Nuclear gene trees and the phylogenetic relationships of the mangabeys (Primates: Papionini)

Phylogenetic relationships of mangabeys within the Old World monkey tribe Papionini are inferred from analyses of nuclear DNA sequences from five unlinked loci. The following conclusions are strongly supported, based on congruence among trees derived for the five separate gene regions: (1) mangabeys are polyphyletic within the Papionini; (2) Cercocebus is the sister taxon to the genus Mandrillus; and (3) Lophocebus belongs to a clade with Papio and Theropithecus, with Papio as its most likely sister taxon. Morphologically based phylogenies positing mangabey monophyly were evaluated by mapping the sequences for each locus on these trees. The data seem to fit these trees poorly in both maximum-parsimony and likelihood analyses. Incongruence among nuclear gene trees occurred in the interrelationships among Lophocebus, Papio, and Theropithecus. Several factors that may account for this incongruence are discussed, including sampling error, random lineage sorting, and introgression.      

Molecular phylogeny of Gastrotricha on the basis of a comparison of the 18S rRNA genes: Rejection of the hypothesis of a relationship between Gastrotricha and Nematoda

Gastrotricha are the small meiobenthic acoelomate worms whose phylogenetic relationships between themselves and other invertebrates remain unclear, despite all attempts to clarify them on the basis of both morphological and molecular analyses. The complete sequences of the 18S rRNA genes (8 new and 7 known) were analyzed in 15 Gastrotricha species to test different hypotheses on the phylogeny of this taxon and to determine the reasons for the contradictions in earlier results. The data were analyzed using both maximum likelihood and Bayesian methods. Based on the results, it was assumed that gastrotrichs form a monophyletic group within the Spiralia clade, which also includes Gnathostomulida, Plathelminthes, Syndermata (Rotifera + Acanthocephala), Nemertea, and Lophotrochozoa. Statistical tests rejected a phylogenetic hypotheses considering Gastrotricha to be closely related to Nematoda and other Ecdysozoa or placing them at the base of the Bilateria tree, close to Acoela or Nemertodermatida. Among gastrotrichs, species belonging to the orders Chaetonotida and Macrodasyida form two well-supported clades. The analysis confirmed monophyly of the families Chaetonotidae and Xenotrichulidae from the order Chaetonida, as well as the families Turbanellidae and Thaumastodermatidae from the order Macrodasyida. Lepidodasyidae is a polyphyletic family, because the genus Mesodasys forms a sister group for Turbanellidae; genus Cephalodasys forms a separate branch at the base of Macrodasyida; and Lepidodasys groups with Neodasys between Thaumastodermatidae and Turbanellidae. To confirm these conclusions and to get an authentic view of the phylogeny of Gastrotricha, it is necessary to study more Gastrotricha species and to analyze some other genes.     

Morphological convergence characterizes the evolution of Xanthophyceae (Heterokontophyta): evidence from nuclear SSU rDNA and plastidial rbcL genes

Xanthophyceae are a group of heterokontophyte algae. Few molecular studies have investigated the evolutionary history and phylogenetic relationships of this class. We sequenced the nuclear-encoded SSU rDNA and chloroplast-encoded rbcL genes of several xanthophycean species from different orders, families, and genera. Neither SSU rDNA nor rbcL genes show intraspecific sequence variation and are good diagnostic markers for characterization of problematic species. New sequences, combined with those previously available, were used to create different multiple alignments. Analyses included sequences from 26 species of Xanthophyceae plus three Phaeothamniophyceae and two Phaeophyceae taxa used as outgroups. Phylogenetic analyses were performed according to Bayesian inference, maximum likelihood, and maximum parsimony methods. We explored effects produced on the phylogenetic outcomes by both taxon sampling as well as selected genes. Congruent results were obtained from analyses performed on single gene multiple alignments as well as on a data set including both SSU rDNA and rbcL sequences. Trees obtained in this study show that several currently recognized xanthophycean taxa do not form monophyletic groups. The order Mischococcales is paraphyletic, while Tribonematales and Botrydiales are polyphyletic even if evidence for the second order is not conclusive. Botrydiales and Vaucheriales, both including siphonous taxa, do not form a clade. The families Botrydiopsidaceae, Botryochloridaceae, and Pleurochloridaceae as well as the genera Botrydiopsis and Chlorellidium are polyphyletic. The Centritractaceae and the genus Bumilleriopsis also appear to be polyphyletic but their monophyly cannot be completely rejected with current evidence. Our results support morphological convergence at any taxonomic rank in the evolution of the Xanthophyceae. Finally, our phylogenetic analyses exclude an origin of the Xanthophyceae from a Vaucheria-like ancestor and favor a single early origin of the coccoid cell form.     

Chroococcidiopsis and heterocyst-differentiating cyanobacteria are each other's closest living relatives

Many filamentous cyanobacteria reduce atmospheric nitrogen in specialized differentiated cells called heterocysts. Here we present evidence that shows that members of the unicellular non-heterocyst-differentiating genus Chroococcidiopsis and the filamentous heterocyst-differentiating cyanobacteria are each other's closest living relatives. Distance, maximum-parsimony, and maximum-likelihood analyses of complete small subunit ribosomal RNA gene sequences yielded highly congruent support for the monophyly of Chroococcidiopsis and the heterocyst-differentiating cyanobacteria. Our results demonstrate that the order Pleurocapsales, which traditionally contains Chroococcidiopsis, is a polyphyletic assemblage with the ability to reproduce by multiple fission having arisen independently at least twice during the cyanobacterial radiation. Our data also reject Myxosarcina as a sister taxon to Chroococcidiopsis, indicating that the numerous presumed shared derived characters thought to unite the two genera evolved independently. The sequence divergence within the Chroococcidiopsis lineage is comparable to and probably exceeds that in the entire heterocyst-differentiating lineage. Chroococcidiopsis forms unique survival cells under nitrogen-limiting conditions, and the sister group relationship with the heterocystous cyanobacteria shown here suggests that differentiation of these cells and heterocysts may be related processes.     

Last of the human protists: the phylogeny and genetic diversity of Iodamoeba

Iodamoeba is the last genus of obligately parasitic human protist whose phylogenetic position is unknown. Iodamoeba small subunit ribosomal DNA sequences were obtained using samples from three host species, and phylogenetic analyses convincingly placed Iodamoeba as a sister taxon to Endolimax. This clade in turn branches among free-living amoeboflagellates of the genus Mastigamoeba. Two Iodamoeba ribosomal lineages (RL1 and RL2) were detected whose sequences differ by 31%, each of which is found in both human and nonhuman hosts.     

Phylogenetic analyses of small subunit ribosomal RNA coding regions reveal a monophyletic lineage of euglyphid testate amoebae (Order Euglyphida)

The Testaceafilosia includes amoebae with filopodia and with a proteinaceous, agglutinated or siliceous test. To explore the deeper phylogeny of this group, we sequenced the small subunit ribosomal RNA coding region of 13 species, including the first sequence of an amoeba with an agglutinated test, Pseudodifflugia sp. Phylogenetic analyses using maximum parsimony and maximum likelihood methods as well as neighbor joining method yielded the following results: the order Euglyphida forms a monophyletic lineage with the sarcomonads as sister group. The next related taxa are the Chlorarachnea and the unidentified filose strain N-Por. In agreement with the previous studies the Phytomyxea branch off at the base of this lineage. The Monadofilosa (Testaceafilosia and Sarcomonadea) appear monophyletic. The Testaceafilosia are polyphyletic, because Pseudodifflugia sp. is positioned as the sister taxon to the sarcomonads. Within the order Euglyphida Paulinella branches off first, together with Cyphoderia followed by Tracheleuglypha. In maximum likelihood and neighbor joining analyses, the genus Euglypha is monophyletic. The branching pattern within the order Euglyphida reflects the evolution of shell morphology from simple to complex built test.     

Molecular phylogenetic evaluation of classification and scenarios of character evolution in calcareous sponges (Porifera, Class Calcarea)

Calcareous sponges (Phylum Porifera, Class Calcarea) are known to be taxonomically difficult. Previous molecular studies have revealed many discrepancies between classically recognized taxa and the observed relationships at the order, family and genus levels; these inconsistencies question underlying hypotheses regarding the evolution of certain morphological characters. Therefore, we extended the available taxa and character set by sequencing the complete small subunit (SSU) rDNA and the almost complete large subunit (LSU) rDNA of additional key species and complemented this dataset by substantially increasing the length of available LSU sequences. Phylogenetic analyses provided new hypotheses about the relationships of Calcarea and about the evolution of certain morphological characters. We tested our phylogeny against competing phylogenetic hypotheses presented by previous classification systems. Our data reject the current order-level classification by again finding non-monophyletic Leucosolenida, Clathrinida and Murrayonida. In the subclass Calcinea, we recovered a clade that includes all species with a cortex, which is largely consistent with the previously proposed order Leucettida. Other orders that had been rejected in the current system were not found, but could not be rejected in our tests either. We found several additional families and genera polyphyletic: the families Leucascidae and Leucaltidae and the genus Leucetta in Calcinea, and in Calcaronea the family Amphoriscidae and the genus Ute. Our phylogeny also provided support for the vaguely suspected close relationship of several members of Grantiidae with giantortical diactines to members of Heteropiidae. Similarly, our analyses revealed several unexpected affinities, such as a sister group relationship between Leucettusa (Leucaltidae) and Leucettidae and between Leucascandra (Jenkinidae) and Sycon carteri (Sycettidae). According to our results, the taxonomy of Calcarea is in desperate need of a thorough revision, which cannot be achieved by considering morphology alone or relying on a taxon sampling based on the current classification below the subclass level.     

Phylogenetic evidence places the coralloid jelly fungus <Emphasis Type="Italic">Tremellodendropsis tuberosa</Emphasis> (Tremellodendropsidales) among early diverging Agaricomycetes

We explored the phylogenetic relationships of Tremellodendropsis tuberosa from western North America. The species has tough, coralloid fruiting bodies that emerge from a basal tuber, as well as unusual, partially septate basidia, large elliptical spores, and regular clamp connections. It has been classified variously in Auriculariales, Tremellales, and in its own order, Tremellodendropsidiales. To evaluate support for these alternatives, we extracted DNA from four specimens and sequenced ～5000 bp from the ribosomal large subunit, small subunit and internal transcribed spacer region from each. We aligned sequences from T. tuberosa with sequences from GenBank that represented 31 Basidiomycota orders and then analyzed the individual and concatenated sequence regions using Bayesian and maximum likelihood approaches. Analyses agreed that T. tuberosa is an early diverging member of Agaricomycetes, but did not provide unequivocal support for its sister group relationships within the class. From the concatenated alignment, after removal of poorly aligned sites using Gblocks, T. tuberosa appeared as the sister group to a clade encompassing four orders, three of them from Phallomycetidae. This relationship had a Bayesian posterior probability of 1.0 and appeared, although without bootstrap support, in maximum likelihood trees. Tree topology tests ruled out placing T. tuberosa within the Auriculariales. We accept that T. tuberosa should be placed in its own order, the Tremellodendropsidales, and not in Auriculariales or Tremellales. As a taxon that diverged early from other Basidiomycota clades, T. tuberosa should be included in further studies of phylogeny and character evolution in Agaricomycetes.     

A molecular phylogeny of the Odonata (Insecta)

Abstract. We estimated the phylogeny of the order Odonata, based on sequences of the nuclear ribosomal genes 5.8 S, 18S, and ITS1 and 2. An 18S‐only analysis resolved deep relationships well: the order Odonata, as well as suborders Zygoptera and Epiprocta (Anisoptera + Epiophlebia), emerged as monophyletic. Some other deep clades resolved well, but support for more recently diverged clades was generally weak. A second, simultaneous, analysis of the 5.8S and 18S genes with the intergenic spacers ITS1 and 2 resolved some recent branches better, but appeared less reliable for deep clades with, for example, suborder Anisoptera emerging as paraphyletic and Epiophlebia superstes recovered as an Anisopteran, embedded within aeshnoid‐like anisopterans and sister to the cordulegastrids. Most existing family levels in the Anisoptera were confirmed as monophyletic clades in both analyses. However, within the corduliids that form a major monophyletic clade with the Libellulidae, several subclades were recovered, of which at least Macromiidae and Oxygastridae are accepted at the family level. In the Zygoptera, the situation is complex. The lestid‐like family groups (here called Lestomorpha) emerged as sister taxon to all other zygopterans, with Hemiphlebia sister to all other lestomorphs. Platystictidae formed a second monophylum, subordinated to lestomorphs. At the next level, some traditional clades were confirmed, but the tropical families Megapodagrionidae and Amphipterygidae were recovered as strongly polyphyletic, and tended to nest within the clade Caloptera, rendering it polyphyletic. Platycnemididae were also non‐monophyletic, with several representatives of uncertain placement. Coenagrionids were diphyletic. True Platycnemididae and non‐American Protoneurids are closely related, but their relationship to the other zygopterans remains obscure and needs more study. New World protoneurids appeared relatively unrelated to old world + Australian protoneurids. Several recent taxonomic changes at the genus level, based on morphology, were confirmed, but other morphology‐based taxonomies have misclassified taxa considered currently as Megapodagrionidae, Platycnemididae and Amphipterygidae and have underestimated the number of family‐level clades.     

Higher level taxonomy and molecular phylogenetics of the Choanoflagellatea

The choanoflagellates (Choanoflagellatea) comprise a major group of nanoflagellates, which are ubiquitous in the aquatic environment. Recent molecular phylogenies have shown them to be the sister group to the Metazoa. However, the phylogeny of the choanoflagellates is still far from understood. We present here a 29 taxon, multigene phylogeny that robustly places the root of the choanoflagellates. One of the original nonloricate families, Codonosigidae is shown to be a polyphyletic assemblage nested within the Salpingoecidae. We elaborate on a revised taxonomy that divides Choanoflagellatea into two orders: Craspedida and Acanthoecida. Craspedida is composed of species that possess an organic cell coating and contains the single family Salpingoecidae. Members of the predominantly marine Acanthoecida produce a siliceous lorica in addition to an organic coat and are contained in two families--the Acanthoecidae and Stephanoecidae fam. n. Previous studies of choanoflagellates have been hindered by cases of taxon misidentification as well as the limited resolution of 18S small subunit (SSU) rDNA phylogenies. Unfortunately, cases of misidentification have been heavily repeated in the literature. In an attempt to avoid further confusion, we highlight known instances of misnamed taxa. We also examine the suitability of SSU rDNA sequences alone for choanoflagellate phylogenetics and recommend the use of protein-coding genes, such as hsp90 and tubA, whenever possible.     

鳇亚科似鳇属鱼类的物种界定和系统发育关系

逗亚科似逗属鱼类的物种界定保持争议, 系统发育关系尚待解决。研究取样似逗属鱼类所有种, 使用核基因多位点序列重建似逗属鱼类的系统发育关系, 运用分子的物种界定方法并结合形态特征分析厘定我国似逗属鱼类的分类。贝叶斯系统发育树结果表明: 桂林似逗与平江似逗是单系种; 似逗与扁嘴似逗是多系种, 前者包括五个谱系A至E, 后者包括两个谱系A与B。POFAD距离分析和Structurama分析的结果表明似逗和扁嘴似逗的每个谱系是独立遗传种群, BP & P分析结果强烈支持它们是不同种。*Beast物种树结果揭示: 扁嘴似逗谱系B位于似逗属鱼类的基部位置; 似逗谱系A与B是姊妹群关系, 似逗谱系C是扁嘴似逗谱系A的姊妹群, 它们一起与桂林似逗形成姊妹群关系; 似逗谱系D与E是姊妹群关系, 它们一起是平江似逗的姊妹群。结合形态证据, 对我国似逗属鱼类分类厘定如下: 限定严格意义似逗包括似逗谱系A+B; 恢复长吻似逗(Pseudogobio longirostris Mori, 1934)给予似逗谱系C分类名; 似逗谱系D与E是隐存种, 桂林似逗与平江似逗是有效种。     

Crocodilian phylogeny inferred from twelve mitochondrial protein-coding genes, with new complete mitochondrial genomic sequences for Crocodylus acutus and Crocodylus novaeguineae

We report complete mitochondrial genomic sequences for Crocodylus acutus and Crocodylus novaeguineae, whose gene orders match those of other crocodilians. Phylogenetic analyses based on the sequences of 12 mitochondrial protein-coding genes support monophyly of two crocodilian taxonomic families, Alligatoridae (genera Alligator, Caiman, and Paleosuchus) and Crocodylidae (genera Crocodylus, Gavialis, Mecistops, Osteolaemus, and Tomistoma). Our results are consistent with monophyly of all crocodilian genera. Within Alligatoridae, genus Alligator is the sister taxon of a clade comprising Caiman and Paleosuchus. Within Crocodylidae, the basal phylogenetic split separates a clade comprising Gavialis and Tomistoma from a clade comprising Crocodylus, Mecistops, and Osteolaemus. Mecistops and Osteolaemus form the sister taxon to Crocodylus. Within Crocodylus, we sampled five Indopacific species, whose phylogenetic ordering is ((C. mindorensis, C. novaeguineae), (C. porosus, (C. siamensis, C. palustris))). The African species C. niloticus and New World species C. acutus form the sister taxon to the Indopacific species, although our sampling lacks three other New World species and an Australian species of Crocodylus.     

Phylogenetic placement of the spider genus Nephila (Araneae: Araneoidea) inferred from rRNA and MaSp1 gene sequences

The family status of the genus Nephila, which belongs to Tetragnathidae currently but Araneidae formerly, was reexamined based on molecular phylogenetic analyses. In the present study, 12S and 18S rRNA gene fragments of eight species of spiders were amplified and sequenced. In addition, 3'-end partial cDNA of major ampullate spidroin-1 (MaSp1) gene of Argiope amoena was cloned and sequenced, and the 3'-end non-repetitive region's cDNA sequence of MaSp1 gene and the predicted amino acid sequence of C-terminal non-repetitive region of MaSp1 were aligned with some previously known sequences. The resulting phylogeny showed that Araneidae and Tetragnathidae are not a sister group in the superfamily Araneoidea, and the genus Nephila is closer to the genera of the family Araneidae rather than to those of Tetragnathidae. We suggest that the genus Nephila should be transferred back to Araneidae. Or the subfamily Nephilinae might be elevated to family level after it was redefined and redelimited. Furthermore, the study showed that 3'-end non-repetitive region's cDNA sequence of MaSp1 gene and C-terminal non-repetitive region's amino acid sequence of MaSp1 are useful molecular markers for phylogenetic analysis of spiders.     

A phylogenetic study of the genus Haligena (Halosphaeriales, Ascomycota)

The genus Haligena (Halosphaeriales, Ascomycota), with two accepted species, is encountered frequently in marine habitats, especially on wood in temperate regions. Phylogenetic analyses of Haligena elaterophora (type species) and H. salina were undertaken, with partial large subunit ribosomal DNA sequences, to determine their relationships with other closely related genera in the order. The genus was shown to be polyphyletic within the Halosphaeriales with the type species forming a basal clade to the order. Haligena salina constituted a sister clade with weak support of Neptunella longirostris in all analyses. Haligena elaterophora and H. salina differ significantly in the nature of their ascospore appendages: wider, more sticky and strap-like in H. elaterophora and spoon-shaped at the point of attachment; in H. salina they are longer and narrower, finely drawn out filaments. A new genus, Morakotiella, is introduced to accommodate H. salina.     

Relationships among the major lineages of Dictyoptera: the effect of outgroup selection on dictyopteran tree topology

Abstract Dictyoptera, comprising Blattaria, Isoptera, and Mantodea, are diverse in appearance and life history, and are strongly supported as monophyletic. We downloaded COII, 16S, 18S, and 28S sequences of 39 dictyopteran species from GenBank. Ribosomal RNA sequences were aligned manually with reference to secondary structure. We included morphological data (maximum of 175 characters) for 12 of these taxa and for an additional 15 dictyopteran taxa (for which we had only morphological data). We had two datasets, a 59‐taxon dataset with five outgroup taxa, from Phasmatodea (2 taxa), Mantophasmatodea (1 taxon), Embioptera (1 taxon), and Grylloblattodea (1 taxon), and a 62‐taxon dataset with three additional outgroup taxa from Plecoptera (1 taxon), Dermaptera (1 taxon) and Orthoptera (1 taxon). We analysed the combined molecular?morphological dataset using the doublet and MK models in Mr Bayes , and using a parsimony heuristic search in paup . Within the monophyletic Mantodea, Mantoida is recovered as sister to the rest of Mantodea, followed by Chaeteessa; the monophyly of most of the more derived families as defined currently is not supported. We recovered novel phylogenetic hypotheses about the taxa within Blattodea (following Hennig, containing Isoptera). Unique to our study, one Bayesian analysis places Polyphagoidea as sister to all other Dictyoptera; other analyses and/or the addition of certain orthopteran sequences, however, place Polyphagoidea more deeply within Dictyoptera. Isoptera falls within the cockroaches, sister to the genus Cryptocercus. Separate parsimony analyses of independent gene fragments suggest that gene selection is an important factor in tree reconstruction. When we varied the ingroup taxa and/or outgroup taxa, the internal dictyopteran relationships differed in the position of several taxa of interest, including Cryptocercus, Polyphaga, Periplaneta and Supella. This provides further evidence that the choice of both outgroup and ingroup taxa greatly affects tree topology.     

First molecular evidence for the phylogenetic placement of the enigmatic snake genus Brachyorrhos (Serpentes: Caenophidia)

BrachyorrhosSchlegel, 1826a is a terrestrial-fossorial snake genus endemic to eastern Indonesia that has been assigned to six different families and subfamilies within Colubroidea (advanced snakes) over the past ~200 years. Here we report the first molecular sequences for Brachyorrhos and use them to test the position of the genus within snake phylogeny. Our Bayesian and Maximum Likelihood analyses of three mitochondrial and one nuclear gene strongly resolve Brachyorrhos within the rear-fanged semiaquatic Homalopsidae (Colubroidea), as the sister taxon to all other genera and sampled species.     

REVIEW Evolution and systematics of the Chelicerata

After approximately 40 years of discussion about the question of whether the Arthropoda are a monophyletic or a paraphyletic group or even a polyphyletic assemblage of unrelated taxa, most morphologists, palaeontologists and molecular taxonomists agree that the Arthropoda are a monophylum. The Euarthropoda are composed of the Arachnomorpha and Mandibulata. Myriapods are usually considered to be mandibulates; however, new molecular data as well as some morphological characters show similarities which the Myriapoda share with the Chelicerata, suggesting that there is no taxon Antennata or Atelocerata. Chelicerata are usually considered to be the sister group of Trilobita or, more correctly, Trilobita branch off from the chelicerate stem line. The first adaptive radiation of the Chelicerata took place in the Cambrian. All extant and some extinct orders were present during the Carboniferous. Two systems are compared. It is suggested that the Chelicerata contain the Pantopoda and Euchelicerata. The Euchelicerata are divided into Xiphosura and terrestrial Arachnida. Scorpiones are considered to be the sister group of all other arachnids, the Lipoctena and these are further divided into the Megoperculata (Uropygi, Amblypygi, and Araneae) and Apulmonata (all other groups). The Acari are tentatively considered to be a monophylum and the sister group of the Ricinulei. However, the Actinotrichida and Anactinotrichida diverged early and therefore have had a long history of independent evolution.     

Phylogeny of the genus Aleochara inferred from mitochondrial cytochrome oxidase sequences (Coleoptera: Staphylinidae)

The phylogeny of the genus Aleochara was previously poorly understood due to difficulties with phylogenetic reconstruction by morphological characters. We present here a phylogeny based on the sequences of a 2022-bp fragment of the COI/II genes; 50 Aleochara and 10 outgroup species were included in the analysis. We used parsimony, minimum-evolution, and maximum-likelihood analyses to infer the phylogeny of the group. Our data do not support the commonly assumed sister group relationship between Aleocharini and Hoplandriini. Aleochara is resolved as a monophylum, although A. clavicornis might not belong to the genus. Within Aleochara, there are two large monophyletic clades. Many of the existing subgenera are shown to be para- or polyphyletic; others are likely to be monophyletic. Tinotus morion, previously assigned to the Hoplandriini, is strongly supported as belonging to Aleochara. According to our data, the mesosternal carina that has been used as an important character for classification has arisen and been reduced independently in several clades within Aleochara.