Phylogeny of Gracilariaceae (Rhodophyta): evidence from plastid and mitochondrial nucleotide sequences

Gracilariaceae are mostly pantropical red algae and include ~230 species in seven genera. Infrafamilial classification of the group has long been based on reproductive characters, but previous phylogenies have shown that traditionally circumscribed groups are not monophyletic. We performed phylogenetic analyses using two plastid (universal plastid amplicon and rbcL) and one mitochondrial (cox1) loci from a greatly expanded number of taxa to better assess generic relationships and understand patterns of character distributions. Our analyses produce the most well‐supported phylogeny of the family to date, and indicate that key characteristics of spermatangia and cystocarp type do not delineate genera as commonly suggested. Our results further indicate that Hydropuntia is not monophyletic. Given their morphological overlap with closely related members of Gracilaria, we propose that Hydropuntia be synonymized with the former. Our results additionally expand the known ranges of several Gracilariaceae species to include Brazil. Lastly, we demonstrate that the recently described Gracilaria yoneshigueana should be synonymized as G. domingensis based on morphological and molecular characters. These results demonstrate the utility of DNA barcoding for understanding poorly known and fragmentary materials of cryptic red algae.     

Phylogeny of the tribe Empoascini (Hemiptera: Cicadellidae: Typhlocybinae) based on morphological characteristics,with reclassification of the Empoasca generic group

A morphology‐based phylogenetic analysis of the tribe Empoascini (Hemiptera: Cicadellidae: Typhlocybinae) is presented for 58 of 83 formerly recognized genera based on 99 morphological characters of adults. The results support excluding the New World Beamerana generic group from Empoascini. The remaining genera of Empoascini were recovered as a monophyletic sister group of Dikraneurini. Previously recognized tribes Jorumini and Helionini are derived from within Empoascini and are considered synonyms of the latter tribe. Three previously recognized informal generic groups, the Empoasca group, Alebroides group and Usharia group were paraphyletic but the Ficiana group was recovered as monophyletic based on five synapomorphies. Genera previously placed in the Alebroides group represent at least six independent lineages, indicating that the hind wing character separating this group from the Empoasca group (CuA and MP veins free) is highly homoplasious. Empoasca (sensu lato) is also paraphyletic. Thus, twelve previously recognized subgenera of Empoasca are elevated to genus status and five species groups of Empoasca from the New World are recognized as separate new genera. Sikkimasca Dworakowska, 1993 is treated as synonym of Marolda Dworakowska, 1977 based on the phylogeny. Biogeographic analysis suggests that Empoascini most likely first evolved in the Oriental region and spread to other biogeographic realms more recently by multiple independent invasions.     

Morphological characterization of infra‐generic lineages in Deparia (Athyriaceae: Polypodiales)

Deparia, including the previously recognized genera Lunathyrium, Dryoathyrium (=Parathyrium), Athyriopsis, Triblemma, and Dictyodroma, is a fern genus comprising about 70 species in Athyriaceae. In this study, we inferred a robust Deparia phylogeny based on a comprehensive taxon sampling (~81% of species) that captures the morphological diversity displayed in the genus. All Deparia species formed a highly supported monophyletic group. Within Deparia, seven major clades were identified, and most of them were characterized by inferring synapomorphies using 14 morphological characters including leaf architecture, petiole base, rhizome type, soral characters, spore perine, and leaf indument. These results provided the morphological basis for an infra‐generic taxonomic revision of Deparia.     

Molecular systematics of the Philippine forest skinks (Squamata: Scincidae: Sphenomorphus): testing morphological hypotheses of interspecific relationships

Skinks of the genus Sphenomorphus are the most diverse clade of squamates in the Philippine Archipelago. Morphological examination of these species has defined six phenotypic groups that are commonly used in characterizations of taxonomic hypotheses. We used a molecular phylogeny based on four mitochondrial and two nuclear genes to assess the group's biogeographical history in the archipelago and examine the phylogenetic validity of the currently recognized Philippine species groups. We re‐examined traditional characters used to define species groups and used multivariate statistics to quantitatively evaluate group structure in morphometric space. Clustering analyses of phenotypic similarity indicate that some (but not all) members of previously defined species groups are phenotypically most similar to other members of the same group. However, when species group membership was mapped on our partitioned Bayesian phylogenetic hypothesis, only one species group corresponds to a clade; all other species group arrangements are strongly rejected by our phylogeny. Our results demonstrate that (1) previously recognized species group relationships were misled by phenotypic convergence; (2) Sphenomorphus is widely paraphyletic; and (3) multiple lineages have independently invaded the Philippines. Based on this new perspective on the phylogenetic relationships of Philippine Sphenomorphus, we revise the archipelago's diverse assemblage of species at the generic level, and resurrect and/or expand four previously recognized genera, and describe two new genera to accommodate the diversity of Philippine skinks of the Sphenomorphus group. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 163 , 1217–1243.     

PHYLOGENY AND SYSTEMATICS OF THE MARINE ALGAL FAMILY GRACILARIACEAE (GRACILARIALES,RHODOPHYTA) BASED ON SMALL SUBUNIT rDNA AND ITS SEQUENCES OF ATLANTIC AND PACIFIC SPECIES1

We sequenced the small subunit rDNA and internal transcribed spacer region of Gracilariaceae from the tropical Atlantic and Pacific, with emphasis on flattened or compressed species. Sequence comparisons confirmed three main lineages of Gracilariaceae: Curdiea/Melanthalia, Gracilariopsis/Gracilariophila, and Gracilaria. The Curdiea/Melanthalia diverged early in the family. Gracilariopsis was paraphyletic, because at least one Gracilariophila species evolved from it. The Atlantic Gracilariopsis were monophyletic and separated from the Pacific lineages. The Gracilaria included all species referable to its own species and to Hydropuntia, which was paraphyletic, formed by distantly related lineages. The new combination Gracilaria pauciramosa (N. Rodríguez Ríos) Bellorin, M. C. Oliveira et E. C. Oliveira is proposed for Polycavernosa pauciramosa N. Rodríguez Ríos. Recognition of subgenera within Gracilaria, based on spermatangial arrangement, was not supported. Instead, infrageneric groups were delineated by geographic origins and combinations of reproductive characters. Most Pacific species with either “textorii” or “verrucosa” type spermatangia were deeply separated from Atlantic species. Within the Atlantic Gracilaria, a lineage encompassing mostly tropical cylindrical species with “henriquesiana” type spermatangia and distinctive cystocarp anatomy was recognized. A lineage was also retrieved for cold water stringy species with verrucosa type spermatangia. Several species from the western Atlantic are closely related to Gracilaria tikvahiae McLachlan with nearly identical morphology. On the other hand, most flattened species from the tropical Atlantic were closely related despite their diverse morphologies. The interpretation of our data in addition to the literature indicates that more populations from the Indo‐Pacific must be studied before a general picture of Gracilariaceae evolution can be framed.     

CHROMOSOME COUNTS OF COMPOSITAE FROM THE UNITED STATES AND MEXICO

Chromosome counts are reported for 126 taxa representing 122 species and 61 genera of Compositae. First reports include two genera, Stylocline (n = 14) and Chromolepis (n = 19), 17 species, two infraspecific taxa, and one interspecific hybrid. Five additional taxa have chromosome numbers differing from previously published accounts. Carminatia is reinstated to generic status.     

A NEW LOOK AT AN ANCIENT ORDER: GENERIC REVISION OF THE BANGIALES (RHODOPHYTA)1

The red algal order Bangiales has been revised as a result of detailed regional studies and the development of expert local knowledge of Bangiales floras, followed by collaborative global analyses based on wide taxon sampling and molecular analyses. Combined analyses of the nuclear SSU rRNA gene and the plastid RUBISCO LSU (rbcL) gene for 157 Bangiales taxa have been conducted. Fifteen genera of Bangiales, seven filamentous and eight foliose, are recognized. This classification includes five newly described and two resurrected genera. This revision constitutes a major change in understanding relationships and evolution in this order. The genus Porphyra is now restricted to five described species and a number of undescribed species. Other foliose taxa previously placed in Porphyra are now recognized to belong to the genera Boreophyllum gen. nov., Clymene gen. nov., Fuscifolium gen. nov., Lysithea gen. nov., Miuraea gen. nov., Pyropia, and Wildemania. Four of the seven filamentous genera recognized in our analyses already have generic names (Bangia, Dione, Minerva, and Pseudobangia), and are all currently monotypic. The unnamed filamentous genera are clearly composed of multiple species, and few of these species have names. Further research is required: the genus to which the marine taxon Bangia fuscopurpurea belongs is not known, and there are also a large number of species previously described as Porphyra for which nuclear SSU ribosomal RNA (nrSSU) or rbcL sequence data should be obtained so that they can be assigned to the appropriate genus.     

The cladistics and biology of the Callajoppa genus-group (Hymenoptera: Ichneumonidae, Ichneumoninae)

A cladistic analysis is presented for the genera of the former ichneumonine tribe Trogini. The tribe Heresiarchini is paraphyletic with respect to the Trogini, and so maintaining Trogini as a separate tribe is unsatisfactory. Within Heresiarchini, the following changes are made: (a) the subtribes Apatetorina and Heresiarchina are referred to as the Apatetor and Heresiarches genus‐groups, (b) the genera of the paraphyletic subtribe Protichneumonina are treated as incerta sedis within Heresiarchini, and (c) the Trogini are referred to as the Callajoppa genus‐group, with the former subtribe Trogina referred to as the Trogus subgroup. Thirty‐five genera are recognized as valid within the Callajoppa genus‐group. Catadelphops, Catadelphus, Cobunus, and Facydes are transferred to this group; Holojoppa is removed and is incertae sedis within Heresiarchini. Three new synonyms are proposed: Araeoscelis and Cryptopyge are junior synonyms of Macrojoppa, and Neamblyjoppa is a junior synonym of Catadelphops. Trogus latipennis Cresson is transferred to Pedinopelte from Macrojoppa, and Trogus mactator Tosquinet and its related species (T. bicolor Radoszkowski, T. heinrichi Uchida, and T. tricephalus Uchida) are transferred to Holcojoppa. Tricyphus is redefined and a neotype is designated for Tricyphus cuspidiger Kriechbaumer, the type‐species of the genus. Thirteen new genera are described (authorship of all is Wahl & Sime): Charmedia (type‐species: Charmedia chavarriai Wahl & Sime, sp. n.) , Daggoo (type‐species: Daggoo philoctetes Wahl & Sime, sp. n.), Dothenia (type‐species: Dothenia hansoni Wahl & Sime, sp. n.), Humbert (type‐species: Humbert humberti Wahl & Sime, sp. n.), Laderrica (type‐species: Laderrica feenyi Wahl & Sime, sp. n.), Mokajoppa (type‐species: Tricyphus respinozai Ward & Gauld), Metallichneumon (type‐species: Metallichneumon neurospastarchus Wahl & Sime, sp. n.), Myocious (type‐species: Myocious orientalis Wahl & Sime, sp. n.) , Quandrus (type‐species: Trogus pepsoides Smith, transferred from Callajoppa), Queequeg (type‐species: Gathetus flavibasalis Uchida, transferred from Neofacydes), Saranaca (type‐species: Trogus elegans Cresson; includes Trogus apicalis Cresson, Tricyphyus ater Hopper, and Tricyphus floridanus Heinrich), Tashtego (type‐species: Tashtego janzeni Wahl & Sime, sp. n.), and Xanthosomnium (type‐species: Xanthosomnium froesei Wahl & Sime, sp. n.). A key to the genera of the Callajoppa genus‐group is provided. The evolution of biological traits within the Callajoppa genus‐group is discussed with reference to the elucidated phylogeny. The groundplan biology is parasitism of Sphingidae, with oviposition into a host pupa/prepupa. There have been two transitions to butterfly parasitism within the Trogus subgroup: one a transition to Papilionidae (followed by a switch to Nymphalidae at Psilomastax) and the other to Nymphalidae (followed by a switch to Papilionidae within Macrojoppa). ©2002 The Linnean Society of London. Zoological Journal of the Linnean Society, 134 , 1–56.     

A global molecular phylogeny of 147 periwinkle species (Gastropoda,Littorininae)

Reid, D. G., Dyal, P. & Williams, S.T. (2012) A global molecular phylogeny of 147 periwinkle species (Gastropoda, Littorininae). —Zoologica Scripta, 41, 125–136. Complete species‐level molecular phylogenies have been published for several genera of Littorinidae (e.g. Echinolittorina, Littoraria). Here we add new sequence data from three genes (28S rRNA, 12S rRNA, cytochrome oxidase c subunit I) for single specimens of an additional 24 species, to make a data set of 147 (97%) of the 152 recognized species of the subfamily Littorininae. This three‐gene data set is analysed to produce a phylogenetic hypothesis for the subfamily, which includes the first complete species‐level phylogeny of the genus Peasiella and the first three‐gene phylogeny of all Littorina species. The non‐planktotrophic species of Littorina have previously been classified together (as subgenus Neritrema), implying a single origin of this developmental mode. Tests of this hypothesis with the new data are inconclusive, and resolution is not improved in a tree constructed from five genes (adding previously published sequences of 16S rRNA and cytochrome b). Using available fossils for calibration we generate a BEAST chronogram, which emphasizes that the radiation of Littorina is more recent than that of other littorinine genera. A database is provided, listing all known species of Littorininae, with their distributions, development, ecology and gene sequences, as a tool for future evolutionary studies of this model group.     

Taxonomic review of the New World tamarins (Primates: Callitrichidae)

Twelve generic names have been ascribed to the New World tamarins but all are currently placed in just one: Saguinus Hoffmannsegg, 1807. Based on geographical distributions, morphology, and pelage patterns and coloration, they have been divided into six species groups: (1) nigricollis, (2) mystax, (3) midas, (4) inustus, (5) bicolor and (6) oedipus. Molecular phylogenetic studies have validated five of these groups; each are distinct clades. Saguinus inustus is embedded in the mystax group. Genetic studies show that tamarins are sister to all other callitrichids, diverging 15?13 Ma. The small‐bodied nigricollis group diverged from the remaining, larger tamarins 11?8 Ma, and the mystax group diverged 7?6 Ma; these radiations are older than those of the marmosets (Callithrix, Cebuella, Mico), which began to diversify 6?5 Ma. The oedipus group diverged from the midas and bicolor groups 5?4 Ma. We review recent taxonomic changes and summarize the history of the generic names. Taking into account the Late Miocene divergence time (11?8 Ma) between the large‐ and small‐bodied tamarin lineages, the small size of the nigricollis group species when compared with other tamarins, and the sympatry of the nigricollis group species with the larger mystax group species, we argue that the nigricollis group be recognized as a distinct genus: Leontocebus Wagner, 1839.     

Phylogenomic analyses of the Photinia complex support the recognition of a new genus Phippsiomeles and the resurrection of a redefined Stranvaesia in Maleae (Rosaceae)

Photinia and its morphologically similar allies in Maleae (Rosaceae) consist of five currently recognized genera: Aronia, Heteromeles, Photinia, Pourthiaea, and Stranvaesia, and 68 species, distributed in Asia and North and Central America. Despite previous efforts to clarify relationships in this group, the generic delimitations have remained uncertain. Our goals were to reconstruct a robust phylogeny of Photinia and its close allies to test the monophyly of the currently recognized genera, especially Photinia and Stranvaesia, and the hybrid origin hypothesis of Photinia bodinieri. This study employs complete plastomes and the entire nuclear ribosomal DNA (nrDNA) repeats assembled from the genome skimming approach with a broad taxon sampling of 81 species in 30 genera of Rosaceae, especially Maleae. Based on three datasets, including the whole plastome, coding sequence, and nrDNA repeats, the results of maximum likelihood and Bayesian inference analyses showed that the previously circumscribed Stranvaesia and Photinia were each non‐monophyletic. Six clades have been recovered herein within Photinia and its allied genera: Aronia, Heteromeles, Photinia s.s., Pourthiaea, Stranvaesia, and a new genus Phippsiomeles consisting of the Central American species formerly placed in Photinia. The strong conflicts between the plastome and nrDNA phylogenies of Phippsiomeles and Stranvaesia tomentosa suggest the possibility that they may have each originated involving hybridization events, while no incongruence among datasets was detected to support the hybrid origin of Photinia bodinieri. We provide 12 new combinations, to transfer eight taxa of the New World Photinia into Phippsiomeles and clarify the generic placements of several species of Photinia and Stranvaesia.     

Phylogeny of the tribe Naupactini (Coleoptera: Curculionidae) based on morphological characters

Naupactini (Curculionidae: Entiminae) is a primarily Neotropical tribe of broad‐nosed weevils with its highest genus and species diversity in South America. Despite several taxonomic contributions published during the last decades, the evolutionary history of Naupactini remains poorly understood. We present the first comprehensive phylogenetic analysis for this tribe based on a data matrix of 100 adult morphological characters scored for 70 species, representing 55 genera of Naupactini (ingroup) and four outgroups belonging to the entimine tribes Otiorhynchini, Entimini, Eustylini and Tanymecini. According to the most parsimonious tree Artipus does not belong to Naupactini; the genera with flat and broad antennae, formerly assigned to other entimine tribes, form a monophyletic group (Saurops (Curiades (Aptolemus (Platyomus)))) related to the clade (Megalostylus (Megalostylodes (Chamaelops Wagneriella))); and the genera distributed along the high Andes, Paramos and Puna form a natural group (Asymmathetes (Amphideritus (Leschenius (Amitrus (Obrieniolus (Melanocyphus Trichocyphus)))))), nested within a larger clade that includes Pantomorus, Naupactus and allied genera. Atrichonotus, Hoplopactus, Mimographus and Naupactus are not recovered as monophyletic. In order to address the taxonomic implications of our phylogenetic analysis, we propose the following nomenclatural changes: to transfer Artipus from Naupactini to Geonemini, to revalidate the genera Mimographopsis (type species M. viridicans), and to revalidate the genus Floresianus (type species F. sordidus). The evolution of selected characters is discussed. This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:C8AA4388‐A2F0‐4E2D‐889A‐500BEA5A9DE1 .     

The suprageneric groups ofthe Pimplinae (Hymenoptera: Ichneumonidae): a cladistic re-evaluationand evolutionary biological study

The phylogenetic relationships of the suprageneric groupsof the ichneumonid subfamily Pimplinae (Hymenoptera) are re‐assessedusing 166 morphological and biological characters for 162 species,representing all of the available described genera and subgenera.The cladistic analysis was repeated using abstracted genera, re‐codedfrom the ­initial set of species, as terminal taxa. Thetopology of the resulting cladograms was similar. In the first (primary) analysisseveral genera (including Neotheronia, Itoplectis, Dolichomitus, Dreisbachia, Polysphincta, Oxyrrhexis and Zonopimpla)were not retrieved as monophyletic groups; however, all except thelast were found to be monophyletic in the second analysis. Theseresults suggest that using abstracted taxa may force a ‘falsemonophyly’ on the preselected groups. Thus we reject theuse of such abstractions, preferring instead to use exemplar speciesthat together show much of the variation that occurs within a hypothesizedgenus. Within the Pimplinae three major groupings were recognized,the Delomeristini (including the Perithoini syn. nov.) , thePimplini and the Ephialtini. Within the Pimplini, two generic groupswere recovered, the Xanthopimpla and Pimpla genus‐groups,but a third postulated group, the Theronia genus‐group, wasfound to be paraphyletic. Within the Ephialtini five groups wererecognized, the Pseudopimpla, Alophosternum, Camptotypus, Ephialtes and Sericopimpla genus‐groups.The spider parasitizing complex of genera (the Polysphincta genus‐complex)was found to nest within the Sericopimpla genus‐group confirmingthe placement of Polysphinctini as a synonym of Ephialtini. Problemswith the status of some existing genera are highlighted, but formalnomenclatural changes are not proposed. The ancestral Pimplinaeare hypothesized to have been solitary ectoparasitic idiobiontson weakly concealed immature Hymenoptera. The major radiations withinthe Pimplinae are shown as: (1) a progressive exploitation of cocooned,then weakly cocooned, lepidopterous pupae in the Pimplini leadingto idiobiont endoparasitism; (2) increasing specialization to attackhosts deeply concealed in wood in the Ephialtes genus‐group,and (3) specialization on a variety of cocooned hosts, includingspider egg sacs, leading to koinobiont ectoparasitism of spiders.A brief synopsis of the distribution of the group is given, and somebiogeographical inferences drawn. The group is presumed to haveoriginated and radiated on Laurasia; no evidence for trans‐Antarcticrelationships can be found. © 2002 The LinneanSociety of London, Zoological Journal of the Linnean Society,2002, 136 , 421?485     

DEFENSE EVOLUTION IN THE GRACILARIACEAE (RHODOPHYTA): SUBSTRATE‐REGULATED OXIDATION OF AGAR OLIGOSACCHARIDES IS MORE ANCIENT THAN THE OLIGOAGAR‐ACTIVATED OXIDATIVE BURST1

Combined phylogenetic, physiological, and biochemical approaches revealed that differences in defense‐related responses among 17 species belonging to the Gracilariaceae were consistent with their evolutionary history. An oxidative burst response resulting from activation of NADPH oxidase was always observed in two of the subgenera of Gracilaria sensu lato (Gracilaria, Hydropuntia), but not in Gracilariopsis and in species related to Gracilaria chilensis (“chilensis” clade). On the other hand, all species examined except Gracilaria tenuistipitata var. liui and Gracilariopsis longissima responded with up‐regulation of agar oligosaccharide oxidase to an challenge with agar oligosaccharides. As indicated by pharmacological experiments conducted with Gracilaria chilensis and Gracilaria sp. “dura,” the up‐regulation of agar oligosaccharide oxidase involved an NAD(P)H‐dependent signaling pathway, but not kinase activity. By contrast, the activation of NADPH oxidase requires protein phosphorylation. Both responses are therefore independent, and the agar oligosaccharide‐activated oxidative burst evolved after the capacity to oxidize agar oligosaccharide, probably providing additional defensive capacity to the most recently differentiated clades of Gracilariaceae. As demonstrated with Gracilaria gracilis, Gracilaria dura, and Gracilariopsis longissima, the different responses to agar oligosaccharides allow for a fast and nondestructive distinction among different clades of gracilarioids that are morphologically convergent. Based upon sequences of the chloroplast‐encoded rbcL gene, this study suggests that at least some of the samples from NW America recorded as Gs. lemanaeiformis are probably Gs. chorda. Moreover, previous records of Gracilaria conferta from Israel are shown to be based upon misidentification of Gracilaria sp. “dura,” a species that belongs to the Hydropuntia subgenus.