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Mitochondrial genomes are readily sequenced with recent technology and thus evolutionary lineages can be densely sampled. This permits better phylogenetic estimates and assessment of potential biases resulting from heterogeneity in nucleotide composition and rate of change. We gathered 245 mitochondrial sequences for the Coleoptera representing all 4 suborders, 15 superfamilies of Polyphaga, and altogether 97 families, including 159 newly sequenced full or partial mitogenomes. Compositional heterogeneity greatly affected 3rd codon positions, and to a lesser extent the 1st and 2nd positions, even after RY coding. Heterogeneity also affected the encoded protein sequence, in particular in the nad2, nad4, nad5, and nad6 genes. Credible tree topologies were obtained with the nhPhyML ("nonhomogeneous") algorithm implementing a model for branch-specific equilibrium frequencies. Likelihood searches using RAxML were improved by data partitioning by gene and codon position. Finally, the PhyloBayes software, which allows different substitution processes for amino acid replacement at various sites, produced a tree that best matched known higher level taxa and defined basal relationships in Coleoptera. After rooting with Neuropterida outgroups, suborder relationships were resolved as (Polyphaga (Myxophaga (Archostemata + Adephaga))). The infraorder relationships in Polyphaga were (Scirtiformia (Elateriformia ((Staphyliniformia + Scarabaeiformia) (Bostrichiformia (Cucujiformia))))). Polyphagan superfamilies were recovered as monophyla except Staphylinoidea (paraphyletic for Scarabaeiformia) and Cucujoidea, which can no longer be considered a valid taxon. The study shows that, although compositional heterogeneity is not universal, it cannot be eliminated for some mitochondrial genes, but dense taxon sampling and the use of appropriate Bayesian analyses can still produce robust phylogenetic trees.

The family Sporormiaceae (Pleosporales, Dothideomycetes, Ascomycota) occur worldwide and a majority of the species are coprophilous. The taxonomy and classification of the family are based on a small number of morphological and ecological characters. Several taxa are easily confused by their shared morphological features, and the relationships between genera are poorly known and in need of critical study. The aims of this study were to resolve the phylogenetic relationships within the Sporormiaceae, test the current generic classification, and study the utility of traditional characters for the taxonomy in the group. To resolve these questions, we analysed combined data sets of ITS-nLSU rDNA, mtSSU rDNA and beta-tubulin sequences with parsimony and Bayesian methods. The results showed that many characters, which previously have been used in the taxonomy and classification of the Sporormiaceae, such as the substrate choice, presence or absence of an ostiole, and presence or absence of germ slits, were all homoplastic and not useful for circumscribing monophyletic groups. A number of characters may be useful for circumscribing smaller clades if used in combination with other features, such as the shape of the ascus with the shape of the ascospores. Our phylogenetic analyses show that Preussia and Sporormiella are non-monophyletic, and a constrained analysis forcing these genera into monophyly resulted in significantly worse trees. Spororminula is nested in Preussia s. lat., and Eremodothis and Pycnidiophora are nested within Westerdykella. Finally, we suggest a new generic classification for the family Sporormiaceae, including Sporormia, Preussia (including Sporomiella and Spororminula) and Westerdykella (including Eremodothis and Pycnidiophora). We also propose 14 new combinations: Preussia alloiomera (S.I. Ahmed & Cain) Kruys, Preussia antarctica (Speg.) Kruys, Preussia bipartis (Cain) Kruys, Preussia borealis (I.Egeland) Kruys, Preussia dubia (S.I. Ahmed &

We present a comprehensive phylogeny derived from 5 genes, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, for 356 isolates and 41 families (six newly described in this volume) in Dothideomycetes. All currently accepted orders in the class are represented for the first time in addition to numerous previously unplaced lineages. Subclass Pleosporomycetidae is expanded to include the aquatic order Jahnulales. An ancestral reconstruction of basic nutritional modes supports numerous transitions from saprobic life histories to plant associated and lichenised modes and a transition from terrestrial to aquatic habitats are confirmed. Finally, a genomic comparison of 6 dothideomycete genomes with other fungi finds a high level of unique protein associated with the class, supporting its delineation as a separate taxon

The aim of this study was to describe mitotic and meiotic chromosomes of Cycloneda sanguinea using C-banding, flourescent in situ hybridization (FISH) rDNA probes, and sequential FISH/Ag-NOR staining. The chromosome number was 2n = 18 + XX for females and 2n = 18 + Xy for males. The X chromosome was metacentric and the Y chromosome was very small. During meiosis, the karyotypic meioformula was n = 9 + Xyp, and sex chromosomes configured a parachute at metaphase I. At the beginning of pachytene, bivalents were still individualized, and sex chromosomes were associated end-to-end through the heteropycnotic region of the X chromosome. Later in pachytene, further condensation led to the formation of a pseudo-ring by the sex bivalent. All chromosomes showed pericentromeric heterochromatin. FISH and sequential FISH/Ag-NOR staining evidenced the location of the nucleolar organizer region in one pair of autosomes (at spermatogonial metaphase). During meiosis, these genes were mapped to a region outside the sex vesicle by FISH, although Xyp was deeply stained with silver at metaphase I. These results suggest that these argyrophilic substances are of a nucleolar protein nature, and seem to be synthesized by a pair of autosomes and imported during meiosis (prophase I) to the sex pair, during the association of the sex chromosomes. Copyright by the Brazilian Society of Genetics.

The aim of this study was to describe mitotic and meiotic chromosomes of Cycloneda sanguinea using C-banding, flourescent in situ hybridization (FISH) rDNA probes, and sequential FISH/Ag-NOR staining. The chromosome number was 2n = 18 + XX for females and 2n = 18 + Xy for males. The X chromosome was metacentric and the Y chromosome was very small. During meiosis, the karyotypic meioformula was n = 9 + Xyp, and sex chromosomes configured a parachute at metaphase I. At the beginning of pachytene, bivalents were still individualized, and sex chromosomes were associated end-to-end through the heteropycnotic region of the X chromosome. Later in pachytene, further condensation led to the formation of a pseudo-ring by the sex bivalent. All chromosomes showed pericentromeric heterochromatin. FISH and sequential FISH/Ag-NOR staining evidenced the location of the nucleolar organizer region in one pair of autosomes (at spermatogonial metaphase). During meiosis, these genes were mapped to a region outside the sex vesicle by FISH, although Xyp was deeply stained with silver at metaphase I. These results suggest that these argyrophilic substances are of a nucleolar protein nature, and seem to be synthesized by a pair of autosomes and imported during meiosis (prophase I) to the sex pair, during the association of the sex chromosomes. Copyright by the Brazilian Society of Genetics.