Barrier to Gene Flow of Grey Mangrove Avicennia marina Populations in the Malay Peninsula as Revealed From Nuclear Microsatellites and Chloroplast Haplotypes
23 Sep 2021-Vol. 2
TL;DR: In this article, the authors assessed the genetic diversity and structure of Avicennia marina populations in Malay Peninsula using nuclear microsatellite markers and chloroplast sequences, and three evolutionary significant units were obtained with nuclear and cytoplasmic markers.
Abstract: Contemporary mangrove forest areas took shape historically and their genetic connectivity depends on sea-faring propagules, subsequent settlement, and persistence in suitable environments. Mangrove species world-wide may experience genetic breaks caused by major land barriers or opposing ocean currents influencing their population genetic structure. For Malay Peninsula, several aquatic species showed strong genetic differentiation between East and West coast regions due to the Sunda shelf flooding since the Last Glacial Maximum. In this study genetic diversity and structure of Avicennia marina populations in Malay Peninsula were assessed using nuclear microsatellite markers and chloroplast sequences. Even though all populations showed identical morphological features of A. marina, three evolutionary significant units were obtained with nuclear and cytoplasmic markers. Avicennia marina along a 586 km stretch of the West coast differed strongly from populations along an 80 km stretch of the East coast featuring chloroplast capture of Avicennia alba in an introgressive A. marina. Over and above this expected East-West division, an intra-regional subdivision was detected among A. marina populations in the narrowest region of the Strait of Malacca. The latter genetic break was supported by an AMOVA, STRUCTURE and BARRIER analysis whereas RST>FST indicated an evolutionary signal of long-lasting divergence. Two different haplotypes along the Western coast showed phylogeographic relationship with either a northern or a putative southern lineage, thereby assuming two Avicennia sources facing each other during Holocene occupation with prolonged separation in the Strait of Malacca. MIGRATE-n model testing supported a northward unidirectional stepping-stone migration route, although with an unclear directionality at the genetic break position, most likely due to weak oceanic currents. Low levels of genetic diversity and southward connectivity was detected for East coast Avicennia populations. We compared the fine-scale spatial genetic structure (FSGS) of Avicennia populations along the exposed coast in the East versus the sheltered coast in the West. A majority of transects from both coastlines revealed no within-site kinship-based FSGS, although the remoteness of the open sea is important for Avicennia patches to maintain a neighborhood. The results provide new insights for mangrove researchers and managers for future in-depth ecological-genetic-based species conservation efforts in Malay Peninsula.
Citations
More filters
01 Jan 2016
TL;DR: The the botany of mangroves is universally compatible with any devices to read and is available in the digital library an online access to it is set as public so you can get it instantly.
Abstract: Thank you very much for reading the botany of mangroves. As you may know, people have look hundreds times for their favorite books like this the botany of mangroves, but end up in harmful downloads. Rather than enjoying a good book with a cup of coffee in the afternoon, instead they cope with some infectious virus inside their computer. the botany of mangroves is available in our digital library an online access to it is set as public so you can get it instantly. Our book servers saves in multiple locations, allowing you to get the most less latency time to download any of our books like this one. Kindly say, the the botany of mangroves is universally compatible with any devices to read.
416 citations
TL;DR: In this article , the authors discuss a range of potential aims and goals of mangrove (re-) establishment along with potential pitfalls along the way from conceiving the initial idea to its realization.
Abstract: Protecting existing mangrove forests is a priority for global conservation because of the wide range of services that these coastal forests provide to humankind. Despite the recent reduction in global rates of mangrove loss, high historical loss rates mean that there are at least 800,000 ha globally that are potentially suitable for mangrove re-establishment. Recently deposited mud banks or intertidal, previously terrestrial, land might provide additional habitat for expanding mangrove areas locally. There is a long history of mangrove rehabilitation. However, despite numerous good examples of, and growing expertise in, natural or assisted (re-)establishment activities, most mangrove planting efforts, for instance, either fail entirely or meet with only limited success. Exposed to waves and currents and subject to tidal inundation, mangroves differ from terrestrial forests, and approaches to, or tools for, terrestrial forest restoration cannot easily be transferred to mangrove forests. Successful mangrove (re-)establishment usually requires a robust understanding of the abiotic and biotic conditions of the chosen site, the ecological requirements of the mangrove species used or facilitated, the reasons for previous mangrove loss or degradation, as well as the barriers–both societal and ecological–that have prevented natural recovery to date. Because most mangrove forests are socio-ecological systems, with which local human populations are intimately engaged, (re-)establishment will normally require the support of, and engagement with, local communities and other local stakeholders. Here, we summarize where, when and why (re-)establishment of mangroves is needed and how to assess this need. We discuss a range of potential aims and goals of mangrove (re-)establishment along with potential pitfalls along the way from conceiving the initial idea to its realization. We compare different technical and conceptual approaches to mangrove (re-)establishment, their challenges and opportunities, and their design and financial requirements, as well as potential solutions. We ground our final outlook and recommendations on examples of successful efforts and the factors that rendered (re-)establishment successful in the past.
4 citations
TL;DR: In this article , a total of 73 Bruguiera gymnorhiza accessions in 15 provinces were sequenced using RAD-seq to generate their SNPs, and the topology of the maximum likelihood phylogenetic tree clearly presented two genetically distinct groups corresponding to two geographic regions, the Gulf of Thailand and the Andaman Sea coasts.
Abstract: Bruguiera gymnorhiza (L.) Savigny is one of the most important and widespread mangrove species in the Indo-West Pacific region. Here, the population structure and genetic diversity of B. gymnorhiza along the coastlines of Thailand were examined. A total of 73 B. gymnorhiza accessions in 15 provinces were sequenced using RAD-seq to generate their SNPs. Based on the high-quality SNPs, the topology of the maximum likelihood phylogenetic tree clearly presented two genetically distinct groups corresponding to two geographic regions, the Gulf of Thailand and the Andaman Sea coasts. The results for the population structure provided by STRUCTURE and PCA also showed two main genetic clusters and their genetic admixture. A moderate genetic diversity was observed among the accessions, with average observed and expected heterozygosity values of 0.397 and 0.317, respectively. A high genetic differentiation (FST = 0.16, p < 0.001) between the two subpopulations was significantly found. An analysis of molecular variance revealed 83.95% of the genetic variation within populations and 16.05% of the genetic variation among populations. A high genetic variation within the populations and admixture may facilitate adaptation to local environments and climate changes. These results provide important information on the population genetic structure and genetic diversity of B. gymnorhiza in Thailand for further mangrove management.
TL;DR: In this paper , the authors used 10× Genomics technology to obtain a comprehensive whole-genome sequence, and restriction site associated DNA sequencing (RAD-seq) to genotype the population.
Abstract: Simple Summary In order to examine the genetic diversity and population structure of the Rhizophora mucronata population in Thailand, we utilized 10× Genomics technology to obtain a comprehensive whole-genome sequence, and restriction site associated DNA sequencing (RAD-seq) to genotype the population. Using SNPs discovered from the R. mucronata genome sequence, we detected moderate levels of genetic diversity and differentiation across 80 R. mucronata accessions collected from the coastal regions of Thailand. Both population structure and principal component analysis (PCA) converged on a clustering of two subpopulations. However, the results of two genetic groups did not correspond to the Gulf of Thailand or the Andaman Sea. Several factors could have influenced the R. mucronata genetic pattern, such as hybridization and anthropogenic factors. Abstract Unique and biodiverse, mangrove ecosystems provide humans with benefits and contribute to coastal protection. Rhizophora mucronata, a member of the Rhizophoraceae family, is prevalent in the mangrove forests of Thailand. R. mucronata’s population structure and genetic diversity have received scant attention. Here, we sequenced the entire genome of R. mucronata using 10× Genomics technology and obtained an assembly size of 219 Mb with the N50 length of 542,540 bases. Using 2857 single nucleotide polymorphism (SNP) markers, this study investigated the genetic diversity and population structure of 80 R. mucronata accessions obtained from the mangrove forests in Thailand. The genetic diversity of R. mucronata was moderate (I = 0.573, Ho = 0.619, He = 0.391). Two subpopulations were observed and confirmed from both population structure and principal component analysis (PCA). Analysis of molecular variance (AMOVA) showed that there was more variation within populations than between them. Mean pairwise genetic differentiation (FST = 0.09) showed that there was not much genetic difference between populations. Intriguingly, the predominant clustering pattern in the R. mucronata population did not correspond to the Gulf of Thailand and the Andaman Sea, which are separated by the Malay Peninsula. Several factors could have influenced the R. mucronata genetic pattern, such as hybridization and anthropogenic factors. This research will provide important information for the future conservation and management of R. mucronata in Thailand.
References
More filters
TL;DR: Pritch et al. as discussed by the authors proposed a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations, which can be applied to most of the commonly used genetic markers, provided that they are not closely linked.
Abstract: We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci— e.g. , seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/~pritch/home.html.
27,454 citations
DOI•
27 Oct 2010
20,272 citations
"Barrier to Gene Flow of Grey Mangro..." refers background in this paper
...However, the forestry measures such as planting, sustainable use, legal protection of areas, etc., are still applicable to A. marina in all countries wherever is needed Frontiers in Conservation Science | www.frontiersin.org 8 September 2021 | Volume 2 | Article 727819 (IUCN, 2021)....
[...]
TL;DR: It is found that in most cases the estimated ‘log probability of data’ does not provide a correct estimation of the number of clusters, K, and using an ad hoc statistic ΔK based on the rate of change in the log probability between successive K values, structure accurately detects the uppermost hierarchical level of structure for the scenarios the authors tested.
Abstract: The identification of genetically homogeneous groups of individuals is a long standing issue in population genetics. A recent Bayesian algorithm implemented in the software STRUCTURE allows the identification of such groups. However, the ability of this algorithm to detect the true number of clusters (K) in a sample of individuals when patterns of dispersal among populations are not homogeneous has not been tested. The goal of this study is to carry out such tests, using various dispersal scenarios from data generated with an individual-based model. We found that in most cases the estimated 'log probability of data' does not provide a correct estimation of the number of clusters, K. However, using an ad hoc statistic DeltaK based on the rate of change in the log probability of data between successive K values, we found that STRUCTURE accurately detects the uppermost hierarchical level of structure for the scenarios we tested. As might be expected, the results are sensitive to the type of genetic marker used (AFLP vs. microsatellite), the number of loci scored, the number of populations sampled, and the number of individuals typed in each sample.
18,572 citations
TL;DR: STRUCTURE HARVESTER is presented, a web-based program for collating results generated by the program STRUCTURE, which provides a fast way to assess and visualize likelihood values across multiple values of K and hundreds of iterations for easier detection of the number of genetic groups that best fit the data.
Abstract: We present STRUCTURE HARVESTER (available at http://taylor0.biology.ucla.edu/structureHarvester/
), a web-based program for collating results generated by the program STRUCTURE. The program provides a fast way to assess and visualize likelihood values across multiple values of K and hundreds of iterations for easier detection of the number of genetic groups that best fit the data. In addition, STRUCTURE HARVESTER will reformat data for use in downstream programs, such as CLUMPP.
9,960 citations
TL;DR: MICRO - CHECKER estimates the frequency of null alleles and, importantly, can adjust the allele and genotype frequencies of the amplified alleles, permitting their use in further population genetic analysis.
Abstract: DNA degradation, low DNA concentrations and primer-site mutations may result in the incorrect assignment of microsatellite genotypes, potentially biasing population genetic analyses. MICRO - CHECKER is WINDOWS ®-based software that tests the genotyping of microsatellites from diploid populations. The program aids identification of genotyping errors due to nonamplified alleles (null alleles), short allele dominance (large allele dropout) and the scoring of stutter peaks, and also detects typographic errors. MICRO - CHECKER estimates the frequency of null alleles and, importantly, can adjust the allele and genotype frequencies of the amplified alleles, permitting their use in further population genetic analysis. MICRO CHECKER can be freely downloaded from http://www.microchecker.hull.ac.uk/.
9,953 citations