Low genetic diversity indicating the threatened status of Rhizophora apiculata (Rhizophoraceae) in Malaysia: declined evolution meets habitat destruction

Abstract

Worldwide, many mangrove species are experiencing significant population declines, including Rhizophora apiculata, which is one of the most widespread and economically important species in tropical Asia. In Malaysia, there has been an alarming decline in R. apiculata populations driven primarily by anthropogenic activities. However, the lack of genetic and demographic information on this species has hampered local efforts to conserve it. To address these gaps, we generated novel genetic information for R. apiculata, based on 1,120 samples collected from 39 natural populations in Peninsular Malaysia. We investigated its genetic diversity and genetic structure with 19 transcriptome and three nuclear microsatellite markers. Our analyses revealed a low genetic diversity (mean He: 0.352) with significant genetic differentiation (FST: 0.315) among populations of R. apiculata. Approximately two-third of the populations showed significant excess of homozygotes, indicating persistent inbreeding which might be due to the decrease in population size or fragmentation. From the cluster analyses, the populations investigated were divided into two distinct clusters, comprising the west and east coasts of Peninsular Malaysia. The western cluster was further divided into two sub-clusters with one of the sub-clusters showing strong admixture pattern that harbours high levels of genetic diversity, thus deserving high priority for conservation.

Barrier to Gene Flow of Grey Mangrove Avicennia marina Populations in the Malay Peninsula as Revealed From Nuclear Microsatellites and Chloroplast Haplotypes

“…Inbreeding and genetic diversity that are common to mangrove populations were also observed for A. marina (Maguire et al, 2000b;Dodd et al, 2002;Yan et al, 2016). Therefore, continued monitoring and in-depth research are necessary to provide further scientific insights on this population diversity, especially from the areas like Malay Peninsula where land blockage effect is protuberant (Azman et al, 2020;Wee et al, 2020;Fairuz-Fozi et al, 2021).…”

Genetic and molecular mechanisms underlying mangrove adaptations to intertidal environments

“…The change in genetic diversity diagnosed by the excess of homozygotes can be related to habitat destruction due to anthropogenic means and the subsequent inbreeding. Human activities such as logging and developments near mangrove habitats can disrupt the gene flow leading to population size reduction ( Azman et al., 2020 ). Spatial genetic structure analysis among populations of A. germinans and R. mangle of Pacific and Caribbean coastal lines revealed significant differences in genetic structure of estuaries from the same coastline, while A. germinans showed higher levels of genetic diversity as compared to R. mangle.…”

“…Exploiting mangrove habitats by largely converting them into aquaculture ponds for fish, shellfish, and shrimp farming could reduce mangrove areas, alter the hydrology, and eventually cause eutrophication ( Friess et al., 2019 ; Hong et al., 2018 ). The other deteriorative effects of human activities such as logging and developments near mangrove habitats impart long-term consequences by acting as a barrier of gene flow resulting in low genetic diversity ( Azman et al., 2020 ; Meng et al., 2016 ). Microsatellite studies on Rhizophora apiculata serve as a typical example of a similar situation which revealed low genetic diversity among the populations and reduction in population size due to habitat fragmentation ( Azman et al., 2020 ).…”

“…The other deteriorative effects of human activities such as logging and developments near mangrove habitats impart long-term consequences by acting as a barrier of gene flow resulting in low genetic diversity ( Azman et al., 2020 ; Meng et al., 2016 ). Microsatellite studies on Rhizophora apiculata serve as a typical example of a similar situation which revealed low genetic diversity among the populations and reduction in population size due to habitat fragmentation ( Azman et al., 2020 ). Moreover, climate change, rising sea level, and fluctuating tidal cycles have influenced the distribution and growth of mangroves ( Friess et al., 2019 ; Parida et al., 2014 ; Rippel et al, 2021 ; Servino et al., 2018 ).…”

Genetic diversity and population structure of Eurycoma apiculata in Eastern Sumatra, Indonesia

“…The results of this study are in line with those reported by Panda et al (2015) on Plumbago zeylanica L. plants in which fragmented populations have lower genetic diversity values than other populations that are not fragmented. According to Azman et al (2020) that populations that have low genetic diversity values indicate that these populations are in a condition of threatening, fragmented, and damaged by human activities. In contrast, The high genetic diversity in the Pokomo population could be caused by several factors, namely i) the genetic diversity has been high from the beginning of the population established, ii) the population has not been a lot disturbed by human activities, so its condition is more maintained, and iii) the occurrence of random mating among individuals resulting in genetic recombination and increasing genetic diversity within population.…”