Donald J. Colgan

Arthropod Cladistics: Combined Analysis of Histone H3 and U2 snRNA Sequences and Morphology

Morphological, developmental, ultrastructural, and gene order characters are catalogued for the same set of arthropod terminals as we have scored in a recent study of histone H3 and U2 snRNA sequences (D. J. Colgan et al., 1998, Aust. J. Zool. 46, 419–437). We examine the implications of separate and simultaneous analyses of sequence and non‐sequence data for arthropod relationships. The most parsimonious trees based on 211 non‐sequence characters (273 apomorphic states) support traditional higher taxa as clades, including Mandibulata, Crustacea, Atelocerata, Myriapoda, and Hexapoda. Combined analysis of morphology with histone H3 and U2 sequences with equal character weights differs from the morphological results alone in supporting Progoneata + Hexapoda (= Labiophora) in favor of a monophyletic Myriapoda, resolves the entognathous hexapods as a grade, and supports pycnogonids as sister group to Euchelicerata (rather than as basal euarthropods). Monophyly of Chelicerata (including pycnogonids), Mandibulata, Crustacea, Progoneata, Chilopoda, and Hexapoda is maintained under a range of transition/transversion and third codon weights, whereas Atelocerata and Myriapoda/Labiophora do not withstand all sensitivity analyses.

Gastropod phylogeny based on six segments from four genes representing coding or non-coding and mitochondrial or nuclear DNA

Significant differences remain between gastropod phylogenetic hypotheses based on morphological and molecular datasets. We collected additional data from three gene segments (28S rDNA expansion region D1 (36 taxa plus two from GenBank), cytochrome c oxidase subunit 1 (35 species plus one from Genbank) and small nuclear RNA U2 (24 species)). These were combined with data available for the same species for histone H3 and two other segments of 28S rDNA. Analyses of these data using cladistic, maximum likelihood or Bayesian methodologies were conducted in an attempt to resolve some of the differences between current hypotheses of gastropod relationships based on morphological and molecular data. The results were of particular interest in four areas. (1) Patellogastropoda in most analyses are included in a derived clade with some Vetigastropoda. In an analysis with Nautilus as the sole outgroup, transversions weighted threefold as costly as transitions and, with third codon position data ignored, Patellogastropoda are excluded from an otherwise monophyletic Gastropoda. (2) Cocculiniformia was never monophyletic in our analyses, although this possibility is not statistically rejected. (3) Nerita, the only representative of Neritopsina in this dataset, is placed anomalously in most analyses, but is, in a few cases, shown as a sister-group to the Apogastropoda, in accord with some morphological hypotheses. (4) Heterobranchia is rarely monophyletic in our analyses owing to the variable placement of the architectonicoid Philippea. This genus, even judged by the high levels of divergence within Heterobranchia, has undergone extreme rates of substitution. The Euthyneura is invariably monophyletic and nearly always included in a clade with the valvatoidean Cornirostra as its sister-group.

ASSESSING THE USEFULNESS OF HISTONE H3, U2 SNRNA AND 28S RDNA IN ANALYSES OF POLYCHAETE RELATIONSHIPS

DNA sequence data from for histone H3 (34 species), U2 snRNA (34 species) and two segments (D1 and D9–10 expansion regions) of 28S rDNA (28 and 26 species, respectively) have been collected to investigate the relationships of polychaetes. Representatives of all of the major morphologically identified clades were used, as well as members of the Sipuncula, Echiura, Turbellaria, Clitellata and Siboglinidae (formerly the phyla Pogonophora and Vestimentifera). Maximum parsimony analyses of the separate data sets gave conflicting results and none conformed closely to previous results based on morphology. Instead each data set provided corroboration of a few of the morphological groupings, usually pairing, though inconsistently, members of the same family. Higher groupings proposed on morphological grounds were rarely recovered. Maximum parsimony analysis of the combined data, excluding areas of uncertain alignment, recovered some morphological groupings such as Cirratulidae, Terebellidae, scale worms and eunicimorphs, and did not significantly contradict others. However, some expected groupings were not recovered. Surprisingly, the fanworms (Sabellidae and Serpulidae) were not shown as sister taxa, and monophyly of Phyllodocida, a morphologically well corroborated clade, required four more steps than most parsimonious trees. Aciculata was not seen in our analyses, although it was the most strongly supported large clade in Rouse and Fauchald (1997, Cladistics and polychaetes. Zoologica Scripta 26, 138–204). Trees constrained to show Aciculata as monophyletic were 18 steps longer than the most parsimonious trees. If trees are rooted on sipunculans rather than the nematode, Aciculata is nearly recovered, being rendered paraphyletic by the inclusion of the sister-pair of Oweniidae and Chaetopteridae. As suggested by some recent morphological and molecular analyses, Siboglinidae and Clitellata may well have sister groups among polychaetes. The morphologically aberrant Sternaspidae are closest to members of Terebellida in the present analyses, supporting the placement of Rouse and Fauchald. Interesting results deserving further assessment concern the placement of Chaetopteridae, Oweniidae and Sipuncula.

Phylogenetic relationships within the Terebellomorpha

Terebellomorpha is a clade of predominantly tube-dwelling polychaetes, some of whose species are very abundant and whose habitats range from shallow to very deep waters. The group contains five families (Terebellidae, Ampharetidae, Pectinariidae, Trichobranchidae and Alvinellidae). This study of their inter-relationships uses DNA sequence data from five gene segments. Including outgroups, sequences were available for 15 species for 15 U2 snRNA, 14 for Histone H3, 23 for the D1 expansion region of 28S rDNA, 15 for the D9-10 region of 28S rDNA and 17 for subunit I of cytochrome oxidase. Outgroups included representatives of the polychaete families Cirratulidae, Sabellidae and Siboglinidae, and the clitellate Lumbricus . These sequences include eight GenBank entries for 28S D1 and one for CO1. Generally, and in all analyses restricted to the data collected in this laboratory, but including all of these, Terebellomorpha is monophyletic. Within Terebellomorpha, the single maximum parsimony tree indicates that Alvinellidae (all data from GenBank) belongs to a clade with Terebellidae and some Trichobranchidae, contradicting morphological expectations. Terebellidae is paraphyletic with respect to Trichobranchus , this being associated with the subfamily Thelepodinae. The second trichobranchid genus Terebellides (for which only 28S D1 data is available from GenBank) is topologically very distinct to Trichobranchus . Additional data are needed to establish the familys monophyly. Also within Terebellidae, subfamily Terebellinae is paraphyletic with respect to Polycirrinae, supporting the suggestion that this subfamilys morphological simplicity is derived.

Relationships of Placostylus from Lord Howe Island: an investigation using the mitochondrial cytochrome c oxidase 1 gene

Large (5–9 cm in length) land snails of the genus Placostylus are found in New Caledonia and the Loyalty Islands, northern New Zealand, the Three Kings Islands just north of New Zealand and on Lord Howe Island. Their presence on Lord Howe, an oceanic island less than 6 million years old, has been an intriguing biogeographical question. Maximum parsimony and maximum likelihood analyses using cytochrome c oxidase subunit I sequence data suggest that the Lord Howe Island and mainland New Zealand taxa are sisters, but that the Three Kings taxon is independently derived, possibly from New Caledonian stock. Placostylus colonies throughout the area of the present study are under considerable threat, with many intraspecific forms and some species threatened and some listed as endangered species. The taxonomic and conservation status of the Lord Howe Island populations are discussed.

A transcriptome resource for the koala ( Phascolarctos cinereus ): insights into koala retrovirus transcription and sequence diversity

BackgroundThe koala, Phascolarctos cinereus, is a biologically unique and evolutionarily distinct Australian arboreal marsupial. The goal of this study was to sequence the transcriptome from several tissues of two geographically separate koalas, and to create the first comprehensive catalog of annotated transcripts for this species, enabling detailed analysis of the unique attributes of this threatened native marsupial, including infection by the koala retrovirus.ResultsRNA-Seq data was generated from a range of tissues from one male and one female koala and assembled de novo into transcripts using Velvet-Oases. Transcript abundance in each tissue was estimated. Transcripts were searched for likely protein-coding regions and a non-redundant set of 117,563 putative protein sequences was produced. In similarity searches there were 84,907 (72%) sequences that aligned to at least one sequence in the NCBI nr protein database. The best alignments were to sequences from other marsupials. After applying a reciprocal best hit requirement of koala sequences to those from tammar wallaby, Tasmanian devil and the gray short-tailed opossum, we estimate that our transcriptome dataset represents approximately 15,000 koala genes. The marsupial alignment information was used to look for potential gene duplications and we report evidence for copy number expansion of the alpha amylase gene, and of an aldehyde reductase gene.Koala retrovirus (KoRV) transcripts were detected in the transcriptomes. These were analysed in detail and the structure of the spliced envelope gene transcript was determined. There was appreciable sequence diversity within KoRV, with 233 sites in the KoRV genome showing small insertions/deletions or single nucleotide polymorphisms. Both koalas had sequences from the KoRV-A subtype, but the male koala transcriptome has, in addition, sequences more closely related to the KoRV-B subtype. This is the first report of a KoRV-B-like sequence in a wild population.ConclusionsThis transcriptomic dataset is a useful resource for molecular genetic studies of the koala, for evolutionary genetic studies of marsupials, for validation and annotation of the koala genome sequence, and for investigation of koala retrovirus. Annotated transcripts can be browsed and queried at http://koalagenome.org.

The phylogenetic position of Neritimorpha based on the mitochondrial genome of Nerita melanotragus (Mollusca: Gastropoda).

This is the first report of the mitochondrial gene order and almost-complete DNA sequence of a representative of the Neritimorpha, the highest-ranking gastropod clade lacking such data. Mitochondrial gene order in Nerita is largely plesiomorphic. Its only difference from the cephalopod Octopus vulgaris is a tRNA transposition shared by Vetigastropoda and Caenogastropoda. Genome arrangements were not informative enough to resolve the evolutionary relationships of Neritimorpha, Vetigastropoda and Caenogastropoda. The sister-group taxon of Neritimorpha varied in sequence-based analyses. Some suggested that Neritimorpha is the sister group of Caenogastropoda plus Heterobranchia and some that Neritimorpha and Caenogastropoda are sister groups. No analysis significantly supported the hypothesis that Vetigastroda is more closely related to Caenogastropoda than is Neritimorpha.

Setting the Molecular Phylogenetic Framework for the Dermaptera

The insect group Dermaptera is traditionally divided into the Forficulina, comprising the majority of the species, the African rodent commensals, Hemimerina, and the Indo-Malayan bat commensals, Arixeniina. Numerous contrasting classifications and phylogenies exist for the Dermaptera, based on morphological, molecular and biogeographic data. We have collected varying number of sequences from fifteen Forficulina and six outgroups to establish a molecular hypothesis of the groups phylogeny. Despite repeated attempts, we were unable to obtain sequence data for Arixeniina and Hemimerina. We obtained partial sequences for four taxa for cytochrome oxidase 1 (with two additional taxa from GenBank), twelve for 16S rDNA, fifteen for 28S rDNA expansion region 1, seven for expansion region 9-10, and nine for 18S rDNA (plus seven sequences from GenBank). In combined analyses, the root of the Dermaptera lies between Anisolabididae and other families. This position is not directly supported by bootstrap analyses. Indirect evidence for the basal position of Anisolabididae, Pygidicranidae and Apachyidae is however found in the association of the four other studied groups (Labiduridae, Spongiphoridae, Chelisochidae and Forficulidae) in a derived clade with significant bootstrap support. The division of Forficulina into Catadermaptera and Eudermaptera is not supported as the former is paraphyletic in the present analyses. Eudermaptera is monophyletic with bootstrap support but is sister group to Labiduridae, a taxon usually assigned to the Catadermaptera.

Pulmonate phylogeny based on 28S rRNA gene sequences: A framework for discussing habitat transitions and character transformation

Pulmonate snails occupy a wide range of marine, estuarine, freshwater and terrestrial environments. Non-terrestrial forms are supposed to be basal in pulmonate evolution but the groups phylogeny is not well resolved either morphologically or on the basis of available DNA sequence data. The lack of a robust phylogeny makes it difficult to understand character polarization and habitat transformation in pulmonates. We have investigated pulmonate relationships using 27 new sequences of 28S rRNA from pulmonates and outgroups, augmented with data from GenBank. The complete alignments comprised about 3.8kb. Maximum parsimony, maximum likelihood and Bayesian analyses of alignments generated under different assumptions are reported. Complete alignments appear to have a degree of substitution saturation so where there is conflict between hypothesised relationships more weight is given to analyses where regions of random similarity are excluded and which are not affected by this complication. Monophyly of the five main pulmonate groups was robustly supported in almost all analyses. The marine group Amphiboloidea and the freshwater Glacidorbidae are the most basal. The remaining pulmonates (Siphonariidae, Hygrophila and Eupulmonata) form a moderately-supported monophyletic group in all analyses bar one probably affected by saturation of substitutions. Siphonariidae, a predominantly marine and intertidal family, and Eupulmonata (mainly terrestrial with marine, estuarine and freshwater species) form a strongly supported clade that is the sister group to Hygrophila (freshwater). Multiple colonizations of freshwater and terrestrial habitats by pulmonate snails are suggested. No analyses strongly support the possibility of habitat reversions. The colonizations of freshwater by Hygrophila and of land by Stylommatophora were apparently phylogenetically independent although it cannot yet be excluded that there were transient terrestrial phases in the history of the former group or freshwater phases in the latter.

Phylogenetic relationships among the black fly species (Diptera: Simuliidae) of Thailand based on multiple gene sequences

Simulium is a very speciose genus of the black fly family Simuliidae that includes many important pests of humans and animals. Cytotaxonomic and morphological studies have made substantial progress in Simulium systematics. 16S rRNA and ITS-1 DNA sequence studies have assisted this progress. Intensive multi-gene molecular systematic investigations will, however, be required for a comprehensive understanding of the genus’ taxonomy and evolution. Our research was conducted to investigate the relationships of Thai Simulium at the subgeneric, species group and species levels. We also examined the possibility of using mitochondrial DNA sequences to facilitate Simulium species identification. Data were collected from three mitochondrial genes (COI, ND4 and 16S rRNA) and two segments of the nuclear 28S ribosomal RNA (the D1 to D2 and the D4 expansion regions). The subgenera Simulium and Gomphostilbia were monophyletic in most analyses. Nevermannia included Montisimulium but was otherwise monophyletic in multigene analyses. In most analyses, Simulium and Nevermannia were more closely related to each other than to Gomphostilbia which was usually basal. Species groups were generally monophyletic. Within Gomphostilbia, however, the batoense species group was always paraphyletic to the other two species groups found in Thailand. Three species groups in Simulium were not monophyletic. The tendency to gill filament number reduction for some species groups in the subgenus Simulium was associated with a derived position in multigene analyses. Most species were monophyletic with two exceptions that probably represent species complexes and will present difficulties for rapid mitochondrial DNA identification.