Effects of Pleistocene sea-level fluctuations on mangrove population dynamics: a lesson from Sonneratia alba

Abstract

BackgroundA large-scale systematical investigation of the influence of Pleistocene climate oscillation on mangrove population dynamics could enrich our knowledge about the evolutionary history during times of historical climate change, which in turn may provide important information for their conservation.ResultsIn this study, phylogeography of a mangrove tree Sonneratia alba was studied by sequencing three chloroplast fragments and seven nuclear genes. A low level of genetic diversity at the population level was detected across its range, especially at the range margins, which was mainly attributed to the steep sea-level drop and associated climate fluctuations during the Pleistocene glacial periods. Extremely small effective population size (Ne) was inferred in populations from both eastern and western Malay Peninsula (44 and 396, respectively), mirroring the fragility of mangrove plants and their paucity of robustness against future climate perturbations and human activity. Two major genetic lineages of high divergence were identified in the two mangrove biodiversity centres: the Indo-Malesia and Australasia regions. The estimated splitting time between these two lineages was 3.153 million year ago (MYA), suggesting a role for pre-Pleistocene events in shaping the major diversity patterns of mangrove species. Within the Indo-Malesia region, a subdivision was implicated between the South China Sea (SCS) and the remaining area with a divergence time of 1.874 MYA, corresponding to glacial vicariance when the emerged Sunda Shelf halted genetic exchange between the western and eastern coasts of the Malay Peninsula during Pleistocene sea-level drops. Notably, genetic admixture was observed in populations at the boundary regions, especially in the two populations near the Malacca Strait, indicating secondary contact between divergent lineages during interglacial periods. These interregional genetic exchanges provided ample opportunity for the re-use of standing genetic variation, which could facilitate mangrove establishment and adaptation in new habitats, especially in the context of global climate changes.ConclusionPhylogeogrpahic analysis in this study reveal that Pleistocene sea-level fluctuations had profound influence on population differentiation of the mangrove tree S. alba. Our study highlights the fragility of mangrove plants and offers a guide for the conservation of coastal mangrove communities experiencing ongoing changes in sea-level.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0849-z) contains supplementary material, which is available to authorized users.

Vicariance and Oceanic Barriers Drive Contemporary Genetic Structure of Widespread Mangrove Species Sonneratia alba J. Sm in the Indo-West Pacific

“…Both our SSR and cpDNA data supported a genetic divide between SCS and EIO, as previously observed in S. alba [11] and other mangrove species (see Introduction). We specifically tested for the effect of the Malay Peninsula as a genetic barrier with and without accounting for distance, and found a significant effect in both instances.…”

“…Instead, the haplotype in the Indian Ocean could be found throughout the distribution range, while another haplotype was largely confined within the South China Sea. The seclusion of the South China Sea haplotype in our study agreed with the findings from Yang et al (2017) [11], though our cpDNA data did not demonstrate two clades corresponding to the Indo-Malesia and Australasia regions.…”

“…An important feature of our results is the occurrence of a main phylogeographic break between populations from Northern Australia and Southwest Pacific Ocean cluster, and the other populations from the IWP (Table 3; Figure 3a). This complements the findings of Yang et al(2017) [11].Even though the genetic divergence between populations from North Australia to Southwest Pacific Ocean and the rest of IWP has been observed in other mangrove species, it was never the strongest genetic break range wide, except for in R. stylosa [8]. Populations from Australia were observed to be genetically close to populations from the South China Sea in Ceriops spp.…”

“…The genetic structure of S. alba showed two major lineages corresponding to the Indo-Malesia and Australasia regions that diverged ca. 3.15 million years ago, prior to Pleistocene [11]. A later divergence estimated at 1.87 million years ago was detected within the Indo-Malesia region, resulting in a lineage within the South China Sea and another spread out across the region.…”

“…This study clearly demonstrated the strong influence of Pleistocene sea-level fluctuations on the genetic structure. However, due to the slower mutation rate in the single nucleotide polymorphism loci employed by Yang et al (2017) and the inherent low levels of genetic diversity in S. alba [11,12], the data may be limited when it comes to inferences on the fine-scale genetic patterns, especially contemporary gene flow mirrored by more recent demographic history. This is essential in understanding the biogeography of S. alba, as most of the studied populations are connected by sea in the present day, and gene flow can be more extensive than glacial periods.…”