Systematics and phylogeny of the tribe Paragini (Diptera: Syrphidae) based on molecular and morphological characters

We studied the phylogeny and systematics of the tribe Paragini (Diptera: Syrphidae) using morphological and molecular data. The paper presents separate parsimony analyses of both adult morphological characters and partial DNA sequence data from mitochondrial cytochrome c oxidase I and nuclear ribosomal 28S rRNA gene, as well as a combined analysis of all the data. The data set of morphological characters included some features of the male terminalia (i.e. shape of the ejaculatory apodeme; relative position of elements of the aedeagal complex; shape of surstylar apodeme; shape of the aedeagal apodeme) not previously used in the systematics of the Paragini. The trees obtained from separate parsimony analyses of molecular and morphological data produced almost identical topologies. Four lineages are supported by the combined data set, and we establish two new subgenera, i.e. Serratoparagus Vujić et Radenković subgen. nov., and Afroparagus Vujić et Radenković subgen. nov., and redefine Pandasyopthalmus Stuckenberg, 1954 stat. rev. and Paragus Latreille, 1804, stat. rev. The monophyly of the Pandasyopthalmus clade, including the species fitting neither of the current species groups ( jozanus -group) of Paragini, is established. Diagnoses of all known species groups are presented, including a new arrangement of almost all valid species of Paragini.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 152 , 507–536.     

A morphological and molecular assessment of the genus Sinotubimorpha (Halymeniaceae, Rhodophyta)

A critical reassessment of the morphological features of two closely related red algal genera,Grateloupia C.Agardh and Sinotubimorpha W.X.Li & Z.F.Ding (Halymeniaceae),pointed out that members of the t...     

Phylogenetic relationships within the tribe Janieae (Corallinales,Rhodophyta) based on molecular and morphological data: a reappraisal of Jania1

Generic boundaries among the genera Cheilosporum, Haliptilon, and Jania—currently referred to the tribe Janieae (Corallinaceae, Corallinales, Rhodophyta)—were reassessed. Phylogenetic relationships among 42 corallinoidean taxa were determined based on 26 anatomical characters and nuclear SSU rDNA sequence data for 11 species (with two duplicate plants) referred to the tribe Corallineae and 15 species referred to the tribe Janieae (two species of Cheilosporum, seven of Haliptilon, and six of Jania, with five duplicate plants). Results from our approach were consistent with the hypothesis that the tribe Janieae is monophyletic. Our data indicate, however, that Jania and Haliptilon as currently delimited are not monophyletic, and that Cheilosporum should not be recognized as an independent genus within the Janieae. Our data resolved two well‐supported biogeographic clades for the included Janieae, an Indian‐Pacific clade and a temperate North Atlantic clade. Among anatomical characters, reproductive structures reflected the evolution of the Janieae. Based on our results, three genera, Cheilosporum, Haliptilon, and Jania, should be merged into a single genus, with Jania having nomenclatural priority. We therefore propose new combinations where necessary of some species previously included in Cheilosporum and Haliptilon.     

Marbleseeds are gromwells – Systematics and evolution of Lithospermum and allies (Boraginaceae tribe Lithospermeae) based on molecular and morphological data

Phylogenetic relationships are complex within the Lithospermeae, a large subgroup of the Boraginaceae s.str. The relationships of New World Lasiarrhenum, Macromeria, Nomosa, Onosmodium, Perittostoma, and Psilolaemus to subcosmopolitan and much larger Lithospermum have not been critically investigated in the recent past. No molecular data on the phylogeny of these genera and Lithospermum have so far been published. We investigated the relationships within Lithospermeae using three loci (nuclear ITS plus 5.8S rRNA, chloroplast trnL-F-spacer, and trnS-G-spacer) and micromorphological character traits (pollen, nutlets). Lithospermum s.l. constitutes the sistergroup of Asian Ulugbekia and is monophyletic only when its American segregates “Macromeria”, monotypic Nomosa, and Onosmodium are included. Both the African and the South American species groups of Lithospermum are monophyletic, but North American representatives are not resolved in a single clade. Morphological characters that have been considered as important for generic delimitation in the past (such as large, yellow corollas without faucal scales, particular pollen types, coarsely veined leaves, shrubby habit) have evolved in at least two only distantly related lineages within Lithospermum s.l. The reduction of American “Macromeria”, Nomosa, and Onosmodium as well as Asian Ulugbekia under Lithospermum is proposed to render the latter monophyletic. This redefined Lithospermum s.l. appears to have undergone a type of recent “island radiation” in the Americas, reflected in a morphological diversity far exceeding that found in the Old World.     

A morphological and molecular assessment of the genus Prionitis J. Agardh (Halymeniaceae, Rhodophyta)

A critical reassessment of the morphological features of two closely related red algal genera, Grateloupia C. Agardh and Prionitis J. Agardh (Halymeniaceae), shows that members of the two genera share very similar reproductive (including the Grateloupia‐type auxiliary‐cell ampullae) and vegetative characters. Diagnostic features hitherto used for distinguishing these two genera, the texture of blades (lubricous to leathery in Grateloupia vs cartilaginous in Prionitis) and the position of reproductive structures (scattered over the entire blade in Grateloupia vs confined to particular portions of the blade in Prionitis), are continuous across some 75 species of both genera, thus making it difficult to draw a clear‐cut distinction between the two genera. In ribulose‐1,5‐bisphosphate carboxylase/oxygenase gene (rbcL) sequence analyses, the species of Grateloupia and Prionitis, including the two generitypes, constitute a large monophyletic clade in the Halymeniaceae. It is therefore proposed that Prionitis be included in the synonymy under Grateloupia and the appropriate combinations are proposed.     

Phylogeny,biogeography, and morphological ancestral character reconstruction in the Mediterranean genus Fumana (Cistaceae)

Fumana is a diverse genus of the Cistaceae family, consisting of 21 currently accepted species. In this study, nuclear (ITS) and plastid (matK, trnT‐L) molecular markers were used to reconstruct the phylogeny and to estimate divergence times, including 19 species of Fumana. Phylogenetic analyses (Bayesian Inference, Maximum Parsimony and Maximum Likelihood) confirmed the monophyly of Fumana and did not support the infrageneric divisions previously established. The results support four main clades that group species that differ in vegetative and reproductive characters. Given the impossibility to define morphological characters common to all species within the clades, our proposal is to reject infrageneric divisions. Molecular dating and ancestral area analyses provide evidence for a Miocene diversification of the genus in the north‐western Mediterranean. Ancestral state reconstructions revealed ancestral character states for some traits related to xeric and arid habitats, suggesting a preadaptation to the Mediterranean climate.     

A revised classification of subtribe Helianthinae (Asteraceae: Heliantheae) II. Derived lineages

Sequence data for internal transcribed spacer (ITS) and partial external transcribed spacer (ETS) regions were combined in a phylogenetic analysis with previously obtained plastid DNA restriction site data to provide a comprehensive molecular phylogenetic hypothesis for derived members of subtribe Helianthinae. Analyses of the two molecular datasets provided conflicting evidence on relationships among some groups, supporting the hypothesis that hybridization has played a significant role in the divergence of the subtribe. A revised generic‐level classification is presented that divides the approximately 350 species of the subtribe among 21 genera. The paraphyletic Viguiera is narrowed to embrace only the type species, V. dentata. Four newly described genera, Dendroviguiera, Gonzalezia, Heiseria and Sidneya, are composed of species formerly included in Viguiera. Aldama is expanded to include 118 species extending from southwestern North America and Mexico to South America. This requires 116 new combinations, including 58 that were recently transferred into Rhysolepis, which is a synonym of Aldama, based on molecular phylogenetic results. One species of Viguiera is transferred to Tithonia, and two combinations in Hymenostephium are validated. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 167 , 311–331.     

The blackburni/murchisona species complex in Australian Pseudotetracha (Coleoptera: Carabidae: Cicindelinae: Megacephalini): evaluating molecular and karyological evidence

Our phylogenetic analysis of three endemic species of the Australian tiger beetle genus Pseudotetracha (Fleutiaux, 1864) from South Australia used sequences of two fragments of the mitochondrial genes 16S rRNA and cytochrome oxidase III. A matrix for each gene and two combined matrices were constructed. We compared these three riparian species, together with data from nine taxa of this genus available in GenBank, using parsimony and Bayesian methods. These molecular results are in agreement with the phylogenetic hypothesis for the blackburni/murchisona species complex previously proposed based on morphology, whereas other recent molecular analyses have questioned the existence of this species complex. In all of our analyses, samples of P. blackburni divided into two statistically supported clades, one of which is more closely related to P. mendacia and P. pulchra than to the other P. blackburni clade. This suggests the existence of a cryptic new species. Additionally, we analysed chromosomes of the second metaphase cells of members of the two clades. The observations showed different karyotypes as blackburni‐1 has two types of second meiotic metaphase cells with 11 and 12 chromosomes, whereas in blackburni‐2, all cells have 12 chromosomes, adding evidence for the putative existence of two species.     

A revised classification of subtribe Helianthinae (Asteraceae: Heliantheae). I. Basal lineages

Results for nuclear ITS sequences were combined with previously obtained data from cpDNA restriction site studies to provide a comprehensive molecular phylogeny for subtribe Helianthinae. Results from the two molecular data sets were mostly congruent for basally diverging branches of the subtribe. Based on the results, combined with morphological observations, the basally diverging branches are placed in six genera, including one newly described. Bahiopsis is resurrected to accommodate species previously placed in Viguiera subgenus Bahiopsis . Calanticaria is newly proposed for the five species of Viguiera ser. Brevifolieae . Heliomeris is retained for the group sometimes included within Viguiera as sect. Heliomeris . Hymenostephium is revived and enlarged to include a number of species of similar habit and involucre, including members of Viguiera sect. Diplostichis , Haploca-lymma and Garcilassa . Although cpDNA results place the morphologically distinctive Sclerocarpus within the clade including species of Hymenostephium , the ITS data were consistent with morphology in suggesting it to be a distinctive lineage.  © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 140 , 65–76.     

A new species of Haplophyllum A. Juss. (Rutaceae) from the Iberian Peninsula: evidence from morphological, karyological and molecular analyses

BACKGROUND AND AIMS: The discovery of a new species, Haplophyllum bastetanum F.B. Navarro, V.N. Suárez-Santiago & Blanca sp. nov., in the south-east of Spain has prompted the comparative study of species of the Iberian Peninsula, and others related, through morphological, cytogenetic, molecular, distributional and ecological characterization. METHODS: The morphological study involved a quantitative analysis of the species present in the Iberian Peninsula and a comparative analysis of the morphological characteristics between H. bastetanum and other related species. Mitotic analyses were made with root meristems taken from germinating seeds. Phylogenetic analyses of the internal transcribed spacer sequences of nuclear ribosomal DNA were performed using neighbour-joining (NJ) and maximum-parsimony methods. KEY RESULTS: Haplophyllum bastetanum is a diploid species (2n = 18) distinguished primarily for its non-trifoliate glabrous leaves, lanceolate sepals, dark-green petals with a dorsal band of hairs, and a highly hairy ovary with round-apex locules. The other two Iberian species (H. linifolium and H. rosmarinifolium) are tetraploid (2n = 36) and have yellow petals. Both phylogenetic methods generated a well-supported clade grouping H. linifolium with H. rosmarinifolium. In the NJ tree, the H. linifolium-H. rosmarinifolium clade is a sister group to H. bastetanum, while in the parsimony analysis this occurred only when the gaps were coded as a fifth base and the characters were reweighted according to the rescaled consistency index. This latter group is supported by the sequence divergence among taxa. CONCLUSIONS: The phylogenies established from DNA sequences together with morphological and cytogenetic analyses support the separation of H. bastetanum as a new species. The results suggest that the change in the number of chromosomes may be the key mechanism of speciation of the genus Haplophyllum in the Iberian Peninsula. An evolutionary scheme for them is propounded.     

Further fragmentation of the polyphyletic genus Polyalthia (Annonaceae): molecular phylogenetic support for a broader delimitation of Marsypopetalum

The species-rich genus Polyalthia has previously been shown to be highly polyphyletic, with species represented in at least five different clades. The Polyalthia species that are associated with Marsypopetalum and Trivalvaria (as revealed either by previous phylogenetic studies or inferred on the basis of comparative morphology) were included in a molecular phylogenetic study based on three chloroplast DNA regions (matK, rbcL and trnL-F). Maximum parsimony, maximum likelihood and Bayesian analyses consistently revealed that several Polyalthia species form a well-supported clade with Marsypopetalum pallidum, and that this clade is sister to Trivalvaria. Diagnostic morphological characters for the clades are re-evaluated and shown to be congruent with the molecular phylogeny. Five Polyalthia species (P. crassa, P. littoralis, P. lucida, P. modesta and P. tristis) are accordingly transferred to Marsypopetalum.     

Phylogenetic placement of Yunnanopilia (Opiliaceae) inferred from molecular and morphological data

Yunnanopilia longistaminea (W.Z. Li) C.Y. Wu & D.Z. Li, which is a controversial species in Opiliaceae, is treated as a variety of Champereia manillana (Blume) Merrill in the Flora of China and morphological analysis has produced conflicting results regarding its affinity to Melientha and Champereia. To determine the systematic position of Yunnanopilia in Opiliaceae, we selected two nuclear regions (internal transcribed spacer [ITS4‐ITS5] and 18S rDNA) and four chloroplast regions (rbcL, matK, psbA‐trnH, and trnS‐trnG) to test the phylogenetics of the family Opiliaceae using maximum likelihood and Bayesian inference analysis. Morphological characteristics were also examined to clarify the similarities and differences among Y. longistaminea and two closely related species. Agonandra was located at the basal position in the family Opiliaceae; in the large clade including other remaining genera, two main clades were clearly identified and correlated with inflorescence morphological characteristics. All samples of Y. longistaminea formed a clade. Yunnanopilia, Melientha, and Champereia were more closely related than other genera of Opiliaceae. Yunnanopilia longistaminea was sister to M. suavis Pierre and was more closely related to M. suavis than to C. manillana. Morphological analysis also showed that differences in the inflorescences and flowers between Y. longistaminea and M. suavis were substantial enough to warrant the retention of Y. longistaminea in its current genus. Thus, we suggest that the monotypic Yunnanopilia be treated as a distinct genus and that the name Y. longistaminea should be adopted.     

A revision of Calvoa Hook. f. (Melastomataceae)

A revision of the genus Calvoa Hook. f. (Melastomataceae) is presented. Principal Component Analyses (PCA) and Cluster Analyses (UPGMA) were performed to elucidate three cases of difficult species delimitation and infraspecific variation, with the following results. (1) The separation between C. crassinoda Hook. f. and C. grandifolia Cogn. was clear in the results obtained with both methods. (2) The group of the West-Central African species Calvoa angolensis A. Fern. & R. Fern., C. calliantha Jacq.-Fél., C. monticola A. Chev., C. pulcherrima Gilg ex Engl., C. sapinii De Wild., C. seretii De Wild., C. sinuata Hook. f. and C. subquinquenervia De Wild, proved difficult to resolve with either analysis, but the Cluster Analysis produced results which are more consistent with the identification of the specimens. (3) Neither of the two analyses supported the recognition of infraspecific categories in Calvoa orientalis Taub. Eighteen species are recognized in the genus. The new species Calvoa Jacques-felixii E. Figueiredo is described and the new combination Calvoa seretii subsp. wildemaniana (Exell) E. Figueiredo is made. Four lectotypes are designated. The conservation status of some taxa is discussed. Six species are considered rare and possibly under threat.     

Phylogeny of Acomys spinosissimus (Rodentia, Muridae) from north Malawi and Tanzania: evidence from morphological and molecular analysis

New specimens of Acomys spinosissimus from northern Malawi and southern Tanzania were subjected to morphological, molecular (cytochrome b mitochondrial gene) and cytogenetical analysis in order to establish the phylogenetic position of these populations among A. spinosissimus, as well as their relationships with other species (A. subspinosus and A. wilsoni). The monophyly of the spinosissimus clade is supported by morphological and molecular phylogenies. Cytogenetics and morphology, but not the cytochrome b phylogeny show the possible existence of two sibling species within spinosissimus. Incongruences are noted between molecular and morphological trees, especially concerning the position of the Transvaal specimens. Two different biogeographic scenarios for the origin and dispersal of A. spinosissimus are discussed in the light of available palaeontological data.     

Species relationships in the genus Vasconcellea (Caricaceae) based on molecular and morphological evidence

Validity of the taxa currently recognized in the genus Vasconcellea was analyzed by investigating morphological and molecular data from 105 specimens of this genus and six specimens of the related genus Carica. Taxon identification of these specimens was compared with clustering in two phenetic dendrograms generated with 36 morphological characters and 254 amplified fragment length polymorphic (AFLP) markers. Moreover, cytoplasmic haplotypes were assessed using polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) of one mitochondrial and two chloroplast DNA regions. Results show that the morphological data set, containing mainly vegetative characteristics, merely reveals external resemblance between specimens, which is not directly associated with genetic relationships and taxon validity. Phenotypic plasticity and intercompatibility between several species are likely to confuse morphological delimitation of the taxa. Based on the results of our study, several specimens that could not be identified with the currently used identification key (1) could be attributed to a known taxon, which should be extended to include a higher range of morphological variability or (2) could be hypothesized to be of hybrid origin. Because of the high intraspecific variation within V. microcarpa and V. × heilbornii, revision of these taxa is recommended.     

Suprageneric relationships of galliform birds (Aves, Galliformes): a cladistic analysis of morphological characters

Of the basal clades of extant birds (Neornithes) the 'landfowl' or galliforms (Aves, Galliformes) are the most speciose. Cladistic analysis of more than 100 morphological characters coded at the generic level for most putative galliform genera confirms that the megapodes ('mound builders'; Megapodiidae) are the most basal clade within the order. They are followed successively by the curassows, guans and chachalacas (Cracidae), which comprise the sister-group to all other extant Galliformes (i.e. Phasianoidea). Within this large 'phasianoid' clade, analyses suggest that the guineafowl (Numididae) are the most basal taxon, although monophyly of this 'family' is not strictly supported on the basis of the morphological characters employed. An additional major clade within the phasianoid Galliformes is recovered by this analysis, comprising the traditional groupings of New World quails (Odontophoridae) and Old World quails ('Perdicini'), yet only monophyly of the former is supported unambiguously by morphological characters. Relationships within the remainder of the phasianoid taxa, including the grouse (Tetraonidae), turkeys (i.e. Meleagris / Agriocharus spp.) as well as other 'pavonine' galliforms (i.e. peafowl; Pavo , Afropavo , Rheinardia , Argusianus and Polyplectron spp.) remain largely unresolved on the basis of morphological characters, yet monophyly of the major subdivisions is supported here. Although there are a number of important differences, especially with regard to relationships within the nonquail phasianoids, the results of this morphological phylogenetic (cladistic) analysis are broadly congruent both with traditional classifications and existing molecular hypotheses of galliform phylogenetic relationships.     

Phylogeny of the spider genus Ixchela Huber, 2000 (Araneae: Pholcidae) based on morphological and molecular evidence (CO1 and 16S), with a hypothesized diversification in the Pleistocene

The genus Ixchela Huber is composed of 20 species distributed from north‐eastern Mexico to Central America, including the five new species described here from Mexico: I xchela azteca sp. nov. , I xchela jalisco sp. nov. , I xchela mendozai sp. nov. , I xchela purepecha sp. nov. and I xchela tlayuda sp. nov. We test the monophyly and investigate the phylogenetic relationships among species of the genus Ixchela using morphological and molecular data. Parsimony (PA) analysis of 24 taxa and 40 morphological characters with equal and implied weights supported the monophyly of Ixchela with eight morphological synapomorphies. The PA analyses with equal and implied weights, and separate Bayesian inference (BI) analyses for the CO1 gene (506 characters), concatenated gene fragments CO1 + 16S (885 characters), morphology + CO1 (546 characters) and the combined evidence data set (morphology + CO1 + 16S) (925 characters) support the monophyly of Ixchela. Our preferred topology shows two large clades; clade 1 has a natural distribution in the Mesoamerican biotic component, whereas clade 2 predominates in the Mexican Montane biotic component. The genus Ixchela diverged in the late Miocene, and the divergence between the internal clades in the genus occurred in the late Pliocene; by contrast, most of the speciation events seem to have occurred mainly during the Pleistocene, where climatic changes brought on by repeated glaciations played an important role in the diversification of the genus. © 2015 The Linnean Society of London