Journal articles: 'RaxML'

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Kozlov, Alexey M., Diego Darriba, Tomáš Flouri, Benoit Morel, and Alexandros Stamatakis. "RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference." Bioinformatics 35, no. 21 (May 9, 2019): 4453–55. http://dx.doi.org/10.1093/bioinformatics/btz305.

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Abstract Motivation Phylogenies are important for fundamental biological research, but also have numerous applications in biotechnology, agriculture and medicine. Finding the optimal tree under the popular maximum likelihood (ML) criterion is known to be NP-hard. Thus, highly optimized and scalable codes are needed to analyze constantly growing empirical datasets. Results We present RAxML-NG, a from-scratch re-implementation of the established greedy tree search algorithm of RAxML/ExaML. RAxML-NG offers improved accuracy, flexibility, speed, scalability, and usability compared with RAxML/ExaML. On taxon-rich datasets, RAxML-NG typically finds higher-scoring trees than IQTree, an increasingly popular recent tool for ML-based phylogenetic inference (although IQ-Tree shows better stability). Finally, RAxML-NG introduces several new features, such as the detection of terraces in tree space and the recently introduced transfer bootstrap support metric. Availability and implementation The code is available under GNU GPL at https://github.com/amkozlov/raxml-ng. RAxML-NG web service (maintained by Vital-IT) is available at https://raxml-ng.vital-it.ch/. Supplementary information Supplementary data are available at Bioinformatics online.

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Silvestro, Daniele, and Ingo Michalak. "raxmlGUI: a graphical front-end for RAxML." Organisms Diversity & Evolution 12, no. 4 (September 1, 2011): 335–37. http://dx.doi.org/10.1007/s13127-011-0056-0.

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Lutteropp, Sarah, Alexey M. Kozlov, and Alexandros Stamatakis. "A fast and memory-efficient implementation of the transfer bootstrap." Bioinformatics 36, no. 7 (November 22, 2019): 2280–81. http://dx.doi.org/10.1093/bioinformatics/btz874.

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Abstract Motivation Recently, Lemoine et al. suggested the transfer bootstrap expectation (TBE) branch support metric as an alternative to classical phylogenetic bootstrap support for taxon-rich datasets. However, the original TBE implementation in the booster tool is compute- and memory-intensive. Results We developed a fast and memory-efficient TBE implementation. We improve upon the original algorithm by Lemoine et al. via several algorithmic and technical optimizations. On empirical as well as on random tree sets with varying taxon counts, our implementation is up to 480 times faster than booster. Furthermore, it only requires memory that is linear in the number of taxa, which leads to 10× to 40× memory savings compared with booster. Availability and implementation Our implementation has been partially integrated into pll-modules and RAxML-NG and is available under the GNU Affero General Public License v3.0 at https://github.com/ddarriba/pll-modules and https://github.com/amkozlov/raxml-ng. The parallel version that also computes additional TBE-related statistics is available at: https://github.com/lutteropp/raxml-ng/tree/tbe. Supplementary information Supplementary data are available at Bioinformatics online.

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Stamatakis, A., A. J. Aberer, C. Goll, S. A. Smith, S. A. Berger, and F. Izquierdo-Carrasco. "RAxML-Light: a tool for computing terabyte phylogenies." Bioinformatics 28, no. 15 (May 24, 2012): 2064–66. http://dx.doi.org/10.1093/bioinformatics/bts309.

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Stamatakis, Alexandros, Paul Hoover, and Jacques Rougemont. "A Rapid Bootstrap Algorithm for the RAxML Web Servers." Systematic Biology 57, no. 5 (October 1, 2008): 758–71. http://dx.doi.org/10.1080/10635150802429642.

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Zhang, Qi-Lin, Run-Qiu Feng, Min Li, Zhong-Long Guo, Li-Jun Zhang, Fang-Zhen Luo, Ya Cao, and Ming-Long Yuan. "The Complete Mitogenome of Pyrrhocoris tibialis (Hemiptera: Pyrrhocoridae) and Phylogenetic Implications." Genes 10, no. 10 (October 18, 2019): 820. http://dx.doi.org/10.3390/genes10100820.

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We determined the complete mitogenome of Pyrrhocoris tibialis (Hemiptera: Heteroptera: Pyrrhocoridae) to better understand the diversity and phylogeny within Pentatomomorpha, which is the second largest infra-order of Heteroptera. Gene content, gene arrangement, nucleotide composition, codon usage, ribosomal RNA (rRNA) structures, and sequences of the mitochondrial transcription termination factor were well conserved in Pyrrhocoroidea. Different protein-coding genes have been subject to different evolutionary rates correlated with the G + C content. The size of control regions (CRs) was highly variable among mitogenomes of three sequenced Pyrrhocoroidea species, with the P. tibialis CR being the largest. All the transfer RNA genes found in Pyrrhocoroidea had the typical clover leaf secondary structure, except for trnS1 (AGN), which lacked the dihydrouridine arm and possessed an unusual anticodon stem (9 bp vs. the normal 5 bp). A total of three different phylogenetic relationships among the five super-families of Pentatomomorpha were obtained using three analytical methods (MrBayes and RAxML under site-homogeneous models and PhyloBayes under a site-heterogeneous CAT + GTR model) and two mitogenomic datasets (nucleotides and amino acids). The tree topology test using seven methods statistically supported a phylogeny of (Aradoidea + (Pentatomoidea + (Lygaeoidea + (Pyrrhocoroidea + Coreoidea)))) as the best topology, as recognized by both RAxML and MrBayes based on the two datasets.

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Liu, Kevin, C. Randal Linder, and Tandy Warnow. "RAxML and FastTree: Comparing Two Methods for Large-Scale Maximum Likelihood Phylogeny Estimation." PLoS ONE 6, no. 11 (November 21, 2011): e27731. http://dx.doi.org/10.1371/journal.pone.0027731.

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Stamatakis, A., F. Blagojevic, D. S. Nikolopoulos, and C. D. Antonopoulos. "Exploring New Search Algorithms and Hardware for Phylogenetics: RAxML Meets the IBM Cell." Journal of VLSI Signal Processing Systems for Signal, Image, and Video Technology 48, no. 3 (August 9, 2007): 271–86. http://dx.doi.org/10.1007/s11265-007-0067-4.

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FRISCH, ANDREAS, MARTIN GRUBE, HIROYUKI KASHIWADANI, and YOSHIHITO OHMURA. "Arthoniaceae with reddish, K+ purple ascomata in Japan." Phytotaxa 356, no. 1 (June 13, 2018): 19. http://dx.doi.org/10.11646/phytotaxa.356.1.2.

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Arthonia sanguinaria is described as new to science. The East Asian Arthonia lopingensis and the widely distributed Arthonia picea are reported as new to Japan from Honshu and the Ogasawara Islands, respectively. The phylogenetic position of A. picea, A. sanguinaria and Coniocarpon cinnabarinum from the Ogasawara Islands is shown by RAxML and Bayesian analysis of mtSSU, nLSU and RPB2 sequence data. Our results confirm the polyphyletic origin of quinoid pigments in Arthoniaceae. A key is presented to the Arthoniaceae with reddish ascomata in Japan.

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Molloy, Erin K., and Tandy Warnow. "TreeMerge: a new method for improving the scalability of species tree estimation methods." Bioinformatics 35, no. 14 (July 2019): i417—i426. http://dx.doi.org/10.1093/bioinformatics/btz344.

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Abstract Motivation At RECOMB-CG 2018, we presented NJMerge and showed that it could be used within a divide-and-conquer framework to scale computationally intensive methods for species tree estimation to larger datasets. However, NJMerge has two significant limitations: it can fail to return a tree and, when used within the proposed divide-and-conquer framework, has O(n5) running time for datasets with n species. Results Here we present a new method called ‘TreeMerge’ that improves on NJMerge in two ways: it is guaranteed to return a tree and it has dramatically faster running time within the same divide-and-conquer framework—only O(n2) time. We use a simulation study to evaluate TreeMerge in the context of multi-locus species tree estimation with two leading methods, ASTRAL-III and RAxML. We find that the divide-and-conquer framework using TreeMerge has a minor impact on species tree accuracy, dramatically reduces running time, and enables both ASTRAL-III and RAxML to complete on datasets (that they would otherwise fail on), when given 64 GB of memory and 48 h maximum running time. Thus, TreeMerge is a step toward a larger vision of enabling researchers with limited computational resources to perform large-scale species tree estimation, which we call Phylogenomics for All. Availability and implementation TreeMerge is publicly available on Github (http://github.com/ekmolloy/treemerge). Supplementary information Supplementary data are available at Bioinformatics online.

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KARUNARATHNA, ANURUDDHA, PAWEŁ DZIAŁAK, RUVISHIKA S. JAYAWARDENA, SAMANTHA CHANDRANATH KARUNARATHNA, CHANG-HSIN KUO, NAKARIN SUWANNARACH, SAOWALUCK TIBPROMMA, and SAISAMORN LUMYONG. "A novel addition to the Pezizellaceae (Rhytismatales, Ascomycota)." Phytotaxa 480, no. 3 (January 22, 2021): 251–61. http://dx.doi.org/10.11646/phytotaxa.480.3.4.

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In previous studies Apiculospora was introduced in Leotiomycetes genera incertae sedis. With our phylogenetic analyses based on large subunit rDNA (LSU) and internal transcribed spacer (ITS1, 5.8S, ITS2), we transfer Apiculospora to Pezizellaceae (Rhytismatales). We introduce Apiculospora penniseti from Pennisetum purpureum. Apiculospora penniseti differs from the closely related A. spartii by the presence of clear apiculi at both apices of the smooth-walled ascospores. Apiculospora penniseti is phylogenetically distinct from A. spartii with moderate support and high BYPP support (69 RAxML/0.97 BYPP). Herein, we discuss the taxonomy and phylogeny of A. penniseti.

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Stamatakis, Alexandros, Thomas Ludwig, and Harald Meier. "RAxML-II: a program for sequential, parallel and distributed inference of large phylogenetic trees." Concurrency and Computation: Practice and Experience 17, no. 14 (2005): 1705–23. http://dx.doi.org/10.1002/cpe.954.

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Stamatakis, A., T. Ludwig, and H. Meier. "RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees." Bioinformatics 21, no. 4 (December 17, 2004): 456–63. http://dx.doi.org/10.1093/bioinformatics/bti191.

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14

Stamatakis, Alexandros. "RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies." Bioinformatics 30, no. 9 (January 21, 2014): 1312–13. http://dx.doi.org/10.1093/bioinformatics/btu033.

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Kalaghatgi, Prabhav, Nico Pfeifer, and Thomas Lengauer. "Family-Joining: A Fast Distance-Based Method for Constructing Generally Labeled Trees." Molecular Biology and Evolution 33, no. 10 (July 19, 2016): 2720–34. http://dx.doi.org/10.1093/molbev/msw123.

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Abstract The widely used model for evolutionary relationships is a bifurcating tree with all taxa/observations placed at the leaves. This is not appropriate if the taxa have been densely sampled across evolutionary time and may be in a direct ancestral relationship, or if there is not enough information to fully resolve all the branching points in the evolutionary tree. In this article, we present a fast distance-based agglomeration method called family-joining (FJ) for constructing so-called generally labeled trees in which taxa may be placed at internal vertices and the tree may contain polytomies. FJ constructs such trees on the basis of pairwise distances and a distance threshold. We tested three methods for threshold selection, FJ-AIC, FJ-BIC, and FJ-CV, which minimize Akaike information criterion, Bayesian information criterion, and cross-validation error, respectively. When compared with related methods on simulated data, FJ-BIC was among the best at reconstructing the correct tree across a wide range of simulation scenarios. FJ-BIC was applied to HIV sequences sampled from individuals involved in a known transmission chain. The FJ-BIC tree was found to be compatible with almost all transmission events. On average, internal branches in the FJ-BIC tree have higher bootstrap support than branches in the leaf-labeled bifurcating tree constructed using RAxML. 36% and 25% of the internal branches in the FJ-BIC tree and RAxML tree, respectively, have bootstrap support greater than 70%. To the best of our knowledge the method presented here is the first attempt at modeling evolutionary relationships using generally labeled trees.

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Soop, K., B. Dima, J. A. Cooper, D. Park, and B. Oertel. "A phylogenetic approach to a global supraspecific taxonomy of Cortinarius (Agaricales) with an emphasis on the southern mycota." Persoonia - Molecular Phylogeny and Evolution of Fungi 42, no. 1 (July 19, 2019): 261–90. http://dx.doi.org/10.3767/persoonia.2019.42.10.

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A section-based taxonomy of Cortinarius, covering large parts of the temperate North and South Hemispheres, is presented. Thirty-seven previously described sections are reviewed, while another forty-two sections are proposed as new or as new combinations. Twenty additional clades are recovered but not formally described. Furthermore, six new or combined species names are introduced, and one species is neotypified. The structure is supported by morphological characters and molecular evidence, based on two (nrITS and nrLSU) and four (nrITS, nrLSU, rpb1 and rpb2) loci datasets and analysed by Maximum Likelihood methods (PhyML, RAxML). Altogether 789 Cortinarius samples were included in the study.

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DIMA, BÁLINT, and KARL SOOP. "The ‘xenosmatoid’ group of Cortinarius (Agaricales) in New Zealand." Phytotaxa 438, no. 4 (April 9, 2020): 223–36. http://dx.doi.org/10.11646/phytotaxa.438.4.1.

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Cortinarius section Xenosmatae, originally based on solely morphological characters, was subsequently shown to contain phylogenetically distantly related species. The type species C. xenosma is a singleton, and this study aims to revise the other members of the section using combined molecular (nrDNA ITS and LSU) and morphological data. Based on phylogenetic analyses using RAxML, PhyML and Bayesian Inference and additional morphological features one new species (C. paraxenosma) and one new section (sect. Olorinati) are proposed. Furthermore sect. Carbonelli is extended and emended to include two former members of sect. Xenosmatae. A key to the species in New Zealand with xenosmatoid morphology is provided.

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Stamatakis, Alexandros. "RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models." Bioinformatics 22, no. 21 (August 23, 2006): 2688–90. http://dx.doi.org/10.1093/bioinformatics/btl446.

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ERTZ, Damien, Neil SANDERSON, Brian J. COPPINS, Jon T. KLEPSLAND, and Andreas FRISCH. "Opegrapha multipuncta and Schismatomma quercicola (Arthoniomycetes) belong to the Lecanoromycetes." Lichenologist 51, no. 5 (September 2019): 395–405. http://dx.doi.org/10.1017/s002428291900029x.

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AbstractOpegrapha multipuncta and Schismatomma quercicola are two sterile European lichens reproducing only vegetatively by means of soredia. RAxML and Bayesian analyses of newly generated sequence data from the mitochondrial ribosomal RNA small subunit provide clear evidence that these two species do not belong to the Arthoniomycetes, but to the Lecanoromycetes. In our phylogenetic analyses, O. multipuncta is nested in the genus Porina (Porinaceae) as sister to P. austroatlantica, while S. quercicola is nested in the genus Schizotrema (Graphidaceae) as sister to S. zebrinum. The following new combinations are introduced: Porina multipuncta (Coppins & P. James) Ertz, Coppins & Frisch and Schizotrema quercicola (Coppins & P. James) Ertz, Frisch & Sanderson. Schizotrema quercicola represents the first record of the genus Schizotrema for Europe and the first sorediate member in this genus. The species is newly recorded from Norway. The lichenicolous habit of Arthonia invadens is confirmed.

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Dai, Dong-Qin, Nalin N. Wijayawardene, Li-Zhou Tang, Chao Liu, Li-Hong Han, Hong-Long Chu, Hai-Bo Wang, et al. "Rubroshiraia gen. nov., a second hypocrellin-producing genus in Shiraiaceae (Pleosporales)." MycoKeys 58 (August 28, 2019): 1–26. http://dx.doi.org/10.3897/mycokeys.58.36723.

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Shiraiaceae is an important family in Pleosporales (Dothideomycetes), which includes medical fungi and plant pathogens. Two hypocrellin-producing taxa, Shiraia bambusicola and a novel genus Rubroshiraiagen. nov., typified by Rubroshiraia bambusae are treated in this article. Maximum likelihood analysis, generated via RAxML (GTR+G model), using a combined SSU, LSU, TEF1 and RPB2 sequence dataset, shows that Rubroshiraia is close to Shiraia and belongs to the family Shiraiaceae. Descriptions, illustrations and a taxonomic key are provided for the genera in Shiraiaceae. Rubroshiraia morphologically differs from Shiraia in having small and dark ascostromata and filiform ascospores. Production of the ascostromatal metabolites, hypocrellin A and B, were examined by HPLC and spectrophotometer. The content of hypocrellin A and B of specimen HKAS 102255 (R. bambusae) is twice that produced by HKAS 102253 (S. bambusicola). To clarify the relationship between R. bambusae and Hypocrella bambusae, type material of the latter was examined and provided the illustration.

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Hermawan, Rudy, Mega Putri Amelya, and Za'Aziza Ridha Julia. "Trichaleurina javanica from West Java." Jurnal Mikologi Indonesia 4, no. 2 (December 4, 2020): 175. http://dx.doi.org/10.46638/jmi.v4i2.85.

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Trichaleurina is a fleshy mushroom with goblet-shaped within Pezizales. Many genera have a morphology similar to Trichaleurina, such as Bulgaria and Galiella. Some previous reports had been described fungi like Trichaleurina as Sarcosoma. Indonesia has been reported that has Trichaleurina specimen (the new name of Sarcosoma) by Boedijn. This research aimed to obtain, characterize, and determine the Trichaleurina around IPB University. Field exploration for fungal samples was used in the Landscape Arboretum of IPB University. Ascomata of Trichaleurina were collected, observed, and preserved using FAA. The specimen was deposited into Herbarium Bogoriense with collection code BO 24420. The molecular phylogenetic tree using RAxML was used to identify the species of the specimen. Morphological data were used to support the species name of the specimen. Specimen BO 24420 was identified as Tricahleurina javanica with 81% bootstrap value. Molecular identification was supported by the morphological data, such as the two oil globules and the size of mature ascospores.

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Park, Minhyuk, Paul Zaharias, and Tandy Warnow. "Disjoint Tree Mergers for Large-Scale Maximum Likelihood Tree Estimation." Algorithms 14, no. 5 (May 7, 2021): 148. http://dx.doi.org/10.3390/a14050148.

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The estimation of phylogenetic trees for individual genes or multi-locus datasets is a basic part of considerable biological research. In order to enable large trees to be computed, Disjoint Tree Mergers (DTMs) have been developed; these methods operate by dividing the input sequence dataset into disjoint sets, constructing trees on each subset, and then combining the subset trees (using auxiliary information) into a tree on the full dataset. DTMs have been used to advantage for multi-locus species tree estimation, enabling highly accurate species trees at reduced computational effort, compared to leading species tree estimation methods. Here, we evaluate the feasibility of using DTMs to improve the scalability of maximum likelihood (ML) gene tree estimation to large numbers of input sequences. Our study shows distinct differences between the three selected ML codes—RAxML-NG, IQ-TREE 2, and FastTree 2—and shows that good DTM pipeline design can provide advantages over these ML codes on large datasets.

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Stamatakis, Alexandros, and Michael Ott. "Efficient computation of the phylogenetic likelihood function on multi-gene alignments and multi-core architectures." Philosophical Transactions of the Royal Society B: Biological Sciences 363, no. 1512 (October 7, 2008): 3977–84. http://dx.doi.org/10.1098/rstb.2008.0163.

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The continuous accumulation of sequence data, for example, due to novel wet-laboratory techniques such as pyrosequencing, coupled with the increasing popularity of multi-gene phylogenies and emerging multi-core processor architectures that face problems of cache congestion, poses new challenges with respect to the efficient computation of the phylogenetic maximum-likelihood (ML) function. Here, we propose two approaches that can significantly speed up likelihood computations that typically represent over 95 per cent of the computational effort conducted by current ML or Bayesian inference programs. Initially, we present a method and an appropriate data structure to efficiently compute the likelihood score on ‘gappy’ multi-gene alignments. By ‘gappy’ we denote sampling-induced gaps owing to missing sequences in individual genes (partitions), i.e. not real alignment gaps. A first proof-of-concept implementation in RAxML indicates that this approach can accelerate inferences on large and gappy alignments by approximately one order of magnitude. Moreover, we present insights and initial performance results on multi-core architectures obtained during the transition from an OpenMP-based to a Pthreads-based fine-grained parallelization of the ML function.

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Lu, Jinming, Yuan Zhang, and Hongwei Chen. "Integrative taxonomy of the genus Pseudostegana (Diptera, Drosophilidae) from China, with descriptions of eleven new species." PeerJ 6 (September 5, 2018): e5160. http://dx.doi.org/10.7717/peerj.5160.

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The genus Pseudostegana (Okada, 1978) currently contains thirty-nine described species. A number of Pseudostegana were collected from the fieldwork in southwestern China from 2010 to 2017. Eleven new species were discovered and are described from southwestern China: Pseudostegana alpina Zhang & Chen, sp. nov.; Pseudostegana amnicola Zhang & Chen, sp. nov.; Pseudostegana amoena Zhang & Chen, sp. nov.; Pseudostegana mailangang Zhang & Chen, sp. nov.; Pseudostegana meiduo Zhang & Chen, sp. nov.; Pseudostegana meiji Zhang & Chen, sp. nov.; Pseudostegana mystica Zhang & Chen, sp. nov.; Pseudostegana stictiptrata Zhang & Chen, sp. nov.; Pseudostegana stigmatptera Zhang & Chen, sp. nov.; Pseudostegana ximalaya Zhang & Chen, sp. nov. and Pseudostegana zhuoma Zhang & Chen, sp. nov. A key to all Chinese Pseudostegana species based on morphological characters is provided. Two mitochondrial loci (COI and ND2) and one nuclear locus (28S rRNA) were sequenced for the Pseudostegana specimens, and Bayesian and RAxML concatenated analyses were run. Molecular species delimitation is performed using the distance-based automatic barcode gap discovery (ABGD) method. Molecular data support the morphological characteristics observed among these Chinese species and confirm the new species as being distinctly different.

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Wang, Jun, Xin-Yi Dai, Xiao-Dong Xu, Zi-Yi Zhang, Dan-Na Yu, Kenneth B. Storey, and Jia-Yong Zhang. "The complete mitochondrial genomes of five longicorn beetles (Coleoptera: Cerambycidae) and phylogenetic relationships within Cerambycidae." PeerJ 7 (September 5, 2019): e7633. http://dx.doi.org/10.7717/peerj.7633.

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Cerambycidae is one of the most diversified groups within Coleoptera and includes nearly 35,000 known species. The relationships at the subfamily level within Cerambycidae have not been convincingly demonstrated and the gene rearrangement of mitochondrial genomes in Cerambycidae remains unclear due to the low numbers of sequenced mitogenomes. In the present study, we determined five complete mitogenomes of Cerambycidae and investigated the phylogenetic relationship among the subfamilies of Cerambycidae based on mitogenomes. The mitogenomic arrangement of all five species was identical to the ancestral Cerambycidae type without gene rearrangement. Remarkably, however, two large intergenic spacers were detected in the mitogenome of Pterolophia sp. ZJY-2019. The origins of these intergenic spacers could be explained by the slipped-strand mispairing and duplication/random loss models. A conserved motif was found between trnS2 and nad1 gene, which was proposed to be a binding site of a transcription termination peptide. Also, tandem repeat units were identified in the A + T-rich region of all five mitogenomes. The monophyly of Lamiinae and Prioninae was strongly supported by both MrBayes and RAxML analyses based on nucleotide datasets, whereas the Cerambycinae and Lepturinae were recovered as non-monophyletic.

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Zhang, Yuanmeng Miles, Julia Stigenberg, Jacqueline Hope Meyer, and Barbara Jo-Anne Sharanowski. "Multilocus phylogeny of the parasitic wasps in the tribe Euphorini (Hymenoptera: Braconidae) with revised generic classifications." PeerJ 6 (May 21, 2018): e4783. http://dx.doi.org/10.7717/peerj.4783.

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BackgroundParasitic wasps in the family Braconidae are important regulators of insect pests, particularly in forest and agroecosystems. Within Braconidae, wasps in the tribe Euphorini (Euphorinae) attack economically damaging plant bugs (Miridae) that are major pests of field and vegetable crops. However, the evolutionary relationships of this tribe have been historically problematic. Most generic concepts have been based on ambiguous morphological characters which often leads to misidentification, complicating their use in biological control.MethodsUsing a combination of three genes (COI,28S, andCAD) and 80 taxa collected worldwide, we conducted Bayesian inference using MrBayes, and maximum likelihood analyses using RAxML and IQ-Tree on individual gene trees as well as the concatenated dataset.ResultsThe monophyly of the tribe Euphorini and the two generaPeristenusandLeiophronwere confirmed using maximum likelihood and Bayesian inference. The subgeneric classifications ofLeiophron sensu latowere not supported, and the monotypic genusMamawas also not supported.DiscussionEuphoriella,Euphoriana,Euphorus, andMamasyn. n,have been synonymized underLeiophron. Mama mariaesyn. nwas placed as a junior synonym ofLeiophron reclinator. The generic concepts ofPeristenusandLeiophronwere refined to reflect the updated phylogeny. Further we discuss the need for revising Euphorini given the number of undescribed species within the tribe.

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HARRISON, SOPHIE E., MICHAEL G. RIX, MARK S. HARVEY, and ANDREW D. AUSTIN. "Systematics of the Australian spiny trapdoor spiders of the genus Blakistonia Hogg (Araneae: Idiopidae)." Zootaxa 4518, no. 1 (November 12, 2018): 1. http://dx.doi.org/10.11646/zootaxa.4518.1.1.

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A combined molecular and morphological approach was used to revise the Australian spiny trapdoor spiders of the genus Blakistonia Hogg. Where possible, our molecular approach used sequence data from the COI barcoding gene, which were analysed using Bayesian, RAxML and neighbour-joining approaches. These molecular data were combined with morphology to describe and diagnose the genus, to redescribe the type (and only previously valid) species, B. aurea Hogg, 1902, and to diagnose, describe and map 19 new species: B. bassi sp. n., B. bella sp. n., B. birksi sp. n., B. carnarvon sp. n., B. emmottiorum sp. n., B. gemmelli sp. n., B. hortoni sp. n., B. mainae sp. n., B. maryae sp. n., B. newtoni sp. n., B. nullarborensis sp. n., B. olea sp. n., B. parva sp. n., B. pidax sp. n., B. plata sp. n., B. raveni sp. n., B. tariae sp. n., B. tunstilli sp. n., and B. wingellina sp. n. The genus Blakistonia is found to be distributed throughout the Australian arid and semi-arid zones, from the Wheatbelt region of Western Australia to central Queensland and western Victoria.

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Cabra-García, Jimmy, and Gustavo Hormiga. "Exploring the impact of morphology, multiple sequence alignment and choice of optimality criteria in phylogenetic inference: a case study with the Neotropical orb-weaving spider genus Wagneriana (Araneae: Araneidae)." Zoological Journal of the Linnean Society 188, no. 4 (November 30, 2019): 976–1151. http://dx.doi.org/10.1093/zoolinnean/zlz088.

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Abstract We present a total evidence phylogenetic analysis of the Neotropical orb-weaving spider genus Wagneriana and discuss the phylogenetic impacts of methodological choices. We analysed 167 phenotypic characters and nine loci scored for 115 Wagneriana and outgroups, including 46 newly sequenced species. We compared total evidence analyses and molecular-only analyses to evaluate the impact of phenotypic evidence, and we performed analyses using the programs POY, TNT, RAxML, GARLI, IQ-TREE and MrBayes to evaluate the effects of multiple sequence alignment and optimality criteria. In all analyses, Wagneriana carimagua and Wagneriana uropygialis were nested in the genera Parawixia and Alpaida, respectively, and the remaining species of Wagneriana fell into three main clades, none of which formed a pair of sister taxa. However, sister-group relationships among the main clades and their internal relationships were strongly influenced by methodological choices. Alignment methods had comparable topological effects to those of optimality criteria in terms of ‘subtree pruning and regrafting’ moves. The inclusion of phenotypic evidence, 2.80–3.05% of the total evidence matrices, increased support irrespective of the optimality criterion used. The monophyly of some groups was recovered only after the addition of morphological characters. A new araneid genus, Popperaneus gen. nov., is erected, and Paraverrucosa is resurrected. Four new synonymies and seven new combinations are proposed.

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GRAY, DAVID A., DAVID B. WEISSMAN, JEFFREY A. COLE, and EMILY MORIARTY LEMMON. "Multilocus phylogeny of Gryllus field crickets (Orthoptera: Gryllidae: Gryllinae) utilizing anchored hybrid enrichment." Zootaxa 4750, no. 3 (March 12, 2020): 328–48. http://dx.doi.org/10.11646/zootaxa.4750.3.2.

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We present the first comprehensive molecular phylogeny of Gryllus field cricket species found in the United States and Canada, select additional named Gryllus species found in Mexico and the Bahamas, plus the European field cricket G. campestris Linnaeus and the Afro-Eurasian cricket G. bimaculatus De Geer. Acheta, Teleogryllus, and Nigrogryllus were used as outgroups. Anchored hybrid enrichment was used to generate 492,531 base pairs of DNA sequence from 563 loci. RAxML analysis of concatenated sequence data and Astral analysis of gene trees gave broadly congruent results, especially for older branches and overall tree structure. The North American Gryllus are monophyletic with respect to the two Old World taxa; certain sub-groups show rapid recent divergence. This is the first Anchored Hybrid Enrichment study of an insect group done for closely related species within a single genus, and the results illustrate the challenges of reconstructing the evolutionary history of young rapidly diverged taxa when both incomplete lineage sorting and probable hybridization are at play. Because Gryllus field crickets have been used extensively as a model system in evolutionary ecology, behavior, neuro-physiology, speciation, and life-history and life-cycle evolution, these results will help inform, interpret, and guide future research in these areas.

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Deng, Xi-Ling, Adrien Favre, Emily Moriarty Lemmon, Alan R. Lemmon, and Steffen U. Pauls. "Gene Flow and Diversification in Himalopsyche martynovi Species Complex (Trichoptera: Rhyacophilidae) in the Hengduan Mountains." Biology 10, no. 8 (August 23, 2021): 816. http://dx.doi.org/10.3390/biology10080816.

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The Hengduan Mountains are one of the most species-rich mountainous areas in the world. The origin and evolution of such a remarkable biodiversity are likely to be associated with geological or climatic dynamics, as well as taxon-specific biotic processes (e.g., hybridization, polyploidization, etc.). Here, we investigate the mechanisms fostering the diversification of the endemic Himalopsyche martynovi complex, a poorly known group of aquatic insects. We used multiple allelic datasets generated from 691 AHE loci to reconstruct species and RaxML phylogenetic trees. We selected the most reliable phylogenetic tree to perform network and gene flow analyses. The phylogenetic reconstructions and network analysis identified three clades, including H. epikur, H. martynovi sensu stricto and H. cf. martynovi. Himalopsyche martynovi sensu stricto and H. cf. martynovi present an intermediate morphology between H. epikur and H. viteceki, the closest known relative to the H. martynovi-complex. The gene flow analysis revealed extensive gene flow among these lineages. Our results suggest that H. viteceki and H. epikur are likely to have contributed to the evolution of H. martynovi sensu stricto and H. cf. martynovi via gene flow, and thus, our study provides insights in the diversification process of a lesser-known ecological group, and hints at the potential role of gene flow in the emergence of biological novelty in the Hengduan Mountains.

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Pershing, Nicole L., Aurelie Kapusta, Shannon Nielsen, Hillary Crandall, Kent Korgenski, Carrie L. Byington, Krow Ampofo, and Anne Blascke. "43. The Capsule and Beyond: Genetic Determinants of Pediatric streptococcus Pneumoniae empyema." Open Forum Infectious Diseases 7, Supplement_1 (October 1, 2020): S23. http://dx.doi.org/10.1093/ofid/ofaa417.042.

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Abstract Background Streptococcus pneumoniae is the most common cause of pneumonia in children, including empyema, a severe complication with increasing incidence in the post-pneumococcal vaccine era. Only a subset of > 90 serotypes cause empyema. Virulence determinants of empyema remain largely unknown. Methods We performed Illumina sequencing of invasive Pneumococcal isolates from pediatric patients at Primary Children’s Hospital (Salt Lake City, UT) isolated between 1996–2018, de novo genome assembly (SPADES), annotation (PROKKA), serotyping (Quelling and SeroBA), and pan-genome assembly (ROARY). SCOARY and pyseer were used for microbial GWAS. Maximum likelihood phylogeny was calculated using RAxML/Gubbins. Results 366 pneumococcal isolates were analyzed from 39 serotypes and multiple phenotypes including pneumonia (n=76), empyema (n=63), CNS infection (n=54), and isolated bacteremia (n=79). Serotypes and empyema phenotype clustered roughly by phylogeny. Most analyzed empyema isolates after 2010 were serotype 3 (19/25); prior to PCV-13 introduction serotypes 1 (8/38), 7F (7/38), and 19A (11/38) were more highly represented. Genes implicated in capsule synthesis, transposases, and metabolism were statistically correlated with the empyema phenotype. Conclusion Specific capsular or metabolic genes may confer optimal fitness for pleural disease. Further characterization of these genetic associations is needed and will inform future treatment and prevention. Disclosures Carrie L. Byington, MD, BioFire (Other Financial or Material Support, Royalties for Intellectual Property)IDbyDNA (Advisor or Review Panel member) Krow Ampofo, MBChB, Merck (Grant/Research Support)

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Arteaga-Figueroa, Luis A., Valentina Sánchez-Bermúdez, and Nicolás D. Franco-Sierra. "Revisiting the phylogeny of phylum Ctenophora: a molecular perspective." F1000Research 5 (August 21, 2017): 2881. http://dx.doi.org/10.12688/f1000research.10426.2.

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The phylogenetic relationships of deep metazoans, specifically in the phylum Ctenophora (inside and outside the phylum), are not totally understood. Several loci (protein coding and ribosomal RNA) from organisms belonging to this phylum are currently available on public databases (e.g. GenBank). Previous studies take into account the ribosomal data and the protein data separately. In this study, we perform a meta-analysis of previously published data together. The published data of this phylum have been used in previous phylogenetic analyses inside the phylum and consist in nuclear ribosomal data, such as 18S, 5.8S, ITS1, ITS2, and protein-coding markers such as NFP (non-fluorescent protein). Previous studies concentrate their efforts toward the analyses of ribosomal data or the protein-coding marker separately. Now we take into account these markers together for an upgrade of the phylogenetic analysis of this phylum. We also test several markers such as 28S, IPNS, Tyrosine aminotransferase and HLH domaincontaining protein for the improvement of the study. This markers were analyzed by Bayesian Inference (MrBayes) and Maximum Likelihood (Garli and RAxML), individually and concatenated, showing improvement in the orders placement and presenting new interesting relationship between the paraphyletic order Cydippida and the other ctenophores. These analyses also include sequences from undescribed species that have been reported in GenBank which improved the alignment matrices and support values of some nodes. Adding the undescribed species suggests interesting and well supported clades, the posterior identification of this species would led to an improvement on the ctenophore’s taxonomy.

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Ott, Michael, Jaroslaw Zola, Srinivas Aluru, Andrew D. Johnson, Daniel Janies, and Alexandros Stamatakis. "Large-Scale Phylogenetic Analysis on Current HPC Architectures." Scientific Programming 16, no. 2-3 (2008): 255–70. http://dx.doi.org/10.1155/2008/395908.

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Phylogenetic inference is considered a grand challenge in Bioinformatics due to its immense computational requirements. The increasing popularity and availability of large multi-gene alignments as well as comprehensive datasets of single nucleotide polymorphisms (SNPs) in current biological studies, coupled with rapid accumulation of sequence data in general, pose new challenges for high performance computing. By example of RAxML, which is currently among the fastest and most accurate programs for phylogenetic inference under the Maximum Likelihood (ML) criterion, we demonstrate how the phylogenetic ML function can be efficiently scaled to current supercomputer architectures like the IBM BlueGene/L (BG/L) and SGI Altix. This is achieved by simultaneous exploitation of coarse- and fine-grained parallelism which is inherent to every ML-based biological analysis. Performance is assessed using datasets consisting of 270 sequences and 566,470 base pairs (haplotype map dataset), and 2,182 sequences and 51,089 base pairs, respectively. To the best of our knowledge, these are the largest datasets analyzed under ML to date. Experimental results indicate that the fine-grained parallelization scales well up to 1,024 processors. Moreover, a larger number of processors can be efficiently exploited by a combination of coarse- and fine-grained parallelism. We also demonstrate that our parallelization scales equally well on an AMD Opteron cluster with a less favorable network latency to processor speed ratio. Finally, we underline the practical relevance of our approach by including a biological discussion of the results from the haplotype map dataset analysis, which revealed novel biological insights via phylogenetic inference.

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Murillo-Ramos, Leidys, Gunnar Brehm, Pasi Sihvonen, Axel Hausmann, Sille Holm, Hamid Reza Ghanavi, Erki Õunap, et al. "A comprehensive molecular phylogeny of Geometridae (Lepidoptera) with a focus on enigmatic small subfamilies." PeerJ 7 (August 27, 2019): e7386. http://dx.doi.org/10.7717/peerj.7386.

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Our study aims to investigate the relationships of the major lineages within the moth family Geometridae, with a focus on the poorly studied Oenochrominae-Desmobathrinae complex, and to translate some of the results into a coherent subfamilial and tribal level classification for the family. We analyzed a molecular dataset of 1,206 Geometroidea terminal taxa from all biogeographical regions comprising up to 11 molecular markers that includes one mitochondrial (COI) and 10 protein-coding nuclear gene regions (wingless, ArgK, MDH, RpS5, GAPDH, IDH, Ca-ATPase, Nex9, EF-1alpha, CAD). The molecular data set was analyzed using maximum likelihood as implemented in IQ-TREE and RAxML. We found high support for the subfamilies Larentiinae, Geometrinae and Ennominae in their traditional scopes. Sterrhinae becomes monophyletic only if Ergavia Walker, Ametris Hübner and Macrotes Westwood, which are currently placed in Oenochrominae, are formally transferred to Sterrhinae. Desmobathrinae and Oenochrominae are found to be polyphyletic. The concepts of Oenochrominae and Desmobathrinae required major revision and, after appropriate rearrangements, these groups also form monophyletic subfamily-level entities. Oenochrominae s.str. as originally conceived by Guenée is phylogenetically distant from Epidesmia and its close relatives. The latter is hereby described as the subfamily Epidesmiinae Murillo-Ramos, Sihvonen & Brehm, subfam. nov. Epidesmiinae are a lineage of “slender-bodied Oenochrominae” that include the genera Ecphyas Turner, Systatica Turner, Adeixis Warren, Dichromodes Guenée, Phrixocomes Turner, Abraxaphantes Warren, Epidesmia Duncan & Westwood and Phrataria Walker. Archiearinae are monophyletic when Dirce and Acalyphes are formally transferred to Ennominae. We also found that many tribes were para- or polyphyletic and therefore propose tens of taxonomic changes at the tribe and subfamily levels. Archaeobalbini stat. rev. Viidalepp (Geometrinae) is raised from synonymy with Pseudoterpnini Warren to tribal rank. Chlorodontoperini Murillo-Ramos, Sihvonen & Brehm, trib. nov. and Drepanogynini Murillo-Ramos, Sihvonen & Brehm, trib. nov. are described as new tribes in Geometrinae and Ennominae, respectively.

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GERASIMOVA, Julia V., Aleksandr K. EZHKIN, and Andreas BECK. "Four new species of Bacidia s.s. (Ramalinaceae, Lecanorales) in the Russian Far East." Lichenologist 50, no. 6 (November 2018): 603–25. http://dx.doi.org/10.1017/s0024282918000397.

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AbstractThe molecular phylogeny of Bacidia s.s. in the Russian Far East was investigated using 62 nucleotide sequences from the ITS nrDNA region, 22 of which were newly obtained. Phylogenetic reconstructions employed Bayesian inference and maximum likelihood searches using MrBayes and RAxML. In addition, ITS2 secondary structures added further support using Compensatory Base Changes. As a result of morphological and phylogenetic studies, four new species of Bacidia are described. Bacidia areolata sp. nov. belongs to the suffusa group. It was collected once in Khabarovskiy Krai, the Russian Far East, on the bark of Acer tegmentosum and is closely related to B. suffusa but differs in having a smooth, cracked to areolate thallus and shorter spores. Bacidia elongata sp. nov. is a member of the fraxinea group and is similar to B. fraxinea but differs in having a wide zone of cells with enlarged lumina along the edge of the exciple. In fact, this zone of enlarged cells, in combination with its overall habit, places it morphologically close to B. suffusa, B. millegrana and B. campalea. Bacidia kurilensis sp. nov. is a basal member of the laurocerasi group and closely related to B. biatorina, B. heterochroa, B. laurocerasi and B. salazarensis. However, the combination of a granular thallus, large black apothecia and a green hue in the upper part of the exciple edge as well as in the epihymenium sets it apart from the species mentioned above. Bacidia sachalinensis sp. nov. resolves as a strongly supported member of the polychroa group and is known from a single locality in Sakhalin, the Russian Far East. Its thallus structure and apothecium colour are variable, which is typical for the polychroa group, but it differs from B. polychroa by having shorter spores with fewer septa and a mainly smooth to areolate thallus.

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Lees, John A., Michelle Kendall, Julian Parkhill, Caroline Colijn, Stephen D. Bentley, and Simon R. Harris. "Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study." Wellcome Open Research 3 (May 29, 2018): 33. http://dx.doi.org/10.12688/wellcomeopenres.14265.2.

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Background: Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods: We simulated data from a defined 'true tree' using a realistic evolutionary model. We built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions. We also used real data from Streptococcus pneumoniae alignments to compare individual core gene trees to a core genome tree. Results: We found that, as expected, maximum likelihood trees from good quality alignments were the most accurate, but also the most computationally intensive. Using less accurate phylogenetic reconstruction methods, we were able to obtain results of comparable accuracy; we found that approximate results can rapidly be obtained using genetic distance based methods. In real data we found that highly conserved core genes, such as those involved in translation, gave an inaccurate tree topology, whereas genes involved in recombination events gave inaccurate branch lengths. We also show a tree-of-trees, relating the results of different phylogenetic reconstructions to each other. Conclusions: We recommend three approaches, depending on requirements for accuracy and computational time. For the most accurate tree, use of either RAxML or IQ-TREE with an alignment of variable sites produced by mapping to a reference genome is best. Quicker approaches that do not perform full maximum likelihood optimisation may be useful for many analyses requiring a phylogeny, as generating a high quality input alignment is likely to be the major limiting factor of accurate tree topology. We have publicly released our simulated data and code to enable further comparisons.

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Vernygora, Oksana V., Tiago R. Simões, and Erin O. Campbell. "Evaluating the Performance of Probabilistic Algorithms for Phylogenetic Analysis of Big Morphological Datasets: A Simulation Study." Systematic Biology 69, no. 6 (March 19, 2020): 1088–105. http://dx.doi.org/10.1093/sysbio/syaa020.

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Abstract Reconstructing the tree of life is an essential task in evolutionary biology. It demands accurate phylogenetic inference for both extant and extinct organisms, the latter being almost entirely dependent on morphological data. While parsimony methods have traditionally dominated the field of morphological phylogenetics, a rapidly growing number of studies are now employing probabilistic methods (maximum likelihood and Bayesian inference). The present-day toolkit of probabilistic methods offers varied software with distinct algorithms and assumptions for reaching global optimality. However, benchmark performance assessments of different software packages for the analyses of morphological data, particularly in the era of big data, are still lacking. Here, we test the performance of four major probabilistic software under variable taxonomic sampling and missing data conditions: the Bayesian inference-based programs MrBayes and RevBayes, and the maximum likelihood-based IQ-TREE and RAxML. We evaluated software performance by calculating the distance between inferred and true trees using a variety of metrics, including Robinson-Foulds (RF), Matching Splits (MS), and Kuhner-Felsenstein (KF) distances. Our results show that increased taxonomic sampling improves accuracy, precision, and resolution of reconstructed topologies across all tested probabilistic software applications and all levels of missing data. Under the RF metric, Bayesian inference applications were the most consistent, accurate, and robust to variation in taxonomic sampling in all tested conditions, especially at high levels of missing data, with little difference in performance between the two tested programs. The MS metric favored more resolved topologies that were generally produced by IQ-TREE. Adding more taxa dramatically reduced performance disparities between programs. Importantly, our results suggest that the RF metric penalizes incorrectly resolved nodes (false positives) more severely than the MS metric, which instead tends to penalize polytomies. If false positives are to be avoided in systematics, Bayesian inference should be preferred over maximum likelihood for the analysis of morphological data.

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WEAVER, DANA, JOSEPH C. SPAGNA, and PATINA K. MENDEZ. "Phylogenetics of a small caddisfly genus (Thremmatidae: Oligophlebodes): comparison among multiple hypotheses from DNA barcode data." Zoosymposia 14, no. 1 (July 15, 2019): 193–203. http://dx.doi.org/10.11646/zoosymposia.14.1.21.

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Barcoding datasets can serve as a resource for species associations and delineations, but single-gene trees estimated by distance methods do not provide strong estimates of phylogeny. Using DNA data from the Barcode of Life Database (BOLD), we calculate a phylogenetic tree for Oligophlebodes (Trichoptera: Thremmatidae), a small genus of caddisfly endemic to the Western United States. Here we estimate a preliminary phylogeny for Oligophlebodes using Bayesian likelihood, and compare it to trees produced by distance and standard likelihood methods. Using the barcode region of the cytochrome oxidase 1 (COI) gene, we analyzed 44 individuals representing five species (and 2 unknowns) and a sister-genus outgroup (Neophylax) from locations ranging from Southern New Mexico northwest into British Columbia. Partitioned Bayesian likelihood analysis under the F81 (1st codon positions) and HKY80 + I + Γ (for both the 2nd and 3rd codon positions) model gave the consensus topology (Neophylax toshi, (O. sierra, (O. ruthae inc. spc. 1 & 2, O. sigma, (spc. 3 & 4, (O. ardis, O. minutus)))). Species identifications were supported by monophyly of most species-level taxa. However, confirmation of species identifications of unknowns was complicated by incomplete taxon sampling for spc. 1 & 2. Placement of spc. 3 & 4 may serve as support for taxonomic review of O. minutus. Compared with an existing published phylogeny of Oligophlebodes BOLD sequences constructed under RAxML, the Bayesian hypothesis had higher resolution at the basal node of Oligophlebodes. Because of their support values, both likelihood trees are recommended over the BOLD TaxonID tree (an unrooted neighbor joining tree using the Kimura 2-parameter model). The novel topology produced in the Bayesian tree supports further explorations by likelihood-based methods, including partitioned analyses, of our preliminary Oligophlebodes dataset that can be used as additional lines of evidence to support morphological work.

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Welker, Frido, Geoff M. Smith, Jarod M. Hutson, Lutz Kindler, Alejandro Garcia-Moreno, Aritza Villaluenga, Elaine Turner, and Sabine Gaudzinski-Windheuser. "Middle Pleistocene protein sequences from the rhinoceros genusStephanorhinusand the phylogeny of extant and extinct Middle/Late Pleistocene Rhinocerotidae." PeerJ 5 (March 14, 2017): e3033. http://dx.doi.org/10.7717/peerj.3033.

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BackgroundAncient protein sequences are increasingly used to elucidate the phylogenetic relationships between extinct and extant mammalian taxa. Here, we apply these recent developments to Middle Pleistocene bone specimens of the rhinoceros genusStephanorhinus. No biomolecular sequence data is currently available for this genus, leaving phylogenetic hypotheses on its evolutionary relationships to extant and extinct rhinoceroses untested. Furthermore, recent phylogenies based on Rhinocerotidae (partial or complete) mitochondrial DNA sequences differ in the placement of the Sumatran rhinoceros (Dicerorhinus sumatrensis). Therefore, studies utilising ancient protein sequences from Middle Pleistocene contexts have the potential to provide further insights into the phylogenetic relationships between extant and extinct species, includingStephanorhinusandDicerorhinus.MethodsZooMS screening (zooarchaeology by mass spectrometry) was performed on several Late and Middle Pleistocene specimens from the genusStephanorhinus, subsequently followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) to obtain ancient protein sequences from a Middle PleistoceneStephanorhinusspecimen. We performed parallel analysis on a Late Pleistocene woolly rhinoceros specimen and extant species of rhinoceroses, resulting in the availability of protein sequence data for five extant species and two extinct genera. Phylogenetic analysis additionally included all extant Perissodactyla genera (Equus,Tapirus), and was conducted using Bayesian (MrBayes) and maximum-likelihood (RAxML) methods.ResultsVarious ancient proteins were identified in both the Middle and Late Pleistocene rhinoceros samples. Protein degradation and proteome complexity are consistent with an endogenous origin of the identified proteins. Phylogenetic analysis of informative proteins resolved the Perissodactyla phylogeny in agreement with previous studies in regards to the placement of the families Equidae, Tapiridae, and Rhinocerotidae.Stephanorhinusis shown to be most closely related to the generaCoelodontaandDicerorhinus. The protein sequence data further places the Sumatran rhino in a clade together with the genusRhinoceros, opposed to forming a clade with the black and white rhinoceros species.DiscussionThe first biomolecular dataset available forStephanorhinusplaces this genus together with the extinct genusCoelodontaand the extant genusDicerorhinus. This is in agreement with morphological studies, although we are unable to resolve the order of divergence between these genera based on the protein sequences available. Our data supports the placement of the genusDicerorhinusin a clade together with extantRhinocerosspecies. Finally, the availability of protein sequence data for both extinct European rhinoceros genera allows future investigations into their geographic distribution and extinction chronologies.

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Pershing, Nicole L., Aurélie Kapusta, Shannon Nielsen, Hillary Crandall, E. Kent Korgenski, Carrie L. Byington, Krow Ampofo, and Anne J. Blaschke. "#64: An odyssey Beyond the Capsule: Genetic Determinants of Pediatric Invasive Streptococcus pneumoniae Empyema." Journal of the Pediatric Infectious Diseases Society 10, Supplement_1 (March 1, 2021): S7. http://dx.doi.org/10.1093/jpids/piaa170.021.

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Abstract Background Streptococcus pneumoniae is among the most common causes of invasive bacterial infections in children, including pneumonia, bacteremia, and meningitis. Over 90 different serotypes (ST) of pneumococcus exist, with enrichment of some ST within specific invasive phenotypes. Other than capsular genes, molecular determinants of particular invasive phenotypes remain largely unknown. Although vaccination targeting especially invasive ST capsular antigens has successfully decreased the incidence of invasive pneumococcal disease (IPD), new ST have emerged, suggesting methods to target other aspects of pneumococcal invasiveness are needed. Methods Pneumococcal isolates from IPD were collected from children presenting to Primary Children’s Hospital from 1996–2018. All viable isolates underwent next-generation sequencing (Illumina), quality control filtering for contamination and low coverage, de novo genome assembly with SPADES, and annotation with PROKKA. Clinical phenotypes were manually validated with physician chart review. Isolates were serotyped via Quelling and in silico using SeroBA. ROARY was used for pan-genome assembly, and SCOARY for microbial genome-wide association studies. RAxML was used for phylogenetic analysis. Results A total of 354 viable pneumococcal isolates were available for genomic analysis including a spectrum of invasive phenotypes: pneumonia (n = 138, of which 54 were complicated by empyema), CNS infection (n = 50), SSTI/bone infections (n = 42), and isolated bacteremia (n = 68). Thirteen samples were censored for poor coverage or genetic contamination. Invasive isolates spanned 37 capsular ST. The pneumococcal pan-genome comprised 6462 genes, of which only 23% were shared by at least 99% of samples. Phylogenetic relatedness resulted in clustering of some ST (e.g., ST1, ST3), whereas others (eg ST19A) were more broadly distributed. Empyema and meningitis phenotypes were distributed across the phylogenetic tree, but enriched in distinct clusters that crossed ST clusters. Genes involved in empyemagenic pneumococcal capsule production, and those implicated in sensing of preferred sugars or non-preferred sugar metabolism were statistically correlated with the empyema phenotype. Conclusion There is marked genetic diversity among invasive pneumococcal isolates, potentially contributing to the variability of disease phenotypes observed. Clustering of invasive phenotypes across ST suggests a genetic signature for invasive phenotypes other than capsule genes alone, further supported by enrichment of specific genes associated with alternative sugar metabolism in empyema isolates. Critical determinants of invasive phenotypes will inform future efforts at disease prevention and treatment.

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Sakagami, Kiyo, Akiko Ishii, Naoko Shimada, and Kunio Yasuda. "RaxL regulates chick ganglion cell development." Mechanisms of Development 120, no. 8 (August 2003): 881–95. http://dx.doi.org/10.1016/s0925-4773(03)00163-1.

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Grossberg, Michael D., and Shree K. Nayar. "The Raxel Imaging Model and Ray-Based Calibration." International Journal of Computer Vision 61, no. 2 (February 2005): 119–37. http://dx.doi.org/10.1023/b:visi.0000043754.56350.10.

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Ramlakhan, Kiran, and Bernet Elzinga. "Ouder-adolescent conflicten en depressieve stemming bij Surinaams-Hindostaanse jonge vrouwen in Nederland." Pedagogiek 39, no. 2 (September 1, 2019): 207–24. http://dx.doi.org/10.5117/ped2019.2.005.raml.

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Berres, Axel, Kyle Post, Andrius Armonas, Myron Hecht, Tomas Juknevičius, and Dave Banham. "OMG RAAML standard for model‐based Fault Tree Analysis." INCOSE International Symposium 31, no. 1 (July 2021): 1349–62. http://dx.doi.org/10.1002/j.2334-5837.2021.00905.x.

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Burrows*, Rhoda L., and Ismail Ahmed. "Fungicidal Seed Treatments and Formonetin Affect Arbuscular-Mycorrhizal Fungi Colonization of Muskmelon." HortScience 39, no. 4 (July 2004): 758A—758. http://dx.doi.org/10.21273/hortsci.39.4.758a.

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Fungicides applied as soil drenches affect arbuscular-mycorrhizal (AM) fungal colonization of plant roots to different degrees, depending on the chemical used. However, the effect of fungicides applied as seed treatments has been less studied, and is of particular interest to growers who want to encourage beneficial mutualisms while protecting seedlings against pathogens. We tested the effects of four common seed treatments, Apron (mefenoxam), Thiram, Raxil (tebuconzaole), and Captan on colonization of `Superstar' muskmelon roots by the AM fungus Glomus intraradices in the greenhouse. By 30 days after planting, colonization was very high (>90% root length) for all treatments, with relatively minor (<10%) differences in percent length root with AM hyphae. The Apron seed treatment had the highest percent root length with hyphae, but the lowest amount of vesicles, while roots from Raxil and Captan-treated seeds had the lowest hyphal colonization and highest vesicle formation. Myconate ®, a commercial formulation of formononetin, an isoflavone previously shown to increase AM colonization, significantly increased the percent colonization of roots from the Raxil treatment, but not other treatments. Myconate also increased vesicle numbers in all but the Captan treatments, but not significantly.

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Binti Syed Mudzhar, Sharifah NurDurrah, and Mohd Yusran Othman. "Huge Renal Angiomyolipoma in a Child with Tuberous Sclerosis Complex: A Diagnostic and Therapeutic Dilemma." International Journal of Human and Health Sciences (IJHHS) 5, no. 0-2 (September 23, 2021): 26. http://dx.doi.org/10.31344/ijhhs.v5i0-2.344.

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Tuberous Sclerosis Complex (TSC) is a rare neuro-cutaneous disorder that is associated with the development of benign hamartomas including renal angiomyolipoma (RAML). TSC associated RAML are usually asymptomatic, but it carries a life-threatening bleeding risk. We are sharing a case of a 5-year-old girl who was diagnosed to have TSC with associated subependymal giant cell astrocytoma, cardiac rhabdomyoma and autism. She presented with a history of worsening abdominal distension over 3 weeks duration and clinically noted to be pale with a ballotable left flank mass. Ultrasound and CT scan found to have multiple RAML in both kidneys with a huge mass on the left side. The mass represented a huge RAML (8cm) with aneurysmal formation with suspicion of intratumoral bleeding. The option of conservative management with mammalian target of rapamycin inhibitor followed with partial nephrectomy has been questioned with its life-threatening risk of bleeding and inability to do biopsy to rule out the possibility of renal cell carcinoma. Decision for nephrectomy was then made clearer following a MAG-3 scan which revealed only 11% differential function of the left kidney. She underwent a total left nephrectomy uneventfully and intraoperatively noted to have an enlarging lesion as compared to the previous imaging; 15cm in largest diameter. Histopathological finding was consistent with multifocal angiomyolipoma with intratumoral haematoma. Decision for nephrectomy in TSC-associated RAML need to be justified carefully in view of its risk of losing the contralateral kidney following the disease progression which may end up with life-long renal replacement therapy.International Journal of Human and Health Sciences Supplementary Issue-2: 2021 Page: S26

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Xiang, Mingfeng, Feng Du, Jing Dai, Ling Chen, Ruijin Geng, Huiming Huang, and Baogang Xie. "Exploring serum metabolic markers for the discrimination of ccRCC from renal angiomyolipoma by metabolomics." Biomarkers in Medicine 14, no. 8 (June 2020): 675–82. http://dx.doi.org/10.2217/bmm-2019-0215.

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Abstract:

Aim: The discrimination of renal cell carcinoma from renal angiomyolipoma (RAML) is crucial for the effective treatment of each. Materials & methods: Serum samples were analyzed by nuclear magnetic resonance spectroscopy-based metabolomics and a number of metabolites were further quantified by HPLC–UV. Results: Clear-cell renal carcinoma (ccRCC) was characterized by drastic disruptions in energy, amino acids, creatinine and uric acid metabolic pathways. A logistic model for the differential diagnosis of RAML from ccRCC was established using the combination of serum levels of uric acid, the ratio of uric acid to hypoxanthine and the ratio of hypoxanthine to creatinine as variables with area under the curve of the receiver operating characteristic curve value of 0.907. Conclusion: Alterations in serum purine metabolites may be used as potential metabolic markers for the differential diagnosis of ccRCC and RAML.

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Xu, Chunli, Yaxin Wang, Shiyao Liu, Qingbiao Xie, Na He, Chenyi Shi, Xiaolei Niu, Chaozu He, Chunxia Li, and Jun Tao. "RaxM regulates the AvrXa21 (RaxX)-mediated immune response." Molecular Plant Pathology 19, no. 11 (September 4, 2018): 2363–69. http://dx.doi.org/10.1111/mpp.12703.

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Zheng, Zhi, Pingyi Liu, Liting Xu, Zhiqiang Peng, Yayue Zhang, Xinyi Chen, Li Hou, et al. "Metabolomics analysis of salvage chemotherapy on refractory acute myeloid leukemia patients." RSC Advances 8, no. 26 (2018): 14445–53. http://dx.doi.org/10.1039/c7ra13298k.

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Zhang, Bo, Shaowei Liao, and Tianrui Ren. "Utilization of the fermentation residues of validamycin as a potential platform for seed treatment." RSC Advances 8, no. 18 (2018): 9956–62. http://dx.doi.org/10.1039/c7ra12298e.

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Validamycin fermentation residue (VFR) is used as a pesticide carrier for seed treatment (FS). FS coated wheat seeds have higher germination and antibacterial rates and better protection against wheat powdery mildew than those treated with Raxil.

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Journal articles on the topic 'RaxML'

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