Assessing Diversity of Crocidura monticola sensu lato from Malaysia using Genetic Markers and Morphology

Sunda shrew, (Soricidae: Crocidura monticola) is one of the most highly complex species. It has three synonyms and to date, researchers still have disparities about the species either C. monticola is a Javan endemic, or is it a widely distributed species. Plus, the lack of information on their ecolo...

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Main Author:	Muhd Amsyari, Morni
Format:	Thesis
Language:	English
Published:	2019
Subjects:	Q Science (General) QH426 Genetics
Online Access:	http://ir.unimas.my/id/eprint/25807/2/Muhd%20Amsyari.pdf
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spelling	my-unimas-ir.258072023-03-21T08:54:35Z Assessing Diversity of Crocidura monticola sensu lato from Malaysia using Genetic Markers and Morphology 2019-07-12 Muhd Amsyari, Morni Q Science (General) QH426 Genetics Sunda shrew, (Soricidae: Crocidura monticola) is one of the most highly complex species. It has three synonyms and to date, researchers still have disparities about the species either C. monticola is a Javan endemic, or is it a widely distributed species. Plus, the lack of information on their ecology, behaviour and taxonomic relationship may lead to species misidentification (e.g. with C. neglecta). This is especially true as populations of such species from Malaysia are poorly studied due to lack of voucher specimens. Therefore, the study aimed to generate the data through genetic analyses and morphological characters in attempt to identify unique lineages that are consistent in both of these markers. A total of 22 samples were sequenced using cytochrome b and cytochrome oxidase I gene. Genetic analyses using MEGA7 recovered lineages with high genetic variation that are unique within the samples from Malaysia. None of the samples collected are grouped together with paratype of C. monticola, as shown in the phylogenetic analysis, where the biggest cytochrome b p-distance value is 20.1%. Crocidura neglecta was also included in the analyses, however they were not grouped together except one individual (GB 15244).Thus, this study discovered five plausible new species with two of them may represent two new undescribed genus. To investigate on Crocidura diversification events, Bayesian evolutionary analysis sampling trees (BEAST) and reconstruct ancestral state in phylogenies (RASP) analysis were done. The radiation of Crocidura in Southeast Asia started to occur during late Miocene (~7.58 mya). Major Crocidura diversification event happened during Pliocene (~3.06 mya) and the most recent event was during Pleistocene (~0.63 mya). Morphologically, this study was performed using both conventional and geometric morphometric methods. Principal Component Analysis (PCA) on fourteen cranial measurements of 51 skull samples of C. monticola sensu lato from Malaysia recovered two v major variations according to elevation: highland samples (>1100m a.s.l) vs lowland samples(<300m a.s.l). The highest loading characters were observed in Function 1 with Greatest Length of Skull (GLS) and Function 2 with Rostral breadth (ROB) as the characters with eigenvalue of 9.6 and 1.9 respectively. These two characters are therefore inferred as the best morphological characters to group this species in accordance with their habitat altitude. Geometric morphometric analyses from dorsal, ventral and mandible views of the skulls showed the shape variations were mostly detected at dentition part. Diet was hypothesised as the main factor that influence the variations. In conclusion, both genetic and morphometric analyses from this study suggested that there are hidden diversities within C. monticola complex from Malaysia. Universiti Malaysia Sarawak (UNIMAS) 2019-07 Thesis http://ir.unimas.my/id/eprint/25807/ http://ir.unimas.my/id/eprint/25807/2/Muhd%20Amsyari.pdf text en validuser masters Universiti Malaysia Sarawak Faculty of Resource Science and Technology
institution	Universiti Malaysia Sarawak
collection	UNIMAS Institutional Repository
language	English
topic	Q Science (General) QH426 Genetics
spellingShingle	Q Science (General) QH426 Genetics Muhd Amsyari, Morni Assessing Diversity of Crocidura monticola sensu lato from Malaysia using Genetic Markers and Morphology
description	Sunda shrew, (Soricidae: Crocidura monticola) is one of the most highly complex species. It has three synonyms and to date, researchers still have disparities about the species either C. monticola is a Javan endemic, or is it a widely distributed species. Plus, the lack of information on their ecology, behaviour and taxonomic relationship may lead to species misidentification (e.g. with C. neglecta). This is especially true as populations of such species from Malaysia are poorly studied due to lack of voucher specimens. Therefore, the study aimed to generate the data through genetic analyses and morphological characters in attempt to identify unique lineages that are consistent in both of these markers. A total of 22 samples were sequenced using cytochrome b and cytochrome oxidase I gene. Genetic analyses using MEGA7 recovered lineages with high genetic variation that are unique within the samples from Malaysia. None of the samples collected are grouped together with paratype of C. monticola, as shown in the phylogenetic analysis, where the biggest cytochrome b p-distance value is 20.1%. Crocidura neglecta was also included in the analyses, however they were not grouped together except one individual (GB 15244).Thus, this study discovered five plausible new species with two of them may represent two new undescribed genus. To investigate on Crocidura diversification events, Bayesian evolutionary analysis sampling trees (BEAST) and reconstruct ancestral state in phylogenies (RASP) analysis were done. The radiation of Crocidura in Southeast Asia started to occur during late Miocene (~7.58 mya). Major Crocidura diversification event happened during Pliocene (~3.06 mya) and the most recent event was during Pleistocene (~0.63 mya). Morphologically, this study was performed using both conventional and geometric morphometric methods. Principal Component Analysis (PCA) on fourteen cranial measurements of 51 skull samples of C. monticola sensu lato from Malaysia recovered two v major variations according to elevation: highland samples (>1100m a.s.l) vs lowland samples(<300m a.s.l). The highest loading characters were observed in Function 1 with Greatest Length of Skull (GLS) and Function 2 with Rostral breadth (ROB) as the characters with eigenvalue of 9.6 and 1.9 respectively. These two characters are therefore inferred as the best morphological characters to group this species in accordance with their habitat altitude. Geometric morphometric analyses from dorsal, ventral and mandible views of the skulls showed the shape variations were mostly detected at dentition part. Diet was hypothesised as the main factor that influence the variations. In conclusion, both genetic and morphometric analyses from this study suggested that there are hidden diversities within C. monticola complex from Malaysia.
format	Thesis
qualification_level	Master's degree
author	Muhd Amsyari, Morni
author_facet	Muhd Amsyari, Morni
author_sort	Muhd Amsyari, Morni
title	Assessing Diversity of Crocidura monticola sensu lato from Malaysia using Genetic Markers and Morphology
title_short	Assessing Diversity of Crocidura monticola sensu lato from Malaysia using Genetic Markers and Morphology
title_full	Assessing Diversity of Crocidura monticola sensu lato from Malaysia using Genetic Markers and Morphology
title_fullStr	Assessing Diversity of Crocidura monticola sensu lato from Malaysia using Genetic Markers and Morphology
title_full_unstemmed	Assessing Diversity of Crocidura monticola sensu lato from Malaysia using Genetic Markers and Morphology
title_sort	assessing diversity of crocidura monticola sensu lato from malaysia using genetic markers and morphology
granting_institution	Universiti Malaysia Sarawak
granting_department	Faculty of Resource Science and Technology
publishDate	2019
url	http://ir.unimas.my/id/eprint/25807/2/Muhd%20Amsyari.pdf
_version_	1783728302312128512

Assessing Diversity of Crocidura monticola sensu lato from Malaysia using Genetic Markers and Morphology

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