Genetic diversity of the green (Chelonia mydas) and hawksbill (Eretmochel YS imbricata) turtles and the prevalence of chelonid fibropapilloma-associated Herpesvirus (CFPHV) in Mabul Island, Sabah, Malaysia

The plummeting number of the Green and Hawksbill turtles in Malaysia is a rising concern due to the possible effects towards the population of these endangered species. Mabul Island, Sabah is an important feeding ground for both Green (Che/onia mydas) and Hawksbill turtles (Eretmochelys imbricata)....

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Main Author:	Aswini Leela Loganathan
Format:	Thesis
Language:	English English
Published:	2018
Subjects:	QL640-669.3 Reptiles and amphibians
Online Access:	https://eprints.ums.edu.my/id/eprint/38297/1/24%20PAGES.pdf https://eprints.ums.edu.my/id/eprint/38297/2/FULLTEXT.pdf
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id	my-ums-ep.38297
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spelling	my-ums-ep.382972024-02-20T03:35:58Z Genetic diversity of the green (Chelonia mydas) and hawksbill (Eretmochel YS imbricata) turtles and the prevalence of chelonid fibropapilloma-associated Herpesvirus (CFPHV) in Mabul Island, Sabah, Malaysia 2018 Aswini Leela Loganathan QL640-669.3 Reptiles and amphibians The plummeting number of the Green and Hawksbill turtles in Malaysia is a rising concern due to the possible effects towards the population of these endangered species. Mabul Island, Sabah is an important feeding ground for both Green (Che/onia mydas) and Hawksbill turtles (Eretmochelys imbricata). An important aspect of conservation efforts today is the use of genetic markers to study endangered and threatened species. This study aims to first, evaluate levels of genetic diversity and gene flow in foraging turtles from Mabul Island using microsatellite markers. Secondly, mitochondrial (mtDNA) markers were used to analyse the migration pattern and origin of the sea turtles in Mabul Island. Lastly, a test to determine the occurrence of Fibropapillomatosis (FP) in sea turtle was also carried out using validated PCR assay. A total of 131 turtle samples (115 Green and 16 Hawksbill turtles) were obtained from foraging grounds in Mabul Island. Microsatellite discovery was performed on a Pacific Biosciences single molecule real time sequencer using circular consensus sequencer (CCS). From the CCS reads, a total of 4,070 microsatellites from Green and 3,411 microsatellites from Hawksbill turtles were identified using Msatcommander software, from which 60 pairs of primers were designed . The microsatellite markers were analysed using QIAxcel DNA high-resolution kit and subsequently tested on the foraging turtle samples from Mabul Island. A total of 49 novel polymorphic markers were developed in this study. The genetic diversity for both Green and Hawksbill turtle population in Mabul Island were estimated to be high with the mean expected heterozygosity (HE) and observed heterozygosity (Ho) of 0. 95 and 0.83 respectively for the Green turtle population. As for the Hawksbill turtle, the mean expected heterozygosity (HE) and observed heterozygosity (Ho) was 0.88 and 0. 77 respectively. Besides that, a ~800 bp fragment of the mtDNA control region D-Loop was amplified using the primers LTEi9 and H950 to investigate the population structure and determine the natal origin of sea turtle populations from Mabul Island. A total of 26 haplotypes were identified from 97 Green turtle individuals. Consequently, the statistical analysis showed a high estimation of nucleotide and haplotype diversity indices of n= 0.0097 and h= 0.9980 respectively for the Mabul Green turtle population. In addition, a PCR-based assay that targets 4 conserved CFPHV genes (UL18, UL22, UL27 and UL30) was used to screen 131 Green and Hawksbill turtles from Mabul Island. The screening included both FP tumour-exhibiting and clinically healthy individuals. From the analysis, nine Green turtles were positive for the FP tumours. This is the first reported case of Fibropapillomatosis in Sabah. Data estimated from this thesis could be used to infer the loss of the genetic diversity and to develop conservation strategies for enforcement agencies in Sabah. Furthermore, the data provides a new perspective and evidence into the occurrence and phylogeographic variation of FP in Mabul Island. In conclusion, this research provided a platform that contributes invaluable resources to construct future functional studies and collaborations in order to reinforce protection of these endangered species. 2018 Thesis https://eprints.ums.edu.my/id/eprint/38297/ https://eprints.ums.edu.my/id/eprint/38297/1/24%20PAGES.pdf text en public https://eprints.ums.edu.my/id/eprint/38297/2/FULLTEXT.pdf text en validuser dphil doctoral Universiti Malaysia Sabah Institut Penyelidikan Bioteknologi
institution	Universiti Malaysia Sabah
collection	UMS Institutional Repository
language	English English
topic	QL640-669.3 Reptiles and amphibians
spellingShingle	QL640-669.3 Reptiles and amphibians Aswini Leela Loganathan Genetic diversity of the green (Chelonia mydas) and hawksbill (Eretmochel YS imbricata) turtles and the prevalence of chelonid fibropapilloma-associated Herpesvirus (CFPHV) in Mabul Island, Sabah, Malaysia
description	The plummeting number of the Green and Hawksbill turtles in Malaysia is a rising concern due to the possible effects towards the population of these endangered species. Mabul Island, Sabah is an important feeding ground for both Green (Che/onia mydas) and Hawksbill turtles (Eretmochelys imbricata). An important aspect of conservation efforts today is the use of genetic markers to study endangered and threatened species. This study aims to first, evaluate levels of genetic diversity and gene flow in foraging turtles from Mabul Island using microsatellite markers. Secondly, mitochondrial (mtDNA) markers were used to analyse the migration pattern and origin of the sea turtles in Mabul Island. Lastly, a test to determine the occurrence of Fibropapillomatosis (FP) in sea turtle was also carried out using validated PCR assay. A total of 131 turtle samples (115 Green and 16 Hawksbill turtles) were obtained from foraging grounds in Mabul Island. Microsatellite discovery was performed on a Pacific Biosciences single molecule real time sequencer using circular consensus sequencer (CCS). From the CCS reads, a total of 4,070 microsatellites from Green and 3,411 microsatellites from Hawksbill turtles were identified using Msatcommander software, from which 60 pairs of primers were designed . The microsatellite markers were analysed using QIAxcel DNA high-resolution kit and subsequently tested on the foraging turtle samples from Mabul Island. A total of 49 novel polymorphic markers were developed in this study. The genetic diversity for both Green and Hawksbill turtle population in Mabul Island were estimated to be high with the mean expected heterozygosity (HE) and observed heterozygosity (Ho) of 0. 95 and 0.83 respectively for the Green turtle population. As for the Hawksbill turtle, the mean expected heterozygosity (HE) and observed heterozygosity (Ho) was 0.88 and 0. 77 respectively. Besides that, a ~800 bp fragment of the mtDNA control region D-Loop was amplified using the primers LTEi9 and H950 to investigate the population structure and determine the natal origin of sea turtle populations from Mabul Island. A total of 26 haplotypes were identified from 97 Green turtle individuals. Consequently, the statistical analysis showed a high estimation of nucleotide and haplotype diversity indices of n= 0.0097 and h= 0.9980 respectively for the Mabul Green turtle population. In addition, a PCR-based assay that targets 4 conserved CFPHV genes (UL18, UL22, UL27 and UL30) was used to screen 131 Green and Hawksbill turtles from Mabul Island. The screening included both FP tumour-exhibiting and clinically healthy individuals. From the analysis, nine Green turtles were positive for the FP tumours. This is the first reported case of Fibropapillomatosis in Sabah. Data estimated from this thesis could be used to infer the loss of the genetic diversity and to develop conservation strategies for enforcement agencies in Sabah. Furthermore, the data provides a new perspective and evidence into the occurrence and phylogeographic variation of FP in Mabul Island. In conclusion, this research provided a platform that contributes invaluable resources to construct future functional studies and collaborations in order to reinforce protection of these endangered species.
format	Thesis
qualification_name	Doctor of Philosophy (PhD.)
qualification_level	Doctorate
author	Aswini Leela Loganathan
author_facet	Aswini Leela Loganathan
author_sort	Aswini Leela Loganathan
title	Genetic diversity of the green (Chelonia mydas) and hawksbill (Eretmochel YS imbricata) turtles and the prevalence of chelonid fibropapilloma-associated Herpesvirus (CFPHV) in Mabul Island, Sabah, Malaysia
title_short	Genetic diversity of the green (Chelonia mydas) and hawksbill (Eretmochel YS imbricata) turtles and the prevalence of chelonid fibropapilloma-associated Herpesvirus (CFPHV) in Mabul Island, Sabah, Malaysia
title_full	Genetic diversity of the green (Chelonia mydas) and hawksbill (Eretmochel YS imbricata) turtles and the prevalence of chelonid fibropapilloma-associated Herpesvirus (CFPHV) in Mabul Island, Sabah, Malaysia
title_fullStr	Genetic diversity of the green (Chelonia mydas) and hawksbill (Eretmochel YS imbricata) turtles and the prevalence of chelonid fibropapilloma-associated Herpesvirus (CFPHV) in Mabul Island, Sabah, Malaysia
title_full_unstemmed	Genetic diversity of the green (Chelonia mydas) and hawksbill (Eretmochel YS imbricata) turtles and the prevalence of chelonid fibropapilloma-associated Herpesvirus (CFPHV) in Mabul Island, Sabah, Malaysia
title_sort	genetic diversity of the green (chelonia mydas) and hawksbill (eretmochel ys imbricata) turtles and the prevalence of chelonid fibropapilloma-associated herpesvirus (cfphv) in mabul island, sabah, malaysia
granting_institution	Universiti Malaysia Sabah
granting_department	Institut Penyelidikan Bioteknologi
publishDate	2018
url	https://eprints.ums.edu.my/id/eprint/38297/1/24%20PAGES.pdf https://eprints.ums.edu.my/id/eprint/38297/2/FULLTEXT.pdf
_version_	1794022712765579264

Genetic diversity of the green (Chelonia mydas) and hawksbill (Eretmochel YS imbricata) turtles and the prevalence of chelonid fibropapilloma-associated Herpesvirus (CFPHV) in Mabul Island, Sabah, Malaysia

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