8TH ASIAN PACIFIC PHYCOLOGICAL FORUM A genetic diversity assessment of Halymenia malaysiana (Halymeniaceae, Rhodophyta) from Malaysia and the Philippines based on COI-5P and rbcL sequences Pui-Ling Tan 1,2 & Phaik-Eem Lim 1 & Showe-Mei Lin 3 & Siew-Moi Phang 1,2 & Stefano G.A. Draisma 4 & Lawrence M. Liao 5 Received: 25 January 2018 /Revised and accepted: 16 April 2018 # Springer Science+Business Media B.V., part of Springer Nature 2018 Abstract Little is known about the genetic diversity and phylogeographic structure of seaweeds in Southeast Asia particularly for Halymenia species. Herein, molecular analyses based on DNA sequences of the COI-5P and rbcL were performed to assess the genetic structure within the foliose Halymenia species H. malaysiana in Malaysia and the Philippines. A total of ten COI-5P haplotypes and eight rbcL haplotypes were recognized from 42 specimens of H. malaysiana examined in this study. The genetic diversities of H. malaysiana were relatively higher based on the COI-5P sequences compared with the rbcL sequences. The results showed that populations from Peninsular Malaysia (East, South, and West coast) were genetically homogenous and exhibited low level of genetic divergence from populations from East Malaysia. In contrast, populations from the Philippines were distinct from Malaysian populations. Site-specific distribution was also evident in the Philippine populations of H. malaysiana. Keywords COI-5P . Halymenia malaysiana . Rhodophyta . Genetic variation . Phylogeography . rbcL . Red algae Introduction Southeast Asia, of which Malaysia and the Philippines are part, is a world-renowned biodiversity hotspot (Briggs 2005; Hughes 2017). Owing to its high species richness and com- plex geological history, it encompasses plenty of interesting study sites for genetic diversity studies. Malaysia consists of Peninsular Malaysia (part of the mainland Southeast Asia) and East Malaysia (northern part of Borneo Island), which are separated by the southern part of South China Sea, but con- nected during the Last Glacial Maximum (23,000 – 19,000 years ago) when the Sunda Shelf was exposed (Wurster et al. 2010). The surface current circulation in the South China Sea is affected by monsoon seasons and may promoted genetic connectivity between populations (Wyrtki 1961). The isolation of northern South China Sea as refugium during the late Pleistocene and postglacial recolonization of the southern South China Sea may have impaired the genetic connectivity in the region and caused subsequent diversifica- tion within Malaysian populations (Chan et al. 2013). Likewise, the Philippines, consisting of more than 7000 islands, has caught much attention as an area of exceptional endemism that is in critical need of conservation (Heaney et al. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10811-018-1484-4) contains supplementary material, which is available to authorized users. * Pui-Ling Tan aquariusling29@yahoo.com; aquariusling292@gmail.com * Phaik-Eem Lim phaikeem@um.edu.my 1 Institute of Ocean and Earth Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia 2 Institute of Biological Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia 3 Institute of Marine Biology, National Taiwan Ocean University, Keelung20224, Taiwan, Republic of China 4 Excellence Center for Biodiversity of Peninsular Thailand, Department of Biology, Faculty of Science, Prince of Songkla University, Hatyai, Songkhla 90112, Thailand 5 Graduate School of Biosphere Science, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima 739-8528, Japan Journal of Applied Phycology https://doi.org/10.1007/s10811-018-1484-4