Substantial genetic divergence among subspecies
In this study we comprehensively sampled A. marina populations across their geographical range, assembled an extensive SNP data set, and used it to quantify the genetic differentiation among the three morphologically recognized subspecies. Our study finds a robust genetic split of A. marina into three groups, noting that this divergence was observed both in the genetic distance DXYmatrix and in PCA clustering based on a SNP frequency matrix. The genetic grouping pattern is generally consistent with the morphological classification of the three subspecies, marina ,eucalyptifolia , and australasica . The levels of within-subspecies genetic diversity are found to differ among subspecies, implying that gene pools of the three subspecies are separated to some degree.
Genetic differentiation among populations, usually attributed to isolation by distance or isolation by geographic barriers, have been documented in many mangrove species, such as the deep genetic differentiation between populations on the opposite sides of the Malay Peninsula in Rhizophora (Guo et al., 2016; Wee et al., 2015), Ceriops (Tan et al., 2005) , Lumnitzera (J. Li et al., 2016), and Xylocarpus (Guo et al., 2018b). Like previous findings, the differentiation on the two sides of Malay Peninsula is also observed in populations of the subspeciesmarina and is attributed to isolation of the Malay Peninsula currently and the whole Sundaland historically. Although propagules of A. marina are buoyant on sea water and disperse over via currents (Steinke & Ward, 2003), they are reported to be relatively weak in dispersal (Clarke, Kerrigan, & Westphal, 2001; Duke et al., 1998). Our estimates of differentiation among A. marinasubspecies exceed those based on geographical isolation. In addition, there is no geographical barrier inferred between the regions inhabited by australasica and eucalyptifolia. There must be some other factors causing their substantial genetic divergence. These findings indicate that the subspecies designation in A. marinaindeed represents a stage beyond structured populations on the speciation continuum.
Despite substantial divergence, these subspecies are not completely isolated. Genetics is not in concordance with morphology in some populations where two subspecies occur in coexistence or adjacently. The individuals from Bunbury, Australia, (BB) are morphologically diagnosed as marina, but genetically closer to eucalyptifolia as shown by the neighbor-joining tree and MDS clustering ofDXY . A recently published study focusing on theA. marina population on the west coast of Australia revealed genetic differentiation across geographical distance but not between subspecies, though the samples likely contain both marina andeucalyptifolia (Binks et al., 2019). This implies that constraint on gene flow between subspecies appears to be relaxed once geographical isolation (by distance or barrier) is removed. This is compatible with a subspecies designation because full species are less likely to allow gene flow, although accidental introgression via hybridization cannot be completely ruled out.