Bioinformatic methods in mammalian genomics: applications towards conservation and health

Three bioinformatic investigations are conducted to address complex challenges in wildlife conservation and human health. Each study applies computational approaches to distinct biological systems, collectively demonstrating the versatility and impact of bioinformatics in solving real-world problems. The first study focuses on the conservation of African lions (Panthera leo) by developing the Lion Localizer, an interactive software platform designed to infer the geographic provenance of confiscated lion body parts using mitochondrial DNA. By compiling a curated database of cytochrome b sequences from published sources and mapping haplotypes to known geographic origins, Lion Localizer enables users to submit query sequences and receive automated provenance predictions. The platform is intended to enable law enforcement and forensic teams to rapidly assess origin and potential trafficking patterns. The second study examines the genetic composition of giraffes housed in North American zoos and private ranches. Using whole-genome sequencing of 52 ex situ giraffes and comparing them to 63 wild individuals from all four recognized giraffe species, population genomic analyses—including admixture, local ancestry inference, and mitochondrial phylogenetics—reveal extensive hybridization in ex situ populations. Most ex situ individuals exhibit mixed ancestry, primarily between northern and reticulated giraffe lineages, with only a small subset retaining high assignment to a single species. These findings raise concerns about the conservation value of existing giraffe assurance populations in North America and call for strategic reassessment of breeding programs to preserve lineage-specific genetic diversity. The third study explores the role of insertionally polymorphic human endogenous retrovirus K (HERV-K) loci in disease, using a case-control dataset of amyotrophic lateral sclerosis (ALS) patients and neurologically healthy individuals. By leveraging previously reported HERV-K loci, applying k-mer-based genotyping, and incorporating Hardy-Weinberg Equilibrium analysis, this approach demonstrates its potential for detecting loci that may be under selective pressure or associated with disease. Notably, one locus (chr12:55727215) showed a significant deviation from HWE, potentially due solo-LTRs—rather than the initially hypothesized distinction between HERV insertions and pre-insertion alleles. This raises the possibility that solo-LTRs represent an alternative allelic state at this locus and warrant further investigation. These findings highlight the value of the proposed methodological framework, which offers a scalable and generalizable strategy for evaluating ERV-disease associations and can be readily extended to other repetitive elements and clinical conditions. Collectively, these studies demonstrate how bioinformatics can be applied across diverse biological domains—from wildlife conservation to human genomics—to trace lineage origins, uncover patterns of genetic structure, and identify loci of potential functional importance.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Informatics

Grantor

University of Illinois Urbana-Champaign

Year dc:date

2025

Author dc:creator

• Au, Wesley

Contributors dc:contributor

• Roca, Alfred L.
• Roca, Alfred L
• Malhi, Ripan S
• Catchen, Julian
• Tan, Milton

• Bioinformatics
• Mammalian Genomics
• Cytochrome B
• Forensics
• Haplotype
• Lions
• Poaching
• Wildlife Trafficking
• Admixture
• Assurance Populations
• Ex Situ Conservation
• Hybridization
• Population Genomics
• Whole-genome Analysis
• Herv-k
• Structural Variant

Statement dc:rights

• Copyright 2025 Wesley Au

Language dc:language

en, eng

Handle dc:identifier

https://hdl.handle.net/2142/129836

OAI record oai:identifier

https://www.ideals.illinois.edu/oai-pmh?verb=GetRecord&metadataPrefix=etdms&identifier=oai%3Awww.ideals.illinois.edu%3A2142%2F129836