Staff View: Genomic phylogeography of the endemic Mountain Black-eye of Borneo (Chlorocharis emiliae): Montane and lowland populations differ in patterns of Pleistocene diversification

Genomic phylogeography of the endemic Mountain Black-eye of Borneo (Chlorocharis emiliae): Montane and lowland populations differ in patterns of Pleistocene diversification

Aim: Our understanding of population diversification in the lowlands of Sundaland has improved substantially over the last 20 years through phylogeographical study, but we know almost nothing about population diversification in the mountains of the region. Here, we apply genomic analysis and habitat...

Full description

Saved in:

Bibliographic Details
Main Authors:	Manthey, Joseph D., Moyle, Robert G., Gawin, Dency F.A., Mustafa Abdul, Rahman, Mohamad Fizl Sidq, Ramji, Sheldon, Frederick H.
Format:	Article
Language:	English
Published:	Blackwell Publishing Ltd 2017
Subjects:	GE Environmental Sciences
Online Access:	http://ir.unimas.my/id/eprint/17781/3/Genomic.pdf http://ir.unimas.my/id/eprint/17781/ https://www.researchgate.net/publication/318160376
Tags:	Add Tag No Tags, Be the first to tag this record!

id	my.unimas.ir.17781
record_format	eprints
spelling	my.unimas.ir.177812022-06-21T07:21:00Z http://ir.unimas.my/id/eprint/17781/ Genomic phylogeography of the endemic Mountain Black-eye of Borneo (Chlorocharis emiliae): Montane and lowland populations differ in patterns of Pleistocene diversification Manthey, Joseph D. Moyle, Robert G. Gawin, Dency F.A. Mustafa Abdul, Rahman Mohamad Fizl Sidq, Ramji Sheldon, Frederick H. GE Environmental Sciences Aim: Our understanding of population diversification in the lowlands of Sundaland has improved substantially over the last 20 years through phylogeographical study, but we know almost nothing about population diversification in the mountains of the region. Here, we apply genomic analysis and habitat modelling to the phylogeography of Chlorocharis emiliae, the Mountain Black-eye, an endemic montane bird of Borneo with a sky-island distribution, to investigate the structure and interconnectivity of its populations. In the process, we consider factors driving population diversification in the mountains versus lowlands on the island, and how population structure of C. emiliae compares with structure of previously studied lowland species. Location: Borneo. Methods: Using RAD-seq, we produced thousands of SNPs in 25 individuals from five sky-island populations of C. emiliae. These populations represent the species entire range across Borneo. Genetic structure and species tree analyses were applied to measure population relationships and connectivity. Ecological niche modelling was used to estimate habitat distributions during current and LGM time periods. Results: We identified slight to moderate genetic distinctiveness among all populations. Based on demographic models, isolation with migration was the main pattern of divergence, and the most admixture occurred among three populations in north-eastern Borneo: Kinabalu, Trus Madi and Murud. The most divergent population, Pueh, in north-western Borneo, has low genetic diversity and a small effective population size, is geographically isolated and has diverged in isolation without notable gene flow. These results, based on a large genomic dataset, contradict the evolutionary relationships identified in an earlier mitochondrial DNA study. Main conclusions: Genomic phylogeographical comparisons indicate that diversification among sky-island populations of C. emiliae was driven largely by distance and historical habitat distribution, resulting in isolation but also some inter-population gene flow. During Pleistocene glacial events, cooler temperatures would have caused montane forest to descend and spread, thereby increasing connectivity among sky-island populations. However, despite increased montane habitat, the north-western population of Pueh remained isolated. This montane pattern contrasts with phylogeographical patterns in the Bornean lowlands, where populations often display evidence of vicariance followed by secondary contact. © 2017 John Wiley & Sons Ltd. Blackwell Publishing Ltd 2017 Article PeerReviewed text en http://ir.unimas.my/id/eprint/17781/3/Genomic.pdf Manthey, Joseph D. and Moyle, Robert G. and Gawin, Dency F.A. and Mustafa Abdul, Rahman and Mohamad Fizl Sidq, Ramji and Sheldon, Frederick H. (2017) Genomic phylogeography of the endemic Mountain Black-eye of Borneo (Chlorocharis emiliae): Montane and lowland populations differ in patterns of Pleistocene diversification. Journal of Biogeography, 44 (Supp.1). ISSN 0305-0270 https://www.researchgate.net/publication/318160376 DOI: 10.1111/jbi.13028
institution	Universiti Malaysia Sarawak
building	Centre for Academic Information Services (CAIS)
collection	Institutional Repository
continent	Asia
country	Malaysia
content_provider	Universiti Malaysia Sarawak
content_source	UNIMAS Institutional Repository
url_provider	http://ir.unimas.my/
language	English
topic	GE Environmental Sciences
spellingShingle	GE Environmental Sciences Manthey, Joseph D. Moyle, Robert G. Gawin, Dency F.A. Mustafa Abdul, Rahman Mohamad Fizl Sidq, Ramji Sheldon, Frederick H. Genomic phylogeography of the endemic Mountain Black-eye of Borneo (Chlorocharis emiliae): Montane and lowland populations differ in patterns of Pleistocene diversification
description	Aim: Our understanding of population diversification in the lowlands of Sundaland has improved substantially over the last 20 years through phylogeographical study, but we know almost nothing about population diversification in the mountains of the region. Here, we apply genomic analysis and habitat modelling to the phylogeography of Chlorocharis emiliae, the Mountain Black-eye, an endemic montane bird of Borneo with a sky-island distribution, to investigate the structure and interconnectivity of its populations. In the process, we consider factors driving population diversification in the mountains versus lowlands on the island, and how population structure of C. emiliae compares with structure of previously studied lowland species. Location: Borneo. Methods: Using RAD-seq, we produced thousands of SNPs in 25 individuals from five sky-island populations of C. emiliae. These populations represent the species entire range across Borneo. Genetic structure and species tree analyses were applied to measure population relationships and connectivity. Ecological niche modelling was used to estimate habitat distributions during current and LGM time periods. Results: We identified slight to moderate genetic distinctiveness among all populations. Based on demographic models, isolation with migration was the main pattern of divergence, and the most admixture occurred among three populations in north-eastern Borneo: Kinabalu, Trus Madi and Murud. The most divergent population, Pueh, in north-western Borneo, has low genetic diversity and a small effective population size, is geographically isolated and has diverged in isolation without notable gene flow. These results, based on a large genomic dataset, contradict the evolutionary relationships identified in an earlier mitochondrial DNA study. Main conclusions: Genomic phylogeographical comparisons indicate that diversification among sky-island populations of C. emiliae was driven largely by distance and historical habitat distribution, resulting in isolation but also some inter-population gene flow. During Pleistocene glacial events, cooler temperatures would have caused montane forest to descend and spread, thereby increasing connectivity among sky-island populations. However, despite increased montane habitat, the north-western population of Pueh remained isolated. This montane pattern contrasts with phylogeographical patterns in the Bornean lowlands, where populations often display evidence of vicariance followed by secondary contact. © 2017 John Wiley & Sons Ltd.
format	Article
author	Manthey, Joseph D. Moyle, Robert G. Gawin, Dency F.A. Mustafa Abdul, Rahman Mohamad Fizl Sidq, Ramji Sheldon, Frederick H.
author_facet	Manthey, Joseph D. Moyle, Robert G. Gawin, Dency F.A. Mustafa Abdul, Rahman Mohamad Fizl Sidq, Ramji Sheldon, Frederick H.
author_sort	Manthey, Joseph D.
title	Genomic phylogeography of the endemic Mountain Black-eye of Borneo (Chlorocharis emiliae): Montane and lowland populations differ in patterns of Pleistocene diversification
title_short	Genomic phylogeography of the endemic Mountain Black-eye of Borneo (Chlorocharis emiliae): Montane and lowland populations differ in patterns of Pleistocene diversification
title_full	Genomic phylogeography of the endemic Mountain Black-eye of Borneo (Chlorocharis emiliae): Montane and lowland populations differ in patterns of Pleistocene diversification
title_fullStr	Genomic phylogeography of the endemic Mountain Black-eye of Borneo (Chlorocharis emiliae): Montane and lowland populations differ in patterns of Pleistocene diversification
title_full_unstemmed	Genomic phylogeography of the endemic Mountain Black-eye of Borneo (Chlorocharis emiliae): Montane and lowland populations differ in patterns of Pleistocene diversification
title_sort	genomic phylogeography of the endemic mountain black-eye of borneo (chlorocharis emiliae): montane and lowland populations differ in patterns of pleistocene diversification
publisher	Blackwell Publishing Ltd
publishDate	2017
url	http://ir.unimas.my/id/eprint/17781/3/Genomic.pdf http://ir.unimas.my/id/eprint/17781/ https://www.researchgate.net/publication/318160376
_version_	1736838263283384320
score	13.211869

Genomic phylogeography of the endemic Mountain Black-eye of Borneo (Chlorocharis emiliae): Montane and lowland populations differ in patterns of Pleistocene diversification

Similar Items