Ancient geograpical barriers drive differentiation among Sonneratia caseolaris populations and recent divergence from S. Ianceolata

Yang, Yuchen, Duke, Norman C., Peng, Fangfang, Li, Jianfang, Yang, Shuhuan, Zhong, Cairong, Zhou, Renchao, and Shi, Suhua (2016) Ancient geograpical barriers drive differentiation among Sonneratia caseolaris populations and recent divergence from S. Ianceolata. Frontiers in Plant Science, 7. 1618. pp. 1-14.

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Glacial vicariance is thought to influence population dynamics and speciation of many marine organisms. Mangroves, a plant group inhabiting intertidal zones, were also profoundly influenced by Pleistocene glaciations. In this study, we investigated phylogeographic patterns of a widespread mangrove species Sonneratia caseolaris and a narrowly distributed, closely related species S. lanceolata to infer their divergence histories and related it to historical geological events. We sequenced two chloroplast fragments and five nuclear genes for one population of S. lanceolata and 12 populations of S. caseolaris across the Indo-West Pacific (IWP) region to evaluate genetic differentiation and divergence time among them. Phylogenetic analysis based on sequences of nuclear ribosomal internal transcribed spacer and a nuclear gene rpl9 for all Sonneratia species indicate that S. lanceolata individuals are nested within S. caseolaris. We found strong genetic structure among geographic regions (South China Sea, the Indian Ocean, and eastern Australia) inhabited by S. caseolaris. We estimated that divergence between the Indo-Malesia and Australasia populations occurred 4.035 million years ago (MYA), prior to the onset of Pleistocene. BARRIERS analysis suggested that complex geographic features in the IWP region had largely shaped the phylogeographic patterns of S. caseolaris. Furthermore, haplotype analyses provided convincing evidence for secondary contact of the South China Sea and the Indian Ocean lineages at the Indo-Pacific boundary. Demographic history inference under isolation and migration (IM) model detected substantial gene flow from the Sri Lanka populations to the populations in the Java Island. Moreover, multi-locus sequence analysis indicated that S. lanceolata was most closely related to the Indian Ocean populations of S. caseolaris and the divergence time between them was 2.057 MYA, coinciding with the onset of the Pleistocene glaciation. Our results suggest that geographic isolation driven by the Pleistocene ice age resulted in the recent origin of S. lanceolata.

Item ID: 46346
Item Type: Article (Research - C1)
ISSN: 1664-462X
Keywords: genetic differentiation, secondary contact, Pleistocene glaciations, Sonneratia, mangroves
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© 2016 Yang, Duke, Peng, Li, Yang, Zhong, Zhou and Shi. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s)or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

Funders: National Natural Science Foundation of China (NNSFC), 985 Project, Science Foundation of State Key Laboratory of Biocontrol (SFSKLB), Chang Hungta Science Foundation (CHSF), Sun Yat-sen University (SYSU)
Projects and Grants: NNSFC 1130208, 91331202 & 31130069, 985 Project 33000-18811202, SFSKLB SKLBC13A03
Date Deposited: 15 Nov 2016 22:06
FoR Codes: 31 BIOLOGICAL SCIENCES > 3104 Evolutionary biology > 310406 Evolutionary impacts of climate change @ 40%
31 BIOLOGICAL SCIENCES > 3105 Genetics > 310599 Genetics not elsewhere classified @ 30%
41 ENVIRONMENTAL SCIENCES > 4104 Environmental management > 410401 Conservation and biodiversity @ 30%
SEO Codes: 96 ENVIRONMENT > 9605 Ecosystem Assessment and Management > 960503 Ecosystem Assessment and Management of Coastal and Estuarine Environments @ 40%
96 ENVIRONMENT > 9608 Flora, Fauna and Biodiversity > 960802 Coastal and Estuarine Flora, Fauna and Biodiversity @ 30%
96 ENVIRONMENT > 9613 Remnant Vegetation and Protected Conservation Areas > 961304 Remnant Vegetation and Protected Conservation Areas in Coastal and Estuarine Environments @ 30%
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