No full-text available
To read the full-text of this research,
you can request a copy directly from the authors.
Pseudobangia corderoi sp. nov. (Bangiales, Rhodophyta) from the Philippines View supplementary material Pseudobangia corderoi sp. nov. (Bangiales, Rhodophyta) from the Philippines
Abstract
A new filamentous bangialean alga, Pseudobangia corderoi sp. nov., is described from the northern Philippines. Locally known as a sea vegetable, this species was previously identified as 'Bangia fusco-purpurea'. Inferred combined analyses of the nucleus-encoded SSU rDNA and the plastid-encoded RubisCO LSU (rbcL) gene indicate that P. corderoi is sister to another unidentified species of Pseudobangia (originally referred to also as 'Bangia fuscopurpurea') from Taiwan. Together, these two taxa formed the closest diverging lineage from Pseudobangia kaycoleae (generitype). Current molecular phylogenies have also yielded monophyly of Pseudobangia and strong support for a sister relationship with the 'Bangia 2' lineage. Molecular and geographic analyses clearly differentiate P. corderoi from other filamentous Bangiales, whereas morpho-anatomical analysis identified only one distinguishing character, i.e. larger dimensions of the thalli. ARTICLE HISTORY
ResearchGate has not been able to resolve any citations for this publication.
The trend in naming genera based almost exclusively on molecular data, and not on morphological diagnostic characters, is increasing. In bifurcating phylogenetic trees generic cut-offs are arbitrary, but at the bare minimum nomenclatural changes should be supported by multiple phylogenetic methodologies using appropriate models for all the various gene partitions, strong support with all branch support methods, and should also result in adding to our knowledge of the interrelationships of taxa. We believe that a recent taxonomic treatment of the genus Pyropia (Yang et al. 2020) into several genera is unwarranted. We reanalysed the data presented in the recent article, using additional phylogenetic methods. Our results show that many of the newly established genera are not well supported by all methods, and the new circumscription of the genus Pyropia renders it unsupported. We also tested additional outgroups, which were previously suggested as sister to Pyropia, but this did not substantially change our conclusions. These generic nomenclatural changes of the previously strongly supported genus Pyropia, do not shed light on the evolution of this group and have serious consequences in these commercially important algae, that are also governed by a plethora of regulation and by-laws that now need to be amended. We suggest that the over-splitting of groups based only on poorly produced and modestly supported phylogenies should not be accepted and that the genus Pyropia sensu Sutherland et al. (2011) be restored.
A new filamentous marine red alga, Kuwaitiella rubra gen. et sp. nov. (Bangiales, Rhodophyta), is described from Kuwait in the north‐western Arabian Gulf (also referred to as the Persian Gulf). It was found on a submerged fishing line. The intensively red upright thallus of up to 1 cm in length consists of cells containing a single stellate plastid. The thallus is initially uniseriate but becomes biseriate in its distal part upon transformation into globular reproductive cells, possibly archaeospores. The biseriate fertile part is the only morphological difference from other filamentous species of the Bangiales, in which this region is parenchymatous. In culture, bipolar asymmetric germination of the spores of Kuwaitiella led to a new generation of identical erect thalli, fixed to the substratum by colourless rhizoids. According to phylogenetic analyses of partial small subunit nuclear ribosomal DNA (18S) and of the plastid‐encoded ribulose‐1,5‐bisphosphate carboxylase/oxygenase large subunit (rbcL), the new species forms an additional lineage of the Bangiales, genetic similarity with other taxa being limited (maximum 91% in SSU and 90% in rbcL). It was no clear member of any known lineage of the Bangiales but was weakly associated with the filamentous species Minerva and Dione from New Zealand. In a SSU phylogeny, it formed a basal branch in the Bangiales and clustered with M. aenigmata and D. arcuata as sister clade to all other species of the order. In a rbcL phylogeny, it was part of a large polytomy of lineages, its closest relative being D. arcuata. Kuwaitiella forms the 8th lineage of filamentous Bangiales detected so far.
Edible seaweeds in the northern Philippines have been reported earlier, but detailed information on the utilization and distribution for most of these recorded species remains limited. A case in point is that of Bangia cf. fuscopurpurea, locally known as "bubuok," which appeared in a listing of edible seaweeds of the province of Ilocos Norte. A survey across 12 areas in the northern Philippines revealed that knowledge about the use of bubuok is limited only to locals from two sites in Ilocos Norte (Burgos and Laoag) and one site in Cagayan (Claveria). Like most edible seaweeds in the northern Philippines, B. cf. fuscopurpurea is consumed mainly as a salad. It is not widely sold in the market and is mostly used for personal subsistence. It is confirmed to be thriving in the rocky intertidal areas of Burgos in Ilocos Norte and growing abundantly only during the wet season (November-January). Additional studies on the taxonomy, phylogeography, and possible use of Bangia cf. fuscopurpurea as a seaweed crop for the northern Philippines are highlighted.
The Molecular Evolutionary Genetics Analysis (MEGA) software has matured to contain a large collection of methods and tools of computational molecular evolution. Here, we describe new additions that make MEGA a more comprehensive tool for building timetrees of species, pathogens, and gene families using rapid relaxed-clock methods. Methods for estimating divergence times and confidence intervals are implemented to use probability densities for calibration constraints for node-dating and sequence sampling dates for tip-dating analyses, which will be supported by new options for tagging sequences with spatiotemporal sampling information, an expanded interactive Node Calibrations Editor, and an extended Tree Explorer to display timetrees. We have now added a Bayesian method for estimating neutral evolutionary probabilities of alleles in a species using multispecies sequence alignments and a machine learning method to test for the autocorrelation of evolutionary rates in phylogenies. The computer memory requirements for the maximum likelihood analysis are reduced significantly through reprogramming, and the graphical user interface (GUI) has been made more responsive and interactive for very big datasets. These enhancements will improve the user experience, quality of results, and the pace of biological discovery. Natively compiled GUI and command-line versions of MEGA11 are available for Microsoft Windows, Linux, and macOS from www.megasoftware.net.
Species circumscription based on phenotypes has frequently masked the actual species diversity in foliose Bangiales. Application of DNA sequence differences in this group has removed dependence on the utility of morphological characters traditionally considered for species discrimination. This study currently represents an extensive analysis of phylogeny and species discrimination of foliose Bangiales across most of their distributional range in the northern Philippines, particularly in Luzon Strait. Molecular assessment based on plastid rbcL and two mitochondrial loci, COI-5P, and cox2–3 spacer, suggested four major groups diagnostic of species lineage. As supported by the results from the four molecular species delimitation methods: PTP, bPTP, ABGD, and SPN, the confirmed Philippine foliose Bangiales species included Pyropia acanthophora, Py. tanegashimensis, and two cryptic taxa from Batanes Islands. The number of species detected in this study suggested that the true species composition of Philippine foliose Bangiales might be considerably lower than what was previously thought. It is possible however that a greater sampling effort in complete seasonal range of collections will reveal more species and extent of their actual distributions. Although the influence of northeast monsoon significantly affects the growth of foliose Bangiales in the Philippines, its role in shaping their present-day distribution remains unclear. Our molecular datasets however suggested that their current biogeographic distribution might reflect past vicariant events and is therefore more complex than have been previously regarded.
The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches.
Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 times (median) faster than SBS and 8.4 times (median) faster than RAxML rapid bootstrap on tested datasets. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.
Samples of the freshwater red algae, Bangiadulcis atropurpurea, collected from the mountain waterfalls and its close species, Bangia fuscopurpurea, collected from coasts, were phylogenetically analyzed. The sequences of the rbcL gene and RuBisCO spacer region of the freshwater Bangiadulcis atropurpurea species were identical or similar to those of B. atropurpurea from Japan, North America and Europe. This result indicated that the freshwater Bangiadulcis species from Taiwan shared a common ancestor with the three above-mentioned populations and formed a distinct clade from the marine Bangia species in the phylogenetic trees. It is suggested that all the previous records on marine Bangia species should be revised and the name B. fuscopurpurea be used for the marine species in Taiwan. In this study, the freshwater alga B. atropurpurea presents a new record in the algal flora of Taiwan. This finding is important for the protection of the biodiversity of red algal flora, and provides useful information on the ecological conservation of the species in Taiwan.
Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast
programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus,
there is need for additional approaches that employ different search strategies to find ML trees and that are at the same
time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation
method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found
higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use
the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein
alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3–97.1%. IQ-TREE
is freely available at http://www.cibiv.at/software/iqtree.
Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community.
I present some of the most notable new features and extensions of RAxML, such as, a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX, and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date, 50 page user manual covering all new RAxML options is available.
The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML.
Alexandros.Stamatakis@h-its.org.
Foliose species of the Bangiales (Porphyra sensu lato) have a long history of study in the N Atlantic, but there are still regions, especially in the northern parts of the N Atlantic that need more attention. A molecular study using rbcL and cox1 sequences was undertaken to assess the diversity of foliose Bangiales species in Iceland and the Faroe Islands. Herbarium collections from the intertidal and subtidal of Iceland (summer and winter) and the Faroe Islands (all seasons) revealed a total of 13 species (11 common to both areas), which were referred to four of the genera recognized in a recent two-gene global phylogeny. Boreophyllum birdiae, Porphyra dioica, P. linearis, P. purpurea, P. umbilicalis, Pyropia ‘leucosticta’ A, Pyropia njordii Mols-Mortensen, J. Brodie & Neefus, sp. nov., Wildemania amplissima and W. miniata were common to both areas, while Pyropia thulaea and Wildemania abyssicola (Kjellman) A. Mols-Mortensen & J. Brodie, comb. nov. (=Porphyra abyssicola Kjellman) were reported from Iceland but not from the Faroe Islands; Porphyra sp. FO and Pyropia elongata were reported from the Faroe Islands but not from Iceland. Boreophyllum birdiae is reported for the first time for Iceland and Porphyra sp. FO is reported for the first time for the Faroe Islands. Pyropia njordii is described from the Faroe Islands and is also recorded for Iceland, Greenland, New England, USA and Nova Scotia, Canada. A total of 25 foliose Bangiales species are now reported from the N Atlantic and these results demonstrate the importance of investigating as many areas as possible to reach a more complete understanding of species diversity and distribution.
A red alga collected from the Virgin Islands (VIS7) superficially resembles Bangia but was found to have characteristics distinct from known members of the Bangiales. This alga is distinguished by having multiple chloroplasts per cell; as many as nine were observed in one cell. Each chloroplast has a single pyrenoid. In the 18S ribosomal RNA (rRNA) gene sequence analyses, this entity is well supported as being a member of the Bangiales. The relationship between this collection and other bangialean collections is unclear; it appears to be associated with a clade of B. fuscopurpurea from the Atlantic and the Pacific, but this relationship is only moderately supported by neighbour-joining bootstrap. The sequence divergence between the VIS7 collection and other collections of Bangia and Porphyra ranged from 6.9% to 12.6%. This amount of divergence is greater than that observed within many of the clades in the 18S rRNA gene sequence analyses and is slightly less than that noted between the Bangiales and the outgroups used in the analyses (11.6-17.8%). Based on these data, we propose a new genus and species within the Bangiales, Pseudobangia kaycoleia. Molecular analyses showed that neither Bangia nor Porphyra is monophyletic and both may encompass several genera.
Marine and freshwater populations of the red alga Bangia were sampled throughout most of the known geographic range in North America. Marine samples were obtained from the Pacific and Atlantic coasts, central Arctic, Gulf of Mexico, and the Virgin Islands. Freshwater samples came from populations in the Laurentian Great Lakes, St. Lawrence River, and Lake Simcoe. In addition, specimens from freshwater populations from Italy, England, and Ireland were included for comparison. DNA sequence analyses of the Rubisco spacer, rbcL gene, and 18S rRNA gene, plus morphometric analysis, were used to discern possible biogeographic and taxonomic trends. No correlation was detected between the molecular and morphological analyses; however, some trends were consistent among the three molecular analyses. For example, all the freshwater collections were nearly identical, indicating that a single lineage may exist in freshwater systems. In addition, the Virgin Islands sample was distinct from all others in both the rbcL and 18S rRNA gene sequences, but quite similar in morphology to those collections with small filament diameter. The Alaska sample clustered consistently with a primarily Atlantic clade with few sequence differences. This finding may indicate a transarctic invasion. Sequence analysis of the 18S rRNA gene yielded a previously unreported intron (in Bangia) located between helices 21 and 20'. All freshwater collections contained this intron, but it was present only in some marine collections. Considerable sequence divergence occurred among groups of collections in both the rbcL (0-16%) and 18S rRNA (0-10.6%) genes with little corresponding diversity in morphology. These values are higher than those reported previously for intergeneric, intrafamilial, or interfamilial comparisons in higher red algal taxa, but are consistent with those reported for the members of the Bangiales. Sequence analysis of the 18S rRNA gene of Bangia collections with six Porphyra species yielded a tree in which Porphyra is paraphyletic within Bangia. In addition, the molecular divergence appears to be quite low between the two genera.
The phylogenetic relationships of Porphyra collected from the Falkland Islands have been examined using molecular data from two loci, the plastid rbcL gene and the nuclear nSSU gene, in conjunction with morphological observations. Nine species have been distinguished, belonging to four distinct lineages within the Bangiales, differing from one another by 16137 substitutions in the rbcL gene. One species is closely related to P. amplissima, a north Atlantic taxon, three are resolved in a clade that includes several species from New Zealand, Australia and South Africa, as well as P. umbilicalis, whereas four others are more closely related to Southern Ocean species, including P. cinnamomea, P. virididentata and several as yet unnamed taxa from New Zealand, Australia and South Africa. Three species, one of which we identify as P. columbina, appear to be widely distributed in the Southern Ocean, with representatives on the Falkland Islands and on islands of the Australian and New Zealand subantarctic.
The red algal order Bangiales has been revised as a result of detailed regional studies and the development of expert local knowledge of Bangiales floras, followed by collaborative global analyses based on wide taxon sampling and molecular analyses. Combined analyses of the nuclear SSU rRNA gene and the plastid RUBISCO LSU (rbcL) gene for 157 Bangiales taxa have been conducted. Fifteen genera of Bangiales, seven filamentous and eight foliose, are recognized. This classification includes five newly described and two resurrected genera. This revision constitutes a major change in understanding relationships and evolution in this order. The genus Porphyra is now restricted to five described species and a number of undescribed species. Other foliose taxa previously placed in Porphyra are now recognized to belong to the genera Boreophyllum gen. nov., Clymene gen. nov., Fuscifolium gen. nov., Lysithea gen. nov., Miuraea gen. nov., Pyropia, and Wildemania. Four of the seven filamentous genera recognized in our analyses already have generic names (Bangia, Dione, Minerva, and Pseudobangia), and are all currently monotypic. The unnamed filamentous genera are clearly composed of multiple species, and few of these species have names. Further research is required: the genus to which the marine taxon Bangia fuscopurpurea belongs is not known, and there are also a large number of species previously described as Porphyra for which nuclear SSU ribosomal RNA (nrSSU) or rbcL sequence data should be obtained so that they can be assigned to the appropriate genus.
We investigated species diversity and distribution patterns of the marine red alga Portieria in the Philippine archipelago. Species boundaries were tested based on mitochondrial, plastid and nuclear encoded loci, using a general mixed Yule-coalescent (GMYC) model-based approach and a Bayesian multilocus species delimitation method. The outcome of the GMYC analysis of the mitochondrial encoded cox2-3 dataset was highly congruent with the multilocus analysis. In stark contrast with the current morphology-based assumption that the genus includes a single, widely distributed species in the Indo-West Pacific (Portieria hornemannii), DNA-based species delimitation resulted in the recognition of 21 species within the Philippines. Species distributions were found to be highly structured with most species restricted to island groups within the archipelago. These extremely narrow species ranges and high levels of intra-archipelagic endemism contrast with the wide-held belief that marine organisms generally have large geographical ranges and that endemism is at most restricted to the archipelagic level. Our results indicate that speciation in the marine environment may occur at spatial scales smaller than 100 km, comparable with some terrestrial systems. Our finding of fine-scale endemism has important consequences for marine conservation and management.
Understanding the evolutionary history of living organisms is a central problem in biology. Until recently the ability to infer evolutionary relationships was limited by the amount of DNA sequence data available, but new DNA sequencing technologies have largely removed this limitation. As a result, DNA sequence data are readily available or obtainable for a wide spectrum of organisms, thus creating an unprecedented opportunity to explore evolutionary relationships broadly and deeply across the Tree of Life. Unfortunately, the algorithms used to infer evolutionary relationships are NP-hard, so the dramatic increase in available DNA sequence data has created a commensurate increase in the need for access to powerful computational resources. Local laptop or desktop machines are no longer viable for analysis of the larger data sets available today, and progress in the field relies upon access to large, scalable high-performance computing resources. This paper describes development of the CIPRES Science Gateway, a web portal designed to provide researchers with transparent access to the fastest available community codes for inference of phylogenetic relationships, and implementation of these codes on scalable computational resources. Meeting the needs of the community has included developing infrastructure to provide access, working with the community to improve existing community codes, developing infrastructure to insure the portal is scalable to the entire systematics community, and adopting strategies that make the project sustainable by the community. The CIPRES Science Gateway has allowed more than 1800 unique users to run jobs that required 2.5 million Service Units since its release in December 2009. (A Service Unit is a CPU-hour at unit priority).
Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d(N)/d(S) rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.
The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data.
AVAILABILITY: The MODELTEST package, including the source code and some documentation is available at http://bioag.byu. edu/zoology/crandall_lab/modeltest.html.
Red algae of the order Bangiales are notable for exhibiting flexible promotion of sexual and asexual reproductive processes by environmental stresses. This flexibility indicates that a trade-off between vegetative growth and reproduction occurs in response to environmental stresses that influence the timing of phase transition within the life cycle. Despite their high phylogenetic divergence, both filamentous and foliose red alga in the order Bangiales exhibit a haploid–diploid life cycle, with a haploid leafy or filamentous gametophyte (thallus) and a diploid filamentous sporophyte (conchocelis). Unlike haploid–diploid life cycles in other orders, the gametophyte in Bangiales is generated independently of meiosis; the regulation of this generation transition is not fully understood. Based on transcriptome and gene expression analyses, the originally proposed biphasic model for alternation of generations in Bangiales was recently updated to include a third stage. Along with the haploid gametophyte and diploid sporophyte, the triphasic framework recognizes a diploid conchosporophyte—a conchosporangium generated on the conchocelis-phase and previously considered to be part of the sporophyte. In addition to this sexual life cycle, some Bangiales species have an asexual life cycle in which vegetative cells of the thallus develop into haploid asexual spores, which are then released from the thallus to produce clonal thalli. Here, we summarize the current knowledge of the triphasic life cycle and life cycle trade-off in Neopyropia yezoensis and ‘Bangia’ sp. as model organisms for the Bangiales.
Challenges in morphology come to bear when assigning specific names in foliose Bangiales. Recent studies suggest that the integration of molecular and phenotypic data is essential, particularly in setting species boundaries and revealing the true species diversity of a given area. In an attempt to further elucidate the diversity of foliose Bangiales in the Philippines, two new species, Pyropia lunae sp. nov. and Pyropia islae sp. nov. are described. Each species differs from other closely related taxa by a combination of morphological and anatomical characters, and nucleotide sequences. Phylogenetic reconstruction based on rbcL gene sequences supports the sister relationship of P. lunae and Pyropia acanthophora, whereas P. islae is recovered as a species allied to Pyropia tanegashimensis and Pyropia denticulata. These two previously undescribed species increase the number of confirmed Philippine Pyropia species to four. So far, P. lunae and P. islae are found only from the Batanes Islands while P. acanthophora and P. tanegashimensis are known to extend their native distributions across into the Indo-Pacific waters. Questions remain, however, with regard to the true species diversity of foliose Bangiales in the Philippines. A wider sampling effort and the application of molecular methods will make it possible to resolve the remaining gaps in the taxonomy of Philippine foliose Bangiales.
Causes of taxonomic confusion are lamentably well known in foliose Bangiales. A magnitude of these uncertainties stems from the paucity of available taxonomic traits in morphologically homoplastic species. At present, the taxonomic identity and systematics of many of the Philippine foliose Bangiales are in a state of flux. A critical examination of published literature on Philippine records of 10 species of foliose Bangiales has rendered the need for re-confirmation of the presence of Porphyra atropurpurea, Porphyra marcosii, Pyropia denticulata, and Pyropia suborbiculata while records of Porphyra umbilicalis, Pyropia vietnamensis, Wildemania variegata, and the invalid name Porphyra crispata have been omitted from the list. Currently, there are only two confirmed species of foliose Bangiales in the Philippines, which are Pyropia acanthophora and Pyropia tanegashimensis. Thus, this review exhorts a re-examination of collected Philippine foliose Bangiales materials using both morphological and molecular analysis.
Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.
Pyropia acanthophora is a foliose Bangiales with widely known endemic populations in Indo-Pacific region. This alga has expanded its range recently as a consequence of introduction. In an attempt to explore the genetic diversity of Py. acanthophora within the Philippines and the impact of the introduction of the species from elsewhere, an examination of molecular differentiation and distribution was undertaken using the mitochondrial COI-5P and plastid rbcL gene sequences. The results revealed that the populations of Py. acanthophora in the Philippines exhibited high haplotypic and genetic diversities, and were found to be distinct from those previously reported as conspecific populations found in Taiwan, India, Japan, Hawaii, and from those introduced populations from Brazil. The network analyses as inferred from rbcL and from the combined COI-5P and rbcL genes showed evidence that the Philippine populations of Py. acanthophora exhibited a chaotic patchiness pattern characterized by a population with highly site-exclusive haplotypes, wide genetic variability and lack of local geographic patterns. The distribution of Py. acanthophora within the Philippines was also found to be greater than what was previously known, ranging from the extreme northwest to extreme northeast mainland Luzon coasts, including Camiguin Is., Cagayan. Understanding the genetic diversity and distribution of Py. acanthophora in the Philippines provides valuable information in relation to the conservation and effective resource management of native populations of Py. acanthophora in the tropical Asian region.
The known morphological features in identifying common species of foliose Bangiales (e.g., members of Pyropia and Porphyra), which are very few and often overlapping, are recently resolved using comparative analysis of DNA sequences and statistics. Records of foliose Bangiales in the Philippines were historically identified based on morphology. Considering the recent radical changes in the taxonomy among these rhodophytes and problems posed by morphology-based identification, taxonomic re-appraisal of Philippine foliose Bangiales based on critical morphological and molecular studies is needed. This study used plastid rbcL and mitochondrial COI-5P gene sequences to investigate the identity of foliose Bangiales collected in Palaui Is., Sta. Ana, Cagayan, Philippines. Observation of key phenotypes revealed the identity of the collected materials as Py. tanegashimensis. Resulting phylogenetic trees showed placement of our collected specimens into a highly supported Py. tanegashimensis clade from Japan and Brazil. Our molecular analysis also suggested that the Philippine Py. tanegashimensis includes endemic populations distinct from the introduced strain originally reported from Brazil.
Summary Ultrastructural observations of dividing cells inBangia vermicularis revealed a type of chloroplast division (plastokinesis) not previously reported in the red algae. The polarity of this prekaryokinetic process serves as a reliable marker of the plane of cytokinesis, a key factor in establishing thallus morphology. At the onset of division one or more invaginations develop in the envelope of the large, lobed chloroplast and proceed centripetally through the stroma in the plane of the thylakoids, forming narrow cytoplasmic channels (CCs). The thylakoids are realigned somewhat, but are not constricted as the chloroplast is divided into two or more units. The number of resulting chloroplasts and the orientation of the CCs are dependent on cell type. Distinctive cylindrical cells at the base of the filamentous region, immediately distal to the holdfast, are shorter than broad and contain a central nucleus surrounded by a doughnutshaped chloroplast. The cylindrical morphology of the thallus is established early in the first periclinal division as multiple plastokinesis commences, generating several radially-arranged daughter chloroplasts. Cleavage of the original chloroplast is completed during subsequent cell divisions in the initial developmental stage, finally resulting in eight chloroplasts that are distributed to an equal number of wedge-shaped radial cells. Cells distal to the actively dividing basal cells are cuboidal and have a peripheral nucleus. Division of the single chloroplast prior to karyokinesis in these cells results in two or four daughter chloroplasts according to cell type. During or following plastokinesis, multilamellar bodies derived from the CE appear to serve as the source of membranes for the developing septum in the channels. Septa link to proliferations of the plasmalemma in areas of slight cell wall (CW) indentations, and are completed between daughter nuclei after karyokinesis, producing a cleavage channel. Subsequently, primary CW material is deposited between the two septal membranes. The shape and arrangement of daughter cells in each of the developmental stages in the thallus are defined by the planes of cell division. These are indicated by both the orientation of CCs and the polar orientation of nuclear division which is always at right angles to the CC.
The identification of Porphyra species hashistorically been difficult because of the lack of distinguishing morphologicaland ecological characters. We developed a restriction fragment lengthpolymorphism (RFLP) assay, based on inter-specific sequence variation inthe ribulose bisphosphate carboxylase oxygenase largesubunit (rbcL) gene andrbcL-rbcS intergenic spacer, toprovide a simple and effective tool for screening and sorting large collectionsof Porphyra from the Northwest Atlantic. A singlerestriction digest (Hae III) discriminates betweenmultiplePorphyra species including one cryptic taxon; anadditionalenzyme (Hind III) was necessary to distinguish between theclosely related P. leucosticta and an introducedspecies P. yezoensis.
The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment
of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order
to downweight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are
varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific
gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather
than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced
gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new
program, CLUSTAL W which is freely available.
Edible seaweeds of Ilocos Norte: food preparations, other local uses and market potentials
- Z M Agngarayngay
- A F C Llaguno
- S G Aquino
- L B Taclan
- E S Galacgac
Agngarayngay Z.M., Llaguno A.F.C., Aquino S.G., Taclan L.B. &
Galacgac E.S. 2005. Edible seaweeds of Ilocos Norte: food preparations,
other local uses and market potentials. Sulu-Celebes Sea Sustainable
Fisheries Management Project. South Triangle, Quezon City,
Philippines. 27 pp.
AlgaeBase. World-wide electronic publication
- M D Guiry
- G M Guiry
Guiry M.D. & Guiry G.M. 2022. AlgaeBase. World-wide electronic publication, National University of Ireland, Galway. http://www.algaebase.
org; searched on 4 June 2022.
Phycological results of the Smithsonian Institution: Philippines expeditions of 1978 and 1979 in Central Visayas
- E G Meñez
- H P Calumpong
Meñez E.G. & Calumpong H.P. 1981. Phycological results of the
Smithsonian Institution: Philippines expeditions of 1978 and 1979 in
Central Visayas, Philippines. In: Proceedings of the 4th International
Coral Reef Symposium (Ed. by E.D. Gomez, C.E. Birkeland, R.
W. Buddemeier, R.E. Johannes, J.A. Marsh Jr. & R.T. Tsuda), pp
379-384. Marine Science Center, University of the Philippines,
Manila, Philippines.
Sulu-Celebes Sea Sustainable Fisheries Management Project
- Z M Agngarayngay
- A F C Llaguno
- S G Aquino
- L B Taclan
- E S Galacgac