The phylogenetic placement of Ostropales within Lecanoromycetes (Ascomycota) revisited

Results of molecular studies regarding the phylogenetic placement of the order Ostropales and related taxa within Lecanoromycetes were thus far inconclusive. Some analyses placed the order as sister to the rest of Lecanoromycetes, while others inferred a position nested within Lecanoromycetes. We assembled a data set of 101 species including sequences from nuLSU rDNA, mtSSU rDNA, and the nuclear protein-coding RPB1 for each species to examine the cause of incongruencies in previously published phylogenies. MP, minimum evolution, and Bayesian analyses were performed using the combined three-region data set and the single-gene data sets. The position of Ostropales nested in Lecanoromycetes is confirmed in all single-gene and concatenated analyses, and a placement as sister to the rest of Lecanoromycetes is significantly rejected using two independent methods of alternative topology testing. Acarosporales and related taxa (Acarosporaceae group) are basal in Lecanoromycetes. However, if the these basal taxa are excluded from the analyses, Ostropales appear to be sister to the rest of Lecanoromycetes, suggesting different ingroup rooting as the cause for deviating topologies in previously published phylogenies.     

The ITS region of groundwater amphipods: length,secondary structure and phylogenetic information content in Crangonyctoids and Niphargids

The phylogenetic analysis of groundwater amphipods is challenging due to the lack of suitable morphological characters. However, molecular phylogenies based on the 18S and 28S nuclear genes of two Crangonyctoidea species endemic to Iceland, Crymostygius thingvallensis and Crangonyx islandicus, support the taxonomy of these species on the basis of morphological characters. Molecular analyses suggest that the genus Crangonyx is paraphyletic, with the species that is found in Eurasia being highly divergent genetically from the species present in North America and Iceland. Studies of the phylogenetic relationships within the genus Niphargus also warrant further work. The nuclear ITS2 region has recently been proposed as a barcoding marker for plants and animals. In addition, ITS2 has been used to build phylogenies at high taxonomic levels by including its secondary structure. In this study, we want to evaluate the applicability of the ITS region for this group of species and describe its characteristics. The taxonomy of C. thingvallensis, as well as the paraphyly of the genus Crangonyx, is supported herein by phylogenies based on the ITS2 variation. The secondary structure and the length of the ITS2 sequences of the Crangonyctoidea and the Niphargidae species studied are highly variable and are characterized by duplications. The ITS2 sequence of Niphargus plateaui is the longest metazoan sequence deposited in the ITS2 database so far. Although saturation was observed in the nucleotide variation of this marker, the addition of the secondary structure information for the reconstruction of the phylogeny did not add support to the phylogenetic trees. The ITS1 region, which is known to be more variable than ITS2 and bears a large duplication within C. islandicus, was found to be less useful for phylogenetic reconstruction.     

Incongruent gene trees, complex evolutionary processes, and the phylogeny of a group of North American minnows (Hybognathus Agassiz 1855)

Hybognathus is a putatively monophyletic group of North American minnows containing seven extant species. Although much is known about the taxonomy, biology, and life history of Hybognathus species, their phylogenetic relations with each other remain unclear. We address this problem with partial sequences of mitochondrial cytochrome-b, 16S rRNA, and ND4 mtDNA genes and nuclear growth hormone (GH) and S7 introns from representatives of all Hybognathus species and four outgroup taxa. Phylogenetic analyses of these data corroborated previous studies on the monophyly of seven recognized species of Hybognathus, and indicated weak support for monophyly of the genus. Topological tests, however, revealed significant (all P < 0.001) conflict among molecular data sets. Ad hoc removal of taxa from topologies and subsequent testing indicated that incongruence was localized to two specific ingroup taxa (H. hayi and H. regius) and suggested that the conflict is a function of underlying processes that have generated the observed phylogenetic patterns. Hybridization (ancestral), which is commonplace in cyprinids, may best explain topological disagreements among datasets; however, retention of ancestral polymorphism and natural selection remain as alternative hypotheses. Our results highlight methodological and topological problems associated with estimating interspecific phylogenies from multiple genes.     

Phylogenetic Relationships of the Silver Saxifrages (Saxifraga, Sect. Ligulatae Haworth): Implications for the Evolution of Substrate Specificity, Life Histories, and Biogeography

The silver saxifrages (Saxifraga sect. Ligulatae Haworth; Saxifragaceae) exhibit remarkable variation of substrate specialization, with strictly calcicole to calcifuge species, as well as life histories which range from semelparity to iteroparity. They occur almost exclusively in the European mountain ranges and display high levels of endemism. Sequences from chloroplast and nuclear ribosomal DNA were obtained to resolve phylogenetic relationships among the silver saxifrages and related taxa and to gain insight into the evolution of substrate specificity, life history, and biogeography. The resulting phylogenies suggested that (1) Saxifraga sect. Ligulatae, as traditionally defined, does not constitute a monophyletic group; (2) lime-secreting hydathodes in calcifuge species apparently represent a secondary nonaptation; (3) semelparity evolved independently two or three times in the silver saxifrages and allied sections, possibly in response to climatic changes that occured during the Pleistocene; and (4) narrow endemics, for example S. cochlearis, likely evolved from the fragmentation of the widespread S. paniculata into refugial populations that became isolated during the glacial maxima of the Pleistocene.     

Molecular taxonomy and ecology of Pseudallescheria, Petriella and Scedosporium prolificans (Microascaceae) containing opportunistic agents on humans

The main purpose of the present paper is to establish the connection between phylogenetic and morphological data and ecological features of strains of Pseudallescheria, Petriella, and Scedosporium. For the phylogenetic analysis sequences of the ITS region and the large subunit (partial sequences) of the rDNA were used. Cultural characteristics were observed on MEA 2 % and Weitzman-Silva Hutner Agar. Results showed, that three major groups could be differentiated, corresponding to Pseudallescheria, Petriella and S. prolificans. Among Petriella species only Pe. setifera is reasonably delimited. Pe. musispora was found to be synonymous with Pe. setifera. S. prolificans proved to be a homogenous species on the basis of ITS-sequences. Morphologically, Pseudallescheria and Petriella are distinguished by ostiolate vs non-ostiolate ascomata, a bipartition reflected also in ITS sequence data. We hypothesise a secondary loss of the ostiole of Pseudallescheria due to its ecological preferences. Infraspecific grouping within the highly variable species P. boydii is consistent for at least one clade in the ITS tree. The evolution of lineages with increased virulence within P. boydii is discussed.     

轮叶蒲桃叶绿体基因组特征及系统发育分析

轮叶蒲桃(Syzygium grijsii)系桃金娘科(Myrtaceae)蒲桃属(Syzygium)常绿灌木，其开发前景较好，但其叶绿体基因组特征及系统发育关系尚未有相关报道。为弥补轮叶蒲桃基因组学方面的空缺，该文对轮叶蒲桃的叶绿体基因组进行了系统的研究。运用Illumina高通量测序，并在GetOrganelle平台进行完整组装，同时利用组装好的数据分析轮叶蒲桃叶绿体基因组的结构特征和系统发育关系，其中包括轮叶蒲桃叶绿体基因组结构、功能及特征、密码子偏好性分析、叶绿体基因组的比较分析和系统发育的分析。结果表明：(1)轮叶蒲桃叶绿体基因组大小为158 591 bp,包含129个基因。其中，rRNA基因8个，tRNA基因37个，蛋白编码基因84个。分析检测到39个重复序列和84个SSR位点。(2)密码子偏好性分析发现轮叶蒲桃叶绿体基因组中末端存在对A/U的偏性，使用最多的是编码亮氨酸的密码子。(3)与近缘种比较，轮叶蒲桃的边界长度保守，边界处的基因种类与多个蒲桃属物种相似；轮叶蒲桃叶绿体基因组在LSC和SSC区变异度较大，有45处0.010i<0....     

Phylogeny, Biogeography, and Processes of Molecular Differentiation in Quercus Subgenus Quercus (Fagaceae)

Quercus is one of the most abundant and economically important genera of woody plants in the Northern Hemisphere. To infer phylogenetic relationships within Quercus subgenus Quercus, chloroplast DNA (cpDNA) restriction sites and nucleotide sequences of the internal transcribed spacers (ITS) and the 5.8S coding region of the nuclear ribosomal DNA repeat were obtained for 44 individuals, including 25 species, intraspecific samples, and three outgroups. Separate parsimony analyses of each data set showed that individual gene trees were congruent and often complementary in supporting clades that generally corresponded to previously recognized taxonomic groups. Only one instance of strongly supported gene tree incongruence was detected and this anomalous pattern was explained best by ancient introgression of cpDNA across sectional boundaries. Simultaneous parsimony analysis of the pruned data sets supported the recognition of the strictly Eurasian section Cerris and resolved a novel hypothesis for the major infrageneric groups (Cerris- (Lobatae- (Protobalanus + Quercus sensu stricto))). The biogeographic hypothesis that all major oak lineages evolved locally at middle latitudes within the general distribution of their fossil ancestors was fully supported. This set of relationships also suggested a New World origin for the widespread white oaks of the Northern Hemisphere (section Quercus s. s.). For both data sets, inter- and intraspecific sampling within section Protobalanus showed little correspondence to morphological species. Greater cladistic structure among the samples was obtained by cpDNA restriction sites and two well-delimited plastomes types comprising a total of 15 distinct haplotypes were resolved. Haplotypes of 2 of the peripheral species in this species complex occupy terminal portions of one of the plastome clades, suggesting a more recent origin relative to those of more widespread species. The phylogeography of the two divergent plastome types suggested a north–south pattern, consistent with a Late Tertiary disjunction in the ancestral distribution of section Protobalanus.     

Is 16S rDNA a Reliable Phylogenetic Marker to Characterize Relationships Below the Family Level in the Enterobacteriaceae?

The phylogenetic relationships of multiple enterobacterial species were reconstructed based on 16S rDNA gene sequences to evaluate the robustness of this housekeeping gene in the taxonomic placement of the enteric plant pathogens Erwinia, Brenneria, Pectobacterium, and Pantoea. Four data sets were compiled, two of which consisted of previously published data. The data sets were designed in order to evaluate how 16S rDNA gene phylogenies are affected by the use of different plant pathogen accessions and varying numbers of animal pathogen and outgroup sequences. DNA data matrices were analyzed using maximum likelihood (ML) algorithms, and character support was determined by ML bootstrap and Bayesian analyses. As additional animal pathogen sequences were added to the phylogenetic analyses, taxon placement changed. Further, the phylogenies varied in their placement of the plant pathogen species, and only the genus Pantoea was monophyletic in all four trees. Finally, bootstrap and Bayesian support values were low for most of the nodes, and all nonterminal branches collapsed in strict consensus trees. Inspection of 16S rDNA nucleotide alignments revealed several highly variable blocks punctuated by regions of conserved sequence. These data suggest that 16S rDNA, while effective for both species-level and family-level phylogenetic reconstruction, may underperform for genus-level phylogenetic analyses in the Enterobacteriaceae.     

Phylogeny of bumble bees in the New World subgenus Fervidobombus (Hymenoptera: Apidae): congruence of molecular and morphological data

We present new DNA sequence data (12S, 16S, and opsin gene fragments) and morphological characters of the male genitalia for a phylogenetic analysis of the bumble bee subgenus Fervidobombus. There is no significant incongruence between the three molecular data sets, and little incongruence between the DNA and morphology. Simultaneous analysis of all the data partitions resulted in a tree that was entirely congruent with the All-DNA tree. Optimization of the geographic locations of the taxa onto the tree topology using dispersal/vicariance analysis suggests a complex picture of spread and diversification of Fervidobombus from the Old World into the southern New World. There is a phylogenetic component to their spread into tropical rain forest, as the two primary rain forest species (Bombus transversalis and Bombus pullatus) comprise a monophyletic clade, along with a third species, Bombus atratus, which is widely distributed in South America, including lowland subtropical habitats.     

Molecular Systematics of Zopfiella and allied genera: evidence from multi-gene sequence analyses

This study aims to reveal the phylogenetic relationships of Zopfiella and allied genera in the Sordariales. Multiple gene sequences (partial 28 S rDNA, ITS/5.8 S rDNA and partial β-tubulin) were analysed using MP and Bayesian analyses. Analyses of different gene datasets were performed individually and then combined to infer phylogenies. Phylogenetic analyses show that currently recognised Zopfiella species are polyphyletic. Based on sequence analyses and morphology, it appears that Zopfiella should be restricted to species having ascospores with a septum in the dark cell. Our molecular analysis also shows that Zopfiella should be placed in Lasiosphaeriaceae rather than Chaetomiaceae. Cercophora and Podospora are also polyphyletic, which is in agreement with previous studies. Our analyses show that species possessing a Cladorrhinum anamorph are phylogenetically closely related. In addition, there are several strongly supported clades, characterised by species possessing divergent morphological characters. It is difficult to predict which characters are phylogenetically informative for delimiting these clades.     

Phylogeny of Salmonine Fishes Based on Growth Hormone Introns: Atlantic (Salmo) and Pacific (Oncorhynchus) Salmon Are Not Sister Taxa

Though salmonid fishes are a well-studied group, phylogenetic questions remain, especially with respect to genus-level relationships. These questions were addressed with duplicate growth hormone (GH) introns. Intron sequences from each duplicate gene yielded phylogenetic trees that were not significantly different from each other in topology. Statistical tests supported validity of the controversial monotypic genusParahucho,monophyly ofOncorhynchus,and inclusion ofAcantholingua ohridanawithinSalmo.Suprisingly, GH1 intron C (GH1C) did not support the widely accepted hypothesis thatOncorhynchus(Pacific salmon and trout) andSalmo(Atlantic salmon and trout) are sibling genera; GH2C was ambiguous at this node. Previously published data were also examined for support ofSalmoandOncorhynchusas sister taxa and only morphology showed significant support. If not sister taxa, the independent evolution of anadromy—the migration to sea and return to freshwater for spawning—is most parsimonious. While there was incongruence with and among published data sets, the GH1C intron phylogeny was the best hypothesis, based on currently available molecular data.     

山西陵川南方红豆杉自然保护区鹅耳枥植物群落谱系结构特征

分析植物群落谱系结构,可以探究乔木层、灌木层和草本层物种对环境变化的响应情况。以山西陵川南方红豆杉自然保护区鹅耳枥群落为研究对象,采用样方法,分别从不同径级和不同坡向对鹅耳枥群落净谱系亲缘关系指数(Net relatedness index,NRI)和净最近种间亲缘关系指数(Nearest taxon index,NTI)进行研究,探讨了鹅耳枥群落沿着径级梯度形成群落谱系结构特征,进而分析了鹅耳枥群落构建的历史进程。结果表明:(1)该保护区鹅耳枥群落乔木层(26种)、灌木层(32种)和草本层(39种)谱系结构树可分为5个类群、5个类群和4个类群;乔木层(86.67%的样地,下同)和灌木层(73.33%)物种群落谱系结构呈谱系发散格局(NRI0,NTI0),但草本层(86.67%)物种群落谱系结构呈谱系聚集格局(NRI0,NTI0)。(2)鹅耳枥群落乔木层中,DBH在Ⅰ级至Ⅱ级间,NRI指数随着DBH的增大而减小,NTI指数随着DBH的增大而增大;在Ⅱ级至Ⅴ级之间,随着植物DBH增大NRI指数和NTI指数值均呈下降趋势;而且在不同DBH水平上群落NRI和NTI指数均差异显著(P0.05),说明随着径级的增大,群落谱系结构由谱系聚集变为谱系发散。(3)灌木层物种谱系结构在阴坡和阳坡均呈聚集型,乔木层阴坡物种的谱系结构呈发散型(NRI0,NTI0),乔木层阳坡和草本层阴阳坡群落均无法判定群落谱系结构是聚集还是发散。     

Genetic diversity of Paramecium species on the basis of multiple loci analysis and ITS secondary structure models

Among ciliates, Paramecium has become a privileged model for the study of “species problem” particularly in the case of the “Paramecium aurelia complex” that has been intensely investigated. Despite extensive studies, the taxonomy of Paramecium is still challenging. The major problem is an uneven sampling of Paramecium with relatively few representatives of each species. To investigate species from the less discovered region (Pakistan), 10 isolates of Paramecium species including a standing-alone FT8 strain previously isolated by some of us were subjected to molecular characterization. Fragments of 18S recombinant DNA (rDNA), ITS1-5.8S-ITS2-5′LSU rDNA, cytochrome c oxidase subunit II, and hsp70 genes were used as molecular markers for phylogenetic analysis of particular isolates. The nucleotide sequences of polymerase chain reaction products of all markers were compared with the available sequences of relevant markers of other Paramecium species from GenBank. Phylogenetic trees based on all molecular markers showed that all the nine strains had a very close relationship with Paramecium primaurelia except for the FT8 strain. FT8 consistently showed its unique position in comparison to all other species in the phylogenetic trees. Available sequences of internal transcribed spacer 1 (ITS1) and ITS2 and some other ciliate sequences from GenBank were used for the construction of secondary models. Two highly conserved helices supported by compensatory base changes among all ciliates of ITS2 secondary structures were found similar to other eukaryotes. Therefore, the most conserved 120 to 180 base pairs regions were identified for their comparative studies. We found that out of the three helices in ITS1 structure, helix B was more conserved in Paramecium species. Despite various substitutions in the primary sequence, it was observed that secondary structures of ITS1 and ITS2 could be helpful in interpreting the phylogenetic relationships both at species as well as at generic level.     

Phylogeography and phylogeny of the epineritic cosmopolitan bonitos of the genus Sarda (Cuvier): inferred patterns of intra‐ and inter‐oceanic connectivity derived from nuclear and mitochondrial DNA data

Aim To reconstruct the phylogenetic relationships of the four species of the genus Sarda (Sarda sarda, Sarda orientalis, Sarda australis and Sarda chilensis) and their phylogeographic history in the context of historical and ecological biogeography. Also, to reconstruct within‐species phylogenetic relationships to test whether the North Atlantic and Mediterranean populations of Atlantic bonito (S. sarda) warrant subspecies status, and the validity of the allopatric northern and southern populations of eastern Pacific bonito (S. chiliensis), recognized as S. chiliensis lineolata and S. chiliensis chiliensis. Location Representative samples of all four Sarda species collected world‐wide were analysed. Methods Phylogenetic inference was carried out with neighbour‐joining, maximum parsimony and maximum likelihood, employing nucleotide sequences of the mitochondrial DNA (mtDNA) control region I (CR‐I) and of the single‐copy nuclear DNA (nDNA) Tmo‐4c4 gene. Analysis of molecular variance was used on the mtDNA data to estimate the extent of geographic population structuring. Results Gene trees derived from mtDNA and nDNA data yielded concordant phylogenies that support the monophyly of the genus Sarda. The following sibling pairs received strong statistical support: striped bonito (S. orientalis) with Australian bonito (S. australis), and Atlantic bonito (S. sarda) with eastern Pacific bonito (S. chiliensis). Furthermore, the origin of S. sarda mtDNA is paraphyletic with respect to S. chiliensis, and these results are indicative of introgression. The analysis of Tmo‐4c4 sequences corroborates the ancestral hybridization between these allopatric species. Comparisons of north‐west Atlantic and Mediterranean populations of S. sarda using mtDNA CR‐I data revealed substantial genetic differentiation. By contrast, no differences between the putative northern and southern allopatric subspecies of S. chiliensis were detected. Main conclusions The monophyly of the genus Sarda as indicated by morphology is corroborated using both molecular markers. However, molecular phylogenies depicted a paraphyletic relationship between S. sarda and S. chiliensis. This phylogeographical relationship is better explained by an ancestral introgression facilitated by trans‐Arctic contact during the Pleistocene. The pronounced genetic differentiation between S. sarda samples from the north‐west Atlantic and the Mediterranean is consistent with the differentiation of these two regions, but not with the amphi‐Atlantic speciation hypothesis. Finally, the S. chiliensis lineolata and S. chiliensis chiliensis subspecies status is not supported by the molecular data.     

Phylogenetic reconstruction using secondary structures of Internal Transcribed Spacer 2 (ITS2, rDNA): finding the molecular and morphological gap in Caribbean gorgonian corals

Background  

Most phylogenetic studies using current methods have focused on primary DNA sequence information. However, RNA secondary structures are particularly useful in systematics because they include characteristics, not found in the primary sequence, that give "morphological" information. Despite the number of recent molecular studies on octocorals, there is no consensus opinion about a region that carries enough phylogenetic resolution to solve intrageneric or close species relationships. Moreover, intrageneric morphological information by itself does not always produce accurate phylogenies; intra-species comparisons can reveal greater differences than intra-generic ones. The search for new phylogenetic approaches, such as by RNA secondary structure analysis, is therefore a priority in octocoral research.     

Phylogenetic and mixed Yule‐coalescent analyses reveal cryptic lineages within two South American marine snails of the genus Crepipatella (Gastropoda: Calyptraeidae)

The presence of sibling species within the marine gastropod genus Crepipatella has complicated the taxonomy of members of the group. Since the establishment of the genus, 15 species have been described, but recent studies have indicated that there are only five valid species, two of which inhabit the coasts of Chile, namely C. dilatata and C. fecunda. The two species are morphologically indistinguishable as adults, but can be differentiated on the basis of their encapsulated developmental stages. The primary aim of this study was to reconstruct phylogeny within the genus, and to establish species limits of C. dilatata and C. fecunda, using mitochondrial DNA data. To this end, we used maximum parsimony, maximum likelihood, and Bayesian inference to reconstruct phylogenies using 589 bp of the cytochrome oxidase I (COI) gene. The mtDNA phylogenies were then used as input in a general mixed Yule‐coalescent (GMYC) analysis to estimate species boundaries. In addition, quarter likelihood mapping was used to test a posteriori the confidence of inner branch patterns in the phylogenetic tree. Both DNA tree‐based and GMYC methods provide support for five isolated lineages within this species complex. Our data also suggest that Late Pleistocene and Holocene fragmentation and subsequent range expansion events may have shaped contemporary genetic patterns of Crepipatella in South America.     

A Test and Refinement of Folding Free Energy Nearest Neighbor Parameters for RNA Including N6-Methyladenosine

RNA folding free energy change parameters are widely used to predict RNA secondary structure and to design RNA sequences. These parameters include terms for the folding free energies of helices and loops. Although the full set of parameters has only been traditionally available for the four common bases and backbone, it is well known that covalent modifications of nucleotides are widespread in natural RNAs. Covalent modifications are also widely used in engineered sequences. We recently derived a full set of nearest neighbor terms for RNA that includes N⁶-methyladenosine (m⁶A). In this work, we test the model using 98 optical melting experiments, matching duplexes with or without N⁶-methylation of A. Most experiments place RRACH, the consensus site of N⁶-methylation, in a variety of contexts, including helices, bulge loops, internal loops, dangling ends, and terminal mismatches. For matched sets of experiments that include either A or m⁶A in the same context, we find that the parameters for m⁶A are as accurate as those for A. Across all experiments, the root mean squared deviation between estimated and experimental free energy changes is 0.67 kcal/mol. We used the new experimental data to refine the set of nearest neighbor parameter terms for m⁶A. These parameters enable prediction of RNA secondary structures including m⁶A, which can be used to model how N⁶-methylation of A affects RNA structure.