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Seagrass, as marine angiosperms, plays an important role in coastal ecosystems. Understanding the population connectivity between geographic regions is important for their future restoration. Halophila ovalis is distributed in the Indo- West Pacific and can produce recruits through both asexual and sexual reproduction. The former uses rhizomatous rametes or rhizome fragments to disperse, the latter uses seeds to achieve the purpose of expanding their population. Since it’s fruits and seeds have negative buoyance and the seeds of H. ovalis could pass through the digestive tract of waterfowls and lead to higher germination rates than un-ingested controls. Therefore, biological vectors (i.e. migratory birds) may be a possible mechanism for long-distance dispersal. In this study, we collected 625 samples from 23 sites to understand the population connectivity of H. ovalis in the Indo-West Pacific. ITS and microsatellite loci were used to barcode and reveal the population connectivity pattern, respectively. According to the result, 432 samples of H. ovalis from 17 sites were used in this study. High level genetic diversity was found within 17 populations. The results of FST analysis showed that significant genetic differentiation was found among H. ovalis populations in the Indo- West Pacific. The results of STRUCTURE analysis showed that most of H. ovalis populations in the Indo- West Pacific possess unique genetic composition. Indicate that the gene flow between H. ovalis populations in the Indo- West Pacific is limited, therefore, long-distance dispersal by migratory birds is unlikely the main mechanism for shaping their connectivity pattern, and we suggest at least three cryptic species may occur within its distribution.
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