Phylogeny of the Spiny African Daisies (Compositae, tribe Arctotideae, subtribe Gorteriinae) based on trnL-F, ndhF, and ITS sequence data

The tribe Arctotideae (African Daisies), of the flowering plant family Compositae (Asteraceae), is a diverse and interesting group with a primarily southern African distribution (ca. 13 genera, 215 species) and many species in the Cape Floristic Region. It is divided into two subtribes: Arctotidinae (ca. 5 genera, 85 species) and Gorteriinae (ca. 8 genera, 130 species). The monophyly of the genera within the subtribe Gorteriinae and their relationship to one another was investigated using 71 samples/212 sequences including 64/141 of which are newly reported from three phylogenetic markers, two from chloroplast DNA (trnL-F and ndhF) and one from the nuclear genome (ITS). The outgroup was composed of seven members from the sister subtribe. Results show the subtribe Gorteriinae to be divided into three monophyletic groups, the Gazania-Hirpicium-Gorteria group, the Didelta group, and the Berkheya-Cullumia group. Within these three groups are 13 sub-groups, one of which has sub-clades. The genus Berkheya Ehrh. is paraphyletic, falling into five different sub-groups. The two monotypic genera, Cuspidia and Heterorhachis are not nested within any of the Berkheya clades. Hirpicium and Cullumia each have most of their taxa in a monophyletic group, but they also have one or two taxa associated with other clades. Four of the five sub-groups of Berkheya have morphologically recognizable shared characters, such as habit and spines that have been recognized by past studies. However, the grouping of one species with Didelta is difficult to explain. Support for the major clades and most of the sub-groups is strong but the relationships among some of the terminal taxa are variable.     

Comparative micromorphology of nectariferous and nectarless labellar spurs in selected clades of subtribe Orchidinae (Orchidaceae)

Floral nectar spurs are widely considered to influence pollinator behaviour in orchids. Spurs of 21 orchid species selected from within four molecularly circumscribed clades of subtribe Orchidinae (based on Platanthera s.l., Gymnadenia–Dactylorhiza s.l., Anacamptis s.l., Orchis s.s.) were examined under light and scanning electron microscopes in order to estimate correlations between nectar production (categorized as absent, trace, reservoir), interior epidermal papillae (categorized as absent, short, medium, long) and epidermal cell striations (categorized as apparently absent, weak, moderate, strong). Closely related congeneric species scored similarly, but more divergent species showed less evidence of phylogenetic constraints. Nectar secretion was negatively correlated with striations and positively correlated with papillae, which were especially frequent and large in species producing substantial reservoirs of nectar. We speculate that the primary function of the papillae is conserving energy through nectar resorption and explain the presence of large papillae in a minority of deceit‐pollinated species by arguing that the papillae improve pollination because they are a tactile expectation of pollinating insects. In contrast, the prominence of striations may be a ‘spandrel’, simply reflecting the thickness of the overlying cuticle. Developmentally, the spur is an invagination of the labellum; it is primarily vascularized by a single ‘U’‐shaped primary strand, with smaller strands present in some species. Several suggestions are made for developing further, more targeted research programmes. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 160 , 369–387     

Recognition of two major clades and early diverged groups within the subfamily Cyperoideae (Cyperaceae) including Korean sedges

We aim to present phylogenetic major groups within the subfamily Cyperoideae (Cyperaceae) on the basis of three molecular data sets; nuclear ribosomal internal transcribed spacer and 5.8S ribosomal RNA region, the ribulose-1, 5-bisphosphate carboxylase/oxygenase large subunit gene, and trnL intron and trnL-F intergenic spacer. Three molecular data and two combined data sets were used to obtain robust and detailed phylogenetic trees by using maximum parsimony and Bayesian inference, respectively. We analyzed 81 genera and 426 species of Cyperaceae, including Korean species. We suggest one early diverged group (EDGs), and two major clades (FAEC and SDC) within the subfamily Cyperoideae. And the clade EDGs comprises six tribes (Schoeneae, Bisboeckelereae, Sclerieae, Cryptangieae, Trilepideae, and Rhynchosporeae) at the basal nodes of Cyperoideae. The FAEC clade (posterior probability [PP]/bootstrap value [BS] = 1.00/85) comprises four tribes (Fuireneae, Abildgaardieae, Eleocharideae, Cypereae), and the SDC clade (PP/BS = 1.00/86) comprises three tribes (Scirpeae, Dulichieae, Cariceae). These three clades used for phylogenetic groups in our study will be useful for establishing the major lineage of the sedge family. The phylogeny of Korean sedges was also investigated within the whole phylogeny of Cyperaceae. The 20 genera of Korean sedges were placed in 10 tribes forming 14 clades.     

First molecular phylogeny of the major clades of Pseudoscorpiones (Arthropoda: Chelicerata)

The phylogenetic relationships of the major lineages of the arachnid order Pseudoscorpiones are investigated for the first time using molecular sequence data from two nuclear ribosomal genes and one mitochondrial protein-encoding gene. The data were analyzed using a dynamic homology approach with the new program POY v.4 under parsimony as the optimality criterion. The data show monophyly of Pseudoscorpiones as well as many of its superfamilies (Feaelloidea, Chthonioidea, Cheiridioidea and Sternophoroidea), but not for Neobisiodea or Garypoidea. Cheliferoidea was not monophyletic either due to the position of Neochelanops, which grouped with some garypoids. In all the analyses, Feaelloidea constituted the sister group to all other pseudoscorpions; Chthonioidea is the sister group to the remaining families, which constitute the group Iocheirata sensu Harvey--a clade including pseudoscorpions with venom glands within the pedipalpal fingers. This phylogenetic pattern suggests that venom glands evolved just once within this order of arachnids.     

Morphological and molecular concordance of Rhynchozoon clades (Bryozoa, Cheilostomata) from Alaska

Abstract. Alpha‐level taxonomy in the bryozoan order Cheilostomata relies almost exclusively on hard‐part morphology. Geographical, ecophenotypic, and intracolony variation often make it difficult to distinguish intra‐ from interspecific variation and to recognize taxonomically informative characters. DNA sequences provide a source of data independent of morphology by which to gauge the relative reliability of various morphological characters for taxonomy. We present a case study involving a limited number of specimens of Rhynchozoon sp. from Ketchikan, Alaska to show the utility of DNA data in identifying genetic lineages for subsequent morphological analysis. The study illustrates that the use of genetic data need not involve massive, broad‐scale phylogenetic studies to address problems in invertebrate α‐level taxonomy. Phylogeny reconstruction with a 430‐bp fragment of the 16S mitochondrial ribosomal RNA gene showed two moderately diverged clades, here termed Rhynchozoon clades A and B, separated by an average genetic distance of 2.38% (K2P+Γ). Comparison of voucher specimens by scanning electron microscopy showed two congruent, morphologically distinct forms (forms A and B, respectively) distinguishable by a polythetic suite of characters including degree of frontal costation, range of spine number, number of beads on the primary orifice, number of areolar pores, and peri‐orificial sculpturing. Orifice shape and ovicell form proved not to be good diagnostic characters. The status of the two forms as biological species is unclear, although maintenance of distinct suites of morphological characters in the two mitochondrial lineages suggests they may be reproductively isolated from one another. For Rhynchozoon form B, which tends to have a highly costate frontal wall, we suggest a resurrection of the name Rhynchozoon tumulosum, which had been previously synonymized with R. rostratum. Rhynchozoon form A may be conspecific with “Rhynchozoon sp. A” previously reported from Washington state.     

Influence of data conflict and molecular phylogeny of major clades in Cimicomorphan true bugs (Insecta: Hemiptera: Heteroptera)

Cimicomorpha, which consists of 16 families representing more than 19,400 species, is the largest infraorder in Heteroptera, Insecta. We present the first molecular phylogenetic investigation of family relationships of Cimicomorpha, including 46 taxa from 12 of 16 Cimicomorphan families. Three genes, with a total of 3277 bp of sequence data (nuclear 18S rDNA: 2022 bp, 28S rDNA: 755 bp, and mitochondrial 16S rDNA: 498 bp) were analyzed. Data partitions were analyzed separately and in combination, by employing ML (maximum likelihood), MP (maximum parsimony), and Bayesian methods. As saturation was detected in substitutions of 16S rDNA, influence of data conflict in combined analyses was further explored by three methods: the incongruence length difference (ILD) test, the partitioned Bremer support (PBS), and the partition addition bootstrap alteration approach (PABA). PBS and PABA approaches suggested that 16S rDNA was not very suitable for addressing relationships at this level in Cimicomorpha. Our results also supported the nabid-cimicoid lineage for Cimicoidea proposed by Schuh and Stys [Schuh, R.T., Stys, P., 1991. Phylogenetic analysis of Cimicomorphan family relationships (Heteroptera). J. NY Entomol. Soc. 99 (3), 298-350]. Data incongruence and the utility of the three genes were briefly discussed.     

Molecular phylogeny and divergence of major clades in the Puntius complex (Teleostei: Cypriniformes)

Puntius sensu lato (s.l.) was one of the most speciose genera in the family Cyprinidae. There are around 120 valid species widely distributed in South-East and South Asia, and South China. Puntius has long been known as an artificial assemblage and ‘catch-all’ genus in which a large number of small, unrelated cyprinids have been placed. With new species and genera being described each year, obtaining detailed knowledge of the phylogenetic relationships of this complex is critically important in the assessment of a natural classification. In the present study, two mitochondrial and four nuclear genes were used to examine the inter-specific and inter-generic relationships of the Puntius complex and to test the monophyly of the current genera. Divergence time analysis was performed to explore the origin, evolution, and divergence of major clades in Puntius s.l. Results revealed that the genera Puntius seusu stricto (s.s.), Systomus, Pethia, Haludaria, Desmopuntius and Puntigrus were monophyletic with high support. However, monophyly of Barbodes, Striuntius and Sahyadria was not supported. Dawkinsia and Sahyadria formed a highly supported clade. Puntius semifasciolatus and P. snyderi from South China and Taiwan represent a new lineage. Inferences from divergence time analysis indicated that Puntius s.l. likely dated to early Miocene. Major clades in Puntius s.l. diverged during Miocene as well.     

Pollen morphology of the subtribe Cuspariinae (Rutaceae)

The neotropical subtribe Cuspariinae (Rutaceae) comprises as many as 26 genera and over 125 species. Pollen grains from 111 collections representing 71 species and 24 genera were examined by LM, SEM, and TEM. The pollen morphology of this subtribe is very diverse. Grains are mostly 3–6-aperturate and colporate, rarely porate (Spiranthera) or pantocolporate (Almeidea). Exine sculpturing is most commonly reticulate, sometimes perforate, foveolate-perforate, foveolate, foveolate-reticulate, reticulate, striate-reticulate, echinate, clavate, or baculate. The exine structure is columellate and tectate-perforate, columellate and semitectate, or intectate and is stratified into ektexine and endexine. The exine ofLeptothyrsa is distinctive in that the ektexine of the mesocolpium is longitudinally deeply ridged. The pollen ofHortia, characterized by a psilate exine with rare perforations, a very thick foot-layer, and reduced columellae, is unlike that of any member of the Cuspariinae and offers no support for the transfer of this genus from the Toddalioideae. The pollen data correlate with macromorphological characters and are taxonomically useful.     

Leaf anatomy of the subtribe Hyptidinae (Labiatae)

The leaf anatomy of the subtribe Hyptidinae (Labiatae), which consists of four small genera and the largr genus Hyplis , is dercribed. The leaves may be dorsiventral or isobilateral. Variable characters of the lainina include: frequency and forms of trichomes, cuticular markings, presence of adaxial stoinata, thickness of leaf, thickness of adaxial epidermis, presence of a hypodermis, occurrence of sclcrified tissues (especially sclerified bundle sheath extensions, phloem and xylem fibres), mesophyll structure and venation pattern. Petiole vasculature varies from simple to complex, sometimes with medullary traces present. Most of the variable characters are related to xeromorphy and are tax-onomically useful within the framework of the present classification.     

Fragmented mitochondrial genomes are present in both major clades of the blood-sucking lice (suborder Anoplura): evidence from two Hoplopleura rodent lice (family Hoplopleuridae)

Background

The suborder Anoplura contains 540 species of blood-sucking lice that parasitize over 840 species of eutherian mammals. Fragmented mitochondrial (mt) genomes have been found in the lice of humans, pigs, horses and rats from four families: Pediculidae, Pthiridae, Haematopinidae and Polyplacidae. These lice, eight species in total, are from the same major clade of the Anoplura. The mt genomes of these lice consist of 9–20 minichromosomes; each minichromosome is 1.5–4 kb in size and has 1–8 genes. To understand mt genome fragmentation in the other major clade of the Anoplura, we sequenced the mt genomes of two species of rodent lice in the genus Hoplopleura (family Hoplopleuridae).

Results

We identified 28 mt genes on 10 minichromosomes in the mouse louse, Ho. akanezumi; each minichromosome is 1.7–2.7 kb long and has 1–6 genes. We identified 34 mt genes on 11 minichromosomes in the rat louse, Ho. kitti; each minichromosome is 1.8–2.8 kb long and has 1–5 genes. Ho. akanezumi also has a chimeric minichromosome with parts of two rRNA genes and a full-length tRNA gene for tyrosine. These two rodent lice share the same pattern for the distribution of all of the protein-coding and rRNA genes but differ in tRNA gene content and gene arrangement in four minichromosomes. Like the four genera of blood-sucking lice that have been investigated in previous studies, the Hoplopleura species have four minichromosomes that are only found in this genus.

Conclusions

Our results indicate that fragmented mt genomes were present in the most recent common ancestor of the two major clades of the blood-sucking lice, which lived ~75 million years ago. Intra-genus variation in the pattern of mt genome fragmentation is common in the blood-sucking lice (suborder Anoplura) and genus-specific minichromosomes are potential synapomorphies. Future studies should expand into more species, genera and families of blood-sucking lice to explore further the phylogenetic utility of the novel features associated with fragmented mt genomes.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-751) contains supplementary material, which is available to authorized users.     

Leaf anatomy of the subtribe Conceveibinae (Euphorbiaceae)

A comparative study of the leaf anatomy of the subtribe Conceveibinae was carried out. Leaves show a similar structural arrangement in all species, however, there are small variations among the taxa that allow definitions of species or groups. It is not possible to recognize infrageneric divisions or to maintain some genera as different from Conceveiba. The analysis included the study of 11 characters of taxonomic importance of the leaf: the form, the size and the apex of the papillae of the lower side of the blade, the number of layers of the palisade parenchyma, the presence or absence of the midrib pith, the number of vascular bundles of petiole as well as the central cylinder and the medulla, and the presence or absence of the sclerenchyma in the different levels of the petiole. The results are evaluated from a taxonomical point of view. With leaf anatomy characters only, it is possible to separate the genus Conceveiba in the subtribe.     

Flower anatomy of the subtribe Hyptidinae (Labiatae)

Flowers of 34 species, representing 4 of the 6 genera of the morphologically diverse South American subtribe Hyptidinae and including members of many of the sections of the genus Hyptis are investigated. Floral anatomy is basically uniform, with some minor variations which are mainly related to differences in flower size. Marsypianthes differs from the other genera in that the style is fused to the ovary, the hypogynous disc is relatively massive, and there are 12 or 13 calyx traces rather than the usual number of 10. The stylopodium, which is characteristic of Eriope and certain sections of Hyptis, is a fold of stylar tissue which develops in the bud prior to opening of the flower and is probably an abscission layer.     

Cladistic interrelationships and major clades of theEricales

A cladistic analysis of theEricales based on morphological, anatomical, embryological, and phytochemical data has been undertaken. Resulting from the analysis, 56 equally parsimonious cladograms were obtained. The tribeEnkiantheae was found to be the sister-group of the rest of theEricaceae, in which theEmpetraceae, theEpacridaceae, Pyrolaceae, andMonotropaceae are forming derived ingroups. It is thus concluded that theEricaceae are a paraphyletic assemblage as presently circumscribed, and thatEmpetraceae andEpacridaceae are better treated as members of theEricaceae.     

Using molecular data to test the monophyly of Lallemantia in the subtribe Nepetinae (Mentheae,Lamiaceae)

Phylogenetic relationships among the species of Lallemantia and its close allies (Lamiaceae, Mentheae) were investigated using nuclear (ITS) and plastid (trnL, trnL/F, trnS/G, rpl32, and rpl32-trnL) DNA sequences. Phylogenetic results from Bayesian and parsimony analyses show that (1) Lallemantia is monophyletic, (2) Hymenocrater is nested within Nepeta, and (3) Lallemantia is more closely related to Dracocephalum than other genera in Nepetinae. Based on the molecular results, the genus Lallemantia comprises two disparate lineages, with each lineage supported by distinct morphological characters (e.g. floral structures and pollen grains).     

Morphological and molecular evidence indicates that the Gulf Coast box turtle (Terrapene carolina major) is not a distinct evolutionary lineage in the Florida Panhandle

Four extant subspecies of Terrapene carolina in eastern North America, Terrapene carolina bauri, Terrapene carolina carolina, Terrapene carolina triunguis, and Terrapene carolina major, are recognized based on morphological studies. A fifth subspecies, Terrapene carolina putnami, has been described from Pleistocene deposits but is very similar morphologically to T. c. major. Questions concerning the relationship of the Gulf Coast box turtle (T. c. major) to other box turtles have been pervasive ever since it was described. We used a combined morphological and genetic analysis to address the status of T. c. major and other T. carolina lineages. Terrapene c. bauri, T. c. carolina, and T. c. triunguis are distinct based on a discriminate function analysis of 25 morphological characters, including characters traditionally used to assign subspecies. The results of the present study confirm that box turtles phenotypically diagnosed as T. c. bauri, T. c. carolina, and T. c. triunguis all occur within the hypothesized range of T. c. major, and that the latter does not possess a diagnosable morphology. The three morphological lineages also possess divergent mitochondrial haplotypes that are present within the hypothesized range of T. c. major. In addition, a fourth distinct mtDNA lineage co‐occurs within the putative range of T. c. major. This unique lineage may include mitochondrial DNA variation from the Pleistocene T. c. putnami. Analysis of nine nuclear DNA microsatellites revealed no population structure in box turtles currently assigned to T. c. major from the Florida Panhandle, suggesting a complete admixture of lineages in this region. The results of the present study indicate that box turtles traditionally assigned to T. c. major based on phenotype are the result of introgression between eastern extant (predominantly T. c. carolina) and an extinct subspecies, T. c. putnami. Published 2011. This article is a US Government work and is in the public domain in the USA. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 889–901.