A plastome phylogeny of Rumex (Polygonaceae) illuminates the divergent evolutionary histories of docks and sorrels.

The genus Rumex L. (Polygonaceae) provides a unique system for investigating the evolutionary development of sex determination and molecular rate evolution. Historically, Rumex has been divided, both taxonomically and colloquially into two groups: 'docks' and 'sorrels'. A well-resolved phylogeny can help evaluate a genetic basis for this division. Here we present a plastome phylogeny for 34 species of Rumex, inferred using maximum likelihood criteria. The historical 'docks' (Rumex subgenus Rumex) were resolved as monophyletic. The historical 'sorrels' (Rumex subgenera Acetosa and Acetosella) were resolved together, though not monophyletic due to the inclusion of R. bucephalophorus (Rumex subgenus Platypodium). Emex is supported as its own subgenus within Rumex, instead of resolved as sister taxa. We found remarkably low nucleotide diversity among the docks, consistent with recent diversification in that group, especially as compared to the sorrels. Fossil calibration of the phylogeny suggested that the common ancestor for Rumex (including Emex) has origins in the lower Miocene (22.13 MYA). The sorrels appear to have subsequently diversified at a relatively constant rate. The origin of the docks, however, was placed in the upper Miocene, but with most speciation occurring in the Plio-Pleistocene.

Osteomyelitis infection caused by Arcanobacterium haemolyticum in a diabetic patient: A first case report.

Arcanobacterium haemolyticum can cause deep infections, including osteomyelitis. In this study, an automated system misidentified this causal agent as Cellulomonas species but 16 s rRNA sequencing correctly identified it as A. haemolyticum. Recognizing the capability of A. haemolyticum to establish the disease is of great importance to enable accurate diagnosis and begin the suitable antibiotic therapy. Here we present the first case of successfully treated A. haemolyticum infective osteomyelitis in a 64-year-old Saudi patient with diabetes mellitus type 2 and review the characteristics of this seldom pathogenic agent.

Taxonomic Reappraisal of Lineus longifissus Auct. (Nemertea: Pilidiophora) from Japan for the First Time in 122 Years.

Having been reported in 1898 for the first time from Japanese waters, the lineid heteronemertean Lineus longifissus auct. is known to inhabit tidal flats under the influence of the warm Kuroshio Current along the coasts of Honshu and southwestward, characteristically with a uniformly raisin-colored to black body lacking a caudal cirrus. The taxonomic identity of the Japanese L. longifissus auct. has been questioned by specialists because of some obvious morphological differences between Lineus longifissus (Hubrecht, 1887) s.str. (now in Heteronemertes Chernyshev, 1995), originally described from the subantarctic region. In the present study, we describe the Japanese L. longifissus auct. as Corsoua takakurai sp. nov. Before the present study, the genus Corsoua Corrêa, 1963 had been monotypic with the type species Corsoua kristenseni Corrêa, 1963 from the Caribbean. We infer the phylogenetic position of Corsoua takakurai within Lineidae based on the mitochondrial 16S rRNA and cytochrome c oxidase subunit I, and the nuclear 18S rRNA, 28S rRNA, and histone H3 genes.

Update on the classification of higher ranks in the phylum Actinobacteria.

Genome analysis is one of the main criteria for description of new taxa. Availability of genome sequences for all the actinobacteria with a valid nomenclature will, however, require another decade's works of sequencing. This paper describes the rearrangement of the higher taxonomic ranks of the members of the phylum 'Actinobacteria', using the phylogeny of 16S rRNA gene sequences and supported by the phylogeny of the available genome sequences. Based on the refined phylogeny of the 16S rRNA gene sequences, we could arrange all the members of the 425 genera of the phylum 'Actinobacteria' with validly published names currently in use into six classes, 46 orders and 79 families, including 16 new orders and 10 new families. The order Micrococcales Prévot 1940 (Approved Lists 1980) emend. Nouioui et al. 2018 is now split into 11 monophyletic orders: the emended order Micrococcales and ten proposed new orders Aquipuribacterales, Beutenbergiales, Bogoriellales, Brevibacteriales, Cellulomonadales, Demequinales, Dermabacterales, Dermatophilales, Microbacteriales and Ruaniales. Further, the class 'Actinobacteria' Stackebrandt et al. 1997 emend. Nouioui et al. 2018 was described without any nomenclature type, and therefore the name 'Actinobacteria' is deemed illegitimate. In accordance to Rule 8 of the International Code of Nomenclature of Prokaryotes, Parker et al. 2019, we proposed the name Actinomycetia which is formed by using the stem of the name Actinomycetales Buchanan 1917 (Approved Lists 1980) emend. Zhi et al. 2009, to replace the name 'Actinobacteria'. The nomenclature type of the proposed new class Actinomycetia is the order Actinomycetales Buchanan 1917 (Approved Lists 1980) emend. Zhi et al. 2009.

Molecular systematics of the heteronemertean genus Dushia (Nemertea, Pilidiophora), with descriptions of D. wijnhoffae sp. nov. and D. nigra species complex comb. nov.

The heteronemertean genus Dushia Corrêa, 1963 was established for what was identified as D. atra (Girard, 1851) (originally Meckelia atra) based on material from littoral, shallow waters in Curaçao, while the nominal species Meckelia atra was originally described from deep water off Florida Cape. In this paper, we conclude that the type species for Dushia has been misidentified. Based on specimens from the Caribbean, we establish D. wijnhoffae Schwartz Norenburg sp. nov. to represent the true identity of the genus, according to Article 70.3.2 of the International Code of Zoological Nomenclature; Meckelia atra should be regarded as a nomen dubium. While the genus has remained monotypic since its establishment, our molecular analysis discovered a second member-or rather a group of members-from the West Pacific. This 'group of members', herein termed Dushia nigra (Stimpson, 1855) species complex comb. nov., involves i) at least two genetically separated biological entities, 0.136-0.148 (p-distance) and 0.152-0.168 (K2P) apart in terms of 513-bp COI sequences, which we interpret as likely to represent cryptic species, ii) three color forms, orange, brown, and black, with the last one occurring most frequently, and iii) four nominal species, Meckelia nigra Stimpson, 1855 (now Cerebratulus niger), Meckelia rubella Stimpson, 1855 (now Cerebratulus rubellus), Micrura formosana Yamaoka, 1939, and Micrura japonica Iwata, 1952. At present, however, we have no objective ground as to which of the four potentially available names (i.e., formosana, japonica, nigra, and rubella) should be allotted to the two cryptic species discovered in the analysis, because i) a single locality can harbor two cryptic species, ii) a single cryptic species may contain three different color morphs (i.e., orange, brown, black), and iii) no data from the type localities for these four nominal species are available at the moment. Our multi-locus analysis of heteronemerteans-for which 16S rRNA, COI, 18S rRNA, 28S rRNA, histone H3 genes are available in public databases-shows that Dushia wijnhoffae sp. nov. and Dushia nigra species complex comb. nov. form a clade, which is closely related to Gorgonorhynchus albocinctus Kajihara, 2015 and an undetermined heteronemertean that has been misidentified as Cerebratulus leucopsis (Coe, 1901). Members of Dushia thus show a vicariant Caribbean-West-Pacific distribution, indicating that the lineage predates the rise of the Isthmus of Panama.

Molecular Evolution of Spider Vision: New Opportunities, Familiar Players.

Spiders are among the world's most species-rich animal lineages, and their visual systems are likewise highly diverse. These modular visual systems, composed of four pairs of image-forming "camera" eyes, have taken on a huge variety of forms, exhibiting variation in eye size, eye placement, image resolution, and field of view, as well as sensitivity to color, polarization, light levels, and motion cues. However, despite this conspicuous diversity, our understanding of the genetic underpinnings of these visual systems remains shallow. Here, we review the current literature, analyze publicly available transcriptomic data, and discuss hypotheses about the origins and development of spider eyes. Our efforts highlight that there are many new things to discover from spider eyes, and yet these opportunities are set against a backdrop of deep homology with other arthropod lineages. For example, many (but not all) of the genes that appear important for early eye development in spiders are familiar players known from the developmental networks of other model systems (e.g., Drosophila). Similarly, our analyses of opsins and related phototransduction genes suggest that spider photoreceptors employ many of the same genes and molecular mechanisms known from other arthropods, with a hypothesized ancestral spider set of four visual and four nonvisual opsins. This deep homology provides a number of useful footholds into new work on spider vision and the molecular basis of its extant variety. We therefore discuss what some of these first steps might be in the hopes of convincing others to join us in studying the vision of these fascinating creatures.

Integration of complete chloroplast genome sequences with small amplicon datasets improves phylogenetic resolution in Acacia.

Combining whole genome data with previously obtained amplicon sequences has the potential to increase the resolution of phylogenetic analyses, particularly at low taxonomic levels or where recent divergence, rapid speciation or slow genome evolution has resulted in limited sequence variation. However, the integration of these types of data for large scale phylogenetic studies has rarely been investigated. Here we conduct a phylogenetic analysis of the whole chloroplast genome and two nuclear ribosomal loci for 65 Acacia species from across the most recent Acacia phylogeny. We then combine this data with previously generated amplicon sequences (four chloroplast loci and two nuclear ribosomal loci) for 508 Acacia species. We use several phylogenetic methods, including maximum likelihood bootstrapping (with and without constraint) and ExaBayes, in order to determine the success of combining a dataset of 4000bp with one of 189,000bp. The results of our study indicate that the inclusion of whole genome data gave a far better resolved and well supported representation of the phylogenetic relationships within Acacia than using only amplicon sequences, with the greatest support observed when using a whole genome phylogeny as a constraint on the amplicon sequences. Our study therefore provides methods for optimal integration of genomic and amplicon sequences.

A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway.

The CIPRES Science Gateway is a community web application that provides public access to a set of parallel tree inference and multiple sequence alignment codes run on large computational resources. These resources are made available at no charge to users by the NSF Extreme Science and Engineering Discovery Environment (XSEDE) project. Here we describe the CIPRES RESTful application programmer interface (CRA), a web service that provides programmatic access to all resources and services currently offered by the CIPRES Science Gateway. Software developers can use the CRA to extend their web or desktop applications to include the ability to run MrBayes, BEAST, RAxML, MAFFT, and other computationally intensive algorithms on XSEDE. The CRA also makes it possible for individuals with modest scripting skills to access the same tools from the command line using curl, or through any scripting language. This report describes the CRA and its use in three web applications (Influenza Research Database - www.fludb.org, Virus Pathogen Resource - www.viprbrc.org, and MorphoBank - www.morphobank.org). The CRA is freely accessible to registered users at https://cipresrest.sdsc.edu/cipresrest/v1; supporting documentation and registration tools are available at https://www.phylo.org/restusers.

Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars.

Next Generation Sequencing (NGS) may enable estimating relationships among genotypes using allelic variation of multiple nuclear genes simultaneously. We explored the potential and caveats of this strategy in four genetically distant Lilium cultivars to estimate their genetic divergence from transcriptome sequences using three approaches: POFAD (Phylogeny of Organisms from Allelic Data, uses allelic information of sequence data), RAxML (Randomized Accelerated Maximum Likelihood, tree building based on concatenated consensus sequences) and Consensus Network (constructing a network summarizing among gene tree conflicts). Twenty six gene contigs were chosen based on the presence of orthologous sequences in all cultivars, seven of which also had an orthologous sequence in Tulipa, used as out-group. The three approaches generated the same topology. Although the resolution offered by these approaches is high, in this case there was no extra benefit in using allelic information. We conclude that these 26 genes can be widely applied to construct a species tree for the genus Lilium.

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.

Novel information theory-based measures for quantifying incongruence among phylogenetic trees.

Phylogenies inferred from different data matrices often conflict with each other necessitating the development of measures that quantify this incongruence. Here, we introduce novel measures that use information theory to quantify the degree of conflict or incongruence among all nontrivial bipartitions present in a set of trees. The first measure, internode certainty (IC), calculates the degree of certainty for a given internode by considering the frequency of the bipartition defined by the internode (internal branch) in a given set of trees jointly with that of the most prevalent conflicting bipartition in the same tree set. The second measure, IC All (ICA), calculates the degree of certainty for a given internode by considering the frequency of the bipartition defined by the internode in a given set of trees in conjunction with that of all conflicting bipartitions in the same underlying tree set. Finally, the tree certainty (TC) and TC All (TCA) measures are the sum of IC and ICA values across all internodes of a phylogeny, respectively. IC, ICA, TC, and TCA can be calculated from different types of data that contain nontrivial bipartitions, including from bootstrap replicate trees to gene trees or individual characters. Given a set of phylogenetic trees, the IC and ICA values of a given internode reflect its specific degree of incongruence, and the TC and TCA values describe the global degree of incongruence between trees in the set. All four measures are implemented and freely available in version 8.0.0 and subsequent versions of the widely used program RAxML.

Maximum Likelihood Analyses of 3,490 rbcL Sequences: Scalability of Comprehensive Inference versus Group-Specific Taxon Sampling.

The constant accumulation of sequence data poses new computational and methodological challenges for phylogenetic inference, since multiple sequence alignments grow both in the horizontal (number of base pairs, phylogenomic alignments) as well as vertical (number of taxa) dimension. Put aside the ongoing controversial discussion about appropriate models, partitioning schemes, and assembly methods for phylogenomic alignments, coupled with the high computational cost to infer these, for many organismic groups, a sufficient number of taxa is often exclusively available from one or just a few genes (e.g., rbcL, matK, rDNA). In this paper we address scalability of Maximum-Likelihood-based phylogeny reconstruction with respect to the number of taxa by example of several large nested single-gene rbcL alignments comprising 400 up to 3,491 taxa. In order to test the effect of taxon sampling, we employ an appropriately adapted taxon jackknifing approach. In contrast to standard jackknifing, this taxon subsampling procedure is not conducted entirely at random, but based on drawing subsamples from empirical taxon-groups which can either be user-defined or determined by using taxonomic information from databases. Our results indicate that, despite an unfavorable number of sequences to number of base pairs ratio, i.e., many relatively short sequences, Maximum Likelihood tree searches and bootstrap analyses scale well on single-gene rbcL alignments with a dense taxon sampling up to several thousand sequences. Moreover, the newly implemented taxon subsampling procedure can be beneficial for inferring higher level relationships and interpreting bootstrap support from comprehensive analysis.

A nuclear ribosomal DNA phylogeny of acer inferred with maximum likelihood, splits graphs, and motif analysis of 606 sequences.

The multi-copy internal transcribed spacer (ITS) region of nuclear ribosomal DNA is widely used to infer phylogenetic relationships among closely related taxa. Here we use maximum likelihood (ML) and splits graph analyses to extract phylogenetic information from approximately 600 mostly cloned ITS sequences, representing 81 species and subspecies of Acer, and both species of its sister Dipteronia. Additional analyses compared sequence motifs in Acer and several hundred Anacardiaceae, Burseraceae, Meliaceae, Rutaceae, and Sapindaceae ITS sequences in GenBank. We also assessed the effects of using smaller data sets of consensus sequences with ambiguity coding (accounting for within-species variation) instead of the full (partly redundant) original sequences. Neighbor-nets and bipartition networks were used to visualize conflict among character state patterns. Species clusters observed in the trees and networks largely agree with morphology-based classifications; of de Jong's (1994) 16 sections, nine are supported in neighbor-net and bipartition networks, and ten by sequence motifs and the ML tree; of his 19 series, 14 are supported in networks, motifs, and the ML tree. Most nodes had higher bootstrap support with matrices of 105 or 40 consensus sequences than with the original matrix. Within-taxon ITS divergence did not differ between diploid and polyploid Acer, and there was little evidence of differentiated parental ITS haplotypes, suggesting that concerted evolution in Acer acts rapidly.

Phylogenetics: Applications, Software and Challenges.

Inference of phylogenetic trees comprising hundreds of organisms based on elaborate statistical models of evolution is an intensive computational task. However, in recent years there has been an impressive improvement in search algorithms, which currently allow for inference of huge phylogenetic trees comprising more than 1,000 taxa within a couple of hours on a single PC. This paper provides an overview of applications of phylogenetic trees to various areas of biological and medical research and reviews some of the most efficient software available for phylogenetic inference. Finally, some of the new challenges that the field currently faces in the areas of high performance computing and information visualization are discussed.