Generic concept in Chlorella‐related coccoid green algae (Chlorophyta,Trebouxiophyceae)

Using a combined set of sequences of SSU and ITS regions of nuclear‐encoded ribosomal DNA, the concept of the experimental algal genus Chlorella was evaluated. Conventionally in the genus Chlorella, only coccoid, solitary algae with spherical morphology that do not possess any mucilaginous envelope were included. All Chlorella species reproduce asexually by autospores. However, phylogenetic analyses showed that within the clade of ‘true’Chlorella species (Chlorella vulgaris, C. lobophora, and C. sorokiniana), taxa with a mucilaginous envelope and colonial lifeform have also evolved. These algae, formerly designated as Dictyosphaerium, are considered as members of the genus Chlorella. In close relationship to Chlorella, five different genera were supported by the phylogenetic analyses: Micractinium (spherical cells, colonial, with bristles), Didymogenes (ellipsoidal cells, two‐celled coenobia, with or without two spines per cell), Actinastrum (ellipsoidal cells within star‐shaped coenobia), Meyerella (spherical cells, solitary, without pyrenoids), and Hegewaldia (spherical cells, colonial, with or without bristles, oogamous propagation). Based on the secondary structures of SSU and ITS rDNA sequences, molecular signatures are provided for each genus of the Chlorella clade.     

Molecular and morphological delimitation and generic classification of the family Oocystaceae (Trebouxiophyceae,Chlorophyta)

The family Oocystaceae (Chlorophyta) is a group of morphologically and ultrastructurally distinct green algae that constitute a well‐supported clade in the class Trebouxiophyceae. Despite the family's clear delimitation, which is based on specific cell wall features, only a few members of the Oocystaceae have been examined using data other than morphological. In previous studies of Trebouxiophyceae, after the establishment of molecular phylogeny, the taxonomic status of the family was called into question. The genus Oocystis proved to be paraphyletic and some species were excluded from Oocystaceae, while a few other species were newly redefined as members of this family. We investigated 54 strains assigned to the Oocystaceae using morphological, ultrastructural and molecular data (SSU rRNA and rbcL genes) to clarify the monophyly of and diversity within Oocystaceae. Oonephris obesa and Nephrocytium agardhianum clustered within the Chlorophyceae and thus are no longer members of the Oocystaceae. On the other hand, we transferred the coenobial Willea vilhelmii to the Oocystaceae. Our findings combined with those of previous studies resulted in the most robust definition of the family to date. The division of the family into three subfamilies and five morphological clades was suggested. Taxonomical adjustments in the genera Neglectella, Oocystidium, Oocystis, and Ooplanctella were established based on congruent molecular and morphological data. We expect further taxonomical changes in the genera Crucigeniella, Eremosphaera, Franceia, Lagerheimia, Oocystis, and Willea in the future.     

Species delimitation in northern European water scavenger beetles of the genus Hydrobius (Coleoptera,Hydrophilidae)

The chiefly Holarctic Hydrobius species complex (Coleoptera, Hydrophilidae) currently consists of Hydrobius arcticus Kuwert, 1890, and three morphological variants of Hydrobius fuscipes (Linnaeus, 1758): var. fuscipes, var. rottenbergii and var. subrotundus in northern Europe. Here molecular and morphological data are used to test the species boundaries in this species complex. Three gene segments (COI, H3 and ITS2) were sequenced and analyzed with Bayesian methods to infer phylogenetic relationships. The Generalized Mixed Yule Coalescent (GMYC) model and two versions of the Bayesian species delimitation method BPP, with or without an a priori defined guide tree (v2.2 & v3.0), were used to evaluate species limits. External and male genital characters of primarily Fennoscandian specimens were measured and statistically analyzed to test for significant differences in quantitative morphological characters. The four morphotypes formed separate genetic clusters on gene trees and were delimited as separate species by GMYC and by both versions of BPP, despite specimens of Hydrobius fuscipes var. fuscipes and Hydrobius fuscipes var. subrotundus being sympatric. Hydrobius arcticus and Hydrobius fuscipes var. rottenbergii could only be separated genetically with ITS2, and were delimited statistically with GMYC on ITS2 and with BPP on the combined data. In addition, six or seven potentially cryptic species of the Hydrobius fuscipes complex from regions outside northern Europe were delimited genetically. Although some overlap was found, the mean values of six male genital characters were significantly different between the morphotypes (p < 0.001). Morphological characters previously presumed to be diagnostic were less reliable to separate Hydrobius fuscipes var. fuscipes from Hydrobius fuscipes var. subrotundus, but characters in the literature for Hydrobius arcticus and Hydrobius fuscipes var. rottenbergii were diagnostic. Overall, morphological and molecular evidence strongly suggest that Hydrobius arcticus and the three morphological variants of Hydrobius fuscipes are separate species and Hydrobius rottenbergii Gerhardt, 1872, stat. n. and Hydrobius subrotundus Stephens, 1829, stat. n. are elevated to valid species. An identification key to northern European species of Hydrobius is provided.     

中国二头孢盘菌属的分类研究（英文）

提供了中国二头孢盘菌属的分类研究概况和已知种类。对属的概念进行了修订;基于形态学特征和序列分析的结果,将兰斯盘菌属的3个种转入二头孢盘菌属,建立3个新组合(黄二头孢盘菌、黄山二头孢盘菌、暗丝二头孢盘菌);描述了一新种(缩孢二头孢盘菌)。该属目前已知的10个种中,在我国分布9个种。编制了该属世界已知种的分种检索表。     

Phylogenetic relationships of green algae assigned to the genus Planophila (Chlorophyta): evidence from 18S rDNA sequence data and ultrastructure

Phylogenetic analyses, based upon nuclear small-subunit ribosomal RNA gene sequences, of four ‘chlorosarcinoid’ species referred to Planophila Gerneck show that the genus is polyphyletic. The type species, P. laetevirens Gerneck, is closely related to species in the Ulotrichales, Ulvophyceae. The monotypic sarcinoid genus Pseudendocloniopsis is the closest relative of Planophila; the two genera represent the addition of a new morphological type to the Ulotrichales. Planophila microcystis (Dangeard) Kornmann & Sahling forms a clade at the base of the Ulvophyceae with Oltmannsiellopsis, and thus belongs to the Oltmannsiellopsidales. This result is also supported by the Oltmannsiellopsis-like ultrastructure of P. microcystis zoospores. Planophila sp. B from Antarctica, which has Trebouxia-like pyrenoid structure, is a trebouxiophyte closely related to Chlorella-like unicellular coccoids, Stichococcus bacillaris and Prasiola species. This is the first robustly supported molecular phylogenetic analysis that places Prasiola in the Trebouxiophyceae. As shown previously, P. terrestris Groover & Hofstetter belongs to the Chaetopeltidales, Chlorophyceae. Dangemannia gen. nov. (type species : D. microcystis (Dangeard) comb. nov.), Floydiella gen. nov. (type species : F. terrestris (Groover & Hofstetter) comb. nov.) and Pabia gen. nov. (type: P. signiensis sp. nov.) are proposed.     

Taxonomic revision of the genus Galictis (Carnivora: Mustelidae): species delimitation,morphological diagnosis,and refined mapping of geographical distribution

Although critical for enabling in‐depth evolutionary, ecological, or conservation‐orientated studies, taxonomic knowledge is still scarce for many groups of organisms, including mammals of the order Carnivora. For some of these taxa, even basic aspects such as species limits and geographical distribution are still uncertain. This is the case for the Neotropical mustelid genus Galictis, considered one of the least studied carnivoran genera in the Americas. To address this issue, we performed a comprehensive assessment of morphological and molecular characters to test the number of species within Galictis, and to characterize their distinctiveness and evolutionary history. In addition, we reviewed and consolidated the available information on the taxonomy of this genus, so as to provide a historical framework upon which we could interpret our data. Our analyses demonstrated that two Galictis species can be clearly delimited and diagnosed using metric and nonmetric morphological characters as well as DNA sequences from mitochondrial and nuclear gene segments. On the basis of this clarified species‐level delimitation, we reassessed the geographical range of each Galictis taxon, identifying possible areas of sympatry between them. These results provide a solid taxonomic framework for Galictis, enabling the development of additional studies focusing on this poorly known taxon. © 2013 The Linnean Society of London, Zoological Journal of the Linnean Society, 2013, 167 , 449–472.     

Taxonomic review of the genus Trisopterus(Teleostei: Gadidae) with recognition of the capelan Trisopterus capelanus as a valid species

Trisopterus is demonstrated to be monophyletic, including four distinct species: T. capelanus, T. esmarkii, T. luscus and T. minutus. The capelan T. capelanus is resurrected from the synonymy of poor cod T. minutus, and is shown to be morphologically more similar to T. luscus, to which species it is also more closely related, indicated by a phylogenetic analysis presented here. A lectotype is designated for T. luscus. Trisopterus fasciatus, the type species of Trisopterus, is a junior synonym of T. luscus, and the lectotype of T. luscus is designated as the neotype of T. fasciatus. The lectotype of T. luscus is also designated as the neotype of Gadus barbatus. Gadus barbatus has priority over T. luscus but the name is suppressed by prevailing usage of T. luscus. A neotype is designated also for T. minutus. A phylogenetic analysis using mitochondrial cytochrome b, and a fragment of the nuclear rhodopsin gene, shows that T. capelanus and T. luscus are sister species, and in turn sister to a clade formed by T. minutus and T. esmarkii.     

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

The monotypic genus Auxenochlorella with its type species 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 in this study revealed that all strains showed similar morphology but differed in their SSU and ITS rDNA sequences. The Hydra endosymbiont formed a 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.     

Large-scale diversity reassessment,evolutionary history,and taxonomic revision of the green macroalgae family Udoteaceae (Bryopsidales,Chlorophyta)

Udoteaceae is a morphologically diverse family of the order Bryopsidales. Despite being very widespread geographically, this family is little known as compared with the closely related Halimedaceae or Caulerpaceae. Using the most extensive Udoteaceae collection to date and a multilocus genetic data set (tufA, rbcL, and 18S rDNA), we reassessed the species diversity of the family, as well as the phylogenetic relationships, the diagnostic morphoanatomical characters, and evolutionary history of its genera, toward a proposed taxonomic revision. Our approach included a combination of molecular and morphological criteria, including species delimitation methods, phylogenetic reconstruction, and mapping of trait evolution. We successfully delimited 62 species hypotheses, of which 29 were assigned (existing) species names and 13 represent putative new species. Our results also led us to revise the genera Udotea s.s., Rhipidosiphon s.s., and Chlorodesmis s.s., to validate the genus Rhipidodesmis, and to propose three new genera: Glaukea gen. nov., Ventalia gen. nov., and Udoteopsis gen. nov. We also identified two large species complexes, which we refer to as the “Penicillus–Rhipidosiphon–Rhipocephalus–Udotea complex” and the “Poropsis–Penicillus–Rhipidodesmis complex”. Using a time-calibrated phylogeny, we estimated the origin of the family Udoteaceae at Late Triassic (ca. 216 Ma), whereas most of the genera originated during Paleogene. Our morphological inference results indicated that the thallus of the Udoteaceae ancestor was likely entirely corticated and calcified, composed of a creeping axis with a multisiphonous stipe and a pluristromatic flabellate frond. The frond shape, cortication, and calcification are still symplesiomorphies for most extant Udoteaceae genera and represent useful diagnostic characters.     

New genus Koliellopsis (Trebouxiophyceae, Chlorophyta): its phylogenetic position inferred from ultrastructure and nuclear ribosomal DNA sequences

Koliellopsis inundata Lokhorst gen. & sp. nov. (Trebouxiophyceae) is described from periodically flooded agricultural fields in the borderland of Belgium and the Netherlands. This new, unbranched, filamentous alga is typified by relatively long vegetative cells, which have a bilobed, laminate chloroplast with a nucleus positioned in its median constriction. Its filaments lack a distinct basal‐distal differentiation and both ends terminate in about equally shaped, rounded or, more often (slightly) tapering cells. Despite its semiterres‐trial occurrence the new alga does not attach to hard substrate, presumably owing to the lack of end cells to produce mucilage and to function as a holdfast. The systematic position of Koliellopsis among the green algae is inferred from ultrastructural examinations of the cell division patterns and from phylogenetic analyses of partial 18S rRNA gene sequences.     

Widespread desert affiliation of trebouxiophycean algae (Trebouxiophyceae,Chlorophyta) including discovery of three new desert genera

Unlike most other green algae, trebouxiophyceans are predominantly aerophytic and contain many symbiotic representatives. In recent years, a number of new terrestrial trebouxiophycean taxa were described from soils, tree bark, and lichens. The present phylogenetic study reveals three new lineages of free‐living trebouxiophyceans found in North American desert soil crusts and proposes new generic names to accommodate them: Desertella, Eremochloris, and Xerochlorella. This survey of desert isolates also led to discovery of representatives of seven existing genera of trebouxiophyceans. Two of these genera have never been reported to contain desert representatives and one was known previously only from aquatic habitats. Furthermore, we expand the known geographic range of the recently described genus Chloropyrula, heretofore only known from the Ural Mountains. We demonstrate that the diversity of trebouxiophyceans is still underestimated and poorly understood, and that most major trebouxiophycean lineages contain desert‐dwelling taxa.     

Taxonomic revision of oil‐producing green algae,Chlorococcum oleofaciens (Volvocales,Chlorophyceae), and its relatives

Historically, species in Volvocales were classified based primarily on morphology. Although the taxonomy of Chlamydomonas has been re‐examined using a polyphasic approach including molecular phylogeny, that of Chlorococcum (Cc.), the largest coccoid genus in Volvocales, has yet to be reexamined. Six species thought to be synonymous with the oil‐producing alga Cc. oleofaciens were previously not confirmed by molecular phylogeny. In this study, seven authentic strains of Cc. oleofaciens and its putative synonyms, along with 11 relatives, were examined based on the phylogeny of the 18S ribosomal RNA (rRNA) gene, comparisons of secondary structures of internal transcribed spacer 1 (ITS1) and ITS2 rDNA, and morphological observations by light microscopy. Seven 18S rRNA types were recognized among these strains and three were distantly related to Cc. oleofaciens. Comparisons of ITS rDNA structures suggested possible separation of the remaining four types into different species. Shapes of vegetative cells, thickness of the cell walls in old cultures, the size of cells in old cultures, and stigma morphology of zoospores also supported the 18S rRNA grouping. Based on these results, the 18 strains examined were reclassified into seven species. Among the putative synonyms, synonymy of Cc. oleofaciens, Cc. croceum, and Cc. granulosum was confirmed, and Cc. microstigmatum, Cc. rugosum, Cc. aquaticum, and Cc. nivale were distinguished from Cc. oleofaciens. Furthermore, another related strain is described as a new species, Macrochloris rubrioleum sp. nov.     

Chloroplast gene arrangement variation within a closely related group of green algae (Trebouxiophyceae, Chlorophyta)

The 22 published chloroplast genomes of green algae, representing sparse taxonomic sampling of diverse lineages that span over one billion years of evolution, each possess a unique gene arrangement. In contrast, many of the >190 published embryophyte (land plant) chloroplast genomes have relatively conserved architectures. To determine the phylogenetic depth at which chloroplast gene rearrangements occur in green algae, a 1.5-4 kb segment of the chloroplast genome was compared across nine species in three closely related genera of Trebouxiophyceae (Chlorophyta). In total, four distinct gene arrangements were obtained for the three genera Elliptochloris, Hemichloris, and Coccomyxa. In Elliptochloris, three distinct chloroplast gene arrangements were detected, one of which is shared with members of its sister genus Hemichloris. Both species of Coccomyxa examined share the fourth arrangement of this genome region, one characterized by very long spacers. Next, the order of genes found in this segment of the chloroplast genome was compared across green algae and land plants. As taxonomic ranks are not equivalent among different groups of organisms, the maximum molecular divergence among taxa sharing a common gene arrangement in this genome segment was compared. Well-supported clades possessing a single gene order had similar phylogenetic depth in green algae and embryophytes. When the dominant gene order of this chloroplast segment in embryophytes was assumed to be ancestral for land plants, the maximum molecular divergence was found to be over two times greater in embryophytes than in trebouxiophyte green algae. This study greatly expands information about chloroplast genome variation in green algae, is the first to demonstrate such variation among congeneric green algae, and further illustrates the fluidity of green algal chloroplast genome architecture in comparison to that of many embryophytes.     

With eyes wide open: a revision of species within and closely related to the Pocillopora damicornis species complex (Scleractinia; Pocilloporidae) using morphology and genetics

Molecular studies have been instrumental for refining species boundaries in the coral genus Pocillopora and revealing hidden species diversity within the extensively studied global species Pocillopora damicornis. Here we formally revise the taxonomic status of species closely related to and within the P. damicornis species complex, taking into account both genetic evidence and new data on morphometrics, including fine‐scale corallite and coenosteum structure. We found that mitochondrial molecular phylogenies are congruent with groups based on gross‐morphology, therefore reflecting species‐level differentiation. However, high levels of gross morphological plasticity and shared morphological characteristics mask clear separation for some groups. Fine‐scale morphological variation, particularly the shape and type of columella, was useful for differentiating between clades and provides an excellent signature of the evolutionary relationships among genetic lineages. As introgressive hybridization and incomplete lineage sorting complicate the delineation of species within the genus on the basis of a single species concept, the Unified Species Concept may represent a suitable approach in revising Pocillopora taxonomy. Eight species are herein described (P. damicornis, P. acuta, P. aliciae, P. verrucosa, P. meandrina, P. eydouxi, P. cf. brevicornis), including a novel taxon – P ocillopora bairdi sp. nov. (Schmidt‐Roach, this study). Citation synonyms and type materials are presented. © 2014 The Linnean Society of London     

Multilocus phylogeny and species delimitation within the genus Glauconycteris (Chiroptera,Vespertilionidae), with the description of a new bat species from the Tshopo Province of the Democratic Republic of the Congo

The genus Glauconycteris Dobson, 1875 currently contains 12 species of butterfly bats, all endemic to sub‐Saharan Africa. Most species are rarely recorded, with half of the species known from less than six geographic localities. The taxonomic status of several species remains problematic. Here, we studied the systematics of butterfly bats using both morphological and molecular approaches. We examined 45 adult specimens for external anatomy and skull morphology, and investigated the phylogeny of Glauconycteris using DNA sequences from three mitochondrial genes and 116 individuals, which in addition to outgroup taxa, included nine of the twelve butterfly bat species currently recognized. Four additional nuclear genes were sequenced on a reduced sample of 69 individuals, covering the outgroup and Glauconycteris species. Our molecular results show that the genus Glauconycteris is monophyletic, and that it is the sister‐group of the Asian genus Hesperoptenus. Molecular dating estimates based on either Cytb or RAG2 data sets suggest that the ancestor of Glauconycteris migrated into Africa from Asia during the Tortonian age of the Late Miocene (11.6–7.2 Mya), while the basal diversification of the crown group occurred in Africa at around 6 ± 2 Mya. The species G. superba is found to be the sister‐group of G. variegata, questioning its placement in the recently described genus Niumbaha. The small species living in tropical rainforests constitute a robust clade, which contains three divergent lineages: (i) the “poensis” group, which is composed of G. poensis, G. alboguttata, G. argentata, and G. egeria; (ii) the “beatrix” group, which contains G. beatrix and G. curryae; and (iii) the “humeralis” group, which includes G. humeralis and a new species described herein. In the “poensis” group, G. egeria is found to be monophyletic in the nuclear tree, but polyphyletic in the mitochondrial tree. The reasons for this mito‐nuclear discordance are discussed.     

Prasiolales (Trebouxiophyceae,Chlorophyta) of the Svalbard Archipelago: diversity,biogeography and description of the new genera Prasionella and Prasionema

Species of Prasiolales (Trebouxiophyceae, Chlorophyta) are among the most common terrestrial and freshwater algae in polar regions. Comprehensive molecular studies of this group are available for Antarctica, but not yet for Arctic regions. We examined the diversity of the Prasiolales in the Svalbard Archipelago combining morphological observations of field-collected material, culture studies, molecular data (plastid rbcL and tufA sequences) and literature records. We confirmed the widespread occurrence of Prasiola crispa and P. fluviatilis, species recorded from Spitsbergen since the 19th century. Molecular phylogenetic analyses led to the discovery of two new genera of Prasiolales. Prasionema payeri is morphologically identical to filamentous stages of P. crispa, but represents an early-diverging lineage in the order. Prasionella wendyae is a colonial alga reproducing by aplanospores; its phylogenetic position is among the basal lineages of the order, but it could not be reliably reconstructed due to weak statistical support. The inclusion of P. wendyae in the prasiolalean phylogeny determined the paraphyly of Rosenvingiella, requiring the establishment of the new genus Rosenvingiellopsis for R. constricta. A poorly known species described from Spitsbergen, Ulothrix discifera, is transferred here to Rosenvingiella. Whereas some species of Prasiolales have bipolar distribution (P. crispa), others appear to be restricted to one or other of the poles. Our results suggest that polar regions are still a major repository of unknown algal diversity and highlight the importance of continued field surveys and the use of molecular data.     

Lunachloris lukesovae gen. et sp. nov. (Trebouxiophyceae,Chlorophyta), a novel coccoid green alga isolated from soil in South Bohemia,Czech Republic

Culture collections of microorganisms can still hold undiscovered biodiversity; with molecular techniques, considerable progress has been made in characterizing microalgae which were isolated in the past and misidentified due to a lack of morphological features. However, many strains are still awaiting taxonomic reassessment. Here we analysed the phylogenetic position, morphology and ultrastructure of the strain CCALA 307 previously identified as Coccomyxa cf. gloeobotrydiformis Reysigl isolated in 1987 from field soil in South Bohemia, Czech Republic. Molecular phylogenetic analyses based on SSU rDNA and the plastid rbcL gene revealed that the strain CCALA 307 formed a distinct sister lineage to Neocystis and Prasiola clades within the Trebouxiophyceae. We describe this strain as a new genus and species, Lunachloris lukesovae. Multiple conserved nucleotide positions identified in the secondary structures of the highly variable ITS2 rDNA barcoding marker provide further evidence of the phylogenetic position of Lunachloris. Minute vegetative cells of this newly recognized species are spherical or ellipsoid, with a single parietal chloroplast without a pyrenoid. Asexually, it reproduces by the formation of 2–6 autospores. Since the majority of recent attention has been paid to algae from the tropics or extreme habitats, the biodiversity of terrestrial microalgae in temperate regions is still notably unexplored and even a ‘common’ habitat like agricultural soil can contain new, as yet unknown species. Moreover, this study emphasizes the importance of culture collections of microorganisms even in the era of culture-independent biodiversity research, because they may harbour novel and undescribed organisms as well as preserving strains for future studies.