Genetic species identification and population structure of Halophila (Hydrocharitaceae) from the Western Pacific to the Eastern Indian Ocean

Ghani NI, Bujang JS. Morphological and genetic identification of Halophila species and a new distribution record of Halophila nipponica at the Tanjung Adang Laut shoal, Johor, Malaysia

The Halophila species exhibit complex characteristics due to their high degree of variation across different bioregions. This study delves into the intricate characteristics of Halophila species in the Tanjung Adang Laut shoal, Johor, Malaysia, and offers valuable insights through morphological and genetic evidence. Employing internal transcribed sequences (ITS), we investigated the phylogeny of Halophila species, revealing distinct clades for H. ovalis, H. major, H. spinulosa, and the newly recorded H. nipponica. Notably, H. nipponica from the Tanjung Adang Laut shoal formed a conspecific relationship with its counterparts from Japan and Korea (98.3-98.5% similarity; 5-11 bp differences). Morphologically, distinguishing features, including the ratio of the half-lamina width (1:4.76-6.13 mm) and cross-vein count (4-7 pairs), supported the identification of H. nipponica. Genetic distance analyses revealed differences between H. nipponica, H. ovalis, and H. major, indicating haplotype diversity. Geographical variations were evident, as H. nipponica presented unique haplotypes (H24) in its clade. The 47 haplotypes network identified significant mutation sites, providing a comprehensive understanding of genetic and morphological distinctions. In conclusion, this study highlights the intricate characteristics and phylogeny of Halophila species in the Tanjung Adang Laut shoal, Johor, and provides valuable insights into their genetic and morphological diversity.

Complete Genome of Rose Myrtle, Rhodomyrtus tomentosa, and Its Population Genetics in Thai Peninsula

Several parts of rose myrtle, Rhodomyrtus tomentosa, exhibited profound antibacterial and anti-inflammatory activities, suggesting its potential in healthcare and cosmetics applications. During the past few years, the demand for biologically active compounds in the industrial sectors increased. Therefore, gathering comprehensive information on all aspects of this plant species is essential. Here, the genome sequencing using short and long reads was used to understand the genome biology of R. tomentosa. Inter-simple sequence repeats (ISSR) and simple sequence repeats (SSR) markers, and geometric morphometrics of the leaves of R. tomentosa collected across Thai Peninsula, were determined for population differentiation analysis. The genome size of R. tomentosa was 442 Mb, and the divergence time between R. tomentosa and Rhodamnia argentea, the white myrtle of eastern Australia, was around 15 million years. No population structure was observed between R. tomentosa on the eastern and western sides of the Thai Peninsula using the ISSR and SSR markers. However, significant differences in leaf size and shape of R. tomentosa were observed in all locations.

Current advances in seagrass research: A review from Viet Nam

Seagrass meadows provide valuable ecosystem services but are fragile and threatened ecosystems all over the world. This review highlights the current advances in seagrass research from Viet Nam. One goal is to support decision makers in developing science-based conservation strategies. In recent years, several techniques were applied to estimate the size of seagrass meadows. Independent from the method used, there is an alarming decline in the seagrass area in almost all parts of Viet Nam. Since 1990, a decline of 46.5% or 13,549 ha was found. Only in a few protected and difficult-to-reach areas was an increase observed. Conditions at those sites could be investigated in more detail to make suggestions for conservation and recovery of seagrass meadows. Due to their lifestyle and morphology, seagrasses take up compounds from their environment easily. Phytoremediation processes of Thalassia hemprichii and Enhalus acoroides are described exemplarily. High accumulation of heavy metals dependent on their concentration in the environment in different organs can be observed. On the one hand, seagrasses play a role in phytoremediation processes in polluted areas; on the other hand, they might suffer at high concentrations, and pollution will contribute to their overall decline. Compared with the neighboring countries, the total C _org stock from seagrass beds in Viet Nam was much lower than in the Philippines and Indonesia but higher than that of Malaysia and Myanmar. Due to an exceptionally long latitudinal coastline of 3,260 km covering cool to warm water environments, the seagrass species composition in Viet Nam shows a high diversity and a high plasticity within species boundaries. This leads to challenges in taxonomic issues, especially with the Halophila genus, which can be better deduced from genetic diversity/population structures of members of Hydrocharitaceae. Finally, the current seagrass conservation and management efforts in Viet Nam are presented and discussed. Only decisions based on the interdisciplinary cooperation of scientists from all disciplines mentioned will finally lead to conserve this valuable ecosystem for mankind and biodiversity.

ITS DNA Barcoding Reveals That Halophila stipulacea Still Remains the Only Non-Indigenous Seagrass of the Mediterranean Sea

Non-indigenous species (NIS) are one of the major threats to the native marine ecosystems of the Mediterranean Sea. Halophila stipulacea was the only exotic seagrass of the Mediterranean until 2018, when small patches of a species morphologically identified as Halophila decipiens were reported in Salamina Island, Greece. Given the absence of reproductive structures during the identification and the taxonomic ambiguities known to lead to misidentifications on this genus, we reassessed the identity of this new exotic record using DNA barcoding (rbcL, matK and ITS) and the recently published taxonomic key. Despite their morphologic similarity to H. decipiens based on the new taxonomic key, the specimens showed no nucleotide differences with H. stipulacea specimens (Crete) for the three barcodes and clustered together on the ITS phylogenetic tree. Considering the high species resolution of the ITS region and the common morphological variability within the genus, the unequivocal genetic result suggests that the Halophila population found in Salamina Island most likely corresponds to a morphologically variant H. stipulacea. Our results highlight the importance of applying an integrated taxonomic approach (morphological and molecular) to taxonomically complex genera such as Halophila, in order to avoid overlooking or misreporting species range shifts, which is essential for monitoring NIS introductions.

Morphological and biochemical responses of tropical seagrasses (Family: Hydrocharitaceae) under colonization of the macroalgae Ulva reticulata Forsskål

BACKGROUND

Coastal land development has deteriorated the habitat and water quality for seagrass growth and causes the proliferation of opportunist macroalgae that can potentially affect them physically and biochemically. The present study investigates the morphological and biochemical responses of seagrass from the Hydrocharitaceae family under the macroalgal bloom of Ulva reticulata, induced by land reclamation activities for constructing artificial islands.

METHODS

Five seagrass species, Enhalus acoroides, Thalassia hemprichii, Halophila ovalis, Halophila major, and Halophila spinulosa were collected at an Ulva reticulata-colonized site (MA) shoal and a non-Ulva reticulata-colonized site (MC) shoal at Sungai Pulai estuary, Johor, Malaysia. Morphometry of shoots comprising leaf length (LL), leaf width (LW), leaf sheath length (LSL), leaflet length (LTL), leaflet width (LTW), petiole length (PL), space between intra-marginal veins (IV) of leaf, cross vein angle (CVA) of leaf, number of the cross vein (NOC), number of the leaf (NOL) and number of the leaflet (NOLT) were measured on fresh seagrass specimens. Moreover, in-situ water quality and water nutrient content were also recorded. Seagrass extracts in methanol were assessed for total phenolic content (TPC), total flavonoid content (TFC), 2,2-diphenyl-1-picrylhydrazyl radical scavenging activity (DPPH), 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid radical cation scavenging activity (ABTS), and ferric reducing antioxidant power (FRAP).

RESULTS

Seagrasses in the U. reticulata-colonized site (MA) had significantly higher (t-test, p < 0.05) leaf dimensions compared to those at the non-U. reticulata colonized site (MC). Simple broad-leaved seagrass of H. major and H. ovalis were highly sensitive to the colonization of U. reticulata, which resulted in higher morphometric variation (t-test, p < 0.05) including LL, PL, LW, and IV. Concerning the biochemical properties, all the seagrasses at MA recorded significantly higher (t-test, p < 0.05) TPC, TFC, and ABTS and lower DPPH and FRAP activities compared to those at MC. Hydrocharitaceae seagrass experience positive changes in leaf morphology features and metabolite contents when shaded by U. reticulata. Researching the synergistic effect of anthropogenic nutrient loads on the interaction between seagrasses and macroalgae can provide valuable information to decrease the negative effect of macroalgae blooms on seagrasses in the tropical meadow.

Liao L, Papenbrock J. Analysis of rDNA reveals a high genetic diversity of Halophila major in the Wallacea region

The genus Halophila shows the highest species diversity within the seagrass genera. Southeast Asian countries where several boundary lines exist were considered as the origin of seagrasses. We hypothesize that the boundary lines, such as Wallace's and Lydekker's Lines, may act as marine geographic barriers to the population structure of Halophila major. Seagrass samples were collected at three islands in Vietnamese waters and analyzed by the molecular maker ITS. These sequences were compared with published ITS sequences from seagrasses collected in the whole region of interest. In this study, we reveal the haplotype and nucleotide diversity, linking population genetics, phylogeography, phylogenetics and estimation of relative divergence times of H. major and other members of the Halophila genus. The morphological characters show variation. The results of the ITS marker analysis reveal smaller groups of H. major from Myanmar, Shoalwater Bay (Australia) and Okinawa (Japan) with high supporting values. The remaining groups including Sri Lanka, Viet Nam, the Philippines, Thailand, Malaysia, Indonesia, Two Peoples Bay (Australia) and Tokushima (Japan) showed low supporting values. The Wallacea region shows the highest haplotype and also nucleotide diversity. Non-significant differences were found among regions, but significant differences were presented among populations. The relative divergence times between some members of section Halophila were estimated 2.15-6.64 Mya.

The Genetic Component of Seagrass Restoration: What We Know and the Way Forwards

Seagrasses are marine flowering plants providing key ecological services and functions in coasts and estuaries across the globe. Increased environmental changes fueled by human activities are affecting their existence, compromising natural habitats and ecosystems’ biodiversity and functioning. In this context, restoration of disturbed seagrass environments has become a worldwide priority to reverse ecosystem degradation and to recover ecosystem functionality and associated services. Despite the proven importance of genetic research to perform successful restoration projects, this aspect has often been overlooked in seagrass restoration. Here, we aimed to provide a comprehensive perspective of genetic aspects related to seagrass restoration. To this end, we first reviewed the importance of studying the genetic diversity and population structure of target seagrass populations; then, we discussed the pros and cons of different approaches used to restore and/or reinforce degraded populations. In general, the collection of genetic information and the development of connectivity maps are critical steps for any seagrass restoration activity. Traditionally, the selection of donor population preferred the use of local gene pools, thought to be the best adapted to current conditions. However, in the face of rapid ocean changes, alternative approaches such as the use of climate-adjusted or admixture genotypes might provide more sustainable options to secure the survival of restored meadows. Also, we discussed different transplantation strategies applied in seagrasses and emphasized the importance of long-term seagrass monitoring in restoration. The newly developed information on epigenetics as well as the application of assisted evolution strategies were also explored. Finally, a view of legal and ethical issues related to national and international restoration management is included, highlighting improvements and potential new directions to integrate with the genetic assessment. We concluded that a good restoration effort should incorporate: (1) a good understanding of the genetic structure of both donors and populations being restored; (2) the analysis of local environmental conditions and disturbances that affect the site to be restored; (3) the analysis of local adaptation constraints influencing the performances of donor populations and native plants; (4) the integration of distribution/connectivity maps with genetic information and environmental factors relative to the target seagrass populations; (5) the planning of long-term monitoring programs to assess the performance of the restored populations. The inclusion of epigenetic knowledge and the development of assisted evolution programs are strongly hoped for the future.

Taxonomy of the Genus Halophila Thouars (Hydocharitaceae): A Review

The seagrass genus Halophila Thouars has more than twenty described species and is predominately distributed over a wide geographic range along the tropical and the warm temperate coastlines in the Indo-West Pacific Oceans. A brief history of the Halophila taxonomic development is presented. Based on reproductive and vegetative morphology, the genus is divided into eight sections including three new sections: section Australes, section Stipulaceae and section Decipientes. A rewritten taxonomic description of the type species for the genus Halophila,H. madagascariensis Steudel ex Doty et B.C. Stone, is provided. The lectotype of H. engelmannii Asch. as well as neotypes of H. hawaiiana Doty et B.C. Stone and H. spinulosa (Br.) Asch. are designated. Furthermore, H. ovalis ssp. bullosa, ssp. ramamurthiana and ssp. linearis together with H. balforurii have been recognised as distinct species. Nomenclature, typification, morphological description and botanical illustrations are presented for each taxon. Recent molecular phylogenetic surveys on certain Halophila taxa are also discussed. Field surveys for the deep water Halophila in West Pacific regions are suggested. Morphological studies combined with molecular investigations for the Halophila on the east coast of Africa and the West Indian Ocean are urgently needed and highly recommended.

Genetic identification and hybridization in the seagrass genus Halophila (Hydrocharitaceae) in Sri Lankan waters

Seagrasses, as marine angiosperms, play important roles in coastal ecosystems. With increasing anthropogenic impacts, they are facing dramatic declines on a global scale. Halophila is well-known as a complex taxonomic challenge mainly due to high morphological plasticity. By using only a morphological approach, the genus could be over-split or similar species could be erroneously lumped, thus masking its true biodiversity. In the present study, we incorporated genetic identification with morphological examination to reveal the identity of Halophila plants in southern and northwestern Sri Lankan waters. The nuclear ribosomal internal transcribed spacer (ITS) region and chloroplast ribulose-bisphosphate carboxylase gene (rbcL) were used to identify plants collected from the Gulf of Mannar, Puttalam Lagoon, and Matara, Sri Lanka. Based on genetic identification, H. major (Zoll.) Miquel is reported for the first time from Sri Lanka, which might have been misidentified as H. ovalis in previous literature based on morphology alone. We also observed a first hybridization case of Halophila cross between H. ovalis and H. major. Two potential cryptic species were found, herein designated Halophila sp. 1 (allied to H. minor) and Halophila sp. 2 (closely related to H. decipiens). In order to clarify taxonomic ambiguity caused by morphological plasticity and the low resolution of genetic markers, further comparative phylogenomic approaches might be needed to solve species boundary issues in this genus.

Strong genetic differentiation in tropical seagrass Enhalus acoroides (Hydrocharitaceae) at the Indo-Malay Archipelago revealed by microsatellite DNA

The Indo-Malay Archipelago is regarded as a barrier that separates organisms of the Indian and Pacific Oceans. Previous studies of marine biota from this region have found a variety of biogeographic barriers, seemingly dependent on taxon and methodology. Several hypotheses, such as emergence of the Sunda Shelf and recent physical oceanography, have been proposed to account for the genetic structuring of marine organisms in this region. Here, we used six microsatellite loci to infer genetic diversity, population differentiation and phylogeographic patterns of Enhalus acoroides across the Indo-Malay Archipelago. Heterozygosities were consistently high, and significant isolation-by-distance, consistent with restricted gene flow, was observed. Both a neighbour joining tree based on D_A distance and Bayesian clustering revealed three major clusters of E. acoroides. Our results indicate that phylogeographic patterns of E. acoroides have possibly been influenced by glaciation and deglaciation during the Pleistocene. Recent physical oceanography such as the South Java Current and the Seasonally Reversing Current may also play a role in shaping the genetic patterns of E. acoroides.

Aquatic long-distance dispersal and vicariance shape the evolution of an ostracod species complex (Crustacea) in four major Brazilian floodplains

Cladogenesis is often driven by the interplay of dispersal and vicariance. The importance of long-distance dispersal in biogeography and speciation is increasingly recognised, but still ill-understood. Here, we study faunal interconnectivity between four large Brazilian floodplains, namely the Amazon, Araguaia, Pantanal (on Paraguay River) and Upper Paraná River floodplains, investigating a species complex of the non-marine ostracod genus Strandesia. We use DNA sequence data from the mitochondrial COI and the nuclear Elongation Factor 1 alpha genes to construct molecular phylogenies and minimum spanning networks, to identify genetic species, analyse biogeographic histories and provide preliminary age estimates of this species complex. The Strandesia species complex includes five morphological and eleven genetic species, which doubles the known diversity in this lineage. The evolutionary history of this species complex appears to comprise sequences of dispersal and vicariance events. Faunal and genetic patterns of connectivity between floodplains in some genetic species are mirrored in modern hydrological connections. This could explain why we find evidence for (aquatic) long-distance dispersal between floodplains, thousands of kilometres apart. Our phylogenetic reconstructions seem to mostly indicate recent dispersal and vicariance events, but the evolution of the present Strandesia species complex could span up to 25 Myr, which by far exceeds the age of the floodplains and the rivers in their current forms.

Genetic identification and evolutionary trends of the seagrass Halophila nipponica in temperate coastal waters of Korea

Although seagrass species in the genus Halophila are generally distributed in tropical or subtropical regions, H. nipponica has been reported to occur in temperate coastal waters of the northwestern Pacific. Because H. nipponica occurs only in the warm temperate areas influenced by the Kuroshio Current and shows a tropical seasonal growth pattern, such as severely restricted growth in low water temperatures, it was hypothesized that this temperate Halophila species diverged from tropical species in the relatively recent evolutionary past. We used a phylogenetic analysis of internal transcribed spacer (ITS) regions to examine the genetic variability and evolutionary trend of H. nipponica. ITS sequences of H. nipponica from various locations in Korea and Japan were identical or showed very low sequence divergence (less than 3-base pair, bp, difference), confirming that H. nipponica from Japan and Korea are the same species. Halophila species in the section Halophila, which have simple phyllotaxy (a pair of petiolate leaves at the rhizome node), were separated into five well-supported clades by maximum parsimony analysis. H. nipponica grouped with H. okinawensis and H. gaudichaudii from the subtropical regions in the same clade, the latter two species having quite low ITS sequence divergence from H. nipponica (7–15-bp). H. nipponica in Clade I diverged 2.95 ± 1.08 million years ago from species in Clade II, which includes H. ovalis. According to geographical distribution and genetic similarity, H. nipponica appears to have diverged from a tropical species like H. ovalis and adapted to warm temperate environments. The results of divergence time estimates suggest that the temperate H. nipponica is an older species than the subtropical H. okinawensis and H. gaudichaudii and they may have different evolutionary histories.