Phylogeny and biogeography of the lamioid genus <Emphasis Type="Italic">Phlomis</Emphasis> (Lamiaceae)

The genus Phlomis is one of the largest genera of subfamily Lamioideae (Lamiaceae) with more than 100 recognised species distributed in Asia, southern Europe and northern Africa. Morphological studies have suggested that the species can be split into two morphologically distinct groups that have previously been recognised as either sections or separate genera. The current study represents the first molecular phylogenetic study of the genus in which taxa representative of the entire genus are included. In contrast to considerable morphological and ecological variation among taxa, sequence variation in the trnL intron, the trnL – F intergenic spacer, and the rps16 intron was low, resulting in sparse phylogenetic resolution, particularly among the South West Asian and Mediterranean taxa. However, the results support a split of the genus into two separate groups that are recognised here as the genera Phlomoides and Phlomis in order to decrease taxonomic complexity. The close relationship between Phlomis s.l. and Eremostachys, pointed out by several authors, is confirmed, and in a noteworthy new finding, the small Asian genus Notochaete, is more closely related to the Phlomis s.l. lineage than previously assumed. The two monotypic genera Pseuderemostachys and Lamiophlomis as well as Notochaete hamosa are transferred to Phlomoides and three new combinations are made. Character optimisation analyses based on geographic distributions of all taxa show that the groups obtained by molecular phylogenetic analysis correlate well with biogeography. The results suggest that the Phlomis s.l. lineage has a Central Asian origin in an area around Western China.     

Sibling species of fragrant orchids (Gymnadenia: Orchidaceae, Magnoliophyta) in Russia

Recent molecular phylogenetic studies of the genus Gymnadenia have demonstrated that it contains sibling taxa, i.e., species that are hardly distinguishable according to morphological traits, yet are phylogenetically rather distant and distinctly distinguishable by molecular methods, which is a rare phenomenon for angiosperms. By sequencing the ITS1-5.8S rDNA-ITS2 fragment the presence of G. densiflora was confirmed for Russia. Our data supported a high degree of genetic differentiation between G. conopsea s. str. and G. densiflora, which confirms their taxonomic rank of species. Morphological analysis has shown that the features that are best for the discrimination between these two species in Northwestern Russia are the length of the lower bract, length of the mid-lobe of the lip, and width of leaves. The ecological and phenological differentiation between G. conopsea s. str. and G. densiflora is briefly reviewed. The ITS sequence variation in these species has been analyzed; the molecular genetic differences of the G. conopsea individuals from the eastern part of the distribution area have been discovered for the first time. Different taxonomic interpretations of Gymnadenia phylogenetic tree topology taking into account the presence of sibling species are discussed in general.     

Chromosome analysis of five Brazilian species of poison frogs (Anura: Dendrobatidae)

Dendrobatid frogs have undergone an extensive systematic reorganization based on recent molecular findings. The present work describes karyotypes of the Brazilian species Adelphobates castaneoticus, A. quinquevittatus, Ameerega picta, A. galactonotus and Dendrobates tinctorius which were compared to each other and with previously described related species. All karyotypes consisted of 2n = 18 chromosomes, except for A. picta which had 2n = 24. The karyotypes of the Adelphobates and D. tinctorius species were highly similar to each other and to the other 2n = 18 previously studied species, revealing conserved karyotypic characteristics in both genera. In recent phylogenetic studies, all Adelphobates species were grouped in a clade separated from the Dendrobates species. Thus, we hypothesized that their common karyotypic traits may have a distinct origin by chromosome rearrangements and mutations. In A. picta, with 2n = 24, chromosome features of pairs from 1 to 8 are shared with other previously karyotyped species within this genus. Hence, the A. picta data reinforced that the C-banding pattern and the NOR location are species-specific traits in the genus Ameerega. Moreover, the Ameerega monophyletism proposed by previous phylogenetic studies indicates that the karyotypic differences among species in this genus result from a long divergence time.     

MORPHOLOGY AND MOLECULAR PHYLOGENY OF ANKISTRODINIUM GEN. NOV. (DINOPHYCEAE), A NEW GENUS OF MARINE SAND‐DWELLING DINOFLAGELLATES FORMERLY CLASSIFIED WITHIN AMPHIDINIUM1

The classical athecate dinoflagellate genera (Amphidinium, Gymnodinium, Gyrodinium) have long been recognized to be polyphyletic. Amphidinium sensu lato is the most diverse of all marine benthic dinoflagellate genera; however, following the redefinition of this genus ～100 species remain now of uncertain or unknown generic affiliation. In an effort to improve our taxonomic and phylogenetic understanding of one of these species, namely Amphidinium semilunatum, we re‐investigated organisms from several distant sites around the world using light and scanning electron microscopy and molecular phylogenetic methods. Our results enabled us to describe this species within a new heterotrophic genus, Ankistrodinium. Cells of A. semilunatum were strongly laterally flattened, rounded‐quadrangular to oval in lateral view, and possessed a small asymmetrical epicone. The sulcus was wide and characteristically deeply incised on the hypocone running around the antapex and reaching the dorsal side. The straight acrobase with hook‐shaped end started at the sulcal extension and continued onto the epicone. The molecular phylogenetic results clearly showed that A. semilunatum is a distinct taxon and is only distantly related to species within the genus Amphidinium sensu stricto. The nearest sister group to Ankistrodinium could not be reliably determined.     

Molecular phylogenetics and evolution of Orchidinae and selected Habenariinae (Orchidaceae)

Internal transcribed spacer (ITS nuclear rDNA) data have been obtained from 190 terrestrial orchid species, encompassing all genera and the great majority of the widely recognized species of Orchidinae, a heterogeneous selection of species of Habenariinae, and single species of Satyriinae and Disinae (the latter serving as outgroup). The resulting parsimony‐based phylogeny reveals 12 well‐resolved clades within the Orchidinae, based on Anacamptis s.l., Serapias, Ophrys, Steveniella–Himantoglossum s.l. (including ‘Comperia’ and ‘Barlia’, most species being 2n = 36), Neotinea s.l., Traunsteinera–Chamorchis, Orchis s.s., Pseudorchis–Amerorchis–Galearis–Neolindleya–Platanthera s.l. (most 2n = 42), Dactylorhiza s.l., Gymnadenia s.l. (most 2n = 40, 80), Ponerorchis s.l.–Hemipilia s.l.–Amitostigma–Neottianthe, and Brachycorythis (most 2n = 42). Relationships are less clearly resolved among these 12 clades, as are those within Habenariinae; the subtribe appears either weakly supported as monophyletic or as paraphyletic under maximum parsimony, and the species‐rich genus Habenaria is clearly highly polyphyletic. The triphyly of Orchis as previously delimited is confirmed, and the improved sampling allows further generic transfers to Anacamptis s.l. and Neotinea s.l. In addition, justifications are given for: (1) establishing Steveniella as the basally divergent member of an appreciably expanded Himantoglossum that incorporates the former genera ‘Barlia’ and ‘Comperia’, (2) reuniting ‘Piperia’ with a broadly defined Platanthera as section Piperia, necessitating ten new combinations, (3) broadening Ponerorchis to include Chusua, and Hemipilia to include single ‘orphan’ species of Ponerorchis and Habenaria, and (4) recognizing ‘Gymnadenia’camtschatica as the monotypic Neolindleya camtschatica within the Pseudorchis～Platanthera clade. Few further generic transfers are likely in Orchidinae s.s., but they are anticipated among habenariid genera, on acquisition of additional morphological and molecular evidence; one probable outcome is expansion of Herminium. Species‐level relationships are also satisfactorily resolved within most of the major clades of Orchidinae, with the notable exceptions of Serapias, the derived sections of Ophrys, Himantoglossum s.s., some sections within Dactylorhiza, the former genus ‘Nigritella’ (now tentatively placed within Gymnadenia s.l.), Hemipilia s.l., and possibly Ponerorchis s.s. Relationships among the 12 major clades broadly accord with bona fide records of intergeneric hybridization. Current evidence supports the recently recognized 2n = 36 clade; it also indicates a 2n = 40 clade that is further diagnosed by digitate root‐tubers, and is derived relative to the recently recognized clade of exclusively Asian genera (Ponerorchis s.l.–Hemipilia s.l.–Amitostigma–Neottianthe). This in turn appears derived relative to the Afro‐Asiatic Brachycorythis group; together, these two clades identify the plesiomorphic chromosome number as 2n = 42. If the African genus Stenogolottis is correctly placed as basally divergent within a monophyletic Habenariinae, the tribe Orchideae and subtribes Orchidinae and Habenariinae could all have originated in Africa, though in contrast the Asiatic focus of the basally divergent members of most major clades of Orchidinae suggests an Asiatic radiation of the subtribe. Morphological characters informally ‘mapped’ across the molecular phylogeny and showing appreciable levels of homoplasy include floral and vegetative pigmentation, flower shape, leaf posture, gynostemium features, and various pollinator attractants. Qualitative comparison of, and reciprocal illumination between, degrees of sequence and morphological divergence suggests a nested set of radiations of progressively decreasing phenotypic magnitude. Brief scenarios, both adaptive and non‐adaptive, are outlined for specific evolutionary transitions. Recommendations are made for further species sampling, concentrating on Asian Orchidinae (together with the Afro‐Asiatic Brachycorythis group) and both Asian and Southern Hemisphere Habenariinae, and adding plastid sequence data. Taxonomic changes listed are: Anacamptis robusta (T.Stephenson) R.M.Bateman, comb. nov. , A. fragrans (Pollini) R.M.Bateman, comb. nov. , A. picta (Loiseleur) R.M.Bateman, comb. nov. , Neotinea commutata (Todari) R.M.Bateman, comb. nov. , N. conica (Willdenow) R.M.Bateman, comb. nov. , Platanthera elegans Lindley ssp. maritima (Rydberg) R.M.Bateman, comb. nov. , P. elegans Lindley ssp. decurtata (R.Morgan & Glicenstein) R.M.Bateman, comb. nov. , P. elongata (Rydberg) R.M.Bateman, comb. nov. , P. michaelii (Greene) R.M.Bateman, comb. nov. , P. leptopetala (Rydberg) R.M.Bateman, comb. nov. , P. transversa (Suksdorf) R.M.Bateman, comb. nov. , P. cooperi (S.Watson) R.M.Bateman, comb. nov. , P. colemanii (R.Morgan & Glicenstein) R.M.Bateman, comb. nov. , P. candida (R.Morgan & Ackerman) R.M.Bateman, comb. nov. and P. yadonii (R.Morgan & Ackerman) R.M.Bateman, comb. nov. © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society, 2003, 142 , 1–40.     

Refuting the six‐genus classification of Penaeus s.l. (Dendrobranchiata,Penaeidae): a combined analysis of mitochondrial and nuclear genes

Ma, K. Y., Chan, T. ‐Y & Chu, K. H. (2011). Refuting the six‐genus classification of Penaeus s.l. (Dendrobranchiata, Penaeidae): a combined analysis of mitochondrial and nuclear genes. —Zoologica Scripta, 40, 498–508. The taxonomic revision in 1997 of the shrimps formerly classified in Penaeus s.l. has been one of the most controversial issues on systematics of the decapods in recent years. Since Pérez Farfante & Kensley (Penaeoid and Sergestoid Shrimps and Prawns of the World, 1997) split this long‐accepted taxon into six genera, much debate has been devoted to their proposed new classification scheme; this has taken place because there are serious doubts whether the said scheme could reflect the evolutionary relationships among the 29 Penaeus s.l. species. Although these shrimps can be easily separated into several groups morphologically, whether these subdivisions are truly monophyletic and warrant a generic rank continues to be hotly debated among taxonomists. This study examined a total of 2425 bp sequences from three nuclear protein genes (enolase, phosphoenolpyruvate carboxykinase and sodium–potassium ATPase α‐subunit), and the mitochondrial 16S and 12S rRNA gene of 18 Penaeus s.l. shrimps and 13 other species in the family Penaeidae. Our phylogenetic analyses strongly support the monophyly of Penaeus s.l. and, concurring with previous studies that used the mitochondrial genes alone, the paraphyly of both Penaeus s.s. (sensu Pérez Farfante & Kensley, Penaeoid and Sergestoid Shrimps and Prawns of the World, 1997) and Melicertus, rendering them non‐natural groupings. Our study reveals two lineages: Penaeus s.s. + Fenneropenaeus + Litopenaeus + Farfantepenaeus and Melicertus + Marsupenaeus, which exhibit genetic divergences comparable with those among other penaeid genera. However, all the morphological characters, which are emphasized by Pérez Farfante and Kensley and used to separate Penaeus s.l., do not correlate with the grouping revealed by the present, perhaps decisive, phylogenetic result. Such disparity may arise from selection on the morphology of genitalia and convergent evolution. Our molecular data clearly refute the six‐genus classification, and we advocate the restoration of the old Penaeus genus (=Penaeus s.l.) definition which is the only classification scheme with both the morphological and the molecular data being in agreement.     

Phylogeny of <Emphasis Type="Italic">Litsea</Emphasis> and related genera (Laureae-Lauraceae) based on analysis of <Emphasis Type="Italic">rpb2</Emphasis> gene sequences

The relationship between Litsea and related genera is currently unclear. Previous molecular studies on these taxa using cpDNA and nrITS were unable to produce well-resolved phylogenetic trees. In this study, we explored the potential of the rpb2 gene as a source of molecular information to better resolve the phylogenetic analysis. Although rpb2 was believed to be a single-copy gene, our cloning results showed that most species examined possessed several copies of these sequences. However, the genetic distance among copies from any one species was low, and these copies always formed monophyletic groups in our molecular trees. Our phylogenetic analyses of rpb2 data resulted in better resolved tree topologies compared to those based on cpDNA or nrITS data. Our results show that monophyly of the genus Litsea is supported only for section Litsea. As a genus, Litsea was shown to be polyphyletic. The genera Actinodaphne and Neolitsea were resolved as monophyletic groups in all analyses. They were also shown to be sisters and closer to the genus Lindera than to the genus Litsea. Our results also revealed that the genus Lindera is not a monophyletic group.     

Taxonomic Study of Korean <Emphasis Type="Italic">Scirpus</Emphasis> L. s.l. (Cyperaceae) II: Pattern of Phenotypic Evolution Inferred from Molecular Phylogeny

Scirpus L. s.l. is well known as one of the polyphyletic groups in Cyperaceae. Recent molecular phylogenetic studies clearly suggested that Scirpus s.l. should be separated into several independent genera. In this study, we intend to present the morphological variations and patterns of phenotypic evolution based on molecular phylogeny of Korean Scirpus s.l. Five genera, including 21 taxa from Korean Scirpus s.l., were examined: three species of Bolboschoenus, three species of Schoenoplectus, eight species of Schoenoplectiella including one hybrid, five species of Scirpus, and two species of Trichophorum. For morphological analyses, 23 and 48 characters were selected from vegetative and reproductive organs, respectively. Molecular phylogeny was inferred from a nuclear ribosomal internal transcribed spacer, the chloroplast rbcL gene, and the chloroplast trnL-F region. Distinct characteristics and quantitative variation was presented for identification of the five genera and their species. A pronounced pattern of morphological character change was reduction, although many other character states seem to be homoplastic. We suggest that the reduction of phenotypic characteristics has been expressed in terms of condensation of internodes, reduction of leaf blade, and simplification of inflorescence among five genera of Korean Scirpus s.l.     

Phylogenetic relationships of the enigmatic species Serratula chinensis and Serratula forrestii (Asteraceae - Cardueae)

The phylogenetic relationships of the Chinese species Serratula forrestii and S. chinensis within the subtribe Centaureinae (Asteraceae – Cardueae) were investigated based on nuclear ribosomal DNA external and internal transcribed spacer sequences. Results indicated that Serratula s. l. is clearly polyphyletic, none of the two species showing close affinities to either Serratula s. str. or Klasea, a genus traditionally included in Serratula. Serratula forrestii has a basal position within the subtribe and has retained most plesiomorphic character states. Serratula chinensis is related to the genera of the Rhaponticum group. Its chromosome number was determined as 2n = 26, and the relationship between this species and the Rhapon-ticum group is discussed from a morphological and karyological point of view.     

Phylogenetic Position of <Emphasis Type="Italic">Corchoropsis</Emphasis> Siebold &; Zucc. (Malvaceae s.l.) Inferred from Plastid DNA Sequences

Recent phylogenetic research suggests that Malvaceae s.l. comprises formerly Tiliaceae, Byttneriaceae, Bombacaceae, and Sterculiaceae. Corchoropsis is traditionally included in Tiliaceae or Sterculiaceae and is distributed in China, Korea, and Japan. One to three species have been recognized for this genus. Phylogenetic relationships among the Malvacean taxa have been intensively studied with molecular data, and the evolution of their morphological characteristics has been re-interpreted accordingly. However, no Corchoropsis species have been included for their phylogenetic position. Here, three chloroplast coding regions—rbcL, atpB, and ndhF, from Corchoropsis psilocarpa and Corchoropsis crenata—were amplified and sequenced, then compared with other Malvacean taxa. This analysis of the three plastid gene sequences now places Corchoropsis species in Dombeyoideae, as previously proposed by Takeda (Bull Misc Inform Kew 365, 1912), Tang (Cathaya 4:131–150, 1992), and Bayer and Kubitzki (2003). Within Dombeyoideae, Corchoropsis forms a strongly supported sister relationship with the Dombeya–Ruizia clade.     

Increasing the number of molecular markers resolves the phylogenetic relationship of ‘Cepaea’ vindobonensis (Pfeiffer 1828) with Caucasotachea Boettger 1909 (Gastropoda: Pulmonata: Helicidae)

‘Cepaea’ vindobonensis has been shown to be closely related to Caucasotachea in recent molecular studies. The phylogenetic relationships within this clade and especially the phylogenetic position of ‘Cepaea’ vindobonensis were, however, not well resolved. Our phylogenetic analyses on the basis of an increased number of molecular genetic loci from the mitochondrial and nuclear genomes unambiguously demonstrate that ‘Cepaea’ vindobonensis represents the sister group of the Caucasotachea taxa, with C. leucoranea from the Caspian region of Azerbaijan and Iran being the sister species of the remaining Caucasian and eastern Pontic Caucasotachea species. We argue for the inclusion of ‘Cepaea’ vindobonensis in Caucasotachea rather than for a re‐erection of a monotypic genus Austrotachea for the species because of the overall low degree of morphological differentiation and the low number of species in the group.     

A novel clade of sporocarp-forming species of glomeromycotan fungi in the <Emphasis Type="Italic">Diversisporales</Emphasis> lineage

In the early times of taxonomy of arbuscular mycorrhizal fungi (Glomeromycota), exclusively sporocarpic species were described. Since then the focus has mainly shifted to species forming spores singly. For many of the sporocarpic species, no molecular data have been made available, and their phylogenetic position has remained unclear. We obtained small subunit ribosomal rDNA and internal transcribed spacer data from specimens of glomeromycotan sporocarps from tropical areas that were assigned to three morphospecies. The complete sequence of the 18S small rDNA subunit sequence, internal transcribed spacers (ITS) 1 and 2 and 5.8S rDNA subunit, was determined from a sporocarp of Glomus fulvum. Partial sequences of the small subunit and the other regions were obtained from Glomus pulvinatum and the newly described species Glomus megalocarpum. Molecular phylogenetic analyses placed all species analyzed as a monophyletic sister group to the Diversispora spurca/Glomus versiforme clade group (“Glomus group C”) within the Diversisporales. The phylogenetic divergence from other known species suggests that this clade may constitute a new genus. These findings will have important consequences for taxon definition in the Diversisporales. They will facilitate identification of these fungi using rDNA sequences within colonized roots or the environment. Taxonomic novelties: Glomus megalocarpum D. Redecker     

Systematic relationships within and between Peucedanum and Angelica (Umbelliferae–Peucedaneae) inferred from immunological studies of seed proteins

 Immunochemical investigation of the seed storage proteins of some large genera in the tribe Peucedaneae (Umbelliferae) has clearly demonstrated the heterogeneity of Angelica and Peucedanum and the comparative homogeneity of Ferula. Among the taxa included in Angelica, Ostericum appears to be the most distant from the type species A. sylvestris, and should be treated as an independent genus. On the contrary, Archangelica is serologically similar to Angelica s. str. A rather complicated picture has been revealed within Peucedanum s. l. Serotaxonomical studies show a relationship pattern largely corresponding to the infrageneric classification of Thellung (1926). The splitting of satellite genera from Peucedanum s. l. is only partially supported. Received June 25, 2002; accepted October 3, 2002     

Unusual intragenomic and interspecific variability of <Emphasis Type="Italic">Geobacillus</Emphasis> 16S-23S rRNA internal transcribed spacers

The aim of this study was to evaluate the inter-and intraspecific as well as intragenomic variability of Geobacillus 16S–23S rRNA internal transcribed spacers without tRNA genes and to compare these sequences with sequences bearing tRNA genes. In this study the structural analysis was performed in a unique way because the length and the sequence of the structural blocks were adjusted to fit the structure of 16S–23S rRNA internal transcribed spacers of five different Geobacillus species. Our study demonstrated the mosaic-like structure of 16S–23S rRNA internal transcribed spacers in Geobacillus. Some characteristics of these spacers of geobacilli were not previously reported for other bacteria: unusually short conserved sequence in the 5′ end region, some identical conserved blocks in both 5′ and 3′ regions of 16S–23S rRNA internal transcribed spacers, the same sequence blocks in both 16S–23S and 23S–5S rRNA intergenic spacers. Our study demonstrated quite uniform arrangement of the sequence blocks in Geobacillus thermodenitrificans. This species diverged early in the phylogenetic tree of the genus Geobacillus. For the phylogenetically recent species Geobacillus kaustophilus and Geobacillus lituanicus the low inter-and intraspecific, but high intragenomic variability, as a consequence of recent phylogenetic events, was established.