Compensatory Base Research Articles

An evaluation of the genus Amphidinium (Dinophyceae) combining evidence from morphology, phylogenetics, and toxin production, with the introduction of six novel species

The genus Amphidinium is an important group of athecated dinoflagellates because of its high abundance in marine habitats, its member’s ability to live in a variety of environmental conditions and ability to produce toxins. Furthermore, the genus is of particular interest in the biotechnology field for its potential in the pharmaceutical arena. Taxonomically the there is a history of complication and confusion over the proper identities and placements of Amphidinium species due to high genetic variability coupled with high morphological conservation. Thirteen years has passed since the most recent review of the group, and while many issues were resolved, some remain. The present study used microscopy, phylogenetics of the 28S region of rDNA, secondary structure of the ITS2 region of rDNA, compensatory base change data, and cytotoxicity data from Amphidinium strains collected world-wide to elucidate remaining confusion. This holistic approach using multiple lines of evidence resulted in a more comprehensive understanding of the morphological, ecological, and genetic characteristics that are attributed to organisms belonging to Amphidinium, including six novel species: A. fijiensis, A. magnum, A. paucianulatum, A. pseudomassartii, A. theodori, and A. tomasii.

Molecular phylogeny of Oncaeidae (Copepoda) using nuclear ribosomal internal transcribed spacer (ITS rDNA).

Copepods belonging to the Oncaeidae family are commonly and abundantly found in marine zooplankton. In the Mediterranean Sea, forty-seven oncaeid species occur, of which eleven in the Gulf of Naples. In this Gulf, several Oncaea species were morphologically analysed and described at the end of the XIX century by W. Giesbrecht. In the same area, oncaeids are being investigated over seasonal and inter-annual scales at the long-term coastal station LTER-MC. In the present work, we identified six oncaeid species using the nuclear ribosomal internal transcribed spacers (ITS rDNA) and the mitochondrial cytochrome c oxidase subunit I (mtCOI). Phylogenetic analyses based on these two genomic regions validated the sisterhood of the genera Triconia and the Oncaea sensu stricto. ITS1 and ITS2 phylogenies produced incongruent results about the position of Oncaea curta, calling for further investigations on this species. We also characterised the ITS2 region by secondary structure predictions and found that all the sequences analysed presented the distinct eukaryotic hallmarks. A Compensatory Base Change search corroborated the close relationship between O. venusta and O. curta and between O. media and O. venusta already identified by ITS phylogenies. The present results, which stem from the integration of molecular and morphological taxonomy, represent an encouraging step towards an improved knowledge of copepod biodiversity: The two complementary approaches, when applied to long-term copepod monitoring, will also help to better understanding their genetic variations and ecological niches of co-occurring species.

RNAscClust: clustering RNA sequences using structure conservation and graph based motifs.

MotivationClustering RNA sequences with common secondary structure is an essential step towards studying RNA function. Whereas structural RNA alignment strategies typically identify common structure for orthologous structured RNAs, clustering seeks to group paralogous RNAs based on structural similarities. However, existing approaches for clustering paralogous RNAs, do not take the compensatory base pair changes obtained from structure conservation in orthologous sequences into account.ResultsHere, we present RNAscClust, the implementation of a new algorithm to cluster a set of structured RNAs taking their respective structural conservation into account. For a set of multiple structural alignments of RNA sequences, each containing a paralog sequence included in a structural alignment of its orthologs, RNAscClust computes minimum free-energy structures for each sequence using conserved base pairs as prior information for the folding. The paralogs are then clustered using a graph kernel-based strategy, which identifies common structural features. We show that the clustering accuracy clearly benefits from an increasing degree of compensatory base pair changes in the alignments.Availability and Implementation RNAscClust is available at http://www.bioinf.uni-freiburg.de/Software/RNAscClust.Supplementary information Supplementary data are available at Bioinformatics online.

Molecular and phylogenetic characterization of Ostreopsis (Dinophyceae) and the description of a new species, Ostreopsis rhodesae sp. nov., from a subtropical Australian lagoon

Cryptic and pseudo-cryptic species are common amongst marine phytoplankton, and may cause misleading inferences of ecological and physiological data of plankton community studies. Deciphering the diversity and distribution of species of the benthic dinoflagellate Ostreopsis is one example, as there are many morphologically indistinct clades that differ greatly genetically and toxicologically from one another. In this study, a new species, Ostreopsis rhodesae from the southern Great Barrier Reef was described. While it initially appeared to be highly similar to several other Ostreopsis species, we found O. rhodesae can be distinguished based on the relative size of the second apical plate (2′), which is twice as long as the APC plate, and separates the third apical (3′) from the third precingular (3′′) plate. Phylogenetic trees based on the SSU, ITS/5.8S and D1-D2 and D8-D10 regions of the LSU rRNA were well supported, and showed a clear difference to other Ostreopsis clades. Compensatory base changes (CBCs) were identified in helices of the ITS2 between O. rhodesae and O. cf. ovata and O. cf. siamensis, which were also present in the same habitat. Fish gill cell lines were toxic to O. rhodesae, cell extracts but no palytoxin-like analogues were found in them. The findings highlight a case of pseudo-cryptic speciation, found in sympatry with closely related and morphologically similar species, but biologically and functionally distinct.

From the Tunnels into the Treetops: New Lineages of Black Yeasts from Biofilm in the Stockholm Metro System and Their Relatives among Ant-Associated Fungi in the Chaetothyriales.

Rock-inhabiting fungi harbour species-rich, poorly differentiated, extremophilic taxa of polyphyletic origin. Their closest relatives are often well-known species from various biotopes with significant pathogenic potential. Speleothems represent a unique rock-dwelling habitat, whose mycobiota are largely unexplored. Isolation of fungi from speleothem biofilm covering bare granite walls in the Kungsträdgården metro station in Stockholm yielded axenic cultures of two distinct black yeast morphotypes. Phylogenetic analyses of DNA sequences from six nuclear loci, ITS, nuc18S and nuc28S rDNA, rpb1, rpb2 and β-tubulin, support their placement in the Chaetothyriales (Ascomycota). They are described as a new genus Bacillicladium with the type species B. lobatum, and a new species Bradymyces graniticola. Bacillicladium is distantly related to the known five chaetothyrialean families and is unique in the Chaetothyriales by variable morphology showing hyphal, meristematic and yeast-like growth in vitro. The nearest relatives of Bacillicladium are recruited among fungi isolated from cardboard-like construction material produced by arboricolous non-attine ants. Their sister relationship is weakly supported by the Maximum likelihood analysis, but strongly supported by Bayesian inference. The genus Bradymyces is placed amidst members of the Trichomeriaceae and is ecologically undefined; it includes an opportunistic animal pathogen while two other species inhabit rock surfaces. ITS rDNA sequences of three species accepted in Bradymyces and other undescribed species and environmental samples were subjected to phylogenetic analysis and in-depth comparative analysis of ITS1 and ITS2 secondary structures in order to study their intraspecific variability. Compensatory base change criterion in the ITS2 secondary structure supported delimitation of species in Bradymyces, which manifest a limited number of phenotypic features useful for species recognition. The role of fungi in the speleothem biofilm and relationships of Bacillicladium and Bradymyces with other members of the Chaetothyriales are discussed.

ITS2 secondary structure for species circumscription: case study in southern African Strychnos L. (Loganiaceae).

Recently developed computational tools in ITS2 sequence-structure phylogenetics are improving tree robustness by exploitation of the added information content of the secondary structure. Despite this strength, however, their adoption for species-level clarifications in angiosperms has been slow. We investigate the utility of combining ITS2 sequence and secondary structure to separate species of southern African Strychnos, and assess correlation between compensatory base changes (CBCs) and currently recognised species boundaries. Combined phylogenetic analysis of sequence and secondary structure datasets performed better, in terms of robustness and species resolution, than analysis involving primary sequences only, achieving 100 and 88.2% taxa discriminations respectively. Further, the Strychnos madagascariensis complex is well-resolved by sequence-structure phylogenetic analysis. The 17 Strychnos species corresponded to 14 ITS2 CBC clades. Four of the five taxa in section Densiflorae belong to a single CBC clade, whose members tend to form natural hybrids. Our finding supports the application of ITS2 as a complementary barcoding marker for species identification. It also highlights the potential of comparative studies of ITS2 CBC features among prospective parental pairs in breeding experiments as a rapid proxy for cross compatibility assessment. This could save valuable time in crop improvement. Patterns of CBC evolution and species boundaries in Strychnos suggests a positive correlation. We conclude that the CBC pattern coupled with observed ITS2 sequence paraphyly in section Densiflorae points to a speciation work-in-progress.

High diversity of Pseudo-nitzschia along the northern coast of Sarawak (Malaysian Borneo), with descriptions of P.bipertita sp. nov. and P.limii sp. nov. (Bacillariophyceae).

Forty-eight isolates of Pseudo-nitzschia species wereestablished from the Miri coast of Sarawak (Malaysian Borneo) and underwent TEM observation and molecular characterization. Ten species werefound: P.abrensis, P.batesiana, P.fukuyoi, P.kodamae, P.lundholmiae, P.multistriata, P.pungens, P.subfraudulenta, as well as two additional new morphotypes, herein designated as P.bipertita sp. nov. and P.limii sp. nov. This is the first report of P.abrensis, P.batesiana, P.kodamae, P.fukuyoi, and P.lundholmiae in coastal waters of Malaysian Borneo. Pseudo-nitzschia bipertita differs from its congeners by the number of sectors that divide the poroids, densities of band striae, and its cingular band structure. Pseudo-nitzschia limii, a pseudo-cryptic species in the P.pseudodelicatissima complex sensu lato, is distinct by having wider proximal and distal mantles, a higher number of striae, and greater poroid height in the striae of the valvocopula. The species were further supported by the phylogenetic reconstructions of the nuclear-encoded large subunit ribosomal gene and the second internal transcribed spacer. Phylogenetically, P.bipertita clustered with its sister taxa (P.subpacifica + P.heimii); P.limii appears as a sister taxon to P.kodamae and P.hasleana in the ITS2 tree. Pairwise comparison of ITS2 transcripts with its closest relatives revealed the presence of bothhemi- and compensatory base changes. Toxicity analysis showed detectable levels of domoic acid inP.abrensis, P.batesiana, P.lundholmiae, and P.subfraudulenta, but both new species tested below the detection limit.

Molecular phylogeny of Botryococcus braunii strains (race A) – An integrative approach

Botryococcus braunii is a green colonial microalga which produces large quantities of liquid hydrocarbons similar to fossil petroleum. Exploring Botryococcus genus diversity entailed morphological, biochemical and phylogenetic studies. The majority of scientific literature specifies B. braunii as the only species with strains classified in three chemical races (A, B and L) which superpose the phylogenetic clusters built on 18S rDNA sequences. The cohesion of data provided by the three main research directions relies on the integrative analysis of the Botryococcus strains. The present work addresses the diversity of B. braunii race A strains by taking into account the morphology, the hydrocarbon and fatty acid profiles, and the phylogeny of 10 strains, isolated from several Romanian aquatic environments. The newly sequenced B. braunii strains increased the resolution of the analyses and yielded at least two distinct phylogenetic clades within race A cluster. This outcome was sustained by the genetic information coded by the 18S rRNA genes and both sequence- and sequence-structure analysis of ITS2. The Compensatory Base Changes occurrence within the secondary structure of ITS2 and the presence of one intron in the 18S rDNA sequences gave extra credibility to our phylogenetic results.

Molecular phylogeny and species delimitation within the ciliate genus Spirostomum (Ciliophora, Postciliodesmatophora, Heterotrichea), using the internal transcribed spacer region

Morphological and molecular delimitation of Spirostomum species is currently under debate. We addressed species boundaries within the genus Spirostomum, using the ITS1-5.8S-ITS2 region and the secondary structure of the ITS2 molecule, and 18S and 28S (D1D2) sequences additionally. The Spirostomum ITS region is among the shortest within the ciliates hitherto studied. The Spirostomum ITS2 molecule matches the “ring model”, but exhibits only two helices radiating from a common loop. According to comparative analyses, they very likely correspond to helices II and III of other eukaryotes. Our phylogenetic analyses of the ITS region revealed a complex genealogical structure within the genus Spirostomum. However, boundaries among Spirostomum species could not be unambiguously determined either by phylogenetic trees, networks or sequence divergence cutoffs, because ITS2 sequences transcended species boundaries of the following morphospecies: S. ambiguum, S. minus, S. subtilis and S. teres. According to molecular diversity analysis, this is very likely caused by polymorphism in S. minus and S. teres, and by the lack of variability in S. ambiguum and S. subtilis. No compensatory base changes (CBCs) were detected in helices of the ITS2 molecule between different Spirostomum species, documenting that CBC analysis per se is not able to effectively discriminate Spirostomum species.

Pseudo-nitzschia arctica sp. nov., a new cold-water cryptic Pseudo-nitzschia species within the P.pseudodelicatissima complex.

A new nontoxic Pseudo-nitzschia species belonging to the P.pseudodelicatissima complex, P.arctica, was isolated from different areas of the Arctic. The erection of P.arctica is mainly supported by molecular data, since the species shares identical ultrastructure with another species in the complex, P.fryxelliana, and represents a new case of crypticity within the genus. Despite their morphological similarity, the two species are not closely related in phylogenies based on LSU, ITS and rbcL. Interestingly, P.arctica is phylogenetically most closely related to P.granii and P.subcurvata, from which the species is, however, morphologically different. P.granii and P.subcurvata lack the central larger interspace which is one of the defining features of the P.pseudodelicatissima complex. The close genetic relationship between P.arctica and the two species P.granii and P.subcurvata is demonstrated by analysis of the secondary structure of ITS2 which revealed no compensatory base changes, two hemi-compensatory base changes, and two deletions in P.arctica with respect to the other two species. These findings emphasize that rates of morphological differentiation, molecular evolution and speciation are often incongruent for Pseudo-nitzschia species, resulting in a restricted phylogenetic value for taxonomic characters used to discriminate species. The description of a new cryptic species, widely distributed in the Arctic and potentially representing an endemic component of the Arctic diatom flora, reinforces the idea of the existence of noncosmopolitan Pseudo-nitzschia species and highlights the need for combined morphological and molecular analyses to assess the distributional patterns of phytoplankton species.

New insights into the morphology and phylogeny of Heterosigma akashiwo (Raphidophyceae), with the description of Heterosigma minor sp. nov.

:Heterosigma akashiwo is one of the smallest raphidophytes and is known for its ability to form dense, fish-killing blooms. In many parts of the world, H. akashiwo is a permanent resident of the algal community, and blooms have caused extensive financial losses for the aquaculture industry. Different aspects of its biology have been the focus of numerous investigations over the last two decades but, perhaps because of its small size and fragile nature, few morphological studies have been carried out. We conducted phylogenetic and morphological studies of 24 strains of Heterosigma from the coastal waters of Europe, North America, Australia and New Zealand. Complete 18S, ITS region and the D1–D2 region of 28S rDNA were sequenced and compared with all available raphidophyte sequences, revealing a novel species of Heterosigma, Heterosigma minor sp. nov. All strains of H. akashiwo were genetically very similar across the rDNA region (> 99.8% similarity) and morphologically very similar in light microscopy and scanning electron microscopy. Heterosigma minor shared only 98.2% similarity with H. akashiwo, and there were several morphological differences: it was smaller, rounder and had fewer mucocysts than H. akashiwo. The secondary structure of ITS2 was reconstructed, revealing three compensatory base changes between the two species, further indicating that H. minor is a sister to H. akashiwo. The phylogeny of Raphidophyceae was reconstructed to include all currently described raphidophytes.

Contrasting evolutionary patterns of 28S and ITS rRNA genes reveal high intragenomic variation in Cephalenchus (Nematoda): Implications for species delimitation

Concerted evolution is often assumed to be the evolutionary force driving multi-family genes, including those from ribosomal DNA (rDNA) repeat, to complete homogenization within a species, although cases of non-concerted evolution have been also documented. In this study, sequence variation of 28S and ITS ribosomal RNA (rRNA) genes in the genus Cephalenchus is assessed at three different levels, intragenomic, intraspecific, and interspecific. The findings suggest that not all Cephalenchus species undergo concerted evolution. High levels of intraspecific polymorphism, mostly due to intragenomic variation, are found in Cephalenchus sp1 (BRA-01). Secondary structure analyses of both rRNA genes and across different species show a similar substitution pattern, including mostly compensatory (CBC) and semi-compensatory (SBC) base changes, thus suggesting the functionality of these rRNA copies despite the variation found in some species. This view is also supported by low sequence variation in the 5.8S gene in relation to the flanking ITS-1 and ITS-2 as well as by the existence of conserved motifs in the former gene. It is suggested that potential cross-fertilization in some Cephalenchus species, based on inspection of female reproductive system, might contribute to both intragenomic and intraspecific polymorphism of their rRNA genes. These results reinforce the potential implications of intragenomic and intraspecific genetic diversity on species delimitation, especially in biodiversity studies based solely on metagenetic approaches. Knowledge of sequence variation will be crucial for accurate species diversity estimation using molecular methods.

DNA Barcoding Green Microalgae Isolated from Neotropical Inland Waters.

This study evaluated the feasibility of using the Ribulose Bisphosphate Carboxylase Large subunit gene (rbcL) and the Internal Transcribed Spacers 1 and 2 of the nuclear rDNA (nuITS1 and nuITS2) markers for identifying a very diverse, albeit poorly known group, of green microalgae from neotropical inland waters. Fifty-one freshwater green microalgae strains isolated from Brazil, the largest biodiversity reservoir in the neotropics, were submitted to DNA barcoding. Currently available universal primers for ITS1-5.8S-ITS2 region amplification were sufficient to successfully amplify and sequence 47 (92%) of the samples. On the other hand, new sets of primers had to be designed for rbcL, which allowed 96% of the samples to be sequenced. Thirty-five percent of the strains could be unambiguously identified to the species level based either on nuITS1 or nuITS2 sequences’ using barcode gap calculations. nuITS2 Compensatory Base Change (CBC) and ITS1-5.8S-ITS2 region phylogenetic analysis, together with morphological inspection, confirmed the identification accuracy. In contrast, only 6% of the strains could be assigned to the correct species based solely on rbcL sequences. In conclusion, the data presented here indicates that either nuITS1 or nuITS2 are useful markers for DNA barcoding of freshwater green microalgae, with advantage for nuITS2 due to the larger availability of analytical tools and reference barcodes deposited at databases for this marker.

Morphological and Molecular Phylogenetic Position of Prorocentrum micans sensu stricto and Description of Prorocentrum koreanum sp. nov. from Southern Coastal Waters in Korea and Japan

Prorocentrum micans is an extremely variable dinoflagellate species, with many different local forms reported worldwide. Because of this morphological diversity, it is important to establish whether these various forms belong to P. micans sensu stricto. For this study, P. micans-like specimens were isolated from several localities in the southern coastal waters of Korea and Japan. The morphological characteristics and the molecular signatures of P. micans were re-examined. Moreover, a new Prorocentrum species, Prorocentrum koreanum sp. nov. was established through detailed light microscopy and scanning electron microscopy observations. Examination of the periflagellar platelets revealed that P. koreanum sp. nov. differs from P. micans. Furthermore, P. koreanum and P. micans exhibited different distribution patterns of trichocyst pores. Through molecular phylogeny analysis of small subunit (SSU) rRNA, internal transcribed spacer (ITS), and large subunit (LSU) rRNA sequence, we found P. koreanum to be more closely related to P. mexicanum and P. rhathymum than to P. micans. Additionally, ITS2 compensatory base changes also provide strong evidence to support P. koreanum and P. micans being separate species.

Delineating a New Heterothallic Species of Volvox (Volvocaceae, Chlorophyceae) Using New Strains of "Volvox africanus".

The volvocine algae represent an excellent model lineage in which to study evolution of female and male genders based on comparative analyses of related species. Among these species, Volvox carteri has been extensively studied as a model of an oogamous and complex organism. However, it may have unique derived features that are not present in other species of Volvox. Therefore, information regarding the characteristics of sexual reproduction of other species of Volvox is also important. In 1971, Starr studied four types of sexuality in several global strains identified as Volvox africanus; however, further taxonomic studies of these strains have been lacking, and strains of three of the four sexual types are not available. Here, we studied the morphology, sexual reproduction, and taxonomy of two V. africanus-like species isolated recently from Lake Biwa, Japan. These two species were very similar to two sexual types described by Starr in 1971: one producing dioecious sexual spheroids in heterothallic strains and the other forming both male spheroids and monoecious spheroids in a single strain. The former species produced zygotes with a reticulate cell wall, whereas a smooth zygote wall was observed in the latter species as in V. africanus previously reported from various localities around the world. Our multigene phylogenetic analysis demonstrated that these are sister species to each other. However, the presence of a compensatory base change in the most conserved region of the secondary structure of nuclear ribosomal DNA internal transcribed spacer-2, hybrid inviability demonstrated by intercrossing experiments, and morphological differences in the density of abutment between the gelatinous material of adjacent cells (individual sheaths) in the spheroid supported the recognition of the two species, V. africanus having a smooth zygote wall and V. reticuliferus Nozaki sp. nov. having a reticulate zygote wall.

Species diversity in European Haematococcus pluvialis (Chlorophyceae, Volvocales)

:Haematococcus pluvialis has received much interest because it can accumulate large quantities of the pigment astaxanthin. While different isolates of H. pluvialis seem to differ considerably in their physiology, their phylogenetic diversity has not yet been thoroughly studied. We studied the species diversity in a set of temperate European strains of H. pluvialis based on internal transcribed spacer (ITS) rDNA and rbcL molecular phylogenies and determined their congruence with morphology and temperature preferences. The ITS rDNA phylogeny resolved three lineages with the European strains. Three additional lineages were not represented by our European strains. Both statistical parsimony network analysis and the general mixed Yule coalescent recovered these six lineages as different species. An ITS1 structure analysis revealed up to three compensatory base changes (CBCs) between each of the three European lineages, while one CBC was found between lineages in the ITS2 secondary structure. Yet the CBCs were not always present in all strains of each lineage. The rbcL was much less variable and separated only two of the three ITS lineages. We propose an epitype for H. pluvialis and describe the two lineages containing European strains as new species, Haematococcus rubicundus and Haematococcus rubens. Although there is broad morphological overlap, strains of H. pluvialis and H. rubens have, on average, more elongated cells, more noticeable cytoplasmic strands and a more (extreme) pear-shaped protoplast apex than H. rubicundus. Optimal temperatures for growth were similar for the three species and varied between 17°C and 23°C, which is lower than reported earlier from other strains. This study provides a robust phylogenetic framework for further ecophysiological study of Haematococcus.

Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain.

A distance constrained secondary structural model of the ≈10 kb RNA genome of the HIV-1 has been predicted but higher-order structures, involving long distance interactions, are currently unknown. We present the first global RNA secondary structure model for the HIV-1 genome, which integrates both comparative structure analysis and information from experimental data in a full-length prediction without distance constraints. Besides recovering known structural elements, we predict several novel structural elements that are conserved in HIV-1 evolution. Our results also indicate that the structure of the HIV-1 genome is highly variable in most regions, with a limited number of stable and conserved RNA secondary structures. Most interesting, a set of long distance interactions form a core organizing structure (COS) that organize the genome into three major structural domains. Despite overlapping protein-coding regions the COS is supported by a particular high frequency of compensatory base changes, suggesting functional importance for this element. This new structural element potentially organizes the whole genome into three major domains protruding from a conserved core structure with potential roles in replication and evolution for the virus.

Comparison of five methods for delimitating species in Ophion Fabricius, a diverse genus of parasitoid wasps (Hymenoptera, Ichneumonidae)

DNA taxonomy has been proposed as a method to quickly assess diversity and species limits in highly diverse, understudied taxa. Here we use five methods for species delimitation and two genetic markers (COI and ITS2) to assess species diversity within the parasitoid genus, Ophion. We searched for compensatory base changes (CBC’s) in ITS2, and determined that they are too rare to be of practical use in delimiting species in this genus. The other four methods used both COI and ITS2, and included distance-based (threshold analysis and ABGD) and tree-based (GMYC and PTP) models. We compared the results of these analyses to each other under various parameters and tested their performance with respect to 11 Nearctic species/morphospecies and 15 described Palearctic species. We also computed barcode accumulation curves of COI sequences to assess the completeness of sampling. The species count was highly variable depending on the method and parameters used, ranging from 47 to 168 species, with more conservative estimates of 89–121 species. Despite this range, many of the Nearctic test species were fairly robust with respect to method. We concluded that while there was often good congruence between methods, GMYC and PTP were less reliant on arbitrary parameters than the other two methods and more easily applied to genetic markers other than COI. However, PTP was less successful at delimiting test species than was GMYC. All methods, as well as the barcode accumulation curves, indicate that several Palearctic species remain undescribed and that we have scarcely begun to appreciate the Nearctic diversity within this genus.

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.

Genetic variability and taxonomic revision of the genus Auxenochlorella (Shihira et Krauss) Kalina et Puncocharova (Trebouxiophyceae, Chlorophyta).

The monotypic genus Auxenochlorella with its typespecies A.protothecoides is so far only known from specific habitats such as the sap of several tree species. Several varieties were described according to physiological performances in culture on different organic substrates. However, two strains designated as Auxenochlorella were isolated from other habitats (an endosymbiont of Hydra viridis and an aquatic strain from an acidic volcano stream). We studied those isolates and compared them with six strains of Auxenochlorella belonging to different varieties. The integrative approach used inthis study revealed that all strains showed similar morphology but differed in their SSU and ITS rDNA sequences. The Hydra endosymbiont formeda sister taxon to A.protothecoides, which included the varieties protothecoides, galactophila, and communis. The variety acidicola is not closely related to Auxenochlorella and represented its own lineage within the Trebouxiophyceae. In view of these results, we propose a new species of Auxenochlorella, A.symbiontica, for the Hydra symbiont, and a new genus Pumiliosphaera, with its type species, P.acidophila, for acidophilic strain. These results are supported by several compensatory base changes in the conserved region of ITS-2 and ITS-2 DNA barcodes.