Molecular phylogeny of Alnus (Betulaceae), inferred from nuclear ribosomal DNA ITS sequences

The nuclear ITS region of 19 species of Alnus was amplified and sequenced. The inferred molecular phylogeny shows that all species of the genus Alnus form a monophyletic group close to Betula and that the fundamental dichotomy within the genus lies between the subgenera Alnaster and Gymnothyrsus, sensu Murai (1964). The subgenus Alnaster appears to be basal in the genus, based on archaism of morphological features, and branching close to the root of the trees due to low ITS divergence from genus Betula. The monophyly of the section Clethropsis is not supported by the present data: Alnus nepalensis is positioned in the subgenus Gymnothyrsus, away from A. nitida and A. maritima. Surprisingly, A. formosana sect. Japonicae is closely tied to A. maritima sect. Clethropsis, with which it shares few morphological traits, and is separate from A. japonica sect. Japonicae with which it shares many traits. An increase in substitution rate is noted in the group comprising A. formosana, A. maritima and A. nitida relative to the rest of the genus, which appears to have had, on the average, a very slow mutation rate. Alnus glutinosa, the designated type for the genus, appears to be representative of the genus both for morphological characters and evolutionary rate. North-East Asia is comforted in its position of origin of the genus since not only does it have the highest number of species and representatives in all deep branching lineages, there are also fewer transcontinental migrations when a North-East Asian ancestor is postulated than when a North American ancestor is postulated.     

Molecular phylogeny of Cotoneaster (Rosaceae) inferred from nuclear ITS and multiple chloroplast sequences

Cotoneaster Medik. (Rosaceae, Maloideae) is distributed in Europe, North Africa, and temperate areas of Asia except Japan. Members of the genus exhibit considerable morphological variation. The infrageneric classification is also obscured by polyploidy, hybridization, and apomixis. In this study, phylogenetic analyses were conducted to test infrageneric classifications of this genus using DNA sequence data from the nuclear ITS (nrITS) region and three chloroplast intergenic spacer regions. Maximum parsimony and Bayesian inference analyses of both datasets agreed with the two sections/subgenera of Koehne’s classification system, and suggested that four subsections (Microphylli, Chaenopetalum, Adpressi, and Cotoneaster) and the series of Koehne’s classification system were non-monophyletic. The incongruence length difference test indicated that the nrITS and cpDNA datasets were significantly incongruent (P = 0.001), and the placement of 14 species was discordant in phylogenetic trees derived from the two datasets. Within Cotoneaster, hybridization was indicated to be an important factor contributing to the incongruence between the nrITS and cpDNA data. By mapping nine morphological characters onto the combined nrITS–cpDNA phylogenetic tree, we inferred that a deciduous habit, glabrous fruit, white anthers, erect and light pink petals, and white filaments are plesiomorphic character states in Cotoneaster.     

The placement of South African strains of Beauveria in a phylogeny inferred from rDNA ITS1-5.8S-ITS2 sequences

This study aimed to confirm the identity of three strains of the entomopathogenic fungus Beauveria bassiana from South African soils and to investigate their phylogenetic relationship with non-indigenous strains from other geographic regions. Sequences of the rDNA ITS1-5.8S-ITS2 region of 23 strains were compared with the Genbank reference sequences of 20 other cosmopolitan strains. Fitch parsimony and neighbor-joining analyses of the ITS1-5.8S-ITS2 regions resolved the strains into two distinct clades and matched them to four species groups/lineages: Beauveria bassiana, B. cf. bassiana (pseudobassiana), B. brongniartii and B. caledonica. Two of the South African strains initially identified as B. bassiana grouped with B. caledonica, whereas the third strain was confirmed as B. bassiana. Because of the paucity of Genbank references for B. caledonica, we have designated the two South African B. caledonica strains as B. sp. aff. caledonica. Other reassignments included two strains from Norway, originally classified as B. bassiana, being grouped with B. brongniartii, and three of the B. brongniartii reference taxa from Brazil which were clearly placed in the B. bassiana clade. The study provides a first report of the presence of the B. caledonica lineage in Africa and confirms current Beauveria phylogenies inferred from molecular data.     

A phylogeny of Thermopsideae (Leguminosae: Papilionoideae) inferred from nuclear ribosomal internal transcribed spacer (ITS) sequences

Based on nuclear ribosomal DNA internal transcribed spacer (ITS) sequences, Thermopsideae is phylogenetically studied within a genistoid background. Analysis reveals that the tribe is not supported as a monophyletic group. Some species of Sophora s.s are nested within it. The central Asian desert Ammopiptanthus forms an isolated clade but is relatively remote to other Thermopsideae members. Piptanthus , Anagyris , Baptisia , and Thermopsis are clustered together into a robust clade. We hence propose that the tribe could either be reduced to just the four 'core genera' with Ammopiptanthus excluded, or, as an alternative, that Thermopsideae could become part of a new Sophoreae s.s. if it is re-circumscribed in the future. Both Piptanthus and Baptisia appear as monophyletic. The genus Anagyris is closer to some east Asian Thermopsis species than to Piptanthus . The east Asian and North American disjunct Thermopsis is not monophyletic. The ITS results suggest a geographical division between the Old World and New World Thermopsis . The east Asian species are clustered with Piptanthus and Anagyris , whereas the North American species are allied to Baptisia . Nonetheless, the only two north-eastern east Asian native Thermopsis species appear to be more related to the North American group than to the east Asian one. The related biogeographical significance has therefore been additionally discussed.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 151 , 365–373.     

Molecular phylogeny of the Caryophyllaceae (Caryophyllales) inferred from chloroplast matK and nuclear rDNA ITS sequences

Caryophyllaceae is a principally holarctic family including around 2200 species often classified into the three subfamilies Alsinoideae, Caryophylloideae, and Paronychioideae. Complex and possibly homoplasious morphological characters within the family make taxa difficult to delimit and diagnose. To explore part of the morphological evolution within the family, we investigated the phylogeny of the Caryophyllaceae by means of analyzing plastid and nuclear sequence data with parsimony and Bayesian methods. We describe a mode of tracing a stable phylogenetic signal in ITS sequences, and a significant common signal is shared with the plastid data. Parsimony and Bayesian analyses yield some differences in tree resolution. None of the subfamilies appear monophyletic, but the monophyly of the Caryophylloideae is not contradicted. Alsinoideae are paraphyletic, with Arenaria subg. Eremogone and Minuartia subg. Spergella more closely related to the Caryophylloideae. There is strong support for the inclusion of Spergula-Spergularia in an Alsinoideae-Caryophylloideae clade. Putative synapomorphies for these groupings are twice as many stamens as number of sepals and a caryophyllad-type of embryogeny. Paronychioideae form a basal grade, where tribe Corrigioleae are sister to the rest of the family. Free styles and capsules with simple teeth are possibly plesiomorphic for the family.     

Molecular phylogeny of Pemphiginae (Hemiptera: Aphididae) inferred from nuclear gene EF-1alpha sequences

Three traditional tribes of Fordini, Pemphigini and Eriosomatini comprise Pemphiginae, and there are two subtribes in Fordini and Pemphigini, respectively. Most of the species in this subfamily live heteroecious holocyclic lives with distinct primary host specificity. The three tribes of Pemphigini (except Prociphilina), Eriosomatini and Fordini use three families of plants, Salicaceae (Populus), Ulmaceae (Ulums) and Anacardiaceae (Pistacia and Rhus), as primary hosts, respectively, and form galls on them. Therefore, the Pemphigids are well known as gall makers, and their galls can be divided into true galls and pseudo-galls in type. We performed the first molecular phylogenetic study of Pemphiginae based on molecular data (EF-1alpha sequences). Results show that Pemphiginae is probably not a monophylum, but the monophyly of Fordini is supported robustly. The monophyly of Pemphigini is not supported, and two subtribes in it, Pemphigina and Prociphilina, are suggested to be raised to tribal level, equal with Fordini and Eriosomatini. The molecular phylogenetic analysis does not show definite relationships among the four tribes of Pemphiginae, as in the previous phylogenetic study based on morphology. It seems that the four tribes radiated at nearly the same time and then evolved independently. Based on this, we can speculate that galls originated independently four times in the four tribes, and there is no evidence to support that true galls are preceded by pseudo-galls, as in the case of thrips and willow sawflies.     

Molecular phylogeny of the Chinese ranids inferred from nuclear and mitochondrial DNA sequences

The phylogeny of representative species of Chinese ranids was reconstructed using two nuclear (tyrosinase and rhodopsin) and two mitochondrial (12S rRNA, 16S rRNA) DNA fragments. Maximum parsimony, Bayesian, and maximum likelihood analyses were employed. In comparison with the results from nuclear and mitochondrial data, we used nuclear gene data as our preferred phylogenetic hypothesis. We proposed two families (Ranidae, Dicroglossidae) for Chinese ranids, with the exception of genus Ingerana. Within Dicroglossidae, four tribes were supported including Dicroglossini, Paini, Limnonectini, and Occidozygini. A broader sampling strategy and evidence from additional molecular markers are required to decisively evaluate the evolutionary history of Chinese ranids.     

Molecular phylogeny and radiation time of Erysiphales inferred from the nuclear ribosomal DNA sequences

Phylogenetic relationships of Erysiphales within Ascomycota were inferred from the newly determined sequences of the 18S rDNA and partial sequences of the 28S rDNA including the D1 and D2 regions of 10 Erysiphales taxa. Phylogenetic analyses revealed that the Erysiphales form a distinct clade among ascomycetous fungi suggesting that the Erysiphales diverged from a single ancestral taxon. The Myxotrichaceae of the Onygenales was distantly related to the other onygenalean families and was the sister group to the Erysiphales calde, with which it combined to form a clade. The Erysiphales/Myxotrichaceae clade was also closely related to some discomycetous fungi (Leotiales, Cyttariales and Thelebolaceae) including taxa that form cleistothecial ascomata. The present molecular analyses as well as previously reported morphological observations suggest the possible existence of a novel evolutionary pathway from cleistothecial discomycetous fungi to Erysiphales and Myxotrichaceae. However, since most of these fungi, except for the Erysiphales, are saprophytic on dung and/or plant materials, the questions of how and why an obligate biotroph like the Erysiphales radiated from the saprophytic fungi remain to be addressed. We also estimated the radiation time of the Erysiphales using the 18S rDNA sequences and the two molecular clockes that have been previously reported. The calculation showed that the Erysiphales split from the Myxotrichaceae 190–127 myr ago. Since the radiation time of the Erysiphales does not exceed 230 myr ago, even when allowance is made for the uncertainty of the molecular clocks, it is possible to consider that the Erysiphales evolved after the radiation of angiosperms. The results of our calculation also showed that the first radiation within the Erysiphales (138–92 myr ago) coincided with the date of a major diversification of angiosperms (130–90 myr ago). These results may support our early assumption that the radiation of the Erysiphales coincided with the evolution of angiosperm plants. Contribution No. 152 from the Laboratory of Plant Pathology, Mie University     

Molecular phylogeny of Clupeiformes (Actinopterygii) inferred from nuclear and mitochondrial DNA sequences

The taxonomy of clupeiforms has been extensively studied, yet phylogenetic relationships among component taxa remain controversial or unresolved. Here we test current and new hypotheses of relationships among clupeiforms using mitochondrial rRNA genes (12S and 16S) and nuclear RAG1 and RAG2 sequences (total of 4749bp) for 37 clupeiform taxa representing all five extant families and all subfamilies of Clupeiformes, except Pristigasterinae, plus seven outgroups. Our results, based on maximum parsimony, maximum likelihood, and Bayesian analyses of these data, show that some traditional hypotheses are supported. These include the monophyly of the families Engraulidae, consisting of two monophyletic subfamilies, Engraulinae (Engraulis and Anchoa) and Coilinae (Coilia and Setipinna), and Pristigasteridae (here represented only by Ilisha and Pellona). The basal position of Denticeps among clupeiforms is consistent with the molecular data when base compositional biases are accounted for. However, the monophyly of Clupeidae was not supported. Some clupeids were more closely related to taxa assigned to Pristigasteridae and Chirocentridae (Chirocentrus). These results suggest that a major revision in the classification of clupeiform fishes may be necessary, but should await a more complete taxonomic sampling and additional data.     

A new insight into the phylogeny of vascular cryptogams with special reference to Selaginella and Isoetes inferred from nuclear ITS/5.8S rDNA sequences

In order to provide a better understanding of the evolutionary history of vascular cryptogams, phylogenetic framework was developed based on ITS1, ITS2 and 5.8S rDNA sequences of 102 extant taxa of vascular cryptogams using Maximum Parsimony (MP) analysis. The analysis revealed high GC content in Isoetaceae (60.5 %) in comparison with Selaginellaceae (54.4 %) that was envisaged to be the result of variation in selection, mutational bias, and biased recombination-associated DNA repair within these two plant lineages during evolution. Transition/transversion ratio was observed to be 0.9 in Isoetaceae, 0.68 in Selaginellaceae and 0.57 among all the 102 taxa belonging to lycophytes and ferns. It is hypothesized that the lycophytes have been separated very early during evolution and therefore acquired independent line of evolution from the other plant lineages. Although Selaginellaceae and Isoetaceae are closely related ancient plant groups, pairwise sequence divergence of sampled taxa on the basis of transition and transversion, and disparity index values per site between sampled sequence pairs pointed towards the differential investment of natural selection process. These lead to high rate of nucleotide substitution within nuclear genome of Selaginellaceae with respect to Isoetaceae. MP phylogenetic tree identified Isoetes subinermis, Isoetes durieui and Salvia microphylla as separate group among the studied taxa due to high sequence variation within these species through the time of evolution. Our result interpreted the polyphyletic origin of ferns and provides valuable information regarding the lycophytes and their fern allies.     

Molecular phylogeny of Moenkhausia (Characidae) inferred from mitochondrial and nuclear DNA evidence

Moenkhausia is one of the most speciose genera in Characidae, currently composed of 75 nominal species of small fishes distributed across South American hydrographic basins, primarily the Amazon and Guyanas. Despite the large number of described species, studies involving a substantial number of its species designed to better understand their relationships and putative monophyly are still lacking. In this study, we analysed a large number of species of Moenkhausia to test the monophyly of the genus based on the phylogenetic analysis of DNA sequences of two mitochondrial and three nuclear genes. The in‐group included 29 species of Moenkhausia, and the out‐group was composed of representatives of Characidae and other members of Characiformes. All species of Moenkhausia belong to the same clade (Clade C); however, they appear distributed in five monophyletic groups along with other different genera, which means that Moenkhausia is polyphyletic and indicates the necessity of an extensive revision of the group.     

Molecular phylogeny of Chinese Rubia (Rubiaceae: Rubieae) inferred from nuclear and plastid DNA sequences

Rubia L. is the type genus of the coffee family Rubiaceae and the third largest genus in the tribe Rubieae, comprising ca. 80 species restricted to the Old World. China is an important diversity center for Rubia, where approximately half of its species occur. However, its internal phylogenetic relationships are still poorly understood. The objective of the present study is to contribute to the phylogenetic relationships within Rubia, using the nuclear internal transcribed spacer and six plastid markers and focusing on species from China. Twenty-seven species of Rubia were sampled to infer their phylogeny using Maximum parsimony, Maximum likelihood, and Bayesian analyses. The monophyly of Rubia is supported, provided that R. rezniczenkoana Litv. is excluded from Rubia and transferred to Galium as a new combination: G. rezniczenkoanum (Litv.) L. E Yang & Z. L. Nie. Within Rubia, two clades are clearly supported. They correspond to the traditional sect. Rubias.l. (A) and sect. Oligoneura Pojark. (B), and are morphologically mainly separable by their pinnate (A) versus palmate (B) leaf venation. Plesiomorphic features are the pinnate leaf veining in sect. Rubia s.l. and the occurrence of some species with opposite leaves and true stipules in sect. Oligoneura. In sect. Oligoneura one can assume an evolution from species with opposite leaves and true stipules (as in the R. siamensis Craib group) to those with whorls of two leaves and two leaf-like stipules (as in ser. Chinenses and the R. mandersii Collett & Hemsl. group) and finally with whorls of 6 or even more elements (as in ser. Cordifoliae). The correlation between clades recognized by DNA analyses and available differential morphological features is partly only loose, particularly in the group of R. cordifolia with 2×, 4×, and 6× cytotypes. This may be due to rapid evolutionary divergence and/or hybridization and allopolyploidy.     

A phylogeny of Apiaceae tribe Scandiceae: evidence from nuclear ribosomal DNA internal transcribed spacer sequences

The evolutionary relationships among members of Apiaceae (Umbelliferae) tribe Scandiceae and representatives of all major lineages of Apioideae (including putatively allied Caucalideae) identified in earlier molecular studies were inferred from nucleotide sequence variation in the internal transcribed spacer regions (ITS1 and ITS2) of nuclear ribosomal DNA. In all, 134 accessions representing 18 genera commonly treated in Scandiceae were analyzed. Phylogenies estimated using maximum parsimony and distance methods were generally similar and suggest that: (1) Scandiceae form a well-supported clade, consisting of the genera Anthriscus, Athamanta (in part), Balansaea, Chaerophyllum, Conopodium, Geocaryum, Kozlovia, Krasnovia, Myrrhis, Myrrhoides, Neoconopodium, Osmorhiza, Scandix, Sphallerocarpus, and Tinguarra; (2) Athamanta is polyphyletic, with A. della-cellae allied with Daucus and A. macedonica placed close to Pimpinella; and (3) Rhabdosciadium and Grammosciadium find affinity with the Aegopodium group of umbellifers, whereas the placement of the monotypic Molopospermum cannot be inferred because of its high sequence divergence. The genus Bubon has been restored with two new combinations, B. macedonicum subsp. albanicum and B. macedonicum subsp. arachnoideum. Scandiceae arise within paraphyletic Caucalideae, the latter comprising two major lineages whose relationships to Scandiceae are not clear. Therefore, a broad treatment of Scandiceae is proposed, with subtribes Scandicinae, Daucinae, and Torilidinae (the latter two representing the Daucus and Torilis subgroups, respectively, of recent molecular systematic investigations).     

Worldwide phylogeny of Lactarius section Deliciosi inferred from ITS and glyceraldehyde-3-phosphate dehydrogenase gene sequences

A phylogenetic analysis of Lactarius sect. Deliciosi was performed based on collections of all known species. Several samples of each species were included, originating from a wide geographic range. The two DNA regions we used (ITS and a part of the gene encoding glyceraldehyde-3-phosphate dehydrogenase) showed an incongruent phylogenetic signal. Much attention was paid to carefully observed macro- and micromorphological characters to draw taxonomic conclusions. We currently accept 38 taxa (31 species and seven varieties) in Lactarius sect. Deliciosi worldwide; four species are new to science. More sampling is needed to resolve the status of the North American varieties. Our knowledge of the Asian species in this section remains fragmentary. The monophyly of the section and its position within Lactarius subgenus Piperites, as proposed in recent morphology-based classification schemes, is confirmed. The intrasectional relationships however do not coincide with the color of the latex (as previously supposed). Intercontinental conspecificity is low in general. The name L. deliciosus is wrongfully applied in North and Central America and only two species seem to occur in both Asia and Europe.     

Towards a molecular phylogeny ofApiaceae subfamilyApioideae: Additional information from nuclear ribosomal DNA ITS sequences

Evolutionary relationships among 116 representatives (80 genera) ofApiaceae (Umbelliferae) subfam.Apioideae were investigated by comparative sequencing of the two internal transcribed spacers of the 18S–26S nuclear ribosomal DNA repeat. The resultant phylogenies, inferred using maximum parsimony and neighbor-joining methods, clarified the relationships of several genera whose phylogenetic placements have heretofore been problematic. Comparisons between the phylogenies inferred and the distribution of several phytochemical (coumarins, flavonoids, and phenylpropenes) and morphological (stomates, pollen, and cotyledonary shape) characters were also made, revealing that many of these characters (like those morphological and anatomical characters of the fruit) are highly homoplastic. It is not surprising then that systems of classification ofApioideae based on these characters, particularly with regard to tribal and subtribal designations and relationships, are unsatisfactory. The results of recent serological investigations of the subfamily support several relationships proposed herein using molecular data.     

The molecular phylogeny of the Miarus campanulae (Coleoptera: Curculionidae) species group inferred from CO1 and ITS2 sequences

Miarus is a Holarctic weevil genus with morphologically very similar species, all breeding on Campanula plants or their close relatives. Two European members of this genus, Miarus campanulae (L.), the type species, and Miarus graminis (Bohemann) have recently been split into several new species on the basis of slight external variations. The separation of these new forms has proved impossible and new data was needed. Molecular data were gathered from specimens from a number of locations in Finland, Estonia, Denmark and Sweden. The regions sequenced were mitochondrial CO1 and nuclear ITS2. Both combined and separate datasets were analyzed using the optimization alignment program POY, with parsimony as the optimality criterion. The recently separated Miarus species was found to be indistinguishable from the traditionally recognized form on the basis of this sequence data. On the other hand, the traditionally recognized species were characterized by numerous synapomorphies. Our data suggest that recent studies have underestimated the morphological variation in this genus. We propose that this may also be true for many taxonomically problematic beetle complexes in well‐studied European regions. The idea that molecular evidence will inevitably reveal unnoticed cryptic variation may only apply to poorly known regions. Miarus fennicus Kangas, 1978 is placed as a junior synonym of Miarus campanulae (Linnaeus, 1767) syn. nov . © The Willi Hennig Society 2006.     

Snake phylogeny: evidence from nuclear and mitochondrial genes

We constructed phylogenies of snakes from the c-mos and cytochrome b genes using conventional phylogenetic methods as well as the relatively new method of Bayesian inference. For all methods, there was excellent congruence between the c-mos and cytochrome b genes, implying a high level of support for the shared clades. Our results agree with previous studies in two important respects: first, that the scolecophidians and alethinophidians are monophyletic sister clades; and second, that the Colubroidea is a monophyletic group with the Acrochordidae as its sister clade. However, our results differ from previous studies in the finding that Loxocemus and Xenopeltis cluster with pythons. An additional noteworthy result from our data is that the genera Exiliboa and Ungaliophis, often placed with Tropidophis (and Trachyboa, not included in the present study) in the Tropidophiidae, are in reality boids.     

用nrDNA ITS序列探讨狭蕊龙胆属及其近缘属 (龙胆科)的系统发育

运用核糖体DNA内转录间隔区ITS序列对狭蕊龙胆属Metagentiana10种及其近缘属22种植物进行了系统发育分析。ITS分析结果表明狭蕊龙胆属是一个多系群:在系统发育树上,双蝴蝶属Tripterospermum和蔓龙胆属Crawfurdia的种类位于狭蕊龙胆属各分支中,而且双蝴蝶属和蔓龙胆属的种类也相互交叉;这一结果不支持将3个属各自独立为属。但是,在所有分析中,3个属共同形成一单系分支,是龙胆属Gentiana的姊妹群;这一结果与形态学、花部解剖学、细胞学、孢粉学和胚胎学等证据基本一致,狭蕊龙胆属应该从龙胆属中分离出来,它与双蝴蝶属和蔓龙胆属有更为密切的亲缘关系。根据分支图,在狭蕊龙胆属、双蝴蝶属和蔓龙胆属组成的复合群中,现已知的染色体基数x＝17、21和23可能存在网状和平行进化。     

A molecular phylogeny of the genus Gagea (Liliaceae) in Germany inferred from non-coding chloroplast and nuclear DNA sequences

The systematics of the mainly yellow flowered Gagea species complex (Liliaceae) has long been considered difficult because only a few phenotypic features within this genus and as a result of hypothesized interspecific hybridisation. A molecular phylogenetic study of seven Gagea species (G. bohemica, G. lutea, G. minima, G. pomeranica, G. pratenis, G. spathacea and G. villosa) from Germany has been undertaken, based on plastid DNA sequences (trnL(UAA)-trnF(GAA), psbA-trnH) and on the nuclear ribosomal internal transcribed spacer (ITS). Sequence divergence within the Gagea species ranges up to 15.5% for psbA-trnH, 22.0% for trnL-trnF and 23.7% for ITS (ITS1 + 5.8S rRNA + ITS2). Two subspecies of Gagea bohemica: G. bohemica subsp. saxatilis and G. bohemica subsp. bohemica are characterized by trnL-trnF data and morphological features. Analysis of the ITS region shows that G. pomeranica represents a hybrid of G. pratensis and G. lutea. Lloydia serotina was initially used as an outgroup species, but it was placed within the investigated Gagea species in the psbA-trnH and the trnL-trnF phylogenetic tree.