Life Sciences Commons^™

An Investigation Of Information Structures In Dna, Joel Mohrmann

Department of Electrical and Computer Engineering: Dissertations, Theses, and Student Research

The information-containing nature of the DNA molecule has been long known and observed. One technique for quantifying the relationships existing within the information contained in DNA sequences is an entity from information theory known as the average mutual information (AMI) profile. This investigation sought to use principally the AMI profile along with a few other metrics to explore the structure of the information contained in DNA sequences.

Treating DNA sequences as an information source, several computational methods were employed to model their information structure. Maximum likelihood and maximum a posteriori estimators were used to predict missing bases in DNA sequences. …

Animal Board Invited Review: Practical Applications Of Genomic Information In Livestock, D. P. Berry, Matthew L. Spangler

Department of Animal Science: Faculty Publications

Access to high-dimensional genomic information in many livestock species is accelerating. This has been greatly aided not only by continual reductions in genotyping costs but also an expansion in the services available that leverage genomic information to create a greater return-on-investment. Genomic information on individual animals has many uses including (1) parentage verification and discovery, (2) traceability, (3) karyotyping, (4) sex determination, (5) reporting and monitoring of mutations conferring major effects or congenital defects, (6) better estimating inbreeding of individuals and coancestry among individuals, (7) mating advice, (8) determining breed composition, (9) enabling precision management, and (10) genomic evaluations; genomic …

Error In Dna Mixture Analysis: Why The Application Of Forensic Dna Is Not A Perfect Science, Rachel Bisbee

Honors Theses

Ever since the first use of DNA evidence in 1986, it has been heavily relied on in court as a means of both convicting felons and exonerating wrongfully imprisoned people. It is a valuable tool in investigations, but like everything else, is not perfect. There have been studies on the accuracy of DNA mixture interpretation in the past with varying results. This is because mixture interpretation is a complicated process that is not always as specific as would be ideal. This study attempted to determine if two students with the exact same education in forensic science and, more specifically, DNA …

Incremental Phylogenetics By Repeated Insertions: An Evolutionary Tree Algorithm, Peter Revesz, Zhiqiang Li

School of Computing: Faculty Publications

We introduce the idea of constructing hypothetical evolutionary trees using an incremental algorithm that inserts species one-by-one into the current evolutionary tree. The method of incremental phylogenetics by repeated insertions lead to an algorithm that can be used on DNA, RNA and amino acid sequences. According to experimental results on both synthetic and biological data, the new algorithm generates more accurate evolutionary trees than the UPGMA and the Neighbor Joining algorithms.

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 …

Genome-Wide Prediction Of Age At Puberty And Reproductive Longevity In Sows, Julie Kathleen Tart, Rodger K. Johnson, Justin W. Bundy, N. N. Ferdinand, A. M. Mcknite, Jennifer R. Wood, Phillip S. Miller, M. F. Rothschild, Matthew L. Spangler, Dorian J. Garrick, Stephen D. Kachman, Daniel C. Ciobanu

Department of Animal Science: Faculty Publications

Traditional selection for sow reproductive longevity is ineffective due to low heritability and late expression of the trait. Incorporation of DNA markers into selection programs is potentially a more practical approach for improving sow lifetime productivity. Using a resource population of crossbred gilts, we explored pleiotropic sources of variation that influence age at puberty and reproductive longevity. Of the traits recorded before breeding, only age at puberty significantly affected the probability that females would produce a first parity litter. The genetic variance explained by 1-Mb windows of the sow genome, compared across traits, uncovered regions that influence both age at …

Genome-Wide Association Analyses Of Sow Reproduction And Lifetime Productivity, Daniel Ciobanu

Department of Animal Science: Faculty Publications

Concurrent with increased prolificacy, high sow death losses and replacement rates are serious economic and welfare issues facing producers. Reproductive failure is the most frequent reason for culling sows. Lifetime productivity is characterized by moderate heritability and high phenotypic variance and, as a result, substantial genetic variation is expected to exist in most populations. Traditional selection for sow reproductive longevity results is ineffective due to low heritability and late expression of the trait. The primary goal of this research project was to identify DNA markers associated with reproductive and sow lifetime productivity that can be used in nucleus herds to …

Identification Of Markers Associated With Sow Lifetime Productivity For Whole Genomic Selection, Daniel Ciobanu

Department of Animal Science: Faculty Publications

Sows are more productive today than ever before. However, concurrent with increased prolificacy, high sow death losses and replacement rates are serious economic and welfare issues facing producers. Reproductive failure is the most frequent reason for culling sows. Length of productive life is moderately heritable and has high variance; thus, substantial genetic variation is expected to exist in most populations. Genetic improvement in the swine industry occurs from selection in nucleus herds and is then transmitted through the breeding pyramid in the multiplication process. Thus, it is critical to identify selection methods that can be applied in nucleus herds that …