Phylogenetic systematics of Colotis and associated genera (Lepidoptera: Pieridae): evolutionary and taxonomic implications

We investigated the genetic diversity and phylogenetic placement of the butterflies in the genus Colotis and eight related pierid genera using sequence information from two mitochondrial and two nuclear genes. To establish the status of species, we initially barcoded 632 specimens representative of all genera and most species and subspecies in those genera. A subset was then selected for phylogenetic analysis where additional gene regions were sequenced: 16S rRNA (523 bp), EF‐1α (1126 bp) and wg (404 bp). DNA barcode results were largely congruent with the traditional classification of species in the Colotis group, but deep splits or lack of genetic divergence in some cases supported either species‐level differentiation or synonymy. Despite using information from four genes, the deeper nodes in our phylogeny were not strongly supported, and monophyly of the ‘Colotis group’ and the genera Colotis and Eronia could not be established. To preserve the monophyly of Colotis, we revive the genus Teracolus for three outlying species previously in Colotis (i.e. Colotis eris, Colotis subfasciatus and Colotis agoye), as well as the genus Afrodryas for Eronia leda. The position of Calopieris is unresolved although it appears to be well outside the molecular variation in Colotis (s.l.). A dispersal/vicariance analysis suggested that major diversification in Colotis (s.str.) occurred in Africa with subsequent dispersal to India and Madagascar.     

Phylogeny of the family Trogidae (Coleoptera: Scarabaeoidea) inferred from mitochondrial and nuclear ribosomal DNA sequence data

Trogidae constitute a monophyletic and biologically unique family within Scarabaeoidea, being the only keratinophagous group in the superfamily. Traditionally, the family has been divided into three distinctive genera, Polynoncus Burmeister, Omorgus Erichson and Trox Fabricius. Although the taxonomy of the group is relatively well studied, changes to the existing classification have recently been proposed and the family as currently constituted has not been subjected to phylogenetic analyses. Here we present a molecular phylogeny for this cosmopolitan family based on three partially sequenced gene regions: 16S rRNA, 18S rRNA and 28S rRNA (domain 2). Included in the analyses are representatives belonging to four of the five extant genera (and three of the four subgenera) from all major zoogeographic regions, representing about 20% of the known trogid species diversity in the family. Phylogenetic analyses performed included parsimony and Bayesian inference. We deduce their historical biogeography by using trogid fossils as calibration points for divergence estimates. Our analyses resolved relationships between and within genera and subgenera that are largely congruent with existing phylogeny hypotheses based on morphological data. We recovered four well‐supported radiations: Polynoncus, Omorgus, Holarctic Trox and African Phoberus MacLeay. On the basis of this study, it is proposed that taxonomic changes to the generic classification of the family be made. The subgenera Trox and Phoberus should be elevated to genera to include the Holarctic and all the Afrotropical species, respectively, and Afromorgus returned to subgeneric rank. Estimates of divergence time are consistent with a Pangaean origin of the family in the Early Jurassic. The subsequent diversification of the major lineages is largely attributed to the break‐up of Pangaea and Gondwana in the Middle Jurassic and early Late Cretaceous, respectively.     

Synergistic effects of combining morphological and molecular data in resolving the phylogenetic position of Semispathidium (Ciliophora,Haptoria) with description of Semispathidium breviarmatum sp. n. from tropical Africa

We describe a new species, Semispathidium breviarmatum sp. n., from tropical Africa and analyse its phylogenetic position within the subclass Haptoria, using live observation, various silver impregnation methods, SEM and the 18S rRNA gene. Semispathidium breviarmatum differs from its congeners by the much higher number of ciliary rows and by the shape and size of the extrusomes, that is, extrusive organelles that kill the prey. The phylogenetic position of Semispathidium is controversial due to its ‘hybrid’ morphology. Specifically, the cylindroidal body has a more or less discoidal oral bulge indicating an enchelyodonid origin, while the anteriorly curved somatic kineties suggest a spathidiid ancestor. In order to reconstruct the evolutionary history of Semispathidium and to unravel its affinity to other haptorians, we used synergistic effects of combining morphological and molecular data coming from 34 haptorian taxa. These analyses show that Semispathidium belongs to the order Spathidiida representing a basal lineage that is far from ordinary Spathidium species, but very likely related to Protospathidium and Enchelys. Any closer phylogenetic relationship between Semispathidium and Enchelyodon spp. is not recognized in morphological and molecular phylogenies and is consistently excluded by statistical tree topology tests.     

Phylogeny of Mesoamerican freshwater mussels and a revised tribe‐level classification of the Ambleminae

Evolutionary and ecological hypotheses of the freshwater mussel subfamily Ambleminae are intensely geographically biased—a consequence of the complete exclusion of Mesoamerican taxa in phylogenetic reconstructions of the clade. We set out to integrate a portion of the Mesoamerican freshwater mussel assemblage into existing hypotheses of amblemine classification and evolution by generating a molecular phylogeny that includes four previously unsampled Mesoamerican genera and nine species endemic to that region. Given the traditionally hypothesized affinity to Nearctic mussels and the understanding that classification should reflect common ancestry, we predicted that (a) Mesoamerican genera would be recovered as members of the recognized tribes of the Ambleminae, and (b) genera would be supported as monophyletic. The mutilocus phylogeny (COI + 28S + 16S) reported herein does not fully support either of those hypotheses. Neither Cyrtonaias nor Psorula were supported as monophyletic and we predict several other Mesoamerica genera are also non‐monophyletic. The reconstructed phylogeny recovered four independent lineages of Mesoamerican freshwater mussels and these clades are distributed across the phylogeny of the Ambleminae, including the tribe Quadrulini (Megalonaias), Lampsilini (two lineages: Cyrtonaias explicata/Sphenonaias microdon, and Pachynaias), and a previously unrecognized, exclusively Mesoamerican and Rio Grande clade consisting of the genera Psoronaias, Psorula and Popenaias. The latter clade possesses several morphological characteristics that distinguish it from its sister taxon, tribe Lampsilini, and we recognize this newly identified Mesoamerican clade as a fifth tribe of the Ambleminae attributable to the Popenaiadini Heard & Guckert, 1970. This revised classification more completely recognizes the suprageneric diversity of the Ambleminae.     

Molecular and morphological characterization of a poorly known marine ciliate, Myoschiston duplicatum precht 1935: implications for phylogenetic relationships between three morphologically similar genera -- Zoothamnium, Myoschiston, and Zoothamnopsis (Ciliophora, Peritrichia, Zoothamniidae)

We studied the morphology and molecular phylogeny of Myoschiston duplicatum, a peritrich ciliate that has been recorded as an epibiont of crustaceans, but which we also identified on marine algae from Korea. The important morphological characteristics revealed by silver staining of Myoschiston species have not been described because they are rarely collected. Using morphological methods, we redescribed the type species of the genus, Myoschiston duplicatum, and provided an improved diagnosis of Myoschiston. In addition, the coding regions for nuclear small subunit (SSU) rRNA and internal transcribed spacer 1‐5.8S‐internal transcribed spacer 2 sequences were sequenced. Phylogenetic analyses that included available SSU rDNA sequences of peritrichs from GenBank strongly supported a position of M. duplicatum within the family Zoothamniidae. In addition, phylogenetic analyses were performed with single datasets (ITS1‐5.8S‐ITS2) and combined datasets (SSU rDNA + ITS1‐5.8S‐ITS2) to explore further the phylogenetic relationship in the family Zoothamniidae between the three morphologically similar genera—Zoothamnium, Myoschiston, and Zoothamnopsis.     

A molecular phylogeny of marine amphipods in the herbivorous family Ampithoidae

Ampithoid amphipods dominate invertebrate assemblages associated with shallow‐water macroalgae and seagrasses worldwide and represent the most species‐rich family of herbivorous amphipod known. To generate the first molecular phylogeny of this family, we sequenced 35 species from 10 genera at two mitochondrial genes [the cytochrome c oxidase subunit I (COI) and the large subunit of 16 s (LSU)] and two nuclear loci [sodium–potassium ATPase (NAK) and elongation factor 1‐alpha (EF1)], for a total of 1453 base pairs. All 10 genera are embedded within an apparently monophyletic Ampithoidae (Amphitholina, Ampithoe, Biancolina, Cymadusa, Exampithoe, Paragrubia, Peramphithoe, Pleonexes, Plumithoe, Pseudoamphithoides and Sunamphitoe). Biancolina was previously placed within its own superfamily in another suborder. Within the family, single‐locus trees were generally poor at resolving relationships among genera. Combined‐locus trees were better at resolving deeper nodes, but complete resolution will require greater taxon sampling of ampithoids and closely related outgroup species, and more molecular characters. Despite these difficulties, our data generally support the monophyly of Ampithoidae, novel evolutionary relationships among genera, several currently accepted genera that will require revisions via alpha taxonomy and the presence of cryptic species.     

Molecular and morphological phylogeny of Diplazontinae (Hymenoptera,Ichneumonidae)

Klopfstein, S., Quicke, D. L. J., Kropf, C. & Frick, H. (2011) Molecular and morphological phylogeny of Diplazontinae (Hymenoptera, Ichneumonidae). —Zoologica Scripta, 40, 379–402. Parasitoid wasps are among the most species rich and at the same time most understudied of all metazoan taxa. To understand their diversification and test hypotheses about their evolution, we need robust phylogenetic hypotheses. Here, we reconstruct the phylogeny of the subfamily Diplazontinae using four genes and 66 morphological characters both in separate analyses and in a total evidence approach. The resulting phylogeny is highly resolved, with most clades supported by multiple independent data partitions. It contains three highly supported genus groups, for which we suggest morphological and behavioural synapomorphies. The placement of some of the genera, especially Xestopelta Dasch, is unexpected, but also supported by morphology. Most of the genera are retrieved as monophyletic, with the exception of the morphologically diverse genus Syrphoctonus Förster. We split this genus into three genera, including Fossatyloides gen. n., to restore the phylogeny–classification link. Conflict between the morphological and the molecular topology was mostly resolved in favour of the molecular partition in the total evidence approach. We discuss reasons for this finding, and suggest strategies for future taxon and character sampling in Diplazontinae.     

A global molecular phylogeny of 147 periwinkle species (Gastropoda,Littorininae)

Reid, D. G., Dyal, P. & Williams, S.T. (2012) A global molecular phylogeny of 147 periwinkle species (Gastropoda, Littorininae). —Zoologica Scripta, 41, 125–136. Complete species‐level molecular phylogenies have been published for several genera of Littorinidae (e.g. Echinolittorina, Littoraria). Here we add new sequence data from three genes (28S rRNA, 12S rRNA, cytochrome oxidase c subunit I) for single specimens of an additional 24 species, to make a data set of 147 (97%) of the 152 recognized species of the subfamily Littorininae. This three‐gene data set is analysed to produce a phylogenetic hypothesis for the subfamily, which includes the first complete species‐level phylogeny of the genus Peasiella and the first three‐gene phylogeny of all Littorina species. The non‐planktotrophic species of Littorina have previously been classified together (as subgenus Neritrema), implying a single origin of this developmental mode. Tests of this hypothesis with the new data are inconclusive, and resolution is not improved in a tree constructed from five genes (adding previously published sequences of 16S rRNA and cytochrome b). Using available fossils for calibration we generate a BEAST chronogram, which emphasizes that the radiation of Littorina is more recent than that of other littorinine genera. A database is provided, listing all known species of Littorininae, with their distributions, development, ecology and gene sequences, as a tool for future evolutionary studies of this model group.     

Mitogenomic phylogeny of Trochoidea (Gastropoda: Vetigastropoda): New insights from increased complete genomes

Increased mitochondrial (mt) genomes can provide more sets of genome‐level characteristics for resolving deeper phylogeny. Limited information with respect to the Trochoidea mitochondrial genome organization is available; besides, monophyly and internal relationships of the superfamily still remain a matter of discussion. To resolve the monophyly and internal phylogenetic controversies of Trochoidea and expand our understanding for mt genomic characteristic evolution among Trochoidea, the phylogenetic trees were reconstructed using 13 newly sequenced complete mt genomes and 35 genomes from GenBank, and both the maximum likelihood and Bayesian inference analyses were highly supported. Vetigastropoda phylogenetic analyses recovered the monophyly of Trochoidea. Trochoidea phylogenetic analyses and genetic distances supported the non‐monophyly of Tegulidae and Tegula, indicating that the taxonomic status of several genera (Rochia, Tectus and Cittarium) should be revised and Tegula, Omphalius and Chlorostoma should be placed as a same genus. The close affinity between Tectus virgatus and Rochia was also revealed. Three‐nucleotide insertion in nad1, nine‐nucleotide insertion and six‐nucleotide deletion in nad5 are detected in Tegulidae, Tectus and Rochia, respectively. Gene orders within Trochoidea are stable, with gene rearrangements exclusive to tRNA genes observed. Homoplasious convergences because of trnT rearrangement display translocation in Turbinidae and reversion in Trochidae and Calliostomatida. For trnE and trnG, we identify 11 arrangement types, suggesting that the gene rearrangement history needs to be further evaluated. Our study emphasizes the importance of mt genomes in resolving phylogenetic relationships within Trochoidea. In addition, the mt genomic characters would contribute new insights into the classification of Trochoidea.     

A molecular phylogeny of the tribe Aphidini (Insecta: Hemiptera: Aphididae) based on the mitochondrial tRNA/COII, 12S/16S and the nuclear EF1α genes

Abstract A phylogeny of the tribe Aphidini (Hemiptera: Aphididae) was reconstructed from three gene fragments: two mitochondrial regions, partial tRNA‐leucine + cytochrome oxidase II (tRNA/COII), partial 12S rRNA + tRNA‐valine + 16S rRNA (12S/16S) and one nuclear gene, the elongation factor‐1 alpha (EF1α). Bayesian phylogenetic (BP) analyses were performed on each individual dataset of tRNA/COII, 12S/16S and EF1α, and maximum parsimony (MP), Bremer support test, maximum likelihood (ML) and BP analysis were performed on the combined dataset. After comparing our molecular phylogenetic results with the classic classification based on morphological and ecological data, we analysed three main issues: the monophyletic relationships among tribes and subtribes, the validities of the latest taxonomic positions of genera and species and the status of certain Aphis species groups. Our results indicate that 36 of the species analysed, with the exception of Cryptosiphum artemisiae, are clustered within the clade of Aphidini. Also, the 28 species representative of the subtribe Aphidina were separated from the eight species representative of Rhopalosiphina; each monophyletic subtribe was supported by significant P‐values in the combined analysis. According to our results, Cryptosiphum should be moved to Macrosiphini because it is more closely related to the genera Lipaphis and Brevicoryne. The genus Toxoptera was recovered as non‐monophyletic. In Rhopalosiphina, three genera, Hyalopterus, Rhopalosiphum and Schizaphis, were relatively closer to each other than to the genus Melanaphis. In the relationships between species‐groups among Aphis, most species were separated into two main lineages; the fabae group seemed to be more closely related to the spiraecola and craccivora group rather than to the gossypii group.     

Phylogenetic relationships of Microdontinae (Diptera: Syrphidae) based on molecular and morphological characters

The intrasubfamilial classification of Microdontinae Rondani (Diptera: Syrphidae) has been a challenge: until recently more than 300 out of more than 400 valid species names were classified in Microdon Meigen. We present phylogenetic analyses of molecular and morphological characters (both separate and combined) of Microdontinae. The morphological dataset contains 174 characters, scored for 189 taxa (9 outgroup), representing all 43 presently recognized genera and several subgenera and species groups. The molecular dataset, representing 90 ingroup species of 28 genera, comprises sequences of five partitions in total from the mitochondrial gene COI and the nuclear ribosomal genes 18S and 28S. We test the sister‐group relationship of Spheginobaccha with the other Microdontinae, attempt to elucidate phylogenetic relationships within the Microdontinae and discuss uncertainties in the classification of Microdontinae. Trees based on molecular characters alone are poorly resolved, but combined data are better resolved. Support for many deeper nodes is low, and placement of such nodes differs between parsimony and Bayesian analyses. However, Spheginobaccha is recovered as highly supported sister group in both. Both analyses agree on the early branching of Mixogaster, Schizoceratomyia, Afromicrodon and Paramicrodon. The taxonomical rank in relation to the other Syrphidae is discussed briefly. An additional analysis based on morphological characters only, including all 189 taxa, used implied weighting. A range of weighting strengths (k‐values) is applied, chosen such that values of character fit of the resulting trees are divided into regular intervals. Results of this analysis are used for discussing the phylogenetic relationships of genera unrepresented in the molecular dataset.     

Morphological phylogeny of the variable fly family Stratiomyidae (Insecta,Diptera)

Brammer, C. A. & von Dohlen, C. D. (2010). Morphological phylogeny of the variable fly family Stratiomyidae (Insecta, Diptera). —Zoologica Scripta, 39, 363–377. Stratiomyidae is a dipteran family distributed worldwide and containing 2800 species classified into 12 subfamilies. Previous phylogenetic work on the Stratiomyidae consisted of a 20‐character morphological analysis of the subfamilies [ World Catalog of the Stratiomyidae (Insect: Diptera). Leiden: Backhuys Publishers, 2001 ], and a molecular study using 69 taxa and two gene regions [ Molecular Phylogenetics and Evolution, 43, 2007, 660 ]. In this study, we present an expanded morphological cladistic analysis using 92 characters and 80 taxa, representing 36 of 39 described genera and all 12 Stratiomyidae subfamilies, as well as Xylomyidae and Pantophthalmidae outgroups. Data are analysed under maximum parsimony with all characters unordered and weighted equally; nodal support is assessed with the bootstrap and Bremer index. The strict consensus of all shortest trees is well resolved, and many of the deeper nodes are supported, although the root is ambiguous. Antissinae, Stratiomyinae, Sarginae and the diverse Clitellariinae are not monophyletic. Clitellariinae are positioned across several lineages, with most species grouped into a single, unsupported clade. Many of the well‐supported relationships are consistent with several aspects of the previous studies. The position of Exodontha remains elusive. Character support for subfamilies and other major clades is discussed.     

Phylogenetic relationships within the genus Tetrahymena inferred from the cytochrome c oxidase subunit 1 and the small subunit ribosomal RNA genes

Details of the phylogenetic relationships among tetrahymenine ciliates remain unresolved despite a rich history of investigation with nuclear gene sequences and other characters. We examined all available species of Tetrahymena and three other tetrahymenine ciliates, and inferred their phylogenetic relationships using nearly complete mitochondrial cytochrome c oxidase subunit 1 (cox1) and small subunit (SSU) rRNA gene sequences. The inferred phylogenies showed the genus Tetrahymena to be monophyletic. The three “classical” morphology-and-ecology-based groupings are paraphyletic. The SSUrRNA phylogeny confirmed the previously established australis and borealis groupings, and nine ribosets. However, these nine ribosets were not well supported. Using cox1 gene, the deduced phylogenies based on this gene revealed 12 well supported groupings, called coxisets, which mostly corresponded to the nine ribosets. This study demonstrated the utility of cox1 for resolving the recent phylogeny of Tetrahymena, whereas the SSU rRNA gene provided resolution of deeper phylogenetic relationships within the genus.     

Phylogeny of the freshwater crabs of the Western Ghats (Brachyura,Gecarcinucidae)

The Western Ghats mountain range in India is a biodiversity hotspot for a variety of organisms including a large number of endemic freshwater crab species and genera of the family Gecarcinucidae. The phylogenetic relationships of these taxa, however, have remained poorly understood. Here, we present a phylogeny that includes 90% of peninsular Indian genera based on mitochondrial 16S rRNA and nuclear histone H3 gene sequences. The subfamily Gecarcinucinae was found to be paraphyletic with members of two other subfamilies, Liotelphusinae and Parathelphusinae, nesting within. We identify a well‐supported clade consisting of north Indian species and one clade comprising mostly south Indian species that inhabit the southern ‘sky islands’ of the Western Ghats. Relationships of early diverging genera, however, were resolved with low support. This study also includes newly sampled material from an isolated mountain plateau in the northern part of the Western Ghats, representing a new species of Gubernatoriana, which we describe here as Gubernatoriana basalticola sp. n. The new species is immediately distinguished from its congeners and the related genera Ghatiana and Inglethelphusa by its carapace and cheliped morphology, which are unique among Indian freshwater crabs. This study highlights the urgent need for continued faunistic studies to assess the true diversity of gecarcinucid crabs on the Indian subcontinent, to fully understand the basal phylogenetic relationships within the freshwater crab family Gecarcinucidae, and to evaluate the conservation threat status and biogeography of the montane freshwater crabs of the Western Ghats.     

Phylogenetic relationships within Aglaopheniidae (Cnidaria,Hydrozoa) reveal unexpected generic diversity

Morphology can be misleading in the representation of phylogenetic relationships, especially in simple organisms like cnidarians and particularly in hydrozoans. These suspension feeders are widely distributed in many marine ecosystems, and the family Aglaopheniidae Marktanner‐Turneretscher, 1890 is among the most diverse and visible, especially on tropical coral reefs. The taxonomy of this family is based on morphological characters with emphasis on reproductive structures for the identification of genera. This study is the most comprehensive molecular phylogeny of the Aglaopheniidae to date, including six genera and 38 species, of which 13 were investigated for the first time and sampled on tropical coral reefs throughout the Indo‐Pacific region. For newly sampled individuals, we sequenced the 16S rRNA, the nuclear locus comprising the complete ITS1‐5.8S rRNA gene‐ITS2 and the first intron of the calmodulin nuclear gene. Phylogenetic analyses of the data revealed and confirmed a general polyphyly, or doubtful monophyly, of all sampled genera in tropical regions based on both the mitochondrial and nuclear markers. Our results revealed that several morphological characters used today are unsuited to resolve phylogenetic relationships between species and genera, as well as the high phyletic diversity within this family. Future revision of the classification of this family will require extensive geographic sampling and the use of an integrative approach.     

Phylogenies from genetic and morphological characters do not support a revision of Gigasporaceae (Glomeromycota) into four families and five genera

The family Gigasporaceae consisted of the two genera Gigaspora and Scutellospora when first erected. In a recent revision of this classification, Scutellospora was divided into three families and four genera based on two main lines of evidence: (1) phylogenetic patterns of coevolving small and large rRNA genes and (2) morphology of spore germination shields. The rRNA trees were assumed to accurately reflect species evolution, and shield characters were selected because they correlated with gene trees. These characters then were used selectively to support gene trees and validate the classification. To test this new classification, a phylogenetic tree was reconstructed from concatenated 25S rRNA and β-tubulin gene sequences using 35% of known species in Gigasporaceae. A tree also was reconstructed from 23 morphological characters represented in 71% of known species. Results from both datasets showed that the revised classification was untenable. The classification also failed to accurately represent sister group relationships amongst higher taxa. Only two clades were fully resolved and congruent among datasets: Gigaspora and Racocetra (a clade consisting of species with spores having one inner germinal wall). Other clades were unresolved, which was attributed in part to undersampling of species. Topology of the morphology-based phylogeny was incongruent with gene evolution. Five shield characters were reduced to three, of which two were phylogenetically uninformative because they were homoplastic. Therefore, most taxa erected in the new classification are rejected. The classification is revised to restore the family Gigasporaceae, within which are the three genera Gigaspora, Racocetra, and Scutellospora. This classification does not reflect strict topology of either gene or morphological evolution. Further revisions must await sampling of additional characters and taxa to better ascertain congruence between datasets and infer a more accurate phylogeny of this important group of fungi.     

Phylogenetic Analysis of the Spider Mite Sub-Family Tetranychinae (Acari: Tetranychidae) Based on the Mitochondrial COI Gene and the 18S and the 5′ End of the 28S rRNA Genes Indicates That Several Genera Are Polyphyletic

The spider mite sub-family Tetranychinae includes many agricultural pests. The internal transcribed spacer (ITS) region of nuclear ribosomal RNA genes and the cytochrome c oxidase subunit I (COI) gene of mitochondrial DNA have been used for species identification and phylogenetic reconstruction within the sub-family Tetranychinae, although they have not always been successful. The 18S and 28S rRNA genes should be more suitable for resolving higher levels of phylogeny, such as tribes or genera of Tetranychinae because these genes evolve more slowly and are made up of conserved regions and divergent domains. Therefore, we used both the 18S (1,825–1,901 bp) and 28S (the 5′ end of 646–743 bp) rRNA genes to infer phylogenetic relationships within the sub-family Tetranychinae with a focus on the tribe Tetranychini. Then, we compared the phylogenetic tree of the 18S and 28S genes with that of the mitochondrial COI gene (618 bp). As observed in previous studies, our phylogeny based on the COI gene was not resolved because of the low bootstrap values for most nodes of the tree. On the other hand, our phylogenetic tree of the 18S and 28S genes revealed several well-supported clades within the sub-family Tetranychinae. The 18S and 28S phylogenetic trees suggest that the tribes Bryobiini, Petrobiini and Eurytetranychini are monophyletic and that the tribe Tetranychini is polyphyletic. At the genus level, six genera for which more than two species were sampled appear to be monophyletic, while four genera (Oligonychus, Tetranychus, Schizotetranychus and Eotetranychus) appear to be polyphyletic. The topology presented here does not fully agree with the current morphology-based taxonomy, so that the diagnostic morphological characters of Tetranychinae need to be reconsidered.     

Diatom phylogenetics inferred based on direct optimization of nuclear-encoded SSU rRNA sequences

Direct optimization (DO) of 126 nuclear‐encoded SSU rRNA diatom sequences was conducted. The optimal phylogeny indicated several unique relationships with respect to those recovered from a maximum likelihood (ML) analysis of an alignment based on maximizing primary and secondary structural similarity between 126 nuclear‐encoded SSU rRNA diatom sequences ( Medlin and Kaczmarska, 2004 ). Dividing diatoms into the subdivisions Coscinodiscophytina and Bacillariophytina was not supported by the DO phylogeny, due to the paraphyly of the former. The same pertains to Coscinodiscophyceae, Mediophyceae, Thalassiosira, Fragilaria and Amphora. The ordinal‐level classification of the diatoms proposed by Round et al. (1990 ) was for the most part found to be unsupported. The DO phylogeny represented a more rigorous hypothesis than the ML tree because DO maximized character congruence during the homology testing (i.e., alignment/tree search) process whereas the non‐phylogenetic similarity‐based alignment used in the ML analysis did not. The above statement is supported by “controlled” parsimony analyses of 35 sequences, which strongly suggested that dissimilarities in the DO and ML tree structure were due to the specific homology testing approach used. It could not be precluded that differences in taxon sampling and the use of a dissimilar optimality criteria contributed to discrepancies in the structure of the optimal ML and DO trees.     

PHYLOGENY OF THE DASYCLADALES (CHLOROPHYTA,ULVOPHYCEAE) BASED ON ANALYSES OF RUBISCO LARGE SUBUNIT (rbcL) GENE SEQUENCES1

The phylogeny of the green algal Order Dasycladales was inferred by maximum parsimony and Bayesian analyses of chloroplast‐encoded rbcL sequence data. Bayesian analysis suggested that the tribe Acetabularieae is monophyletic but that some genera within the tribe, such as Acetabularia Lamouroux and Polyphysa Lamouroux, are not. Bayesian analysis placed Halicoryne Harvey as the sister group of the Acetabularieae, a result consistent with limited fossil evidence and monophyly of the family Acetabulariaceae but was not supported by significant posterior probability. Bayesian analysis further suggested that the family Dasycladaceae is a paraphyletic assemblage at the base of the Dasycladales radiation, casting doubt on the current family‐level classification. The genus Cymopolia Lamouroux was inferred to be the basal‐most dasycladalean genus, which is also consistent with limited fossil evidence. Unweighted parsimony analyses provided similar results but primarily differed by the sister relationship between Halicoryne Lamouroux and Bornetella Munier‐Chalmas, thus supporting the monophyly of neither the families Acetabulariaceae nor Dasycladaceae. This result, however, was supported by low bootstrap values. Low transition‐to‐transversion ratios, potential loss of phylogenetic signal in third codon positions, and the 550 million year old Dasycladalean lineage suggest that dasyclad rbcL sequences may be saturated due to deep time divergences. Such factors may have contributed to inaccurate reconstruction of phylogeny, particularly with respect to potential inconsistency of parsimony analyses. Regardless, strongly negative g₁ values were obtained in analyses including all codon positions, indicating the presence of considerable phylogenetic signal in dasyclad rbcL sequence data. Morphological features relevant to the separation of taxa within the Dasycladales and the possible effects of extinction on phylogeny reconstruction are discussed relative to the inferred phylogenies.