Monophyly of Rhizaria and multigene phylogeny of unicellular bikonts

Reconstructing a global phylogeny of eukaryotes is an ongoing challenge of molecular phylogenetics. The availability of genomic data from a broad range of eukaryotic phyla helped in resolving the eukaryotic tree into a topology with a rather small number of large assemblages, but the relationships between these "supergroups" are yet to be confirmed. Rhizaria is the most recently recognized "supergroup," but, in spite of this important position within the tree of life, their representatives are still missing in global phylogenies of eukaryotes. Here, we report the first large-scale analysis of eukaryote phylogeny including data for 2 rhizarian species, the foraminiferan Reticulomyxa filosa and the chlorarachniophyte Bigelowiella natans. Our results confirm the monophyly of Rhizaria (Foraminifera + Cercozoa), with very high bootstrap supports in all analyses. The overall topology of our trees is in agreement with the current view of eukaryote phylogeny with basal division into "unikonts" (Opisthokonts and Ameobozoa) and "bikonts" (Plantae, alveolates, stramenopiles, and excavates). As expected, Rhizaria branch among bikonts; however, their phylogenetic position is uncertain. Depending on the data set and the type of analysis, Rhizaria branch as sister group to either stramenopiles or excavates. Overall, the relationships between the major groups of unicellular bikonts are poorly resolved, despite the use of 85 proteins and the largest taxonomic sampling for this part of the tree available to date. This may be due to an acceleration of evolutionary rates in some bikont phyla or be related to their rapid diversification in the early evolution of eukaryotes.     

The effect of model choice on phylogenetic inference using mitochondrial sequence data: lessons from the scorpions

Chelicerates are a diverse group of arthropods, with around 65,000 described species occupying a wide range of habitats. Many phylogenies describing the relationships between the various chelicerate orders have been proposed. While some relationships are widely accepted, others remain contentious. To increase the taxonomic sampling of species available for phylogenetic study based on mitochondrial genomes we produced the nearly complete sequence of the mitochondrial genome of the scorpion Mesobuthus gibbosus. Mitochondrial gene order in M. gibbosus largely mirrors that in Limulus polyphemus but tRNA secondary structures are truncated. A recent analysis argued that independent reversal of mitochondrial genome strand-bias in several groups of arthropods, including spiders and scorpions, could compromise phylogenetic reconstruction and proposed an evolutionary model that excludes mutational events caused by strand-bias (Neutral Transitions Excluded, NTE). An arthropod dataset of six mitochondrial genes, when analyzed under NTE, yields strong support for scorpions as sister taxon to the rest of Chelicerata. We investigated the robustness of this result by exploring the effect of adding additional chelicerate genes and taxa and comparing the phylogenies obtained under different models. We find evidence that (1) placement of scorpions arising at the base of the Chelicerata is an artifact of model mis-specification and scorpions are strongly supported as basal arachnids and (2) an expanded chelicerate dataset finds support for several proposed interordinal relationships (ticks plus mites [Acari] and spiders plus whip spiders plus whip scorpions [Araneae+Pedipalpi]). Mitochondrial sequence data are subject to systematic bias that is positively misleading for evolutionary inference and thus extreme methodological care must be taken when using them to infer phylogenies.     

Phylogenetic analysis of four nuclear protein-encoding genes largely corroborates the traditional classification of Bivalvia (Mollusca)

Revived interest in molluscan phylogeny has resulted in a torrent of molecular sequence data from phylogenetic, mitogenomic, and phylogenomic studies. Despite recent progress, basal relationships of the class Bivalvia remain contentious, owing to conflicting morphological and molecular hypotheses. Marked incongruity of phylogenetic signal in datasets heavily represented by nuclear ribosomal genes versus mitochondrial genes has also impeded consensus on the type of molecular data best suited for investigating bivalve relationships. To arbitrate conflicting phylogenetic hypotheses, we evaluated the utility of four nuclear protein-encoding genes-ATP synthase β, elongation factor-1α, myosin heavy chain type II, and RNA polymerase II-for resolving the basal relationships of Bivalvia. We sampled all five major lineages of bivalves (Archiheterodonta, Euheterodonta [including Anomalodesmata], Palaeoheterodonta, Protobranchia, and Pteriomorphia) and inferred relationships using maximum likelihood and Bayesian approaches. To investigate the robustness of the phylogenetic signal embedded in the data, we implemented additional datasets wherein length variability and/or third codon positions were eliminated. Results obtained include (a) the clade (Nuculanida+Opponobranchia), i.e., the traditionally defined Protobranchia; (b) the monophyly of Pteriomorphia; (c) the clade (Archiheterodonta+Palaeoheterodonta); (d) the monophyly of the traditionally defined Euheterodonta (including Anomalodesmata); and (e) the monophyly of Heteroconchia, i.e., (Palaeoheterodonta+Archiheterodonta+Euheterodonta). The stability of the basal tree topology to dataset manipulation is indicative of signal robustness in these four genes. The inferred tree topology corresponds closely to those obtained by datasets dominated by nuclear ribosomal genes (18S rRNA and 28S rRNA), controverting recent taxonomic actions based solely upon mitochondrial gene phylogenies.     

Evidence for Eurogondwana: the roles of dispersal,extinction and vicariance in the evolution and biogeography of Indo‐Pacific Hormuridae (Scorpiones: Scorpionoidea)

Scorpions previously assigned to the genus Liocheles Sundevall, 1883, of the family Hormuridae Laurie, 1896, are widely distributed in the tropical forests of the Indo‐Pacific region. Revisionary systematics of these poorly known scorpions has revealed a tremendous diversity of species. As part of an ongoing investigation, the first analysis of Indo‐Pacific hormurid scorpion phylogeny based on morphological data scored for all currently recognized species of Hormiops Fage, 1933 , Hormurus Thorell, 1876, and Liocheles, is presented. The taxonomy of these scorpions is reassessed and their biogeography reinterpreted in the light of the phylogeny. Phylogenetic, morphological, and distributional data support the revalidation of Hormiops and Hormurus, previously synonymized with Liocheles. The phylogeny indicates that the Australasian hormurids are more closely related to the Afrotropical and Neotropical hormurids than to the Indian hormurids, as previously proposed, refuting the “out‐of‐India” origin of Asian hormurids. A recent paleogeographical hypothesis, the “Eurogondwana model”, is supported instead. According to this hypothesis, hormurid scorpions colonized Laurasia from Africa via the Apulia microplate (Europa terrane) in the Cretaceous, subsequently colonized the Australo‐Papuan archipelago in the early‐mid Cenozoic, and then went extinct in the Northern Hemisphere during the second half of the Cenozoic. These results suggest that, contrary to the traditional paradigm, dispersal and extinction may affect spatial and temporal biotic distributions as much as vicariance, even in animals with limited vagility, such as scorpions.     

Phylogeny of feather mite subfamily Avenzoariinae (Acari: Analgoidea: Avenzoariidae) inferred from combined analyses of molecular and morphological data.

Phylogenetic relationships among feather mites of the subfamily Avenzoariinae (Acari: Analgoidea: Avenzoariidae) were reconstructed by parsimony analysis of a combined data matrix. We analyzed 41 morphological characters and 246 molecular characters from a fragment of the 16S rDNA. Morphological trees were well supported at deep branches (genera and above), but showed much less support and resolution within genera. Molecular analyses produced trees with better resolution and support on terminal branches and worse support on basal branches. I(MF) index for the combined matrix pointed to the significant congruence of both data subsets with the whole of the data. The topology of the combined tree was close to the morphological tree in the deep branches and had well-resolved terminal branches as in the molecular tree. This suggests a considerable level of complimentarity between the two data sets. An analysis of association patterns of the mites and their hosts was conducted based on the results of the combined analyses for the Avenzoariinae and a phylogeny of their charadriiform hosts (compiled from various bird phylogeny hypotheses). The trees could be reconciled by the invoking of 12-13 cospeciation events, 6-7 duplications, 2 host shifts, and 26-29 sorting events. This suggests a high degree of cospeciation.     

Phylogeny of firs (genus <Emphasis Type="Italic">Abies</Emphasis>, Pinaceae) based on multilocus nuclear markers (AFLP)

To study the phylogenetic relationships, evolutionary history, and molecular systematics of firs (genus Abies), the phylogenetic reconstruction, based on nuclear multilocus markers—amplified fragment length polymorphism (AFLP)—was conducted. Using seven combinations of selective primers, 84 samples of 39 taxa were genotyped for 553 polymorphic AFLP loci. A comparison with our earlier chloroplast and mitochondrial phylogenies of the genus (in 2014) shows that the nuclear phylogeny generally is more congruent to the chloroplast tree. Most of the clades resolved by the chloroplast phylogeny were supported also in the AFLP tree. Employing the nuclear DNA-based tree, we revealed the presence of new groups and the differences in the topology of several clades. AFLP confirmed the monophyly of Asian species of section Balsamea and their sister position in relation to the American group of species of this section. As shown by the tree of chloroplast DNA, Asian species of section Balsamea do not form a monophyletic group, but belong to the clade comprising the majority of Asian species. Phylogenetically mitochondrial DNA data to a large extent are not congruent to the nuclear and chloroplast DNA trees, and are more in line with geographical distribution of species. Conflicts between nuclear and cytoplasmic phylogeny were analyzed. Taking them into account, we consider the hypothesis of a hybrid origin of particular groups of firs, including ancient hybridization in section Balsamea. A comparison of molecular data with traditional taxonomy of the genus is discussed.     

Effects of sequence alignment and structural domains of ribosomal DNA on phylogeny reconstruction for the protozoan family sarcocystidae

Finding correct species relationships using phylogeny reconstruction based on molecular data is dependent on several empirical and technical factors. These include the choice of DNA sequence from which phylogeny is to be inferred, the establishment of character homology within a sequence alignment, and the phylogeny algorithm used. Nevertheless, sequencing and phylogeny tools provide a way of testing certain hypotheses regarding the relationship among the organisms for which phenotypic characters demonstrate conflicting evolutionary information. The protozoan family Sarcocystidae is one such group for which molecular data have been applied phylogenetically to resolve questionable relationships. However, analyses carried out to date, particularly based on small-subunit ribosomal DNA, have not resolved all of the relationships within this family. Analysis of more than one gene is necessary in order to obtain a robust species signal, and some DNA sequences may not be appropriate in terms of their phylogenetic information content. With this in mind, we tested the informativeness of our chosen molecule, the large-subunit ribosomal DNA (lsu rDNA), by using subdivisions of the sequence in phylogenetic analysis through PAUP, fastDNAml, and neighbor joining. The segments of sequence applied correspond to areas of higher nucleotide variation in a secondary-structure alignment involving 21 taxa. We found that subdivision of the entire lsu rDNA is inappropriate for phylogenetic analysis of the Sarcocystidae. There are limited informative nucleotide sites in the lsu rDNA for certain clades, such as the one encompassing the subfamily Toxoplasmatinae. Consequently, the removal of any segment of the alignment compromises the final tree topology. We also tested the effect of using two different alignment procedures (CLUSTAL W and the structure alignment using DCSE) and three different tree-building methods on the final tree topology. This work shows that congruence between different methods in the formation of clades may be a feature of robust topology; however, a sequence alignment based on primary structure may not be comparing homologous nucleotides even though the expected topology is obtained. Our results support previous findings showing the paraphyly of the current genera Sarcocystis and Hammondia and again bring to question the relationships of Sarcocystis muris, Isospora felis, and Neospora caninum. In addition, results based on phylogenetic analysis of the structure alignment suggest that Sarcocystis zamani and Sarcocystis singaporensis, which have reptilian definitive hosts, are monophyletic with Sarcocystis species using mammalian definitive hosts if the genus Frenkelia is synonymized with Sarcocystis.     

History of study,updated checklist,distribution and key of scorpions (Arachnida：Scorpiones) from China

This review describes the history of taxonomic research on scorpions and provides an updated checklist and key of the scorpions currently known in China. This checklist is based on a thorough review of the extant literatures on scorpion species whose presence has been confirmed in China through field expeditions and examination of scorpion collections, excepting a few members that have no clear distribution or are currently in doubt. Totally, the scorpion fauna of China consists of 53 species and subspecies belonging to 12 genera crossing five families, with 33 species (62.3%) and one genus being recorded as endemic. Additionally, identification key and the distribution of scorpions from China are provided.     

Wide phylogenetic distribution of Scorpine and long-chain beta-KTx-like peptides in scorpion venoms: identification of "orphan" components

Scorpine and toxins specific for potassium channels of the family beta (beta-Ktx) are two types of structurally related scorpion venom components, characterized by an unusually long extended N-terminal segment, followed by a Cys-rich domain with some resemblance to other scorpion toxins. In this communication, we report evidence supporting the ubiquitous presence of Scorpine and beta-KTx-like polypeptides and their precursors in scorpions of the genus Tityus of the family Buthidae, but also included is the first example of such peptides in scorpions from the family Iuridae. Seven new beta-KTxs or Scorpine-like peptides and precursors are reported: five from the genus Tityus (T. costatus, T. discrepans and T. trivittatus) and two from Hadrurus gertschi. The cDNA precursors for all of these peptides were obtained by molecular cloning and their presence in the venoms were confirmed for various peptides. Analysis of the sequences revealed the existence of at least three distinct groups: (1) beta-KTx-like peptides from buthids; (2) Scorpine-like peptides from scorpionid and iurid scorpions; (3) heterogeneous peptides similar to BmTXKbeta of buthids and iurids. The biological function for most of these peptides is not well known; that is why they are here considered "orphan" peptides.     

Phylogeny of the cricket subfamily Eneopterinae (Orthoptera, Grylloidea, Eneopteridae) based on four molecular loci and morphology

The phylogenetic relationships of 39 species of Eneopterinae crickets are reconstructed using four molecular markers (16S rRNA, 12S rRNA, cytochrome b, 18S rRNA) and a large morphological data set. Phylogenetic analysis via direct optimisation of DNA sequence data using parsimony as optimality criterion is done for six combinations of weighting parameter sets in a sensitivity analysis. The results are discussed in a twofold purpose: first, in term of significance of the molecular markers for phylogeny reconstruction in Ensifera, as our study represents the first molecular phylogeny performed for this insect suborder at this level of diversity; second, in term of corroboration of a previous phylogeny of Eneopterinae, built on morphological data alone. The four molecular markers all convey phylogenetic signal, although variously distributed on the tree. The monophyly of the subfamily, that of three over five tribes, and of 10 over 13 genera, are recovered. Finally, previous hypotheses on the evolution of acoustic devices and signals in the Eneopterinae clade are briefly tested, and supported, by our new data set.     

Troglomorphism,trichobothriotaxy and typhlochactid phylogeny (Scorpiones,Chactoidea): more evidence that troglobitism is not an evolutionary dead‐end

The scorpion family Typhlochactidae Mitchell, 1971 is endemic to eastern Mexico and exclusively troglomorphic. Six of the nine species in the family are hypogean (troglobitic), morphologically specialized for life in the cave environment, whereas three are endogean (humicolous) and comparably less specialized. The family therefore provides a model for testing the hypotheses that ecological specialists (stenotopes) evolve from generalist ancestors (eurytopes) and that specialization (in this case to the cavernicolous habitat) is an irreversible, evolutionary dead‐end that ultimately leads to extinction. Due to their cryptic ecology, inaccessible habitat, and apparently low population density, Typhlochactidae are very poorly known. The monophyly of these troglomorphic scorpions has never been rigorously tested, nor has their phylogeny been investigated in a quantitative analysis. We test and confirm their monophyly with a cladistic analysis of 195 morphological characters (142 phylogenetically informative), the first for a group of scorpions in which primary homology of pedipalp trichobothria was determined strictly according to topographical identity (the “placeholder approach”). The phylogeny of Typhlochactidae challenges the conventional wisdom that ecological specialization (stenotopy) is unidirectional and irreversible, falsifying Cope’s Law of the unspecialized and Dollo’s Law of evolutionary irreversibility. Troglobitism is not an evolutionary dead‐end: endogean scorpions evolved from hypogean ancestors on more than one occasion. © The Willi Hennig Society 2009.     

Phylogeny and systematic position of Opiliones: a combined analysis of chelicerate relationships using morphological and molecular data

The ordinal level phylogeny of the Arachnida and the suprafamilial level phylogeny of the Opiliones were studied on the basis of a combined analysis of 253 morphological characters, the complete sequence of the 18S rRNA gene, and the D3 region of the 28S rRNA gene. Molecular data were collected for 63 terminal taxa. Morphological data were collected for 35 exemplar taxa of Opiliones, but groundplans were applied to some of the remaining chelicerate groups. Six extinct terminals, including Paleozoic scorpions, are scored for morphological characters. The data were analyzed using strict parsimony for the morphological data matrix and via direct optimization for the molecular and combined data matrices. A sensitivity analysis of 15 parameter sets was undertaken, and character congruence was used as the optimality criterion to choose among competing hypotheses. The results obtained are unstable for the high-level chelicerate relationships (except for Tetrapulmonata, Pedipalpi, and Camarostomata), and the sister group of the Opiliones is not clearly established, although the monophyly of Dromopoda is supported under many parameter sets. However, the internal phylogeny of the Opiliones is robust to parameter choice and allows the discarding of previous hypotheses of opilionid phylogeny such as the "Cyphopalpatores" or "Palpatores." The topology obtained is congruent with the previous hypothesis of "Palpatores" paraphyly as follows: (Cyphophthalmi (Eupnoi (Dyspnoi + Laniatores))). Resolution within the Eupnoi, Dyspnoi, and Laniatores (the latter two united as Dyspnolaniatores nov.) is also stable to the superfamily level, permitting a new classification system for the Opiliones.     

Systematics of Fraxinus (Oleaceae) and evolution of dioecy

Phylogenetic relationships among 40 of the 43 recognized species of Fraxinus L. (Oleaceae) were estimated on the basis of 106 nuclear ribosomal ITS sequences. ITS trees resulting from maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) are congruent and identify six distinct lineages. These clades allow establishing sections with high molecular and morphological support. The basal resolution generally has low ML bootstrap and MP jackknife support, but the Bayesian posterior probabilities are high for certain relationships. An independent data set of combined sequences from the chloroplast rps16 and trnL-F regions contains few informative sites but corroborate most of the relationships in the ITS tree. The molecular phylogeny is discussed in the light of morphological and other data and a revised infrageneric classification with six sections are presented. The subgenera and subsections are abandoned and the section Pauciflorae is a new combination. Fraxinus quadrangulata and Fraxinus anomala are united with Fraxinus dipetala in the section Dipetalae and Fraxinus platypoda is transferred to the section Fraxinus. Fraxinus chiisanensis, Fraxinus spaethiana and Fraxinus cuspidata are treated as incertae sedis. A sectional key is given, together with a systematic list of the 43 recognized species, with common synonyms and distribution. Breeding system and other traits mapped on the phylogeny show that dioecy has three separate origins, and in each case followed after the transition from insect to wind pollination. In one instance dioecy evolved from hermaphroditism via androdioecy and twice via polygamy.     

Troglobitic scorpions: a new genus and species from Brazil

A new genus and species of troglobitic buthid scorpion are described on the basis of a single specimen collected in Brazil. This is the first cavernicolous scorpion ever found in Brazil, and only the second to be found in South America. Some considerations on troglobitic scorpions are proposed.     

A morphological analysis of marsupial mammal higher-level phylogenetic relationships

Phylogenetic relationships among marsupial taxa have proven to be more complex than the simple grouping of species by continent. Recent marsupials are distributed across the New World, Australia, New Guinea, and certain neighboring islands. Morphological characteristics of various groups bridge different geographical areas. We investigated the origin of these characteristics by assembling a morphological data matrix consisting of a new suite of 149 postcranial characters and incorporated a series of previously published data on the craniodental (76 characters) and soft tissue (5 characters) anatomy. Twenty‐one marsupial terminal taxa representing all the major radiations of marsupials and 10 outgroups, most of which are exceptionally well‐preserved fossils such as Vincelestes, Ukhaatherium, and a few basal metatherian taxa, were investigated. A maximum parsimony analysis was conducted, resulting in one most parsimonious tree. Relationships among outgroups are congruent with current understanding of mammalian phylogeny. All currently accepted marsupial orders were recovered by the analysis. We confirmed previous results showing the South American “monito del monte”Dromiciops nested within the Australasian radiation. Within this australidelphian clade, Dromiciops was closely allied with the Diprotodontia. The South American paucituberculates appeared more closely related to the Australidelphia than to the American Didelphimorphia. The marsupial mole Notoryctes and the Peramelia were closely allied to each other and in turn were the sister group of the Dromiciops plus Diprotodontia clade. This pattern of relationships left Dasyuromorphia as the most basal offshoot of the Australidelphia. Whereas this tree topology recovers some signal that had been detected by previous studies, morphological and/or molecular, some novel hypotheses are also supported.     

Phylogenomic Resolution of Sea Spider Diversification through Integration of Multiple Data Classes

Despite significant advances in invertebrate phylogenomics over the past decade, the higher-level phylogeny of Pycnogonida (sea spiders) remains elusive. Due to the inaccessibility of some small-bodied lineages, few phylogenetic studies have sampled all sea spider families. Previous efforts based on a handful of genes have yielded unstable tree topologies. Here, we inferred the relationships of 89 sea spider species using targeted capture of the mitochondrial genome, 56 conserved exons, 101 ultraconserved elements, and 3 nuclear ribosomal genes. We inferred molecular divergence times by integrating morphological data for fossil species to calibrate 15 nodes in the arthropod tree of life. This integration of data classes resolved the basal topology of sea spiders with high support. The enigmatic family Austrodecidae was resolved as the sister group to the remaining Pycnogonida and the small-bodied family Rhynchothoracidae as the sister group of the robust-bodied family Pycnogonidae. Molecular divergence time estimation recovered a basal divergence of crown group sea spiders in the Ordovician. Comparison of diversification dynamics with other marine invertebrate taxa that originated in the Paleozoic suggests that sea spiders and some crustacean groups exhibit resilience to mass extinction episodes, relative to mollusk and echinoderm lineages.     

cDNA cloning, sequence analysis and molecular modeling of a new peptide from the scorpion Buthotus saulcyi venom

In this study, the cDNA of a new peptide from the venom of the scorpion, Buthotus saulcyi, was cloned and sequenced. It codes for a 64 residues peptide (Bsaul1) which shares high sequence similarity with depressant insect toxins of scorpions. The differences between them mainly appear in the loop1 which connects the beta-strand1 to the alpha-helix and seems to be functionally important in long chain scorpion neurotoxins. This loop is three amino acids longer in Bsaul1 compared to other depressant toxins. A comparative amino acid sequence analysis done on Bsaul1 and some of alpha-, beta-, excitatory and depressant toxins of scorpions showed that Bsaul1 contains all the residues which are highly conserved among long chain scorpion neurotoxins. Structural model of Bsaul1 was generated using Ts1 (a beta-toxin that competes with the depressant insect toxins for binding to Na(+) channels) as template. According to the molecular model of Bsaul1, the folding of the polypeptide chain is being composed of an anti-parallel three-stranded beta-sheet and a stretch of alpha- helix, tightly bound by a set of four disulfide bridges. A striking similarity in the spatial arrangement of some critical residues was shown by superposition of the backbone conformation of Bsaul1 and Ts1.