A taxonomic reassessment of the Vittiaceae (Hypnales, Bryopsida): evidence from phylogenetic analyses of combined chloroplast and nuclear sequence data

The Vittiaceae are a small family of aquatic mosses that are defined based on gametophytic traits whose interpretation has led to conflicting taxonomic arrangements. Phylogenetic analyses of two cpDNA regions, trnL-trnF and atpB-rbcL, indicate that Vittia is nested within the Amblystegiaceae s. str., suggesting that the family Vittiaceae should not be recognized. Platylomella lescurii appears nested within the Thuidiaceae/Leskeaceae. This suggests that the series of character states shared by Vittia and Platylomella, including a differentiated leaf border, short laminal cells, stiff stems, and a thick costa, are convergent features that arose independently in unrelated lineages of aquatic Hypnales. Within the Amblystegiaceae, phylogenetic analyses of the two cpDNA regions combined with ITS sequence data show that Hypnobartlettia, Vittia elimbata spec. nov., V. pachyloma, and V. salina, despite their strong morphological similarity to aquatic Amblystegium species, form a clade that is sister to the Drepanocladus/Pseudo-calliergon complex. This combined clade is unresolved at a polytomy that includes Amblystegium serpens and a clade including all the other Amblystegium species. The occurrence of A. serpens outside the strongly supported clade including other Amblystegium species suggests that A. serpens may be better accommodated in a distinct genus. Amblystegium serpens is the type species of Amblystegium and thus retains the name. The other species are accommodated in their own genus, Hygroamblystegium, including H. fluviatile, H. humile comb. nov., H. noterophyllum, H. tenax, and H. varium.     

Phylogeny of Castanea (Fagaceae) based on chloroplast trnT-L-F sequence data

Species in the genus Castanea are widely distributed in the deciduous forests of the Northern Hemisphere from Asia to Europe and North America. They show floristic similarity but differences in chestnut blight resistance especially among eastern Asian and eastern North American species. Phylogenetic analyses were conducted in this study using sequences of three chloroplast noncoding trnT-L-F regions. The trnT-L region was found to be the most variable and informative region. The highest proportion of parsimony informative sites, more and larger indels, and higher pairwise distances between taxa were obtained at trnT-L than at the other two regions. The high A+T values (74.5%) in the Castanea trnT-L region may explain the high proportion of transversions found in this region where as comparatively lower A+T values were found in the trnL intron (68.35%) and trnL-F spacer (70.07%) with relatively balanced numbers of transitions and transversions. The genus Castanea is supported as a monophyletic clade, while the section Eucastanon is paraphyletic. C. crenata is the most basal clade and sister to the remainder of the genus. The three Chinese species of Castanea are supported as a single monophyletic clade, whose sister group contains the North American and European species. There is consistent but weak support for a sister–group relationship between the North American species and European species.     

Free‐living calamyzin chrysopetalids (Annelida) from methane seeps,anoxic basins,and whale falls

Members of Calamyzinae, a clade of free‐living and ectoparasitic chrysopetalids, are mainly associated with deep‐sea chemosynthetic environments. The three currently known free‐living calamyzin species are placed in Vigtorniella. A new free‐living calamyzin species similar to these is described here. Phylogenetic analyses of Calamyzinae using mitochondrial (cytochrome c oxidase subunit I and 16S rDNA) and nuclear (Histone H3 and 18S rDNA) loci showed that Vigtorniella and the new species form a grade with respect to an ectoparasitic clade, requiring two new genera to be erected. All free‐living calamyzins show a similar anterior end and chaetal morphology. Micospina auribohnorum gen. et sp. nov. is described for the small‐bodied new species from deep‐sea whale falls off California and methane seeps off Costa Rica. The maximum‐likelihood and Bayesian analyses show Micospina gen. nov. as sister to the ectoparasitic clade. Boudemos gen. nov. is named for the clade of two larger‐bodied species: Boudemos flokati gen. et comb. nov. and Boudemos ardabilia gen. et comb. nov., which is sister group to all other Calamyzinae. Vigtorniella is retained for the type species, Vigtorniella zaikai (Kiseleva, 1992), with the adults found amongst bacterial mats at the boundary of the hydrogen sulphide zone in the Black Sea. Micospina gen. nov., Boudemos gen. nov., and Vigtorniella form a grade of free‐living taxa that is associated with feeding on organic‐enriched sediments, and the latter two taxa display ontogenetic jaw change. Jaws are absent in Micospina auribohnorum gen. et sp. nov. and most of the calamyzin clade of parasitic forms.     

Phylogeny of Carpinus and subfamily Coryloideae (Betulaceae) based on chloroplast and nuclear ribosomal sequence data

Phylogenetic studies were conducted for Carpinus and the subfamily Coryloideae (Betulaceae) using sequences of the chloroplast matK gene, the trnL-trnF region (trnL intron, and trnL [UAA] 3' exon-trnF [GAA] intergenic spacer) and the psbA-trnH intergenic spacer, and the nuclear ribosomal ITS regions. The combined analyses of the three chloroplast regions suggest that Coryloideae is monophyletic; Ostryopsis is sister to the Carpinus - Ostrya clade; Corylus is monophyletic and sister to the Ostrya - Carpinus - Ostryopsis clade; Ostrya is paraphyletic; and within Carpinus, species of sect. Carpinus from eastern Asia form a monophyletic group, whereas the positions of C. betulus from Europe and C. caroliniana from eastern North America are unresolved within the Carpinus clade. The cpDNA tree generated in this study is largely congruent with the previously published ITS results, but the ITS tree places Carpinus sect. Distegocarpus as sister to the Ostrya - Carpinus sect. Carpinus clade. Future work is needed to examine the relationships within the Ostrya - Carpinus clade, evaluate the generic status of Ostrya, and test the phylogenetic position of Ostryopsis.     

Further investigations on the PHAEOTHAMNIOPHYCEAE using a multigene phylogeny,with descriptions of five new species

We examined 12 strains representing eight species classified in the algal class Phaeothamniophyceae (Heterokontophyta). Based upon a five-gene molecular phylogeny (nuclear-encoded SSU rRNA and plastid-encoded psaA, psbA, psbC, and rbcL) and light microscopic observations, we describe five new species: Phaeoschizochlamys santosii sp. nov., Phaeoschizochlamys siveri sp. nov., Phaeothamnion wetherbeei sp. nov., Stichogloea dopii sp. nov. and Stichogloea fawleyi sp. nov. The Phaeothamniophyceae, as delimited here, form a natural group that is sister to the Aurearenophyceae. Molecular phylogenetic analyses proved more reliable than morphological characters for distinguishing species. Evolutionary trends with the SI clade of the heterokont algae are discussed.     

The tropical African legume Scorodophloeus clade includes two undescribed Hymenostegia segregate genera and Micklethwaitia,a rare,monospecific genus from Mozambique

Legume subfamily Caesalpinioideae accommodates approximately 2250 species in 171 genera which traditionally are placed in four tribes: Caesalpinieae, Cassieae, Cercideae and Detarieae. The monophyletic tribe Detarieae includes the Amherstieae subclade which contains about 55 genera. Our knowledge of the relationships among those genera is good in some cases but for many other genera phylogenetic relationships have been unclear. The non-monophyletic nature of at least two amherstioid genera, Cynometra and Hymenostegia has also complicated the picture. During the course of a multi-disciplinary study of Hymenostegia sensu lato, which includes phylogenetic analyses based on matK and trnL data, we have recovered the “Scorodophloeus clade”, an exclusively tropical African clade of four genera which includes the eponymous genus Scorodophloeus, two undescribed generic segregates of Hymenostegia sensu lato, and the previously unsampled rare monospecific genus Micklethwaitia from Mozambique. Zenkerella is suggested as a possible sister genus to the Scorodophloeus clade. A distribution map is presented of the seven species that belong to the Scorodophloeus clade.     

Phylogenetic Framework for Trema (Celtidaceae)

We used ITS and trnL sequence data, analyzed separately and combined by MP, to explore species relationships and concepts in Trema (Celtidaceae), a pantropical genus of pioneer trees. Whether Trema is monophyletic or includes Parasponia is still unresolved. Three clades within Trema received moderate to high support, one from the New World and two from the Old World, but their relationships were not resolved. In the New World, specimens of T. micrantha formed two groups consistent with endocarp morphology. Group I, with smaller brown endocarps, is a highly supported clade sister to T. lamarckiana. Group II, with larger black endocarps, is poorly resolved with several subclades, including the highly supported T. integerrima clade. Both Old World clades contain Asian and African species, with three or more species in each region. Trema orientalis is not monophyletic: specimens from Africa formed a highly supported clade sister to T. africana, while those from Asia were sister to T. aspera from Australia.     

Phylogenetic relationships within the South American fish family Anostomidae (Teleostei,Ostariophysi, Characiformes)

Analysis of a morphological dataset containing 152 parsimony‐informative characters yielded the first phylogenetic reconstruction spanning the South American characiform family Anostomidae. The reconstruction included 46 ingroup species representing all anostomid genera and subgenera. Outgroup comparisons included members of the sister group to the Anostomidae (the Chilodontidae) as well as members of the families Curimatidae, Characidae, Citharinidae, Distichodontidae, Hemiodontidae, Parodontidae and Prochilodontidae. The results supported a clade containing Anostomus, Gnathodolus, Pseudanos, Sartor and Synaptolaemus (the subfamily Anostominae sensu Winterbottom) albeit with a somewhat different set of relationships among the species within these genera. Anostomus as previously recognized was found to be paraphyletic and is split herein into two monophyletic components, a restricted Anostomus and the new genus Petulanos gen. nov. , described herein. Laemolyta appeared as sister to the clade containing Anostomus, Gnathodolus, Petulanos, Pseudanos, Sartor and Synaptolaemus. Rhytiodus and Schizodon together formed a well‐supported clade that was, in turn, sister to the clade containing Anostomus, Gnathodolus, Laemolyta, Petulanos, Pseudanos, Sartor and Synaptolaemus. Anostomoides was sister to the clade formed by these nine genera. Leporinus as currently defined was not found to be monophyletic, although certain clades within that genus were supported, including the species with subterminal mouths in the former subgenus Hypomasticus which we recognize herein as a genus. Abramites nested in Leporinus, and Leporellus was found to be the most basal anostomid genus. The presence of cis‐ and trans‐Andean species in Abramites, Leporellus, Leporinus and Schizodon, all relatively basal genera, suggests that much of the diversification of anostomid species pre‐dates the uplift of the Andean Cordilleras circa 11.8 million years ago. Several important morphological shifts in anostomid evolution are illustrated and discussed, including instances of convergence and reversal. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 154 , 70–210.     

Evaluation of six candidate DNA barcoding loci in Ficus (Moraceae) of China

Ficus, with about 755 species, diverse habits and complicated co‐evolutionary history with fig wasps, is a notoriously difficult group in taxonomy. DNA barcoding is expected to bring light to the identification of Ficus but needs evaluation of candidate loci. Based on five plastid loci (rbcL, matK, trnH‐psbA, psbK‐psbI, atpF‐atpH) and a nuclear locus [internal transcribed spacer (ITS)], we calculated genetic distances and DNA barcoding gaps individually and in combination and constructed phylogenetic trees to test their ability to distinguish the species of the genus. A total of 228 samples representing 63 putative species in Ficus (Moraceae) of China were included in this study. The results demonstrated that ITS has the most variable sites, greater intra‐ and inter‐specific divergences, the highest species discrimination rate (72%) and higher primer universality among the single loci. It is followed by psbK‐psbI and trnH‐psbA with moderate variation and considerably lower species discrimination rates (about 19%), whereas matK, rbcL and atpF‐atpH could not effectively separate the species. Among the possible combinations of loci, ITS + trnH‐psbA performed best but only marginally improved species resolution over ITS alone (75% vs. 72%). Therefore, we recommend using ITS as a single DNA barcoding locus in Ficus.     

Phylogenetic confirmation of the genus Robbea (Nematoda: Desmodoridae,Stilbonematinae) with the description of three new species

ABSTRACT

The Stilbonematinae are a monophyletic group of marine nematodes that are characterized by a coat of thiotrophic bacterial symbionts. Among the ten known genera of the Stilbonematinae, the genus Robbea Gerlach 1956 had a problematic taxonomic history of synonymizations and indications of polyphyletic origin. Here we describe three new species of the genus, R. hypermnestra sp. nov., R. ruetzleri sp. nov. and R. agricola sp. nov., using conventional light microscopy, interference contrast microscopy and SEM. We provide 18S rRNA gene sequences of all three species, together with new sequences for the genera Catanema and Leptonemella. Both our morphological analyses as well as our phylogenetic reconstructions corroborate the genus Robbea. In our phylogenetic analysis the three species of the genus Robbea form a distinct clade in the Stilbonematinae radiation and are clearly separated from the clade of the genus Catanema, which has previously been synonymized with Robbea. Surprisingly, in R. hypermnestra sp. nov. all females are intersexes exhibiting male sexual characters. Our extended dataset of Stilbonematinae 18S rRNA genes for the first time allows the identification of the different genera, e.g. in a barcoding approach.

http://zoobank.org/urn:lsid:zoobank.org:pub:D37C3F5A-CF2B-40E6-8B09-3C72EEED60B0     

RFLP analysis of cpDNA in the genus <Emphasis Type="Italic">Hypericum</Emphasis>

The chloroplast DNA of 43 species including 16 sections from the genus Hypericum was studied by PCR-RFLP analysis. The PCR-amplified products of four cpDNA regions, trnC-trnD, psbC-trnS, trnL-trnF and rbcL were digested with four restriction endonucleases. A high level of interspecific variation was detected while intraspecific diversity was not observed. The resulting parsimony analysis indicated the monophyletic assemblage of the sections Androsaemum, Olympia, Drosocarpium and Trigynobrathys. Monophyly of Hypericum is weakly supported, but close relationships of H. perforatum and H. maculatum are indicated. The members of Ascyreia are weakly resolved, but clustering of H. kouytchense and H. oblongifolium is well supported, however, H. reptans is nested with Olympia. CpDNA profiles and the positions on the parsimony tree indicate that the chloroplast donor among the putative parents of the hybrid species H. ×inodorum is H. androsaemum.     

Taxonomic contributions to Hapalidiales (Corallinophycidae,Rhodophyta): Boreolithothamnion gen. nov., Lithothamnion redefined and with three new species and Roseolithon with new combinations

Phylogenetic analyses of rbcL gene sequences and of concatenated rbcL, psbA, and nuclear SSU rRNA gene sequences resolved the generitype of Lithothamnion, L. muelleri, in a clade with three other southern Australian species, L. kraftii sp. nov., L. saundersii sp. nov., and L. woelkerlingii sp. nov. Cold water boreal species currently classified in Lithothamnion and whose type specimens have been sequenced are transferred to Boreolithothamnion gen. nov., with B. glaciale comb. nov. as the generitype. The other species are B. giganteum comb. nov., B. phymatodeum comb. nov., and B. sonderi comb. nov., whose type specimens are newly sequenced, and B. lemoineae comb. nov., B. soriferum comb. nov., and B. tophiforme comb. nov., whose type specimens were already sequenced. Based on rbcL sequences from the type specimens of Lithothamnion crispatum, L. indicum, and L. superpositum, each is recognized as a distinct species and transferred to the recently described Roseolithon as R. crispatum comb. nov., R. indicum comb. nov., and R. superpositum com. nov., respectively. To correctly assign species to these three genera based only on morpho-anatomy, specimens must have multiporate conceptacles and some epithallial cells with flared walls. The discussion provides examples demonstrating that only with phylogenetic analyses of DNA sequences can the evolution of morpho-anatomical characters of non-geniculate corallines be understood and applied at the correct taxonomic rank. Finally, phylogenetic analyses of DNA sequences support recognition of the Hapalidiales as a distinct order characterized by having multiporate tetra/bisporangial conceptacles, and not as a suborder of Corallinales whose tetra/bisporangial conceptacles are uniporate.     

<Emphasis Type="Italic">Rovnoecus</Emphasis>, a new genus of digger wasps (Hymenoptera,Crabronidae, Pemphredoninae) from the Rovno amber

A new fossil digger wasp Rovnoecus klesovicus gen. et sp. nov. (Hymenoptera, Crabronidae, Pemphredoninae, Pemphredonini) is described from the Upper Eocene Rovno amber. The genus Rovnoecus gen. nov. is characterized by an incomplete occipital carina, partly reduced second discoidal cell, and the presence of spines on all tibiae. Rovnoecus gen. nov. is most similar to the fossil genus Eoxyloecus Budrys, 1993 from the Baltic amber. The two genera form a monophyletic group that is a sister group to the group formed by the genera Passaloecus Shuckard, 1837 and Eopinoecus Budrys, 1993. This indirectly corroborates the hypothesis of the geographically different origin of the Rovno and Baltic ambers.     

Descriptions and phylogenetic relationships of a new genus and two new species of Oligo‐Miocene cormorants (Aves: Phalacrocoracidae) from Australia

Tertiary cormorant fossils (Aves: Phalacrocoracidae) from Late Oligocene deposits in Australia are described. They derive from the Late Oligocene – Early Miocene (26–24 Mya) Etadunna and Namba Formations in the Lake Eyre and Lake Frome Basins, South Australia, respectively. A new genus, Nambashag gen. nov. , with two new species ( Nambashag billerooensis sp. nov. , 30 specimens; Nambashag microglaucus sp. nov. , 14 specimens), has been established. Phylogenetic analyses based on 113 morphological and two integumentary characters indicated that Nambashag is the sister taxon to the Early Miocene Nectornis miocaenus of Europe and all extant phalacrocoracids. As Nambashag, Nectornis, and extant phalacrocoracids constitute a strongly supported clade sister to Anhinga species, the fossil taxa have been referred to Phalacrocoracidae. Sulids and Fregata were successive sister taxa to the Phalacrocoracoidea, i.e. phalacrocoracids + Anhinga. As phalacrocoracids lived in both Europe and Australia during the Late Oligocene and no older phalacrocoracid taxa are known, the biogeographical origin of cormorants remains unanswered. The phylogenetic relationships of extant taxa were not wholly resolved, but contrary to previous morphological analyses, considerable concordance was found with relationships recovered by recent molecular analyses. Microcarbo is sister to all other extant phalacrocoracids, and all Leucocarbo species form a well‐supported clade. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 163 , 277–314.     

A new genus in the diverse Andean Pedaliodes complex uncovered using target enrichment (Lepidoptera,Nymphalidae)

A new genus of Neotropical Satyrinae butterflies, Viloriodes Pyrcz & Espeland gen. n. is described in the Pedaliodes Butler complex comprising 11–13 genera and more than 400 species. Support for the new genus is provided by a phylogenetic analysis based on target enrichment (TE) data including 618 nuclear loci with a total of 248,940 nucleotides, and the mitochondrial gene cytochrome oxidase subunit 1 (COI). Five species, whose DNA sequences were obtained by TE during this study, form a strongly supported clade sister to the large clade comprising Pedaliodes and four other genera. Complementary COI analysis confirms the monophyly of Viloriodes gen. n., with the above five plus eight other species clustering in highly supported clades in both Bayesian Inference and Maximum Likelihood analyses, and a TE + COI concatenated tree. Based on molecular and morphological data, 30 species are assigned to Viloriodes gen. n. The new genus can be recognized by a set of subtle morphological characteristics of colour patterns and male and female genitalia. An analysis of divergence times indicates that Viloriodes gen. n. and Steromapedaliodes Forster separated around 5.9 Mya. Viloriodes gen. n. has a wider geographic distribution than any other genus of the Pedaliodes complex, being found from central Mexico to northern Argentina and to the Guyana Shield, typically occurring at lower elevations than Pedaliodes.     

A new genus of schizomids (Arachnida: Schizomida: Hubbardiidae) from Mexico,with notes on its systematics

During the systematic revision of Mayazomus, the third most diverse genus of micro whip-scorpions in North America, we found three species with peculiar morphological variation, which are different from those diagnostic characters for Mayazomus. These species share with Mayazomus the large body size and the unusual development of the male pedipalps; however, these three species share the shape of the female spermathecae with Stenochrus rather than with Mayazomus. Therefore, their phylogenetic placements create a dilemma. Here we perform analyses with morphological evidence, using two different methodologies (Parsimony and Bayesian inference) in order to hypothesize the phylogenetic relationships of the three species mentioned with each other and with respect to other North American and/or Central American genera. The results confirm our initial hypothesis that the species belong to a different genus, Olmeca gen. nov., which is recovered as the sister group of all hubbardiine genera included in these analyses, except for the genus Hubbardia. The results also indicate that despite sharing some morphological similarities, it is distantly related with Mayazomus. Three species are described herein: Olmeca brujo sp. nov., Olmeca cruzlopezi sp. nov., and Olmeca santibanezi sp. nov. Additionally, we provide a hypothesis of the relationships and biogeography of Olmeca gen. nov. with other genera.

http://zoobank.org/urn:lsid:zoobank.org:pub:F64CE801-7D82-4827-A5B9-0C0B41F58043