Putting incertae sedis taxa in their place: a proposal for ten new families and three new genera in Sphaeropleales (Chlorophyceae,Chlorophyta)

Best known for aquatic colonial algae such as Hydrodictyon, Pediastrum, or Scenedesmus, the order Sphaeropleales also contains numerous coccoid taxa from aquatic and terrestrial habitats. Recent findings indicate that coccoid lineages in this order are very diverse genetically and may be the prevalent form, although their diversity is often hidden morphologically. This study characterizes coccoid algae recently discovered from desert soil crusts that share morphological and ecological features with the genera Bracteacoccus, Pseudomuriella, and Chromochloris. Analyses of a multi‐gene data set that includes members from all sphaeroplealean families are used to examine the monophyly of these morphologically similar taxa, which are shown instead to be phylogenetically distinct and very divergent. We propose new generic names for these lineages: Bracteamorpha, Rotundella, and Tumidella. In addition, we propose an updated family‐level taxonomy within Sphaeropleales that includes ten new families of coccoid algae to accommodate the newly presented genera and many incertae sedis taxa in the order: Bracteamorphaceae, Chromochloridaceae, Dictyococcaceae, Dictyochloridaceae, Mychonastaceae, Pseudomuriellaceae, Rotundellaceae, Schizochlamydaceae, Schroederiaceae, and Tumidellaceae.     

Molecular systematics of gerbils and deomyines (Rodentia: Gerbillinae,Deomyinae) and a test of desert adaptation in the tympanic bulla

Recent molecular studies in gerbils found multiple instances of discordance between molecular and morphological phylogenies. In this study, we analyse the largest molecular data set to date of gerbils and their sister group the deomyines to estimate their phylogenetic relationships. Maximum‐likelihood and Bayesian analyses were largely concordant, and both generally had high levels of node support. For gerbils, the results were generally concordant with previous molecular phylogenies based on allozymes, chromosomes, DNA/DNA hybridization and DNA sequences, and discordant with morphological phylogenies. None of the traditional gerbil tribes and subtribes were monophyletic. In addition, paraphyly was found in the genera Gerbillus, Gerbilliscus and Meriones as well as in five subgenera within Dipodillus, Gerbillurus and Meriones. Short branches separating taxa in small clusters within Dipodillus and Meriones suggest synonymy. Within deomyines, all genera and subgenera were monophyletic; however, two species groups within Acomys appear to contain synonymous taxa. We also find support for the discordance between molecular and morphological phylogenies in gerbils being partly due to convergent adaptations to arid environments, primarily in the suite of traits associated with inflation of the tympanic bullae. Relative bullar size does appear to be a desert adaptation and is correlated with aridity independent of phylogeny. Further, it varies more strongly along bioclimatic clines than between binary habitat classifications (desert versus mesic).     

Phantoms of Gondwana?—phylogeny of the spider subfamily Mynogleninae (Araneae: Linyphiidae)

This is the first genus‐level phylogeny of the subfamily Mynogleninae. It is based on 190 morphological characters scored for 44 taxa: 37 mynoglenine taxa (ingroup) representing 15 of the 17 known genera and seven outgroup taxa representing the subfamilies Stemonyphantinae, Linyphiinae (Linyphiini and Micronetini), and Erigoninae, and a representative of the family Pimoidae, the sister‐group to Linyphiidae. No fewer than 147 of the morphological characters used in this study are new and defined for this study, and come mainly from male and female genitalia. Parsimony analysis with equal weights resulted in three most parsimonious trees of length 871. The monophyly of the subfamily Mynogleninae and the genera Novafroneta, Parafroneta, Laminafroneta, Afroneta, Promynoglenes, Metamynoglenes, and Haplinis are supported, whereas Pseudafroneta is paraphyletic. The remaining seven mynoglenine genera are either monotypic or represented by only one taxon. Diagnoses are given for all genera included in the analysis. The evolution of morphological traits is discussed and we summarize the diversity and distribution patterns of the 124 known species of mynoglenines. The preferred topology suggests a single origin of mynoglenines in New Zealand with two dispersal events to Africa, and does not support Gondwana origin.     

High diversity Pleistocene rainforest Dasyurid assemblages with implications for the radiation of the dasyuridae

It is commonly accepted that dasyurids (Marsupialia: Dasyuridae) radiated in the late Miocene or early Pliocene in response to a drying trend in Australia's climate as evidenced from the high diversity of dasyurids from modern arid environments compared with Miocene rainforest assemblages. However, mid‐Pleistocene dasyurid assemblages from cave deposits at Mt Etna, Queensland are more diverse than any previously known from rainforest habitats. New taxa will be described elsewhere, but include three new genera as well as new species of Dasyurus, Antechinus and Phascogale. Comparison of dasyurids from Mt Etna sites that are interpreted as rainforest palaeoenvironments with fossil and extant assemblages indicate that they are at least as diverse as those from modern arid environments. Thus Neogene diversification of dasyurids occurred in both arid and rainforest habitats, but only the former survived continuing aridification. Hence, aridification cannot be invoked for the diversification of all dasyurid lineages.     

Phylogeny and biogeography of tetralophodont rodents of the tribe Oryzomyini (Cricetidae: Sigmodontinae)

Oryzomyini is the richest tribe among the Sigmodontine rodents, encompassing 32 living and extinct genera and including an increasing number of recently described species and genera. Some Oryzomyini are tetralophodont showing a reduction in the number of molar folds to four, while most taxa in this tribe retain the plesiomorphic pentalophodont state. We applied phylogenetic methods, molecular dating techniques and ancestral area analyses to members of an oryzomyini clade informally named ‘D’ in former studies and included related fossil tetralophodont forms. Based on 98 morphological characters and sequences of five gene fragments, we found that the tetralophodont condition is paraphyletic. Among living taxa, Pseudoryzomys is sister to Holochilus, and Lundomys is derived from a basal divergence. A clade formed by living Holochilus and the fossils Noronhomys and Carletonomys is sister to Holochilus primigenus, making Holochilus paraphyletic. Therefore, we describe a new genus that accommodates the fossil H. primigenus. Because trans‐Andean taxa currently share a common ancestor with taxa of cis‐Adean distribution, the northern Andes uplift may have worked as a postdispersal barrier. The tetralophodont lineages diverged during the Pliocene from a cis‐Andean ancestor, and the Great Plains in South America may have favoured the diversification of tetralophodont forms adapted to open habitats during the Pliocene.     

Revised systematics and higher classification of pierid butterflies (Lepidoptera: Pieridae) based on molecular data

The butterfly family Pieridae comprises approximately 1000 described species placed in 85 genera, but the higher classification has not yet been settled. We used molecular data from eight gene regions (one mitochondrial and seven nuclear protein‐coding genes) comprising a total of ~6700 bp from 96 taxa to infer a well‐supported phylogenetic hypothesis for the family. Based on this hypothesis, we revise the higher classification for all pierid genera. We resurrect the tribe Teracolini stat. rev. in the subfamily Pierinae to include the genera Teracolus, Pinacopteryx, Gideona, Ixias, Eronia, Colotis and most likely Calopieris. We transfer Hebomoia to the tribe Anthocharidini and assign the previously unplaced genera Belenois and Dixeia to the subtribe Aporiina. Three lineages near the base of Pierinae (Leptosia, Elodina and Nepheronia + Pareronia) remain unplaced. For each of these, we describe and delineate new tribes: Elodinini Braby tribus nova, Leptosiaini Braby tribus nova and Nepheroniini Braby tribus nova. The proposed higher classification is based on well‐supported monophyletic groups and is likely to remain stable even with the addition of more data.     

SSU rRNA GENE PHYLOGENY OF MORPHOSPECIES AFFILIATED TO THE BIOASSAY ALGA “SELENASTRUM CAPRICORNUTUM” RECOVERED THE POLYPHYLETIC ORIGIN OF CRESCENT‐SHAPED CHLOROPHYTA1

The generic concept of coccoid green algae exhibiting a crescent‐shaped morphotype is evaluated using SSU rRNA gene sequence analyses and light and electron microscopical observations. These common chlorophytes evolved polyphyletically in 10 different clades of the Chlorophyceae and three clades of the Trebouxiophyceae. Six clades are assigned to known genera of Selenastraceae: Kirchneriella, Nephrochlamys, Raphidocelis, Rhombocystis, Selenastrum, and Tetranephris. Four other clades, named following their present genus designation as Ankistrodesmus‐like I and II and Monoraphidium‐like I and II, require further investigation. One crescent‐shaped morphotype, which evolved within the Trebouxiophyceae, is designated as Neocystis mucosa sp. nov. The other two lineages containing trebouxiophycean algae with this morphotype are the Elliptochloris and the Watanabea clades. The taxonomic placement of the widely used bioassay strain “Selenastrum capricornutum” NIVA‐CHL 1 in the genus Raphidocelis (species name Raphidocelis subcapitata) is indicated by molecular data.     

Evolutionary divergence in freshwater insects with contrasting dispersal capacity across a sea of desert

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Duthieeae,a new tribe of grasses (Poaceae) identified among the early diverging lineages of subfamily Pooideae: molecular phylogenetics,morphological delineation,cytogenetics and biogeography

The phylogeny of Pooideae, one of the largest subfamilies of grasses, has been intensively studied during the past years. To investigate the early evolutionary splits in Pooideae we used a broad sample of genera with uncertain placement, some of which have not been studied in molecular phylogenetics before, complemented by representatives from other lineages of this subfamily. Morphological, cytogenetic and biogeographical analyses were added to the molecular sequence work on chloroplast matK–3’trnK and nuclear ITS. According to chloroplast DNA data, a new and well-supported lineage was identified among the early branches. It consisted of Phaenosperma and a larger group of genera encompassing Anisopogon, Danthoniastrum, Duthiea, Metcalfia, Pseudodanthonia (inclusion resting on ITS and morphology), Sinochasea and Stephanachne. Based on structural characters we suggest to keep Phaenosperma under the monotypic tribe Phaenospermateae and to accommodate the other genera under a new tribe Duthieeae, which is morphologically well-defined by synapomorphic spikelet features. Megalachne and Podophorus were not part of the early diverging Pooideae lineages but belong to the Aveneae/Poeae complex. Morphological characteristics of Duthieeae are discussed with respect especially to Stipeae and reveal consistent differences between both tribes. The genera of Duthieeae and the major lineages of Stipeae are keyed. A cytogenetic survey of exemplary taxa corroborates high chromosome base numbers as prevailing within the early diverging lineages of Pooideae, but chromosome sizes are more highly varied than previously reported. Ecogeographical analyses point to warm and humid conditions as the ancestral bioclimatic niche of Phaenosperma and Duthieeae, whereas adaptation to cold and drought occurred only in a part of Duthieeae but was obviously less successful than in the widespread and much more species-rich tribe Stipeae. The distribution of Duthieeae with species-poor or monotypic genera in mountains of the northern hemisphere and Anisopogon as an outlier in Australia suggests relict character.     

DEFINING THE MAJOR LINEAGES OF RED ALGAE (RHODOPHYTA)1

Previous phylogenetic studies of the Rhodophyta have provided a framework for understanding red algal phylogeny, but there still exists the need for a comprehensive analysis using a broad sampling of taxa and sufficient phylogenetic information to clearly define the major lineages. In this study, we determined 48 sequences of the PSI P700 chl a apoprotein A1 (psaA) and rbcL coding regions and established a robust red algal phylogeny to identify the major clades. The tree included most of the lineages of the Bangiophyceae (25 genera, 48 taxa). Seven well‐supported lineages were identified with this analysis with the Cyanidiales having the earliest divergence and being distinct from the remaining taxa; i.e. the Porphyridiales 1–3, Bangiales, Florideophyceae, and Compsopogonales. We also analyzed data sets with fewer taxa but using seven proteins or the DNA sequence from nine genes to resolve inter‐clade relationships. Based on all of these analyses, we propose that the Rhodophyta contains two new subphyla, the Cyanidiophytina with a single class, the Cyanidiophyceae, and the Rhodophytina with six classes, the Bangiophyceae, Compsopogonophyceae, Florideophyceae, Porphyridiophyceae classis nov. (which contains Porphyridium, Flintiella, and Erythrolobus), Rhodellophyceae, and Stylonematophyceae classis nov. (which contains Stylonema, Bangiopsis, Chroodactylon, Chroothece, Purpureofilum, Rhodosorus, Rhodospora, and Rufusia). We also describe a new order, Rhodellales, and a new family, Rhodellaceae (with Rhodella, Dixoniella, and Glaucosphaera).     

Phylogenetic relationships of the ubiquitous coral reef crab subfamily Chlorodiellinae (Decapoda,Brachyura, Xanthidae)

The xanthid subfamily Chlorodiellinae is one of the most ubiquitous coral reef crab taxa in the Indo‐West Pacific region. Many species are common in coral rubble and rocky shores from Hawaii to eastern Africa, often dominating reef cryptofauna in terms of biomass. Phylogenetic analyses of mitochondrial (COX1, 12S rRNA and 16S rRNA) and nuclear (histone H3) gene sequences of 202 specimens indicate that the Chlorodiellinae is polyphyletic as presently defined. Three genera, Pilodius, Cyclodius and Chlorodiella, and two previously undescribed lineages were recovered as a well‐supported clade. In combination with morphological data, the subfamily is redefined and restricted to this clade. Two new genera, Soliella gen. n., and Luniella gen. n., are described based on features of the carapace, male thoracic sternum and male gonopods. The remaining chlorodielline genera and members of the Etisinae, a subfamily with supposedly close morphological affinities to the Chlorodiellinae, were recovered at various positions throughout the xanthid phylogeny, although with relatively low support values. These results reiterate the unresolved status of xanthid subfamilial relationships, but nevertheless provide progress for xanthid systematics.     

PHYLOGENETIC ANALYSES OF THE RED ALGAL ORDER RHODYMENIALES SUPPORTS RECOGNITION OF THE HYMENOCLADIACEAE FAM. NOV., FRYEELLACEAE FAM. NOV., AND NEOGASTROCLONIUM GEN. NOV.1

Systematics of the red algal order Rhodymeniales was investigated using combined large‐subunit nuclear ribosomal DNA (LSU) and elongation factor 2 (EF2) analyses. These data were subjected to distance, parsimony, and Bayesian analyses, and the resulting phylogenies were largely congruent with previously published SSU results in that the four currently recognized rhodymenialean families (Champiaceae, Faucheaceae, Lomentariaceae, and Rhodymeniaceae) were resolved as monophyletic lineages (with the exception of Coelothrix, which is here transferred to the Champiaceae from the Rhodymeniaceae). In addition, taxa presently considered as incertae sedis consisted of two lineages (Fryeella lineage and Hymenocladia lineage). Based on these results, two new families are proposed: (i) the Fryeellaceae fam. nov. to accommodate the genera Fryeella, Hymenocladiopsis, and a new taxon from Tasmania, Australia; and (ii) the Hymenocladiaceae fam. nov., to accommodate Asteromenia, Hymenocladia, and Erythrymenia. In addition to resolving familial relationships, these analyses resolved some novel interspecific affinities, and we propose a new genus, Neogastroclonium gen. nov., for Gastroclonium subarticulatum, a species that differs significantly in both morphology and molecular data from genuine species of Gastroclonium. Relationships among additional faucheacean and lomentariacean taxa were investigated using LSU data only, and these results are discussed. The familial classification of the Rhodymeniales proposed herein is discussed in light of vegetative and reproductive anatomy, most notably the ontogeny of the tetrasporangia.     

An assessment of the status of Polycirridae genera (Annelida: Terebelliformia) and evolutionary transformation series of characters within the family

A phylogenetic analysis was performed to determine the monophyly of non‐monotypic genera of the terebelliform family Polycirridae, i.e. Polycirrus, Amaeana, Lysilla, and Hauchiella, and the evolution of characters among members of this clade. The monotypic genera, Enoplobranchus and Biremis, were also included, together with members of both known species in Hauchiella. Representative species were included for remaining genera: 14 species of Polycirrus, six species of Amaeana, and six species of Lysilla. Out‐groups consisted of representatives of Spionidae, Cirratulidae, and Sabellariidae, as well as several species of Telothelepodidae. A total of 40 in‐ and out‐group species were coded for 50 subjects (‘characters’) and 117 subject–predicate relationships (‘states’). Although results are consistent with recent phylogenetic studies within Terebelliformia that suggest Polycirridae monophyly, only Hauchiella was found to be monophyletic, albeit part of the more inclusive clade comprising remaining polycirrid genera. Evolutionary transformation series are discussed for selected characters in relation to the non‐monophyly of Polycirrus, Lysilla, and Amaeana. Implications for the use of supraspecific taxa as ‘taxonomic surrogates’ are highlighted. The definition of Polycirridae is emended. © 2015 The Linnean Society of London     

A phylogeny of Xanthopygina (Insecta,Coleoptera) reveals major lineages and the origin of myrmecophily

Xanthopygina is a group of colourful, neotropical rove beetles (Staphylinidae) comprising 28 genera and more than 350 species. While many genera are found on rotting fruits, carrion, dung and mushrooms, several taxa have evolved associations with social insects. Previous phylogenetic analyses have used only a subset of genera and were based solely on molecular data. In this paper, we performed Bayesian and maximum likelihood phylogenetic analyses of all known genera, including three potentially new genera, based on molecular (4,797 bp) and morphological (91) characters. Our results reaffirmed the monophyly of the subtribe and divided it into eight major lineages: the Elmas, Gastrisus, Isanopus, Ocyolinus, Plociopterus, Smilax, Trigonopselaphus and Xanthopygus groups. We hypothesized that myrmecophily evolved once in the common ancestor of the Smilax group, and that sphecophily possibly evolved twice, in the Trigonopselaphus and Xanthopygus groups.     

Molecular phylogeny of the ant tribe Myrmicini (Hymenoptera: Formicidae)

The interrelationships within ant subfamilies remain elusive, despite the recent establishment of the phylogeny of the major ant lineages. The tribe Myrmicini belongs to the subfamily Myrmicinae, and groups morphologically unspecialized genera. Previous research has struggled with defining Myrmicini, leading to considerable taxonomic instability. Earlier molecular phylogenetic studies have suggested the nonmonophyly of Myrmicini, but were based on limited taxon sampling. We investigated the composition of Myrmicini with phylogenetic analyses of an enlarged set of taxa, using DNA sequences of eight gene fragments taken from 37 representatives of six of the seven genera (Eutetramorium, Huberia, Hylomyrma, Manica, Myrmica, and Pogonomyrmex), and eight outgroups. Our results demonstrate the invalidity of Myrmicini as currently defined. We recovered sister‐group relationships between the genera Myrmica and Manica, and between Pogonomyrmex and Hylomyrma. This study illustrates that to understand the phylogeny of over 6000 myrmicine species, comprehensive taxon sampling and DNA sequencing are an absolute requisite. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 160 , 482–495.     

Molecular phylogenetics of Erebidae (Lepidoptera,Noctuoidea)

As a step towards understanding the higher‐level phylogeny and evolutionary affinities of quadrifid noctuoid moths, we have undertaken the first large‐scale molecular phylogenetic analysis of the moth family Erebidae, including almost all subfamilies, as well as most tribes and subtribes. DNA sequence data for one mitochondrial gene (COI) and seven nuclear genes (EF‐1α, wingless, RpS5, IDH, MDH, GAPDH and CAD) were analysed for a total of 237 taxa, principally type genera of higher taxa. Data matrices (6407 bp in total) were analysed by parsimony with equal weighting and model‐based evolutionary methods (maximum likelihood), which revealed a well‐resolved skeleton phylogenetic hypothesis with 18 major lineages, which we treat here as subfamilies of Erebidae. We thus present a new phylogeny for Erebidae consisting of 18 moderate to strongly supported subfamilies: Scoliopteryginae, Rivulinae, Anobinae, Hypeninae, Lymantriinae, Pangraptinae, Herminiinae, Aganainae, Arctiinae, Calpinae, Hypocalinae, Eulepidotinae, Toxocampinae, Tinoliinae, Scolecocampinae, Hypenodinae, Boletobiinae and Erebinae. Where possible, each monophyletic lineage is diagnosed by autapomorphic morphological character states, and within each subfamily, monophyletic tribes and subtribes can be circumscribed, most of which can also be diagnosed by morphological apomorphies. All additional taxa sampled fell within one of the four previously recognized quadrifid families (mostly into Erebidae), which are now found to include two unusual monobasic taxa from New Guinea: Cocytiinae (now in Erebidae: Erebinae) and Eucocytiinae (now in Noctuidae: Pantheinae).     

A phylogenetic revision of the true bug genus Heraeus (Hemiptera: Rhyparochromidae: Myodochini), with the description of two new genera and 30 new species

Prior to this study, the genus Heraeus Stål, 1862 included 14 species, all of which are restricted to the Western Hemisphere. Three species are known from the Nearctic Region, nine from the Neotropical Region, and two mainly tropical elements are distributed in both regions. In this contribution, we consider Heraeus cincticornis Stål, 1874 a junior synonym of Heraeus elegans (Walker, 1873), select a lectotype for Heraeus coquilletti Barber, 1914, and neotype for Lygaeus triguttatus Guérin‐Méneville, 1857, and describe 28 new species. In addition, the two new genera, Baranowskiobius gen. nov., to include H. elegans (Baranowskiobius elegans comb. nov.) and two new species, and Paraheraeus gen. nov., to include Heraeus eximius Distant, 1882 (Paraheraeus eximius comb. nov.), are described. Previously described species and new taxa are (re)described and illustrated, including male genitalia. Scanning electron micrographs, general habitus photographs, and distribution maps are included for all species studied. A phylogenetic analysis comprising 46 terminal taxa and 50 morphological characters was performed, and five species groups were hypothesized, including the coquilletti, caliginosus, guttatus, illitus, and plebejus groups. All known species of Heraeus and the new genera are included in the phylogenetic analysis. The type species of the genera Myodocha Latreille, 1807, Orthaea Dallas, 1852, and Paisana Dellapé, 2008 are used as out‐groups.