Phylogenetic reconstruction using secondary structures of Internal Transcribed Spacer 2 (ITS2, rDNA): finding the molecular and morphological gap in Caribbean gorgonian corals

Skimming genomes for systematics and DNA barcodes of corals

Numerous genomic methods developed over the past two decades have enabled the discovery and extraction of orthologous loci to help resolve phylogenetic relationships across various taxa and scales. Genome skimming (or low-coverage genome sequencing) is a promising method to not only extract high-copy loci but also 100s to 1000s of phylogenetically informative nuclear loci (e.g., ultraconserved elements [UCEs] and exons) from contemporary and museum samples. The subphylum Anthozoa, including important ecosystem engineers (e.g., stony corals, black corals, anemones, and octocorals) in the marine environment, is in critical need of phylogenetic resolution and thus might benefit from a genome-skimming approach. We conducted genome skimming on 242 anthozoan corals collected from 1886 to 2022. Using existing target-capture baitsets, we bioinformatically obtained UCEs and exons from the genome-skimming data and incorporated them with data from previously published target-capture studies. The mean number of UCE and exon loci extracted from the genome skimming data was 1837 ± 662 SD for octocorals and 1379 ± 476 SD loci for hexacorals. Phylogenetic relationships were well resolved within each class. A mean of 1422 ± 720 loci was obtained from the historical specimens, with 1253 loci recovered from the oldest specimen collected in 1886. We also obtained partial to whole mitogenomes and nuclear rRNA genes from >95% of samples. Bioinformatically pulling UCEs, exons, mitochondrial genomes, and nuclear rRNA genes from genome skimming data is a viable and low-cost option for phylogenetic studies. This approach can be used to review and support taxonomic revisions and reconstruct evolutionary histories, including historical museum and type specimens.

Mesophotic Gorgonian Corals Evolved Multiple Times and Faster Than Deep and Shallow Lineages

Mesophotic Coral Ecosystems (MCEs) develop on a unique environment, where abrupt environmental changes take place. Using a time-calibrated molecular phylogeny (mtDNA: mtMutS), we examined the lineage membership of mesophotic gorgonian corals (Octocorallia: Cnidaria) in comparison to shallow and deep-sea lineages of the wider Caribbean-Gulf of Mexico and the Tropical Eastern Pacific. Our results show mesophotic gorgonians originating multiple times from old deep-sea octocoral lineages, whereas shallow-water species comprise younger lineages. The mesophotic gorgonian fauna in the studied areas is related to their zooxanthellate shallow-water counterparts in only two clades (Gorgoniidae and Plexauridae), where the bathymetrical gradient could serve as a driver of diversification. Interestingly, mesophotic clades have diversified faster than either shallow or deep clades. One of this groups with fast diversification is the family Ellisellidae, a major component of the mesophotic gorgonian coral assemblage worldwide.

Menzerath-Altmann's Law of Syntax in RNA Accretion History

RNA evolves by adding substructural parts to growing molecules. Molecular accretion history can be dissected with phylogenetic methods that exploit structural and functional evidence. Here, we explore the statistical behaviors of lengths of double-stranded and single-stranded segments of growing tRNA, 5S rRNA, RNase P RNA, and rRNA molecules. The reconstruction of character state changes along branches of phylogenetic trees of molecules and trees of substructures revealed strong pushes towards an economy of scale. In addition, statistically significant negative correlations and strong associations between the average lengths of helical double-stranded stems and their time of origin (age) were identified with the Pearson's correlation and Spearman's rho methods. The ages of substructures were derived directly from published rooted trees of substructures. A similar negative correlation was detected in unpaired segments of rRNA but not for the other molecules studied. These results suggest a principle of diminishing returns in RNA accretion history. We show this principle follows a tendency of substructural parts to decrease their size when molecular systems enlarge that follows the Menzerath-Altmann's law of language in full generality and without interference from the details of molecular growth.

A tropical eastern Pacific invasive brittle star species (Echinodermata: Ophiuroidea) reaches southeastern Florida

The invasive brittle star Ophiothela mirabilis (family Ophiotrichidae), a tropical Indo-Pacific endemic species, first reported in Atlantic waters off southern Brazil in 2000, has extended its range northward to the Caribbean Sea, to the Lesser Antilles in 2011, and was first reported in south Florida in January 2019. Its occurrence in southeast Florida extends along nearly 70km of coastline, from near the Port of Miami, Miami-Dade County, northward to Deerfield Beach, Broward County. It occurs abundantly as an epizoite on octocorals, attaining population densities of 25 individuals and more per 10-cm long octocoral stem. The surface texture of octocoral hosts (rough, smooth) did not affect the densities of the ophiuroid epizoites, and there were significantly greater abundances on octocorals during two winter sampling periods than in the summer. Beige and orange-coloured morphs are sometimes present on the same octocoral stem. Gut content analysis supported a suspension feeding mode, revealing essentially identical ingested items in both colour morphs with a preponderance of amorphous detritus and filamentous algae. Molecular genetic evidence (COI & 16s) has established the identity of O. mirabilis and its relationship to invasive Brazilian populations. The orange and beige morphs form two distinct, but closely related lineages that may represent two separate introductions. The orange morph shares haplotypes with Brazilian and Caribbean specimens suggesting a further range expansion of the 'original' invasion. The beige morph, however, shares haplotypes with specimens from the Mexican Pacific and Peru and potentially represents a secondary introduction. Traits promoting dispersal and establishment of this species in new habitats are manifold: vagility and ability to cling tightly to diverse host taxa (e.g. sponges, cnidarians, bryozoans, and echinoderms), frequent asexual reproduction (fissiparity), suspension feeding, including a wide range of dietary items, possession of integument-covered ossicles and arm spines offering protection from predators, and an effective competitive edge over associated microbiota for substrate space.

Internal transcribed spacer 2 (ITS2) molecular morphometric analysis based species delimitation of foliar endophytic fungi from Aglaia elaeagnoidea, Flacourtia inermis and Premna serratifolia

Molecular morphometrics is an emerging third dimensional aspect of fungal species delimitation. They have been demonstrated to be more informative than conventional barcoding methods. Hence in this study, foliar endophytic fungal (FEF) assemblages in three Magnoliopsida plants were delimited using nuclear ribosomal internal transcribed spacer 2 (ITS2) sequence-secondary structural features based phylogenetic analysis, also known as molecular morphometrics. A total of 392 FEF isolates were obtained from the Aglaia elaeagnoidea, Flacourtia inermis, and Premna serratifolia leaves and grouped into 98 morphotypes. Among these host plants, P. serratifolia showed the maximum percentage of colonization frequency. Representatives of each morphotype was sequenced and subjected to further molecular characterization. The results revealed that morphotypes were belonged to the phylum of Ascomycota, distributed over two classes (Sordariomycetes (68.59%) and Dothideomycetes (31.41%)), 6 orders and 19 genera. Based on compensatory base changes (CBC) analysis and absolute identity of ITS2 structure, 21, 20 and 23 species were recognized from A. elaeagnoidea, F. inermis, and P. serratifolia respectively. Diversity indices were higher in A. elaeagnoidea, despite it accounted for a modest 16.8% of total isolates recorded in this study. The genus Colletotrichum was predominant in A. elaeagnoidea (39%) and P. serratifolia (48%). Similarly, Diaporthe (43%) was dominant in F. inermis. Several host-specific species were also observed. This study concludes that these plants host diverse species of Ascomycota. To the best of our knowledge, this is the first detailed report on FEF diversity from these plants. Also, the inclusion of ITS2 secondary structure information along with the sequence provides a further dimension to resolve the inherent problems in identification of fungal species.

Molecular Authentication of the Medicinal Species of Ligusticum (Ligustici Rhizoma et Radix, "Gao-ben") by Integrating Non-coding Internal Transcribed Spacer 2 (ITS2) and Its Secondary Structure

Ligustici Rhizoma et Radix (LReR), an important Chinese medicine known as "Gao-ben," refers to Ligusticum sinense Oliv. or Ligusticum jeholense Nakai et Kitag. However, a number of other species are commonly sold as "Gao-ben" in the herbal medicine market, which may result in a series of quality control problems and inconsistent therapeutic effects. The "Gao-ben" is commonly sold sliced and dried, making traditional identification methods difficult. Here, the mini barcode ITS2 region was examined on 68 samples representing LReR and 7 potential adulterant or substitute species. The results showed 100% success rates of PCR and sequencing and the existence of a barcoding gap. The neighbor-joining (NJ) tree indicated that all the tested samples could be exactly identified. The ITS2 secondary structure revealed a clear difference between true "Gao-ben" and three adulterant species. We therefore recommend the use of ITS2 as a mini barcode for distinguishing between closely or distantly related plant species that may be used in Chinese medicine.

Barcode ITS2: a useful tool for identifying Trachelospermum jasminoides and a good monitor for medicine market

Trachelospermum jasminoides is commonly used in traditional Chinese medicine. However, the use of the plant's local alternatives is frequent, causing potential clinical problems. The T. jasminoides sold in the medicine market is commonly dried and sliced, making traditional identification methods difficult. In this study, the ITS2 region was evaluated on 127 sequences representing T. jasminoides and its local alternatives according to PCR and sequencing rates, intra- and inter-specific divergences, secondary structure, and discrimination capacity. Results indicated the 100% success rates of PCR and sequencing and the obvious presence of a barcoding gap. Results of BLAST 1, nearest distance and neighbor-joining tree methods showed that barcode ITS2 could successfully identify all the texted samples. The secondary structures of the ITS2 region provided another dimensionality for species identification. Two-dimensional images were obtained for better and easier identification. Previous studies on DNA barcoding concentrated more on the same family, genus, or species. However, an ideal barcode should be variable enough to identify closely related species. Meanwhile, the barcodes should also be conservative in identifying distantly related species. This study highlights the application of barcode ITS2 in solving practical problems in the distantly related local alternatives of medical plants.

Molecular phylogeny of 21 tropical bamboo species reconstructed by integrating non-coding internal transcribed spacer (ITS1 and 2) sequences and their consensus secondary structure

The unavailability of the reproductive structure and unpredictability of vegetative characters for the identification and phylogenetic study of bamboo prompted the application of molecular techniques for greater resolution and consensus. We first employed internal transcribed spacer (ITS1, 5.8S rRNA and ITS2) sequences to construct the phylogenetic tree of 21 tropical bamboo species. While the sequence alone could grossly reconstruct the traditional phylogeny amongst the 21-tropical species studied, some anomalies were encountered that prompted a further refinement of the phylogenetic analyses. Therefore, we integrated the secondary structure of the ITS sequences to derive individual sequence-structure matrix to gain more resolution on the phylogenetic reconstruction. The results showed that ITS sequence-structure is the reliable alternative to the conventional phenotypic method for the identification of bamboo species. The best-fit topology obtained by the sequence-structure based phylogeny over the sole sequence based one underscores closer clustering of all the studied Bambusa species (Sub-tribe Bambusinae), while Melocanna baccifera, which belongs to Sub-Tribe Melocanneae, disjointedly clustered as an out-group within the consensus phylogenetic tree. In this study, we demonstrated the dependability of the combined (ITS sequence+structure-based) approach over the only sequence-based analysis for phylogenetic relationship assessment of bamboo.

Comparative Molecular and Morphological Variation Analysis of Siderastrea (Anthozoa, Scleractinia) Reveals the Presence of Siderastrea stellata in the Gulf of Mexico

The genus Siderastrea exhibits high levels of morphological variability. Some of its species share similar morphological characteristics with congeners, making their identification difficult. Siderastrea stellata has been reported as an intermediary of S. siderea and S. radians in the Brazilian reef ecosystem. In an earlier study conducted in Mexico, we detected Siderastrea colonies with morphological features that were not consistent with some siderastreid species previously reported in the Gulf of Mexico. Thus, we performed a combined morphological and molecular analysis to identify Siderastrea species boundaries from the Gulf of Mexico. Some colonies presented high morphologic variability, with characteristics that corresponded to Siderastrea stellata. Molecular analysis, using the nuclear ITS and ITS2 region, corroborated the morphological results, revealing low genetic variability between S. radians and S. stellata. Since the ITS sequences did not distinguish between Siderastrea species, we used the ITS2 region to differentiate S. stellata from S. radians. This is the first report of Siderastrea stellata and its variability in the Gulf of Mexico that is supported by morphological and molecular analyses.

Microbe-ID: an open source toolbox for microbial genotyping and species identification

Development of tools to identify species, genotypes, or novel strains of invasive organisms is critical for monitoring emergence and implementing rapid response measures. Molecular markers, although critical to identifying species or genotypes, require bioinformatic tools for analysis. However, user-friendly analytical tools for fast identification are not readily available. To address this need, we created a web-based set of applications called Microbe-ID that allow for customizing a toolbox for rapid species identification and strain genotyping using any genetic markers of choice. Two components of Microbe-ID, named Sequence-ID and Genotype-ID, implement species and genotype identification, respectively. Sequence-ID allows identification of species by using BLAST to query sequences for any locus of interest against a custom reference sequence database. Genotype-ID allows placement of an unknown multilocus marker in either a minimum spanning network or dendrogram with bootstrap support from a user-created reference database. Microbe-ID can be used for identification of any organism based on nucleotide sequences or any molecular marker type and several examples are provided. We created a public website for demonstration purposes called Microbe-ID (microbe-id.org) and provided a working implementation for the genus Phytophthora (phytophthora-id.org). In Phytophthora-ID, the Sequence-ID application allows identification based on ITS or cox spacer sequences. Genotype-ID groups individuals into clonal lineages based on simple sequence repeat (SSR) markers for the two invasive plant pathogen species P. infestans and P. ramorum. All code is open source and available on github and CRAN. Instructions for installation and use are provided at https://github.com/grunwaldlab/Microbe-ID.

Application of the Ribosomal DNA ITS2 Region of Physalis (Solanaceae): DNA Barcoding and Phylogenetic Study

Recently, commercial interest in Physalis species has grown worldwide due to their high nutritional value, edible fruit, and potential medicinal properties. However, many Physalis species have similar shapes and are easily confused, and consequently the phylogenetic relationships between Physalis species are poorly understood. This hinders their safe utilization and genetic resource conservation. In this study, the nuclear ribosomal ITS2 region was used to identify species and phylogenetically examine Physalis. Eighty-six ITS2 regions from 45 Physalis species were analyzed. The ITS2 sequences were aligned using Clustal W and genetic distances were calculated using MEGA V6.0. The results showed that ITS2 regions have significant intra- and inter-specific divergences, obvious barcoding gaps, and higher species discrimination rates (82.2% for both the BLASTA1 and nearest distance methods). In addition, the secondary structure of ITS2 provided another way to differentiate species. Cluster analysis based on ITS2 regions largely concurred with the relationships among Physalis species established by many previous molecular analyses, and showed that most sections of Physalis appear to be polyphyletic. Our results demonstrated that ITS2 can be used as an efficient and powerful marker in the identification and phylogenetic study of Physalis species. The technique provides a scientific basis for the conservation of Physalis plants and for utilization of resources.

The Antarctic Circumpolar Current as a diversification trigger for deep-sea octocorals

BACKGROUND

Antarctica is surrounded by the Antarctic Circumpolar Current (ACC), the largest and strongest current in the world. Despite its potential importance for shaping biogeographical patterns, the distribution and connectivity of deep-sea populations across the ACC remain poorly understood. In this study we conducted the first assessment of phylogeographical patterns in deep-sea octocorals in the South Pacific and Southern Ocean, specifically a group of closely related bottlebrush octocorals (Primnoidae: Tokoprymno and Thourella), as a test case to study the effect of the ACC on the population structure of brooding species. We assessed the degree to which the ACC constitutes a barrier to gene flow between northern and southern populations and whether the onset of diversification of these corals coincides with the origin of the ACC (Oligocene-Miocene boundary).

RESULTS

Based on DNA sequences of two nuclear genes from 80 individuals and a combination of phylogeographic model-testing approaches we found a phylogenetic break corresponding to the spatial occurrence of the ACC. We also found significant genetic structure among our four regional populations. However, we uncovered shared haplotypes among certain population pairs, suggesting long-distance, asymmetrical migration. Our divergence time analyses indicated that the separation of amphi-ACC populations took place during the Middle Miocene around 12.6 million years ago, i.e., after the formation of the ACC.

CONCLUSION

We suggest that the ACC constitutes a semi-permeable barrier to these deep-sea octocorals capable of separating and structuring populations, while allowing short periods of gene flow. The fluctuations in latitudinal positioning of the ACC during the Miocene likely contributed to the diversification of these octocorals. Additionally, we provide evidence that the populations from each of our four sampling regions could actually constitute different species.

Identification of commercial Ganoderma (Lingzhi) species by ITS2 sequences

Background

DNA barcoding can be used to authenticate Ganoderma species for safe use. This study aims to identify commercial products containing Ganoderma using DNA barcoding.

Methods

We used 63 internal transcribed spacer (ITS) 2 sequences of Ganoderma species from 33 newly-sequenced wild samples, crude drugs, mycelia, spores, and authentic extracts and spore oils collected from various locations and markets, as well as 30 sequences from GenBank. Sequences were assembled and aligned using CodonCode Aligner V3.71. Intra- and inter-specific distances were estimated by MEGA 6.0, and phylogeny reconstruction was based on the K2P model. SNP(s) and RNA secondary structure of ITS2 were analyzed and compared among closely related Ganoderma species.

Results

G. lucidum cultivated in China was different from those cultivated in Europe. “Chizhi” (G. lucidum) and “Zizhi” (G. sinense) were clustered into two clades that were separated from the other Ganoderma species. The fruiting bodies and commercial products of G. lucidum and G. sinense were successfully distinguished from those of other Ganoderma species by comparing the ITS2 sequences and RNA secondary structures.

Conclusion

The DNA barcoding method is applicable to the authentication of commercial products containing Ganoderma species.

Genetic diversity, paraphyly and incomplete lineage sorting of mtDNA, ITS2 and microsatellite flanking region in closely related Heliopora species (Octocorallia)

Examining genetic diversity and lineage sorting of different genes in closely related species provide useful information for phylogenetic analyses and ultimately for understanding the origins of biodiversity. In this study, we examined inter- and intraspecific genetic variation in internal transcribed spacer 2 (ITS2), partial mitochondrial gene (mtMutS), and nuclear microsatellite flanking region in two closely related octocoral species (Heliopora coerulea, HC-A and HC-B). These species were recently identified in a population genetic study using microsatellite markers. The two species have different reproductive timing, which ecologically promotes lineage sorting. In this study, we examined whether species boundaries could be detected by the commonly used nuclear ITS2 and mtMutS, as well as by possibly neutral microsatellite flanking sequences. Haplotype network analysis of microsatellite flanking region revealed that a possible ancestral haplotype was still shared between the two species, indicating on-going lineage sorting. Haplotype network analysis of ITS2 and microsatellite flanking region revealed shared haplotypes between the two lineages. The two species shared fewer ITS2 sequences than microsatellite flanking region sequences. The almost fixed point mutation at the tip of helix 3 of ITS2 was not associated with the secondary structure or compensatory base changes (CBCs). The phylogenetic tree of ITS2 showed paraphyly and that of the microsatellite flanking region indicated that lineage sorting for the two species may be incomplete. Much higher intra- and inter-individual variation of ITS2 was observed in HC-B than that in HC-A, highlighting the importance of examining ITS2 from multiple individuals to estimate genetic diversity. The mitochondrial mtMutS gene sequences from 39 individuals, including both species collected from Japan and Taiwan, showed no variation because of slow rates of mitochondrial nucleotide substitution. This study suggests caution is warranted when reciprocal monophyly in a phylogenetic tree is used as the criterion for delimiting closely related octocoral species based on ITS2 or mtMtuS sequences. Detection of boundaries between closely related species requires multi-locus analysis, such as genetic admixture analysis using multiple individuals.

Computing the origin and evolution of the ribosome from its structure - Uncovering processes of macromolecular accretion benefiting synthetic biology

Accretion occurs pervasively in nature at widely different timeframes. The process also manifests in the evolution of macromolecules. Here we review recent computational and structural biology studies of evolutionary accretion that make use of the ideographic (historical, retrodictive) and nomothetic (universal, predictive) scientific frameworks. Computational studies uncover explicit timelines of accretion of structural parts in molecular repertoires and molecules. Phylogenetic trees of protein structural domains and proteomes and their molecular functions were built from a genomic census of millions of encoded proteins and associated terminal Gene Ontology terms. Trees reveal a ‘metabolic-first’ origin of proteins, the late development of translation, and a patchwork distribution of proteins in biological networks mediated by molecular recruitment. Similarly, the natural history of ancient RNA molecules inferred from trees of molecular substructures built from a census of molecular features shows patchwork-like accretion patterns. Ideographic analyses of ribosomal history uncover the early appearance of structures supporting mRNA decoding and tRNA translocation, the coevolution of ribosomal proteins and RNA, and a first evolutionary transition that brings ribosomal subunits together into a processive protein biosynthetic complex. Nomothetic structural biology studies of tertiary interactions and ancient insertions in rRNA complement these findings, once concentric layering assumptions are removed. Patterns of coaxial helical stacking reveal a frustrated dynamics of outward and inward ribosomal growth possibly mediated by structural grafting. The early rise of the ribosomal ‘turnstile’ suggests an evolutionary transition in natural biological computation. Results make explicit the need to understand processes of molecular growth and information transfer of macromolecules.

Molecular and Morphological Species Boundaries in the Gorgonian Octocoral Genus Pterogorgia (Octocorallia: Gorgoniidae)

Most gorgonian octocoral species are described using diagnostic characteristics of their sclerites (microscopic skeletal components). Species in the genus Pterogorgia, however, are separated primarily by differences in their calyx and branch morphology. Specimens of a morphologically unusual Pterogorgia collected from Saba Bank in the NE Caribbean Sea were found with calyx morphology similar to P. citrina and branch morphology similar to P. guadalupensis. In order to test morphological species boundaries, and the validity of calyx and branch morphology as systematic characters, a phylogenetic analysis was undertaken utilizing partial gene fragments of three mitochondrial (mtMutS, cytochrome b, and igr4; 726bp total) and two nuclear (ITS2, 166bp; and SRP54 intron, 143bp) loci. The datasets for nuclear and mitochondrial loci contained few phylogenetically informative sites, and tree topologies did not resolve any of the morphological species as monophyletic groups. Instead, the mitochondrial loci and SRP54 each recovered two clades but were slightly incongruent, with a few individuals of P. guadalupensis represented in both clades with SRP54. A concatenated dataset of these loci grouped all P. anceps and P. guadalupensis in a clade, and P. citrina and the Pterogorgia sp. from Saba Bank in a sister clade, but with minimal variation/resolution within each clade. However, in common with other octocoral taxa, the limited genetic variation may not have been able to resolve whether branch variation represents intraspecific variation or separate species. Therefore, these results suggest that there are at least two phylogenetic lineages of Pterogorgia at the species level, and the atypical Pterogorgia sp. may represent an unusual morphotype of P. citrina, possibly endemic to Saba Bank. Branch morphology does not appear to be a reliable morphological character to differentiate Pterogorgia species (e.g., branches "flat" or "3-4 edges" in P. guadalupensis and P. anceps, respectively), and a re-evaluation of species-level characters (e.g., sclerites) is needed.

Octocoral Species Assembly and Coexistence in Caribbean Coral Reefs

BACKGROUND

What are the determinant factors of community assemblies in the most diverse ecosystem in the ocean? Coral reefs can be divided in continental (i.e., reefs that develop on the continental shelf, including siliciclastic reefs) and oceanic (i.e., far off the continental shelf, usually on volcanic substratum); whether or not these habitat differences impose community-wide ecological divergence or species exclusion/coexistence with evolutionary consequences, is unknown.

METHODS

Studying Caribbean octocorals as model system, we determined the phylogenetic community structure in a coral reef community, making emphasis on species coexistence evidenced on trait evolution and environmental feedbacks. Forty-nine species represented in five families constituted the species pool from which a phylogenetic tree was reconstructed using mtDNA. We included data from 11 localities in the Western Caribbean (Colombia) including most reef types. To test diversity-environment and phenotype-environment relationships, phylogenetic community structure and trait evolution we carried out comparative analyses implementing ecological and evolutionary approaches.

RESULTS

Phylogenetic inferences suggest clustering of oceanic reefs (e.g., atolls) contrasting with phylogenetic overdispersion of continental reefs (e.g., reefs banks). Additionally, atolls and barrier reefs had the highest species diversity (Shannon index) whereas phylogenetic diversity was higher in reef banks. The discriminant component analysis supported this differentiation between oceanic and continental reefs, where continental octocoral species tend to have greater calyx apertures, thicker branches, prominent calyces and azooxanthellate species. This analysis also indicated a clear separation between the slope and the remaining habitats, caused by the presence or absence of Symbiodinium. K statistic analysis showed that this trait is conserved as well as the branch shape.

DISCUSSION

There was strong octocoral community structure with opposite diversity and composition patterns between oceanic and continental reefs. Even habitats with similar depths and overall environmental conditions did not share similar communities between oceanic and continental reefs. This indicates a strong regional influence over the local communities, probably due to water transparency differences between major reef types, i.e., oceanic vs. continental shelf-neritic. This was supported by contrasting patterns found in morphology, composition and evolutionary history of the species between atolls and reef banks.

Utilizing ribosomal DNA gene marker regions to characterize the metacercariae (Trematoda: Digenea) parasitizing piscine intermediate hosts in Manipur, Northeast India

Freshwater fishes in Manipur, Northeast India frequently harbour several types of metacercariae, which based on morphological criteria were identified as Clinostomoides brieni, Euclinostomum heterostomum (Clinostomidae) and Polylekithum sp. (Allocreadiidae). Molecular techniques utilizing PCR amplification of rDNA regions of larger subunit (LSU or 28S), smaller subunit (SSU or 18S) and inter transcribed spacers (ITS1, 2) were used for molecular characterization of these types. Sequences generated from the metacercariae were compared with their related sequences available in public databases; an analysis of the identity matrices and phylogenetic trees constructed was also carried out, which confirmed their identification. Similarly, the sequences generated from Polylekithum sp. were found to be highly similar to the species of the same genus. The rDNA ITS2 secondary structure provided additional confirmation of the robustness of the molecular marker as a tool for taxon-specific characterization.

Secondary structure and phylogenetic utility of the ribosomal large subunit (28S) in monogeneans of the genus Thaparocleidus and Bifurcohaptor (Monogenea: Dactylogyridae)

Present communication deals with secondary structure of 28S rDNA of two already known species of monogeneans viz., Bifurcohaptor indicus and Thaparocleidus parvulus parasitizing gill filaments of a freshwater fish, Mystus vittatus for phylogenetic inference. Secondary structure data are best used as accessory taxonomic characters as their phylogenetic resolving power and confidence in validity. Secondary structure of the 28S rDNA transcript could provide information for identifying homologous nucleotide characters, useful for cladistic inference of relationships. Such structure data could be used as taxonomic character. The study supports that species-level sequence variability renders 28S sequence as a unique window for examining the behavior of fast evolving, non-coding DNA sequences. Apart from this it also confirms that molecular similarity present in various species could be host-induced.

The short ITS2 sequence serves as an efficient taxonomic sequence tag in comparison with the full-length ITS

An ideal DNA barcoding region should be short enough to be amplified from degraded DNA. In this paper, we discuss the possibility of using a short nuclear DNA sequence as a barcode to identify a wide range of medicinal plant species. First, the PCR and sequencing success rates of ITS and ITS2 were evaluated based entirely on materials from dry medicinal product and herbarium voucher specimens, including some samples collected back to 90 years ago. The results showed that ITS2 could recover 91% while ITS could recover only 23% efficiency of PCR and sequencing by using one pair of primer. Second, 12861 ITS and ITS2 plant sequences were used to compare the identification efficiency of the two regions. Four identification criteria (BLAST, inter- and intradivergence Wilcoxon signed rank tests, and TaxonDNA) were evaluated. Our results supported the hypothesis that ITS2 can be used as a minibarcode to effectively identify species in a wide variety of specimens and medicinal materials.

PCR-based molecular characterization, phylogenetic analysis and secondary structure of the 28S rDNA of Thaparocleidus wallagonius (Monogenea: Dactylogyridae) - the most primitive species of this genus from India

Species of the monogenean genus Thaparocleidus are specific to freshwater siluriform fish. The infection caused by these gill parasites are a major health problem to fish. But, to focus the control strategies of these parasites, first it is important to establish an accurate discrimination by molecular methods. In the present study, phylogenetic and structural analysis of 28S region of ribosomal DNA of T. wallagonius species collected from fish Wallago attu from Meerut (U.P.), India, was carried out. In the first step, we amplified, sequenced 28S region of ribosomal DNA of T. wallagonius to establish the phylogenetic relationship with other species of this genus. T. wallagonius found on gill filaments of fish W. attu, is the most primitive parasite of this genus from India, was unequivocally discriminate from other species of the same genus in this study. A secondary-structure model of the large subunit rDNA was also predicted using a combined comparative and thermodynamic approach. Molecular morphometric and phylogenetic relationship of T. wallagonius are discussed in detailed that based on molecular analysis using bioinformatic tools.

Cleaning up the 'Bigmessidae': molecular phylogeny of scleractinian corals from Faviidae, Merulinidae, Pectiniidae and Trachyphylliidae

BACKGROUND

Molecular phylogenetic studies on scleractinian corals have shown that most taxa are not reflective of their evolutionary histories. Based principally on gross morphology, traditional taxonomy suffers from the lack of well-defined and homologous characters that can sufficiently describe scleractinian diversity. One of the most challenging clades recovered by recent analyses is 'Bigmessidae', an informal grouping that comprises four conventional coral families, Faviidae, Merulinidae, Pectiniidae and Trachyphylliidae, interspersed among one another with no apparent systematic pattern. There is an urgent need for taxonomic revisions in this clade, but it is vital to first establish phylogenetic relationships within the group. In this study, we reconstruct the evolutionary history of 'Bigmessidae' based on five DNA sequence markers gathered from 76 of the 132 currently recognized species collected from five reef regions in the central Indo-Pacific and the Atlantic.

RESULTS

We present a robust molecular phylogeny of 'Bigmessidae' based on the combined five-gene data, achieving a higher degree of resolution compared to previous analyses. Two Pacific species presumed to be in 'Bigmessidae' are more closely related to outgroup clades, suggesting that other unsampled taxa have unforeseen affinities. As expected, nested within 'Bigmessidae' are four conventional families as listed above, and relationships among them generally corroborate previous molecular analyses. Our more resolved phylogeny supports a close association of Hydnophora (Merulinidae) with Favites + Montastraea (Faviidae), rather than with the rest of Merulinidae, i.e., Merulina and Scapophyllia. Montastraea annularis, the only Atlantic 'Bigmessidae' is sister to Cyphastrea, a grouping that can be reconciled by their septothecal walls, a microstructural feature of the skeleton determined by recent morphological work. Characters at the subcorallite scale appear to be appropriate synapomorphies for other subclades, which cannot be explained using macromorphology. Indeed, wide geographic sampling here has revealed more instances of possible cryptic taxa confused by evolutionary convergence of gross coral morphology.

CONCLUSIONS

Numerous examples of cryptic taxa determined in this study support the assertion that diversity estimates of scleractinian corals are erroneous. Fortunately, the recovery of most 'Bigmessidae' genera with only minor degrees of paraphyly offers some hope for impending taxonomic amendments. Subclades are well defined and supported by subcorallite morphological features, providing a robust framework for further systematic work.

Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees

Background

In several studies, secondary structures of ribosomal genes have been used to improve the quality of phylogenetic reconstructions. An extensive evaluation of the benefits of secondary structure, however, is lacking.

Results

This is the first study to counter this deficiency. We inspected the accuracy and robustness of phylogenetics with individual secondary structures by simulation experiments for artificial tree topologies with up to 18 taxa and for divergency levels in the range of typical phylogenetic studies. We chose the internal transcribed spacer 2 of the ribosomal cistron as an exemplary marker region. Simulation integrated the coevolution process of sequences with secondary structures. Additionally, the phylogenetic power of marker size duplication was investigated and compared with sequence and sequence-structure reconstruction methods. The results clearly show that accuracy and robustness of Neighbor Joining trees are largely improved by structural information in contrast to sequence only data, whereas a doubled marker size only accounts for robustness.

Conclusions

Individual secondary structures of ribosomal RNA sequences provide a valuable gain of information content that is useful for phylogenetics. Thus, the usage of ITS2 sequence together with secondary structure for taxonomic inferences is recommended. Other reconstruction methods as maximum likelihood, bayesian inference or maximum parsimony may equally profit from secondary structure inclusion.

Reviewers

This article was reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin.

Open peer review

Reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin. For the full reviews, please go to the Reviewers' comments section.

Phylogenetic reconstruction using secondary structures and sequence motifs of ITS2 rDNA of Paragonimus westermani (Kerbert, 1878) Braun, 1899 (Digenea: Paragonimidae) and related species

BACKGROUND

Most phylogenetic studies using current methods have focused on primary DNA sequence information. However, RNA secondary structures are particularly useful in systematics because they include characteristics that give "morphological" information, not found in the primary sequence. In several mountainous regions of Northeastern India, foci of Paragonimus (lung fluke) infection reportedly involve species that are known to prevail in neighbouring countries. The present study was undertaken to demonstrate the sequence analysis of the ribosomal DNA (ITS2) of the infective (metacercarial) stage of the lung fluke collected from the edible crab hosts that are abundant in a mountain stream of the area (Miao, Changlang District in Arunachal Pradesh) and to construct its phylogeny. Using the approach of molecular morphometrics that is based on ITS2 secondary structure homologies, phylogenetic relationships of the various isolates of Paragonimus species that are prevalent in the neighbouring Near-eastern countries have been discussed.

RESULTS

Initially, ten predicted RNA secondary structures were reconstructed and the topology based only on the predicted RNA secondary structure of the ITS2 region resolved most relationships among the species studied. We obtained three similar topologies for seven species of the genus Paragonimus on the basis of traditional primary sequence analysis using MEGA and a Bayesian analysis of the combined data. The latter approach allowed us to include both primary sequence and RNA molecular morphometrics; each data partition was allowed to have a different evolution rate. Paragonimus westermani was found to group with P. siamensis of Thailand; this was best supported by both the molecular morphometrics and combined analyses. P. heterotremus, P. proliferus, P. skrjabini, P. bangkokensis and P. harinasutai formed a separate clade in the molecular phylogenies, and were reciprocally monophyletic with respect to other species. ITS2 sequence motifs allowed an accurate in-silico distinction of lung flukes.

CONCLUSION

Data indicate that ITS2 motifs (<or= 50 bp in size) can be considered a promising tool for trematode species identification. RNA secondary structure analysis could be a valuable tool for distinguishing new species and completing Paragonimus systematics, more so because ITS2 secondary structure contains more information than the usual primary sequence alignment.

Use of sequence motifs as barcodes and secondary structures of internal transcribed spacer 2 (ITS2, rDNA) for identification of the Indian liver fluke, Fasciola (Trematoda: Fasciolidae)

Most phylogenetic studies using current methods have focused on primary DNA sequence information. However, RNA secondary structures are particularly useful in systematics because they include characteristics that give “morphological” information which is not found in the primary sequence. Also DNA sequence motifs from the internal transcribed spacer (ITS) of the nuclear rRNA repeat are useful for identification of trematodes. The species of liver flukes of the genus Fasciola (Platyhelminthes: Digenea: Fasciolidae) are obligate parasitic trematodes residing in the large biliary ducts of herbivorous mammals. While Fasciola hepatica has a cosmopolitan distribution, the other major species, i.e., F. gigantica is reportedly prevalent in the tropical and subtropical regions of Africa and Asia. To determine the Fasciola sp. of Assam (India) origin based on rDNA molecular data, ribosomal ITS2 region was sequenced (EF027103) and analysed. NCBI databases were used for sequence homology analysis and the phylogenetic trees were constructed based upon the ITS2 using MEGA and a Bayesian analysis of the combined data. The latter approach allowed us to include both primary sequence and RNA molecular morphometrics and revealed a close relationship with isolates of F. gigantica from China, Indonesia and Japan, the isolate from China with significant bootstrap values being the closest. ITS2 sequence motifs allowed an accurate in silico distinction of liver flukes. The data indicate that ITS2 motifs (≤ 50 bp in size) can be considered promising tool for trematode species identification. Using the novel approach of molecular morphometrics that is based on ITS2 secondary structure homologies, phylogenetic relationships of the various isolates of fasciolid species have been discussed.

Ecological barcoding of corallivory by second internal transcribed spacer sequences: hosts of coralliophiline gastropods detected by the cnidarian DNA in their stomach

The second internal transcribed spacer (ITS2) of the nuclear ribosomal RNA cluster (rDNA) is significantly smaller in the Cnidaria (120-260 bp) than in the rest of the Metazoa. ITS2 is one of the fastest evolving DNA regions among those commonly used in molecular systematics and has been proposed as a possible barcoding gene for Cnidaria to replace the currently problematic mitochondrial sequences used. We have reviewed the intraspecific and interspecific variation of ITS2 rRNA sequences in the Anthozoa. We have observed that the lower limits of the interspecific DNA divergence ranges very often overlap with intraspecific ranges, and identical sequences from individuals of different species are not rare. This finding can result in problems similar to those encountered with the mitochondrial COI, and we conclude that ITS2 does not prove significantly better than COI for standard taxonomic DNA barcoding in Anthozoa. However, ITS2 appears to be a promising gene in the ecological DNA barcoding of corallivory, where taxonomic accuracy at genus or even family level may represent a significant improvement of current knowledge. We have successfully amplified and sequenced ITS2 from template DNA extracted from foot muscle and from stomach contents of corallivorous gastropods, and from their anthozoan hosts. The small size of cnidarian ITS2 makes it a very easy and efficient tool for ecological barcoding of associations. Ecological barcoding of corallivory is an indispensable approach to the study of the associations in deep water, where direct observation is severely limited by logistics and costs.

ProfDistS: (profile-) distance based phylogeny on sequence--structure alignments

MOTIVATION

The Profile Neighbor Joining (PNJ) algorithm as implemented in the software ProfDist is computationally efficient in reconstructing very large trees. Besides the huge amount of sequence data the structure is important in RNA alignment analysis and phylogenetic reconstruction.

RESULTS

For this ProfDistS provides a phylogenetic workflow that uses individual RNA secondary structures in reconstructing phylogenies based on sequence-structure alignments-using PNJ with manual or iterative and automatic profile definition. Moreover, ProfDistS can deal also with protein sequences.

ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales)

Background

Within Chlorophyceae the ITS2 secondary structure shows an unbranched helix I, except for the 'Hydrodictyon' and the 'Scenedesmus' clade having a ramified first helix. The latter two are classified within the Sphaeropleales, characterised by directly opposed basal bodies in their flagellar apparatuses (DO-group). Previous studies could not resolve the taxonomic position of the 'Sphaeroplea' clade within the Chlorophyceae without ambiguity and two pivotal questions remain open: (1) Is the DO-group monophyletic and (2) is a branched helix I an apomorphic feature of the DO-group? In the present study we analysed the secondary structure of three newly obtained ITS2 sequences classified within the 'Sphaeroplea' clade and resolved sphaeroplealean relationships by applying different phylogenetic approaches based on a combined sequence-structure alignment.

Results

The newly obtained ITS2 sequences of Ankyra judayi, Atractomorpha porcata and Sphaeroplea annulina of the 'Sphaeroplea' clade do not show any branching in the secondary structure of their helix I. All applied phylogenetic methods highly support the 'Sphaeroplea' clade as a sister group to the 'core Sphaeropleales'. Thus, the DO-group is monophyletic. Furthermore, based on characteristics in the sequence-structure alignment one is able to distinguish distinct lineages within the green algae.

Conclusion

In green algae, a branched helix I in the secondary structure of the ITS2 evolves past the 'Sphaeroplea' clade. A branched helix I is an apomorph characteristic within the monophyletic DO-group. Our results corroborate the fundamental relevance of including the secondary structure in sequence analysis and phylogenetics.

NOBAI: a web server for character coding of geometrical and statistical features in RNA structure

The Numeration of Objects in Biology: Alignment Inferences (NOBAI) web server provides a web interface to the applications in the NOBAI software package. This software codes topological and thermodynamic information related to the secondary structure of RNA molecules as multi-state phylogenetic characters, builds character matrices directly in NEXUS format and provides sequence randomization options. The web server is an effective tool that facilitates the search for evolutionary history embedded in the structure of functional RNA molecules. The NOBAI web server is accessible at 'http://www.manet.uiuc.edu/nobai/nobai.php'. This web site is free and open to all users and there is no login requirement.

Phenotypic plasticity or speciation? A case from a clonal marine organism

BACKGROUND

Clonal marine organisms exhibit high levels of morphological variation. Morphological differences may be a response to environmental factors but also they can be attributed to accumulated genetic differences due to disruption of gene flow among populations. In this study, we examined the extensive morphological variation (of 14 characters) in natural populations observed in the gorgonian Eunicea flexuosa, a widely distributed Caribbean octocoral. Eco-phenotypic and genetic effects were evaluated by reciprocal transplants of colonies inhabiting opposite ends of the depth gradient and analysis of population genetics of mitochondrial and nuclear genes, respectively.

RESULTS

Significant differences (P < 0.001) in 14 morphological traits were found among colonies inhabiting 12 locations distributed in seven reefs in southwest Puerto Rico. Results from principal component analysis indicated the presence of two groups based on depth distribution, suggesting the presence of two discrete morphotypes (i.e. shallow type < 5 m and deep type > 17 m). A discriminant function analysis based on a priori univariate and multivariate analyses (which separated the colonies in morphotypes) correctly classified 93% of the colonies for each environment. Light, water motion and sediment transport might influence the distribution of the two morphotypes. Reaction norms of morphological characters of colonies reciprocally transplanted showed gradual significant changes through the 15 months of transplantation. Sclerites of shallow water colonies became larger when transplanted to deeper environments and vice versa, but neither of the two transplanted groups overlapped with the residents' morphology. Genetic analysis of mitochondrial and nuclear genes suggested that such discrete morphology and non-overlapping phenotypic plasticity is correlated with the presence of two independent evolutionary lineages. The distribution of the lineages is non-random and may be related to adaptational responses of each lineage to the environmental demands of each habitat.

CONCLUSION

The extensive distribution and ample morphological variation of Eunicea flexuosa corresponds to two distinct genetic lineages with narrower distributions and more rigid phenotypic plasticity than the original description. The accepted description sensu Bayer (1961) of E. flexuosa is a complex of at least two distinct genetic lineages, adapted to different habitats and do not exchange genetic material despite living in sympatry. The present study highlights the importance of correctly defining species, because the unknowingly use of species complexes can overestimate geographical distribution, population abundance, and physiological tolerance.