Species distribution and introgressive hybridization of two Avicennia species from the Western Hemisphere unveiled by phylogeographic patterns

A new computational method to estimate adaptation time in Avicennia by using divergence time

Evolutionary studies of plant groups which are distributed in vast geographical regions and face different ecological and environmental conditions are important as they through light on different mechanisms of local adaptation and species divergence through time. The genus Avicennia is one of these plant groups which inspire of few species show interesting geographical distribution with some degree of species-specific geographical isolations. In general, very limited molecular phylogenetic investigations have been carried out in the genus Avicennia, and therefore we conducted the present study with the following aims: 1. To estimate the species divergence time based on different nuclear and chloroplast DNA regions, separately. This will illustrate how different genetic regions evolved in this genus, 2. To identify the sequences with potential adaptive value against geographical variable by latent factor mixed models (LFMM) analysis, 3. To illustrate the phylogenetic signal of these DNA regions and their role in speciation within the genus and, 4. To introducing a new computational strategy for estimating adaptive time for the sequences. The results showed that different genetic regions may produce different species divergent time, both the nuclear ribosomal internal transcribed spacer (ITS) region and chloroplast DNA sequences, contained potentially adaptive single nucleotide polymorphisms (SNPs).We could present a suggestive time for these adaptive sequences for the first time. In conclusion both local adaptation and independent mutations seem to have played role in Avicennia speciation and evolution.

Fasta2Structure: a user-friendly tool for converting multiple aligned FASTA files to STRUCTURE format

BACKGROUND

The STRUCTURE software has gained popularity as a tool for population structure and genetic analysis. Nevertheless, formatting data to meet STRUCTURE's specific requirements can be daunting and susceptible to errors, especially when handling multilocus data. This article highlights the creation of a graphical user interface (GUI) application tailored to streamline the process of converting multiple sequence alignments into a single, cohesive file that is compatible with the STRUCTURE software.

RESULTS

The application has been developed utilizing Tkinter for the GUI and Biopython for handling FASTA files. This program processes the files, pinpoints variable sites, and converts the sequences into a binary format. Subsequently, the sequences are concatenated and presented within the graphical interface's text area, enabling users to review and confirm the results. Furthermore, the program stores the concatenated results in a file, delivering a ready-to-use input for the STRUCTURE software.

CONCLUSION

This application offers an efficient and dependable solution for transforming multiple aligned FASTA files into a concatenated binary format file, which is compatible with the STRUCTURE software. With its user-friendly graphical interface and error-reduction approach, this tool proves invaluable for researchers engaged in population structure and genetic analysis.

Putative Local Adaptive SNPs in the Genus Avicennia

The genus Avicennia with eight species grow in intertidal zones of tropical and temperate regions, ranging in distribution from West Asia, to Australia, and Latin America. These mangroves have several medicinal applications for mankind. Many genetic and phylogenetic studies have been carried out on mangroves, but none is concerned with geographical adaptation of SNPs. We therefore, used ITS sequences of about 120 Avicennia taxa growing in different parts of the world and undertook computational analyses to identify discriminating SNPs among these species and to study their association with geographical variables. A combination of multivariate and Bayesian approaches such as CCA, RDA, and LFMM were conducted to identify the SNPs with potential adaptation to geographical and ecological variables. Manhattan plot revealed that many of these SNPs are significantly associated with these variables. The genetic changes accompanied by local and geographical adaptation were illustrated by skyline plot. These genetic changes occurred not under a molecular clock model of evolution and probably under a positive selection pressure imposed in different geographical regions in which these plants grow.

Comparative Analysis and Phylogenetic Relationships of Ceriops Species (Rhizophoraceae) and Avicennia lanata (Acanthaceae): Insight into the Chloroplast Genome Evolution between Middle and Seaward Zones of Mangrove Forests

Ceriops and Avicennia are true mangroves in the middle and seaward zones of mangrove forests, respectively. The chloroplast genomes of Ceriops decandra, Ceriops zippeliana, and Ceriops tagal were assembled into lengths of 166,650, 166,083 and 164,432 bp, respectively, whereas Avicennia lanata was 148,264 bp in length. The gene content and gene order are highly conserved among these species. The chloroplast genome contains 125 genes in A. lanata and 129 genes in Ceriops species. Three duplicate genes (rpl2, rpl23, and trnM-CAU) were found in the IR regions of the three Ceriops species, resulting in expansion of the IR regions. The rpl32 gene was lost in C. zippeliana, whereas the infA gene was present in A. lanata. Short repeats (<40 bp) and a lower number of SSRs were found in A. lanata but not in Ceriops species. The phylogenetic analysis supports that all Ceriops species are clustered in Rhizophoraceae and A. lanata is in Acanthaceae. In a search for genes under selective pressures of coastal environments, the rps7 gene was under positive selection compared with non-mangrove species. Finally, two specific primer sets were developed for species identification of the three Ceriops species. Thus, this finding provides insightful genetic information for evolutionary relationships and molecular markers in Ceriops and Avicennia species.

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

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 &gt; 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 vs. 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.

Hurricanes overcome migration lag and shape intraspecific genetic variation beyond a poleward mangrove range limit

Expansion of many tree species lags behind climate change projections. Extreme storms can rapidly overcome this lag, especially for coastal species, but how will storm-driven expansion shape intraspecific genetic variation? Do storms provide recruits only from the nearest sources, or from more distant sources? Answers to these questions have ecological and evolutionary implications, but empirical evidence is absent from the literature. In 2017, Hurricane Irma provided an opportunity to address this knowledge gap at the northern range limit of the neotropical black mangrove (Avicennia germinans) on the Atlantic coast of Florida, USA. We observed massive post-hurricane increases in beach-stranded A. germinans propagules at, and past, this species' present day range margin when compared to a previously surveyed nonhurricane year. Yet, propagule dispersal does not guarantee subsequent establishment and reproductive success (i.e., effective dispersal). We also evaluated prior effective dispersal along this coastline with isolated A. germinans trees identified beyond the most northern established population. We used 12 nuclear microsatellite loci to genotype 896 hurricane-driven drift propagules from nine sites and 10 isolated trees from four sites, determined their sources of origin, and estimated dispersal distances. Almost all drift propagules and all isolated trees came from the nearest sources. This research suggests that hurricanes are a prerequisite for poleward range expansion of a coastal tree species and that storms can shape the expanding gene pool by providing almost exclusively range-margin genotypes. These insights and empirical estimates of hurricane-driven dispersal distances should improve our ability to forecast distributional shifts of coastal species.

Local adaptation of a dominant coastal tree to freshwater availability and solar radiation suggested by genomic and ecophysiological approaches

Local adaptation is often a product of environmental variations in geographical space and has implications for biodiversity conservation. We investigated the role of latitudinal heterogeneity in climate on the organization of genetic and phenotypic variation in the dominant coastal tree Avicennia schaueriana. In a common garden experiment, samples from an equatorial region, with pronounced seasonality in precipitation, accumulated less biomass, and showed lower stomatal conductance and transpiration, narrower xylem vessels, smaller leaves and higher reflectance of long wavelengths by the stem epidermis than samples from a subtropical region, with seasonality in temperature and no dry season. Transcriptomic differences identified between trees sampled under field conditions at equatorial and subtropical sites, were enriched in functional categories such as responses to temperature, solar radiation, water deficit, photosynthesis and cell wall biosynthesis. Remarkably, the diversity based on genome-wide SNPs revealed a north-south genetic structure and signatures of selection were identified for loci associated with photosynthesis, anthocyanin accumulation and the responses to osmotic and hypoxia stresses. Our results suggest the existence of divergence in key resource-use characteristics, likely driven by seasonality in water deficit and solar radiation. These findings provide a basis for conservation plans and for predicting coastal plants responses to climate change.

Molecular responses to freshwater limitation in the mangrove tree Avicennia germinans (Acanthaceae)

Environmental variation along the geographical space can shape populations by natural selection. In the context of global warming and changing precipitation regimes, it is crucial to understand the role of environmental heterogeneity in tropical trees adaptation, given their disproportional contribution to water and carbon biogeochemical cycles. Here, we investigated how heterogeneity in freshwater availability along tropical wetlands has influenced molecular variations of the black mangrove (Avicennia germinans). A total of 57 trees were sampled at seven sites differing markedly in precipitation regime and riverine freshwater inputs. Using 2,297 genome-wide single nucleotide polymorphic markers, we found signatures of natural selection by the association between variations in allele frequencies and environmental variables, including the precipitation of the warmest quarter and the annual precipitation. Additionally, we found candidate loci for selection based on statistical deviations from neutral expectations of interpopulation differentiation. Most candidate loci within transcribed sequences were functionally associated with central aspects of drought tolerance or plant response to drought. Moreover, our results suggest the occurrence of the rapid evolution of a population, probably in response to sudden and persistent limitations in plant access to soil water, following a road construction in 1974. Observations supporting rapid evolution included the reduction in tree size and changes in allele frequencies and in transcript expression associated with increased drought tolerance through the accumulation of osmoprotectants and antioxidants, biosynthesis of cuticles, protection against protein degradation, stomatal closure, photorespiration and photosynthesis. We describe a major role of spatial heterogeneity in freshwater availability in the specialization of this typically tropical tree.

A general framework for propagule dispersal in mangroves

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.

Global-scale dispersal and connectivity in mangroves

Mangroves are of considerable ecological and socioeconomical importance; however, substantial areal losses have been recorded in many regions, driven primarily by anthropogenic disturbances and sea level rise. Oceanic dispersal of mangrove propagules provides a key mechanism for shifting distributions in response to environmental change. Here we provide a model framework for describing global dispersal and connectivity in mangroves. We identify important dispersal routes, barriers, and stepping-stones and quantify the influence of minimum and maximum floating periods on simulated connectivity patterns. Our study provides a baseline to improve our understanding of observed mangrove species distributions and, in combination with climate data, the expected range shifts under climate change.

Dispersal provides a key mechanism for geographical range shifts in response to changing environmental conditions. For mangroves, which are highly susceptible to climate change, the spatial scale of dispersal remains largely unknown. Here we use a high-resolution, eddy- and tide-resolving numerical ocean model to simulate mangrove propagule dispersal across the global ocean and generate connectivity matrices between mangrove habitats using a range of floating periods. We find high rates of along-coast transport and transoceanic dispersal across the Atlantic, Pacific, and Indian Oceans. No connectivity is observed between populations on either side of the American and African continents. Archipelagos, such as the Galapagos and those found in Polynesia, Micronesia, and Melanesia, act as critical stepping-stones for dispersal across the Pacific Ocean. Direct and reciprocal dispersal routes across the Indian Ocean via the South Equatorial Current and seasonally reversing monsoon currents, respectively, allow connectivity between western Indian Ocean and Indo-West Pacific sites. We demonstrate the isolation of the Hawaii Islands and help explain the presence of mangroves on the latitudinal outlier Bermuda. Finally, we find that dispersal distance and connectivity are highly sensitive to the minimum and maximum floating periods. We anticipate that our findings will guide future research agendas to quantify biophysical factors that determine mangrove dispersal and connectivity, including the influence of ocean surface water properties on metabolic processes and buoyancy behavior, which may determine the potential of viably reaching a suitable habitat. Ultimately, this will lead to a better understanding of global mangrove species distributions and their response to changing climate conditions.

Population genetic structure, introgression, and hybridization in the genus Rhizophora along the Brazilian coast

Mangrove plants comprise plants with similar ecological features that have enabled them to adapt to life between the sea and the land. Within a geographic region, different mangrove species share not only similar adaptations but also similar genetic structure patterns. Along the eastern coast of South America, there is a subdivision between the populations north and south of the continent's northeastern extremity. Here, we aimed to test for this north‐south genetic structure in Rhizophora mangle, a dominant mangrove plant in the Western Hemisphere. Additionally, we aimed to study the relationships between R. mangle, R. racemosa, and R. × harrisonii and to test for evidence of hybridization and introgression. Our results confirmed the north‐south genetic structure pattern in R. mangle and revealed a less abrupt genetic break in the northern population than those observed in Avicennia species, another dominant and widespread mangrove genus in the Western Hemisphere. These results are consistent with the role of oceanic currents influencing sea‐dispersed plants and differences between Avicennia and Rhizophora propagules in longevity and establishment time. We also observed that introgression and hybridization are relevant biological processes in the northeastern coast of South America and that they are likely asymmetric toward R. mangle, suggesting that adaptation might be a process maintaining this hybrid zone.

Possible developments for ex situ phytoremediation of contaminated sediments, in tropical and subtropical regions - Review

The growing problem of remediation of contaminated sediments dredged from harbor channels needs to be resolved by a cost effective and sustainable technology. Phytoremediation, by ex situ remediation plants, seems to have the potential to replace traditional methods in case of moderately contaminated sediments. On the other side, the need to mix sediments with soil and/or sand to allow an easier establishment of most employed species causes an increase of the volume of the processed substrate up to 30%. Moreover the majority of phytoremediating species are natives of temperate climate belt. Mangroves, with a special focus on the genus Avicennia - a salt secreting species - should represent an effective alternative in terms of adaptation to salty, anoxic sediments and an opportunity to develop ex situ phytoremediation plants in tropical and subtropical regions. The use of humic acid to increase root development, cell antioxidant activity and the potential attenuation of the "heavy metals exclusion strategy" to increase phytoextraction potentials of mangroves will be reviewed.

Re-Evaluation of Phylogenetic Relationships among Species of the Mangrove Genus Avicennia from Indo-West Pacific Based on Multilocus Analyses

Avicennia L. (Avicenniaceae), one of the most diverse mangrove genera, is distributed widely in tropical and subtropical intertidal zones worldwide. Five species of Avicennia in the Indo-West Pacific region have been previously described. However, their phylogenetic relationships were determined based on morphological and allozyme data. To enhance our understanding of evolutionary patterns in the clade, we carried out a molecular phylogenetic study using wide sampling and multiple loci. Our results support two monophyletic clades across all species worldwide in Avicennia: an Atlantic-East Pacific (AEP) lineage and an Indo-West Pacific (IWP) lineage. This split is in line with biogeographic distribution of the clade. Focusing on the IWP branch, we reconstructed a detailed phylogenetic tree based on sequences from 25 nuclear genes. The results identified three distinct subclades, (1) A. rumphiana and A. alba, (2) A. officinalis and A. integra, and (3) the A. marina complex, with high bootstrap support. The results strongly corresponded to two morphological traits in floral structure: stigma position in relation to the anthers and style length. Using Bayesian dating methods we estimated diversification of the IWP lineage was dated to late Miocene (c. 6.0 million years ago) and may have been driven largely by the fluctuating sea levels since that time.