Life Sciences Commons^™

Annotation Of Non-Model Species’ Genomes, Taiya Jarva

Master's Theses

The innovations in high throughput sequencing technologies in recent decades has allowed unprecedented examination and characterization of the genetic make-up of both model and non-model species, which has led to a surge in the use of genomics in fields which were previously considered unfeasible. These advances have greatly expanded the realm of possibilities in the fields of ecology and conservation. It is now possible to the identification of large cohorts of genetic markers, including single nucleotide polymorphisms (SNPs) and larger structural variants, as well as signatures of selection and local adaptation. Markers can be used to identify species, define population …

Genomic Tools Reveal Complex Social Organization Of An Invasive Large Mammal (Sus Scrofa), Chelsea L. Titus, Courtney F. Bowden, Timothy J. Smyser, Stephen L. Webb, James C. Beasley

USDA Wildlife Services: Staff Publications

A comprehensive understanding of sociality in wildlife is vital to optimizing conservation and management efforts. However, sociality is complicated, especially for widely distributed species that exhibit substantive behavioral plasticity. Invasive wild pigs (Sus scrofa), often representing hybrids of European wild boar and domestic pigs, are among the most adaptable and widely distributed large mammals. The social structure of wild pigs is believed to be similar to European wild boar, consisting of matriarchal groups (sounders) and solitary males. However, wild pig social structure is understudied and largely limited to visual observations. Using a hierarchical approach, we incorporated genomic tools …

Genetic Structure Of Urban White-Tailed Deer In West Michigan, Jacob David Brand

Masters Theses

In urban areas, green spaces are used by humans and wildlife. The proximity between them can lead to both positive and negative interactions, which can make managing urban wildlife difficult. Managers are challenged due to conflicts between wildlife population sizes that can be naturally supported versus those that are socially tolerable. White-tailed deer (Odocoileus virginianus) thrive in urban environments because their habitat requirements are met within green spaces and backyard vegetation. Matrilineal groups of urban white-tailed deer live within the same areas, at times forming high densities that can lead to the spread of diseases or environmental pests, including hemlock …

Connections In The Underworld: A Morphological And Molecular Study Of Diversity And Connectivity Among Anchialine Shrimp., Robert Eugene Ditter

FIU Electronic Theses and Dissertations

This research investigates the distribution and population structure of crustaceans, endemic to anchialine systems in the tropical western Atlantic focusing on cave-dwelling shrimp from the family Barbouriidae. Taxonomic and molecular tools (genetic and genomic) are utilized to examine population dynamics and the presence of phenotypic hypervariation (PhyV) of the critically endangered species Barbouria cubensis (von Martens, 1872). The presence of PhyV and its geographic distribution is investigated among anchialine populations of B. cubensis from 34 sites on Abaco, Eleuthera, and San Salvador, Bahamas. Examination of 54 informative morphological characters revealed PhyV present in nearly 90% (n=463) of specimens with no …

Genetic Studies Of Wildlife, Brittaney L. Buchanan

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

Genetic techniques are being more frequently used to understand the biology and management of wildlife species. The wild turkey is one species of genetic interest because the correct identification of individuals to the subspecies level is difficult using traditional methods. Currently phenotypic differences in plumage, especially the upper tail coverts, are used to assign individuals to subspecies. To hunters wanting to complete a “grand slam,” identification of birds’ subspecies is important. This study focuses on the five extant subspecies: Eastern (M. g. silvestris), Osceola (M. g. osceola), Rio Grande (M. g. intermedia), Merriam’s ( …

Application And Refinement Of Molecular Ecology Techniques For Amphibian Conservation, Stephanie Marie Burgess

Electronic Theses and Dissertations

Wildlife conservation has become increasingly difficult due to habitat loss habitat fragmentation and land use change. Thus conservationists have embraced advances in molecular ecology such as landscape genetics and microbial bioinformatics that employ genetic techniques to further understand the relationship between individuals and their environment. In landscape genetics model inferences can be used to identify features that facilitate or resist gene flow providing a framework for anticipating the impacts of land use changes on a species’ ability to disperse. However the factors that affect the transferability of landscape genetics inferences are poorly understood and little is known about the effect …

The Role Of Reproductive Timing As A Driver Of Genetic Differentiation In Populations Of Pacific Herring, Eleni L. Petrou, Todd Sandell, Dayv Lowry, Lorenz Hauser

Salish Sea Ecosystem Conference

There is growing recognition that maintaining diversity in life history traits contributes to the sustainable management of wild populations. One important life history characteristic is reproductive phenology, and it has been shown that differences in the timing of reproduction can act as a barrier to gene flow between populations. If the difference in reproductive timing determines the level of connectivity, one would expect that genetic differentiation between populations would increase as a function of difference in reproductive date. This pattern, known as “isolation by time” (IBT), has been observed in wild populations of salmonids containing early and late runs. Pacific …

Consequences Of Severe Habitat Fragmentation On Density, Genetics, And Spatial Capture-Recapture Analysis Of A Small Bear Population, Sean Mccarthy Murphy, Ben C. Augustine, Wade Allen Ulrey, Joseph Maddox Guthrie, Brian K Scheick, J. Walter Mccown, John J. Cox

Forestry and Natural Resources Faculty Publications

Loss and fragmentation of natural habitats caused by human land uses have subdivided several formerly contiguous large carnivore populations into multiple small and often isolated subpopulations, which can reduce genetic variation and lead to precipitous population declines. Substantial habitat loss and fragmentation from urban development and agriculture expansion relegated the Highlands-Glades subpopulation (HGS) of Florida, USA, black bears (Ursus americanus floridanus) to prolonged isolation; increasing human land development is projected to cause ≥ 50% loss of remaining natural habitats occupied by the HGS in coming decades. We conducted a noninvasive genetic spatial capture-recapture study to quantitatively describe the …

Cellulose- And Xylan-Degrading Thermophilic Anaerobic Bacteria From Biocompost, M. V. Sizova, J. A. Izquierdo, N. S. Panikov, L. R. Lynd

Dartmouth Scholarship

Nine thermophilic cellulolytic clostridial isolates and four other noncellulolytic bacterial isolates were isolated from self-heated biocompost via preliminary enrichment culture on microcrystalline cellulose. All cellulolytic isolates grew vigorously on cellulose, with the formation of either ethanol and acetate or acetate and formate as principal fermentation products as well as lactate and glycerol as minor products. In addition, two out of nine cellulolytic strains were able to utilize xylan and pretreated wood with roughly the same efficiency as for cellulose. The major products of xylan fermentation were acetate and formate, with minor contributions of lactate and ethanol. Phylogenetic analyses of 16S …

Day 2: Thursday, 18 August 2005: Upper Colorado River Endangered Fish Recovery Program, Bob Muth, Tom Pitts, Dan Luecke

Endangered Species Act Congressional Field Tour (August 17-19)

58 pages (includes illustrations and maps).

Contains references.