Population genetics of the endemic red-chested sea cucumber, Hemiocnus insolens, along the southern coastline of Africa

Simple item page
dc.contributor.advisorRocke, Emma
dc.contributor.advisorKarenyi Natasha
dc.contributor.authorHo, Yi-Ting
dc.date.accessioned2024-04-30T12:56:30Z
dc.date.available2024-04-30T12:56:30Z
dc.date.issued2023
dc.date.updated2024-04-25T14:19:40Z
dc.description.abstractHemiocnus insolens is the endemic red-chested sea cucumber (or holothuroid) of South Africa, found along the coastline spanning from Port Elizabeth, South Africa to Lüderitz, Namibia. They present as three colour variations (red, yellow, and white) prompting the existence of possible cryptic species. The aim of the study is to sequence the genomic markers of each colour variation using Sanger sequencing and metagenomic sequencing to analyse their phylogenetic and associated community structure to delimit whether the colour variations of H. insolens are a single species or a possible species complex. DNA was extracted from tissue of whole preserved (99% ethanol AR) samples and were sequenced for 16S rRNA and COI gene regions (Sanger sequencing) as well as their metagenomes (Oxford Nanopore Technologies). ChromasPro and seaview.exe were used for sequence analysis and tree building, respectively. MGnify and Flye were used for assessing the metagenomics of selected samples. Parsimony-based tree fitting was generated for 16S rRNA and COI which suggested that some differentiation between white samples, and red and yellow samples (BP = 100) (Figure 2.1, Figure 2.2). According to population genetics and phylogeography, these species can be considered as cryptic species due to their phylogeographic breaks bolstering the separation of certain colour variations. Metagenome-assembled genomes (MAGs) were used to further explore the community structure of each sample/colour variation and were holistically compared to the parsimony-based phylogenetic trees to support these differences and provide explanations. Results suggested some differences in gene expression and microbiome diversity between the colour variations; however, these results were preliminary as a result of small sample size and low throughput in sequencing. Metagenome studies provided some insight into creating a conceptual model of how the environment could affect the colour expression of H. insolens.
dc.identifier.apacitationHo, Y. (2023). <i>Population genetics of the endemic red-chested sea cucumber, Hemiocnus insolens, along the southern coastline of Africa</i>. (). ,Faculty of Science ,Department of Biological Sciences. Retrieved from http://hdl.handle.net/11427/39522en_ZA
dc.identifier.chicagocitationHo, Yi-Ting. <i>"Population genetics of the endemic red-chested sea cucumber, Hemiocnus insolens, along the southern coastline of Africa."</i> ., ,Faculty of Science ,Department of Biological Sciences, 2023. http://hdl.handle.net/11427/39522en_ZA
dc.identifier.citationHo, Y. 2023. Population genetics of the endemic red-chested sea cucumber, Hemiocnus insolens, along the southern coastline of Africa. . ,Faculty of Science ,Department of Biological Sciences. http://hdl.handle.net/11427/39522en_ZA
dc.identifier.ris TY - Thesis / Dissertation AU - Ho, Yi-Ting AB - Hemiocnus insolens is the endemic red-chested sea cucumber (or holothuroid) of South Africa, found along the coastline spanning from Port Elizabeth, South Africa to Lüderitz, Namibia. They present as three colour variations (red, yellow, and white) prompting the existence of possible cryptic species. The aim of the study is to sequence the genomic markers of each colour variation using Sanger sequencing and metagenomic sequencing to analyse their phylogenetic and associated community structure to delimit whether the colour variations of H. insolens are a single species or a possible species complex. DNA was extracted from tissue of whole preserved (99% ethanol AR) samples and were sequenced for 16S rRNA and COI gene regions (Sanger sequencing) as well as their metagenomes (Oxford Nanopore Technologies). ChromasPro and seaview.exe were used for sequence analysis and tree building, respectively. MGnify and Flye were used for assessing the metagenomics of selected samples. Parsimony-based tree fitting was generated for 16S rRNA and COI which suggested that some differentiation between white samples, and red and yellow samples (BP = 100) (Figure 2.1, Figure 2.2). According to population genetics and phylogeography, these species can be considered as cryptic species due to their phylogeographic breaks bolstering the separation of certain colour variations. Metagenome-assembled genomes (MAGs) were used to further explore the community structure of each sample/colour variation and were holistically compared to the parsimony-based phylogenetic trees to support these differences and provide explanations. Results suggested some differences in gene expression and microbiome diversity between the colour variations; however, these results were preliminary as a result of small sample size and low throughput in sequencing. Metagenome studies provided some insight into creating a conceptual model of how the environment could affect the colour expression of H. insolens. DA - 2023 DB - OpenUCT DP - University of Cape Town KW - Biological Sciences LK - https://open.uct.ac.za PY - 2023 T1 - Population genetics of the endemic red-chested sea cucumber, Hemiocnus insolens, along the southern coastline of Africa TI - Population genetics of the endemic red-chested sea cucumber, Hemiocnus insolens, along the southern coastline of Africa UR - http://hdl.handle.net/11427/39522 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/39522
dc.identifier.vancouvercitationHo Y. Population genetics of the endemic red-chested sea cucumber, Hemiocnus insolens, along the southern coastline of Africa. []. ,Faculty of Science ,Department of Biological Sciences, 2023 [cited yyyy month dd]. Available from: http://hdl.handle.net/11427/39522en_ZA
dc.language.rfc3066Eng
dc.publisher.departmentDepartment of Biological Sciences
dc.publisher.facultyFaculty of Science
dc.subjectBiological Sciences
dc.titlePopulation genetics of the endemic red-chested sea cucumber, Hemiocnus insolens, along the southern coastline of Africa
dc.typeThesis / Dissertation
dc.type.qualificationlevelMasters
dc.type.qualificationlevelMSc
Files
Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
thesis_sci_2023_ho yi ting.pdf
Size:
1.96 MB
Format:
Adobe Portable Document Format
Description:
Download
License bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
license.txt
Size:
1.72 KB
Format:
Item-specific license agreed upon to submission
Description:
Download
Collections
Masters