects, and reduced population fitness, all of which can increase extinction probability. Population viability is principle to determining the status of reintroduced populations and for guiding management decisions. To attempt to reestablish black bear (Ursus americanus) populations in the central Appalachians, two reintroductions using small founder groups occurred during the 1990s in the Big South Fork area along the Kentucky-Tennessee border (BSF) and in the Jefferson National Forest along the Kentucky-Virginia border (KVP). My objectives were to estimate demographic and genetic parameters, and to evaluate long-term viability …

Draft Genome Sequences For Seven Streptococcus Parauberis Isolates From Wild Fish In The Chesapeake Bay, Ashley Haines, Emily Nebergall, Elvira Besong, Kimaya Council, Onaysha Lambert, David Gauthier

Biological Sciences Faculty Publications

Streptococcus parauberis is a pathogen of cattle and fish, closely related Streptococcus uberis and Streptococcus iniae. We report the genomes of seven S. parauberis strains recovered from striped bass (Morone saxatilis) in the Chesapeake Bay. The availability of these genomes will allow comparative genomic analysis of Chesapeake Bay S. parauberis strains versus S. parauberis cultured from other animal hosts and geographic regions.

Isolation And Characterization Of Eight Polymorphic Microsatellites For The Spotted Spiny Lobster, Panulirus Guttatus, Nathan Truelove, Donald C. Behringer, Mark J. Butler Iv, Richard F. Preziosi

Biological Sciences Faculty Publications

Microsatellite sequences were isolated from enriched genomic libraries of the spotted spiny lobster, Panulirus guttatus using 454 pyrosequencing. Twenty-nine previously developed polymerase chain reaction primer pairs of Panulirus argus microsatellite loci were also tested for cross-species amplification in Panulirus guttatus. In total, eight consistently amplifying, and polymorphic loci were characterized for 57 individuals collected in the Florida Keys and Bermuda. The number of alleles per locus ranged from 8 to 20 and observed heterozygosities ranged from 0.409 to 0.958. Significant deviations from Hardy–Weinberg equilibrium were found in one locus from Florida and three loci from Bermuda. Quality control testing indicated …

Phenotypic And Genetic Analyses Of Adaptation To Geothermal Soils In Yellow Monkeyflowers Of Yellowstone National Park, Peter Breigenzer

Undergraduate Theses, Professional Papers, and Capstone Artifacts

Microgeographic adaptation, which occurs on a spatial scale smaller than the dispersal distance of the evolving organisms, provides a fertile context for understanding the genetic processes that shape natural variation and contribute to biological diversity. In plants, mosaics of distinct soil conditions can select for microgeographic divergence in the face of gene flow, leading to major life history transitions and novel trait evolution. Mimulus (monkeyflowers) is an emerging model genus for ecological genomics, due to tremendous diversity, experimental tractability, and a wealth of genomic resources. In Yellowstone National Park, Mimulus guttatus occurs in both geothermal soils and nearby nonthermal bogs …

Genetic Structure And Connectivity Of The Endangered Giant Kangaroo Rat (Dipodomys Ingens) In A Heterogeneous Environment, Nathan Alexander

Cal Poly Humboldt theses and projects

Movement ecology and dispersal are important aspects of species’ life histories that can inform conservation and management. Dispersal is often cryptic and difficult to detect, but recent advances genetic technology and applications have provided new approaches to identifying and describing dispersal patterns. Giant kangaroo rats (Dipodomys ingens) are an endangered heteromyid that appear to persist in small subpopulations in a heterogeneous environment of their northern range, the Ciervo-Panoche Natural Area, California. Previous work suggested high levels of genetic diversity between populations with genetic distances not being correlated to geographic distances. Here, I identified landscape population structure through clustering …

Resolving Gnetum Evolutionary History, Angela Mcfadden

All Master's Theses

Gnetum are non-flowering seed plants of the tropics, indigenous to South America, Africa, and Asia. This group of about 40 species is fascinating to botanists because it shares distinctive morphological characteristics with flowering plants, such as broad leaves, woody stems, and flower-like strobili. There are still questions surrounding the relationships within the genus of Gnetum. With that in mind, I focused my work on generating phylogenetic hypotheses, using two molecular data sets: a concatenation of over 60 different chloroplast genes (66,815 base pairs), and the whole chloroplast genome (128,772 base pairs). This allowed me to compare the two phylogenies …

Conservation Genetics On The Frontline, Kenneth W. Rand

Graduate Student Theses, Dissertations, & Professional Papers

Conservation genetics stands out as an effective tool for discovering and monitoring rare, endangered or invasive populations of plants and animals. Particularly when compared to traditional search and capture methods, it provides more holistic studies to preserve the disappearing biodiversity of the American West and the world.

Three stories highlight the work done to preserve biodiversity through the use of conservation genetics:

1. Trout Rescue: A new hope for westslope cutthroat in Montana How to save a disappearing westslope cutthroat trout through genetic rescue by adding genetic diversity to ensuring future survival in increasingly warming waters more harm than good. …

Effective Drug Treatment Induces Drug Resistance Through Rapid Genome Alteration-Mediated Cancer Evolution, Steven Horne

Wayne State University Dissertations

The central paradox associated with current cancer therapeutic strategies is initially effective treatment, which eliminates a high tumor cell count, consistently results in successful drug resistance. Mathematical and evolutionary modeling have previously suggested that therapeutic intervention could provide selective pressure for the expansion of resistant variants. Drug-related stress has been associated with genome chaos, a common phenomenon in cancer characterized as rapid, stochastic genomic fragmentation and reorganization. Since cancer represents an evolutionary process, analysis within the context of genome-mediated cancer evolution can shed light on this key problem of therapeutics. We propose that genomic change is a general response to …

Population Genetic Structure Of Necturus Maculosus In Central And Eastern Kentucky, Mason Owen Murphy

Theses and Dissertations--Biology

Population structure is influenced by extrinsic factors, such as landscape architecture and dispersal barriers. Lotic network architecture is known to constrain ecological, demographic and evolutionary processes, including population genetic structure. I assessed the population structure of a widespread aquatic salamander, Necturus maculosus, across three river basins in central and eastern Kentucky. I examined the role of network architecture, anthropogenic barriers, and spatial scale on patterns of population structure. I also provided a review of N. maculosus capture methods and offer an improved trap design. I identified significant structuring between the combined Licking/Kinniconick basin and the Kentucky River basin, with …

Absence Of Mate Choice And Postcopulatory Benefits In A Species With Extreme Sexual Size Dimorphism, Marie Claire Chelini, Eileen Hebets

Eileen Hebets Publications

Most hypotheses related to the evolution of female-biased extreme sexual size dimorphism (SSD) attribute the differences in the size of each sex to selection for reproduction, either through selection for increased female fecundity or selection for male increased mobility and faster development. Very few studies, however, have tested for direct fitness benefits associated with the latter – small male size. Mecaphesa celer is a crab spider with extreme SSD, whose males are less than half the size of females and often weigh 10 times less. Here, we test the hypotheses that larger size in females and smaller size in males …

Low-Head Dams On Habitat, Fish Functional Guilds And Genetic Structuring In A Midwestern River System, Shannon Cassandra Frary Smith

Masters Theses

The natural flow regime of the majority of rivers in the United States has been altered by anthropogenic structures. This loss of connectivity plays a strong role in shaping river ecosystems by altering physical habitat characteristics and shaping fish community assemblages. Although the impacts of large dams on river systems are well documented and often easy to observe, there are fewer studies on the effects of smaller low-head dams. Additionally, the influences of low-head dams on the genetic structuring of small-bodied riverine fishes have yet to be fully explored. I assessed the effects of two low-head dams on the Vermilion …

Independent Origination Of Floral Zygomorphy, A Predicted Adaptive Response To Pollinators: Developmental And Genetic Mechanisms, Ghadeer Bukhari, Wenheng Zhang

Theses and Dissertations

Observations of floral development indicate that floral organ initiation in pentapetalous flowers more commonly results in a medially positioned abaxial petal (MAB) than in a medially positioned adaxial petal (MAD), where the medial plane is defined by the stem and the bract during early floral development. It was proposed that the dominant MAB petal initiation might impose a developmental constraint that leads to the evolution of limited patterns of floral zygomorphy in Asteridae, a family in which the floral zygomorphy develops along the medial plane and results in a central ventral (CV) petal in mature flowers. Here, I investigate whether …

Clusters Of Alpha Satellite On Human Chromosome 21 Are Dispersed Far Onto The Short Arm And Lack Ancient Layers, William Ziccardi, Chongjian Zhao, Valery Shepelev, Lev Uralsky, Ivan Alexandrov, Tatyana Andreeva, Evgeny Rogaev, Christopher Bun, Emily Miller, Catherine Putonti, Jeffrey Doering

Bioinformatics Faculty Publications

Human alpha satellite (AS) sequence domains that currently function as centromeres are typically flanked by layers of evolutionarily older AS that presumably represent the remnants of earlier primate centromeres. Studies on several human chromosomes reveal that these older AS arrays are arranged in an age gradient, with the oldest arrays farthest from the functional centromere and arrays progressively closer to the centromere being progressively younger. The organization of AS on human chromosome 21 (HC21) has not been well-characterized. We have used newly available HC21 sequence data and an HC21p YAC map to determine the size, organization, and location of the …

A Novel Method Of Microsatellite Genotyping-By-Sequencing Using Individual Combinatorial Barcoding, Salla Vartia, Jose L. Villanueva-Cañas, John Finarelli, Edward D. Farrell, Patrick C. Collins, Graham M. Hughes, Jeanette E.L. Carlson, David T. Gauthier, Philip Mcginnity, Thomas F. Cross, Richard D. Fitzgerald, Luca Mirimin, Fiona Crispie, Paul D. Cotter, Jens Carlsson

Biological Sciences Faculty Publications

This study examines the potential of next-generation sequencing based 'genotyping-by-sequencing' (GBS) of microsatellite loci for rapid and cost-effective genotyping in large-scale population genetic studies. The recovery of individual genotypes from large sequence pools was achieved by PCR-incorporated combinatorial barcoding using universal primers. Three experimental conditions were employed to explore the possibility of using this approach with existing and novel multiplex marker panels and weighted amplicon mixture. The GBS approach was validated against microsatellite data generated by capillary electrophoresis. GBS allows access to the underlying nucleotide sequences that can reveal homoplasy, even in large datasets and facilitates cross laboratory transfer. GBS …

Genome Wide Epigenetic Analyses Of Araptus Attenuatus, A Bark Beetle, Chitra Seshadri

Theses and Dissertations

Phylogeographic studies have relied on surveying neutral genetic variation in natural populations as a way of gaining better insights into the evolutionary processes shaping present day population demography. Recent emphasis on understanding putative adaptive variation have brought to light the role of epigenetic variation in influencing phenotypes and the mechanisms underlying local adaptation. While much is known about how methylation acts at specific loci to influence known phenotypes, there is little information on the spatial genetic structure of genome-wide patterns of methylation and the extent to which it can extend our understanding of both neutral and putatively adaptive processes. This …

Mechanisms Of Adaptation In The Newly Invasive Species Brachypodium Sylvaticum (Hudson) Beauv., Gina Lola Marchini

Dissertations and Theses

It is common knowledge that invasive species cause worldwide ecological and economic damage, and are nearly impossible to eradicate. However, upon introduction to a novel environment, alien species should be the underdogs: They are present in small numbers, possess low genetic diversity, and have not adapted to the climate and competitors present in the new habitat. So, how are alien species able to invade an environment occupied by native species that have already adapted to the local environment? To discover some answers to this apparent paradox I conducted four ecological genetic studies that utilized the invasive species Brachypodium sylvaticum (Hudson) …