Phylogenetic position of Madagascan species of Acacia s.l. and new combinations in Senegalia and Vachellia (Fabaceae,Mimosoideae, Acacieae)

The recent worldwide effort to transfer all non‐Australian taxa of Acacia s.l. mostly to the genera Senegalia and Vachellia follows the acceptance of the proposed re‐typification of the genus with an Australian species. The Madagascan species have, as yet, not been included in phylogenetic studies of Acacia s.l. and their position in the new generic classification of Acacia s.l. is therefore still unclear. In this study, plastid DNA sequence data were generated for seven Madagascan species, included in existing matrices for Acacia s.l. and analysed to assess the placement of these species. The results indicate that the Madagascan species are placed either in Senegalia or Vachellia and conform to the morphological characters used to distinguish these genera, despite some taxa having unusual red flowers. New combinations are formalized for Senegalia baronii , S . hildebrandtii , S . kraussiana ssp. madagascariensis , S . menabeensis , S . meridionalis , S . pervillei , S . pervillei ssp. pubescens , S . polhillii , S . sakalava , S . sakalava ssp. hispida , V achellia bellula , V . myrmecophila and V . vigueri . Nomenclatural errors are also corrected for three African taxa and, as such, new combinations are provided for Senegalia fleckii , S . hamulosa and V achellia theronii . © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 288–294.     

Phylogenetic relationships,song and distribution of the endangered Rufous‐headed Robin Larvivora ruficeps

The Rufous‐headed Robin Larvivora ruficeps is one of the world's rarest and least known birds. We summarize the known records since it was first described in 1905 from Shaanxi Province, central China. All subsequent Chinese records are from seven adjacent localities in nearby Sichuan Province. We studied its phylogenetic position for the first time using mitochondrial and nuclear markers for all species of Larvivora and a broad selection of other species in the family Muscicapidae. Our results confirmed that L. ruficeps is appropriately placed in the genus Larvivora, and suggested that it is sister to the Rufous‐tailed Robin Larvivora sibilans, with these two forming a sister clade to a clade comprising both the Japanese Robin Larvivora akahige and Ryukyu Robin Larvivora komadori. Siberian Blue Robin Larvivora cyane and Indian Blue Robin Larvivora brunnea form the sister clade to the other Larvivora species. In contrast, song analyses indicated that the song of L. ruficeps is most similar to that of L. komadori, whereas the song of L. sibilans is relatively more similar to that of L. akahige, and songs of L. cyane and L. brunnea closely resemble each other. We used ecological niche modelling to estimate the suitable habitats of L. ruficeps based on the records from breeding grounds, suggesting that north and central Sichuan, south Gansu, south Shaanxi and south‐east Tibet are likely to contain the most suitable habitats for this species.     

Phylogenetic position and revised classification of Acacia s.l. (Fabaceae: Mimosoideae) in Africa,including new combinations in Vachellia and Senegalia

Previous phylogenetic studies have indicated that Acacia Miller s.l. is polyphyletic and in need of reclassification. A proposal to conserve the name Acacia for the larger Australian contingent of the genus (formerly subgenus Phyllodineae) resulted in the retypification of the genus with the Australian A. penninervis. However, Acacia s.l. comprises at least four additional distinct clades or genera, some still requiring formal taxonomic transfer of species. These include Vachellia (formerly subgenus Acacia), Senegalia (formerly subgenus Aculeiferum), Acaciella (formerly subgenus Aculeiferum section Filicinae) and Mariosousa (formerly the A. coulteri group). In light of this fragmentation of Acacia s.l., there is a need to assess relationships of the non‐Australian taxa. A molecular phylogenetic study of Acacia s.l and close relatives occurring in Africa was conducted using sequence data from matK/trnK, trnL‐trnF and psbA‐trnH with the aim of determining the placement of the African species in the new generic system. The results reinforce the inevitability of recognizing segregate genera for Acacia s.l. and new combinations for the African species in Senegalia and Vachellia are formalized. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172 , 500–523.     

Phylogenetic analysis of cultivation‐resistant terrestrial cyanobacteria with massive sheaths (Stigonema spp. and Petalonema alatum,Nostocales, Cyanobacteria) using single‐cell and filament sequencing of environmental samples

Molecular assessment of a large portion of traditional cyanobacterial taxa has been hindered by the failure to isolate and grow them in culture. In this study, we developed an optimized protocol for single cell/filament isolation and 16S rRNA gene sequencing of terrestrial cyanobacteria with large mucilaginous sheaths, and applied it to determine the phylogenetic position of typical members of the genera Petalonema and Stigonema. A methodology based on a glass‐capillary isolation technique and a semi‐nested PCR protocol enabled reliable sequencing of the 16S rRNA gene from all samples analyzed. Ten samples covering seven species of Stigonema from Europe, North and Central America, and Hawaii, and the type species of Petalonema from Slovakia were sequenced. Contrary to some previous studies, which proposed a relationship with heteropolar nostocalean cyanobacteria, Petalonema appeared to belong to the family Scytonemataceae. Analysis of Stigonema specimens recovered a unique coherent phylogenetic cluster, substantially broadening our knowledge of the molecular diversity within this genus. Neither the uni‐ to biseriate species nor the multiseriate species formed monophyletic subclusters within the genus. Typical multiseriate species of Stigonema clustered in a phylogenetic branch derived from uni‐ to biseriate S. ocellatum Thuret ex Bornet & Flahault in our analysis, suggesting that species with more complex thalli may have evolved from the more simple ones. We propose the technique tested in this study as a promising tool for a future revision of the molecular taxonomy in cyanobacteria.     

Tinocladia sanrikuensis sp. nov. (Ectocarpales s.l., Phaeophyceae) from Japan

The new species Tinocladia sanrikuensis sp. nov. H.Kawai, K.Takeuchi & T.Hanyuda (Ectocarpales s.l., Phaeophyceae) is described from the Pacific coast of the Tohoku region, northern Japan based on morphology and DNA sequences. The species is a spring–summer annual growing on lower intertidal to upper subtidal rocks and cobbles on relatively protected sites. T. sanrikuensis has a slimy, cylindrical, multiaxial erect thallus, slightly hollow when fully developed, branching once to twice, and resembles T. crassa in gross morphology. The erect thalli are composed of a dense medullary layer, long subcortical filaments, and assimilatory filaments of 11–35 cells, up to 425 μm long and curved in the upper portion. Unilocular zoidangia are formed on the basal part of assimilatory filaments. The species is genetically most closely related to T. crassa and has the same basic thallus structures but differs in having thinner and longer assimilatory filaments. DNA sequences of the mitochondrial cox1 and cox3, chloroplast atpB, psaA, psbA and rbcL genes support the distinctness of this species.     

Classification of crucigenoid algae: phylogenetic position of the reinstated genus Lemmermannia,Tetrastrum spp. Crucigenia tetrapedia,and C. lauterbornii (Trebouxiophyceae,Chlorophyta)1

The subfamily Crucigenioideae was traditionally classified within the well‐characterized family Scenedesmaceae (Chlorophyceae). Several morpho‐logical revisions and questionable taxonomic changes hampered the correct classification of crucigenoid species resulting in a high number of synonymous genera. We used a molecular approach to determine the phylogenetic position of several Tetrastrum and Crucigenia species. The molecular results were correlated with morphological and ontogenetic characters. Phylogenetic analyses of the SSU rDNA gene resolved the position of Tetrastrum heteracanthum and T. staurogeniaeforme as a new lineage within the Oocystis clade of the Trebouxiophyceae. Crucigenia tetrapedia, T. triangulare, T. punctatum, and T. komarekii were shown to be closely related to Botryococcus (Trebouxiophyceae) and were transferred to Lemmer‐mannia. Crucigenia lauterbornii was not closely related to the other Crucigenia strains, but was recovered within the Chlorella clade of the Trebouxiophyceae.     

Multilocus phylogeny and taxonomy of East Asian voles Alexandromys (Rodentia,Arvicolinae)

Phylogenetic relationships, taxonomy and nomenclature issues within East Asian voles Alexandromys were addressed using comprehensive species samples, including all 12 valid species of the genus, and multilocus analysis. We examined the mitochondrial cytochrome b (cytb) gene and three nuclear genes in 36 specimens. Additionally, we examined a data set of 106 specimens using only the cytb gene. Our results did not confirm the aggregation of A. kikuchii, A. montebelli and A. oeconomus into a separate clade, namely the subgenus Pallasiinus. Analysis of incomplete lineage sorting using JML software highlighted both the cases of mitochondrial introgression and incomplete lineage sorting within the genus. Thus, the sister position of A. sachalinensis and A. maximowiczii in mitochondrial trees could be explained by mitochondrial introgression, while the sister position of A. limnophilus and A. fortis in mitochondrial trees could be successfully explained by incomplete lineage sorting. Very short genetic distances, together with an absence of monophyly, of the three species, A. evoronensis, A. mujanensis and A. maximowiczii, is supported by multiple morphological data, which indicates that these three taxa should be one species—A. maximowiczii. Analysis of genetic distances and tree topology revealed that three species of short‐tailed voles—A. middendorffii, A. mongolicus and A. gromovi—are more closely related to each other than to other established species of Alexandromys. The lacustrine vole, A. limnophilus, is closely related to the group of short‐tailed voles. Analysis of the type specimens of limnophilus and flaviventris confirmed that these taxa form one species together with A. l. malygini. Our results suggest that the mountains of western Mongolia are inhabited by a new taxon of short‐tailed voles of the same rank as middendorffii, mongolicus and gromovi—A. m. alpinus ssp. n.     

Phylogenetic analyses of the genus Aeromonas based on housekeeping gene sequencing and its influence on systematics

The phylogenies derived from housekeeping gene sequence alignments, although mere evolutionary hypotheses, have increased our knowledge about the Aeromonas genetic diversity, providing a robust species delineation framework invaluable for reliable, easy and fast species identification. Previous classifications of Aeromonas, have been fully surpassed by recently developed phylogenetic (natural) classification obtained from the analysis of so‐called ‘molecular chronometers’. Despite ribosomal RNAs cannot split all known Aeromonas species, the conserved nature of 16S rRNA offers reliable alignments containing mosaics of sequence signatures which may serve as targets of genus‐specific oligonucleotides for subsequent identification/detection tests in samples without culturing. On the contrary, some housekeeping genes coding for proteins show a much better chronometric capacity to discriminate highly related strains. Although both, species and loci, do not all evolve at exactly the same rate, published Aeromonas phylogenies were congruent to each other, indicating that, phylogenetic markers are synchronized and a concatenated multigene phylogeny, may be ‘the mirror’ of the entire genomic relationships. Thanks to MLPA approaches, the discovery of new Aeromonas species and strains of rarely isolated species is today more frequent and, consequently, should be extensively promoted for isolate screening and species identification. Although, accumulated data still should be carefully catalogued to inherit a reliable database.     

Sorting out the Snakebirds: The species status,phylogeny, and biogeography of the Darters (Aves: Anhingidae)

Although the avian family Anhingidae is unequivocally monophyletic, the number and relationships of the component species within the single genus (Anhinga) have long remained unclear. Here, we use extensive mitochondrial and nuclear DNA sequence data (8,878 bp) to show that four species should be recognized. Our fully resolved and well‐supported tree shows that the American Anhinga (Anhinga anhinga) is sister to the three Old World species, with the Oriental (A. melanogaster) and African (A. rufa) Darters sister within the Old World clade, which also includes the Australian Darter (A. novaehollandiae). We estimate that the divergence between the New World and Old World branches occurred 19–22 mya, with the Australian Darter separating from its Old World congeners 14–16 mya and the Oriental and African species splitting ~10 mya. The genus is yet another example of osteological conservatism in the Suliformes, which is comparable to that shown by the cormorants and shags. Nevertheless, the relationships we infer are congruent with recent plumage studies and are biogeographically plausible. We suggest that further investigation of the variation within the African and Australian Darters would be of interest.     

Localization and evolution of septins in algae

Septins are a group of GTP‐binding proteins that are multi‐functional, with a well‐known role in cytokinesis in animals and fungi. Although the functions of septins have been thoroughly studied in opisthokonts (fungi and animals), the function and evolution of plant/algal septins are not as well characterized. Here we describe septin localization and expression in the green algae Nannochloris bacillaris and Marvania geminata. The present data suggest that septins localize at the division site when cytokinesis occurs. In addition, we show that septin homologs may be found only in green algae, but not in other major plant lineages, such as land plants, red algae and glaucophytes. We also found other septin homolog‐possessing organisms among the diatoms, Rhizaria and cryptomonad/haptophyte lineages. Our study reveals the potential role of algal septins in cytokinesis and/or cell elongation, and confirms that septin genes appear to have been lost in the Plantae lineage, except in some green algae.     

Phylogenetic Reappraisal of the Genus Monomorphina (Euglenophyceae) Based on Molecular and Morphological Data

A morphological and molecular examination of the genus Monomorphina was conducted on 46 strains isolated mainly from Korea. The strains were divided into two types based on morphological data: Monomorphina aenigmatica and M. pyrum ‐ like species. Phylogenetic analysis based on a combined data set of nuclear SSU and LSU and plastid SSU and LSU rDNA showed that the strains could be divided into eight clades: Clade A of M. aenigmatica, Clade B of the isolates (M. pyropsis) from Michigan, USA, Clade C of M. pseudopyrum, Clade D of the isolates (M. pyroria) from Bremen, Germany, Clade E of M. soropyrum, Clade F of M. pyriformis, Clade G of M. parapyrum, and Clade H of M. pyrum. Six of these clades came from strains that would be considered M. pyrum sensu Kosmala et Zakry?, one of which could be recognized as a traditional species (M. pyrum) and five were designated as new species; each species had unique molecular signatures at nr SSU rDNA helix 17 and 17′ and spacer E23_14′‐E23_15. The species of Monomorphina had a wide range of genetic diversity with interspecies sequence similarity of 85.6%–97.1% and intraspecies similarity of 96.4%–99.9%. Our results suggested that genetic diversity found in the M. pyrum complex justifies the recognition of a minimum of eight species within this genus, based on specific molecular signatures and gene divergence of the nr SSU rDNA sequences.     

Proteroctopus ribeti in coleoid evolution

Palaeontological data are key elements for inferring ancestral character states and the assembly of character complexes, but cephalopod fossils preserving soft tissues are very rare. The exceptionally well‐preserved, unique specimen of Jurassic Proteroctopus ribeti Fischer & Riou from the Lagerstätte of La‐Voulte‐sur‐Rhône (c. 165 Ma, France) is one of the few fossil octopod related taxa, but is rarely considered in evolutionary studies. In this paper, we used synchrotron microtomography to reappraise its external characters and for the first time, to reveal its internal structures. A unique character association is found with two fins, head fused to the body, eight well‐developed arms with cirri and two rows of oblique suckers, a gladius and absence of an ink sac. The phylogenetic analysis indicates that Proteroctopus is a basal member of the Vampyropoda. However, this result should be interpreted with caution due to the number of unknown character states in the matrix. Contrary to previous assumptions, the phylogenetic position of Proteroctopus, as well as its stratigraphic occurrence, suggest that the arrangement of biserial suckers may be the ancestral condition in Vampyropoda.     

Cyanomargarita gen. nov. (Nostocales,Cyanobacteria): convergent evolution resulting in a cryptic genus

Two populations of Rivularia‐like cyanobacteria were isolated from ecologically distinct and biogeographically distant sites. One population was from an unpolluted stream in the Kola Peninsula of Russia, whereas the other was from a wet wall in the Grand Staircase‐Escalante National Monument, a desert park‐land in Utah. Though both were virtually indistinguishable from Rivularia in field and cultured material, they were both phylogenetically distant from Rivularia and the Rivulariaceae based on both 16S rRNA and rbcLX phylogenies. We here name the new cryptic genus Cyanomargarita gen. nov., with type species C. melechinii sp. nov., and additional species C. calcarea sp. nov. We also name a new family for these taxa, the Cyanomargaritaceae.     

Phylogenetic Position and Molecular Chronology of a Colonial Green Flagellate,Stephanosphaera pluvialis (Volvocales,Chlorophyceae), among Unicellular Algae

The genus Balticola comprises a group of unicellular green flagellate algae and is composed of four species formerly classified in the genus Haematococcus. Balticola is closely related to a colonial green flagellate, Stephanosphaera pluvialis. Although the phylogeny among these genera was previously investigated based on two nuclear gene sequences, the phylogenetic sister of S. pluvialis has yet to be determined. In the present study, the species diversity of Balticola and Stephanosphaera was investigated using 18S rRNA gene sequences, and phylogenetic analyses of combined nuclear and chloroplast gene sequences were performed to understand the evolutionary origin of coloniality in Stephanosphaera. The divergence times of four colonial volvocalean flagellates from their respective unicellular sisters were also estimated. Six Balticola genotypes and a single Stephanosphaera genotype were recognized, and one Balticola genotype was resolved as the sister of S. pluvialis, showing that Balticola is a nonmonophyletic genus. The divergence time of Stephanosphaera from its nearest Balticola relative was estimated to be 4–63 million years ago, and these genera represent the most recently diverged pair of unicellular and colonial flagellates among the Volvocales.     

Taxonomic revision of Chlamydomonas subg. Amphichloris (Volvocales,Chlorophyceae), with resurrection of the genus Dangeardinia and descriptions of Ixipapillifera gen. nov. and Rhysamphichloris gen. nov.

Chlamydomonas (Cd.) is one of the largest but most polyphyletic genera of freshwater unicellular green algae. It consists of 400–600 morphological species and requires taxonomic revision. Toward reclassification, each morphologically defined classical subgenus (or subgroup) should be examined using culture strains. Chlamydomonas subg. Amphichloris is characterized by a central nucleus between two axial pyrenoids, however, the phylogenetic structure of this subgenus has yet to be examined using molecular data. Here, we examined 12 strains including six newly isolated strains, morphologically identified as Chlamydomonas subg. Amphichloris, using 18S rRNA gene phylogeny, light microscopy, and mitochondria fluorescent microscopy. Molecular phylogenetic analyses revealed three independent lineages of the subgenus, separated from the type species of Chlamydomonas, Cd. reinhardtii. These three lineages were further distinguished from each other by light and fluorescent microscopy—in particular by the morphology of the papillae, chloroplast surface, stigmata, and mitochondria—and are here assigned to three genera: Dangeardinia emend., Ixipapillifera gen. nov., and Rhysamphichloris gen. nov. Based on the molecular and morphological data, two to three species were recognized in each genus, including one new species, I. pauromitos. In addition, Cd. deasonii, which was previously assigned to subgroup “Pleiochloris,” was included in the genus Ixipapillifera as I. deasonii comb. nov.     

Molecular and morphological criteria for revision of the genus Microcoleus (Oscillatoriales,Cyanobacteria)

Ninety‐two strains of Microcoleus vaginatus (=nomenclatural‐type species of the genus Microcoleus Desmazières ex Gomont) and Phormidium autumnale Trevisan ex Gomont from a wide diversity of regions and biotopes were examined using a combination of morphological and molecular methods. Phylogenies based on the 16S rDNA and 16S‐23S ITS (partial) demonstrated that the 92 strains, together with a number of strains in GenBank, were members of a highly supported monophyletic clade of strains (Bayesian posterior probability = 1.0) distant from the species‐cluster containing the generitype of Phormidium. Similarity of the 16S rRNA gene exceeded 95.5% among all members of the Microcoleus clade, but was less than 95% between any Microcoleus strains and species outside of the clade (e.g., Phormidium sensu stricto). These findings, which are in agreement with earlier studies on these taxa, necessitate the revision of Microcoleus to include P. autumnale. Furthermore, the cluster of Phormidium species in the P. autumnale group (known as Group VII) must be moved into Microcoleus as well, and these nomenclatural transfers are included in this study. The main diacritical characters defining Microcoleus are related to the cytomorphology of trichomes, including: narrowed trichome ends, calyptra, cells shorter than wide up to more or less isodiametric, and facultative presence of sheaths. The majority of species are 4–10 μm in diameter. The possession of multiple trichomes in a common sheath is present facultatively in many but not all species.