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.     

A new phylogenetic tribal classification of the grape family (Vitaceae)

Vitaceae (the grape family) consist of 16 genera and ca. 950 species primarily distributed in tropical regions. The family is well‐known for the economic importance of grapes, and is also ecologically significant with many species as dominant climbers in tropical and temperate forests. Recent phylogenetic and phylogenomic analyses of sequence data from all three genomes have supported five major clades within Vitaceae: (i) the clade of Ampelopsis, Nekemias, Rhoicissus, and Clematicissus; (ii) the Cissus clade; (iii) the clade of Cayratia, Causonis, Cyphostemma, Pseudocayratia, Tetrastigma, and an undescribed genus “Afrocayratia”; (iv) the clade of Parthenocissus and Yua; and (v) the grape genus Vitis and its close tropical relatives Ampelocissus, Pterisanthes and Nothocissus, with Nothocissus and Pterisanthes nested within Ampelocissus. Based on the phylogenetic and morphological (mostly inflorescence, floral and seed characters) evidence, the new classification places the 950 species and 16 genera into five tribes: (i) tribe Ampelopsideae J.Wen & Z.L.Nie, trib. nov. (47 species in four genera; Ampelopsis, Nekemias, Rhoicissus and Clematicissus); (ii) tribe Cisseae Rchb. (300 species in one genus; Cissus); (iii) tribe Cayratieae J.Wen & L.M.Lu, trib. nov. (370 species in seven genera; Cayratia, Causonis, “Afrocayratia”, Pseudocayratia, Acareosperma, Cyphostemma and Tetrastigma); (iv) tribe Parthenocisseae J.Wen & Z.D.Chen, trib. nov. (ca. 16 spp. in two genera; Parthenocissus and Yua); and (v) tribe Viteae Dumort. (ca. 190 species in two genera; Ampelocissus and Vitis).     

A phylogenetic study of krill (Crustacea: Euphausiacea) reveals new taxa and co-evolution of morphological characters

The first comprehensive phylogenetic study of Euphausiacea (all 86 valid species) is presented. It is based on four molecular markers and 168 morphological characters (including 58 characters of the petasma). Phylogenetic analyses support the monophyly and robustness of the families Bentheuphausidae and Euphausiidae and reveal three major clades for which we erect three new subfamilies: Thysanopodinae, Euphausiinae and Nematoscelinae. All genus-level clades are statistically supported (except Thysanopoda in molecular analyses), deeply nested within the subfamily-level clades, and encompass 14 new species groups. Copulatory structures have a major impact on tree topology in the morphological analysis, the removal of which resulted in only half the number of supported clades and genera. We revealed three groups of morphological characters, which are probably coupled with the same biological role and thus interlinked evolutionarily: (i) antennular peduncle and petasma (copulation); (ii) eyes and anterior thoracopods (feeding); and (iii) shape of carapace and pleon (defence). We analysed the evolutionary pathways of the clades into main oceanic biotopes and compared them with morphological adaptations most likely to be coupled with this process.     

Phylogenetic relationships, character evolution, and taxonomic implications within the slipper lobsters (Crustacea: Decapoda: Scyllaridae)

The slipper lobsters belong to the family Scyllaridae which contains a total of 20 genera and 89 species distributed across four subfamilies (Arctidinae, Ibacinae, Scyllarinae, and Theninae). We have collected nucleotide sequence data from regions of five different genes (16S, 18S, COI, 28S, H3) to estimate phylogenetic relationships among 54 species from the Scyllaridae with a focus on the species rich subfamily Scyllarinae. We have included in our analyses at least one representative from all 20 genera in the Scyllaridae and 35 of the 52 species within the Scyllarinae. Our resulting phylogenetic estimate shows the subfamilies are monophyletic, except for Ibacinae, which has paraphyletic relationships among genera. Many of the genera within the Scyllarinae form non-monophyletic groups, while the genera from all other subfamilies form well supported clades. We discuss the implications of this history on the evolution of morphological characters and ecological transitions (nearshore vs. offshore) within the slipper lobsters. Finally, we identify, through ancestral state character reconstructions, key morphological features diagnostic of the major clades of diversity within the Scyllaridae and relate this character evolution to current taxonomy and classification.     

Molecular phylogenetics of Maxillaria and related genera (Orchidaceae: Cymbidieae) based on combined molecular data sets

The orchid genus Maxillaria is one of the largest and most common of neotropical orchid genera, but its current generic boundaries and relationships have long been regarded as artificial. Phylogenetic relationships within subtribe Maxillariinae sensu Dressler (1993) with emphasis on Maxillaria s.l. were inferred using parsimony analyses of individual and combined DNA sequence data. We analyzed a combined matrix of nrITS DNA, the plastid matK gene and flanking trnK intron, and the plastid atpB-rbcL intergenic spacer for 619 individuals representing ca. 354 species. The plastid rpoC1 gene (ca. 2600 bp) was sequenced for 84 selected species and combined in a more limited analysis with the other data sets to provide greater resolution. In a well-resolved, supported consensus, most clades were present in more than one individual analysis. All the currently recognized minor genera of "core" Maxillariinae (Anthosiphon, Chrysocycnis, Cryptocentrum, Cyrtidiorchis, Mormolyca, Pityphyllum, and Trigonidium) are embedded within a polyphyletic Maxillaria s.l. Our results support the recognition of a more restricted Maxillaria, of some previously published segregate genera (Brasiliorchis, Camaridium, Christensonella, Heterotaxis, Ornithidium, Sauvetrea), and of several novel clades at the generic level. These revised monophyletic generic concepts should minimize further nomenclatural changes, encourage monographic studies, and facilitate more focused analyses of character evolution within Maxillariinae.     

DNA barcoding of Caenogastropoda along coast of China based on the COI gene

DNA barcoding provides an efficient method for species-level identifications. In this study, we have amplified partial sequences of mitochondrial cytochrome c oxidase I (COI) gene from 110 specimens of 45 species of Caenogastropoda collected from the coast along China to evaluate whether DNA barcodes can distinguish these species accurately. The average Kimura 2-parameter (K2P) distances within species, genera and families were 0.44%, 13.96% and 22.27%, respectively. Both the neighbour-joining tree and the Bayesian tree showed a clear discrimination of all the species in our study with highly supported clades. These results proved that the species of Caenogastropoda can be efficiently and accurately identified by DNA barcoding based on the COI gene.     

Testing morphology-based hypotheses of phylogenetic relationships in Parmeliaceae (Ascomycota) using three ribosomal markers and the nuclear RPB1 gene

Parmeliaceae is the largest family of lichen-forming fungi with more than 2000 species and includes taxa with different growth forms. Morphology was widely employed to distinguish groups within this large, cosmopolitan family. In this study we test these morphology-based groupings using DNA sequence data from three nuclear and one mitochondrial marker from 120 taxa that include 59 genera and represent the morphological and chemical diversity in this lineage. Parmeliaceae is strongly supported as monophyletic and six well-supported main clades can be distinguished within the family. The relationships among them remain unresolved. The clades largely agree with the morphology-based groupings and only the placement of four of the genera studied is rejected by molecular data, while four other genera belong to clades previously unrecognised. The classification of these previously misplaced genera, however, has already been questioned by some authors based on morphological evidence. These results support morphological characters as important for the identification of monophyletic clades within Parmeliaceae.     

Born migrators: Historical biogeography of the cosmopolitan family Cannabaceae

Dispersal scenarios have been favored over tectonic vicariance as an explanation for disjunct distributions in many plant taxa during the last two decades. However, this argument has been insufficiently addressed in cosmopolitan groups showing disjunct patterns in both the temperate and tropical regions. In this study, we used the Cannabaceae, an angiosperm family distributed in tropical and temperate regions of both the New World and the Old World, to explore the role of dispersal in shaping disjunct patterns and species diversification of cosmopolitan plants. We reconstructed the phylogenetic relationships of all 10 genera and 75 species of Cannabaceae (ca. 64.1% of recognized species) based on eight DNA regions. Based on fossil calibrations, we estimated the divergence times and net diversification rates. We further inferred the ancestral geographical ranges with several models and compared the fitness of different models. The Cannabaceae and most genera were strongly supported as monophyletic except for the Parasponia being embedded within the Trema. The Celtis were resolved into two strongly supported clades primarily corresponding to temperate and tropical regions. We inferred that the Cannabaceae originated at ca. 93 Ma, and that subsequent rampant and widespread dispersals shaped the intercontinentally disjunct distribution of the Cannabaceae. Dispersal coincides with adaptation to drier and colder climate in the Northern Hemisphere, or humid and warm climate in the tropical regions, followed by rapid species diversification. This study advances our understanding as to the formation of distribution patterns and species diversification of a plant family with tropical to temperate disjunct distributions.     

Relationships among "ancient araliads" and their significance for the systematics of Apiales

The relationship between the angiosperm families Apiaceae and Araliaceae (order Apiales) has been difficult to resolve, due in large part to problems associated with taxa characterized by a mixture of features typical of both families. Among such confounding groups are the araliads Delarbrea, Pseudosciadium, Myodocarpus, Mackinlaya, and Apiopetalum and many members of Apiaceae subfamily Hydrocotyloideae. Traditional systems have often envisioned these taxa as phyletic intermediates or bridges between the two families. To reevaluate the phylogenetic position of the "intermediate" araliad genera, molecular data were collected from nuclear (rDNA ITS) and plastid (matK) sequences from a complete or near-complete sampling of species in each genus. When analyzed with samples representing the other major clades now recognized within Apiales, results confirm and expand the findings of previously published studies. The five araliad "intermediates" are placed within two well-supported clades clearly segregated from the "core" groups of both Apiaceae and Araliaceae. These segregate clades closely parallel traditional definitions of the araliad tribes Myodocarpeae (Delarbrea, Pseudosciadium, and Myodocarpus) and Mackinlayeae (Mackinlaya and Apiopetalum), and relationships among the species within these clades are largely supported by morphological and anatomical data. Based on these results, Myodocarpeae and Mackinlayeae may best be treated as distinct families. This approach would render four monophyletic groups within Apiales, to which a fifth, Pittosporaceae, cannot at present be excluded. Sampling of taxa from Hydrocotyloideae remains preliminary, but results confirm previous studies indicating the polyphyly of this subfamily: hydrocotyloid taxa may be found in no fewer than three major clades in Apiales.     

Fourfold polyphyly of the genus formerly known as Upucerthia, with notes on the systematics and evolution of the avian subfamily Furnariinae

The traditional avian subfamily Furnariinae, a group of terrestrial ovenbirds typical of the Andean and Patagonian arid zones, consists of the genera Furnarius, Cinclodes, Geositta, Upucerthia, Chilia, and Eremobius. We investigated phylogenetic relationships within the Furnariinae, with particular attention to the nine species of the genus Upucerthia, using nuclear and mitochondrial DNA sequences from all genera in the subfamily. Upucerthia was found to be highly polyphyletic, its constituent species forming four non-sister clades: (1) a basal lineage consisting of two Upucerthia species, U. ruficaudus and U. andaecola, as well as the monotypic genera Eremobius and Chilia; (2) a lineage consisting of U. harterti and U. certhioides, two species behaviorally divergent from other Upucerthia species; (3) a lineage consisting of U. serrana, which is not closely related to any other Upucerthia species; and (4) a lineage, sister to Cinclodes, consisting of the four Upucerthia species U. dumetaria, U. albigula, U. validirostris, and U. jelskii. The larger Furnariinae was also found to be highly polyphyletic; the terrestrial open country ecotype characteristic of this subfamily occurs in four unrelated clades in the family Furnariidae, including a basal lineage as well as derived lineages. Although the large degree of divergence among Upucerthia clades was not previously recognized, owing to ecological, behavioral, and morphological similarities, the groupings correspond closely to relationships suggested by plumage. This is in contrast to studies of other avian genera in which plumage patterns have been shown to be extensively convergent. The generic names Upucerthia and Ochetorhynchus are available for two of the former Upucerthia clades; new generic names may be warranted for the other two.     

Molecular phylogeny of Macaranga, Mallotus, and related genera (Euphorbiaceae s.s.): insights from plastid and nuclear DNA sequence data

Macaranga and Mallotus (Euphorbiaceae s.s.) are two closely related, large paleo(sub)tropical genera. To investigate the phylogenetic relationships between and within them and to determine the position of related genera belonging to the subtribe Rottlerinae, we sequenced one plastid (trnL-F) and three nuclear (ITS, ncpGS, phyC) markers for species representative of these genera. The analyses demonstrated the monophyly of Macaranga and the paraphyly of Mallotus and revealed three highly supported main clades. The genera Cordemoya and Deuteromallotus and the Mallotus sections Hancea and Oliganthae form a basal Cordemoya s.l. clade. The two other clades, the Macaranga clade and the Mallotus s.s. clade (the latter with Coccoceras, Neotrewia, Octospermum, and Trewia), are sister groups. In the Macaranga clade, two basal lineages (comprising mostly sect. Pseudorottlera) and a crown group with three geographically homogenous main clades were identified. The phylogeny of the Mallotus s.s. clade is less clear because of internal conflict in all four data sets. Many of the sections and informal infrageneric groups of Macaranga and Mallotus do not appear to be monophyletic. In both the Macaranga and Mallotus s.s. clades, the African and/or Madagascan taxa are nested in Asian clades, suggesting migrations or dispersals from Asia to Africa and Madagascar.     

Test of the monophyly of Odostomiinae and Turbonilliinae (Gastropoda, Heterobranchia, Pyramidellidae) based on 16S mtDNA sequences

Schander, C., Halanych, K. M., Dahlgren, T. & Sundberg, P. (2003) Test of the monophyly of Odostomiinae and Turbonilliinae (Gastropoda, Heterobranchia, Pyramidellidae) based on 16S mtDNA sequences. — Zoologica Scripta, 32 , 243−254.
While gastropod phylogeny has received much recent attention, relationships within some major gastropod clades have still not been studied. The Pyramidellidae is one such group, comprising more than 6000 named species in more than 350 genera. We sequenced part of the mitochondrial 16S gene from 32 species in an attempt to clarify pyramidellid phylogeny and employed a successive alignment approach that allowed us to maximize the phylogenetic signal of the data. Neighbour-joining, maximum parsimony and likelihood analyses recovered two distinct clades. One clade consisted of Noemiamea which nested within Odostomia ( sensu stricto ) . The inclusion of Brachystomia , Megastomia , Jordaniella and Liostomia within Odostomia is not supported. The second clade comprised Spiralinella , Brachystomia , Boonea , Jordaniella , Liostomia and Parthenina . Our results further suggest that Turbonilla, as interpreted by most authors, is polyphyletic. This study shows that the 16S gene is useful in unravelling pyramidellid phylogeny but needs to be combined with other data (including molecular, morphological and developmental) to fully clarify the evolutionary relationships.     

Molecular phylogeny and systematics of flowering plants of the family Crassulaceae DC

Crassulaceae (orpine or stonecrop family) is the most species-rich (ca. 1400 spp) family in the order Saxifragales. Most members of the family are succulent plants. Phenotypic diversity and large number of species complicates systematics of the family and obscures reconstruction of relationship within it. Phylogenetic analyzes based on morphological and molecular markers placed Crassulaceae as one of the crown clades of Saxifragales. In this contribution a review of phylogenetic studies on the family Crassulaceae, based on DNA nucleotide sequence comparisons is presented; major clades established in the family are characterised; their structure and polyphylesis of some genera are discussed. It is shown that the traditional taxonomic structure of Crassulaceae contradicts pattern of phylogenetic relationships between its members. We critically analyzed recent taxonomic systems of the family and stress that homoplasy of morphological characters does not allow to use them to reconstruct relationships between crassulacean taxa even at the low taxonomic levels.     

Large‐scale molecular phylogeny of metallic wood‐boring beetles (Coleoptera: Buprestoidea) provides new insights into relationships and reveals multiple evolutionary origins of the larval leaf‐mining habit

The family Buprestidae (jewel beetles or metallic wood‐boring beetles), contains nearly 15 000 species in 522 genera. Together with the small family Schizopodidae (seven species, three genera), they form the superfamily Buprestoidea. Adult Buprestoidea feed on flowers or foliage, whereas larvae are mostly internal feeders, boring in roots or stems, or mining the leaves of woody or herbaceous plants. The subfamilial and tribal classification of Buprestoidea remains unsettled, with substantially different schemes proposed by different workers based on morphology. Here we report the first large‐scale molecular phylogenetic study of the superfamily Buprestoidea based on data from four genes for 141 ingroup species. We used these data to reconstruct higher‐level relationships and to assess the current classification and the origins of the larval leaf‐mining habit within Buprestoidea. In our analyses, the monophyly of Buprestoidea was strongly supported, as was the monophyly of Schizopodidae and its placement sister to Buprestidae. Our results are largely consistent with the generally accepted major lineages of buprestoids, including clearly‐defined agrilines, buprestines–chrysochroines and early‐branching julodines–polycestines. In addition to Schizopodidae, three of the six subfamilies were monophyletic in our study: Agrilinae, Julodinae and the monogeneric Galbellinae (Galbella). Polycestinae was monophyletic with the exception of the enigmatic Haplostethini. Chrysochroinae and Buprestinae were not monophyletic, but were recovered together in a large mixed clade along with Galbella. The interrelationships of Chrysochroinae and Buprestinae were not well resolved; however they were clearly polyphyletic, with chrysochroine genera falling into several different well‐supported clades otherwise comprising buprestine genera. All Agrilinae were contained in a single strongly supported clade. Coraebini were dispersed throughout Agrilinae, with strong nodal support for several clades representing subtribes. Neither Agrilini nor Tracheini were monophyletic. The leaf‐mining genus Paratrachys (Paratracheini) was recovered within the Acmaeoderioid clade, consistent with the current classification, and confirming the independent origins of leaf‐mining within Polycestinae and Agrilinae. Additionally, our results strongly suggest that the leaf‐mining agriline tribe Tracheini is polyphyletic, as are several of its constituent subtribes. External root feeding was likely the ancestral larval feeding habit in Buprestoidea. The apparent evolutionary transitions to internal feeding allowed access to a variety of additional plant tissues, including leaves. Interestingly, the several genera of leaf‐mining agrilines do not form a monophyletic group. Many of these genera are diverse and highly specialized, possibly indicating adaptive radiations.     

Phylogenetic relationships of Polyporus and morphologically allied genera

Polyporus accommodates morphologically heterogeneous species and is divided into six infrageneric groups based on macromorphological characters. On the other hand allied genera have macro- and microscopic characters similar to those of Polyporus. The phylogenetic relationships of Polyporus and allied genera were established from sequences of RNA polymerase II second largest subunit (RPB2), nuclear ribosomal large subunit (nucLSU) and mitochondrial ATPase subunit 6 (ATP6). The molecular phylogenetic trees confirmed that Polyporus is a polyphyletic genus and recognized six major clades (1-6) containing species of Polyporus and several allied genera. Among the clades one contained three infrageneric groups of Polyporus and two allied genera, Datronia and Pseudofavolus while one other contained group Polyporellus and Lentinus. Five of the six major clades contained species belonging to a single infrageneric group, Favolus, Melanopus, Polyporellus or Polyporus. This suggests that morphological characters used to define these groups have phylogenetic significance and reveals the need for a taxonomic revision of Polyporus and its allied genera.     

A MOLECULAR PHYLOGENY OF THE GELIDIALES (RHODOPHYTA) BASED ON ANALYSIS OF PLASTID rbcL NUCLEOTIDE SEQUENCES1

Parsimony analyses of rbcL nucleotide. sequences were used to develop hypotheses of relationships among taxa in the taxonomically difficult order Celidiales including species from seven currently recognized genera: Capreolia, Gelidiella, Gelidium, Onikusa, Pterocladia, Ptilophora, and Suhria. Nucleotide. sequences of rbcL from red algae are variable and provide a large number of informative characters for phylogenetic analysis, yet the absence of insertion/deletion mutations allows for the unambiguous alignment of sequences. Species were resolved into 10 well-.supported major clades representing genera and species complexes. The topological positions of these 10 clades within trees are also well supported and indicate that Gelidium and Pterocladia as currently circumscribed are not monophyletic. These results call for a revision of the classification of the Gelidiales .