The species representation of public databases is growing rapidly and permits increasingly detailed phylogenetic inferences. We present a supermatrix based on all gene sequences of Coleoptera available in Genbank for two nuclear (18S and 28S rRNA) and two mitochondrial (rrnL and cox1) genes. After filtering for unique species names and the addition of ˜2000 unpublished sequences for cox1 and 18S rRNA, the resulting data matrix included 8441 species‐level terminals and 6600 aligned nucleotide positions. The concatenated matrix represents the equivalent of 2.17% of the 390 000 described species of Coleoptera and includes 152 beetle families. The remaining 29 families constitute small lineages with ˜250 known species in total. Taxonomic coverage remains low for several major lineages, including Buprestidae (0.16% of described species), Staphylinidae (1.03%), Tenebrionidae (0.90%) and Cerambycidae (0.58%). The current taxon sampling was strongly biased towards the Northern Hemisphere. Phylogenetic trees obtained from the supermatrix were in very good agreement with the Linnaean classification, in particular at the family level, but lower for the subfamily and lowest for the genus level. The topology supports the basal split of Derodontidae and Scirtoidea from the remaining Polyphaga, and the broad paraphyly of Cucujoidea. The data extraction pipeline and detailed tree provide a framework for placement of any new sequences, including environmental samples, into a DNA‐based classification system of Coleoptera.

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.

Six research plots were established on a surface mine for the purpose of evaluating the forest productivity potential and hydrological and water quality characteristics of three different loose-graded spoil types. The three spoil types were: (1) predominately brown, weathered sandstone (BROWN); (2) predominately gray, un-weathered sandstone (GRAY); and (3) mixed weathered and un-weathered sandstones and shale material (MIXED). The average area of the six plots was approximately 3,658 m 2 . The physical and chemical soil characteristics that gave the BROWN spoil type a predictably higher productivity potential and natural regeneration than the GRAY and MIXED spoil were its finer soil texture, higher CEC and P concentration, and a pH that was more suitable for native hardwood trees. Four species of tree seedlings were planted into the spoils. Growth and survival of the planted trees were evaluated for three years. As an indicator of natural succession potential, percentage ground cover of volunteer vegetation on the three spoil types was also evaluated. By the third year (2007) after planting, the BROWN spoil type had a significantly higher average tree volume index than the MIXED spoil and MIXED was significantly higher than GRAY. Ground cover from natural regeneration was found to be 66.4% on the BROWN spoil (61 different species), 5.8% on the MIXED spoil (35 different species), and less than 2.0% on the GRAY spoil (12 different species). Results showed that the loose-graded spoil in this experiment was characterized by low discharge volumes, small peak discharges, and long durations of discharge and had hydrologic characteristics of a forested watershed, even at this early stage of development. Generally, concentrations of Ca, Mg, and SO 4 2-decreased over time in GRAY and MIXED and increased in BROWN. The pH of the water discharge from all three spoil types has increased from about 7.5 to 8.5. Although the average electrical conductivity (EC) in water discharged from the BROWN spoil remained relatively level during the study period, the GRAY and MIXED appears to be on a downward trajectory from about 1500 µS cm -1 to about 500 µS cm -1 . The latter value of EC has been reported as the apparent threshold at which the benthic invertebrate community returns to drastically disturbed headwater streams of eastern Kentucky and adjacent coal-producing Appalachian states.

Abstract. In 1996, a multidisciplinary group of researchers at the University of Kentucky initiated a study on the Starfire surface mine in eastern Kentucky to evaluate the effects of soil compaction and two organic amendments on the survivability and growth of high value tree species. Three types of prepared rooting medium were examined: compacted spoil, lightly compacted spoil, and uncompacted spoil. The compacted spoil was prepared using normally accepted spoil handling techniques that resulted in a smooth graded surface. The lightly compacted spoil was loose-dumped and struck-off with one or two passes of a bulldozer. The uncompacted spoil was loose-dumped and not further disturbed. In addition, organic amendments (mulches) were evaluated within the three reclamation techniques. The organic amendments used were processed hardwood bark mulch and a combination of straw and horse manure mulch. The following six species of trees were planted: white oak (Quercus alba), white ash (Fraxinus americana), eastern white pine (Pinus strobus), northern red oak (Quercus rubra), black walnut (Juglans nigra), and yellow poplar (Liriodendron tulipifera). Five of the six species, the exception being white ash, showed increased survivability as compaction was minimized. Additionally, the loose-graded techniques led to enhanced growth in height for the seedlings. The addition of organic amendments also showed additional benefit but results varied by species and by treatment. Results definitively show that strike-off and loose-dump techniques improve seedling height and survival. The data also suggest that even a small amount of traffic (i.e., one or two passes per the strike-off method) may result in enough compaction to significantly reduce survival and growth in some species, such as yellow poplar and white pine. In the backfilling and grading process, spoil material should be placed and compacted according to standard engineering practices so that the required stability and approximate original contour is achieved. However, the top 1.2 to 1.8 meters (4 to 6 feet) of material should not be graded or only lightly graded so that it is as uncompacted as possible.

A phylogenetic tree at the species level is still far off for highly diverse insect orders, including the Coleoptera, but the taxonomic breadth of public sequence databases is growing. In addition, new types of data may contribute to increasing taxon coverage, such as metagenomic shotgun sequencing for assembly of mitogenomes from bulk specimen samples. The current study explores the application of these techniques for large-scale efforts to build the tree of Coleoptera. We used shotgun data from 17 different ecological and taxonomic datasets (5 unpublished) to assemble a total of 1942 mitogenome contigs of >3000 bp. These sequences were combined into a single dataset together with all mitochondrial data available at GenBank, in addition to nuclear markers widely used in molecular phylogenetics. The resulting matrix of nearly 16,000 species with two or more loci produced trees (RAxML) showing overall congruence with the Linnaean taxonomy at hierarchical levels from suborders to genera. We tested the role of full-length mitogenomes in stabilizing the tree from GenBank data, as mitogenomes might link terminals with non-overlapping gene representation. However, the mitogenome data were only partly useful in this respect, presumably because of the purely automated approach to assembly and gene delimitation, but improvements in future may be possible by using multiple assemblers and manual curation. In conclusion, the combination of data mining and metagenomic sequencing of bulk samples provided the largest phylogenetic tree of Coleoptera to date, which represents a summary of existing phylogenetic knowledge and a defensible tree of great utility, in particular for studies at the intra-familial level, despite some shortcomings for resolving basal nodes.