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Background    Borassus flabellifer  or Asian Palmyra palm is an important crop for local economies in the South and Southeast Asia for its fruit and palm sugar production. Archeological and historical evidence indicated the presence of this species in Southeast Asia dating back at least 1500 years.  B. flabellifer  is believed to be originated in Africa, spread to South Asia and introduced into Southeast Asia through commercial routes and dissemination of cultures, however, the nature of its invasion and settlement in Thailand is unclear.    Results  Here, we analyzed genetic data of 230  B. flabellifer  accessions across Thailand using 17 EST-SSR and 12 gSSR polymorphic markers. Clustering analysis revealed that the population consisted of two genetic clusters (STRUCTURE K = 2). Cluster I is found mainly in southern Thailand, while Cluster II is found mainly in the northeastern. Those found in the central are of an extensive mix between the two. These two clusters are in moderate differentiation ( F   ST  = 0.066 and  N   M  = 3.532) and have low genetic diversity (H O  = 0.371 and 0.416; A R  = 2.99 and 3.19, for the cluster I and II respectively). The minimum numbers of founders for each genetic group varies from 3 to 4 individuals, based on simulation using different allele frequency assumptions. These numbers coincide with that  B. flabellifer  is dioecious, and a number of seeds had to be simultaneously introduced for obtaining both male and female founders.    Conclusions  From these data and geographical and historical evidence, we hypothesize that there were at least two different invasive events of  B. flabellifer  in Thailand.  B. flabellifer  was likely brought through the Straits of Malacca to be propagated in the southern Thailand as one of the invasive events before spreading to the central Thailand. The second event likely occurred in Khmer Empire, currently Cambodia, before spreading to the northeastern Thailand.    Electronic supplementary material  The online version of this article (10.1186/s12863-017-0554-y) contains supplementary material, which is available to authorized users.

Genetic evidence of multiple invasions and a small number of founders of Asian Palmyra palm (Borassus flabellifer) in Thailand