Genetic discontinuities in a dominant mangrove Rhizophora apiculata (Rhizophoraceae) in the Indo‐Malesian region

Abstract

Aim Population genomics data were used to determine the genetic diversity, genetic divergence and genetic structure of the mangrove, Rhizophora apiculata, across its distributional range and to re-assess the evolutionary processes that shaped its current distribution.Location The Indo-Malesian region section of the Indo-West Pacific region.Methods Next-generation sequencing technology was used to sequence 81 nuclear loci from a pooled DNA sample of 31-44 individuals of Rhizophora apiculata from 11 populations. Five nuclear loci from six to eight individuals from 18 populations were sequenced using conventional Sanger sequencing technology to validate the results.Results Genetic diversity at the population level was low (p and h were < 1.0 9 10 À3 in most of the populations), but relatively high at the species level (p = 2.419 9 10 À3 and h = 1.362 9 10 À3 ). The populations of R. apiculata in the Indo-Malesian region were genetically differentiated and grouped into three clusters: east Indian Ocean (EIO), South China Sea (SCS) and Australasia (AUA). Based on the genetic distance matrices, two genetic discontinuities were observed, and they correspond to the Malay Peninsula land barrier and the Wallacea zone. The admixture observed in populations from the Malacca Strait was attributed to asymmetric gene flow through the strait, which was simulated by the isolation-with-migration (IM) model.Main conclusion Both the Sunda shelf barrier and ocean currents in Wallacea contributed to the observed genetic discontinuity, which separated R. apiculata into three clusters (SCS, EIO and AUA). The cycle between extinction and recolonization in the SCS in response to Pleistocene sea level fluctuations reduced the genetic diversity within populations. The repeated opening and closing of the gene flow corridors, such as the Malacca Strait, may have blurred the genetic discontinuities to an extent and introduced an admixture into populations in boundary areas.

The presence of a cryptic barrier in the West Pacific Ocean suggests the effect of glacial climate changes on a widespread sea‐dispersed plant, Vigna marina (Fabaceae)

“…A clear genetic break in the West Pacific Ocean has also been observed in some other sea-dispersed plants: Rhizophora stylosa (Wee et al, 2015), R. apiculata (Guo et al, 2016), Xylocarpus granatum (Tomizawa et al, 2017) and Sonneratia alba , and in these cases the locations of the genetic breaks roughly corresponded to the one determined for V. marina. The presence of common genetic structure in multiple widespread sea-dispersed species…”

“…Recent studies have reported genetic structure within oceanic regions where no apparent barriers exist, suggesting that inconspicuous barriers in the marine environment may exist (Duke et al, ). For example, Wee et al () detected clear genetic differentiation between South East Asian (Japan, Vietnam, Philippine and Indonesia) and Oceanian (Fiji, Vanuatu and New Caledonia) populations in Rhizophora stylosa and Guo et al () detected similar genetic structure in Rhizophora apiculata . As the locations of these genetic breaks might correspond to the boundaries of oceanic currents, Wee et al () suggested that oceanic circulation patterns might have acted as “cryptic barriers.” However, the presence of cryptic barriers has not yet been well examined.…”

“…As the locations of these genetic breaks might correspond to the boundaries of oceanic currents, Wee et al () suggested that oceanic circulation patterns might have acted as “cryptic barriers.” However, the presence of cryptic barriers has not yet been well examined. Firstly, previous studies (Guo et al, ; Wee et al, ) did not cover the entire species distributional range and the species studied by them are not widely distributed across the Indo‐West Pacific (IWP) region, which is one of the main biogeographical regions for mangroves. Extensive and detailed sampling is needed to test the presence of cryptic barriers, especially in the West Pacific region (sensu Wee et al, ).…”

“…Firstly, previous studies (Guo et al, 2016;Wee et al, 2015) did not cover the entire species distributional range and the species studied by them are not widely distributed across the Indo-West Pacific (IWP) region, which is one of the main biogeographical regions for mangroves. Extensive and detailed sampling is needed to test the presence of cryptic barriers, especially in the West Pacific region (sensu Wee et al, 2015).…”

Extremely low genetic diversity across mangrove taxa reflects past sea level changes and hints at poor future responses

“…Mangroves, which anchor tropical coastal communities, are particularly vulnerable because they already occupy a niche that is on the extreme margin of the woody plant distribution. We and many others have studied the adaptability of major mangrove taxa as well as their evolutionary diversification (Guo et al, 2016; Urashi, Teshima, Minobe, Koizumi, & Inomata, 2013; Wee et al, *These authors contributed equally to the work. 2015; Xu, He, Guo, et al, 2017;Xu, He, Zhang, et al, 2017;Yang et al, 2017;Zhou et al, 2011).…”