Phylogenetic relationships ofPythium species based on ITS and 5.8S sequences of the ribosomal DNA

The sequences of ITS regions in 30 species and two groups of the genusPythium were resolved. In the phylogenetic trees, the species were generally divided into two clusters, referred to here as the F and S groups. The species in the two groups correspond in terms of their sporangial morphology, with the F group being filamentous/lobulate and the S group being spherical. Genetic divergence within the F group was lower than that within the S group. Other morphological characteristics such as oogonial structure and sexual nature appeared to be unrelated to the groupings in these trees. An alignment analysis revealed common sequences to all the species and arrangements specific to each F or S group. It was found that the ITS region was a good target in designing species-specific primers for the identification and detection ofPythium species. In the tree based on 5.8S rDNA sequences, oomycetes are distantly related to other fungi but separated from algae in Chromista.     

Phylogenetic relationships of species within the tribe Labiostrongylinea (Nematoda: Cloacinidae) from Australian marsupials based on ribosomal DNA spacer sequence data

Parasitic nematodes of the tribe Labiostrongylinea (Family Cloacinidae) occur in the stomachs of a wide variety of potoroid and macropodid marsupials in Australia, Papua Indonesia and Papua New Guinea. The aim of the present study was to infer the evolutionary relationships of the five genera of labiostrongyline nematodes that occur in Australian potoroids and macropodids using sequence data of the nuclear first and second internal transcribed spacers of ribosomal DNA. The phylogenetic analyses resulted in the separation of the Labiostrongylinea into two major groups reflecting coevolution between hosts and parasites. Two nematode species belonging to the genus Potorostrongylus formed a sister group to the remaining species of the Labiostrongylinea. This genus occurs exclusively in potoroid marsupials, which are considered to be basal to the macropodid marsupials. The second major group included species of Labiostrongylus, Labiosimplex, Labiomultiplex and Parazoniolaimus, all of which occur in macropodids. These species formed two distinct clades, one predominating in the host genera Thylogale and Onychogalea, and the second in the genus Macropus, which includes the more recent macropodids. However, there is also evidence of colonisation by both nematode clades of relatively unrelated hosts. In addition, genetic differences among individuals of Lm. eugenii from geographically isolated populations of M. eugenii, and among Ls. longispicularis from different subspecies of M. robustus suggest the existence of sibling species that may have arisen by allopatric speciation. The broad coevolutionary relationship between the labiostrongyline nematodes and their marsupial hosts therefore represents a mixture of potential cospeciation and colonisation events.     

Phylogenetic relationships ofPelvetia andPelvetiopsis (Phaeophyceae) based on small subunit ribosomal DNA sequences

Nucleotide sequences of the small-subunit (SSU) ribosomal DNA were determined forPelvetia babingtonii, P. canaliculate, Pelvetiopsis limitata, andAscophyllum nodosum in the family Fucaceae. A total of 1755 positions were aligned for the whole sequence. The positional differences in the primary structure among the taxa ranged from 16 to 30 nucleotide changes in pairwise comparisons. There was a minimum divergence betweenPs. limitata andP. babingtonii while a maximum betweenPs. limitata andP. canaliculata. The SSU rDNA trees showed that the genusPelvetia was not monophyletic and the genusPelvetiopsis was not closely related toPelvetia. Our results suggest that the taxonomic revision of the genusPelvetia as well as the family Fucaceae is needed based on detailed morphological observations.     

Phylogenetic relationships in the Lejeuneaceae (Hepaticae) inferred using ITS sequences of nuclear ribosomal DNA

Sequences of the ITS1–5.8S–ITS2 region of nuclear ribosomal DNA were generated for 12 species from 9 genera of Lejeuneaceae and a single species of Jubulaceae (outgroup). The taxon sampling of Lejeuneaceae included representatives of the two widely recognized subfamilies, Lejeuneoideae and Ptychanthoideae. The molecular dataset was analysed independently and in combination with a morphological dataset. The nrITS dataset and the combined dataset resulted in identical topologies. The genus Bryopteris, sometimes treated as a separate family Bryopteridaceae, is nested within the Lejeuneaceae subfamily Ptychanthoideae. Lejeuneaceae subfamily Lejeuneoideae proved to be paraphyletic with the tribe Lejeuneeae sister to Ptychanthoideae, albeit without significant bootstrap support. The tribes Brachiolejeuneeae and Cheilolejeuneeae of Lejeuneoideae, established recently based on morphological evidence, are well supported in bootstrap analyses both of the ITS and the combined molecular–morphological datasets. The results support classifications of Lejeuneaceae based on morphological data and demonstrate the usefulness of the ITS region for phylogenetic studies within or among closely related genera of Lejeuneaceae.     

Phylogenetic relationships in Lupinus (Fabaceae: Papilionoideae) based on internal transcribed spacer sequences (ITS) of nuclear ribosomal DNA

Internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA from 44 taxa of the genus Lupinus and five outgroup taxa were used for phylogenetic analysis. Lupinus appears as a strongly supported monophyletic genus, which is unambiguously part of the Genisteae. The lupines are distributed into five main clades in general accordance with their geographical origin. In the Old World, almost all the recognized taxonomic units are well resolved. The ITS data reveal an unexpectedly close relationship between the diverse sections Angustifoli and Lutei. The ITS results suggest a geographical division between the western New World lupines and the eastern ones. They also indicate the presence of some moderately to strongly supported groups of taxa, such as the Microcarpi-Pusilli group, the L. spariflorus-L. arizonicus group, the L. mexicanus-L. elegans group in the western New World, and the notable L. multiflorus-L. paraguariensis group in the eastern New World. The latter group strongly suggests that the eastern South American compound- and simple-leaved perennial lupines derive from a common ancestor. However, apart from some exceptions, relationships within the genus still remain largely unresolved based on ITS data. The lack of resolution at the base of the genus is suggestive of a rapid initial radiation of the lupines subsequent to the dispersal of their common ancestor. Relative rate tests demonstrate the presence of rate heterogeneity of ITS sequences within Lupinus. In many pairwise comparisons between taxa, substitution rate inequalities are correlated with the habit (annual, perennial), suggesting some role for the generation time effects in the evolutionary history of lupines.     

Phylogenetic relationships within the Mysidae (Crustacea, Peracarida, Mysida) based on nuclear 18S ribosomal RNA sequences

Species of the order Mysida (Crustacea, Peracarida) are shrimp-like animals that occur in vast numbers in coastal regions of the world. The order Mysida comprises 1,053 species and 165 genera. The present study covers 25 species of the well-defined Mysidae, the most speciose family within the order Mysida. 18S rRNA sequence analysis confirms that the subfamily Siriellinae is monophyletic. On the other hand the subfamily Gastrosaccinae is paraphyletic and the subfamily Mysinae, represented in this study by the tribes Mysini and Leptomysini, consistently resolves into three independent clades, and hence is clearly not monophyletic. The tribe Mysini is not monophyletic either, and forms two clades of which one appears to be closely related to the Leptomysini. Our results are concordant with a number of morphological differences urging a taxonomic revision of the Mysidae.     

Phylogenetic relationships of Old World Brassicaceae from Iran based on nuclear ribosomal DNA sequences

Phylogenetic analysis of 155 nuclear rDNA ITS sequences among them 19 Iranian endemic genera were used to elucidate phylogenetic relationships of Old World Brassicaceae from Iran in the context of the most recent tribal system suggested by Al-Shehbaz et al. [Al-Shehbaz, I.A., Beilstein, M.A, Kellogg, E.A., 2006. Systematics and phylogeny of the Brassicaceae (Cruciferae): an overview. Plant Syst. Evol. 259, 89–120]. Iranian endemic taxa are assigned to 16 clades, 15 of these correspond to recognized tribes. Our data support the recent tribal recognition of Calepina and relatives and further indicate that the Orychophragmus clade (with Conringia planisiliqua and Orychophragmus) may be recognized as a new tribe. Our data also support the inclusion of 13 genera not previously studied, or with unresolved positions in previous phylogenetic analyses in 10 tribes with the tribal assignment given in parentheses: Acanthocardamum (Aethionemeae), Alyssopsis (Camelineae), Anastatica (Malcolmieae), Asperuginoides (Cochlearieae), Camelinopsis (Thlaspideae), Didymophysa (Thlaspideae), Dielsiocharisi (Camelineae), Lachnoloma (Anchonieae), Micrantha (Anchonieae), Noccidium (Camelineae), Octoceras (Euclidieae), Pseudofortuynia (Sisymbrieae) and Streptoloma (Euclidieae). ITS data and morphological characters further indicate that the remaining five genera, i.e., Acanthocardamum, Olimarabidopsis, Brossardia, Noccidium and Zuvanda may be subsumed under Aethionema, Alyssopsis, Noccaea, Capsella and Conringia, respectively. Alyssum, Chorispora, Fibigia and Goldbachia are paraphyletic and Conringia, Malcolmia, Matthiola are polyphyletic taxa.     

Phylogenetic relationships of freshwater bryozoans (Ectoprocta, Phylactolaemata) inferred from mitochondrial ribosomal DNA sequences

Most species of freshwater bryozoans (Ectoprocta: Phylactolaemata) have few morphological distinctions, and within phylactolaemates, the morphology of the statoblast has been used to determine evolutionary relationships. Here, two controversial phylogenies have been proposed for phylactolaemates with regard to the relationship of Lophopodidae to other families. Two plumatellid genera, Gelatinella and Hyalinella , are candidates for the ancestral type of lophopodids. In addition, the coexistence of spines on the surfaces of the statoblast has led to the suggestion that lophopodids are closely related to the family Cristatellidae. In this study, we analysed mitochondrial DNA sequences of the 12S and 16S rDNA genes of 10 phylactolaemate species. Our results suggest that plumatellids may not be a direct ancestral group of lophopodids and that cristatellids are not a sister group of lophopodids. Fredericella , which was previously thought to be an ancestral group, was revealed to be derived. In addition, our results suggest that Stephanella is the most basal phylactolaemate. Mapping morphological characteristics onto the sequence-based phylogenetic tree revealed convergent evolution of statoblast characters.     

Phylogenetic relationships of functionally dioecious FICUS (Moraceae) based on ribosomal DNA sequences and morphology

Figs (Ficus, Moraceae) are either monoecious or gynodioecious depending on the arrangement of unisexual florets within the specialized inflorescence or syconium. The gynodioecious species are functionally dioecious due to the impact of pollinating fig wasps (Hymenoptera: Agaonidae) on the maturation of fig seeds. The evolutionary relationships of functionally dioecious figs (Ficus subg. Ficus) were examined through phylogenetic analyses based on the internal transcribed spacer (ITS) region of nuclear ribosomal DNA and morphology. Forty-six species representing each monoecious subgenus and each section of functionally dioecious subg. Ficus were included in parsimony analyses based on 180 molecular characters and 61 morphological characters that were potentially informative. Separate and combined analyses of molecular and morphological data sets suggested that functionally dioecious figs are not monophyletic and that monoecious subg. Sycomorus is derived within a dioecious clade. The combined analysis indicated one or two origins of functional dioecy in the genus and at least two reversals to monoecy within a functionally dioecious lineage. The exclusion of breeding system and related characters from the analysis also indicated two shifts from monoecy to functional dioecy and two reversals. The associations of pollinating fig wasps were congruent with host fig phylogeny and further supported a revised classification of Ficus.     

Phylogenetic analysis of the Metastrongyloidea (Nematoda: Strongylida) inferred from ribosomal RNA gene sequences

Phylogenetic relationships among nematodes of the strongylid superfamily Metastrongyloidea were analyzed using partial sequences from the large-subunit ribosomal RNA (LSU rRNA) and small-subunit ribosomal RNA (SSU rRNA) genes. Regions of nuclear ribosomal DNA (rDNA) were amplified by polymerase chain reaction, directly sequenced, aligned, and phylogenies inferred using maximum parsimony. Phylogenetic hypotheses inferred from the SSU rRNA gene supported the monophyly of representative taxa from each of the 7 currently accepted metastrongyloid families. Metastrongyloid taxa formed the sister group to representative trichostrongyloid sequences based on SSU data. Sequences from either the SSU or LSU RNA regions alone provided poor resolution for relationships within the Metastrongyloidea. However, a combined analysis using sequences from all rDNA regions yielded 3 equally parsimonious trees that represented the abursate Filaroididae as polyphyletic, Parafilaroides decorus as the sister species to the monophyletic Pseudaliidae, and a sister group relationship between Oslerus osleri and Metastrongylus salmi. Relationships among 3 members of the Crenosomatidae, and 1 representative of the Skrjabingylidae (Skrjabingylus chitwoodorum) were not resolved by these combined data. However, members of both these groups were consistently resolved as the sister group to the other metastrongyloid families. These relationships are inconsistent with traditional classifications of the Metastrongyloidea and existing hypotheses for their evolution.     

Phylogenetic relationships in Gleditsia (Leguminosae) based on ITS sequences

We used nucleotide sequences from the internal transcribed spacers and 5.8S gene of nuclear ribosomal DNA to test competing phylogenetic and biogeographic hypotheses in Gleditsia. Eleven of 13 Gleditsia species were sampled, along with two species of its sister genus, Gymnocladus. Analyses of ITS data and of a combined data set that included sequences of ITS and two chloroplast genes supported several conclusions that were interpreted in light of fossil data and current legume phylogeny. Gleditsia and Gymnocladus appear to have originated in eastern Asia during the Eocene. Eastern North American species of both genera most likely evolved from ancestors that migrated across the Bering land bridge, but the eastern Asian/eastern North American disjunction appears to be much older in Gymnocladus than in Gleditsia. Gleditsia amorphoides, from temperate South America, is sister to the rest of the genus, suggesting early long-distance dispersal from Asia. The remainder of Gleditsia is divided into three unresolved clades, possibly indicating a split early in the evolution of the genus. Two of those clades contain only Asian species, and one contains Asian and North American species. The North American species, Gleditsia triacanthos and Gleditsia aquatica, are polymorphic and paraphyletic with respect to their ITS and cpDNA sequences, which suggests recent diversification.     

Phylogenetic relationships of bitterlings based on mitochondrial 12S ribosomal DNA sequences

Analysis of the nucleotide sequence of the mitochondrial 12S ribosomal RNA gene of 27 species or sub-species of bitterlings showed that bitterlings comprise an Acheilognathus clade and a Tanakia-Rhodeus clade, partially supporting an earlier classification based on morphology and karyology. The monophyly of Acheilognathus is confirmed, but that of Tanakia and Rhodeus remains poorly resolved. Within the Tanakia–Rhodeus clade, all species or sub-species having a diploid chromosome number of 46 form a monophyletic group. Results support the hypothesis that evolutionary trends of bitterling karyotypes involve reduction from 2 n =48 to either 2 n =44 (by Robertsonian translocation) or 2 n =46 (by non-Robertsonian translocation).     

Phylogenetic relationships ofPolemoniaceae inferred from 18S ribosomal DNA sequences

Cladistic analyses of chloroplast DNA disagree with current classifications by placingPolemoniaceae near sympetalous families with two staminal whorls, includingFouquieriaceae andDiapensiaceae, rather than near sympetalous families with a single staminal whorl, such asHydrophyllaceae andConvolvulaceae. To explore further the affinities ofPolemoniaceae, we sequenced 18S ribosomal DNA for eight genera ofPolemoniaceae and 31 families representing a broadly definedAsteridae. The distribution of variation in these sequences suggest some sites are hypervariable and multiple hits at these sites have obscured much of the hierarchical structure present in the data. Nevertheless, parsimony, least-squares minimum evolution, and maximum likelihood methods all support a monophyleticPolemoniaceae that is placed nearFouquieriaceae, Diapensiaceae and related ericalean families.     

Phylogenetic relationships of Australian strongyloid nematodes inferred from ribosomal DNA sequence data

The sequence of the second internal transcribed spacer of the ribosomal DNA was determined for the following strongyloid nematodes: Cylicocyclus insignis, Chabertia ovina, Oesophagostomum venulosum, Cloacina communis, Cloacina hydriformis, Labiostrongylus labiostrongylus, Parazoniolaimus collaris, Macropostrongylus macropostrongylus, Macropostrongylus yorkei, Rugopharynx australis, Rugopharynx rosemariae, Macropostrongyloides baylisi, Oesophagostomoides longispicularis and Paramacropostrongylus toraliformis, and compared with published sequences for species of Strongylus and for Hypodontus macropi. The resultant phylogenetic trees supported current hypotheses based on morphological evidence for the separation of the families Strongylidae and Chabertiidae, but did not support the separation of the endemic Australian genera as a distinctive clade within the Chabertiidae. The implications of this finding for the phylogenetic origins of the Australian strongyloids are discussed.     

Phylogenetic relationships of coffee-tree species (Coffea L.) as inferred from ITS sequences of nuclear ribosomal DNA

 Phylogenetic relationships of Coffea species were estimated from the sequences of the internal transcribed spacer (ITS 2) region of nuclear ribosomal DNA. The ITS 2 region of 37 accessions belonging to 26 Coffea taxa and to three Psilanthus species was directly sequenced from polymerase chain reaction (PCR)-amplified DNA fragments. The level of variation was high enough to make the ITS 2 a useful tool for phylogenetic reconstruction. However, an unusual level of intraspecific variation was observed leading to some difficulty in interpreting rDNA sequence divergences. Sequences were analysed using Wagner parsimony as well as the neighbour-joining distance method. Coffea taxa were divided into several major groups which present a strong geographical correspondence (i.e. Madagascar, East Africa, Central Africa and West Africa). This organisation is well supported by cytogenetic evidence. On the other hand, the results were in contradiction with the present classification of coffee-tree taxa into two genera, namely Coffea and Psilanthus. Furthermore, additivity of parental rDNA types was not observed in the allotetraploid species C. arabica. Received: 25 July 1996 / Accepted: 18 October 1996     

Phylogenetic relationships of elopomorph fishes inferred from mitochondrial ribosomal DNA sequences

The superorder Elopomorpha, a grouping which includes all teleost fishes that possess a specialized leptocephalous larva [true eels (Anguilliformes), gulpers and bobtail snipe eels (Saccopharyngiformes), bonefishes, spiny eels, and halosaurs (Albuliformes, including Notacanthiformes), ladyfishes and tarpons (Elopiformes, including Megalopiformes)] comprises >800 species for which phylogenetic relationships are poorly understood. In the present study, we analyzed mitochondrial DNA sequences in segments of the 12S and 16S rRNA genes in 33 elopomorph taxa encompassing all of the previously proposed orders, and 9 of the 15 currently recognized families of the Anguilliformes, as well as outgroup representatives from the superorders Osteoglossomorpha (nine species) and Clupeomorpha (three species), to develop phylogenetic hypotheses based on distance and parsimony methods. Both methods failed to support the monophyly of the Elopomorpha, casting doubt on the validity of the leptocephalus as an elopomorph synapomorphy. The orders Elopiformes, Albuliformes, and Anguilliformes, however, were resolved as monophyletic assemblages. Parsimony analysis supported the separation of the Anguilliformes into two groups (primitive and advanced) based on the presence of divided versus fused frontal bones. In addition, the molecular data indicated a close affinity of the anguilliform Thalassenchelys coheni (incertae sedis), known only from the leptocephalus, with the family Serrivomeridae. The implications of these data as regards the evolution of the elopomorph assemblage are discussed.