Eclipta thermalis, a previously common weed, threatened by the expansion of the exotic congener E. alba in Japanese rice paddies

Rice paddies are wetland ecosystems recognized as important habitats for many organisms; however, the hybridization-related extinction risk of native plant species has not been investigated in this system so far. Eclipta L. (Compositae) is a common paddy weed in Japan; however, its genetic composition might be altered due to the hybridization between the native E. thermalis and the closely related exotic E. alba. We examined Eclipta's genetic composition using 12 microsatellite markers (612 samples collected from 109 populations) and found (i) widespread geographical distribution of E. alba in Japan, (ii) hybridization with E. thermalis, and a large number of later-generation hybrids, and (iii) widely varying situations among regions and populations. Eclipta alba appears to have invaded an open niche in northern Japan but has not yet reached southern Japan. Both E. alba and E. thermalis were found in central Japan; however, the latter had become rare due to hybridization-mediated processes such as competition, and demographic and genetic swamping. Notably, endogenous and exogenous selection plays an important role in the invasion of E. alba, but to varying degrees among different areas. In summary, considering the genetic variability in E. thermalis, the genetic cluster of mainland Japan is in a highly critical situation due to the invasion of E. alba.