Taxonomy, phylogeny and biogeography of Kickxia and Nanorrhinum (Scrophulariaceae)

Phylogenetic studies in Kickxia sensu lato, using morphological characters, show that two groups of species appear as distinct clades, one corresponding to sect. Kickxia and the other corresponding to sect. Valvatae. The differences between the two sections are of the same magnitude as those used to separate other closely related genera in the tribe. Therefore, the treatment of sect. Valvatae as a separate genus, Nanorrhinum , is proposed. Results from a dispersal-vicariance analysis indicate that the area of origin for Nanorrhinum is Arabia, whereas for Kickxia sensu stricto it is either Macaronesia, the Mediterranean Region or both these areas combined. The taxonomy of Nanorrhinum is revised in detail, whereas for Kickxia a synoptical treatment is given, mainly based on previous literature. The results indicate that the plasticity of the species of Nanorrhinum , as well as the variation within populations in the field, is often much greater than previously thought, and that, therefore, far too many species have been described. In the present study ten species are recognized in Nanorrhinum. New combinations are N. azraqensis, N. stenanthum, N. hastatum, N. elegans, N. kuriensis, N. asparagoides, N. heterophyllum and N. woodii. Three lectotypes are selected. Keys to all taxa are given, and new information on chromosome numbers and sexual systems are provided for several species.     

Molecular phylogeny of the Australian frog genera Crinia, Geocrinia, and allied taxa (Anura: Myobatrachidae).

We present a mitochondrial gene tree for representative species of all the genera in the subfamily Myobatrachinae, with special emphasis on Crinia and Geocrinia. This group has been the subject of a number of long-standing taxonomic and phylogenetic debates. Our phylogeny is based on data from approximately 780 bp of 12S rRNA and 676 bp of ND2, and resolves a number of these problems. We confirm that the morphologically highly derived monotypic genera Metacrinia, Myobatrachus, and Arenophryne are closely related, and that Pseudophryne forms the sister group to these genera. Uperoleia and the recently described genus Spicospina are also part of this clade. Our data show that Assa and Geocrinia are reciprocally monophyletic and together they form a well-supported clade. Geocrinia is monophyletic and the phylogenetic relationships with the genus are fully resolved with two major species groups identified: G. leai, G. victoriana, and G. laevis; and G. rosea, G. alba, and G. vitellina (we were unable to sample G. lutea). We confirm that Taudactylus forms the sister group to the other myobatrachine genera, but our data are equivocal on the phylogenetic position of Paracrinia. The phylogenetic relationships among Crinia species are well resolved with strong support for a number of distinct monophyletic clades, but more data are required to resolve relationships among these major Crinia clades. Crinia tasmaniensis and Bryobatrachus nimbus form the sister clade to the rest of Crinia. Due to the lack of generic level synapomorphies for a Bryobatrachus that includes C. tasmaniensis, we synonymize Bryobatrachus with Crinia. Crinia georgiana does not form a clade distinct from other Crinia species and so our data do not support recognition of the genus Ranidella for other Crinia species. Crinia subinsignifera, C. pseudinsignifera, and C. insignifera are extremely closely related despite differences in male advertisement call. A preliminary investigation of phylogeographic substructure within C. signifera revealed significant divergence between samples from across the range of this species.     

Molecular phylogeny and biogeography of tribe anthemideae (Asteraceae), based on chloroplast gene ndhF

Anthemideae (Asteraceae) is primarily a north temperate, Old World tribe of 109 genera and approximately 1740 species. We sequenced a 1200-bp portion of chloroplast gene ndhF for representative genera and subtribes and constructed a phylogeny for the tribe. There is support for monophyly of subtribes Chrysantheminae and Gonosperminae and for portions of some subtribes. However, our molecular phylogeny differs significantly from traditional classifications and from previously published morphological phylogenies of the tribe. Many South African genera from several different subtribes form a basal grade, indicating multiple, relictual lineages. Eurasian genera form a recently derived clade that includes the Mediterranean genera of the Iberian Peninsula and North Africa. There is little resolution or support for the placement of eastern Asian genera. Apparently, the tribe originated in the Southern Hemisphere, presumably in Africa, with the Eurasian and Mediterranean members being derived from a common ancestor.     

Molecular evidence for naturalness of genera in the tribe Antirrhineae (Scrophulariaceae) and three independent evolutionary lineages from the New World and the Old

The tribe Antirrhineae consists of 29 genera distributed in the New World and the Old. Phylogenetic analyses of ITS and ndhF sequences served to recognize six main lineages: Anarrhinum group (Anarrhinum, Kickxia); Linaria group (Linaria); Maurandya group (Cymbalaria, Asarina, Maurandella, Rhodochiton, Lophospermum); Schweinfurthia group (Pseudorontium, Schweinfurthia); Antirrhinum group (Antirrhinum, Pseudomisopates, Misopates, Acanthorrhinum, Howeliella, Neogarrhinum, Sairocarpus, Mohavea, Galvezia); Chaenorrhinum group (Chaenorrhinum, Albraunia, Holzneria). Parsimony (cladistics), distance-based (Neighbor-Joining), and Bayesian inference reveal that: (1) the tribe is a natural group; (2) genera such as Linaria, Schweinfurthia, Kickxia, and Antirrhinum also form natural groups; (3) three Antirrhineae lineages containing genera from the New and Old World are the result of three intercontinental disjunctions displaying similar levels of ITS-sequence divergence and differentiation times (Oligocene-Miocene); (4) evolution of flower shapes is not congruent with primitiveness of personate flowers; (5) both polyploidy and dysploidy appear to be responsible for most variation in chromosome number in the six main lineages. Nuclear and chloroplast evidence also supports the split of American and Mediterranean species of Antirrhinum into different genera, a result that should be contemplated in the interest of a more natural (monophyletic) taxonomy. Nucleotide additivity causes poor resolution in the ITS analysis of 22 species of Mediterranean Antirrhinum and lead us to interpret extensive hybridization in the Iberian Peninsula.This research was supported by the Spanish Dirección General de Investigación Científica y Técnica (DGICYT) through the project Flora Iberica (PS91-0070-C03-01). We thank Jorge Martínez and Emilio Cano for his assistance in the lab, Rafael Rubio and Omar Fiz for helping on the Bayesian inferences, the curators/collection managers of BCF, E, JACA, MA, SALA, SALAF, SEV, TARI, VAL for loans and access to specimens, and two anonymous reviewers for improving the quality of this publication.     

Molecular phylogeny of the diatom genera Amphora and Halamphora (Bacillariophyta) with a focus on morphological and ecological evolution

The taxonomic history of the diatom genus Amphora is one of a broad early morphological concept resulting in the inclusion of a diversity of taxa, followed by an extended period of revision and refinement. The introduction of molecular systematics has increased the pace of revision and has largely resolved the relationships between the major lineages, indicating homoplasy in the evolution of amphoroid symmetry. Within the two largest monophyletic lineages, the genus Halamphora and the now taxonomically refined genus Amphora, the intrageneric morphological and ecological relationships have yet to be explored within a phylogenetic framework. Critical among this is whether the range of morphological features exhibited within these diverse genera are reflective of evolutionary groupings or, as with many previously studied amphoroid features, are nonhomologous when examined phylogenetically. Presented here is a four‐marker molecular phylogeny that includes 31 taxa from the genus Amphora and 77 taxa from the genus Halamphora collected from fresh, brackish, and salt waters from coastal and inland habitats of the United States and Japan. These phylogenies illustrate complex patterns in the evolution of frustule morphology and ecology within the genera and the implications of this on the taxonomy, classification, and organization of the genera are discussed.     

Molecular phylogeny and systematics of the tribe Chorisporeae (Brassicaceae)

Sequence data from nuclear (ITS) and chloroplast (trnL-F) regions for 89 accessions representing 56 out of 64 species from all five genera of the tribe Chorisporeae (plus Dontostemon tibeticus) have been studied to test the monophyly of the tribe and its component genera, clarify its boundaries, and elucidate its phylogenetic position in the family. Both data sets showed strong support for the monophyly of the Chorisporeae as currently delimited, though the position of its tentative member D. tibeticus was not resolved by ITS. Parrya and Pseudoclausia are poly- and paraphyletic with regard to each other, and Chorispora is either polyphyletic or at least paraphyletic (comprising Diptychocarpus) within a weakly supported monophyletic clade. The incongruence in branching pattern among the markers was most likely caused by hybridization and possibly influenced by incomplete lineage sorting. The present results suggest uniting Pseudoclausia, Clausia podlechii, and Achoriphragma with Parrya and transferring P. beketovii and P. saposhnikovii to Leiospora (Euclidieae). We also obtained support for splitting Chorispora into two geographically defined groups, one of which is closer to Diptychocarpus. Both data sets revealed a close relationship of the Chorisporeae to Dontostemoneae, while ITS also indicated affinity to Hesperideae. Therefore, the position of Chorisporeae needs further verification.     

Molecular phylogeny of the fungus gnat tribe Exechiini (Mycetophilidae, Diptera)

The phylogenetic relationships within the fungus gnat tribe Exechiini have been left unattended for many years. Recent studies have not shed much light on the intergeneric relationship within the tribe. Here the first attempt to resolve the phylogeny of the tribe Exechiini using molecular markers is presented. The nuclear 18S and the mitochondrial 16S, and cytochrome oxidase subunit I (COI) genes were successfully sequenced for 20 species representing 15 Exechiini genera and five outgroup genera. Bayesian, maximum parsimony and maximum likelihood analyses revealed basically congruent tree topologies and the monophyly of Exechiini, including the genus Cordyla , is confirmed. The molecular data corroborate previous morphological studies in several aspects. Cordyla is found in a basal clade together with Brachypeza , Pseudorymosia and Stigmatomeria . The splitting of the genera Allodiopsis s.l. and Brevicornu s.l. as well as the sistergroup relationship of Exechia and Exechiopsis is also supported. The limited phylogenetic information provided by morphological characters is mirrored in the limited resolution of the molecular markers used in this study. Short internal and long-terminal branches obtained may indicate a rapid radiation of the Exechiini genera during a short evolutionary period.     

Molecular phylogeny reveals the non-monophyly of tribe Yinshanieae(Brassicaceae) and description of a new tribe,Hillielleae

The taxonomic treatment within the unigeneric tribe Yinshanieae(Brassicaceae) is controversial, owing to differences in generic delimitation applied to its species. In this study, sequences from nuclear ITS and chloroplast trn L-F regions were used to test the monophyly of Yinshanieae, while two nuclear markers(ITS, ETS) and four chloroplast markers(trnL-F, trn H-psbA, rps16, rpL32-trnL) were used to elucidate the phylogenetic relationships within the tribe. Using maximum parsimony, maximum likelihood, and Bayesian inference methods, we reconstructed the phylogeny of Brassicaceae and Yinshanieae. The results show that Yinshanieae is not a monophyletic group, with the taxa splitting into two distantly related clades: one clade contains four taxa and falls in Lineage I, whereas the other includes all species previously placed in Hilliella and is embedded in the Expanded Lineage II. The tribe Yinshanieae is redefined, and a new tribe, Hillielleae, is proposed based on combined evidence from molecular phylogeny, morphology, and cytology.     

Molecular phylogeny and adaptive radiation of the endemic Hawaiian Plantago species (Plantaginaceae)

Insular oceanic islands provide excellent opportunities for the study of evolutionary processes and adaptive radiation. The Hawaiian Plantago radiation comprises six endemic taxa showing considerable inter- and intraspecific morphological and ecological diversity. The rDNA internal (ITS) and external (ETS) transcribed spacers and two recently described chloroplast spacers, ndhF-rpl32 and rpl32-trnL, were sequenced to study phylogenetic relationships within this morphologically complex group. Phylogenetic analysis provided strong evidence for the monophyly of Hawaiian Plantago, suggesting that the lineage arose from a single long-distance dispersal event. Inconsistencies between nuclear and chloroplast phylogenies suggest a history of hybridization. The basal, unresolved dichotomy of the combined phylogeny is consistent with rapid phenotypic diversification of the major lineages early in the history of this group. Speciation has largely occurred allopatrically, with divergence a result of intraisland ecological shifts between bog and woodland habitats and interisland dispersal events. Most interisland colonizations were from older to younger islands with initial colonization of Kaua'i. In our analysis, P. pachyphylla is paraphyletic and taxonomic separation of the distinct morphotypes of this species appears justified. Furthermore, the apparent hybrid ancestry and unique morphology and habitat of the endangered P. princeps var. longibracteata support its recognition at the specific rank.     

Systematic significance of seed morphology in the genus Veronica (Plantaginaceae), with special reference to the Egyptian taxa

Seed morphology of 29 taxa including 9 subgenera belonging to the genus Veronica was compared using scanning electron microscopy to assess their diagnostic value for systematic studies. Subgenus Beccabunga is the largest in this study represented by nine taxa. Seed surface often varies from ridged reticulate or verrucose/granulate reticulate to rugose-reticulate. Seed color and size have limited taxonomic significance as their variation is uninformative. Thereagainst, seed shape and seed coat ornamentation present informative characters that can be used efficiently in distinguishing the studied taxa. Our seed features support the DNA sequence data in showing close relationships between V. biloba and V. campylopoda, and between V. fruticans and V. fruticulosa. The present study indicates thatV. anagallis-aquatica, V. anagalloides, V. comosa, and V. catenata have more or less the same seed features; consequently, these four former species are most likely representing a single species as reported by earlier studies. Furthermore, V. polita and V. persica are very similar in terms of seed characteristics. Our results justify placement of V. peregina within subgenus Beccabunga and support the monophyly of the subgenus Veronica.     

Molecular phylogeny of swallowtail butterflies of the tribe Papilionini (Papilionidae, Lepidoptera).

Swallowtail butterflies of the tribe Papilionini number about 225 species and are currently used as model organisms in several research areas, including genetics, chemical ecology and phylogenetics of host plant utilization and mimicry, mechanisms of speciation, and conservation. We have inferred phylogenetic relationships for a sample of 18 species of the genus Papilio (sensu lato) and five outgroup taxa by sequencing two stretches of mitochondrial DNA that correspond to segments 12886-13370 and 12083-12545 of Drosophila melanogaster mitochondrial DNA and consist of sections of the genes for the large ribosomal RNA and subunit 1 of NADH-dehydrogenase. Our data support the monophyly of Papilio and, within it, of several traditionally recognized subgroups. Species belonging to groups that utilize primarily Rutaceae as larval foodplants form two clusters, corresponding to Old World and American taxa, respectively, while two previously recognized clades-of American and South Asian-Austronesian origin-whose members were known to feed mostly on Lauraceae and Magnoliaceae, are observed to form a clade. The sister group of Papilio is found to be the South Asian genus Meandrusa, which also happens to feed on Lauraceae. The latter plant family is therefore the probable larval host of the ancestor Papilio and the shift to Rutaceae (which four-fifths of extant Papilio species use as foodplants) is more likely to have occurred only after the initial diversification of the genus.     

Molecular phylogeny of litostome ciliates (Ciliophora, Litostomatea) with emphasis on free-living haptorian genera

The monophyly of the litostomes was tested using nine newly sequenced and four previously unpublished small subunit ribosomal RNA (SSrRNA) gene sequences from free-living Haptoria as well as from endosymbiotic Trichostomatia: the vestibuliferids Balantidium coli and Isotricha prostoma, the cyclotrichiid Mesodinium pulex, and the haptorids Loxophyllum rostratum, Dileptus sp., Enchelyodon sp., Enchelys polynucleata, Epispathidium papilliferum (isolates A and B), Spathidium stammeri, Arcuospathidium muscorum, Arcuospathidium cultriforme, and the unusual Teuthophrys trisulca. Phylogenetic analyses depicted the litostomes as a monophyletic group consisting of the trichostomes (subclass Trichostomatia) and the free-living haptorians (subclass Haptoria). The cyclotrichiids Mesodinium and Myrionecta (order Cyclotrichiida) branched either basally within or outside the Litostomatea. In most analyses, the haptorians did not receive support as a monophyletic group. Instead, Dileptus branched basally to all litostome taxa, and Epispathidium papilliferum grouped with the Subclass Trichostomatia. Some subgroupings, however, of haptorian genera corresponded to suggested superfamilial taxa (e.g., orders Spathidiida and Pleurostomatida). Within the monophyletic trichostomes, we can distinguish three clades: (1) an Australian clade; (2) the order Entodiniomorphida; and (3) the order Vestibuliferida. However, Balantidium, currently classified in the Vestibuliferida, did not group with the other vestibuliferids, suggesting that this order may be paraphyletic.     

Molecular phylogeny of Acarosporaceae (Ascomycota) with focus on the proposed genus Polysporinopsis

The molecular phylogeny of Acarosporaceae with a focus on the recently proposed genus Polysporinopsis was investigated using maximum parsimony and Bayesian analyses, using nuITS-LSU and mtSSU rDNA sequence datasets. A well-supported monophyletic clade corresponding to Acarospora (including the type species A. schleicheri, A. fuscata, A. nitrophila, A. rugulosa, A. bullata, A. sinopica, A molybdina and A. peliscypha) was present in all analyses. Acarospora as currently delimited is not monophyletic; neither A. smaragdula nor A. badiofusca belongs to the genus in the restricted sense. Polysporinopsis, which comprises three species previously classified in Acarospora (P. sinopica-type species, P. smaragdula, and P. rugulosa) is not a monophyletic group separate from Acarospora s. str. Acarospora sinopica and A. smaragdula are not closely related; A. sinopica belongs to Acarospora s. str., but A. smaragdula is one of the most basal taxa currently known in Acarosporaceae.     

Molecular phylogeny of the Paleogene fungus gnat tribe Exechiini (Diptera: Mycetophilidae) revisited: Monophyly of genera established and rapid radiation confirmed

The phylogeny of the fungus gnat tribe Exechiini (Diptera: Mycetophilidae) is reconstructed based on the combined analysis of five nuclear (18S, two parts of 28S, CAD, EF1α) and two mitochondrial (12S, COI) gene markers. According to known fossil record, and recent higher‐level phylogenies, the tribe constitutes the most apomorphic, distinctly monophyletic clade of the family Mycetophilidae. The tribe originated in the Paleogene and apparently quickly diversified in the Neogene with an unusual rapid radiation of complex male terminalia. Earlier attempts to reconstruct the phylogeny of the tribe, based on both morphology and molecular methods, have not yielded reliable hypotheses, neither in terms of resolution nor in terms of support for major clades. Increased taxon sampling and wider gene sampling have been suggested to achieve better phylogenetic resolution. Aiming at this, we present new phylogenies, for the first time with all known genera and subgenera of Exechiini represented. While many terminal intergeneric relationships are well supported, both in maximum likelihood and in Bayesian analyses, most of the major, deeper clades remain poorly supported. We suggest that a rapid radiation event close to the root may be causing the low resolution at this level in the phylogeny. This contrasts parallel phylogenies of the older subfamilies and tribes of the family Mycetophilidae, where traditional clades have usually been recovered with high support. Further in‐depth studies into the evolutionary history of the tribe are needed to enlighten and coalesce the specific phenomena driving their unique morphological, genetic and phylogeographic histories.     

Molecular phylogeny of Aphyocharacinae (Characiformes, Characidae) with morphological diagnoses for the subfamily and recognized genera

The subfamily Aphyocharacinae was recently redefined to comprise eight genera: Aphyocharax, Prionobrama, Paragoniates, Phenagoniates, Leptagoniates, Xenagoniates, Rachoviscus and Inpaichthys. This new composition, however, is partially incongruent with published results of molecular studies especially concerning the positions of Rachoviscus and Inpaichthys. Our goal was to investigate the monophyly of Aphyocharacinae and its interrelationships using three distinct phylogenetic methodologies: Maximum-likelihood and Bayesian analyses of molecular data, and also Parsimony analysis of a concatenated molecular and morphological dataset. All tree topologies recovered herein suggest that Rachoviscus, Inpaichthys and Leptagoniates pi do not belong to the Aphyocharacinae. The remaining aphyocharacin taxa analyzed do form a monophyletic group, which is itself composed of two subgroups being one comprised of Paragoniates, Phenagoniates, Leptagoniates and Xenagoniates, and the other comprised of Aphyocharax and Prionobrama. Internal relationships among these genera are statistically well supported and morphological synapomorphies are presented at the generic level. All tree topologies also indicate that Aphyocharacidium is closely related to Aphyocharacinae suggesting that it should be included in this subfamily. As recognized in the present study, the Aphyocharacinae is diagnosed by a single morphological synapomorphy: two dorsal-fin rays articulating with the first dorsal pterygiophore.     

Molecular phylogeny and systematics of the Polysphincta group of genera (Hymenoptera,Ichneumonidae, Pimplinae)

The phylogenetic relationships between genera of the Polysphincta group of Pimplinae (Ichneumonidae) were surveyed using molecular markers, partial sequences of cytochrome c oxidase I (COI), 28S rRNA and elongation factor 1α, and maximum likelihood and Bayesian approaches to obtain a robust phylogenetic hypothesis to understand the evolution of the group. The Polysphincta group was recovered as monophyletic, although relationships between genera were different from previous hypotheses based on morphological data. Within the Polysphincta group, three major clades were recognized and phylogenetic relationships among them were well resolved as (Schizopyga subgroup + (Acrodactyla subgroup + Polysphincta subgroup)). The Schizopyga subgroup consisted of the genera Piogaster, Schizopyga, Zabrachypus and Brachyzapus. As the genus Schizopyga was found to be polyphyletic, the genus Dreisbachia, which had been synonymized under Schizopyga, was resurrected and Iania gen.n. is proposed for Dreisbachia pictifrons, to maintain monophyletic genera. Species of the Schizopyga subgroup utilize spiders constructing egg‐laying chambers or funnel webs as hosts. The genus Piogaster was not recovered as the sister to all other members of the genus group, unlike previous hypotheses, but was nested in this clade as (Zabrachypus + ((Brachyzapus + Schizopyga) + (Dreisbachia + (Iania + Piogaster)))). Members of the Acrodactyla and Polysphincta subgroups attack spiders that weave aerial webs. The host range of the former is centred on tetragnathid and linyphiid spiders, the host range of the latter seems to centre mainly on orb‐weaving araneids and partly on theridiids weaving three‐dimensional (3D) irregular webs. Based on the obtained phylogeny of the group, the evolution of larval and cocoon morphology, and the mode of parasitism are discussed. Acrodactyla varicarinata Uchida & Momoi and A. inoperta Kusigemati are transferred to the genus Megaetaira ( comb.n.). This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:0AB1086F‐9F23‐4057‐B7ED‐3A3943E19C61 .