DNA barcoding is a molecular based technique used to separate and identify individual species. Here we establish a DNA Barcode library for the orchid flora of an Andean cloud forest in Northwestern Ecuador. The library contains 135 matK and 136 rbcL DNA Barcodes representing over 33 Orchidaceae genera. Sequence analysis shows percent species resolution was higher for matK (98.8%) than rbcL (70.24%), with a large portion of the unresolved species for the rbcL loci coming from taxonomically complex genera in the subtribe Pleurothallidinae. Neighbor Joining (NJ) trees revealed that the orchid flora of Siempre Verde is divided taxonomically into two large monophyletic clades at the sub family level; Orchidoideae and Epidendroideae. Sequences within Orchidoideae presented with high bootstrap support across all NJ trees (matK, rbcL and matK+rbcL), indicating species within the clade are well resolved. Resolution for sequences within sub family Epidendroideae varied depending on taxonomic clade and loci used. Overall the matK NJ tree outperformed the rbcL NJ tree by delivering monophyletic clades at the subfamily, tribe, and subtribe level with higher bootstrap values, separating a higher number of congeners, particularly those in taxonomically complex genera such as Pleurothallis, Stelis, and Lepanthes. Estimates of evolutionary divergence showed a very low level of intraspecific variation in DNA Barcodes of target cryptic species Oncidium heteranthum, acknowledging that floral traits in Oncidium are often highly plastic, and not indicative of species lines.
","abstract_html":"<p>DNA barcoding is a molecular based technique used to separate and identify individual species. Here we establish a DNA Barcode library for the orchid flora of an Andean cloud forest in Northwestern Ecuador. The library contains 135 <em>matK</em> and 136 <em>rbcL</em> DNA Barcodes representing over 33 Orchidaceae genera. Sequence analysis shows percent species resolution was higher for <em>matK</em> (98.8%) than <em>rbc</em>L (70.24%), with a large portion of the unresolved species for the <em>rbcL</em> loci coming from taxonomically complex genera in the subtribe Pleurothallidinae. Neighbor Joining (NJ) trees revealed that the orchid flora of Siempre Verde is divided taxonomically into two large monophyletic clades at the sub family level; Orchidoideae and Epidendroideae. Sequences within Orchidoideae presented with high bootstrap support across all NJ trees (<em>matK, rbcL and matK+rbc</em>L), indicating species within the clade are well resolved. Resolution for sequences within sub family Epidendroideae varied depending on taxonomic clade and loci used. Overall the <em>matK</em> NJ tree outperformed the <em>rbcL</em> NJ tree by delivering monophyletic clades at the subfamily, tribe, and subtribe level with higher bootstrap values, separating a higher number of congeners, particularly those in taxonomically complex genera such as <em>Pleurothallis, Stelis</em>, and <em>Lepanthes</em>. Estimates of evolutionary divergence showed a very low level of intraspecific variation in DNA Barcodes of target cryptic species <em>Oncidium</em> <em>heteranthum</em>, acknowledging that floral traits in <em>Oncidium</em> are often highly plastic, and not indicative of species lines.</p>","abstract_has_math":false,"creators":["Bucalo, Kylie"],"institution":null,"degree_name":"Biology","degree_level":"Thesis","degree_discipline":"Biology","degree_department":null,"school":null,"contributors":["Dr. Kevin Burgess","Alvaro Perez","Dr. Jennifer Cruse-Sanders"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2016,"date_issued":"2016-01-01T08:00:00Z","date_published":"2016-01-01T08:00:00Z","updated_at":"2026-07-24T01:44:55Z","subjects":["Ecuador","Orchid","DNA Barcode","Pleurothallis","Epidendrum","Stelis","Lepanthes","Oncidium","Biology","Botany","Plant Biology"],"languages":["English"],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://csuepress.columbusstate.edu/theses_dissertations/277","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Dr. Kevin Burgess","Alvaro Perez","Dr. Jennifer Cruse-Sanders"]},{"key":"dc:creator","label":"Author","values":["Bucalo, Kylie"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.available","label":"Dc Date Available","values":["2018-08-09T07:00:00Z"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Biology"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Biology"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Ecuador","Orchid","DNA Barcode","Pleurothallis","Epidendrum","Stelis","Lepanthes","Oncidium","Biology","Botany","Plant Biology"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["English"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://csuepress.columbusstate.edu/theses_dissertations/277"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["DNA barcoding is a molecular based technique used to separate and identify individual species. Here we establish a DNA Barcode library for the orchid flora of an Andean cloud forest in Northwestern Ecuador. The library contains 135 matK and 136 rbcL DNA Barcodes representing over 33 Orchidaceae genera. Sequence analysis shows percent species resolution was higher for matK (98.8%) than rbcL (70.24%), with a large portion of the unresolved species for the rbcL loci coming from taxonomically complex genera in the subtribe Pleurothallidinae. Neighbor Joining (NJ) trees revealed that the orchid flora of Siempre Verde is divided taxonomically into two large monophyletic clades at the sub family level; Orchidoideae and Epidendroideae. Sequences within Orchidoideae presented with high bootstrap support across all NJ trees (matK, rbcL and matK+rbcL), indicating species within the clade are well resolved. Resolution for sequences within sub family Epidendroideae varied depending on taxonomic clade and loci used. Overall the matK NJ tree outperformed the rbcL NJ tree by delivering monophyletic clades at the subfamily, tribe, and subtribe level with higher bootstrap values, separating a higher number of congeners, particularly those in taxonomically complex genera such as Pleurothallis, Stelis, and Lepanthes. Estimates of evolutionary divergence showed a very low level of intraspecific variation in DNA Barcodes of target cryptic species Oncidium heteranthum, acknowledging that floral traits in Oncidium are often highly plastic, and not indicative of species lines.
"]},{"key":"dc:title","label":"Title","values":["Evaluating the Evolutionary and Genetic Relationships of the Andean Orchids of Northwestern Ecuador"]}]}],"canonical_facts":{"dc:contributor":["Dr. Kevin Burgess","Alvaro Perez","Dr. Jennifer Cruse-Sanders"],"dc:creator":["Bucalo, Kylie"],"dc:date.available":["2018-08-09T07:00:00Z"],"dc:description.abstract":["DNA barcoding is a molecular based technique used to separate and identify individual species. Here we establish a DNA Barcode library for the orchid flora of an Andean cloud forest in Northwestern Ecuador. The library contains 135 matK and 136 rbcL DNA Barcodes representing over 33 Orchidaceae genera. Sequence analysis shows percent species resolution was higher for matK (98.8%) than rbcL (70.24%), with a large portion of the unresolved species for the rbcL loci coming from taxonomically complex genera in the subtribe Pleurothallidinae. Neighbor Joining (NJ) trees revealed that the orchid flora of Siempre Verde is divided taxonomically into two large monophyletic clades at the sub family level; Orchidoideae and Epidendroideae. Sequences within Orchidoideae presented with high bootstrap support across all NJ trees (matK, rbcL and matK+rbcL), indicating species within the clade are well resolved. Resolution for sequences within sub family Epidendroideae varied depending on taxonomic clade and loci used. Overall the matK NJ tree outperformed the rbcL NJ tree by delivering monophyletic clades at the subfamily, tribe, and subtribe level with higher bootstrap values, separating a higher number of congeners, particularly those in taxonomically complex genera such as Pleurothallis, Stelis, and Lepanthes. Estimates of evolutionary divergence showed a very low level of intraspecific variation in DNA Barcodes of target cryptic species Oncidium heteranthum, acknowledging that floral traits in Oncidium are often highly plastic, and not indicative of species lines.
"],"dc:identifier":["https://csuepress.columbusstate.edu/theses_dissertations/277"],"dc:language":["English"],"dc:subject":["Ecuador","Orchid","DNA Barcode","Pleurothallis","Epidendrum","Stelis","Lepanthes","Oncidium","Biology","Botany","Plant Biology"],"dc:title":["Evaluating the Evolutionary and Genetic Relationships of the Andean Orchids of Northwestern Ecuador"],"thesis:degree_discipline":["Biology"],"thesis:degree_level":["Thesis"],"thesis:degree_name":["Biology"]},"updated_at":"2026-07-24T01:44:55Z"}