Differentiated population structure of a genetically depauperate mangrove species Ceriops tagal revealed by both Sanger and deep sequencing

Abstract

Ceriops tagal is a long-lived, woody perennial mangrove species, which is expected to maintain high levels of genetic diversity. We used two kinds of molecular markers, including maternally inherited chloroplast intergenic spacers (total ∼2550bp) and bi-parentally inherited nuclear genes (total ∼69,308bp) to examine the genetic variation of C. tagal across East India Ocean (EIO), West Pacific Ocean (WPO) and North Australia (NA), representing the largest range ever investigated. For nuclear genes survey, we adopted deep sequencing technologies to sequence 90 nuclear loci from pooled DNA samples of 100 individuals from each of three populations of C. tagal. Our data showed an extremely low level of polymorphism both at the chloroplast regions (nucleotide diversity: π=3.2×10−4) and nuclear loci (π=3.0×10−4) across the species range investigated. This species appeared to have passed through severe and prolonged demographic bottlenecks in the Pleistocene glaciation. However, a highly differentiated population structure among geographical regions was revealed by both molecular markers. Chlorotype analysis identified three major geographical groups in correspond to the EIO, WPO and NA. The high genetic identities within any local populations of C. tagal and shallow distinct genetic differences between geographical groups suggested recent historical isolation among the populations. Genetic information obtained from this study should help provide a framework for the development of conservation program for this species.