Phylogenetic relationships among Thunnus species inferred from rDNA ITS1 sequence

Intra and interspecific nucleotide sequence variation of rDNA first internal transcribed spacer (ITS1) was analysed using all eight species of the genus Thunnus plus two out‐group species within the same family, skipjack tuna Katsuwonus pelamis and striped bonito Sarda orientalis . Intraspecific nucleotide sequence variation in ITS1, including intra‐genomic variation, was low, ranging from 0·003 to 0·014 [Kimura's two parameter distance (K2P)], whereas variation between species within the genus Thunnus ranged from 0·009 to 0·05. The Atlantic and Pacific northern bluefin tunas Thunnus thynnus thynnus and Thunnus thynnus orientalis , recently proposed to be distinct species, were found to share nearly identical ITS1 sequences (mean K2P = 0·006) well within the range of intraspecific variation. The northern bluefin tuna appeared to be a sister group to albacore Thunnus alalunga , with all other Thunnus species in a distinct clade. The ITS1 phylogeny was consistent with mtDNA phylogeny in clustering the three tropical Thunnus species ( T. albacares , T. atlanticus and T. tonggol ). Southern bluefin Thunnus maccoyii and bigeye Thunnus obesus tunas showed a closer affinity to this tropical tuna group than to the northern bluefin tuna and albacore. The molecular data supported mitochondrial introgression between species and contradicted morphological subdivision of the genus into two subgenera Neothunnus and Thunnus .     

Phylogenetic relationships among Artemisia species based on nuclear ITS and chloroplast psbA-trnH DNA markers

The taxonomic and phylogenetic relationships within the genus Artemisia s.l. (Asteraceae) are controversial, and it has been considered 1 to 8 different genera. This work re-investigated the phylogenetic relationships in Artemisia using nuclear ribosomal (ITS) and chloroplast psbA-trnH DNA sequences using three sections of Artemisia, Dracunculus, and Serphidium. Three phylogenetic trees were conducted separately on the basis of ITS, psbA-trnH and combined sequences using maximum parsimony. The results showed that the three sections were clearly separated from each other, and that the heterogamous Dracunculus and Artemisia are closely related to each other than either to homogamous Serphidium. This may suggest the taxonomic importance of capitulum morphology in Artemisia s.l. Our data also cast doubt on the use of cytogenetic similarity e.g., basic chromosome number in grouping Serphidium and Artemisia s.s. Furthermore, AMOVA analysis showed a higher level of ITS (55.29%) and combined ITS+cppsbA-trnH (55.63%) variations among sections. This provides further evidence for separation of these three sections and supports the phylogenetic results. The higher ITS nucleotide differences detected in Artemisia (30.4737) compared to very low value in Dracunculus (2.3333) and Serphidium (1.23077) may propose that the Artemisia comprises of several incipient sections. This supports the previous suggestion that Artemisia is a complex group.     

Phylogenetic relationships among diploid species of Symphyotrichum (Asteraceae: Astereae) based on two nuclear markers, ITS and GAPDH

The mostly North American subtribe Symphyotrichinae (Asteraceae: Astereae) comprises Canadanthus, Ampelaster, Psilactis, Almutaster, and Symphyotrichum. Intergeneric and interspecific relationships within the subtribe have been investigated in the past, particularly by Nesom [Nesom, G.L., 1994. Review of the taxonomy of Aster sensu lato (Asteraceae: Astereae), emphasizing the new world species, Phytologia 77, 141–297] and Semple [Semple, J.C., 2005. Classification of Symphyotrichum. Available from: <http://www.jcsemple.uwaterloo.ca/Symphyotrichumclassification.htm/>], using morphological and cytological approaches. Symphyotrichum is the largest and most complex genus within the subtribe and includes four subgenera: Symphyotrichum (x = 7, 8), Virgulus (x = 4, 5), Astropolium (x = 5), and Chapmaniani (x = 7). In this study we used two nuclear markers, the nrDNA internal transcribed spacer (ITS) and the low-copy nuclear gene glyceraldehyde 3-phosphate dehydrogenase (GAPDH), to resolve intergeneric and interspecific relationships within the subtribe at the diploid level, and to determine whether our phylogenies validate the classifications of Nesom or Semple. Our results confirm the distinct generic status of Canadanthus and Ampelaster, whereas Psilactis and Almutaster form a polytomy with Symphyotrichum. Within Symphyotrichum, subg. Virgulus is monophyletic based on ITS and appears polyphyletic based on GAPDH. Neither the ITS nor the GAPDH analyses support a distinct status for subg. Astropolium, which groups within subg. Symphyotrichum. In general, interspecific relationships within Symphyotrichum are unresolved. Lack of resolution may be interpreted as a case of recent and rapid evolutionary radiation.     

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.     

Phylogenetics and evolution of the Macaronesian members of the genus Aichryson (Crassulaceae) inferred from nuclear and chloroplast sequence data

Aichryson is a genus of annual or perennial herbs, comprising approximately 13 species. The genus is nearly endemic to Macaronesia, with the center of diversity on the Canary Islands. Previous studies indicate that Aichryson is monophyletic and sister to a clade comprising two other genera, Monanthes and Aeonium. However, phylogenetic relationships within the genus have yet to be investigated. Phylogenetic relationships were estimated for Aichryson using DNA sequence data from both the nuclear and chloroplast genome. Parsimony analyses were conducted using separate nuclear and chloroplast data sets, as well as a combined data set. These combined analyses provide a well-resolved topology that is used to investigate patterns of evolution within the genus. For example, although typically herbaceous in habit, two members display a woody growth form. Our analyses indicate that woodiness is a derived feature in Aichryson that has arisen once. Furthermore, the data presented suggest that the Aichryson pachycaulon group, a group of five subspecies, are in fact not monophyletic and that a reexamination of classification is necessary. The present study indicates that the biogeographical patterns exhibited by Aichryson appear to be rare, occurring in only one other known genus.The authors would like to thank Susana Fontinha of the Madeiran Botanical Garden for plant material of Madeiran Aichryson; Drs. D. Crawford and J. Archibald, as well as two anonymous reviewers for helpful comments; Eastern Illinois Undergraduate Honors Research Fund, and University of Kansas Plant Biology Research Award. Additional financial support for this work was provided by the Department of Ecology and Evolutionary Biology and the Museum of Natural History and Biodiversity Research Center, University of Kansas and a Kansas NSF EPSCoR First Award (NSF 32171) to MEM.     

Phylogenetic relationships on 14 morphologically similar species of Pucciniastrum in Japan based on rDNA sequence data

We analyzed the phylogenetic relationships of 49 specimens comprising 14 morphologically similar species of Pucciniastrum distributed in Japan based on the sequence data of the large subunit rDNA (D1/D2), 5.8S rDNA, and internal transcribed spacer (ITS) regions. Neighbor-joining and parsimony analyses generated six major groups for both the D1/D2 and ITS regions. Pucciniastrum circaeae and P. epilobii formed a single group. P. hydrangeae-petiolaris, P. coryli, P. fagi, P. hikosanense, P. tiliae, and P. boehmeriae were each a distinct clade, and P. fagi formed a close relationship with P. hikosanense. However, these analyses did not support the monophyly of the following species: P. kusanoi, P. actinidiae, P. corni, P. styracinum, P. yoshinagai, and P. miyabeanum. Contribution no. 201, Laboratory of Plant Parasitic Mycology, Graduate School of Life and Environmental Sciences, University of Tsukuba, Japan     

Phylogenetic relationships and biogeography of Fuchsia (Onagraceae) based on noncoding nuclear and chloroplast DNA data

To examine relationships and test previous sectional delimitations within Fuchsia, this study used parsimony and maximum likelihood analyses with nuclear ITS and chloroplast trnL-F and rpl16 sequence data for 37 taxa representing all sections of Fuchsia and four outgroup taxa. Results support previous sectional delimitations, except for F. verrucosa, which is related to a Central American clade rather than to section Fuchsia and is described here as a new section Verrucosa. The basal relationships within Fuchsia are poorly resolved, suggesting an initial rapid diversification of the genus. Among the species sampled, there is strong support for a single South Pacific lineage, a southern South American/southern Brazilian lineage, a tropical Andean lineage, and one or two Central American and Mexican lineages. There is no clear support for an austral origin of the genus, as previously proposed, which is more consistent with Fuchsia's sister group relationship with the boreal Circaea. An ultrametric molecular clock analysis (all minimal dates) places the split between Fuchsia and Circaea at 41 million years ago (mya), with the diversification of the modern-day lineages of Fuchsia beginning at 31 mya. The South Pacific Fuchsia lineage branches off around 30 mya, consistent with fossil records from Australia and New Zealand. The large Andean section Fuchsia began to diversify around 22 mya, preceded by the divergence of the Caribbean F. triphylla at 25 mya. The Brazilian members of section Quelusia separated from the southern Andean F. magellanica around 13 mya, and the ancestor of the Tahitian F. cyrtandroides split off from the New Zealand species of section Skinnera approximately 8 mya.     

Phylogenetic relationships in Elymus (Poaceae: Triticeae) based on the nuclear ribosomal internal transcribed spacer and chloroplast trnL-F sequences

To estimate the phylogenetic relationship of polyploid Elymus in Triticeae, nuclear ribosomal internal transcribed spacer (ITS) and chloroplast trnL-F sequences of 45 Elymus accessions containing various genomes were analysed with those of five Pseudoroegneria (St), two Hordeum (H), three Agropyron (P) and two Australopyrum (W) accessions. The ITS sequences revealed a close phylogenetic relationship between the polyploid Elymus and species from the other genera. The ITS and trnL-F trees indicated considerable differentiation of the StY genome species. The trnL-F sequences revealed an especially close relationship of Pseudoroegneria to all Elymus species included. Both the ITS and trnL-F trees suggested multiple origins and recurrent hybridization of Elymus species. The results suggested that: the St, H, P, and W genomes in polyploid Elymus were donated by Pseudoroegneria, Hordeum, Agropyron and Australopyrum, respectively, and the St and Y genomes may have originated from the same ancestor; Pseudoroegneria was the maternal donor of the polyploid Elymus; and some Elymus species showed multiple origin and experienced recurrent hybridization.     

Phylogenetic analysis of Petunia sensu Jussieu (Solanaceae) using chloroplast DNA RFLP

BACKGROUND AND AIMS: The phylogenetic relationships of Petunia sensu Jussieu (Petunia sensu Wijsman plus Calibrachoa) are unclear. This study aimed to resolve this uncertainty using molecular evidence. METHODS: Phylogenetic trees of 52 taxa of Petunia sensu Jussieu were constructed using restriction fragment length polymorphism (RFLP) of chloroplast DNA digested with 19 restriction enzymes and hybridized with 12 cloned Nicotiana chloroplast DNA fragments as probes. KEY RESULTS: In all, 89 phylogenetically informative RFLPs were detected and one 50 % majority consensus tree was obtained, using the maximum parsimony method, and one distance matrix tree, using the neighbour joining method. Petunia sensu Wijsman and Calibrachoa were monophyletic sister clades in both trees. Calibrachoa parviflora and C. pygmaea, previously thought to differ from the other species in terms of their cross-compatibility, seed morphology, and nuclear DNA content, formed a basal clade that was sister to the remainder of Calibrachoa. Several clades found in the phylogenetic trees corresponded to their distribution ranges, suggesting that recent speciation in the genus Petunia sensu Jussieu occurred independently in several different regions. CONCLUSIONS: The separation of Petunia sensu Wijsman and Calibrachoa was supported by chloroplast DNA analysis. Two groups in the Calibrachoa were also recognized with a high degree of confidence.     

Phylogenetic relationships and hybrid origin of Potamogeton species (Potamogetonaceae) distributed in China: insights from the nuclear ribosomal internal transcribed spacer sequence (ITS)

Hybridization and polyploidization are important evolutionary processes in higher plants and have greatly enriched the diversity of the genus Potamogeton (Potamogetonaceae). To study the phylogenetic relationships and hybrid origin of Potamogeton species, 35 accessions representing 20 species, including diploids, tetraploids and hexaploids, and three hybrids were collected in China and their ribosomal internal transcribed spacers (ITS) were cloned, sequenced and statistically analyzed. The data showed that ITS sequences were informative to analyze the phylogeny of Potamogeton, and the phylogenetic tree revealed that Potamogeton species examined could be mainly divided into two groups (Group I and II), corresponding to subgenus Potamogeton and subgenus Coleogeton, respectively. Then, the evolutionary mechanism on the polyploidy of Potamogeton species was discussed. P. natans probably was an allotetraploid and one of its parent might result from aneuploidy change of species with 2n=28. P. hubeiensis might be derived from the hybridization between P. octandrus and P. cristatus. We suggested that both P. lucens and P. maackianus probably were allotetraploids, and P. obtusifolius might be a diploid hybrid between P. compressus and P. pusillus. Moreover, P. malainoides might have undergone biased concerted evolution toward one of its parent P. wrightii, and P. intortusifolius might be a synonymy of P. × anguillanus.     

Phylogenetic relationships among Lactuca (Asteraceae) species and related genera based on ITS-1 DNA sequences

Internal transcribed spacer (ITS-1) sequences from 97 accessions representing 23 species of Lactuca and related genera were determined and used to evaluate species relationships of Lactuca sensu lato (s.l.). The ITS-1 phylogenies, calculated using PAUP and PHYLIP, correspond better to the classification of Feráková than to other classifications evaluated, although the inclusion of sect. Lactuca subsect. Cyanicae is not supported. Therefore, exclusion of subsect. Cyanicae from Lactuca sensu Feráková is proposed. The amended genus contains the entire gene pool (sensu Harlan and De Wet) of cultivated lettuce (Lactuca sativa). The position of the species in the amended classification corresponds to their position in the lettuce gene pool. In the ITS-1 phylogenies, a clade with L. sativa, L. serriola, L. dregeana, L. altaica, and L. aculeata represents the primary gene pool. L. virosa and L. saligna, branching off closest to this clade, encompass the secondary gene pool. L. virosa is possibly of hybrid origin. The primary and secondary gene pool species are classified in sect. Lactuca subsect. Lactuca. The species L. quercina, L. viminea, L. sibirica, and L. tatarica, branching off next, represent the tertiary gene pool. They are classified in Lactuca sect. Lactucopsis, sect. Phaenixopus, and sect. Mulgedium, respectively. L. perennis and L. tenerrima, classified in sect. Lactuca subsect. Cyanicae, form clades with species from related genera and are not part of the lettuce gene pool.     

用叶绿体ndhF和核核糖体ITS序列推断李属(蔷薇科)的系统发育

Sequences of the chloroplast ndhF gene and the nuclear ribosomal ITS regions are employed to reconstruct the phylogeny of Prunus (Rosaceae), and evaluate the classification schemes of this genus. The two data sets are congruent in that the genera Prunus s.l. and Maddenia form a monophyletic group, with Maddenia nested within Prunus. However, the ndhF data set is incongruent with the ITS data supporting two major groups within Prunus one consisting of subgenera Laurocerasus (including Pygeum) and Padus as well as the genus Maddenia and another of subgenera Amygdalus, Cerasus, and Prunus. The ITS data, on the other hand, support a clade composed of subgenera Amygdalus and Prunus and Prunus sect. Microcerasus in addition to a paraphyletic grade of subgenera Laurocerasus and Padus (and the genus Maddenia) taxa. In general, the subgeneric classifications of Prunus s.l. are not supported. The ITS and ndhF phylogenies differ mainly in interspecific relationships and the relative position of the Padus/Laurocerasus group. Both ITS and ndhF data sets suggest that the formerly recognized genus Pygeum is polyphyletic and that the distinction of the subgenera Padus and Laurocerasus is not supported. The biogeographic interactions of the temperate and tropical members in the Padus/Laurocera- sus/Maddenia alliance including Pygeum are shown to be highly dynamic and complex.     

Phylogenetic relationships among Cucumis species based on the ribosomal internal transcribed spacer sequence and microsatellite markers

The phylogenetic relationships within the genus Cucumis (a total of 25 accessions belonging to 17 species) were studied using the nuclear ribosomal DNA internal transcribed spacer (ITS) region. The analysis included commercially important species such as melon (C. melo L.) and cucumber (C. sativus). Two additional cucurbit species, watermelon and zucchini, were also included as outgroups. The data obtained reflected the clustering of Cucumis species in four main groups, comprising accessions from cucumber, melon, C. metuliferus and the wild African species. Some of the species clustered in different positions from those reported in classifications previously described by other authors. The data obtained clearly identify a division between the 2n=2x = 14 species (C. sativus) and the 2n = 2x = 24 ones (C. melo and wild species). Within the wild species we identified a subgroup that included C. sagittatus and C. globosus. Oreosyce africana, also classified as Cucumis membranifolius, was shown to be nested within Cucumis. Three accessions previously classified as independent species were shown to be genotypes of Cucumis melo. A set of melon and cucumber SSRs were also used to analyse the Cucumis species and the results were compared with the ITS data. The differential amplification of the SSRs among the accessions made it possible to distinguish three main groups: melon, cucumber and the wild species, though with less detail than applying ITS. Some SSRs were shown to be specific for melon, but other SSRs were useful for producing PCR fragments in all species of the genus.We are grateful to NCRPIS, IPK in Gatersleben, Semillas Fitó S.A., Michel Pitrat and Fernando Nuez for providing seeds. We would also like to thank Vanessa Alfaro, Trinidad Martínez and Núria Galofré for their excellent technical assistance. This work was financed by project AGL2000-0360 of Spains Ministerio de Ciencia y Tecnología (MCYT). AJMs work was supported by a postdoctoral contract from Spains MCYT.     

Phylogenetic relationships in the genusStylosanthes (Leguminosae) based upon chloroplast DNA variation

A detailed analysis of chloroplast DNA restriction fragment length variation was undertaken to reconstruct the maternal phylogeny of 18 taxa from both sections of the papilionoid tropical forage legume genusStylosanthes. Data were analysed by means of the computer program PAUP, using an heuristic search with Wagner parsimony. The resulting cladogram dividedStylosanthes into four separate clades, which comprised: (i) theS. guianensis complex and related species (i.e.S. gracilis, S. grandifolia andS. montevidensis); (ii)S. hispida, tetraploidS. hamata s. l.,S. sympodialis, S. humilis, S. leiocarpa, S. angustifolia and certain accesions ofS. scabra; (iii)S. calcicola, S. viscosa, diploidS. hamata s. str., andS. fruticosa, plus accessions ofS. scabra, S. capitata and one accession ofS. grandifolia; and (iv)S. macrocephala and other accessions ofS. capitata not included within clade 3. Results are generally congruent with previously established interspecific relationships and, moreover, enabled identification of putative maternal progenitors for four tetraploid taxa:S. humilis was identified as a likely maternal parent of bothS. sympodialis andS. hamata s. l.,S. viscosa as a maternal parent ofS. scabra, andS. macrocephala as a maternal parent ofS. capitata.     

Phylogenetic relationships of Salix (Salicaceae) based on rbcL sequence data

Nucleotide sequences of the chloroplast-encoded rbcL gene were used to examine phylogenetic relationships of the genus Salix together with other allied genera of the family Salicaceae. Phylogenetic analyses of rbcL sequences strongly suggest the monophyly of three commonly recognized genera (Chosenia, Salix, and Toisusu). Two monophyletic groups are recognized within the larger monophyletic group. They do not correspond with any infrageneric taxa proposed so far. With regard to character evolution, it is thought that the reduction of stamen number from more than two stamens to two might occur in at least three lineages and that fused bud scales evolved several times and/or the reverse evolution occurred from fused to free. Some types of pollen surfaces are considered to have evolved independently.     

Phylogenetic relationships of Betula species (Betulaceae) based on nuclear ADH and chloroplast matK sequences

The phylogenetic relationships within the genus Betula (Betulaceae) were investigated using a part of the nuclear ADH gene and DNA sequences of the chloroplast matK gene with parts of its flanking regions. Two well-supported phylogenetic groups could be identified in the chloroplast DNA sequence: one containing the three American species B. lenta, B. alleghaniensis, and B. papyrifera and the other including all the other species studied. The ADH gene displayed more variation, and three main groups could be identified. In disagreement with the classical division of the genus Betula, B. schmidtii and B. nana grouped with the species in subgenus Betula, and B. ermanii grouped with species in subgenus Chamaebetula, including B. humilis and B. fruticosa. The ADH phylogeny suggests that several independent polyploidizations within the genus Betula could have taken place. The ADH and chloroplast phylogenies were in part incongruent due to the placement of B. papyrifera. The most likely reason for this seems to be cytoplasmic introgression.