Kentucky’s limestone caves and karst water systems are an ecologically important part of its natural heritage and home to many unique subterranean species. In addition to being geologically interesting, it is also home to one, of only three, extant North American atyids: the federally endangered Kentucky Cave Shrimp (Palaemonias ganteri, Hay 1901). However, access for monitoring and management objectives involving this species and other cave inhabitants can be difficult, highly contingent upon environmental conditions, and time consuming with low yields using traditional techniques. Advancements in metabarcoding and Next Generation Sequencing (NGS) technologies provide tools that may allow researchers and managers to address some of the hurdles posed by the difficult environment where P. ganteri lives.
This study was able to identify the presence of P. ganteri DNA at seven locations in addition to inferring six distinct variations between homologous COI shrimp sequences and confirming the presence of one known shrimp variant. Metabarcoding identified some close variations to reference sequences for cave obligates, but more importantly, highlighted the need for better references when conducting cave faunal surveys with eDNA techniques. These findings not only have implications for better surveillance of P. ganteri and other cave inhabitants, but also open up the possibility for improving management goals by incorporating population-level genetic information that can be considered for each groundwater basin.
","abstract_html":"<p>Kentucky’s limestone caves and karst water systems are an ecologically important part of its natural heritage and home to many unique subterranean species. In addition to being geologically interesting, it is also home to one, of only three, extant North American atyids: the federally endangered Kentucky Cave Shrimp (Palaemonias ganteri, Hay 1901). However, access for monitoring and management objectives involving this species and other cave inhabitants can be difficult, highly contingent upon environmental conditions, and time consuming with low yields using traditional techniques. Advancements in metabarcoding and Next Generation Sequencing (NGS) technologies provide tools that may allow researchers and managers to address some of the hurdles posed by the difficult environment where P. ganteri lives. </p> <p>This study was able to identify the presence of P. ganteri DNA at seven locations in addition to inferring six distinct variations between homologous COI shrimp sequences and confirming the presence of one known shrimp variant. Metabarcoding identified some close variations to reference sequences for cave obligates, but more importantly, highlighted the need for better references when conducting cave faunal surveys with eDNA techniques. These findings not only have implications for better surveillance of P. ganteri and other cave inhabitants, but also open up the possibility for improving management goals by incorporating population-level genetic information that can be considered for each groundwater basin. </p>","abstract_has_math":false,"creators":["Stump, Andrew Joseph"],"institution":"Eastern Kentucky University","degree_name":"Master of Science (MS)","degree_level":"Master's","degree_discipline":"Biological Sciences","degree_department":null,"school":null,"contributors":[],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2019,"date_issued":"2019-01-01T08:00:00Z","date_published":"2019-01-01T08:00:00Z","updated_at":"2026-07-24T02:15:53Z","subjects":["environmental DNA","haplotype","Kentucky Cave Shrimp","metabarcoding","Bioinformatics","Terrestrial and Aquatic Ecology"],"languages":[],"rights":["Copyright 2019 Andrew Joseph Stump"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://encompass.eku.edu/etd/651","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:creator","label":"Author","values":["Stump, Andrew Joseph"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:publisher","label":"Institution","values":["Encompass Digital Archive, Eastern Kentucky University"]},{"key":"dc:type","label":"Dc Type","values":["Master Thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Biological Sciences"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Master's"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Master of Science (MS)"]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["Eastern Kentucky University"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["environmental DNA","haplotype","Kentucky Cave Shrimp","metabarcoding","Bioinformatics","Terrestrial and Aquatic Ecology"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2019 Andrew Joseph Stump"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://encompass.eku.edu/etd/651"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Kentucky’s limestone caves and karst water systems are an ecologically important part of its natural heritage and home to many unique subterranean species. In addition to being geologically interesting, it is also home to one, of only three, extant North American atyids: the federally endangered Kentucky Cave Shrimp (Palaemonias ganteri, Hay 1901). However, access for monitoring and management objectives involving this species and other cave inhabitants can be difficult, highly contingent upon environmental conditions, and time consuming with low yields using traditional techniques. Advancements in metabarcoding and Next Generation Sequencing (NGS) technologies provide tools that may allow researchers and managers to address some of the hurdles posed by the difficult environment where P. ganteri lives.
This study was able to identify the presence of P. ganteri DNA at seven locations in addition to inferring six distinct variations between homologous COI shrimp sequences and confirming the presence of one known shrimp variant. Metabarcoding identified some close variations to reference sequences for cave obligates, but more importantly, highlighted the need for better references when conducting cave faunal surveys with eDNA techniques. These findings not only have implications for better surveillance of P. ganteri and other cave inhabitants, but also open up the possibility for improving management goals by incorporating population-level genetic information that can be considered for each groundwater basin.
"]},{"key":"dc:format","label":"Dc Format","values":["application/PDF"]},{"key":"dc:source","label":"Dc Source","values":["Encompass Digital Archive: Online Theses and Dissertations"]},{"key":"dc:title","label":"Title","values":["The use of environmental DNA for the detection of Palaemonias ganteri (Hay, 1901), a federally endangered cave species"]}]}],"canonical_facts":{"dc:creator":["Stump, Andrew Joseph"],"dc:description.abstract":["Kentucky’s limestone caves and karst water systems are an ecologically important part of its natural heritage and home to many unique subterranean species. In addition to being geologically interesting, it is also home to one, of only three, extant North American atyids: the federally endangered Kentucky Cave Shrimp (Palaemonias ganteri, Hay 1901). However, access for monitoring and management objectives involving this species and other cave inhabitants can be difficult, highly contingent upon environmental conditions, and time consuming with low yields using traditional techniques. Advancements in metabarcoding and Next Generation Sequencing (NGS) technologies provide tools that may allow researchers and managers to address some of the hurdles posed by the difficult environment where P. ganteri lives.
This study was able to identify the presence of P. ganteri DNA at seven locations in addition to inferring six distinct variations between homologous COI shrimp sequences and confirming the presence of one known shrimp variant. Metabarcoding identified some close variations to reference sequences for cave obligates, but more importantly, highlighted the need for better references when conducting cave faunal surveys with eDNA techniques. These findings not only have implications for better surveillance of P. ganteri and other cave inhabitants, but also open up the possibility for improving management goals by incorporating population-level genetic information that can be considered for each groundwater basin.
"],"dc:format":["application/PDF"],"dc:identifier":["https://encompass.eku.edu/etd/651"],"dc:publisher":["Encompass Digital Archive, Eastern Kentucky University"],"dc:rights":["Copyright 2019 Andrew Joseph Stump"],"dc:source":["Encompass Digital Archive: Online Theses and Dissertations"],"dc:subject":["environmental DNA","haplotype","Kentucky Cave Shrimp","metabarcoding","Bioinformatics","Terrestrial and Aquatic Ecology"],"dc:title":["The use of environmental DNA for the detection of Palaemonias ganteri (Hay, 1901), a federally endangered cave species"],"dc:type":["Master Thesis"],"thesis:degree_discipline":["Biological Sciences"],"thesis:degree_level":["Master's"],"thesis:degree_name":["Master of Science (MS)"],"thesis:institution_name":["Eastern Kentucky University"]},"updated_at":"2026-07-24T02:15:53Z"}