Family-level sampling of mitochondrial genomes in coleoptera: compositional heterogeneity and phylogenetics

Mitochondrial genomes are readily sequenced with recent technology and thus evolutionary lineages can be sampled more densely. 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 (‘non-homogeneous’) 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, whilst 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

Single-Cell-Genomics-Facilitated Read Binning of Candidate Phylum EM19 Genomes from Geothermal Spring Metagenomes

The vast majority of microbial life remains uncatalogued due to the inability to cultivate these organisms in the laboratory. This “microbial dark matter” represents a substantial portion of the tree of life and of the populations that contribute to chemical cycling in many ecosystems. In this work, we leveraged an existing single-cell genomic data set representing the candidate bacterial phylum “Calescamantes” (EM19) to calibrate machine learning algorithms and define metagenomic bins directly from pyrosequencing reads derived from Great Boiling Spring in the U.S. Great Basin. Compared to other assembly-based methods, taxonomic binning with a read-based machine learning approach yielded final assemblies with the highest predicted genome completeness of any method tested. Read-first binning subsequently was used to extract Calescamantes bins from all metagenomes with abundant Calescamantes populations, including metagenomes from Octopus Spring and Bison Pool in Yellowstone National Park and Gongxiaoshe Spring in Yunnan Province, China. Metabolic reconstruction suggests that Calescamantes are heterotrophic, facultative anaerobes, which can utilize oxidized nitrogen sources as terminal electron acceptors for respiration in the absence of oxygen and use proteins as their primary carbon source. Despite their phylogenetic divergence, the geographically separate Calescamantes populations were highly similar in their predicted metabolic capabilities and core gene content, respiring O2, or oxidized nitrogen species for energy conservation in distant but chemically similar hot springs.This work was supported by NASA exobiology grant EXO-NNX11AR78G, U.S. National Science Foundation grant OISE 0968421, and U.S. Department of Energy grant DE-EE-0000716. B.P.H. acknowledges generous support from Greg Fullmer through the UNLV Foundation, and W.S. acknowledges Northern Illinois University for funding. B.P.H and S.K.M. acknowledge support from an Amazon Web Services Education Research Grant award. The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231. This article is made openly accessible in part by an award from the Northern Illinois University Libraries’ Open Access Publishing Fund

Mirrored one-nucleon knockout reactions to the T-z = +/- 3/2 A=53 mirror nuclei

Background: The study of excited states in mirror nuclei allows us to extract information on charge-dependent (i.e., isospin-nonconserving) interactions in nuclei. Purpose: To extend previous studies of mirror nuclei in the f72 region, investigating charge symmetry breaking of the strong nuclear force. Methods: γ-ray spectroscopy has been performed for the mirror (Tz=±32) pair Ni53 and Mn53, produced via mirrored one-nucleon knockout reactions. Results: Several new transitions have been identified in Ni53 from which a new level scheme has been constructed. Cross sections for knockout have been analyzed and compared with reaction model calculations where evidence is found for knockout from high-spin isomeric states. Mirror energy differences between isobaric analog states have been computed, compared to large scale shell-model calculations, and interpreted in terms of isospin-nonconserving effects. In addition, lifetimes for the long-lived Jπ=52−1 analog states in both Mn53 and Ni53 have been extracted through lineshape analysis, giving half-lives of t12=120(14) ps and t12=198(12) ps, respectively. Conclusions: The inclusion of a set of isovector isospin-nonconserving matrix elements to the shell-model calculations gave the best agreement with the experimental data

Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage

OP9 is a yet-uncultivated bacterial lineage found in geothermal systems, petroleum reservoirs, anaerobic digesters and wastewater treatment facilities. Here we use single-cell and metagenome sequencing to obtain two distinct, nearly complete OP9 genomes, one constructed from single cells sorted from hot spring sediments and the other derived from binned metagenomic contigs from an in situ-enriched cellulolytic, thermophilic community. Phylogenomic analyses support the designation of OP9 as a candidate phylum for which we propose the name ‘Atribacteria’. Although a plurality of predicted proteins is most similar to those from Firmicutes, the presence of key genes suggests a diderm cell envelope. Metabolic reconstruction from the core genome suggests an anaerobic lifestyle based on sugar fermentation by Embden–Meyerhof glycolysis with production of hydrogen, acetate and ethanol. Putative glycohydrolases and an endoglucanase may enable catabolism of (hemi)cellulose in thermal environments. This study lays a foundation for understanding the physiology and ecological role of the ‘Atribacteria’.United States. National Aeronautics and Space Administration (Exobiology Grant EXO-NNX11AR78G)National Science Foundation (U.S.) (Grant MCB 0546865)National Science Foundation (U.S.) (Grant OISE 0968421)United States. Dept. of Energy (Grant DE-EE-0000716)Nevada Renewable Energy ConsortiumUnited States. Dept. of Energy. Office of Science. Joint Genome Institute (Contract DE-AC02-05CH11231

The climatic challenge: which plants will people use in the next century?

More than 31,000 useful plant species have been documented to fulfil needs and services for humans or the animals and environment we depend on. Despite this diversity, humans currently satisfy most requirements with surprisingly few plant species; for example, just three crops – rice, wheat and maize – comprise more than 50% of plant derived calories. Here, we synthesize the projected impact of global climatic change on useful plants across the spectrum of plant domestication. We illustrate the demographic, spatial, ecophysiological, chemical, functional, evolutionary and cultural traits that are likely to characterise useful plants and their resilience in the next century. Using this framework, we consider a range of possible pathways for future human use of plants. These are centred on two trade-offs: i) diversification versus specialization in the range of species we utilize, and ii) substitutionof the species towards those better suited to future climate versus facilitating adaptation in our existing suite of dominant useful plants. In the coming century, major challenges to agriculture and biodiversity will be dominated by increased climatic variation, shifting species ranges, disruption to biotic interactions, nutrient limitation and emerging pests and pathogens. These challenges must be mitigated, whilst enhancing sustainable production to meet the needs of a growing population and a more resource intensive standard of living. With the continued erosion of biodiversity, our future ability to choose among these pathways and trade-offs is likely to be diminished

Time-calibrated phylogenetic trees establish a lag between polyploidisation and diversification in Nicotiana (Solanaceae)

We investigate the timing of diversification in allopolyploids of Nicotiana (Solanaceae) utilising sequence data of maternal and paternal origin to look for evidence of a lag phase during which diploidisation took place. Bayesian relaxed clock phylogenetic methods show recent allopolyploids are a result of several unique polyploidisation events, and older allopolyploid sections have undergone subsequent speciation at the polyploid level (i.e. a number of these polyploid species share a singular origin). The independently formed recent polyploid species in the genus all have mean age estimates below 1 million years ago (Ma). Nicotiana  section Polydicliae (two species) evolved 1.5 Ma, N. section Repandae (four species) formed 4 Ma, and N. section Suaveolentes (*35 species) is about 6 million years old. A general trend of higher speciation rates in older polyploids is evident, but diversification dramatically increases at approximately 6 Ma (in section Suaveolentes). Nicotiana sect. Suaveolentes has spectacularly radiated to form 35 species in Australia and some Pacific islands following a lag phase of almost 6 million years. Species have filled new ecological niches and undergone extensive diploidisation (e.g. chromosome fusions bringing the ancestral allotetraploid number, n = 24, down to n = 15 and ribosomal loci numbers back to diploid condition). Considering the progenitors of Suaveolentes inhabit South America, this represents the colonisation of Australia by polyploids that have subsequently undergone a recent radiation into new environments. To our knowledge, this study is the first report of a substantial lag phase being investigated below the family level

Mirrored one-nucleon knockout reactions to the Tz=± 32 A=53 mirror nuclei

Background: The study of excited states in mirror nuclei allows us to extract information on charge-dependent (i.e., isospin-nonconserving) interactions in nuclei. Purpose: To extend previous studies of mirror nuclei in the f72 region, investigating charge symmetry breaking of the strong nuclear force. Methods: γ-ray spectroscopy has been performed for the mirror (Tz=±32) pair Ni53 and Mn53, produced via mirrored one-nucleon knockout reactions. Results: Several new transitions have been identified in Ni53 from which a new level scheme has been constructed. Cross sections for knockout have been analyzed and compared with reaction model calculations where evidence is found for knockout from high-spin isomeric states. Mirror energy differences between isobaric analog states have been computed, compared to large scale shell-model calculations, and interpreted in terms of isospin-nonconserving effects. In addition, lifetimes for the long-lived Jπ=521- analog states in both Mn53 and Ni53 have been extracted through lineshape analysis, giving half-lives of t12=120(14) ps and t12=198(12) ps, respectively. Conclusions: The inclusion of a set of isovector isospin-nonconserving matrix elements to the shell-model calculations gave the best agreement with the experimental data

Parent Stars of Extrasolar Planets VII: New Abundance Analyses of 30 Systems

The results of new spectroscopic analyses of 30 stars with giant planet and/or brown dwarf companions are presented. Values for Teff and [Fe/H] are used in conjunction with Hipparcos data and Padova isochrones to derive masses, ages, and theoretical surface gravities. These new data are combined with spectroscopic and photometric metallicity estimates of other stars harboring planets and published samples of F, G, and K dwarfs to compare several subsets of planet bearing stars with similarly well-constrained control groups. The distribution of [Fe/H] values continues the trend uncovered in previous studies in that stars hosting planetary companions have a higher mean value than otherwise similar nearby stars. We also investigate the relationship between stellar mass and the presence of giant planets and find statistically marginal but suggestive evidence of a decrease in the incidence of radial velocity companions orbiting relatively less massive stars. If confirmed with larger samples, this would represent a critical constraint to both planetary formation models as well as to estimates of the distribution of planetary systems in our galaxy.Comment: 27 pages, 13 figures. Accepted for publication in The Astronomical Journa