A plastid DNA phylogeny of the genus Acacia Miller (Acacieae, Leguminoseae)

Past classifications of the tribe Acacieae Rchb. are outlined and the confusion concerning the relationships of the three subgenera of Acacia Mill. are highlighted. A plastid DNA analysis of Acacieae shows that the genus Acacia is not monophyletic. Furthermore subgenera Acacia Vassal and Aculeiferum Vassal are sister taxa and neither appear closely related to subgenus Phyllodineae (DC.) Ser. Subgenera Acacia and Aculeiferum form a clade that is basal to a well-supported clade consisting of tribe Ingeae Benth. taxa, Faidherbia albida (Del.) A. Chev. and subgenus Phyllodineae. The series of relationships suggested by the cpDNA data contradicts previous investigations of the tribe. Possible explanations of this conflict are explored, and the taxonomic implications of the plastid DNA data set are considered.     

Cotyledon architecture and anatomy in the Acacieae (Leguminosae: Mimosoideae)

Cotyledon size, shape, venation pattern and anatomy have been investigated in Faidherbia albida and 152 species of Acacia representing the three subgenera Acacia, Aculeiferum and Heterophyllum. Cell volumes of epidermis, palisade and storage tissue, stomatal frequency, stomatal index and frequency of stomatal types have been determined for F. albida and 12 species from each subgenus. The data obtained support the recognition of the subgenera of Acacia as separate taxa but provide no indication of their status. The evidence from cotyledons also supports the separation of Faidherbia from Acacia , and the amalgamation of the Acacieae and Ingeae.     

Molecular systematics of Boraginaceae tribe Boragineae based on ITS1 and trnL sequences, with special reference to Anchusa s.l

BACKGROUND AND AIMS: Boragineae is one of the main tribes of Boraginaceae, but delimitation and intergeneric classification of this group are unclear and have not yet been studied using DNA sequences. In particular, phylogenetic relationships in Anchusa s.l. still need to be elucidated in order to assess its taxonomic boundaries with respect to the controversial segregate genera Hormuzakia, Gastrocotyle, Phyllocara and Cynoglottis. METHODS: Phylogenetic relationships among 51 taxa of tribe Boragineae were investigated by comparative sequencing of the trnL(UAA) intron of the plastid genome and of the ITS1 region of the nuclear ribosomal DNA. Exemplar taxa from 16 genera of Boragineae and all subgenera of Anchusa s.l. were included, along with two selected outgroups from tribes Lithospermeae and Cynoglosseae. KEY RESULTS: Phylogenies generated by maximum parsimony and combined ITS1-trnL sequences support the monophyly of the tribe and a split into two clades, Pentaglottis and the remainder of Boragineae. The latter contains two large monophyletic groups. The first consists of three moderately to well-supported branches, Borago-Symphytum, Pulmonaria-Nonea and Brunnera. In the Pulmonaria-Nonea subclade, the rare endemic Paraskevia cesatiana is sister to Pulmonaria, and Nonea appears to be paraphyletic with respect to Elizaldia. The second main group corresponds to the well-supported clade of Anchusa s.l., with the megaphyllic, polyploid herb Trachystemon orientalis as sister taxon, although with low support. Anchusa s.l. is highly paraphyletic to its segregate genera and falls into four subclades: (1) Phyllocara, Hormuzakia, Anchusa subgenus Buglossum and A. subgenus Buglossoides; (2) Gastrocotyle; (3) A. subgenus Buglossellum and Cynoglottis; and (4) A. subgenus Anchusa, Lycopsis and Anchusella. All species of Anchusa subg. Anchusa, including the South African A. capensis, are included in a single unresolved clade. Anchusa subgenus Limbata is also included here despite marked divergence in floral morphology. The low nucleotide variation of ITS1 suggests a recent partly adaptive radiation within this group. CONCLUSIONS: Molecular data show that nine of the usually accepted genera of the Boragineae consisting of two or more species are monophyletic: Anchusella, Borago, Brunnera, Cynoglottis, Gastrocotyle, Hormuzakia, Nonea, Pulmonaria and Symphytum. In addition, the tribe includes the four monotypic genera Paraskevia, Pentaglottis, Phyllocara and Trachystemon. The morphologically well-characterized segregate genera in Anchusa s.l. are all confirmed by DNA sequences and should be definitively accepted. Most of the traditionally recognized subgenera of Anchusa are also supported as monophyletic groups by both nuclear and plastid sequence data. In order to bring taxonomy in line with phylogeny, the institution of new, independent generic entities for subgenera Buglossum, Buglossellum and Buglossoides and a narrower but more natural concept of Anchusa are advocated.     

Phylogeny and classification of Muscini (Diptera, Muscidae)

Worldwide in distribution, the tribe Muscini comprises 21 accepted genera and about 350 species. In the present study, a cladistic analysis based upon adult morphological characters is carried out in order to discuss the monophyly of the tribe and its genera, the intergeneric relationships and, in some cases, also the intrageneric relationships. As a result, Muscini is supported as a monophyletic tribe sister-group of Stomoxyini. Except for Morellia Robineau-Desvoidy, Curranosia Paterson, and Eudasyphora Townsend, all the remaining genera are monophyletic. The results are dubious for Polietes Rondani, which was then provisionally kept unchanged. Morellia was broadened to include the Neotropical endemic genera Parapyrellia Townsend, Trichomorellia Stein, and Xenomorellia Malloch. Therefore, a new classification is proposed for Morellia in which it is divided into four subgenera: Morellia s.s. , Parapyrellia , Trichomorellia , and Xenomorellia . Furthermore, the previously proposed subgenus Dasysterna Zimin is given new status as a genus; however, as it is preoccupied by Dasysterna Dejean, the new replacement name Ziminellia nom. nov. is proposed herewith. Eudasyphora was found to be a paraphyletic group relative to Dasyphora Robineau-Desvoidy; both genera are hence synonymized, and Dasyphora is classified in three subgenera: Dasyphora s.s. , Eudasyphora , and Rypellia Malloch. The analysis demonstrated that the traditional classification of Musca Linnaeus into subgenera is artificial and, moreover, that the use of characters from male genitalia could be strongly informative for classifying the genus in phylogeny-supported species groups. Finally, the new classification proposal for Muscini recognizes 18 genera and, furthermore, two undescribed genus-ranked taxa are indicated.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 149 , 493–532.     

Molecular phylogenetics of the genus Ceratitis (Diptera: Tephritidae)

The Afrotropical fruit fly genus Ceratitis MacLeay is an economically important group that comprises over 89 species, subdivided into six subgenera. Cladistic analyses of morphological and host use characters have produced several phylogenetic hypotheses for the genus. Only monophyly of the subgenera Pardalaspis and Ceratitis (sensu stricto) and polyphyly of the subgenus Ceratalaspis are common to all of these phylogenies. In this study, the hypotheses developed from morphological and host use characters are tested using gene trees produced from DNA sequence data of two mitochondrial genes (cytochrome oxidase I and NADH-dehydrogenase subunit 6) and a nuclear gene (period). Comparison of gene trees indicates the following relationships: the subgenus Pardalaspis is monophyletic, subsection A of the subgenus Pterandrus is monophyletic, the subgenus Pterandrus may be either paraphyletic or polyphyletic, the subgenus Ceratalaspis is polyphyletic, and the subgenus Ceratitis s. s. might not be monophyletic. In addition, the genera Ceratitis and Trirhithrum do not form reciprocally monophyletic clades in the gene trees. Although the data statistically reject monophyly for Trirhithrum under the Shimodaira-Hasegawa test, they do not reject monophyly of Ceratitis.     

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 of Drosophila and related genera: conflict between molecular and anatomical analyses

Drosophila species are extensively used in biological research; yet, important phylogenetic relationships within the genus and with related genera remain unresolved. The combined data for three genes (Adh, Sod, and Gpdh) statistically resolves outstanding issues. We define the genus Drosophila inclusively so as to include Scaptomyza and Zaprionus (considered distinct genera in the taxonomy of Wheeler, 1981) but excluding Scaptodrosophila. The genus Drosophila so defined is monophyletic. The subgenus Sophophora (including the melanogaster, obscura, and willistoni groups) is monophyletic and the sister clade to all other Drosophila subgenera. The Hawaiian Drosophila (including Scaptomyza) is a monophyletic group, but the subgenus Drosophila is not monophyletic, because the immigrans group is more closely related to the subgenus Hirtodrosophila than to other species of the subgenus Drosophila, such as the virilis and repleta groups.     

Derivation and dispersal of Acacia (Leguminosae), with particular reference to Australia, and the recognition of Senegalia and Racosperma

The morphology of seedlings, leaves, flowers and inflorescences, anatomy of the pod, the occurrence of extra-floral nectaries, free amino acids of the seeds, flavonoid compounds in heartwoods, cyanogenic compounds and porate, colporate and extraporate pollen, and susceptibility to rusts, all indicate that three genera, Acacia Miller, Senegalia Raf. and Racosperma Martius, should be recognized. These correspond to currently accepted subgenera of Acacia. The size of these more narrowly circumscribed genera is in keeping with the size of genera of other tribes of low diversity in Leguminosae. Acacia and Senegalia arose independently from the Ingeae, with Racosperma being derived from Senegalia. Section Filicinae is more advanced than section Senegalia of Senegalia , and sections Racosperma and Pukhella , both with at least some species with bipinnate foliage, are the most advanced of Racosperma , while the other sections Pleurinervia and Lycopodiifolia have only phyllodinous species. Long-range dispersal of Racosperma from the Australian region has occurred, but the broad pattern of distribution is interpreted in terms of plate tectonics. Racosperma was present in Australia in the late Cretaceous but did not become widespread until the general drying of the continent in the Miocene. The flora of SW Australia has been isolated from the rest of the continent by climatic barriers since the late Tertiary and has a high proportion of endemic species. Barriers to plant migration in the east have operated only intermittently and there is no area comparable in endemism to the southwest.     

The Genus Artemisia and its Allies: Phylogeny of the Subtribe Artemisiinae (Asteraceae, Anthemideae) Based on Nucleotide Sequences of Nuclear Ribosomal DNA Internal Transcribed Spacers (ITS)

Abstract: Sequences of the internal transcribed spacers (ITS1 and ITS2) of nuclear ribosomal DNA were analysed for 44 Artemisia species (46 populations) representing all the five classical subgenera and the geographical range of the genus, 11 species from 10 genera closely related to Artemisia, and six outgroup species from five other genera of the Anthemideae. The results definitely support the monophyly of the genus Artemisia in its broadest sense (including some taxa segregated as independent genera, like Oligosporus and Seriphidium ). Eight main clades are established in this molecular phylogeny within Artemisia; they agree in part with the classical subdivision of the genus, but they also suggest that some infrageneric groups must be redefined, especially the subgenus Artemisia. The subgenera Tridentatae and Seriphidium are independent from each other. Some of the satellite genera are clearly placed within Artemisia ( Artemisiastrum, Filifolium, Mausolea, Picrothamnus, Sphaeromeria, Turaniphytum ), whereas some others fall outside the large clade formed by this genus (Brachanthemum, Elachanthemum, Hippolytia, Kaschgaria). Our results, correlated to other data such as pollen morphology, allow us to conclude that the subtribe Artemisiinae as currently defined is a very heterogeneous group. Affinities of the largest genus of the subtribe and tribe, Artemisia, and of other genera of the subtribe to some genera from other subtribes of the Anthemideae strongly suggest that subtribe Artemisiinae needs a deep revision and redefinition. Phylogenetic utility of region trnL-F of the plastid DNA in the genus Artemisia and allies was also evaluated: sequences of the trnL-F region in Artemisia do not provide phylogenetic information.     

Phylogeny of the genus Peperomia (Piperaceae) inferred from the trnK/matK region (cpDNA)

The genus Peperomia is one of the largest genera of basal angiosperms, comprising about 1500-1700 pantropically distributed species. The currently accepted infrageneric classification divides Peperomia into nine subgenera and seven sections. This classification is based on some 200 species, primarily using fruit morphology. The monophyly of these infrageneric taxa has never been tested and molecular phylogenetic studies of a representative sampling within Peperomia do not exist. This paper provides the first molecular phylogeny for the genus Peperomia. Monophyletic clades within Peperomia are identified and previously used morphological characters are critically reviewed. We show that the importance of some morphological characters has been overestimated and that some of these characters presumably have evolved several times independently. Only one previously described subgenus has been confirmed to be monophyletic.     

The plam-feeding planthopper genus Ommatissus (Homoptera: Fulgoroidea: Tropiduchidae)

Abstract The tribe Trypetimorphini, the genus Ommatissus , and its two subgenera and eleven species are redescribed or described as new. Evidence for the monophyly of both the genus and of the tribe to which it belongs is examined; it is concluded that while the genus is monophyletic, the monophyly of the tribe is in doubt. Keys for the separation of the three genera of the tribe and for all of the known species of Ommatissus are presented. A new subgenus of Ommatissus is described: O.(Opatissus) , with the type-species O.vietnamicus . Four new species are described: Ommatissus magribus from Morocco, O.kamerunus from Cameroon, O.natalensis from South Africa and O.vietnamicus from Vietnam. The 'Dubas bug', Ommatissus lybicus Bergevin, formerly regarded as a variety of O.binotatus Fieber, is raised to full species status. Trichoduchus is synonymized with Trypetimorpha resulting in the new combinations Trypetimorpha biermani Dammerman, T.china Wu and T.japonicus Ishihara. Trichoduchus japonicus Fennah is synonymized with Trypetimorpha japonicus Ishihara.     

Molecular phylogenetic analysis of Arenaria (Caryophyllaceae: tribe Arenarieae) and its allies inferred from nuclear DNA internal transcribed spacer and plastid DNA rps16 sequences

The systematics and phylogeny of the genus Arenaria and allied genera are unresolved. The use of morphological data has resulted in contradictory taxonomic concepts in the past due to their homoplastic nature. We present a phylogenetic analysis based on internal transcribed spacer (ITS) and rps16 sequence data of 140 (132 taxa) and 131 (120 taxa) accessions, respectively. Maximum parsimony and Bayesian analyses of each marker produced nearly congruent trees. Monophyly of Arenaria s.s. and Eremogone is confirmed here. Our results corroborate earlier results indicating that Arenaria subgenus Odontostemma is monophyletic, but outside the core group of Arenaria. Arenaria subgenus Solitaria is sister to Odontostemma and also not closely related to the latter; both of these subgenera are excluded from Arenaria and treated as distinct genera. The molecular data indicate that the ‘Arenaria s.s. clade’ consists of a few well‐supported subgroups and that the current subgeneric classification of the genus does not reflect evolutionary history. Arenaria subgenus Leiosperma is clearly monophyletic, but we reduce it to sectional level. Our molecular data show that the monotypic Arenaria subgenera Porphyrantha and Arenariastrum are nested in A. subgenus Arenaria, whereas subgenus Eremogoneastrum is included in Eremogone. None of the species‐rich sections in subgenus Arenaria is monophyletic. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178 , 648–669.     

Phylogeny and classification of diving beetles in the tribe Cybistrini (Coleoptera, Dytiscidae, Dytiscinae)

Phylogenetic relationships among members of the diving beetle tribe Cybistrini (Coleoptera: Dytiscidae) were inferred from analysis of 47 adult and larval morphological characters and sequences from portions of the genes cytochrome oxidase I (COI) and II (COII), histone III (H3) and wingless. Thirty‐three species of Cybistrini were included, representing all genus‐groups except Regimbartina Chatanay and Megadytes (Bifurcitus) Brinck, and most historically recognized species groups and subgenera used in the tribe. Outgroups include six species from other tribes within Dytiscinae and Lancetinae. Analyses included parsimony analysis of the combined data, likelihood analysis of combined molecular data and partitioned Bayesian analysis of the combined data. Results indicate that Cybistrini is well supported as a monophyletic group. Within the tribe, all currently recognized genus groups were found to be monophyletic with the exception of Onychohydrus Schaum, which is paraphyletic with respect to Austrodytes Watts in the parsimony analysis, but monophyletic in the likelihood and Bayesian analyses, and Cybister sensu stricto, which is paraphyletic with respect to C. (Melanectes) Brinck and C. (Scaphinectes) Ádám in the parsimony analysis or only the latter in the likelihood and Bayesian analyses. Results also suggest that some, but not all, historically recognized species groups or subgenera in the large genus Cybister Curtis are monophyletic, and this is discussed and compared. To improve the classification, the name Sternhydrus Brinck is elevated from subgenus to genus rank ( new status ). Four subgenera in the genus Cybister are recognized: C. (Melanectes) Brinck, C. (Megadytoides) Brinck ( resurrected ), C. (Neocybister) Miller, Bergsten and Whiting ( new subgenus ) and C. (Cybister) Curtis. The following new synonyms are established: Trochalus Dejean ( new synonym ), and ScaphinectesÁdám = Cybister (Cybister) ( new synonym ). The Neotropical species Cybister parvus Trémouilles (not examined) apparently does not fit any historical or currently recognized genus‐group diagnosis in Cybistrini, so it is retained in Cybister but incertae sedis with respect to subgenus. In addition to classification, the evolution of the unique character combinations present in cybistrines are discussed. A key to the adults of genera and subgenera is presented.     

Phylogeny of Iris based on chloroplast matK gene and trnK intron sequence data

Phylogenetic analyses of 46 species of Iris, representing all subgenera and all sections except Regelia, Brevituba, and Monolepis, utilized matK gene and trnK intron sequence data. Sequence data show that Iris is paraphyletic because Belamcanda chinensis is resolved within the genus. The two largest subgenera, Iris and Limniris, are both resolved as polyphyletic. With the removal of section Hexapogon, subgenus Iris is weakly supported as monophyletic. Relationships within subgenus Limniris are more complex with the subgenus as currently circumscribed representing eight independent origins among the species included in this study. Several potential monophyletic groups are identified including subgenus Scorpiris, series Spuria (subgenus Limniris section Limniris), and a clade of section Limniris species from North America and Asia.     

Phylogeny of Oriental voles (Rodentia: Muridae: Arvicolinae): molecular and morphological evidence

The systematics of Oriental voles remains controversial despite numerous previous studies. In this study, we explore the systematics of all species of Oriental voles, except Eothenomys wardi, using a combination of DNA sequences and morphological data. Our molecular phylogeny, based on two mitochondrial genes (COI and cyt b), resolves the Oriental voles as a monophyletic group with strong support. Four distinct lineages are resolved: Eothenomys, Anteliomys, Caryomys, and the new subgenus Ermites. Based on morphology, we consider Caryomys and Eothenomys to be valid genera. Eothenomys, Anteliomys, and Ermites are subgenera of Eothenomys. The molecular phylogeny resolves subgenera Anteliomys and Ermites as sister taxa. Subgenus Eothenomys is sister to the clade Anteliomys + Ermites. Caryomys is the sister group to genus Eothenomys. Further, the subspecies E. custos hintoni and E. chinensis tarquinius do not cluster with E. custos custos and E. chinensis chinensis, respectively, and the former two taxa are elevated to species level and assigned to the new subgenus Ermites.     

Phylogenetic analysis of the genus Cheilosia (Diptera, Syrphidae) using mitochondrial COI sequence data

The genus Cheilosia is one of the most diverse and speciose genera of Syrphidae (Diptera). The phylogenetic relationships of the hoverfly genus Cheilosia was investigated for the first time using molecular data. The mitochondrial protein-coding gene cytochrome c oxidase subunit I (COI) was chosen for sequencing; 1341 characters were obtained for 24 ingroup taxa and these were analyzed with parsimony. The monophyly of the genus Cheilosia was well supported. Current taxonomic division of Cheilosia into two subgenera (sg. Nigrocheilosia and sg. Neocheilosia) and most nonformalized species groups based on morphology were supported by the monophyletic groups identified in the molecular analysis. The phylogenetic informativeness of COI in resolving the subtribal relationships within the tribe Cheilosiini remains ambiguous.     

Phylogeny and systematics of the Trogidae (Coleoptera: Scarabaeoidea)

Abstract. A cladistic analysis of the Trogidae using eighteen adult characters resulted in a monophyletic group from which the genera Glaresis Erichson, Afroglaresis Petrovitz and Cryptogenius Westwood are excluded. The Trogidae as here defined comprises three genera, Trox Fabricius (with two subgenera, Trox and Phoberus Macleay), Omorgus Erichson (with three subgenera, Omorgus, Afromorgus subg.n. and Haroldomorgus subg.n.) and Polynoncus Burmeister.     

A review of the tribe Auletini (Coleoptera,Rhynchitidae) from the Russian fauna: 1. Subtribe Auletobiina

The genus Auletobius in the Russian fauna is revised. Five species (A. egorovi, A. irkutensis, A. puberulus, A. sanguisorbae, and A. submaculatus) belonging to two subgenera are revealed. The distribution of these species in Russia is given. The data on the trophic associations of the species are summarized. Keys to the subtribes of the tribe Auletini, subgenera of the genus Auletobius, and species of the subgenus Auletobius s. str. are given. All the taxa are redescribed.