Oceanic currents, not land masses, maintain the genetic structure of the mangrove Rhizophora mucronata Lam. (Rhizophoraceae) in Southeast Asia
TL;DR: Novel evidence is presented that the genetic structure of R. mucronata is maintained by ocean current-facilitated propagule dispersal, which can be explained by the prevailing ocean currents in this region.
Abstract: Aim
Mangroves are intertidal plants with sea-dispersed propagules, hence their population structure can offer valuable insights into the biogeographical processes driving population subdivision in coastal species. In this study, we used molecular markers and ocean circulation simulations to examine the effects of ocean currents and land masses on the genetic structure of the major mangrove species Rhizophora mucronata.
Location
Southeast Asia.
Methods
We assessed the genetic structure of 13 R. mucronata populations from continental Southeast Asia and Sumatra using 10 microsatellite loci. We first examined the relative effects of geographical distance and land mass (the Malay Peninsula) in shaping the genetic structure of R. mucronata in Southeast Asia. We then characterized the genetic structure of R. mucronata and compared it to the simulated ocean circulation patterns within our study region.
Results
Despite the low genetic diversity, significant genetic structuring was detected across R. mucronata populations. Contrary to observations on other mangrove species, genetic differentiation in R. mucronata was not found across the coasts of the Malay Peninsula, nor was it correlated with geographical distance. Instead, the most distinct genetic discontinuity was found at the boundary between the Andaman Sea and the Malacca Strait, and this can be explained by the prevailing ocean currents in this region.
Main conclusions
Our study presents novel evidence that the genetic structure of R. mucronata is maintained by ocean current-facilitated propagule dispersal.
Citations
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TL;DR: It is shown that important dispersal factors remain understudied and that adequate empirical data on the determinants of dispersal are missing for most mangrove species, as well as the mechanisms and ecological processes that are known to modulate the spatial patterns of mangroves dispersal.
Abstract: Dispersal allows species to shift their distributions in response to changing climate conditions. As a result, dispersal is considered a key process contributing to a species' long-term persistence. For many passive dispersers, fluid dynamics of wind and water fuel these movements and different species have developed remarkable adaptations for utilizing this energy to reach and colonize suitable habitats. The seafaring propagules (fruits and seeds) of mangroves represent an excellent example of such passive dispersal. Mangroves are halophytic woody plants that grow in the intertidal zones along tropical and subtropical shorelines and produce hydrochorous propagules with high dispersal potential. This results in exceptionally large coastal ranges across vast expanses of ocean and allows species to shift geographically and track the conditions to which they are adapted. This is particularly relevant given the challenges presented by rapid sea-level rise, higher frequency and intensity of storms, and changes in regional precipitation and temperature regimes. However, despite its importance, the underlying drivers of mangrove dispersal have typically been studied in isolation, and a conceptual synthesis of mangrove oceanic dispersal across spatial scales is lacking. Here, we review current knowledge on mangrove propagule dispersal across the various stages of the dispersal process. Using a general framework, we outline the mechanisms and ecological processes that are known to modulate the spatial patterns of mangrove dispersal. We show that important dispersal factors remain understudied and that adequate empirical data on the determinants of dispersal are missing for most mangrove species. This review particularly aims to provide a baseline for developing future research agendas and field campaigns, filling current knowledge gaps and increasing our understanding of the processes that shape global mangrove distributions.
81 citations
TL;DR: The first evidence of ongoing hybridization between Avicennia species and that these hybrids are fertile is reported, although this interspecific crossing has not contributed to an increase in the genetic diversity the populations where A. germinans and A. schaueriana hybridize.
Abstract: Mangrove plants comprise a unique group of organisms that grow within the intertidal zones of tropical and subtropical regions and whose distributions are influenced by both biotic and abiotic factors. To understand how these extrinsic and intrinsic processes influence a more fundamental level of the biological hierarchy of mangroves, we studied the genetic diversity of two Neotropical mangrove trees, Avicenniagerminans and A. schaueriana, using microsatellites markers. As reported for other sea-dispersed species, there was a strong differentiation between A. germinans and A. schaueriana populations sampled north and south of the northeastern extremity of South America, likely due to the influence of marine superficial currents. Moreover, we observed fine-scale genetic structures even when no obvious physical barriers were present, indicating pollen and propagule dispersal limitation, which could be explained by isolation-by-distance coupled with mating system differences. We report the first evidence of ongoing hybridization between Avicennia species and that these hybrids are fertile, although this interspecific crossing has not contributed to an increase in the genetic diversity the populations where A. germinans and A. schaueriana hybridize. These findings highlight the complex interplay between intrinsic and extrinsic factors that shape the distribution of the genetic diversity in these sea-dispersed colonizer species.
62 citations
10 Nov 2017
TL;DR: Landscape genomics is a rapidly advancing research field that combines population genomics, landscape ecology, and spatial analytical techniques to explicitly quantify the effects of environmental heterogeneity on neutral and adaptive genetic variation and underlying processes.
Abstract: Landscape genomics is a rapidly advancing research field that combines population genomics, landscape ecology, and spatial analytical techniques to explicitly quantify the effects of environmental heterogeneity on neutral and adaptive genetic variation and underlying processes. Landscape genomics has tremendous potential for addressing fundamental and applied research questions in various research fields, including ecology, evolution, and conservation biology. However, the unique combination of different scientific disciplines and analytical approaches also constitute a challenge to most researchers wishing to apply landscape genomics. Here, we present an introductory overview of important concepts and methods used in current landscape genomics. For this, we first define the field and explain basic concepts and methods to capture different hypotheses of landscape influences on neutral genetic variation. Next, we highlight established and emerging genomic tools for quantifying adaptive genetic variation in landscape genomic studies. To illustrate the covered topics and to demonstrate the potential of landscape genomics, we provide empirical examples addressing a variety of research question, i.e., the investigation of evolutionary processes driving population differentiation, the landscape genomics of range expanding species, and landscape genomic patterns in organisms of special interest, including species inhabiting aquatic and terrestrial environments. We conclude by outlining remaining challenges and future research avenues in landscape genomics.
60 citations
Cites background from "Oceanic currents, not land masses, ..."
...For example, estuarine barriers and ocean currents were found to restrict gene flow in the mangrove species Avicennia germinans, Rhizophora mangle, and Rhizophora mucronata (Ceron-Souza et al. 2012; Wee et al. 2014), and ocean barriers limited gene flow in sandalwood (Santalum insular) (Lhuillier et al....
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...…estuarine barriers and ocean currents were found to restrict gene flow in the mangrove species Avicennia germinans, Rhizophora mangle, and Rhizophora mucronata (Ceron-Souza et al. 2012; Wee et al. 2014), and ocean barriers limited gene flow in sandalwood (Santalum insular) (Lhuillier et al. 2006)....
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01 Jan 2017
TL;DR: In this article, an updated account of mangrove biodiversity patterns and evolution based on ancestral biogeography and extant floristics is provided, where the factors influencing current distributional patterns have been looked at closely with the specific distributions of each genotype considering prior historical influences.
Abstract: This treatment provides an updated account of mangrove biodiversity patterns and evolution based on ancestral biogeography and extant floristics. Mangrove plants occur where they do in the world because past and current factors influence their dispersal and establishment. Key limiting factors include: land barriers, dispersal across water, climatic conditions, and availability of biotic material. Over time, each of these factors has morphed and changed as each driver varied during the evolution of the 80 species and hybrids from at least 18 family lineages. In this treatment, the factors influencing current distributional patterns have been looked at closely with the specific distributions of each genotype considering prior historical influences. Distributional patterns, like diversity hot spots spanning large geographic areas, species gradients, and discontinuities are considered tangible evidence of the appearance and evolution of each mangrove entity.
54 citations
Chiba University1, Xishuangbanna Tropical Botanical Garden2, University of Tokyo3, National University of Singapore4, M S Swaminathan Research Foundation5, University of North Sumatra6, Indonesian Institute of Sciences7, Jenderal Soedirman University8, Kasetsart University9, Universiti Malaysia Sabah10, Hanoi National University of Education11, Ateneo de Manila University12, Adventist University of the Philippines13, Universiti Putra Malaysia14, University of Yangon15, University of the Ryukyus16
TL;DR: The results serve as the foundation for the conservation genetics of R. mucronata and R. stylosa and highlighted the need to recognize the genetic distinctiveness of closely-related species, determine their respective genetic structure, and avoid artificially promoting hybridization in mangrove restoration programmes.
Abstract: Mangrove forests are ecologically important but globally threatened intertidal plant communities. Effective mangrove conservation requires the determination of species identity, management units, and genetic structure. Here, we investigate the genetic distinctiveness and genetic structure of an iconic but yet taxonomically confusing species complex Rhizophora mucronata and R. stylosa across their distributional range, by employing a suite of 20 informative nuclear SSR markers. Our results demonstrated the general genetic distinctiveness of R. mucronata and R. stylosa, and potential hybridization or introgression between them. We investigated the population genetics of each species without the putative hybrids, and found strong genetic structure between oceanic regions in both R. mucronata and R. stylosa. In R. mucronata, a strong divergence was detected between populations from the Indian Ocean region (Indian Ocean and Andaman Sea) and the Pacific Ocean region (Malacca Strait, South China Sea and Northwest Pacific Ocean). In R. stylosa, the genetic break was located more eastward, between populations from South and East China Sea and populations from the Southwest Pacific Ocean. The location of these genetic breaks coincided with the boundaries of oceanic currents, thus suggesting that oceanic circulation patterns might have acted as a cryptic barrier to gene flow. Our findings have important implications on the conservation of mangroves, especially relating to replanting efforts and the definition of evolutionary significant units in Rhizophora species. We outlined the genetic structure and identified geographical areas that require further investigations for both R. mucronata and R. stylosa. These results serve as the foundation for the conservation genetics of R. mucronata and R. stylosa and highlighted the need to recognize the genetic distinctiveness of closely-related species, determine their respective genetic structure, and avoid artificially promoting hybridization in mangrove restoration programmes.
49 citations
Cites background or result from "Oceanic currents, not land masses, ..."
...An analysis of regional oceanic circulation patterns suggested that contemporary oceanic currents may act as a cryptic barrier to gene flow that prevents admixture across this genetic boundary [40]....
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...The genetic break we detected at the northern boundary of the Malacca Strait concurred with an earlier study involving a smaller geographical coverage of Southeast Asia [40]....
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...[40] showed that these R....
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References
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Journal Article•
TL;DR: Copyright (©) 1999–2012 R Foundation for Statistical Computing; permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and permission notice are preserved on all copies.
Abstract: Copyright (©) 1999–2012 R Foundation for Statistical Computing. Permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and this permission notice are preserved on all copies. Permission is granted to copy and distribute modified versions of this manual under the conditions for verbatim copying, provided that the entire resulting derived work is distributed under the terms of a permission notice identical to this one. Permission is granted to copy and distribute translations of this manual into another language, under the above conditions for modified versions, except that this permission notice may be stated in a translation approved by the R Core Team.
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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.
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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.
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Abstract: This journal frequently contains papers that report values of F-statistics estimated from genetic data collected from several populations. These parameters, FST, FIT, and FIS, were introduced by Wright (1951), and offer a convenient means of summarizing population structure. While there is some disagreement about the interpretation of the quantities, there is considerably more disagreement on the method of evaluating them. Different authors make different assumptions about sample sizes or numbers of populations and handle the difficulties of multiple alleles and unequal sample sizes in different ways. Wright himself, for example, did not consider the effects of finite sample size. The purpose of this discussion is to offer some unity to various estimation formulae and to point out that correlations of genes in structured populations, with which F-statistics are concerned, are expressed very conveniently with a set of parameters treated by Cockerham (1 969, 1973). We start with the parameters and construct appropriate estimators for them, rather than beginning the discussion with various data functions. The extension of Cockerham's work to multiple alleles and loci will be made explicit, and the use of jackknife procedures for estimating variances will be advocated. All of this may be regarded as an extension of a recent treatment of estimating the coancestry coefficient to serve as a mea-
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