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.     

Subfamilial relationships within Caryophyllaceae as inferred from 5' ndhF sequences

DNA sequences of the 5' end of the chloroplast ndhF gene for 15 species of Caryophyllaceae have been analyzed by parsimony and neighbor-joining analyses. Three major clades are identified, with little or no support for monophyly of traditionally recognized subfamilies. The first of the three major clades identified (Clade I) is constituted by part of the subfamily Paronychioideae. It includes members of the tribe Paronychieae and members of tribe Polycarpeae. The second (Clade II) contains members of the Paronychieae exclusively. Tribe Paronychieae is thus apparently polyphyletic and tribe Polycarpeae is at least paraphyletic. The third clade (Clade III) includes members of subfamilies Alsinoideae and Caryophylloideae along with the genus Spergularia. The genus Scleranthus is also part of Clade III, while Drymaria groups with the other genera of tribe Polycarpeae in Clade II. We conclude that morphological characters previously used to delimit subfamilial groupings in the Caryophyllaceae are apparently unreliable estimators of phylogeny.     

Phylogeny and classification of Marantaceae

Relationships of Marantaceae were estimated from nucleotide sequence variation in the rps16 intron (plastid DNA) and from morphological characters. Fifty-nine species (21 genera) formed the ingroup, and 12 species (12 genera) of other Zingiberales formed the outgroup. There is no support for the traditional subdivision of Marantaceae into a triovulate and a uniovulate tribe or the informal groups previously proposed. The so-called Donax group forms a paraphyletic grade that is basal within Marantaceae. Thalia appears as the distal branch of this grade, but its position is not supported in jackknife analysis. The so-called Calathea group is monophyletic in all shortest trees but not supported with greater than 50% jackknife. The genus Calathea appears to be paraphyletic. The Maranta and Phrynium groups are clearly polyphyletic. Maranta, Koernickanthe , and genera of the Mymsma group, all neotropical, form a strongly supported monophyletic group. The sister of this group is the palaeotropical genus Halopegia. Koernickanthe is nested within Maranta , as this genus is traditionally circumscribed. The African genera Ataenidia and Marantochloa form a strongly supported clade in which Ataenidia is the sister group to Marantochloa . Based on phylogeny it is concluded that Africa, in spite of being much poorer in species, is the most likely ancestral area of Marantaceae     

Molecular phylogeny of the arthrostylidioid bamboos (Poaceae: Bambusoideae: Bambuseae: Arthrostylidiinae) and new genus Didymogonyx

We present the first multi-locus chloroplast phylogeny of Arthrostylidiinae, a subtribe of neotropical woody bamboos. The morphological diversity of Arthrostylidiinae makes its taxonomy difficult and prior molecular analyses of bamboos have lacked breadth of sampling within the subtribe, leaving internal relationships uncertain. We sampled 51 taxa, chosen to span the range of taxonomic diversity and morphology, and analyzed a combined chloroplast DNA dataset with six chloroplast regions: ndhF, trnD-trnT, trnC-rpoB, rps16-trnQ, trnT-trnL, and rpl16. A consensus of maximum parsimony and Bayesian inference analyses reveals monophyly of the Arthrostylidiinae and four moderately supported lineages within it. Six previously recognized genera were monophyletic, three polyphyletic, and two monotypic; Rhipidocladum sect. Didymogonyx is here raised to generic status. When mapped onto our topology, many of the morphological characters show homoplasy.     

Molecular phylogeny of Nyctaginaceae: taxonomy, biogeography, and characters associated with a radiation of xerophytic genera in North America

The four o'clock family (Nyctaginaceae) has a number of genera with unusual morphological and ecological characters, several of which appear to have a "tendency" to evolve repeatedly in Nyctaginaceae. Despite this, the Nyctaginaceae have attracted little attention from botanists. To produce a phylogeny for the Nyctaginaceae, we sampled 51 species representing 25 genera (of 28-31) for three chloroplast loci (ndhF, rps16, rpl16, and nrITS) and included all genera from North America. Parsimony, likelihood, and Bayesian methods were used to reconstruct the phylogeny for the family. The family is neotropical in origin. A radiation of woody taxa unites Pisonia and Pisoniella with the difficult tropical genera Neea and Guapira, which also form a clade, though neither appears to be monophyletic. This group is sister to a clade containing Bougainvillea, Belemia, and Phaeoptilum. A dramatic radiation of genera occurred in the deserts of North America. The tribe Nyctagineae and its subtribes are paraphyletic, due to over-reliance on a few homoplasious characters, i.e., pollen morphology and involucre presence. Two notable characters associated with the desert radiation are cleistogamy and edaphic endemism on gypsum soils. We discuss evolutionary trends in these traits in light of available data about self-incompatibility and gypsum tolerance in Nyctaginaceae.     

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

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

A molecular phylogeny for digger wasps in the tribe Ammophilini (Hymenoptera,Apoidea, Sphecidae)

The evolution of parental care strategies in aculeate (stinging) wasps and bees has been much studied from a functional perspective, but relatively little phylogenetic information is available to place this in a rigorous historical context, especially at the species level. We used mitochondrial cytochrome oxidase I and two nuclear genes, the elongation factor‐1α and LW rhodopsin, to investigate the phylogeny of Sphecidae digger wasps. We focus particularly on the tribe Ammophilini, a clade of nonsocial apoid wasps that exhibit unusually diverse parental care strategies. We analysed a 2232 bp dataset for 40 ammophilines plus nine other taxa from within the remaining Sphecidae. Our Bayesian phylogeny provides strong support for the monophyly of Ammophilini and for the monophyly of all six individual ammophiline genera, except that the position of P. affinis within the genus Podalonia is only weakly supported. The monophyly of some, but not all, previously designated species groups within the genus Ammophila is supported. We discuss the implications of our results for the evolution of morphological traits used previously in ammophiline systematics.     

A molecular phylogeny and classification of Bignoniaceae

Bignoniaceae are woody, trees, shrubs, and lianas found in all tropical floras of the world with lesser representation in temperate regions. Phylogenetic analyses of chloroplast sequences (rbcL, ndhF, trnL-F) were undertaken to infer evolutionary relationships in Bignoniaceae and to revise its classification. Eight clades are recognized as tribes (Bignonieae, Catalpeae, Coleeae, Crescentieae, Jacarandeae, Oroxyleae, Tecomeae, Tourrettieae); additional inclusive clades are named informally. Jacarandeae and Catalpeae are resurrected; the former is sister to the rest of the family, and the latter occupies an unresolved position within the "core" Bignoniaceae. Tribe Eccremocarpeae is included in Tourrettieae. Past classifications recognized a large Tecomeae, but this tribe is paraphyletic with respect to all other tribes. Here Tecomeae are reduced to a clade of approximately 12 genera with a worldwide distribution in both temperate and tropical ecosystems. Two large clades, Bignonieae and Crescentiina, account for over 80% of the species in the family. Coleeae and Crescentieae are each included in larger clades, the Paleotropical alliance and Tabebuia alliance, respectively; each alliance includes a grade of taxa assigned to the traditional Tecomeae. Parsimony inference suggests that the family originated in the neotropics, with at least five dispersal events leading to the Old World representatives.     

Genome relationship among nine species of Millettieae (Leguminosae: Papilionoideae) based on random amplified polymorphic DNA (RAPD)

Random amplified polymorphic DNA (RAPD) marker was used to establish intergeneric classification and phylogeny of the tribe Millettieae sensu Geesink (1984) (Leguminosae: Papilionoideae) and to assess genetic relationship between 9 constituent species belonging to 5 traditionally recognized genera under the tribe. DNA from pooled leaf samples was isolated and RAPD analysis performed using 25 decamer primers. The genetic similarities were derived from the dendrogram constructed by the pooled RAPD data using a similarity index, which supported clear grouping of species under their respective genera, inter- and intra-generic classification and phylogeny and also merger of Pongamia with Millettia. Elevation of Tephrosia purpurea var. pumila to the rank of a species (T. pumila) based on morphological characteristics is also supported through this study of molecular markers.     

Phylogenetic placement of the anamorphic tribe Ustilaginoideae (Hypocreales, Ascomycota)

Tribe Ustilaginoideae (Hypocreales, Ascomycetes) is made up of three anamorph genera, Munkia, Neomunkia and Ustilaginoidea. Species of Munkia and Neomunkia develop on the culms of bamboo (Chusquea spp.) and have a neotropical distribution while species of Ustilaginoidea infect the florets of various grasses and are pantropical in distribution. In this study we evaluated the phylogeny of the tribe and assessed hypotheses regarding its affinity to clavicipitalean teleomorphic groups. To support phylogenetic analyses, morphology of representatives of several key species of Ustilaginoideae was examined also. Phylogenetic analyses using sequences of the large subunit of the ribosomal RNA gene suggest that members of Ustilaginoideae are distinct from teleomorphic genera of Clavicipitaceae and that Ustilaginoideae should be recognized as a monophyletic group within Hypocreales. However, phylogenetic analyses did not resolve the placement of Ustilaginoideae in Clavicipitaceae or Hypocreaceae, suggesting that it might be a distinct lineage within Hypocreales. This evaluation supported the monophyly of tribes Balansieae and Clavicipeae in the family Clavicipitaceae.     

A molecular phylogeny of the grass subfamily Panicoideae (Poaceae) shows multiple origins of C4 photosynthesis

DNA sequence data from the chloroplast gene ndhF were analyzed to estimate the phylogeny of the subfamily Panicoideae, with emphasis on the tribe Paniceae. Our data suggest that the subfamily is divided into three strongly supported clades, corresponding to groups with largely identical base chromosome numbers. Relationships among the three clades are unclear. In unweighted parsimony analyses, the two major clades with x = 10 (Andropogoneae and x = 10 Paniceae) are weakly supported as sister taxa. The third large clade corresponds to x = 9 Paniceae. In analyses under implied weight, the two clades of Paniceae are sisters, making the tribe monophyletic. Neither resolution is strongly supported.Our molecular phylogenies are not congruent with previous classifications of tribes or subtribes. Based on this sample of species, we infer that C(4) photosynthesis has evolved independently several times, although a single origin with multiple reversals and several reacquisitions is only slightly less parsimonious. The phosphoenol pyruvate carboxykinase (PCK) subtype of C(4) photosynthesis has evolved only once, as has the NAD-malic enzyme (ME) subtype; all other origins are NADP-ME. Inflorescence bristles are apparently homologous in the genera Setaria and Pennisetum, contrary to opinions of most previous authors. Some genera, such as Digitaria, Echinochloa, and Homolepis are supported as monophyletic. The large genus Paspalum is shown to be paraphyletic, with Thrasya derived from within it. As expected, Panicum is polyphyletic, with lineages derived from multiple ancestors across the tree. Panicum subg. Panicum is monophyletic. Panicum subg. Dichanthelium, subg. Agrostoides, and subg. Phanopyrum are unrelated to each other, and none is monophyletic. Only Panicum subg. Dichanthelium sect. Dichanthelium, represented by P. sabulorum and P. koolauense, is monophyletic. Panicum subg. Megathyrsus, a monotypic subgenus including only the species P. maximum, is better placed in Urochloa, as suggested by other authors.     

Phylogeny and morphological evolution of tribe Menispermeae (Menispermaceae) inferred from chloroplast and nuclear sequences

The Menispermaceae family contains ca. 72 genera with 450 species that are almost entirely tropical. Its phylogeny at the tribal level has never been examined using molecular data. Here we used DNA sequences of the chloroplast matK gene and trnL-F regions, and the nuclear ITS region to study the delimitation and position of the tribe Menispermeae within the family and its subtribal monophyletic groups. Family-wide phylogenetic analyses of the chloroplast data produced two strongly supported clades. The first clade contains two subclades: Coscinieae including Arcangelisia and Anamirta, and Tinosporeae sensu lato including Fibraureae, supported by morphological characters, such as traits of the cotyledon, stylar scar and embryo. The second clade consists of the tribes Menispermeae sensu DC. and Tiliacoreae Miers. All our analyses surprisingly recognized that tribe Menispermeae is not monophyletic unless tribe Tiliacoreae is included, suggesting that characters of cotyledon and stylar scar are very important for the infrafamilial classification, and that endosperm presence vs. absence was over-emphasized in traditionally tribal division of the family. Our topologies indicate a secondary loss of endosperm. The monophyly of two subtribes of the tribe Menispermeae, Stephaniinae and Cissampelinae, is supported by the cpDNA and ITS data, as well as by morphological characters, including aperture types and shapes, and colpal membrane features of pollen grains, and sepal number of male flowers. The Cocculinae was recognized as a paraphyletic group containing the remaining genera of the tribe Menispermeae.     

Madagasikaria (Malpighiaceae): a new genus from Madagascar with implications for floral evolution in Malpighiaceae

Madagasikaria andersonii is described here as a new genus and species of Malpighiaceae from Madagascar. The phylogenetic placement of Madagasikaria was estimated by using combined data from ndhF and trnL-F chloroplast sequences and phytochrome (PHYC) and ITS nuclear sequences. It forms a strongly supported clade with the Malagasy endemic genera Rhynchophora and Microsteira. Despite nearly identical floral morphology among species in this clade (here called the madagasikarioid clade), these genera are easily distinguishable on the basis of their fruits. The schizocarpic fruits of Madagasikaria have distinctive mericarps. Each mericarp has a lateral wing, which completely encircles the nut, and a peculiar dorsal wing, which folds over on itself. The morphology of this fruit suggests that the homology of the unusual wing in Rhynchophora is lateral in nature and represents a reduced wing similar to the lateral wing in Madagasikaria. Taxa in the madagasikarioid clade all appear to be morphologically androdioecious and functionally dioecious, producing both staminate and "bisexual" (i.e., functionally carpellate) individuals. This condition appears to be exceedingly rare in flowering plants and has important implications for floral evolution within Malpighiaceae. Neotropical Malpighiaceae are pollinated by specialized oil-collecting anthophorine bees of the tribe Centridini and exhibit highly conserved floral morphology despite tremendous diversity in fruit morphology and habit. These oil-collecting bees are absent from the paleotropics, where most members of the Malpighiaceae lack both the oil glands and the typical floral orientation crucial to pollination by neotropical oil-collecting bees. The madagasikarioids represent one shift from the neotropical pollination syndrome among Old World Malpighiaceae.     

The distribution of iridoids in Bignoniaceae

The distribution of iridoids among the tribes of Bignoniaceae is shown. In the present work, 18 species from the tribes Bignonieae and Tecomeae as well as one from Eccremocarpeae have been investigated. These data combined with those obtained through a literature review were analysed and showed that iridoids occur predominantly in the tribe Tecomeae. In this tribe, a chemical distintion between the genera Tabebuia and Tecoma was observed: The iridoids in Tabebuia are decarboxylated whereas in Tecoma they are C-4 formylated. The species from Bignonieae are poorly investigated and only few reports have been published, however, the iridoids found are mainly C-4 carboxylated. The only exception, Dolichandra cynanchoides (=Macfadyena cynanchoides), with decarboxylated iridoids, is also morphologically abnormal in Bignonieae.     

Evolution of floral morphology and pollination system in Bignonieae (Bignoniaceae)

The radiation of angiosperms is associated with shifts among pollination modes that are thought to have driven the diversification of floral forms. However, the exact sequence of evolutionary events that led to such great diversity in floral traits is unknown for most plant groups. Here, we characterize the patterns of evolution of individual floral traits and overall floral morphologies in the tribe Bignonieae (Bignoniaceae). We identified 12 discrete traits that are associated with seven floral types previously described for the group and used a penalized likelihood tree of the tribe to reconstruct the ancestral states of those traits at all nodes of the phylogeny of Bignonieae. In addition, evolutionary correlations among traits were conducted using a maximum likelihood approach to test whether the evolution of individual floral traits followed the correlated patterns of evolution expected under the "pollination syndrome" concept. The ancestral Bignonieae flower presented an Anemopaegma-type morphology, which was followed by several parallel shifts in floral morphologies. Those shifts occurred through intermediate stages resulting in mixed floral morphologies as well as directly from the Anemopaegma-type morphology to other floral types. Positive and negative evolutionary correlations among traits fit patterns expected under the pollination syndrome perspective, suggesting that interactions between Bignonieae flowers and pollinators likely played important roles in the diversification of the group as a whole.     

Molecular phylogeny of the family of apes and humans

The morphological picture of primate phylogeny has not unambiguously identified the nearest outgroup of Anthropoidea and has not resolved the branching pattern within Hominoidea. The molecular picture provides more resolution and clarifies the systematics of Hominoidea. Protein and DNA evidence divides Hominoidea into Hylobatidae (gibbons) and Hominidae, family Hominidae into Ponginae (orangutan) and Homininae, and subfamily Homininae into two tribes, one for Gorilla, and the other for Pan (chimpanzee) and Homo. Parsimony and maximum likelihood analyses, carried out on orthologous noncoding nucleotide sequences from primate beta-globin gene clusters, provide significant evidence for the human-chimpanzee tribe and overwhelming evidence for the human-chimpanzee-gorilla clade. These analyses also indicate that the rate of molecular evolution became slower in hominoids than in other primates and mammals.     

Higher level molecular phylogeny of darkling beetles (Coleoptera: Tenebrionidae)

Insect diversity represents about 60% of the estimated million‐and‐a‐half described eukaryotic species worldwide, yet comprehensive and well‐resolved intra‐ordinal phylogenies are still lacking for the majority of insect groups. This is the case especially for the most species‐rich insect group, the beetles (Coleoptera), a group for which less than 4% of the known species have had their DNA sequenced. In this study, we reconstruct the first higher level phylogeny based on DNA sequence data for the species‐rich darkling beetles, a family comprising at least 20 000 species. Although amongst all families of beetles Tenebrionidae ranks seventh in terms of species diversity, the lack of knowledge on the phylogeny and systematics of the group is such that its monophyly has been questioned (not to mention those of the subfamilies and tribes contained within it). We investigate the evolutionary history of Tenebrionidae using multiple phylogenetic inference methods (Bayesian inference, maximum likelihood and parsimony) to analyse a dataset consisting of eight gene fragments across 404 taxa (including 250 tenebrionid species). Although the resulting phylogenetic framework only encompasses a fraction of the known tenebrionid diversity, it provides important information on their systematics and evolution. Whatever the methods used, our results provide strong support for the monophyly of the family, and highlight the likely paraphyletic or polyphyletic nature of several important tenebrionid subfamilies and tribes, notably the polyphyletic subfamilies Diaperinae and Tenebrioninae that clearly require substantial revision in the future. Some interesting associations in several groups are also revealed by the phylogenetic analyses, such as the pairing of Aphtora Bates with Phrenapatinae. Furthermore this study advances our knowledge of the evolution of the group, providing novel insights into much‐debated theories, such as the apparent relict distribution of the tribe Elenophorini.