{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/129836"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/129836","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Bioinformatic methods in mammalian genomics: applications towards conservation and health","abstract":"Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2025-10-20 without embargo terms","abstract_html":"Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2025-10-20 without embargo terms","abstract_has_math":false,"creators":["Au, Wesley"],"institution":"University of Illinois Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Informatics","degree_department":null,"school":null,"contributors":["Roca, Alfred L.","Roca, Alfred L","Malhi, Ripan S","Catchen, Julian","Tan, Milton"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2025,"date_issued":"2025-07-11","date_published":"2025-07-11","updated_at":"2026-07-22T22:25:05Z","subjects":["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"],"languages":["en","eng"],"rights":["Copyright 2025 Wesley Au"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/2142/129836","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Roca, Alfred L.","Roca, Alfred L","Malhi, Ripan S","Catchen, Julian","Tan, Milton"]},{"key":"dc:creator","label":"Author","values":["Au, Wesley"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2025-07-11","2025-08"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Informatics"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["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"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en","eng"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2025 Wesley Au"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://hdl.handle.net/2142/129836"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2025-10-20 without embargo terms","The student, Wesley Au, accepted the attached license on 2025-07-01 at 10:59.","The student, Wesley Au, submitted this Dissertation for approval on 2025-07-01 at 11:14.","This Dissertation was approved for publication on 2025-07-11 at 14:45.","DSpace SAF Submission Ingestion Package generated from Vireo submission #22391 on 2025-10-20 at 16:57:24","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."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Bioinformatic methods in mammalian genomics: applications towards conservation and health"]}]}],"canonical_facts":{"dc:contributor":["Roca, Alfred L.","Roca, Alfred L","Malhi, Ripan S","Catchen, Julian","Tan, Milton"],"dc:creator":["Au, Wesley"],"dc:date":["2025-07-11","2025-08"],"dc:description":["Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2025-10-20 without embargo terms","The student, Wesley Au, accepted the attached license on 2025-07-01 at 10:59.","The student, Wesley Au, submitted this Dissertation for approval on 2025-07-01 at 11:14.","This Dissertation was approved for publication on 2025-07-11 at 14:45.","DSpace SAF Submission Ingestion Package generated from Vireo submission #22391 on 2025-10-20 at 16:57:24","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."],"dc:format":["application/pdf"],"dc:identifier":["https://hdl.handle.net/2142/129836"],"dc:language":["en","eng"],"dc:rights":["Copyright 2025 Wesley Au"],"dc:subject":["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"],"dc:title":["Bioinformatic methods in mammalian genomics: applications towards conservation and health"],"dc:type":["text"],"thesis:degree_discipline":["Informatics"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois Urbana-Champaign"]},"updated_at":"2026-07-22T22:25:05Z"}