Profiling Populations Using Neutral Markers, Major Histocompatibility Complex Genes and Volatile Organic Compounds as Modeled in Equus caballus Linnaeus

Authors

Ketaki Deshpande, Florida International UniversityFollow

Document Type

Dissertation

Degree

Doctor of Philosophy (PhD)

Major/Program

Biology

First Advisor's Name

DeEtta Mills

First Advisor's Committee Title

Committee Chair

Second Advisor's Name

Kenneth Furton

Second Advisor's Committee Title

Committee member

Third Advisor's Name

Robert Lickliter

Third Advisor's Committee Title

Committee member

Fourth Advisor's Name

Jeffrey Wells

Fourth Advisor's Committee Title

Committee member

Fifth Advisor's Name

Eric von Wettberg

Fifth Advisor's Committee Title

Committee member

Sixth Advisor's Committee Title

Committee member

Keywords

Equine, Volatilome, Major histocompatibility complex, odor, kinship, fecal, PCT, wild horses

Date of Defense

10-3-2016

Abstract

Assessing the genetics of wild animal populations aims to understand selective pressures, and factors whether it be inbreeding or adaptation, that affect the genome. Although numerous techniques are available for assessing population structure, a major obstacle in studying wild populations is obtaining samples from the animals without having to capture them, which can lead to undue distress and injury. Therefore, biologists often use non-invasive sampling methods (i.e., collection of feces, hair) to extract host DNA. In this study, new DNA extraction protocols were developed that improved the quality and quantity of DNA obtained from fecal matter. Fecal samples aged up to Day 6 as well as field samples with unknown days since defecation were successful in individualization of the contributors using microsatellites and were further used to demonstrate kinship. Neutral markers such as short tandem repeat, and mitochondrial D-loop sequences are used for assessing relatedness and evolutionary relationships and can mutate without detrimental effects on the organism. Loci, such as the major histocompatibility complex (MHC), adapt more rapidly under selective pressure such as parasite load, or resistance to diseases and support natural selection processes. Analysis of the neutral microsatellites in Big Summit feral horse population demonstrated a population lacking diversity and trending towards being an inbred population. However, examination of the MHC genes showed maintenance of greater variation that may be the result of selection pressures. The MHC similarity and lower genetic demarcation between geographically separated horse populations further indicated effect of selection pressures in preserving diversity at the MHC genes. Although such molecular markers are used in profiling populations, the current study was also successful in demonstrating the use of individual odor profiles as an additional profiling tool. Volatile organic compounds (VOC) obtained from hair of domestic horses were able to individualize horses as well as differentiate between horse breeds and display kinship. The relation of genetics to odor phenotype is of interest as the inherent polymorphic nature of MHC genes has the potential to generate unique combinations of genotypes that presumably produce distinct odor phenotypes. Subsequently, this study was able to show a significant correlation between MHC genotypes and VOC odor profiles in horses. Understanding the relationship between MHC and odor using domestic horses with known relatedness provides evidence that these same correlations may be applicable to wild equids and dictates their harem hierarchal social structure.

Identifier

FIDC001190

ORCID

orcid.org/0000-0002-3131-5748

Recommended Citation

Deshpande, Ketaki, "Profiling Populations Using Neutral Markers, Major Histocompatibility Complex Genes and Volatile Organic Compounds as Modeled in Equus caballus Linnaeus" (2016). FIU Electronic Theses and Dissertations. 3044.
https://digitalcommons.fiu.edu/etd/3044