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Open accessJournal ArticleDOI: 10.1038/S41598-021-84304-8

Expansion of the mangrove species Rhizophora mucronata in the Western Indian Ocean launched contrasting genetic patterns

02 Mar 2021-Scientific Reports (Springer Science and Business Media LLC)-Vol. 11, Iss: 1, pp 4987-4987
Abstract: Estimates of population structure and gene flow allow exploring the historical and contemporary processes that determine a species’ biogeographic pattern. In mangroves, large-scale genetic studies to estimate gene flow have been conducted predominantly in the Indo-Pacific and Atlantic region. Here we examine the genetic diversity and connectivity of Rhizophora mucronata across a > 3,000 km coastal stretch in the Western Indian Ocean (WIO) including WIO islands. Based on 359 trees from 13 populations and using 17 polymorphic microsatellite loci we detected genetic breaks between populations of the (1) East African coastline, (2) Mozambique Channel Area (3) granitic Seychelles, and (4) Aldabra and northern Madagascar. Genetic structure, diversity levels, and patterns of inferred connectivity, aligned with the directionality of major ocean currents, driven by bifurcation of the South Equatorial Current, northward into the East African Coastal Current and southward into the Mozambique Channel Area. A secondary genetic break between nearby populations in the Delagoa Bight coincided with high inbreeding levels and fixed loci. Results illustrate how oceanographic processes can connect and separate mangrove populations regardless of geographic distance.

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Topics: Rhizophora mucronata (55%), Genetic structure (55%), Genetic diversity (52%) ... show more

5 results found

Open accessJournal ArticleDOI: 10.3389/FMARS.2021.643982
Abstract: Avicennia dominated mangrove forests occur from seaward to landward sites and hence are subject to different dynamics within estuarine ecosystems. Regeneration of mangrove forests primarily depends on the extent of propagule spread and subsequent establishment in suitable habitats. The complex nature of estuarine systems induces a wide variety of local conditions for within-site propagule retention and settlement thereby allowing spontaneous regeneration of mangroves. In this study, we estimated the fine-scale spatial genetic structure (FSGS) of Avicennia populations and examined whether their position relative to the seaside or the size of mangrove patches could have influenced the extant local population genetic structure. A kinship-based FSGS was performed using microsatellite markers in 523 A. marina, 189 A. rumphiana and 60 A. alba adult trees of 24 sites in The Philippines. Transects within each estuary were taken both parallel and perpendicular to the coastline or tidal river edge. The extent of local mangrove areas and various human-induced encroachments as such did not show any trend in allele diversity, heterozygosity values or inbreeding levels. However, farther inland situated mangrove patches showed a larger FSGS extent across the neighborhood (up to 75 m) though less diversity along with inbreeding, most likely due to retention of related propagules and lowered chance of external propagule input. Estimation of connectivity along a same coastline stretch supported a unidirectional steppingstone or adjacent migration model for populations of either A. marina, A. alba or A. rumphiana. These were congruent with ocean currents across mangrove estuaries of the Tablas Strait and along Western Leyte, thereby emphasizing the relevance of coastal connectivity for long term persistence. From this study, we conclude that both proximity to open water and narrowness of mangrove patches may affect their captured diversity, inbreeding and fine-scale structure caused by propagule movement within or beyond a local mangrove fragment during recent generations. Higher levels of allele diversity for seaward sites and highest likelihood of migration for adjacent mangroves both add to the importance of coastal connectivity that is the only natural cohesive force on longer term and necessary to counteract short term effects of increasingly encroached mangrove environments.

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Topics: Mangrove (58%), Avicennia (57%), Propagule (54%)

3 Citations

Open accessJournal ArticleDOI: 10.1111/EDE.12388
Abstract: The capacity to respond to environmental challenges ultimately relies on phenotypic variation which manifests from complex interactions of genetic and nongenetic mechanisms through development. While we know something about genetic variation and structure of many species of conservation importance, we know very little about the nongenetic contributions to variation. Rhizophora mangle is a foundation species that occurs in coastal estuarine habitats throughout the neotropics where it provides critical ecosystem functions and is potentially threatened by anthropogenic environmental changes. Several studies have documented landscape-level patterns of genetic variation in this species, but we know virtually nothing about the inheritance of nongenetic variation. To assess one type of nongenetic variation, we examined the patterns of DNA sequence and DNA methylation in maternal plants and offspring from natural populations of R. mangle from the Gulf Coast of Florida. We used a reduced representation bisulfite sequencing approach (epi-genotyping by sequencing; epiGBS) to address the following questions: (a) What are the levels of genetic and epigenetic diversity in natural populations of R. mangle? (b) How are genetic and epigenetic variation structured within and among populations? (c) How faithfully is epigenetic variation inherited? We found low genetic diversity but high epigenetic diversity from natural populations of maternal plants in the field. In addition, a large portion (up to ~25%) of epigenetic differences among offspring grown in common garden was explained by maternal family. Therefore, epigenetic variation could be an important source of response to challenging environments in the genetically depauperate populations of this foundation species.

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Topics: Genetic variation (56%), Genetic diversity (54%), Rhizophora mangle (51%)

2 Citations

Open accessJournal ArticleDOI: 10.3389/FCOSC.2021.727819
23 Sep 2021-
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.

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Topics: Avicennia marina (63%), Avicennia (60%), Avicennia alba (57%) ... show more

1 Citations

Open accessJournal ArticleDOI: 10.3389/FCOSC.2021.726676
23 Sep 2021-
Abstract: Historical processes of long-distance migration and ocean-wide expansion feature the global biogeographic pattern of Rhizophora species. Throughout the Indian Ocean, R. stylosa and R. mucronata appear as a young phylogenetic group with expansion of R. mucronata towards the Western Indian Ocean (WIO) driven by the South Equatorial Current. Nuclear microsatellites revealed genetic patterns and breaks, however, estimating propagule dispersal routes requires maternally inherited cytoplasmic markers. Here, we examine the phylogeography of 21 R. mucronata provenances across a >4,200 km coastal stretch in the WIO using R. stylosa as outgroup. Full length chloroplast genome (164,474 bp) and nuclear ribosomal RNA cistron (8,033 bp) sequences were assembled. Boundaries, junction point, sequence orientation and stretch between LSC/IRb/SSC/IRa/LSC showed no differences with the R. stylosa chloroplast genome. A total of 58 mutations in R. mucronata encompassing transitions/transversions, insertion-deletions and mononucleotide repeats revealed three major haplogroups. Haplonetwork, Bayesian ML and Approximate Bayesian Computation (ABC) analyses supported discrete historical migration events. An ancient haplogroup A in the Seychelles and eastern Madagascar was as divergent from other R. mucronata haplogroups as it was from R. stylosa. A star-like haplonetwork referred to recent range expansion of haplogroup B from northern Madagascar towards the African mainland coastline, including a single variant spanning >1,800 km across the Mozambique Channel Area. Populations south of Delagoa Bight contained haplogroup C and originate from a unique bottleneck dispersal event. Divergence estimates of pre- and post-Last Glacial Maximum illustrated a recent emergence of WIO Rhizophora mangroves compared to other oceans. Connectivity patterns could be aligned with directionality of major ocean currents. Madagascar and the Seychelles each harbored haplogroups A and B, albeit among spatially separated populations, explained from a different migration era. Likewise, the Aldabra Atoll harbored spatially distinct haplotypes. Nuclear ribosomal cistron (8,033bp) variants corresponded to haplogroups and confirmed admixtures in the Seychelles and Aldabra. These findings shed new light on the origins and dispersal routes of R. mucronata lineages that have shaped their contemporary populations in large regions of the WIO, which may be important information for defining marine conservation units, both at ocean scale and at level of small islands.

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Topics: Haplogroup (55%), Biological dispersal (51%)

1 Citations

Open accessJournal ArticleDOI: 10.3389/FCOSC.2021.746461
08 Oct 2021-
Abstract: Dispersal plays a crucial role in the connectivity of established mangrove populations and in species range dynamics. As species ranges shift in response to climate change, range expansions can occur from incremental short-distance dispersal events and from stochastic long-distance dispersal events. Most population genetic research dealt with historically accumulated events though evidence of actual propagule dispersal allows to estimate genotypic features and origin of founders. In this study we aim to disentangle a contemporary dispersal event. Using microsatellite markers, we genotyped 60 Rhizophora racemosa drift propagules obtained on a bare unforested coastal area in southern Cameroon, estimated their relationship to 109 adult trees from most proximate sites (which were 3 to 85 km away), and assessed their relative difference with 873 trees of major mangrove areas (> 300 km) along the Cameroonian coastline. Proximate mangrove populations were considered as potential source populations in assignment tests. However, drift propagules could not be assigned to any of the Cameroonian mangrove sites and were genetically isolated from Cameroonian populations. Drift propagules showed higher levels of genetic diversity and private alleles giving a higher relatedness to each other than to any putative source population. Chloroplast sequences were used to confirm the identity of drift propagules as R. racemosa. We postulate that a complex interaction of ocean currents, estuarine geomorphology, and tidal patterns explain drift propagule dispersal to an area. Most likely the investigated cohort of propagules originated from more southern mangrove areas of the West African range beyond the Cameroonian border. This study unraveled the allelic, genetic, and genotypic features of stranded propagules following a stochastic long-distance dispersal. Transboundary dispersal of these propagules highlights the need for intergovernmental efforts in the management of biodiversity.

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Topics: Biological dispersal (67%), Propagule (59%), Species distribution (54%) ... show more

83 results found

Open accessJournal ArticleDOI: 10.1093/GENETICS/155.2.945
01 Jun 2000-Genetics
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

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Topics: Human population genetics (60%), Effective population size (55%), Population (55%) ... show more

25,033 Citations

Open accessJournal ArticleDOI: 10.1111/J.1365-294X.2005.02553.X
01 Jul 2005-Molecular Ecology
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.

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Topics: Bayes' theorem (52%), Population (52%), Sample size determination (50%)

16,374 Citations

Journal ArticleDOI: 10.1111/J.1471-8286.2005.01155.X
Rodney Peakall1, Peter E. Smouse2Institutions (2)
Abstract: genalex is a user-friendly cross-platform package that runs within Microsoft Excel, enabling population genetic analyses of codominant, haploid and binary data. Allele frequency-based analyses include heterozygosity, F statistics, Nei's genetic distance, population assignment, probabilities of identity and pairwise relatedness. Distance-based calculations include amova, principal coordinates analysis (PCA), Mantel tests, multivariate and 2D spatial autocorrelation and twogener. More than 20 different graphs summarize data and aid exploration. Sequence and genotype data can be imported from automated sequencers, and exported to other software. Initially designed as tool for teaching, genalex 6 now offers features for researchers as well. Documentation and the program are available at

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Topics: Population (53%)

14,741 Citations

Journal ArticleDOI: 10.1111/J.1471-8286.2004.00684.X
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

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Topics: Genotyping (56%), Genotype frequency (54%), Population (52%) ... show more

9,353 Citations

Journal ArticleDOI: 10.1007/S12686-011-9548-7
Dent Earl1, Bridgett M. vonHoldt2Institutions (2)
Abstract: We present STRUCTURE HARVESTER (available at ), 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.

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8,329 Citations