Non-monophyly of fish in the Sinipercidae (Perciformes) as inferred from cytochrome <Emphasis Type="Italic">b</Emphasis> gene

The sinipercids represent a group of 12 species of freshwater percoid fish, including nine in Siniperca and three species in Coreoperca. Despite several classification attempts and a preliminary molecular phylogeny, the phylogenetic relationships and systematic position of sinipercids remained still unsolved. The complete cytochrome b gene sequences from nine sinipercid species four non-sinipercid fish species were cloned, and a total of 12 cyt b sequences from 10 species of sinipercids and 11 cyt b sequences from 10 species of non-sinipercid fish also in Perciformes were included in the phylogenetic analysis. As expected, the two genera Siniperca and Coreoperca within sinipercids are recovered as monophyletic. However, nine species representing Moronidae, Serranidae, Centropomidae, Acropomatidae, Emmelichtyidae, Siganidae and Centrarchidae included in the present study are all nested between Coreoperca and Siniperca, which provides marked evidence for a non-monophyly of sinipercid fishes. Coreoperca appears to be closest to Centrachus representing the family Centrarchidae. Coreoperca whiteheadi and C. herzi are sibling species, which together are closely related to C. kawamebari. In the Siniperca, the node between S. roulei and the remaining species is the most ancestral, followed by that of S. fortis. S. chuatsi and S. kneri are sibling species, sister to S. obscura. However, the sinipercids do not seem to have a very clear phylogenetic history, for different methods of phylogenetic reconstruction result in different tree topologies, and the only conclusive result in favor of a paraphyletic origin of the two sinipercid genera is the parametric bootstrap test. The paraphyly of Sinipercidae may suggest that the “synapomorphs” such as cycloid scales, upon which this family is based, were independently derived at least twice within sinipercid fishes, and further study should be carried out to include the other two Siniperca species and to incorporate other genes. Handling editor: C. Sturmbauer     

Phylogenetic and systematic study of Korean <Emphasis Type="Italic">Orius</Emphasis> species (Heteroptera: Anthocoridae) on the basis of molecular and morphological data

A phylogenetic and systematic study of Orius species (Heteroptera: Anthocoridae) from Korea has been conducted using both morphological and molecular characters. Thirty morphological character states were coded for 10 strains of 9 species. Five molecular markers, partial cytochrome c oxidase I (COI), cytochrome b (CytB), 16S rRNA (16S), 18S rRNA (18S), and 28S rRNA (28S), from mitochondrial and nuclear genes, were tested. Phylogenetic analyses based on molecular data were conducted by minimum evolution, maximum parsimony, maximum likelihood, and Bayesian phylogenetic (BP) analyses. Analysis of morphological data was performed using the parsimony programs NONA, and the combined dataset of morphological and molecular data was analyzed using BP analyses. The results of this study indicate that use of COI and CytB enabled relatively effective identification of species, whereas the sequences of 16S, 18S and 28S did not enable identification of closely related species such as Orius minutus and O. strigicollis. We discuss the usefulness of the five molecular markers for determining phylogenetic relationships and identifying the species.     

A Three-Gene Dinoflagellate Phylogeny Suggests Monophyly of Prorocentrales and a Basal Position for <Emphasis Type="Italic">Amphidinium</Emphasis> and <Emphasis Type="Italic">Heterocapsa</Emphasis>

Many outstanding questions about dinoflagellate evolution can potentially be resolved by establishing a robust phylogeny. To do this, we generated a data set of mitochondrial cytochrome b (cob) and mitochondrial cytochrome c oxidase 1 (cox1) from a broad range of dinoflagellates. Maximum likelihood, maximum parsimony, and Bayesian methods were used to infer phylogenies from these genes separately and as a concatenated alignment with and without small subunit (SSU) rDNA sequences. These trees were largely congruent in topology with previously published phylogenies but revealed several unexpected results. Prorocentrum benthic and planktonic species previously placed in different clusters formed a monophyletic group in all trees, suggesting that the Prorocentrales is a monophyletic group. More strikingly, our analyses placed Amphidinium and Heterocapsa as early splits among dinoflagellates that diverged after the emergence of O. marina. This affiliation received strong bootstrap support, but these lineages exhibited relatively long branches. The approximately unbiased (AU-) test was used to assess this result using a three-gene (cob + cox1 + SSU rDNA) DNA data set and the inferred tree. This analysis showed that forcing Amphidinium or Heterocapsa to relatively more derived positions in the phylogeny resulted in significantly lower likelihood scores, consistent with the phylogenies. The position of these lineages needs to be further verified. Reviewing Editor: Dr. Martin Kreitman     

Gene Sequence Phylogenies of the Family <Emphasis Type="Italic">Microbacteriaceae</Emphasis>

The type strains of 32 species of 13 genera of the family Microbacteriaceae were analysed with respect to gene-coding phylogeny for DNA gyrase subunit B (gyrB), RNA-polymerase subunit B (rpoB), recombinase A (recA), and polyphosphate kinase (ppk). The resulting gene trees were compared with the 16S rRNA gene phylogeny of the same strains. The topology of neighbour-joining and maximum parsimony phylogenetic trees, based on nucleic-acid sequences and protein sequences of housekeeping genes, differed from one another, and no gene tree was identical to that of the 16S rRNA gene tree. Most genera analysed containing >1 strain formed phylogenetically coherent taxa. The three pathovars of Curtobacterium flaccumfaciens clustered together to the exclusion of the type strains of other Curtobacterium species in all DNA - and protein-based analyses. In no tree did the distribution of a major taxonomic marker, i.e., diaminobutyric acid versus lysine and/or ornithine in the peptidoglycan, or acyl type of peptidoglycan, correlate with the phylogenetic position of the organisms. The changing phylogenetic position of Agrococcus jenensis was unexpected: This strain defined individual lineages in the trees based on 16S rRNA and gyrB and showed identity with Microbacterium saperdae in the other three gene trees.     

Phylogeny of kangaroo apples (<Emphasis Type="Italic">Solanum</Emphasis> subg. <Emphasis Type="Italic">Archaesolanum</Emphasis>, Solanaceae)

Kangaroo apples, subgenus Archaesolanum, are a unique and still poorly known group within the genus Solanum. Here we aimed to reveal phylogeny, historical biogeography and age of diversification of Archaesolanum. We sampled all recognized species of the group and sequenced three chloroplast regions, the trnT-trnL spacer, trnL intron and trnL-trnF spacer to calibrate a molecular clock to estimate the age of the group. Distributional data were combined with the results of phylogenetic analysis to track the historical processes responsible for the current range of the group. Our analysis supported the monophyly of the kangaroo apples and the biogeographical disjunction between the two subclades within the group. Based on the divergence time estimates the most recent common ancestor of kangaroo apples is from the late Miocene age (~9 MYA). Based on the age estimate the common ancestors of the kangaroo apples are presumed to have arrived in Australia by long-distance dispersal. The two distinct lineages within the group have separated during the aridification of the continent and further speciated in the brief resurgence of rainforests during the Pliocene.     

Phylogeny of members of the <Emphasis Type="Italic">Frankia</Emphasis> genus based on <Emphasis Type="Italic">gyr</Emphasis>B, <Emphasis Type="Italic">nif</Emphasis>H and <Emphasis Type="Italic">gln</Emphasis>II sequences

To construct an evolutionary hypothesis for the genus Frankia, gyrB (encoding gyrase B), nifH (encoding nitrogenase reductase) and glnII (encoding glutamine synthetase II) gene sequences were considered for 38 strains. The overall clustering pattern among Frankia strains based on the three analyzed sequences varied among themselves and with the previously established 16S rRNA gene phylogeny and they did not reliably reflect clear evolution of the four discerned Frankia clusters (1, 2, 3 and 4). Based on concatenated gyrB, nifH and glnII, robust phylogenetic trees were observed with the three treeing methods (Maximum Likelihood, Parsimony and Neighbor-Joining) and supported by strong bootstrap and posterior probability values (>75%) for overall branching. Cluster 4 (non-infective and/or non-nitrogen-fixing Frankia) was positioned at a deeper branch followed by cluster 3 (Rhamnaceae and Elaeagnaceae infective Frankia), while cluster 2 represents uncultured Frankia microsymbionts of the Coriariaceae, Datiscaceae, Rosaceae and of Ceanothus sp. (Rhamnaceae); Cluster 1 (Betulaceae, Myricaceae and Casuarinaceae infective Frankia) appears to have diverged more recently. The present study demonstrates the utility of phylogenetic analyses based upon concatenated gyrB, nifH and glnII sequences to help resolve previously unresolved or poorly resolved nodes and will aid in describing species among the genus Frankia.     

Phylogenetic relationships among <Emphasis Type="Italic">Fagopyrum</Emphasis> species based on analysis of the <Emphasis Type="Italic">nad1</Emphasis> Gene b/c intron

For the first time, the b/c intron of the nad1 gene was characterized in 13 species of Fagopyrum and the applicability of the intron was demonstrated for identification of buckwheat species. The length of the b/c intron of the nad1 gene varied from 1217 bp in F. tataricum and F. cymosum to 1239 bp in F. capillatum. Species-specific SNPs and indels were identified. The genus phylogeny that was determined with the molecular approach correlated with phylogenetic data that are based on morphological characteristics. The NJ and MP dendrograms revealed distinct division of the analyzed species into two main groups, cymosum and urophyllum. The species of the urophyllum group were characterized by the presence of several synapomorphic substitutions and indels, including the insertion of 11 nucleotides, which is flanked by direct repeats.     

Comparative genomic analysis of CIPK gene family in <Emphasis Type="Italic">Arabidopsis</Emphasis> and <Emphasis Type="Italic">Populus</Emphasis>

Calcium serves as a second messenger in various signal transduction pathways in plants. CBL-interacting protein kinases (CIPKs), which have a variety of functions, are involved in calcium signal transduction. Previous, the studies on CIPK family members focused on Arabidopsis and rice. Here, we present a comparative genomic analysis of the CIPK gene family in Arabidopsis and poplar, a model tree species. Twenty-seven potential CIPKs were identified from poplar using genome-wide analysis. Like the CIPK gene family from Arabidopsis, CIPK genes from poplar were also divided into intron-free and intron-harboring groups. In the intron-harboring group, the intron distribution of CIPKs is rather conserved during the genome evolutionary process. Many homologous gene pairs were found in the CIPK gene family, indicating duplication events might contribute to the amplification of this gene family. The phylogenetic comparison of CIPKs in combination with intron distribution analysis revealed that CIPK genes from both Arabidopsis and poplar might have an ancient origin, which formed earlier than the separation of these two eudicot species. Our genomic and bioinformatic analysis will provide an important foundation for further functional dissection of the CBL-CIPK signaling network in poplars. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Phylogeny of Chinese <Emphasis Type="Italic">Polystichum</Emphasis> (Dryopteridaceae) based on chloroplast DNA sequence data (<Emphasis Type="Italic">trnL-F</Emphasis> and <Emphasis Type="Italic">rps4-trnS</Emphasis>)

Polystichum is one of the largest and most taxonomically complex fern genera in China. The evolutionary relationships of Chinese Polystichum and related genera, and the relationship between our Polystichum phylogeny and ecogeographic distribution, were tested by the use of DNA sequence data. Fifty-one species of Polystichum and 21 species in allied genera were sequenced for the plastid intergenic spacers rps4-trnS and trnL-F. Maximum parsimony and Bayesian phylogenetic analyses of both individual and combined data sets showed that Chinese Polystichum as commonly recognized was paraphyletic: one clade (the CCPC clade) included Cyrtomidictyum lepidocaulon, two Cyrtogonellum species, three Cyrtomium species, and a small number of Polystichum species usually occurring on limestone. A second clade, Polystichum sensu stricto, included the remainder of the Polystichum species; these often occur on non-limestone substrates. The remaining Cyrtomium species formed the third clade. Three subclades resolved within Polystichum sensu stricto (s.s.) clade do not correspond with recent sectional classifications, and we outline the issues relevant to a new classification for the genus. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Phylogeny of <Emphasis Type="Italic">Litsea</Emphasis> and related genera (Laureae-Lauraceae) based on analysis of <Emphasis Type="Italic">rpb2</Emphasis> gene sequences

The relationship between Litsea and related genera is currently unclear. Previous molecular studies on these taxa using cpDNA and nrITS were unable to produce well-resolved phylogenetic trees. In this study, we explored the potential of the rpb2 gene as a source of molecular information to better resolve the phylogenetic analysis. Although rpb2 was believed to be a single-copy gene, our cloning results showed that most species examined possessed several copies of these sequences. However, the genetic distance among copies from any one species was low, and these copies always formed monophyletic groups in our molecular trees. Our phylogenetic analyses of rpb2 data resulted in better resolved tree topologies compared to those based on cpDNA or nrITS data. Our results show that monophyly of the genus Litsea is supported only for section Litsea. As a genus, Litsea was shown to be polyphyletic. The genera Actinodaphne and Neolitsea were resolved as monophyletic groups in all analyses. They were also shown to be sisters and closer to the genus Lindera than to the genus Litsea. Our results also revealed that the genus Lindera is not a monophyletic group.     

mtDNA Diversity and genetic lineages of eighteen cattle breeds from <Emphasis Type="Italic">Bos taurus </Emphasis>and<Emphasis Type="Italic"> Bos indicus</Emphasis> in China

In order to clarify the origin and genetic diversity of indigenous cattle breeds in China, we carried out phylogenetic analysis of representatives of those breeds by employing mitochondrial gene polymorphism. Complete cyt b gene sequences, 1140 bp in length, were determined for a total of 136 individuals from 18 different breeds and these sequences were clustered into two distinct genetic lineages: taurine (Bos taurus) and zebu (Bos indicus). In analysis of the cyt b gene diversity, Chinese cattle showed higher nucleotide (0.00923) and haplotype diversity (0.848) than the reports from other studies, and the animals from the taurine lineage indicated higher nucleotide diversity (0.00330) and haplotype diversity (0.746) than the ones from the zebu lineage (0.00136; 0.661). The zebu mtDNA dominated in the southern breeds (63.3–100%), while the taurine dominated in the northern breeds (81.8–100%). Six cattle breeds from the central area of China exhibited intermediate frequencies of zebu mtDNA (25–71.4%). This polymorphism revealed a declining south-to-north gradient of female zebu introgression and a geographical hybrid zone of Bos taurus and Bos indicus in China.     

Molecular phylogeny of tribe Forsythieae (Oleaceae) based on nuclear ribosomal DNA internal transcribed spacers and plastid DNA <Emphasis Type="Italic">trnL</Emphasis>-<Emphasis Type="Italic">F</Emphasis> and <Emphasis Type="Italic">matK</Emphasis> gene sequences

The tribe Forsythieae comprises 2 genera (Forsythia and Abeliophyllum) and 14 species distributed mostly in the Far East. Although Forsythieae is considered monophyletic, with many symplesiomorphic characters, the phylogenetic status of Abeliophyllum remains controversial. We assessed the phylogenetic relationships of Forsythieae, based on a 3.3-kb plastid fragment (trnL-F region and matK gene) and nuclear internal transcribed spacer (ITS) region DNA sequences. We obtained a highly resolved and strongly supported topology with possible outgroups. The topology of the combined tree was congruent with those of the ITS region and matK gene. Maximum parsimony, maximum likelihood, and Bayesian inference tree analyses for the combined data also yielded identical relationships. Combined sequence data strongly supported the monophyly of Forsythieae and the close relationship between Fontanesia and Jasminum. Oleaceae, not Fontanesia, was found to be a sister group to Forsythieae. Moreover, the genus Abeliophyllum was distinctly independent of Forsythia. Three Forsythia lineages were suggested: (a) ONJ (ovata-nakaii-japonica clade), (b) VGE (viridissima-giraldiana-europaea), and (c) KISS (koreana-intermedia-saxatilis-suspensa). Our results indicated that F. × intermedia is not a hybrid between F. suspensa and F. viridissima, but further studies are needed to determine its taxonomic identity. Furthermore, the diverse fruit shapes in Oleaceae are assumed to be the result of parallelism or convergence.     

A new primer set for amplification of the cytochrome <Emphasis Type="Italic">b</Emphasis> gene in lantern fishes (Myctophidae)

New universal primers are offered for amplification of complete sequence of mitochondrial cyt b gene in lantern fishes of the family Myctophidae. Analysis of cyt b variability in the species of seven genera (Bolinichthys, Ceratoscopelus, Diaphus, Diogenichthys, Lampanyctus, Lepidophanes, Nannobrachium) demonstrates considerable divergence between species: an average of 18.2% (p-distances). Diversity (nucleotide diversity, number of segregating and phylogenetically informative sites, average number of nucleotide differences) and divergence significantly exceed those of another widely used mitochondrial marker, a fragment of cytochrome c oxidase subunit 1 sequence (cox 1). The mitochondrial cyt b gene amplified with the developed primers can be recommended as an informative tool for phylogenetic and population studies of lantern fishes.     

A PCR-RFLP method on faecal samples to distinguish <Emphasis Type="Italic">Martes martes</Emphasis>, <Emphasis Type="Italic">Martes foina</Emphasis>, <Emphasis Type="Italic">Mustela putorius</Emphasis> and <Emphasis Type="Italic">Vulpes vulpes</Emphasis>

A non-invasive genetic approach has been recently employed in the population genetics of wild species, using faeces that could be easily collected, particularly of elusive or endangered species. However, faeces of pine (Martes martes) and beech marten (M. foina) can be morphologically similar and could be confused with those of polecat (Mustela putorius) and red fox (Vulpes vulpes). On this basis, a rapid, simple and inexpensive RFLP protocol using a cytochrome b (Cyt b) gene fragment of mtDNA, isolated from faecal samples, was performed to distinguish the above-mentioned species.     

Detection of <Emphasis Type="Italic">Lactobacillus</Emphasis> species using a gene fragment of the RNA polymerase beta subunit <Emphasis Type="Italic">rpoB</Emphasis>

In this paper, we report on the comparative analysis of nucleotide sequences of the rpoB gene to assess its potential for use as a genetic marker for identification of Lactibacillus spp. recovered from acid milk products in different regions of Kazakhstan. The discriminatory power of the rpoB gene sequence was shown to be significantly higher for identification of closely related species of the Lactobacillus genus as compared to that of the 16S rRNA gene. The phylogeny based on the rpoB gene proved identical to that of the 16S rRNA gene and could be used as a supplement phylogenetic marker.     

Chloroplast DNA phylogeography of <Emphasis Type="Italic">Pedicularis</Emphasis> ser. <Emphasis Type="Italic">Gloriosae</Emphasis> (Orobanchaceae) in Japan

Phylogeographic analyses using chloroplast DNA (cpDNA) variation were performed for Pedicularis ser. Gloriosae (Orobanchaceae). Eighty-one plants of 18 populations of 6 species (P. gloriosa, P. iwatensis, P. nipponica, P. ochiaiana, P. sceptrum-carolinum and P. grandiflora) were analyzed. Fifteen distinct haplotypes were identified based on six cpDNA regions: the intergenic spacer between the trnT and trnL 3′exon, trnL 3′exon-trnF, atpB-rbcL, accD–psaI, the rpl16 intron and the trnK region (including the matK gene). Via phylogenetic analyses of the haplotypes, two continental species, P. sceptrum-carolinum and P. grandiflora, were placed at the most ancestral position in the trees. The former species is widely distributed in the Eurasian continent, and the latter is distributed in Far East Asia. Two robust major cpDNA clades (clades I and II) were revealed in the Japanese archipelago, although the statistical values of monophyly of these clades were weak. Clade I included the haplotypes (A-1, A-2, B-1, B-2 and J) of three species (P. gloriosa, P. iwatensis and P. ochiaiana), and Clade II included seven haplotypes (C-D, E-1, E-2 and F-H) of P. nipponica. These results suggest that this series originated on the Eurasian continent and that subsequently populations at the eastern edge of the continent differentiated into the two Japanese lineages. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

<Emphasis Type="Italic">Diaporthe</Emphasis> from walnut tree (<Emphasis Type="Italic">Juglans regia</Emphasis>) in China,with insight of the <Emphasis Type="Italic">Diaporthe eres</Emphasis> complex

Species of Diaporthe are important plant pathogenic fungi that commonly occur on a wide range of hosts. They are relatively difficult to identify due to their extreme similarity in morphology and confusing multigene phylogeny, especially in the Diaporthe eres complex. In the present study, isolates were collected from diseased branches of Juglans regia in China. Most strains were clustered into the D. eres species complex based on the combined internal transcribed spacer (ITS) region, partial calmodulin (CAL), histone H3 (HIS), translation elongation factor 1-alpha (TEF1-α) and beta-tubulin (TUB) genes. To focus on this complex, CAL, TEF1-α and TUB were selected in further phylogenetic analyses that showed a better topology compared with combined five-gene phylogeny. Results revealed that all strains which clustered in the Diaporthe eres complex from Juglans regia in China were Diaporthe eres. Results suggested a revised species criterion in the Diaporthe eres complex. The current study uncovered a new species here described as Diaporthe. tibetensis.     

Phylogeny and taxonomy of <Emphasis Type="Italic">Cladosporium</Emphasis>-like hyphomycetes,including <Emphasis Type="Italic">Davidiella</Emphasis> gen. nov., the teleomorph of <Emphasis Type="Italic">Cladosporium s. str.</Emphasis>

A phylogenetic study employing sequence data from the internal transcribed spacers (ITS1, ITS2) and 5.8S gene, as well as the 18S rRNA gene of various Cladosporium-like hyphomycetes revealed Cladosporium s. lat. to be heterogeneous. The genus Cladosporium s. str. was shown to represent a sister clade to Mycosphaerella s. str., for which the teleomorph genus Davidiella is proposed. The morphology, phylogeny and taxonomy of the cladosporioid fungi are discussed on the basis of this phylogeny, which consists of several clades representing Cladosporium-like genera. Cladosporium is confined to Davidiella (Mycosphaerellaceae) anamorphs with coronate conidiogenous loci and conidial hila. Pseudocladosporium is confined to anamorphs of Caproventuria (Venturiaceae). Cladosporium-like anamorphs of the Venturia (conidia catenate) are referred to Fusicladium. Human-pathogenic Cladosporium species belong in Cladophialophora (Capronia, Herpotrichiellaceae) and Cladosporium fulvum is representative of the Mycosphaerella/Passalora clade (Mycosphaerellaceae). Cladosporium malorum proved to provide the correct epithet for Pseudocladosporium kellermanianum (syn. Phaeoramularia kellermaniana, Cladophialophora kellermaniana) as well as Cladosporium porophorum. Based on differences in conidiogenesis and the structure of the conidiogenous loci, further supported by molecular data, C. malorum is allocated to Alternaria.     

Phylogenetic Studies of <Emphasis Type="Italic">Gordonia</Emphasis> Species Based on <Emphasis Type="Italic">gyrB</Emphasis> and <Emphasis Type="Italic">secA1</Emphasis> Gene Analyses

Phylogenetic relations within the genus Gordonia were analyzed using partial gyrB and secA1 gene sequences of 23 type species in comparison with those of 16S rRNA gene. The gyrB and secA1 phylogenies showed agreement with that constructed using 16S rRNA gene sequences. The degrees of divergence of the gyrB and secA1 genes were approximately 3.4 and 1.7 times greater, respectively, than that of 16S rRNA gene. The gyrB gene showed more discriminatory power than either the secA1 or 16S rRNA gene, facilitating clear differentiation of any two Gordonia species using gyrB gene analysis. Our data indicate that gyrB and secA1 gene sequences are useful as markers for phylogenetic study and identification at the species level of the genus Gordonia.