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1.
Sequences of the end of the 5.8S gene and the internal transcribed spacer 2 (ITS‐2) of nuclear ribosomal DNA have been determined for 19 species of the brown algal genus Sargassum (Sargassaceae), representing three subgenera and eight sections (sections are in parentheses): Phyllotrichia, Bactrophycus (Teretia, Spongocarpus, Halochloa and Repentia) and Sargassum (Acanthocarpicae, Malacocarpicae, Zygocarpicae) to assess the taxonomic position of the section Phyllocystae traditionally included within the Bactrophycus. The sequence of Myagropsis myagroides (Mertens ex Turner) Fensholt (Sargassaceae) was used as an outgroup. Sequences of ITS‐2 were analyzed using neighbor‐joining, parsimony and maximum likelihood methods. The results showed the existence of three clades in Sargassum, corresponding to the three subgenera. The subgenus Phyllotrichia is positioned near the outgroup. Two robust clades were obtained, one corresponding to the subgenus Bactrophycus and the other to the subgenus Sargassum. Sargassum mcclurei Setchell and Sargassum quinhonense Nguyen, the two Phyllocystae investigated, are close to species belonging to the section Zygocarpicae in the subgenus Sargassum. A transfer of the section Phyllocystae to the subgenus Sargassum is therefore proposed on the basis of molecular data (ITS‐2) and morphological data (receptacles and basal leaf).  相似文献   

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The taxonomic and phylogenetic concepts within the Sargassum C. Agardh (Sargassaceae) species complex were evaluated through molecular phylogenetic analyses using portions of the chloroplast encoded rbcLS Operon. According to more conservative sequences (rbcL), Turbinaria (Turner) J. Agardh is a close and well‐supported sister lineage to the Sargassum species complex and an appropriate external outgroup for analyses of subgenera and subsections within Sargassum. Both rbcL and more rapidly evolving rbcLS spacer sequences indicated that the East Asiatic genus Myagropsis (Mertens et Turner) Fensholt, along with Sargassum sinicola Setchell et Gardner, represent the closest lineage to Sargassum and form appropriate internal outgroups. The rbcLS spacer region supported three of four subgeneric designations by J. Agardh and sectional levels within the subgenus Sargassum. However, some aspects of Agardh's system were not supported: many of the subsectional ranks or the phyletic concepts; Phyllotrichia was not monophyletic as a subgenus, and its species were also not the most ancestral of Sargassum; and subgenus Sargassum was not the most derived subgenus within the genus. This modern phylogeny suggests a deep evolutionary history for subgenus Sargassum with rapid speciation in closely related subsections and series, and a sister relationship between subgenera Arthrophycus and Bactrophycus.  相似文献   

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Thanwisai A  Kuvangkadilok C  Baimai V 《Genetica》2006,128(1-3):177-204
The sequences of the second internal transcribed spacer (ITS2) of ribosomal DNA (rDNA) were determined for 40 black fly species from Thailand, belonging to 4 subgenera of the genus Simulium, namely Gomphostilbia (12 species), Nevermannia (5 species), Montisimulium (1 species), Simulium sensu stricto (21 species), and an unknown subgenus with one species (Simulium baimaii). The length of the ITS2 ranged from 247 to 308 bp. All black fly species had high AT content, ranging from 71 to 83.8%. Intraindividual variation (clonal variation) occurred in 13 species, ranging from 0.3 to 1.1%. Large intrapopulation and interpopulation heterogeneities exist in S. feuerboni from the same and different locations in Doi Inthanon National Park, northern Thailand. Phylogenetic relationships among 40 black fly species were examined using PAUP (version 4.0b10) and MrBAYS (version 3.0B4). The topology of the trees revealed two major monophyletic clades. The subgenus Simulium and Simulium baimaii were placed in the first monophyletic clade, whereas the subgenera Nevermannia + Montisimulium were placed as the sister group to the subgenus Gomphostilbia in the second monophyletic clade. Our results suggest that S. baimaii belongs to the malyschevi-group or variegatum-group in the subgenus Simulium. The molecular phylogeny generally agrees with existing morphology-based phylogenies.  相似文献   

6.
The genus Corydalis is recognized as one of the most taxonomically challenging plant taxa. It is mainly distributed in the Himalaya–Hengduan Mountains, a global biodiversity hotspot. To date, no effective solution for species discrimination and taxonomic assignment in Corydalis has been developed. In this study, five nuclear and chloroplast DNA regions, ITS, ITS2, matK, rbcL, and psbA‐trnH, were preliminarily assessed based on their ability to discriminate Corydalis to eliminate inefficient regions, and the three regions showing good performance (ITS, ITS2 and matK) were then evaluated in 131 samples representing 28 species of 11 sections of four subgenera in Corydalis using three analytical methods (NJ, ML, MP tree; K2P‐distance and BLAST). The results showed that the various approaches exhibit different species identification power and that BLAST shows the best performance among the tested approaches. A comparison of different barcodes indicated that among the single barcodes, ITS (65.2%) exhibited the highest identification success rate and that the combination of ITS + matK (69.6%) provided the highest species resolution among all single barcodes and their combinations. Three Pharmacopoeia‐recorded medicinal plants and their materia medica were identified successfully based on the ITS and ITS2 regions. In the phylogenetic analysis, the sections Thalictrifoliae, Sophorocapnos, Racemosae, Aulacostigma, and Corydalis formed well‐supported separate lineages. We thus hypothesize that the five sections should be classified as an independent subgenus and that the genus should be divided into three subgenera. In this study, DNA barcoding provided relatively high species discrimination power, indicating that it can be used for species discrimination in this taxonomically complicated genus and as a potential tool for the authentication of materia medica belonging to Corydalis.  相似文献   

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Phylogenetic relationships among 108 oak species (genus Quercus L.) were inferred using DNA sequences of six nuclear genes selected from the existing genomic resources of the genus. Previous phylogenetic reconstructions based on traditional molecular markers are inconclusive at the deeper nodes. Overall, weak phylogenetic signals were obtained for each individual gene analysis, but stronger signals were obtained when gene sequences were concatenated. Our data support the recognition of six major intrageneric groups Cyclobalanopsis, Cerris, Ilex, Quercus, Lobatae and Protobalanus. Our analyses provide resolution at deeper nodes but with moderate support and a more robust infrageneric classification within the two major clades, the ‘Old World Oaks’ (Cyclobalanopsis, Cerris, Ilex) and ‘New World Oaks’ (Quercus, Lobatae, Protobalanus). However, depending on outgroup choice, our analysis yielded two alternative placements of the Cyclobalanopsis clade within the genus Quercus. When Castanea Mill. was chosen as outgroup, our data suggested that the genus Quercus comprised two clades corresponding to two subgenera as traditionally recognized by Camus: subgenus Euquercus Hickel and Camus and subgenus Cyclobalanopsis Øersted (Schneider). However, when Notholithocarpus Manos, Cannon and S. Oh was chosen as an outgroup subgenus Cyclobalanopsis clustered with Cerris and Ilex groups to form the Old World clade. To assess the placement of the root, we complemented our dataset with published data of ITS and CRC sequences. Based on the concatenated eight gene sequences, the most likely root position is at the split between the ‘Old World Oaks’ and the ‘New World Oaks’, which is one of the alternative positions suggested by our six gene analysis. Using a dating approach, we inferred an Eocene age for the primary divergences in Quercus and a root age of about 50–55 Ma, which agrees with palaeobotanical evidence. Finally, irrespective of the outgroup choice, our data boost the topology within the New World clade, where (Protobalanus + Quercus) is a sister clade of Lobatae. Inferred divergence ages within this clade and the Cerris–Ilex clade are generally younger than could be expected from the fossil record, indicating that morphological differentiation pre-dates genetic isolation in this clade.  相似文献   

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Chloroplast DNA (cpDNA) restriction site variation was examined in 32 species, representing five subgenera, of Bromus (Poaceae). Thirty-seven phylogenetically informative restriction sites were detected. Cladistic analysis of the restriction site data produced a single most-parsimonious tree of 50 steps. The cladogram indicated two major clades within the genus. One clade included B. trinii of subgenus Neobromus and species of subgenus Ceratochloa. The other was composed of subgenera Festucaria, Stenobromus, and Bromus. Within the second clade, species of subgenus Festucaria appeared in three lineages. The second clade also contained an assemblage of species belonging to subgenera Stenobromus and Bromus in a separate lineage. There was very little resolution of relationships in this assemblage since several species appeared individually in separate lineages. The cpDNA phylogenetic hypothesis did not separate species of subgenera Stenobromus and Bromus into well-defined clades as circumscribed by morphology and cytogenetics. The cpDNA tree is in agreement with the phylogenetic scheme based on traditional data in that: 1) subgenera Neobromus and Ceratochloa were the first to diverge, while Bromus and Stenobromus diverged later; 2) within the genus Bromus species with small chromosomes are ancestral; and 3) subgenera Bromus and Stenobromus probably originated from similar ancestors as Festucaria. The tree based on cpDNA data does not support that: 1) subgenera Neobromus and Ceratochloa did not have a common origin; 2) subgenus Festucaria is monophyletic; and 3) subgenera Stenobromus and Bromus are distinct entities. The mean nucleotide sequence divergence values between pairs of subgenera ranged from p = 0.0 to 0.9. These values suggest that cpDNA evolution in Bromus is slow.  相似文献   

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The lizard genus Liolaemus and different clades within it have been the focus of several recent phylogenetic studies mainly based on morphology and mtDNA. Although there is general consensus for recognizing two clades (subgenera) within the genus, [Liolaemus (sensu stricto) and Eulaemus], phylogenetic relationships within each subgenus remain difficult to elucidate, given incomplete taxonomic sampling and large discordance between published studies. Here, new phylogenetic relationships for the Eulaemus subgenus are proposed based on the largest molecular data set ever used for this clade, which includes 188 individuals and 14 loci representing different parts of the genome (mtDNA, anonymous nuclear loci and nuclear protein‐coding loci). This data set was analysed using two species tree approaches (*beast and MDC). Levels of discordance among methods were found, and with previously published studies, but results are robust enough to propose new phylogenetic hypotheses for the Eulaemus clade. Specifically well‐resolved and well‐supported novel hypotheses are provided within the lineomaculatus section, and we formally recognize the zullyae clade, the sarmientoi clade and the hatcheri group. We also resolve species relationships within the montanus section, and particularly within the melanops series. We found discordance between mitochondrial and nuclear trees and discussed alternative hypotheses for the lineomaculatus and montanus sections, as well as the challenge in resolving phylogenetic relationships for large clades in general.  相似文献   

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Laparocerus are plant‐chewing flightless weevils distributed on oceanic islands in Macaronesia, with a single species in Morocco. The genus has a complicated taxonomic history with several subgenera described. To assist in a taxonomical revision of the group, a molecular study was undertaken. In this first contribution, the species from the Azores and Madeira archipelagos are studied together with representatives of subgenera from the Canary Islands and the single known continental species (46 OTUs). Phylogenetic analyses are based on sequence data from mitochondrial cytochrome oxidase II (COII) and the ribosomal 16S ribosomal RNA (16S rRNA) genes (combined data set 1023 bp), with additional data from the nuclear elongation factor 1α (EF‐1α) for some selected species. Maximum likelihood (ML) and Bayesian analyses show that all Madeiran species are monophyletic and form a monophyletic group with the Afro‐Canarian samples. Species of the genus Lichenophagus appear within the Madeiran and Canarian Laparocerus clades, but separated in accordance with their respective island origin. Thus, Lichenophagus is here restricted to Madeiran species and proposed as subgenus (status novo) of Laparocerus. Conversely, the Laparocerus subgenus Drouetius from the Azores is revealed to be a separate and distant outgroup, in agreement with its morphological distinctiveness, deserving an independent genus status. Internal relationships within the Madeiran clade are discussed and compared with morphologically defined species groups. The Madeiran monotypic subgenus Cyphoscelis is not supported by the genetic data and synonymized (nov. syn.) with Laparocerus. Subgenera Laparocerus and Atlantis prove to be polyphyletic. Consequently a restriction to monophyletic and morphologically congruent clades is proposed. A cryptic species vicariant of Laparocerus morio was detected and recognized as L. chaoensis, status novo. Other cases of discrepancy between the genetic results and the traditional taxonomy are discussed in detail in the light of mitochondrial introgression, incomplete lineage sorting or poor taxonomy hypotheses.  相似文献   

11.
Sargassum subgenus Phyllotricha currently includes seven species restricted to Australian and New Zealand coasts. A recent study of Cystoseira and other Sargassaceae genera based on mitochondrial 23S DNA and chloroplast‐encoded psbA sequences resulted in the most widely distributed species of subgenus Phyllotricha, Sargassum decurrens, being transferred to the reinstated monospecific Sargassopsis Trevisan. The fate of the residual six Phyllotricha species, however, was not considered. The present study examines these Phyllotricha species, alongside other Sargassum subgenera, Sargassopsis, Sirophysalis trinodis (formerly Cystoseira trinodis) and the New Zealand endemic Carpophyllum Greville, using morphological evidence and the molecular phylogenetic markers cox3, ITS‐2 and the rbcL–S spacer. Our results suggest both the genus Sargassum and Sargassum subgenus Phyllotricha are polyphyletic as currently circumscribed. Four S. subgen. Phyllotricha species, i.e. S. sonderi, S. decipiens, S. varians and S. verruculosum, form a monophyletic group sister to the genus Carpophyllum, and S. peronii is genetically identical to S. decurrens with regard to all three loci. We propose the resurrection of the genus Phyllotricha Areschoug, with type species Phyllotricha sonderi, and include the new combinations Phyllotricha decipiens, Phyllotricha varians and Phyllotricha verruculosum. Sargassum peronii, S. heteromorphum and S. kendrickii are transferred to Sargassopsis and Sargassum peronii is considered a synonym of Sargassopsis decurrens.  相似文献   

12.
The taxonomy and phylogeny of Asian Meconopsis (Himalayan blue poppy) remain largely unresolved. We used the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA) and the chloroplast DNA (cpDNA) trnL-F region for phylogenetic reconstruction of Meconopsis and its close relatives Papaver, Roemeria, and Stylomecon. We identified five main clades, which were well-supported in the gene trees reconstructed with the nrDNA ITS and cpDNA trnL-F sequences. We found that 41 species of Asian Meconopsis did not constitute a monophyletic clade, but formed two solid clades (I and V) separated in the phylogenetic tree by three clades (II, III and IV) of Papaver and its allies. Clade V includes only four Asian Meconopsis species, with the remaining 90 percent of Asian species included in clade I. In this core Asian Meconopsis clade, five subclades (Ia–Ie) were recognized in the nrDNA ITS tree. Three species (Meconopsis discigera, M. pinnatifolia, and M. torquata) of subgenus Discogyne were imbedded in subclade Ia, indicating that the present definition of subgenera in Meconopsis should be rejected. These subclades are inconsistent with any series or sections of the present classifications, suggesting that classifications of the genus should be completely revised. Finally, proposals for further revision of the genus Meconopsis were put forward based on molecular, morphological, and biogeographical evidences.  相似文献   

13.
In this study, we used sequences of two mitochondrial genes, cytochrome c oxidase I (COI) and 16S rRNA, and one nuclear gene, 28S rRNA, to test the monophyly of the sea star genus Echinaster, and understand the phylogenetic relationships among species and subgenera within this genus. Phylogenetic analyses based on Bayesian inference and maximum likelihood methods revealed three clades with high values of genetic divergence among them (K2P distances for COI over 23%). One of the clades grouped all Echinaster (Othilia) species, and the other two clades included Echinaster (non‐Othilia) species and Henricia species, respectively. Although the relationships among Henricia, Othilia, and Echinaster could not be completely clarified, the Othilia clade was a well‐supported group with shared diagnostic morphological characters. Moreover, the approximately unbiased test applied to the phylogenetic reconstruction rejected the hypothesis of the genus Echinaster as a monophyletic group. According to these results, we suggest the revalidation of Othilia as a genus instead of a subgenus within Echinaster. Our study clarifies important points about the phylogenetic relationships among species of Echinaster. Other important systematic questions about the taxonomic classification of Echinaster and Henricia still remain open, but this molecular study provides bases for future research on the topic.  相似文献   

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In the present study, we investigated the intrageneric and intergeneric phylogenetic relationships of the heterotrophic marine dinoflagellate genus Protoperidinium. Using single‐cell polymerase chain reaction methods, we determined small subunit ribosomal RNA gene sequences for 10 Protoperidinium species belonging to four sections and two subgenera. Phylogenetic trees were constructed using maximum parsimony, neighbor joining and maximum likelihood methods. We found intraspecific variability of small subunit rDNA sequences in Protoperidinium conicum (Gran) Balech, Protoperidinium crassipes (Kofoid) Balech and Protoperidinium denticulatum (Gran et Braarud) Balech, but not in other species. The small subunit rDNA phylogeny revealed that the genus is monophyletic, but its phylogenetic position within the Dinophyceae could not be determined because of ambiguous basal topologies. Within the genus Protoperidinium, species of the subgenus Archaeperidinium with two anterior intercalary plates (2a) were shown to be monophyletic, but species of the subgenus Protoperidinium with three anterior intercalary plates (3a) were resolved as paraphyletic. The sections Avellana, Divergentia and Protoperidinium were shown to be monophyletic, while the section Conica was paraphyletic. Based on the trees obtained in the present study, most of the traditionally defined sections are supported by molecular phylogeny. It was also indicated that the section Avellana evolved from one of the Conica‐type dinoflagellates.  相似文献   

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We used nuclear ribosomal DNA internal transcribed spacer region (ITS 1 - 5.8S - ITS 2; ITS) sequences to generate the first phylogeny of Rubus based on a large, molecular data set. We sampled 57 taxa including 20 species of subgenus Rubus (blackberries), one to seven species from each of the remaining 11 subgenera, and the monotypic and closely related Dalibarda. In Rubus, ITS sequences are most informative among subgenera, and variability is low between closely related species. Parsimony analysis indicates that Rubus plus Dalibarda form a strongly supported clade, and D. repens may nest within Rubus. Of the subgenera with more than one species sampled, only subgenus Orobatus appears monophyletic. Three large clades are strongly supported: one contains all sampled species of nine of the 12 subgenera; another includes extreme Southern Hemisphere species of subgenera Comaropsis, Dalibarda, and Lampobatus; and a third clade consists of subgenus Rubus plus R. alpinus of subgenus Lampobatus. Rubus ursinus appears to be a hybrid between a close relative of R. macraei (subgenus Idaeobatus, raspberries) and an unidentified subgenus Rubus species. ITS sequences are generally consistent with biogeography and ploidy, but traditionally important morphological characters, such as stem armature and leaf type, appear to have limited phylogenetic value in Rubus.  相似文献   

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The genus Gephyromantis is a clade within the Malagasy-Comoroan family Mantellidae composed of rainforest frogs that live and breed to varying degrees independently from water. Based on DNA sequences of five mitochondrial and five nuclear genes we inferred the phylogeny of these frogs with full taxon coverage at the species level. Our preferred consensus tree from a partitioned Bayesian analysis of 5843 base pairs of 51 nominal and candidate species supports various major clades within the genus although the basal relationships among these remain unresolved. The data provide strong evidence for the monophyly of the subgenera Gephyromantis (after exclusion of Gephyromantis klemmeri), Laurentomantis, Vatomantis, and Phylacomantis. Species assigned to the subgenus Duboimantis belong to two strongly supported clades of uncertain relationships. G. klemmeri, previously in the subgenus Gephyromantis, was placed with high support sister to the Laurentomantis clade, and the Laurentomantis + G. klemmeri clade was sister to Vatomantis. A reconstruction of ancestral distribution areas indicates a diversification of several subgenera in the northern biogeographic regions of Madagascar and the dispersal out of northern Madagascar for several clades.  相似文献   

17.
The three brown banded land snail genus Humboldtiana (Pulmonata: Humboldtianidae) comprises 50 species of insular distribution from southern Texas to central México; its low vagility and dispersal potential are reflected in high levels of endemism and highly restricted distributions. A current scheme of classification recognizes six subgenera: Polyomphala, Oreades, Gymnopallax, Clydonacme, Aglotrochus, and Humboldtiana (the latter containing three species groups). In the present work, mitochondrial 16S rDNA and partial ITS region and ribosomal large subunit (5.8S+ITS-2+28S) sequences from 26 recognized species and 2 populations of unknown identity were studied to assess phylogenetic relationships of Humboldtiana species using parsimony and Bayesian analysis, and AU test was used to compare the different phylogenetic hypotheses. The same four major clades were recovered by both methods (buffoniana, queretaroana, montezumae and fortis), although none of them support the current scheme of classification, with the only exception being the subgenus Gymnopallax included in the clade buffoniana. The results suggest that speciation patterns observed in the genus Humboldtiana could be explained as a morphostatic radiation.  相似文献   

18.
Jeon, M.‐J., Song, J.‐H. & Ahn, K.‐J. (2012). Molecular phylogeny of the marine littoral genus Cafius (Coleoptera: Staphylinidae: Staphylininae) and implications for classification. —Zoologica Scripta, 41, 150–159. A phylogenetic analysis of the marine littoral genus Cafius Stephens is presented based on molecular characters. The data set comprised partial mitochondrial COI (910 bp), COII (369 bp), 12S rDNA (351–354 bp), 16S rDNA (505–509 bp) and nearly complete sequences of 18S rDNA (1814–1830 bp) for 37 species. Twenty‐seven Cafius species, representing five of six subgenera, two Remus Holme species, three Phucobius Sharp species, monotypic Thinocafius Steel and four outgroups were included. The sequences were analysed simultaneously by parsimony analysis in Tree Analysis Using New Technology (TNT) with traditional manual alignment, direct optimization (DO) in the program POY4 under a variety of gap costs and partitioned Bayesian analysis for the combined data. The genus Cafius and nearly all of its subgenera were not supported as being monophyletic. Instead, all analyses (parsimony trees, DO tree under equal weighting and Bayesian tree) showed monophyly of Cafius + Phucobius + Remus + Thinocafius (clade Z) and all seven nested clades (A–G). However, the phylogenetic relationships among clades A–G differed among the analyses. The genus Phucobius was recovered as a monophyletic group within Cafius. The genus Remus was not monophyletic but formed a clade with C. rufescens Sharp and C. rufifrons Bierig within Cafius. The genus Thinocafius formed a clade with C. caviceps Broun, C. litoreus (Broun) and C. quadriimpressus (White) within Cafius. We propose new concepts for the genus Cafius and its related genera, and the seven nested clades.  相似文献   

19.
 Intrageneric phylogeny among ten representative Ceanothus species was investigated using DNA sequences of the chloroplast encoded ndhF and rbcL genes. Parsimony analysis of the ndhF sequences identified two main clades corresponding to two subgenera Ceanothus and Cerastes. The phylogenetic results suggest that three monophyletic clades within the subgenus Ceanothus can be delimited on the basis of (1) evergreen or (2) deciduous leaves and (3) thorn presence within the evergreen clade. The estimated divergence time based on rbcL sequences suggests that the two subgenera diverged 18–39 million years ago whereas species within each subgenus diverged more recently. Taken together, the results support the division of Ceanothus into two monophyletic subgenera and are consistent with the postulated recent divergence of many species within each subgenus. Received: 25 September 1996/Accepted: 8 November 1996  相似文献   

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