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opencc-zeroFeb 2024View details →

Supplementary information for: The artefactual branch effect and phylogenetic conflict: Species delimitation with gene flow in mangrove pit vipers (Trimeresurus purpureomaculatus-erythrurus complex)

Mangrove pit vipers of the Trimeresurus purpureomaculatus-erythrurus complex are the only species of viper known to naturally inhabit mangroves. Despite serving integral ecological functions in mangrove ecosystems, the evolutionary history, distribution, and species boundaries of mangrove pit vipers remain poorly understood, partly due to overlapping distributions, confusing phenotypic variations, and the lack of focused studies. Here, we present the first genomic study on mangrove pit vipers and introduce a robust hypothesis-driven species delimitation framework that considers gene flow and phylogenetic uncertainty in conjunction with a novel application of a new class of speciation-based delimitation model implemented through the program Delineate. Our results showed that gene flow produced phylogenetic conflict in our focal species and substantiated the artefactual branch effect where highly admixed populations appear as divergent nonmonophyletic lineages arranged in a stepwise manner at the basal position of clades. Despite the confounding effects of gene flow, we were able to obtain unequivocal support for the recognition of a new species based on the intersection and congruence of multiple lines of evidence. This study demonstrates that an integrative hypothesis-driven approach predicated on the consideration of multiple plausible evolutionary histories, population structure/ differentiation, gene flow, and the implementation of a speciation-based delimitation model can effectively delimit species in the presence of gene flow and phylogenetic conflict.

opencc-by-4.0Mar 2024View details →

Mangroves as nature-based mitigation for ENSO-driven compound flood risks in a large river delta: supporting data - high water levels

This dataset contains modelled high water levels in the Guayas delta supporting the paper 'Mangroves as nature-based mitigation for ENSO-driven compound flood risks in a large river delta' published in HESS 2024. The dataset is organised through two folders: <ul> <li>mangroves: all data from the scenarios with mangroves included in the domain</li> <li>no_mangroves: all data from the scenarios without mangroves included in the domain</li> </ul> Each folder is further divided along 6 subfolders: <ul> <li>I: El Niño Ocean & river</li> <li>II: El Niño Ocean</li> <li>III: El Niño river</li> <li>IV: Neutral</li> <li>I_50per: 50 % increase in seaward El Niño anomalies</li> <li>I_150per: 150 % increase in seaward El Niño anomalies</li> </ul> Each folder contains two files: <ul> <li>vars.csv - each row represents a mesh node and there are three columns: <ul> <li>X: x value of the model mesh node [m]</li> <li>Y: y value of the model mesh node [m]</li> <li>HIGH_WATER: high water level [m]</li> </ul> </li> </ul>

opencc-by-4.0Mar 2021View details →

Figure 4 in Population biology of the fiddler crab Uca maracoani (Crustacea, Ocypodidae) inhabiting an impacted mangrove area on the southern coast of São Paulo state, Brazil

Figure 4. Frequency of juveniles (%) of Uca maracoani by month.

Figure 7 in Animal diversity in the mangrove forest at Bichitrapur of Balasore district, Odisha, India- A case study

Figure 7. Onchidium typhae on the wooden hole of mangrove.

Figure 9. Omobranchus zebra, a in Animal diversity in the mangrove forest at Bichitrapur of Balasore district, Odisha, India- A case study

Figure 9. Omobranchus zebra, a blennid fish.

Figure 6 in Animal diversity in the mangrove forest at Bichitrapur of Balasore district, Odisha, India- A case study

Figure 6. Europila withersi on the leaf of mangroves.

Figure 4 in Animal diversity in the mangrove forest at Bichitrapur of Balasore district, Odisha, India- A case study

Figure 4. Coenobita cavipes climbing on Exocearia aggolacha, mangrove.

Figure 5 in Animal diversity in the mangrove forest at Bichitrapur of Balasore district, Odisha, India- A case study

Figure 5. Balanus amhritrite and Nerita articulata on the mangrove.

Figure 2 in Animal diversity in the mangrove forest at Bichitrapur of Balasore district, Odisha, India- A case study

Figure 2. Mangrove area of Subarnarekha estuary at Bichitrapur.

Figure 1 in Animal diversity in the mangrove forest at Bichitrapur of Balasore district, Odisha, India- A case study

Figure 1. Satellite Map showing the mangrove area of Bichitrapur (Courtsey: Google earth.com).

opencc-zeroDec 2023View details →

Metagenomic analysis of gut microbiome illuminates the mechanisms and evolution of lignocellulose degradation in mangrove herbivorous crabs

Background: Sesarmid crabs dominate mangrove habitat as the major primary consumers, which facilitates the trophic link and nutrient recycling in the ecosystem. Therefore, the adaptations and mechanisms of sesarmid crabs to herbivory is not only crucial to terrestrialization and its evolutionary success, but also to the healthy functioning of mangrove forest ecosystems. Although endogenous cellulases expressions were reported in crab species, it remains unknown if the endogenous enzymes alone can complete the whole lignocellulolytic pathway, or they also depend on the contribution from their intestinal microbiome. We attempt to investigate the role of gut symbiotic microbes of mangrove-feeding sesarmid crabs in plant digestion using a comparative metagenomic approach. Results: Metagenomics analyses on 43 crab gut samples from 23 species of mangrove crabs revealed a wide coverage of 127 CAZy families and nine KOs targeting lignocellulose and their derivatives in all species analyzed, including predominantly carnivorous species, suggesting the crab species gut microbiome have lignocellulolytic capacity regardless of dietary preference. Microbial cellulase, hemicellulase and pectinase genes in herbivorous and detritivorous crabs were differentially more abundant when compared to omnivorous and carnivorous crabs, indicating the importance of gut symbionts in lignocellulose degradation in mangrove crabs and the enrichment of lignocellulolytic microbes in response to diet with higher lignocellulose content. The herbivorous and detritivorous crabs showed highly similar CAZyme composition compared to dissimilarities observed in taxonomic profiles observed in both groups, suggesting a stronger selection force to gut microbiota by its functional capacity than by taxonomy. The gut microbiota in herbivorous sesarmid crabs were also enriched with nitrogen reduction and fixation genes, implying possible roles of the gut microbiota in supplementing nitrogen that is deficient in plant diet. Conclusions: Endosymbiotic cellulolytic microbes play an important role in lignocellulose degradation in most crab species but their abundance is strongly correlated with dietary preference, and they are highly enriched in herbivorous sesarmids, thus enhancing their capacity for digestion of mangrove leaves. Dietary preference is a stronger driver in determining the microbial CAZyme composition and taxonomic profile in mangrove crab microbiome, resulting in functional redundancy of endosymbiotic microbes. Our results showed that crabs implement a mixed mode of digestion utilizing both endogenous and microbial enzymes in lignocellulose degradation, as observed in most of the more advanced herbivorous invertebrate species.

opencc-by-4.0Dec 2017View details →

Figure 1 in Notes on specimens of the Glossy Mangrove Snake (Gerarda prevostiana) in the collection of the Zoological Survey of India, Kolkata along with past records from India

Figure 1. Gerarda prevostiana.

opencc-by-4.0Jun 2024View details →

Exotic Laguncularia racemosa drives rapid shifts in pond-to-mangrove restoration communities

The global degradation of mangrove ecosystems necessitates urgent restoration efforts. In China and many Southeast Asian regions, pond-to-mangrove restoration (PTMR) has become a key method for mangrove recovery. PTMR involves creating suitable habitats for mangroves through artificial terrain modification and planting. However, an overlooked issue is whether invasive exotic species benefit from PTMR. This study examines plant communities in a typical PTMR area, comparing community composition at four (PTMR4) and eight (PTMR8) years post-restoration. Results show that the exotic species Laguncularia racemosa rapidly increases in PTMR areas, significantly inhibiting native species growth and altering community composition. The relative abundance of L. racemosa rose from 8% at PTMR4 to 57% at PTMR8. By PTMR8, L. racemosa was taller than native species, with many seedlings present. Given the rapid growth and reproductive capacity of L. racemosa, and the high hydrological connectivity of mangrove wetlands, we recommend incorporating exotic species monitoring during PTMR. This study highlights the threat of biological invasions to ecological restoration projects, not just mangrove restoration. It emphasizes the need to prevent invasive species introduction during early restoration stages.

opencc-by-4.0Apr 2024View details →

The global fish and invertebrate abundance value of mangroves dataset

This dataset is the species and species group predictions of the density of 37 commercially important fish and invertebrates that are known to extensively use mangroves. All methods are provided in detail in the accompanying manuscript, zu Ermgassen et al. (2025) Mangroves support an estimated annual abundance of over 700 billion juvenile fish and invertebrates.  <h2>Description of files</h2> <ul> <li>Mangrove_commercial_fauna_density_data_references.csv: this is the raw data used to create the linear model using generalized least squares relating the fish density values to the covariate data</li> </ul> R Scripts & Data <ul> <li>This folder contain several R scripts and data files to used calculate the values in zu Ermgassen et al. (2025) Mangroves support an estimated annual abundance of over 700 billion juvenile fish and invertebrates. </li> </ul> Predictions* Species Predictions <ul> <li>all_sp_fit_fn.csv: the mean predicted species density for 37 commercially important fish and invertebrates for a grid with a spatial resolution of 1km2.</li> <li>all_sp_fit_fn_lower.csv: the lower (1.96 * standard error of the model fit) predicted species density for 37 commercially important fish and invertebrates for a grid with a spatial resolution of 1km2.</li> <li>all_sp_fit_fn_upper.csv: the upper (1.96 * standard error of the model fit) predicted species density for 37 commercially important fish and invertebrates for a grid with a spatial resolution of 1km2.</li> </ul> Species Group Predictions <ul> <li>all_sp_fit_fn_total.csv: the mean, lower and upper (1.96 * standard error of the model fit) predicted species density for 37 commercially important fish and invertebrates for a grid with a spatial resolution of 1km2, with species summed into finfishes (n = 29), crabs (n = 4), bivalves (n = 1), and prawns (n = 3).</li> </ul> Prediction Shapefiles <ul> <li>Species Name Contractions.csv: file with key to name contractions in the shapefile datasets</li> <li>Shapfiles: spatial representations of the Predictions datasets based on the 1km2 grid</li> </ul> * N.B. data labeled Neosarmatium meinerti in the above files has been corrected to Neosarmatium africanum

opencc-zeroDec 2021View details →

Data from: Establishing community-wide DNA barcode references for conserving mangrove forests in China

Background: Mangrove ecosystems have been the focus of global attention for their crucial role in sheltering coastal communities and retarding global climate change by sequestering 'blue carbon'. China is relatively rich in mangrove diversity, with one-third of the ca. 70 true mangrove species and a number of mangrove associate species occurring naturally along the country's coasts. Mangrove ecosystems, however, are widely threatened by intensifying human disturbances and rising sea levels. The urgent need to protect mangrove ecosystems could be assisted by using barcoding technology, which provides rapid species identification. Results: To investigate this potential, 898 plant specimens were collected from 33 of the major mangrove sites in China. Based on the morphologic diagnosis, the specimens were assigned to 72 species, including all 28 true mangrove species and all 12 mangrove associate species recorded in China. Three chloroplast DNA markers rbcL, trnH-psbA, matK, and one nuclear marker ITS2 were chosen to investigate the utility of using barcoding to identify these species. According to the criteria of barcoding gaps in genetic distance, sequence similarity and phylogenetic monophyly, we propose that a single marker, ITS2, is sufficient to barcode the species of mangroves and their associates in China. Furthermore, rbcL or trnH-psbA can also be used to gather supplement confirming data. In using these barcodes, we revealed a very low level of genetic variation among geographic locations in the mangrove species, which is an alert to their vulnerability to climate and anthropogenic disturbances. Conclusion: We suggest to use ITS2 to barcode mangrove species and terrestrial coastal plants in South China. The DNA barcode sequences we obtained would be valuable in monitoring biodiversity and the restoration of ecosystems, which are essential for mangrove conservation.

opencc-by-4.0Jul 2021View details →

Data from: Inheritance of DNA methylation differences in the mangrove Rhizophora mangle

This record contains supplementary information for the article "Inheritance of DNA methylation differences in the mangrove Rhizophora mangle" published in Evolution&Development. It contains the barcodes (barcodes.txt), the reference contigs (contigs.fasta.gz), the annotation of the reference contigs (mergedAnnot.csv.gz), the SNPs (snps.vcf.gz), the methylation data (methylation.txt.gz), and the experimental design (design.txt). All data are unfiltered. Short reads are available on SRA (PRJNA746695). Note that demultiplexing of the pooled reads (SRX11452376) will fail because the barcodes are already removed and the header information is lost during SRA submission. Instead, use the pre-demultiplexed reads that are as well linked to PRJNA746695.   Table S13 (TableS13_DSSwithGeneAnnotation.offspringFams.csv.gz): Differential cytosine methylation between families using the mother data set. The first three columns fragment number ("chr"), the position within the fragment ("pos"), and the sequence context ("context"). Columns with the pattern FDR_<X>_vs_<Y> contain false discovery rates of a test comparing population X with population Y. Average DNA methylation levels for each population are given in the columns "AC", "FD", "HI", "UTB", "WB", and "WI". The remaining columns contain the annotation of the fragment, for example whether it matches to a gene and if yes, the gene name ID and description are provided.

opencc-zeroJul 2022View details →

Data From: Evolution of woody plants to the land‐sea interface: The atypical genomic features of mangroves with atypical phenotypic adaptation

How plants adapt and diverge in extreme environments is a key question of plant evolution and ecology. Mangrove invasion of intertidal environments is facilitated by adaptive phenotypes such as aerial roots, salt-secreting leaf, and viviparity, and genomic mechanisms including whole genome duplication and transposable element number reduction. However, a number of mangroves lack these typical phenotypes. The question we ask is whether these phenotypically atypical mangroves also have distinct genomic features? The sibling mangrove species Lumnitzera littorea and Lumnitzera racemosa provide a model to study this question. We sequenced and assembled their genomes to chromosome level, together with a closely related species Combretum micranthum. While most mangroves have small genomes, the genomes of both Lumnitzera species are large (1443 and 1317 Mb) and carry a high proportion of repeat sequences (~75%). Moreover, Lumnitzera species have not undergone post-gamma whole-genome duplications. Their genome size increased mainly due to the expansion of repeat sequences in their ancestors. However, Lumnitzera genomes have reduced transposable elements by constraining the proliferation of new LTR-RTs. Meanwhile, the two species have more gene families contracted than expanded, and some gene families with reversed size change may underlie their differentiation in root morphology and local distribution. We identified 86 chromosomal inversions, five of which are measured between 6.5 and 12.8 megabases. A number of genes located in these inversions function in pigment biosynthesis, a process likely involved in flower color differentiation between the Lumnitzera species. We conclude that the mangroves with atypical phenotypes also have atypical genomic evolution.

opencc-zeroAug 2022View details →

Data from: Hindcast-validated species distribution models reveal future vulnerabilities of mangroves and salt marsh species

Rapid climate change threatens biodiversity via habitat loss, range shifts, increases in invasive species, novel species interactions, and other unforeseen changes. Coastal and estuarine species are especially vulnerable to the impacts of climate change due to sea level rise and may be severely impacted in the next several decades. Species distribution modeling can project the potential future distributions of species under scenarios of climate change using bioclimatic data and georeferenced occurrence data. However, models projecting suitable habitat into the future are impossible to ground truth. One solution is to develop species distribution models for the present and project them to periods in the recent past where distributions are known to test model performance before making projections into the future. Here, we develop models using abiotic environmental variables to quantify the current suitable habitat available to eight Neotropical coastal species: four mangrove species and four salt marsh species. Using a novel model validation approach that leverages newly available monthly climatic data from 1960-2018, we project these niche models into two time periods in the recent past (i.e., within the past half-century) when either mangrove or salt marsh dominance was documented via other data sources. Models were hindcast-validated and then used to project the suitable habitat of all species at four time periods in the future under a model of climate change. For all future time periods, the projected suitable habitat of mangrove species decreased, and suitable habitat declined more severely in salt marsh species.

opencc-zeroOct 2022View details →

A biogeographical approach to characterising the climatic, physical and geomorphic niche of the most widely distributed mangrove species, Avicennia marina

Aim: Mangroves are coastal ecosystems exposed to terrestrial, marine, geomorphic and climatic forcings operating in concert, making the mangrove niche hard to define, as evidenced by extremely poor restoration outcomes. We have developed a set of high-resolution species distribution models and interpreted the variables that have the largest impact on the niche of Avicennia marina, the most globally widespread mangrove species, to comprehensively detail the forcings driving habitat suitability. Location: Australia. Time period: 1970–2020. Major taxa studied: Avicennia marina (Forssk.) Vierh. Methods: We modelled the suitable habitat for A. marina in Australia using the maxent method incorporating 38 environmental variables and the Global Mangrove Watch baseline for the presence records. Using k-means grouping we identified sub-regions where similar suites of environmental variables influence habitat suitability, while also identifying biogeographical commonalities among the sub-regions. To better understand the low realisation of the fundamental niche we analysed the other land covers occupying the niche. Results: A. marina in Australia occupies six different environmental sub-regions. Maxent distribution models accurately predicted the presence of A. marina in each subpopulation (AUC > 0.9). A. marina's presence in all sub-regions was strongly determined by its proximity to freshwater. Precipitation and temperature extreme values were more important than average values in predicting the species' presence. The species requires low-energy coastlines with high solar radiation. The suitable areas are primarily shared with salt marshes, seagrass and buildings or cleared land. Main conclusions: Our results offer a baseline for the suitable area of A. marina's presence that includes a range of environmental conditions, A. marina currently occupies <50% of its suitable habitat and there is scope for restoration with significant ecosystem service gains. The six different sub-regions in Australia map to known phylogenetically distinct populations indicating genetic plasticity in response to region-specific climatic conditions.