Parsimony Bootstrap Research Articles

Luteodorsum huanglongense (Gomphaceae, Gomphales), a New Genus and Species of Gomphoid Fungus from the Loess Plateau, Northwest China.

During an investigation of the macrofungal flora in the Huanglong Mountains of the Loess Plateau, northwest China, a unique gomphoid fungus was discovered and collected. After morphological identification and molecular phylogenetic analyses, a new genus named Luteodorsum and its type species, L. huanglongense, were proposed. Phylogenetic analyses were conducted using datasets of nuclear ribosomal DNA 28S large subunit (LSU), mitochondrial (mt) adenosine triphosphatase (ATPase) subunit 6 (atp6), and mt small-subunit rDNA (mtSSU). The results confirmed that L. huanglongense forms an independent clade within Gomphales, with full maximum likelihood bootstrap support (MLBS), maximum parsimony bootstrap support (MPBS), and Bayesian posterior probability (BPP). L. huanglongense is characterized by its sandy-brown, orange-brown, or coffee-brown color; clavate to infundibuliform shape; wrinkled and ridged hymenophore; ellipsoid to obovoid warted basidiospores; cylindrical to clavate flexuous pleurocystidia; and crystal basal mycelium. Overall, this study contributes to the growing body of knowledge on the diversity and evolution of Gomphales and provides valuable insights into the unique fungal flora found in the Huanglong Mountains.

Supplementary files

Fig. S1. Maximum Likelihood phylogram (log likelihood -7961.52) of our isolated Mortierellaceae species based on the concatenation of the rDNA-ITS and LSU region. Our isolates were grouped into five genera: the colour-indicated lineages representing the genera Podila, Entomortierella, the new genus Tyroliella, Mortierella and Linnemannia. Branch support values ≥ 70 (Bayesian Posterior Probabilities / Parsimony Bootstrap support) are shown above the respective branches. Sequences generated from typus are highlighted in red.<br />Table S1. Information on the Mortierellaceae strains used in this study including GenBank accession numbers, CBS numbers, JMRC numbers, IBF herbarium numbers and data concerning the isolation of the respective strain. ITS sequences with 100 % sequence identity were submitted to GenBank only for 2–3 representative strains for each species, respectively (100 % identitiy).

Supplementary files

Fig. S1. Multilocus phylogeny of Aspergillus series Nigri based on three loci (benA, CaM and RPB2) without species A. chiangmaiensis, A. pseudopiperis and A. pseudotubingensis. Best-scoring Maximum Likelihood (ML) tree inferred in the IQ-TREE is shown; ultrafast bootstrap support values (ML bs) are appended to nodes; only support values ≥95 % are shown; the ex-type strains are designated with a bold print; the information on geographic origin and isolation source is plotted on the tree (see the legend). <br />Fig. S2. Comparison of single-gene genealogies based on the benA, CaM and RPB2 loci and created by three different phylogenetic methods (only one isolate per unique multilocus haplotype is included in each phylogeny). Best-scoring single-locus maximum likelihood (ML) trees are shown; ML ultrafast bootstrap support values (ML bs), maximum parsimony bootstrap support values (MP bs) and Bayesian inference posterior probabilities (BI pp) are appended to nodes. Only support values ≥95 %, ≥70 % and ≥0.95, respectively, are shown. A dash indicates lower statistical support for a specific node, or the absence of a node in the phylogeny, while an asterisk indicates full support. The ex-type strains are designated with a bold print. Alignment characteristics, partitioning schemes and substitution models are listed in Supplementary Table S1.<br />Fig. S3. Best scoring maximum likelihood tree inferred in IQ-TREE based on ITS rDNA region sequences of series Nigri members (Table 1). It is apparent from the tree that a limited variability present in this locus can only differentiate the three main lineages, and more detailed differentiation is not possible. The ITS sequence of the A. vadensis ex-type was excluded from the analysis because it contains numerous errors and unresolved positions (accession number AY585549). Alignment characteristics, partitioning schemes and substitution models are listed in Supplementary Table S1.<br />Table S1. Characteristics of alignments, partition-merging results and best substitution model for each partition according to the Bayesian information criterion.<br />Table S2. Assignment of strains into populations for analysis in DELINEATE based on BPP v. 4.3.<br />Table S3. Aspergillus series Nigri genomes analyzed in this study and their basic characteristics.<br />Table S4. Distribution of 200 orthologous genes into ten separate STACEY analyses.<br />Table S5. List of unique multilocus haplotypes.<br />Table S6. Maximum sequence dissimilarity between isolates of the same Aspergillus species whose species limits have been delimited using methods based on a multispecies coalescent model; only species represented by isolates from at least three countries were included.

Isolation, biochemical characterization and phylogeny of a cellulose-degrading ruminal bacterium

Background: The isolation of cellulolytic bacteria, which hydrolyze cellulose to cellobiose and glucose, can provide useful information about rumen diversity. Objective: To identify and characterize a microorganism capable of hydrolyzing cellulose, isolated from a cow rumen. Methods: Anaerobic culture techniques were used for isolating cellulose-degrading rumen bacteria. Congo red staining was used to evaluate β-D-glucanase activity, and carbohydrate fermentation pattern was obtained with the kit API 50CHB/E. DNA extraction was performed and the 16S rDNA gene was amplified using 8F (5'-AGA GTT TGA TCC TGG CTC AG-3'), and 1492R (5' GGT TAC CTT GTT ACG ACT T 3') primers. The phylogenetic tree was reconstructed with the algorithm of maximum parsimony (bootstrap 5000), and 16S rDNA sequence was deposited in the NCBI database (accession number: KM094184). Results: The isolated bacterium showed cellulolytic activity detected with Congo red; besides, glycerol, ribose, xylose, sucrose, galactose and glucose were fermented by this bacterium. However, biochemical tests did not identify the bacteria because no match was found at database of API WEB Software. The phylogenetic inference indicated that this bacterium belongs to Shigella genus, with 98% maximal identity respect to the other taxonomic species. Conclusions: Phylogenetic analysis of 16S rRNA genes showed that the rumen isolated bacterium was a member of the genus Shigella, which, under mesophilic conditions, is an interesting candidate for obtaining oligosaccharides from lignocellulosic biomass.Keywords: cellulolytic, fermentation, monophyletic, rumen, Shigella. Resumen Antecedentes: El aislamiento de las bacterias celulolíticas, que hidrolizan la celulosa a celobiosa y glucosa, proporciona valiosa información sobre la diversidad del rumen,. Objetivo: Identificar y caracterizar un microorganismo capaz de hidrolizar celulosa, aislado de un rumen vacuno. Métodos: Se utilizaron técnicas de cultivo anaeróbico para aislar bacterias ruminales que degradan celulosa. La tinción con rojo Congo se usó para evaluar la actividad β-D-glucanasa y el patrón de fermentación de carbohidratos se obtuvo con el kit API 50CHB/E. Se realizó la extracción de DNA y se amplificó el gen de 16S rDNA utilizando los cebadores 8F (5'-AGA GTT TGA TCC TGG CTC AG-3'), y 1492R (5' GGT TAC CTT GTT ACG ACT T 3'). El árbol filogenético se reconstruyó con el algoritmo de máxima parsimonia (replicas 5000) y la secuencia 16S rDNA se depositó en la base de datos del NCBI (número de acceso: KM094184). Resultados: La bacteria aislada mostró actividad celulolítica detectada con la tinción de rojo Congo; además, esta bacteria fermenta glicerol, ribosa, xilosa, sacarosa, galactosa y glucosa. Sin embargo, las pruebas bioquímicas no permitieron identificar a la bacteria aislada, por no encontrar coincidencias en la base de datos del software API WEB. La inferencia filogenética indicó que esta bacteria pertenece al género Shigella, con 98% de identidad máxima respecto a las otras especies taxonómicas. Conclusiones: El análisis filogenético del gen 16S rRNA mostró que la bacteria aislada del rumen es un miembro del género Shigella que, en condiciones mesófilas, es un candidato interesante para obtener oligosacáridos a partir de biomasa lignocelulósica.Palabras clave: celulolítica, fermentación, monofilético, rumen, Shigella. ResumoAntecedentes: As bactérias celulolíticas hidrolizam a celulosa em celobiose e glicose, e o isolamento desses microrganismos fornece informações sobre a diversidade do rúmen. Objetivo: Identificar e caracterizar um microorganismo isolada do rúmen de uma vaca, com capacidade para hidrolisar a celulose. Métodos: Técnicas de cultura anaeróbica foram utilizadas para isolar bactérias ruminais que degradam a celulose. A atividade β-D-glucanase foi mostrada utilizando mancha de vermelho Congo, e o padrão de fermentação de carbohidratos foi obtida com o kit API 50CHB/E. A extracção foi realizada de DNA e amplificou-se os genes 16S rDNA utilizando os iniciadores 8F (AGA GTT TGA 5'-TCC TGG CTC AG-3'), e 1492R (5' CTT GGT TAC GTT ACG TCA T 3'). A árvore filogenética foi reconstruída com o algoritmo de máxima parcimônia (réplicas 5000). A sequência de rDNA 16S foi depositada no banco de dados do NCBI (número de acesso: KM094184). Resultados: O isolado mostrou uma atividade celulolítica com coloração vermelho Congo; además esta bactéria fermentação de glicerol, ribose, xilose, sacarose, galactose e glicose. No entanto, com as provas bioquímicas não se identificou a bactérias isolada, já que não se encontrou na base de dados do software API WEB. A inferência filogenética indicou que esta bactéria pertence ao género Shigella, com 98% de identidade de máximo respeito para outras espécies taxonômicas. Conclusão: A análise filogenética do gene 16S rRNA mostrou as bactérias isoladas do ambiente ruminal como um membro do género Shigella, que condições mesofilicas é um candidato atraente para obter oligossacarídeos da biomassa lignocelulósica.Palavras-chave: celulolítica, fermentação, monofilético, rúmen, Shigella.

MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation

BackgroundThe nonparametric bootstrap is widely used to measure the branch support of phylogenetic trees. However, bootstrapping is computationally expensive and remains a bottleneck in phylogenetic analyses. Recently, an ultrafast bootstrap approximation (UFBoot) approach was proposed for maximum likelihood analyses. However, such an approach is still missing for maximum parsimony.ResultsTo close this gap we present MPBoot, an adaptation and extension of UFBoot to compute branch supports under the maximum parsimony principle. MPBoot works for both uniform and non-uniform cost matrices. Our analyses on biological DNA and protein showed that under uniform cost matrices, MPBoot runs on average 4.7 (DNA) to 7 times (protein data) (range: 1.2–20.7) faster than the standard parsimony bootstrap implemented in PAUP*; but 1.6 (DNA) to 4.1 times (protein data) slower than the standard bootstrap with a fast search routine in TNT (fast-TNT). However, for non-uniform cost matrices MPBoot is 5 (DNA) to 13 times (protein data) (range:0.3–63.9) faster than fast-TNT. We note that MPBoot achieves better scores more frequently than PAUP* and fast-TNT. However, this effect is less pronounced if an intensive but slower search in TNT is invoked. Moreover, experiments on large-scale simulated data show that while both PAUP* and TNT bootstrap estimates are too conservative, MPBoot bootstrap estimates appear more unbiased.ConclusionsMPBoot provides an efficient alternative to the standard maximum parsimony bootstrap procedure. It shows favorable performance in terms of run time, the capability of finding a maximum parsimony tree, and high bootstrap accuracy on simulated as well as empirical data sets. MPBoot is easy-to-use, open-source and available at http://www.cibiv.at/software/mpboot.

The Utility of Single-Copy Nuclear Genes for Phylogenetic Resolution ofAcerandDipteronia(Acereae, Sapindaceae)

We sought to test the utility of two single-copy nuclear genes for resolving phylogenetic relationships within the woody plant tribe, Acereae (Sapindaceae). Acereae comprises Acer (125 spp.) and Dipteronia (2 spp.), two genera that possess schizocarpic fruits, which split into two winged mericarps. In Acer, the mericarps are elongated with a basally arranged locule and a dorsal or distal wing. In Dipteronia, the mericarp is obovate, and the locule is located centrally and surrounded by the wing. We analyzed 35 species of Acer representing 12 of 16 taxonomic sections plus Dipteronia sinensis to elucidate the phylogeny of Acereae using the single-copy nuclear genes AT103 and SQD1. Both genes exhibited limited variation in Acereae and, therefore, provided limited support for phylogenetic relationships. The phylogeny of concatenated AT103 and SQD1 showed Dipteronia sinensis within Acer with negligible support (0.14 posterior probability, < 50% maximum parsimony bootstrap, MP-BS), a position that is congruent with results from prior studies using chloroplast DNA and internal transcribed spacer (ITS). Based on our results and results from prior studies, we discuss implications for leaf and fruit evolution in Acereae.

Anastomosis Groups and Pathogenicity of Rhizoctonia solani and Binucleate Rhizoctonia from Potato in South Africa.

A survey of anastomosis groups (AG) of Rhizoctonia spp. associated with potato diseases was conducted in South Africa. In total, 112 Rhizoctonia solani and 19 binucleate Rhizoctonia (BNR) isolates were recovered from diseased potato plants, characterized for AG and pathogenicity. The AG identity of the isolates was confirmed using phylogenetic analysis of the internal transcribed spacer region of ribosomal DNA. R. solani isolates recovered belonged to AG 3-PT, AG 2-2IIIB, AG 4HG-I, AG 4HG-III, and AG 5, while BNR isolates belonged to AG A and AG R, with frequencies of 74, 6.1, 2.3, 2.3, 0.8, 12.2, and 2.3%, respectively. R. solani AG 3-PT was the most predominant AG and occurred in all the potato-growing regions sampled, whereas the other AG occurred in distinct locations. Different AG grouped into distinct clades, with high maximum parsimony and maximum-likelihood bootstrap support for both R. solani and BNR. An experiment under greenhouse conditions with representative isolates from different AG showed differences in aggressiveness between and within AG. Isolates of AG 2-2IIIB, AG 4HG-III, and AG R were the most aggressive in causing stem canker while AG 3-PT, AG 5, and AG R caused black scurf. This is the first comprehensive survey of R. solani and BNR on potato in South Africa using a molecular-based approach. This is the first report of R. solani AG 2-2IIIB and AG 4 HG-I causing stem and stolon canker and BNR AG A and AG R causing stem canker and black scurf on potato in South Africa.

Entorrhizomycota: A New Fungal Phylum Reveals New Perspectives on the Evolution of Fungi.

Entorrhiza is a small fungal genus comprising 14 species that all cause galls on roots of Cyperaceae and Juncaceae. Although this genus was established 130 years ago, crucial questions on the phylogenetic relationships and biology of this enigmatic taxon are still unanswered. In order to infer a robust hypothesis about the phylogenetic position of Entorrhiza and to evaluate evolutionary trends, multiple gene sequences and morphological characteristics of Entorrhiza were analyzed and compared with respective findings in Fungi. In our comprehensive five-gene analyses Entorrhiza appeared as a highly supported monophyletic lineage representing the sister group to the rest of the Dikarya, a phylogenetic placement that received but moderate maximum likelihood and maximum parsimony bootstrap support. An alternative maximum likelihood tree with the constraint that Entorrhiza forms a monophyletic group with Basidiomycota could not be rejected. According to the first phylogenetic hypothesis, the teliospore tetrads of Entorrhiza represent the prototype of the dikaryan meiosporangium. The alternative hypothesis is supported by similarities in septal pore structure, cell wall and spindle pole bodies. Based on the isolated phylogenetic position of Entorrhiza and its peculiar combination of features related to ultrastructure and reproduction mode, we propose a new phylum Entorrhizomycota, for the genus Entorrhiza, which represents an apparently widespread group of inconspicuous fungi.

Molecular phylogeny of the ‘Cape snow’ genus Syncarpha (Asteraceae: Gnaphalieae) reveals a need for generic re-delimitation

A phylogenetic hypothesis is presented for the charismatic but taxonomically poorly-known Cape daisy genus Syncarpha, based on near-complete ingroup sampling and good coverage of outgroup taxa. A combination of nuclear ribosomal and chloroplast spacer DNA sequence data gives a well-resolved phyogenetic hypothesis, the robustness of which is assessed via both parsimony bootstrap and Bayesian posterior probabilities based on the uncorrelated lognormal relaxed clock model. Syncarpha species fall into two well-supported and distantly-related clades that last shared a common ancestor in the mid-Miocene. The larger Syncarpha 1 grouping contains the type species and corresponds to African ‘Helipterum’; this clade is sister to Edmondia and belongs in a larger clade which also includes the Australian Gnaphalieae. The Syncarpha 2 clade contains the taxa associated with Syncarpha paniculata (formerly Helichrysum paniculatum) and is more closely related to Plecostachys and some species of Gnaphalium. Formal assessment of monophyly lays the groundwork for future revisionary taxonomic work.

Niche specificity of ammonia-oxidizing archaeal and bacterial communities in a freshwater wetland receiving municipal wastewater in Daqing, Northeast China.

Ecophysiological differences between ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) enable them to adapt to different niches in complex freshwater wetland ecosystems. The community characters of AOA and AOB in the different niches in a freshwater wetland receiving municipal wastewater, as well as the physicochemical parameters of sediment/soil samples, were investigated in this study. AOA community structures varied and separated from each other among four different niches. Wetland vegetation including aquatic macrophytes and terrestrial plants affected the AOA community composition but less for AOB, whereas sediment depths might contribute to the AOB community shift. The diversity of AOA communities was higher than that of AOB across all four niches. Archaeal and bacterial amoA genes (encoding for the alpha-subunit of ammonia monooxygenases) were most diverse in the dry-land niche, indicating O2 availability might favor ammonia oxidation. The majority of AOA amoA sequences belonged to the Soil/sediment Cluster B in the freshwater wetland ecosystems, while the dominant AOB amoA sequences were affiliated with Nitrosospira-like cluster. In the Nitrosospira-like cluster, AOB amoA gene sequences affiliated with the uncultured ammonia-oxidizing beta-proteobacteria constituted the largest portion (99%). Moreover, independent methods for phylogenetic tree analysis supported high parsimony bootstrap values. As a consequence, it is proposed that Nitrosospira-like amoA gene sequences recovered in this study represent a potentially novel cluster, grouping with the sequences from Gulf of Mexico deposited in the public databases.

Dubious resolution and support from published sparse supermatrices: The importance of thorough tree searches

We re-analyzed 10 sparse supermatrices wherein the original authors relied primarily or entirely upon maximum likelihood phylogenetic analyses implemented in RAxML and quantified branch support using the bootstrap. We compared the RAxML-based topologies and bootstrap values with both superficial- and relatively thorough-tree-search parsimony topologies and bootstrap values. We tested for clades that were resolved by RAxML but properly unsupported by checking if the SH-like aLRT equals zero and/or if the parsimony-optimized minimum branch length equals zero. Four of our conclusions are as follows. (1) Despite sampling nearly 50,000 characters, highly supported branches in a RAxML tree may be entirely unsupported because of missing data. (2) One should not rely entirely upon RAxML SH-like aLRT, RAxML bootstrap, or superficial parsimony bootstrap methods to rigorously quantify branch support for sparse supermatrices. (3) A fundamental factor that favors thorough parsimony analyses of sparse supermatrices is being able to distinguish between clades that are unequivocally supported by the data from those that are not; superficial likelihood analyses that quantify branch support using the bootstrap cannot be relied upon to always make this distinction. (4) The SH-like aLRT and parsimony-optimized-minimum-branch-length tests generally identify the same properly unsupported clades; the latter is a more severe test.

On the systematic position of some Asian enigmatic genera of Asclepiadoideae (Apocynaceae)

The phylogenetic structure of Asclepiadoideae (Apocynaceae) has been elucidated at the tribal and subtribal levels in the last two decades. However, to date, the systematic positions of seven Asian genera, Cosmostigma, Graphistemma, Holostemma, Pentasachme, Raphistemma, Seshagiria and Treutlera, have not been investigated. In this study, we examine the evolutionary relationships among these seven small enigmatic Asian genera and clarify their positions in Asclepiadoideae, using a combination of plastid sequences of rbcL, rps16, trnL and trnL- F regions. Cosmostigma and Treutlera are resolved as members of the non-Hoya clade of Marsdenieae with strong support (maximum parsimony bootstrap support value BSMP = 96, maximum likelihood bootstrap support value BSML = 98, Bayesian-inferred posterior probability PP = 1.0). Pentasachme is resolved as sister of Stapeliinae to Ceropegieae with moderate support (BSMP = 64, BSML = 66, PP = 0.94). Graphistemma, Holostemma, Raphistemma and Seshagiria are all nested in the Asclepiadeae-Cynanchinae clade (BSMP = 97, BSML = 100, PP = 1.0). The study confirms the generally accepted tribal and subtribal structure of the subfamily. One exception is Eustegia minuta, which is placed here as sister to all Asclepiadeae (BSMP = 58, BSML = 76, PP = 0.99) and not as sister to the Marsdenieae + Ceropegieae clade. The weak support and conflicting position indicate the need for a placement of Eustegia as an independent tribe. In Asclepiadeae, a sister group position of Cynanchinae to the Asclepiadinae + Tylophorinae clade is favoured (BSMP = 84, BSML = 88, PP = 1.0), whereas Schizostephanus is retrieved as unresolved. Oxystelma appears as an early-branching member of Asclepiadinae with weak support (BSMP = 52, BSML = 74, PP = 0.69). Calciphila and Solenostemma are also associated with Asclepiadinae with weak support (BSMP = 37, BSML = 45, PP = 0.79), but all alternative positions are essentially without support. The position of Indian Asclepiadoideae in the family phylogeny is discussed. (c) 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174, 601-619.

An artifact caused by undersampling optimal trees in supermatrix analyses of locally sampled characters

Empirical and simulated examples are used to demonstrate an artifact caused by undersampling optimal trees in data matrices that consist mostly or entirely of locally sampled (as opposed to globally, for most or all terminals) characters. The artifact is that unsupported clades consisting entirely of terminals scored for the same locally sampled partition may be resolved and assigned high resampling support—despite their being properly unsupported (i.e., not resolved in the strict consensus of all optimal trees). This artifact occurs despite application of random-addition sequences for stepwise terminal addition. The artifact is not necessarily obviated with thorough conventional branch swapping methods (even tree-bisection-reconnection) when just a single tree is held, as is sometimes implemented in parsimony bootstrap pseudoreplicates, and in every GARLI, PhyML, and RAxML pseudoreplicate and search for the most likely tree for the matrix as a whole. Hence GARLI, RAxML, and PhyML-based likelihood results require extra scrutiny, particularly when they provide high resolution and support for clades that are entirely unsupported by methods that perform more thorough searches, as in most parsimony analyses.

Isolation and characterization of bacteriophages infecting Xanthomonas arboricola pv. juglandis, the causal agent of walnut blight disease

Walnut orchards suffer from a blight caused by the bacteria Xanthomonas arboricola pv. juglandis. These bacteria can be infected by viral bacteriophages and this study was carried out to isolate and characterize bacteriophages from walnut orchards located throughout the South Island of New Zealand. Twenty six X. arboricola phages were isolated from three hundred and twenty six samples of plant material representing phyllosphere and rhizosphere ecosystems. The phage isolates were characterized by host-range, plaque and particle morphology, restriction digest and phylogenetic analysis and stability under various storage conditions. From capsid and tail dimensions the bacteriophages were considered to belong to the double-stranded DNA families Podoviridae and Siphoviridae. Of the twenty six bacteriophages, sixteen belonged to Podoviridae and were found both in the phyllosphere and rhizosphere. In contrast, Siphoviridae were present only in the rhizosphere isolates. Phage genome sizes ranged from 38.0 to 52.0 kb from a Hind III restriction digestion and had in common a 400 kb fragment that was identical at the DNA level. Despite the similar restriction patterns, maximum parsimony bootstrap analysis showed that the phage were members of different groups. Finally, we hypothesise that these phage might have use in a biocontrol strategy and therefore storage stability and efficacy was tested. Titres declined more than 50% over a 12-months storage period. Deep-freezing temperatures (-34°C) increased while chloroform decreased the stability.

Taxonomic recommendations for British birds: seventh report

Taxonomic recommendations for British birds: seventh report

Phylogenetic relationships among arecoid palms (Arecaceae: Arecoideae).

The Arecoideae is the largest and most diverse of the five subfamilies of palms (Arecaceae/Palmae), containing >50 % of the species in the family. Despite its importance, phylogenetic relationships among Arecoideae are poorly understood. Here the most densely sampled phylogenetic analysis of Arecoideae available to date is presented. The results are used to test the current classification of the subfamily and to identify priority areas for future research. DNA sequence data for the low-copy nuclear genes PRK and RPB2 were collected from 190 palm species, covering 103 (96 %) genera of Arecoideae. The data were analysed using the parsimony ratchet, maximum likelihood, and both likelihood and parsimony bootstrapping. Despite the recovery of paralogues and pseudogenes in a small number of taxa, PRK and RPB2 were both highly informative, producing well-resolved phylogenetic trees with many nodes well supported by bootstrap analyses. Simultaneous analyses of the combined data sets provided additional resolution and support. Two areas of incongruence between PRK and RPB2 were strongly supported by the bootstrap relating to the placement of tribes Chamaedoreeae, Iriarteeae and Reinhardtieae; the causes of this incongruence remain uncertain. The current classification within Arecoideae was strongly supported by the present data. Of the 14 tribes and 14 sub-tribes in the classification, only five sub-tribes from tribe Areceae (Basseliniinae, Linospadicinae, Oncospermatinae, Rhopalostylidinae and Verschaffeltiinae) failed to receive support. Three major higher level clades were strongly supported: (1) the RRC clade (Roystoneeae, Reinhardtieae and Cocoseae), (2) the POS clade (Podococceae, Oranieae and Sclerospermeae) and (3) the core arecoid clade (Areceae, Euterpeae, Geonomateae, Leopoldinieae, Manicarieae and Pelagodoxeae). However, new data sources are required to elucidate ambiguities that remain in phylogenetic relationships among and within the major groups of Arecoideae, as well as within the Areceae, the largest tribe in the palm family.

Non-monophyly and intricate morphological evolution within the avian family Cettiidae revealed by multilocus analysis of a taxonomically densely sampled dataset

BackgroundThe avian family Cettiidae, including the genera Cettia, Urosphena, Tesia, Abroscopus and Tickellia and Orthotomus cucullatus, has recently been proposed based on analysis of a small number of loci and species. The close relationship of most of these taxa was unexpected, and called for a comprehensive study based on multiple loci and dense taxon sampling. In the present study, we infer the relationships of all except one of the species in this family using one mitochondrial and three nuclear loci. We use traditional gene tree methods (Bayesian inference, maximum likelihood bootstrapping, parsimony bootstrapping), as well as a recently developed Bayesian species tree approach (*BEAST) that accounts for lineage sorting processes that might produce discordance between gene trees. We also analyse mitochondrial DNA for a larger sample, comprising multiple individuals and a large number of subspecies of polytypic species.ResultsThere are many topological incongruences among the single-locus trees, although none of these is strongly supported. The multi-locus tree inferred using concatenated sequences and the species tree agree well with each other, and are overall well resolved and well supported by the data. The main discrepancy between these trees concerns the most basal split. Both methods infer the genus Cettia to be highly non-monophyletic, as it is scattered across the entire family tree. Deep intraspecific divergences are revealed, and one or two species and one subspecies are inferred to be non-monophyletic (differences between methods).ConclusionsThe molecular phylogeny presented here is strongly inconsistent with the traditional, morphology-based classification. The remarkably high degree of non-monophyly in the genus Cettia is likely to be one of the most extraordinary examples of misconceived relationships in an avian genus. The phylogeny suggests instances of parallel evolution, as well as highly unequal rates of morphological divergence in different lineages. This complex morphological evolution apparently misled earlier taxonomists. These results underscore the well-known but still often neglected problem of basing classifications on overall morphological similarity. Based on the molecular data, a revised taxonomy is proposed. Although the traditional and species tree methods inferred much the same tree in the present study, the assumption by species tree methods that all species are monophyletic is a limitation in these methods, as some currently recognized species might have more complex histories.

Molecular phylogenetics of Ruscaceae sensu lato and related families (Asparagales) based on plastid and nuclear DNA sequences.

Previous phylogenetics studies of Asparagales, although extensive and generally well supported, have left several sets of taxa unclearly placed and have not addressed all relationships within certain clades thoroughly (some clades were relatively sparsely sampled). One of the most important of these is sampling within and placement of Nolinoideae (Ruscaceae s.l.) of Asparagaceae sensu Angiosperm Phylogeny Group (APG) III, which subfamily includes taxa previously referred to Convallariaceae, Dracaenaaceae, Eriospermaceae, Nolinaceae and Ruscaceae. A phylogenetic analysis of a combined data set for 126 taxa of Ruscaceae s.l. and related groups in Asparagales based on three nuclear and plastid DNA coding genes, 18S rDNA (1796 bp), rbcL (1338 bp) and matK (1668 bp), representing a total of approx. 4·8 kb is presented. Parsimony and Bayesian inference analyses were conducted to elucidate relationships of Ruscaceae s.l. and related groups, and parsimony bootstrap analysis was performed to assess support of clades. The combination of the three genes results in the most highly resolved and strongly supported topology yet obtained for Asparagales including Ruscaceae s.l. Asparagales relationships are nearly congruent with previous combined gene analyses, which were reflected in the APG III classification. Parsimony and Bayesian analyses yield identical relationships except for some slight variation among the core asparagoid families, which nevertheless form a strongly supported group in both types of analyses. In core asparagoids, five major clades are identified: (1) Alliaceae s.l. (sensu APG III, Amarylidaceae-Agapanthaceae-Alliaceae); (2) Asparagaceae-Laxmanniaceae-Ruscaceae s.l.; (3) Themidaceae; (4) Hyacinthaceae; (5) Anemarrhenaceae-Behniaceae-Herreriaceae-Agavaceae (clades 2-5 collectively Asparagaceae s.l. sensu APG III). The position of Aphyllanthes is labile, but it is sister to Themidaceae in the combined maximum-parsimony tree and sister to Anemarrhenaceae in the Bayesian analysis. The highly supported clade of Xanthorrhoeaceae s.l. (sensu APG III, including Asphodelaceae and Hemerocallidaceae) is sister to the core asparagoids. Ruscaceae s.l. are a well-supported group. Asparagaceae s.s. are sister to Ruscaceae s.l., even though the clade of the two families is weakly supported; Laxmanniaceae are strongly supported as sister to Ruscaceae s.l. and Asparagaceae. Ruscaceae s.l. include six principal clades that often reflect previously named groups: (1) tribe Polygonateae (excluding Disporopsis); (2) tribe Ophiopogoneae; (3) tribe Convallarieae (excluding Theropogon); (4) Ruscaceae s.s. + Dracaenaceae + Theropogon + Disporopsis + Comospermum; (5) Nolinaceae, (6) Eriospermum. The analyses here were largely conducted with new data collected for the same loci as in previous studies, but in this case from different species/DNA accessions and greater sampling in many cases than in previously published analyses; nonetheless, the results largely mirror those of previously conducted studies. This demonstrates the robustness of these results and answers questions often raised about reproducibility of DNA results, given the often sparse sampling of taxa in some studies, particularly the earliest ones. The results also provide a clear set of patterns on which to base a new classification of the subfamilies of Asparagaceae s.l., particularly Ruscaceae s.l. (= Nolinoideae of Asparagaceae s.l.), and examine other putatively important characters of Asparagales.

Phylogenetic analysis of Biomphalaria tenagophila (Orbigny, 1835) (Mollusca: Gastropoda)

Mitochondrial DNA of Biomphalaria tenagophila, a mollusc intermediate host of Schistosoma mansoni in Brazil, was sequenced and characterised. The genome size found for B. tenagophila was 13,722 bp and contained 13 messenger RNAs, 22 transfer RNAs (tRNA) and two ribosomal RNAs (rRNA). In addition to sequencing, the mitochondrial DNA (mtDNA) genome organization of B. tenagophila was analysed based on its content and localization of both coding and non-coding regions, regions of gene overlap and tRNA nucleotide sequences. Sequences of protein, rRNA 12S and rRNA 16S nucleotides as well as gene organization were compared between B. tenagophila and Biomphalaria glabrata, as the latter is the most important S. mansoni intermediate host in Brazil. Differences between such species were observed regarding rRNA composition. The complete sequence of the B. tenagophila mitochondrial genome was deposited in GenBank (accession EF433576). Furthermore, phylogenetic relationships were estimated among 28 mollusc species, which had their complete mitochondrial genome deposited in GenBank, using the neighbour-joining method, maximum parsimony and maximum likelihood bootstrap. B. tenagophila was positioned at a branch close to B. glabrata and Pulmonata molluscs, collectively comprising a paraphyletic group, contrary to Opistobranchia, which was positioned at a single branch and constituted a monophyletic group.

Identical Skin Toxins by Convergent Molecular Adaptation in Frogs

The Tree of Life is rife with adaptive convergences at all scales and biological levels of complexity. However, natural selection is not likely to result in the independent evolution of identical gene products. Here we report such a striking example of evolutionary convergence in the toxic skin secretions of two distantly related frog lineages. Caeruleins are important decapeptides in pharmacological and clinical research [1] and are commonly believed to represent a single evolutionary class of peptides [2-4]. Instead, our phylogenetic analyses combining transcriptome and genome data reveal that independently evolved precursor genes encode identical caeruleins in Xenopus and Litoria frogs. The former arose by duplication from the cholecystokinin (cck) gene, whereas the latter was derived from the gastrin gene. These hormone genes that are involved in many physiological processes diverged early in vertebrate evolution, after a segmental duplication during the Cambrian period. Besides implicating convergent mutations of the peptide-encoding sequence, recurrent caerulein origins entail parallel shifts of expression from the gut-brain axis to skin secretory glands. These results highlight extreme structural convergence in anciently diverged genes as an evolutionary mechanism through which recurrent adaptation is attained across large phylogenetic distances.