The phylogenetic relationships ofByblis andRoridula (Byblidaceae-Roridulaceae) inferred from partial 18S ribosomal RNA sequences

The phylogenetic relationships of the angiosperm generaByblis andRoridula have been the subject of ongoing taxonomic controversy. Twenty-eight taxa of varying degrees of alleged relationship, including 3 members of theWinteraceae (as an outgroup), were investigated using partial sequences of 18S rRNA (small subunit) and also compared against the morphological data set fromHufford's (1992) cladistic treatment of 80 members of theRosidae-Asteridae. The morphological analysis placed the two genera in a clade with theSarraceniaceae in theCorniflorae-Asterid group as a sister taxon to anEricales-Hydrangeales clade. The 18S rRNA analysis supports the recently publishedrbcL DNA analysis ofAlbert & al. (1992), withRoridula joined to taxa in the lowerRosidae, butByblis joining instead to members of theAsteridae near theSolanaceae. Comparisons for congruence between the three analyses placeByblis in the higher Asterid group near theSolanaceae, andRoridula possibly nearer theSarraceniaceae andEricales. These results imply that the traditional morphological characters used to relate the two genera are possibly the result of convergence towards similar ecological and life-history strategies rather than synapomorphies.     

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.     

The phylogenetic position of taxaceae based on 18S rRNA sequences

The evolutionary position of the yew family, Taxaceae, has been very controversial. Some plant taxonomists strongly advocate excluding Taxaceae from the conifer order and raising its taxonomic status to a new order or even class because of its absence of seed cones, contrary to the case in the majority of conifers. However, other authors believe that the Taxaceae are not fundamentally different from the rest of the conifers except in that they possess the most reduced solitary-ovule cones. To resolve the controversy, we have sequenced the 18S rRNA genes from representative gymnosperms: Taxus mairei (Taxaceae), Podocarpus nakaii (Podocarpaceae), Pinus luchuensis (Pinaceae), and Ginkgo biloba (Ginkgoales). Our phylogenetic analysis of the new sequence data with the published 18S rRNA sequence of Zamia pumila (a cycad) as an outgroup strongly indicates that Taxus, Pinus, and Podocarpus form a monophyletic group with the exclusion of Ginkgo and that Taxus is more closely related to Pinus than to Podocarpus. Therefore, Taxaceae should be classified as a family of Coniferales. Our finding that Taxaceae, Pinaceae, and Podocarpaceae form a clade contradicts both the view that the uniovulate seed of Taxaceae is a primitive character and the view that the Taxaceae are descendants of the Podocarpaceae. Rather, the uniovulate seed of Taxaceae and that of some species of Podocarpus appear to have different origins, probably all reduced from multiovulate cones. Correspondence to: W.-H. Li     

Detecting possibly saturated positions in 18S and 28S sequences and their influence on phylogenetic reconstruction of Annelida (Lophotrochozoa)

Phylogenetic reconstructions may be hampered by multiple substitutions in nucleotide positions obliterating signal, a phenomenon called saturation. Traditionally, plotting ti/tv ratios against genetic distances has been used to reveal saturation by assessing when ti/tv stabilizes at 1. However, interpretation of results and assessment of comparability between different data sets or partitions are rather subjective. Herein, we present the new C factor, which quantifies convergence of ti/tv ratios, thus allowing comparability. Furthermore, we introduce a comparative value for homoplasy, the O/E ratio, based on alterations of tree length. Simulation studies and an empirical example, based on annelid rRNA-gene sequences, show that the C factor correlates with noise, tree length and genetic distance and therefore is a proxy for saturation. The O/E ratio correlates with the C factor, which does not provide an intrinsic threshold of exclusion, and thus both together can objectively guide decisions to exclude saturated nucleotide positions. However, analyses also showed that, for reconstructing annelid phylogeny using Maximum Likelihood, an increase in numbers of positions improves tree reconstruction more than does the exclusion of saturated positions.     

Monophyly and phylogenetic relationships of the catfish genus Glyptothorax (Teleostei: Sisoridae) inferred from nuclear and mitochondrial gene sequences

GlyptothoraxBlyth (1860) is the most species-diverse and widely-distributed genus in the Sisoridae, but few studies have examined monophyly of the genus and phylogenetic relations within it. We used the nuclear RAG2 gene and mitochondrial COI and Cyt b genes from 50 of the approximately 70 species to examine monophyly of Glyptothorax and phylogenetic relationships within the genus. Molecular phylogenetic trees were constructed using maximum parsimony, maximum likelihood and Bayesian inference methods. All methods strongly supported monophyly of Glyptothorax, with Bagarius as its sister group. Both analyses of two- and three-gene datasets recovered nine major subclades of Glyptothorax, but some internal nodes remained poorly resolved. The phylogenetic relationships within the genus and existing taxonomic problems are discussed.     

18S ribosomal RNA gene sequences of Cochliopodium (Himatismenida) and the phylogeny of Amoebozoa

Cochliopodium is a very distinctive genus of discoid amoebae covered by a dorsal tectum of carbohydrate microscales. Its phylogenetic position is unclear, since although sharing many features with naked "gymnamoebae", the tectum sets it apart. We sequenced 18S ribosomal RNA genes from three Cochliopodium species (minus, spiniferum and Cochliopodium sp., a new species resembling C. minutum). Phylogenetic analysis shows Cochliopodium as robustly holophyletic and within Amoebozoa, in full accord with morphological data. Cochliopodium is always one of the basal branches within Amoebozoa but its precise position is unstable. In Bayesian analysis it is sister to holophyletic Glycostylida, but distance trees mostly place it between Dermamoeba and a possibly artifactual long-branch cluster including Thecamoeba. These positions are poorly supported and basal amoebozoan branching ill-resolved, making it unclear whether Discosea (Glycostylida, Himatismenida, Dermamoebida) is holophyletic; however, Thecamoeba seems not specifically related to Dermamoeba. We also sequenced the small-subunit rRNA gene of Vannella persistens, which constantly grouped with other Vannella species, and two Hartmannella strains. Our trees suggest that Vexilliferidae, Variosea and Hartmannella are polyphyletic, confirming the existence of two very distinct Hartmannella clades: that comprising H. cantabrigiensis and another divergent species is sister to Glaeseria, whilst Hartmannella vermiformis branches more deeply.     

Phylogenetic relationship of Alexandrium monilatum (Dinophyceae) to other Alexandrium species based on 18S ribosomal RNA gene sequences

The phylogenetic relationship of Alexandrium monilatum to other Alexandrium spp. was explored using 18S rDNA sequences. Maximum likelihood phylogenetic analysis of the combined rDNA sequences established that A. monilatum paired with Alexandrium taylori and that the pair was the first of the Alexandrium taxa to diverge, followed by Alexandrium margalefii. All three are members of the Alexandrium subgenus Gessnerium Halim nov. comb.     

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.     

The phylogenetic relationships of Cynoglottis (Boraginaceae- Boragineae) inferred from ITS, 5.8S and trnL sequences

A molecular phylogenetic analysis of Cynoglottis was performed to evaluate previous hypotheses based on non-molecular evidence concerning the position of this genus within Boraginaceae tribe Boragineae. ITS-5.8S and trnL_UAA sequences from the nuclear and chloroplast non-coding genomes were obtained for four Cynoglottis taxa and selected members of the related genera Anchusa, Anchusella, Gastrocotyle, Brunnera and Pentaglottis. Cynoglottis is monophyletic, but neither trnL nor ITS support a close relationship with Brunnera, unlike previously supposed on morphological grounds. Brunnera is, instead, related to the southwestern European monotypic genus Pentaglottis, with which it forms a basal clade. ITS-5.8S sequences show that Anchusa thessala, a southeastern European annual species of Anchusa subg. Buglossellum, is sister to Cynoglottis and that the two taxa form a clade which also includes the Balkan endemic Gastrocotyle macedonica. Species of Anchusa subg. Anchusa form a separate lineage with high bootstrap support, suggesting that this heterogeneous genus is paraphyletic with respect to Cynoglottis. ITS sequences also discriminate between the Balkan-Apenninic diploid C. barrelieri and the Anatolian tetraploid C. chetikiana, albeit with low support. The molecular results are discussed in the light of karyological, morphological and chorological aspects.This work has been supported by M.I.U.R. 40% 2003 and the University of Firenze.     

A phylogenetic analysis of the genus Leuconostoc based on reverse transcriptase sequencing of 16 S rRNA

The phylogenetic interrelationships of members of the genus Leuconostoc and some heterofermentative lactobacilli, which phenotypically resemble leuconostocs, were investigated by comparative analysis of their 16 S rRNA sequences. The six species, Leuconostoc mesenteroides, Leu. carnosum, Leu. citreum, Leu. gelidum, Leu. lactis and Leu. pseudomesenteroides exhibited a high degree of sequence similarity with each other and formed a phylogenetically coherent group, quite separate from all other lactic acid bacteria investigated. The species Leu. paramesenteroides was found to be phylogenetically distinct from the Leu. mesenteroides group of species and formed a natural grouping with the heterofermentative lactobacilli, Lb. confusus, Lb. kandleri, Lb. minor and Lb. viridescens. The rRNA sequence of the acidophilic species, Leu. oenos, displayed exceptionally low levels of homology with all of the other taxa examined. The 16 S sequence of Leu. oenos showed major nucleotide differences in relatively highly conserved positions of the molecule indicating this species is phylogenetically distinct and warrants a separate genus.     

Systematics of Chaetognatha under the light of molecular data, using duplicated ribosomal 18S DNA sequences

While the phylogenetic position of Chaetognatha has became central to the question of early bilaterian evolution, the internal systematics of the phylum are still not clear. The phylogenetic relationships of the chaetognaths were investigated using newly obtained small subunit ribosomal RNA nuclear 18S (SSU rRNA) sequences from 16 species together with 3 sequences available in GenBank. As previously shown with the large subunit ribosomal RNA 28S gene, two classes of Chaetognatha SSU rRNA gene can be identified, suggesting a duplication of the whole ribosomal cluster; allowing the rooting of one class of genes by another in phylogenetic analyses. Maximum Parsimony, Maximum Likelihood and Bayesian analyses of the molecular data, and statistical tests showed (1) that there are three main monophyletic groups: Sagittidae/Krohnittidae, Spadellidae/Pterosagittidae, and Eukrohniidae/Heterokrohniidae, (2) that the group of Aphragmophora without Pterosagittidae (Sagittidae/Krohnittidae) is monophyletic, (3) the Spadellidae/Pterosagittidae and Eukrohniidae/Heterokrohniidae families are very likely clustered, (4) the Krohnittidae and Pterosagittidae groups should no longer be considered as families as they are included in other groups designated as families, (5) suborder Ctenodontina is not monophyletic and the Flabellodontina should no longer be considered as a suborder, and (6) the Syngonata/Chorismogonata and the Monophragmophora/Biphragmophora hypotheses are rejected. Such conclusions are considered in the light of morphological characters, several of which are shown to be prone to homoplasy.     

Molecular phylogenetic analysis of Violaceae (Malpighiales) based on plastid and nuclear DNA sequences

A phylogenetic analysis of Violaceae is presented using sequences from rbcL, atpB, matK and 18S rDNA from 39 species and 19 genera. The combined analysis of four molecular markers resulted in only one most parsimonious tree, and 33 of all 38 nodes within Violaceae are supported by a bootstrap proportion of more than 50%. Fusispermum is in a basal-most position and Rinorea, Decorsella, Rinoreocarpus and the other Violaceae are successively diverged. The monogeneric subfamily Fusispermoideae is supported, and it shares a number of plesiomorphies with Passifloraceae (a convolute petal aestivation, actinomorphic flowers and connate filaments). The other monogeneric subfamily Leonioideae is sunken within the subfamily Violoideae and is sister to Gloeospermum, sharing some seed morphological characteristics. The present molecular phylogenetic analysis suggests that the convolute, apotact and quincuncial petal aestivation is successively derived within the family. The evolutionary trends of the other morphological characteristics, such as a filament connation, the number of carpels and floral symmetry, are discussed. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Complex estimates of evolutionary relationships in Tarentola mauritanica (Reptilia: Gekkonidae) derived from mitochondrial DNA sequences

Mitochondrial DNA (12S rRNA, 16S rRNA) sequences were analysed within Tarentola mauritanica and other selected species of Tarentola. Several highly genetically distinct lineages occur in North Africa, revealing phylogroups in southern and central Morocco, northern Morocco, Algeria, Tunisia, and Libya. A single haplotype characterizes populations across Spain, Portugal, Italy, Menorca, Crete, and Tunisia raising the possibility of an anthropogenic introduction followed by rapid population expansion throughout southern Europe. T. mauritanica is paraphyletic with respect to T. angustimentalis, a Canary islands endemic. The high genetic diversity observed across North Africa suggests T. mauritanica may represent a species complex.     

Phylogeny of Oedogoniales (Chlorophyceae, Chlorophyta) inferred from 18S rDNA sequences with emphasis on the relationships in the genus Oedogonium based on ITS-2 sequences

The phylogeny of Oedogoniales was investigated by using nuclear 18S rDNA sequences. Results showed that the genus Oedocladium, as a separated clade, was clustered within the clade of Oedogonium; whereas the genus Bulbochaete was in a comparatively divergent position to the other two genera. The relationship among the species of Oedogonium was discussed, focusing on ITS-2 phylogeny analyzed combining with some morphological characteristics. Our results showed that all the dioecious nannandrous taxa involved in this study were resolved into one clade, while all the monocious taxa were clustered into another clade as a sister group to the former. The report also suggests that the dioecious macrandrous taxa form a paraphyly and could be more basally situated than the dioecious nannandrous and the monoecious taxa by means of molecular phylogeny and morphotype investigations.     

Species boundaries,phylogenetic relationships,and ecological differentiation inAnthriscus (Apiaceae)

Species boundaries and phylogenetic relationships of 17 taxa ofAnthriscus (Apiaceae), with special emphasis on the critical sect.Cacosciadium, were explored using morphological data with principal component analysis, phenetics, and phylogenetics. The analyses did not provide satisfactory resolution of taxa from sect.Cacosciadium and only four species were retained. The total number of species was reduced to nine. Sect.Cacosciadium is distinguished by only two synapomorphies while sects.Anthriscus andCaroides are better supported. Present geographic and ecological variation suggests that the radiation ofAnthriscus occurred through divergence of peripheral isolated populations adapting to different habitats: high montane meadows and screes, shady climax forests, and seasonally dry habitats at lower altitudes. The adaptive significance of particular morphological traits is discussed.     

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.     

A phylogenetic study ofSaxifraga sect.Saxifraga (Saxifragaceae) based on nrDNA ITS sequences

Parsimony analyses of 54 nrDNA ITS (Internal Transcribed Spacer) sequences ofSaxifraga sect.Saxifraga were performed. In addition to some unresolved clades, there is strong disagreement between the ITS phylogeny and previous classifications based primarily on morphology. The extensive cytological instability of sect.Saxifraga prevents previous cytotaxonomical results from resolving the incongruence between molecular and morphological data. Dissimilar topologies between chloroplast (matK) and nuclear (ITS) trees for eight species of sect.Saxifraga suggest that gene trees and the true species tree are not coincident. Recent and mid-term reticulation is proposed as an explanation for the incongruence between morphological, cytological, organellar, and nuclear data. Homogenization in multigene families, such as the ITS region, via concerted evolution may be the key to the interpretation of results based on ITS sequences within sect.Saxifraga. The use of organellar genes in a larger sample should help to determine whether extensive reticulation occurs in sect.Saxifraga, as has been documented in various genera of Saxifragaceae.     

Redefinition and phylogenetic relationships of the family Pinguipedidae (Teleostei: Perciformes)

The phylogenetic relationships of the family Pinguipedidae plus the genus Cheimarrichthys von Haast, 1874, were studied to redefine the family. Based on a phylogenetic analysis using derived characters belonging to 21 transformation series, accepting the monophyly of Pinguipedidae plus Cheimarrichthys provisionally for the operational procedure of the analysis, it was hypothesized that Cheimarrichthys is not closely related to Parapercis Bleeker, 1863, although these genera had been considered as having a close affinity. Although the Pinguipedidae and Cheimarrichthys share nine derived characters, it was determined that these characters are also found in other trachinoid families. In addition, several families, such as the Leptoscopidae, Uranoscopidae, and Trichodontidae, have many more derived characters in common with Cheimarrichthys than the pinguipedids have with that genus. The conclusion drawn here is that it is not parsimonious to recognize the monophyly of the Pinguipedidae and Cheimarrichthys based on these nine derived characters, and that these characters are not compelling enough to link these groups. The redefined Pinguipedidae is proposed to include the following five genera: Parapercis, Prolatilus Gill, 1865, Pinguipes Cuvier, 1829, Pseudopercis de Miranda-Ribeiro, 1903, and Kochichthys Kamohara, 1960. Cheimarrichthys, excluded from the Pinguipedidae, is put into its own family, Cheimarrichthyidae.     

The phylogenetic positions of the conifer genera Amentotaxus,Phyllocladus, and Nageia inferred from 18s rRNA sequences

To determine the evolutionary positions of the conifer genera Amentotaxus, Phyllocladus, and Nageia, we obtained 18S rRNA sequences from 11 new taxa representing the major living orders and families of gymnosperms. With the published Chlamydomonas as an outgroup, phylogenetic analyses of our new data and available sequences indicate that (1) the Gnetales form a monophyletic group, which is an outgroup to the conifers, (2) the conifers are monophyletic, (3) Taxaceae, Cephalotaxaceae, Cupressaceae, and Taxodiaceae form a monophyletic group, (4) Amentotaxus is closer to Torreya than to Cephalotaxus, suggesting that Amentotaxus is better to be classified as a member of Taxaceae, (5) Phyllocladus, Dacrycarpus, Podocarpus, and Nageia form a monophyletic group, and (6) Pinaceae is an outgroup to the other families of conifers. Our finding that Phyllocladus is a sister group of the Podocarpaceae disagrees with the suggestion that the phylloclade of the genus is an ancient structure and that the genus is a terminal taxon within the Podocarpaceae. The genus Nageia is more closely related to Podocarpus than to Dacrycarpus and was derived from within the Podocarpaceae. In conclusion, our data indicate that in conifers, the uniovulate cone occurred independently in Taxacaeae and Cephalotaxaceae, and in Podocarpaceae after the three families separated from Pinaceae, and support the hypothesis that the uniovulate cone is derived from reduction of a multiovulate cone.Correspondence to: S.-M. Chaw