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https://www.readbyqxmd.com/read/28742928/shotgun-mitogenomics-across-body-size-classes-in-a-local-assemblage-of-tropical-diptera-phylogeny-species-diversity-and-mitochondrial-abundance-spectrum
#1
Le Qin Choo, Alex Crampton-Platt, Alfried P Vogler
Mitochondrial genomes can be assembled readily from shotgun sequenced DNA mixtures of mass-trapped arthropods ('mitochondrial metagenomics'), speeding up the taxonomic characterization. Bulk sequencing was conducted on some 800 individuals of Diptera obtained by canopy-fogging of a single tree in Borneo dominated by small (<1.5 mm) individuals. Specimens were split into five body-size classes for DNA extraction, to equalize read numbers across specimens and to study how body size, a key ecological trait, interacts with species and phylogenetic diversity...
July 25, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28742843/sequencing-of-the-complete-mitochondrial-genomes-of-eight-freshwater-snail-species-exposes-pervasive-paraphyly-within-the-viviparidae-family-caenogastropoda
#2
Ju-Guang Wang, Dong Zhang, Ivan Jakovlić, Wei-Min Wang
Phylogenetic relationships among snails (Caenogastropoda) are still unresolved, and many taxonomic categories remain non-monophyletic. Paraphyly has been reported within a large family of freshwater snails, Viviparidae, where the taxonomic status of several species remains questionable. As many endemic Chinese viviparid species have become endangered during the last few decades, this presents a major obstacle for conservation efforts. Mitochondrial genomes (mitogenomes) carry a large amount of data, so they can often provide a much higher resolution for phylogenetic analyses in comparison to the traditionally used molecular markers...
2017: PloS One
https://www.readbyqxmd.com/read/28742006/flavobacterium-soyangense-sp-nov-a-psychrotolerant-bacterium-isolated-from-an-oligotrophic-freshwater-lake
#3
Gi Gyun Nam, Yochan Joung, Miri Park, Suhyun Kim, Hyoung Tae Jeon, Jang-Cheon Cho
A bacterial strain, designated IMCC26223T, was isolated from an oligotrophic freshwater lake, Lake Soyang, Korea. Cells of strain IMCC26223T were Gram-staining negative, strictly aerobic, non-motile and short-rod-shaped. Growth occurred at pH 6-8 (optimum, pH 7.0), at 4-25 °C (optimum, 15 °C) and with 0-0.5 % (w/v) NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain IMCC26223T was identified as a member of the genus Flavobacterium and most closely related to Flavobacterium fluvii H7T (97...
July 26, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28741861/parvularia-atlantis-gen-et-sp-nov-a-nucleariid-filose-amoeba-holomycota-opisthokonta
#4
David López-Escardó, Purificación López-García, David Moreira, Iñaki Ruiz-Trillo, Guifré Torruella
The opisthokonts constitute a eukaryotic supergroup divided into two main clades: the holozoans, which include animals and their unicellular relatives, and the holomycotans, which include fungi, opisthosporidians and nucleariids. Nucleariids are phagotrophic filose amoebae that phenotypically resemble more their distant holozoan cousins than their holomycotan phylogenetic relatives. Despite their evolutionary interest, the diversity and internal phylogenetic relationships within the nucleariids remain poorly studied...
July 25, 2017: Journal of Eukaryotic Microbiology
https://www.readbyqxmd.com/read/28739372/an-improved-and-general-streamlined-phylogenetic-protocol-applied-to-the-fatty-acid-desaturase-family
#5
Matthew Wilding, Matthias Nachtschatt, Robert Speight, Colin Scott
Numerous tools to generate phylogenetic estimates are available, but there is no single protocol that will produce an accurate phylogenetic tree for any dataset. Here, we investigated some of those tools, paying particular attention to different alignment algorithms, in order to produce a phylogeny for the integral membrane fatty acid desaturase (FAD) family. Herein, we report a novel streamlined protocol which utilises peptide pattern recognition (PPR). This protocol can theoretically be applied universally to generate accurate multiple sequence alignments and improve downstream phylogenetic analyses...
July 21, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28738824/visibiome-an-efficient-microbiome-search-engine-based-on-a-scalable-distributed-architecture
#6
Syafiq Kamarul Azman, Muhammad Zohaib Anwar, Andreas Henschel
BACKGROUND: Given the current influx of 16S rRNA profiles of microbiota samples, it is conceivable that large amounts of them eventually are available for search, comparison and contextualization with respect to novel samples. This process facilitates the identification of similar compositional features in microbiota elsewhere and therefore can help to understand driving factors for microbial community assembly. RESULTS: We present Visibiome, a microbiome search engine that can perform exhaustive, phylogeny based similarity search and contextualization of user-provided samples against a comprehensive dataset of 16S rRNA profiles environments, while tackling several computational challenges...
July 24, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28735426/diet-versus-phylogeny-a-comparison-of-gut-microbiota-in-captive-colobine-monkey-species
#7
Vanessa L Hale, Chia L Tan, Kefeng Niu, Yeqin Yang, Rob Knight, Qikun Zhang, Duoying Cui, Katherine R Amato
Both diet and host phylogeny shape the gut microbial community, and separating out the effects of these variables can be challenging. In this study, high-throughput sequencing was used to evaluate the impact of diet and phylogeny on the gut microbiota of nine colobine monkey species (N = 64 individuals). Colobines are leaf-eating monkeys that fare poorly in captivity-often exhibiting gastrointestinal (GI) problems. This study included eight Asian colobines (Rhinopithecus brelichi, Rhinopithecus roxellana, Rhinopithecus bieti, Pygathrix nemaeus, Nasalis larvatus, Trachypithecus francoisi, Trachypithecus auratus, and Trachypithecus vetulus) and one African colobine (Colobus guereza)...
July 22, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28735325/characterization-of-endolithic-culturable-microbial-communities-in-carbonate-rocks-from-a-typical-karst-canyon-in-guizhou-china
#8
Yuan Tang, Jian-Zhong Cheng, Bin Lian
The endolithic environment is a ubiquitous habitat for microorganisms and a critical interface between biology and geology. In this study, a culture-based method and the phylogenetic analysis based on 16S rRNA and internal transcribed spacer (ITS) sequences were used to investigate the diversity of endolithic bacteria and fungi in two main types of carbonate rocks (namely dolomite and limestone) from Nanjiang Canyon in Guizhou karst area, China. The results of bacterial diversity indicated that all bacteria isolated from dolomite and limestone rocks were divided into 4 bacterial groups, including Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes...
January 2, 2017: Polish Journal of Microbiology
https://www.readbyqxmd.com/read/28734138/ghrelin-plasma-concentration-does-not-covary-with-energy-demand-in-adult-laying-hens
#9
A Höhne, L Schrader, S Weigend, S Petow
The peptide hormone ghrelin is suggested to be involved in food intake regulation in young growing chicken. Whether ghrelin is involved in the regulation of energetic balance associated with laying performance in adult laying hens was studied by use of 4 chicken lines that differ in laying performance and phylogeny (4 lines; 16 hens per line). As housing conditions are also known to affect energy demand, half of the hens per line were housed in single cages and the other half of hens were maintained in a floor housing system...
June 29, 2017: Domestic Animal Endocrinology
https://www.readbyqxmd.com/read/28733989/detecting-ancient-co-dispersals-and-host-shifts-by-double-dating-of-host-and-parasite-phylogenies-application-in-proctophyllodid-feather-mites-associated-with-passerine-birds
#10
Pavel B Klimov, Sergey V Mironov, Barry M OConnor
Inferring co-phylogeographic events requires matching the timing of these events on both host and symbiont (e.g., parasites) phylogenies because divergences of hosts and their symbionts may not temporally coincide, and host switches may occur. We investigate a large radiation of birds (Passeriformes) and their permanent symbionts, the proctophyllodid feather mites (117 species from 116 bird species; 6 genes, 11,468 nt aligned) using two time-calibration strategies for mites: fossils only and host phylogeography only...
July 22, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28733783/perianth-organs-in-nymphaeaceae-comparative-study-on-epidermal-and-structural-characters
#11
Lucía Melisa Zini, Beatriz Gloria Galati, María Silvia Ferrucci
The perianth organs of six species of Nymphaeaceae, representing Euryale, Nymphaea and Victoria, were studied on the basis of macroscopical, micromorphological, and anatomical characters. The aims were to determine whether perianth is differentiated among tepal whorls considering the presence of sepaloid and petaloid characters, and to evaluate the occurrence of both features in individual tepals. Selected perianth series were examined macroscopically, with light microscopy, and scanning electron microscopy...
July 21, 2017: Journal of Plant Research
https://www.readbyqxmd.com/read/28732465/genome-wide-signals-of-positive-selection-in-strongylocentrotid-sea-urchins
#12
Kord M Kober, Grant H Pogson
BACKGROUND: Comparative genomics studies investigating the signals of positive selection among groups of closely related species are still rare and limited in taxonomic breadth. Such studies show great promise in advancing our knowledge about the proportion and the identity of genes experiencing diversifying selection. However, methodological challenges have led to high levels of false positives in past studies. Here, we use the well-annotated genome of the purple sea urchin, Strongylocentrotus purpuratus, as a reference to investigate the signals of positive selection at 6520 single-copy orthologs from nine sea urchin species belonging to the family Strongylocentrotidae paying careful attention to minimizing false positives...
July 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28731793/phylogeny-traits-and-biodiversity-of-a-neotropical-bat-assemblage-close-relatives-show-similar-responses-to-local-deforestation
#13
Hannah K Frank, Luke O Frishkoff, Chase D Mendenhall, Gretchen C Daily, Elizabeth A Hadly
If species' evolutionary pasts predetermine their responses to evolutionarily novel stressors, then phylogeny could predict species survival in an increasingly human-dominated world. To understand the role of phylogenetic relatedness in structuring responses to rapid environmental change, we focused on assemblages of Neotropical bats, an ecologically diverse and functionally important group. We examined how taxonomic and phylogenetic diversity shift between tropical forest and farmland. We then explored the importance of evolutionary history by ascertaining whether close relatives share similar responses to environmental change and which species traits might mediate these trends...
August 2017: American Naturalist
https://www.readbyqxmd.com/read/28731792/the-evolution-of-energetic-scaling-across-the-vertebrate-tree-of-life
#14
Josef C Uyeda, Matthew W Pennell, Eliot T Miller, Rafael Maia, Craig R McClain
Metabolism is the link between ecology and physiology-it dictates the flow of energy through individuals and across trophic levels. Much of the predictive power of metabolic theories of ecology derives from the scaling relationship between organismal size and metabolic rate. There is growing evidence that this scaling relationship is not universal, but we have little knowledge of how it has evolved over macroevolutionary time. Here we develop a novel phylogenetic comparative method to investigate how often and in which clades the macroevolutionary dynamics of the metabolic scaling have changed...
August 2017: American Naturalist
https://www.readbyqxmd.com/read/28731473/ninety-nine-de-novo-assembled-genomes-from-the-moose-alces-alces-rumen-microbiome-provide-new-insights-into-microbial-plant-biomass-degradation
#15
Olov Svartström, Johannes Alneberg, Nicolas Terrapon, Vincent Lombard, Ino de Bruijn, Jonas Malmsten, Ann-Marie Dalin, Emilie El Muller, Pranjul Shah, Paul Wilmes, Bernard Henrissat, Henrik Aspeborg, Anders F Andersson
The moose (Alces alces) is a ruminant that harvests energy from fiber-rich lignocellulose material through carbohydrate-active enzymes (CAZymes) produced by its rumen microbes. We applied shotgun metagenomics to rumen contents from six moose to obtain insights into this microbiome. Following binning, 99 metagenome-assembled genomes (MAGs) belonging to 11 prokaryotic phyla were reconstructed and characterized based on phylogeny and CAZyme profile. The taxonomy of these MAGs reflected the overall composition of the metagenome, with dominance of the phyla Bacteroidetes and Firmicutes...
July 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28731469/novel-chaperonins-are-prevalent-in-the-virioplankton-and-demonstrate-links-to-viral-biology-and-ecology
#16
Rachel L Marine, Daniel J Nasko, Jeffrey Wray, Shawn W Polson, K Eric Wommack
Chaperonins are protein-folding machinery found in all cellular life. Chaperonin genes have been documented within a few viruses, yet, surprisingly, analysis of metagenome sequence data indicated that chaperonin-carrying viruses are common and geographically widespread in marine ecosystems. Also unexpected was the discovery of viral chaperonin sequences related to thermosome proteins of archaea, indicating the presence of virioplankton populations infecting marine archaeal hosts. Virioplankton large subunit chaperonin sequences (GroELs) were divergent from bacterial sequences, indicating that viruses have carried this gene over long evolutionary time...
July 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28729857/nutrient-acquisition-and-the-metabolic-potential-of-photoferrotrophic-chlorobi
#17
Katharine J Thompson, Rachel L Simister, Aria S Hahn, Steven J Hallam, Sean A Crowe
Anoxygenic photosynthesis evolved prior to oxygenic photosynthesis and harnessed energy from sunlight to support biomass production on the early Earth. Models that consider the availability of electron donors predict that anoxygenic photosynthesis using Fe(II), known as photoferrotrophy, would have supported most global primary production before the proliferation of oxygenic phototrophs at approximately 2.3 billion years ago. These photoferrotrophs have also been implicated in the deposition of banded iron formations, the world's largest sedimentary iron ore deposits that formed mostly in late Archean and early Proterozoic Eons...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28729652/a-genomic-glance-through-the-fog-of-plasticity-and-diversification-in-pocillopora
#18
Erika C Johnston, Zac H Forsman, Jean-François Flot, Sebastian Schmidt-Roach, Jorge H Pinzón, Ingrid S S Knapp, Robert J Toonen
Scleractinian corals of the genus Pocillopora (Lamarck, 1816) are notoriously difficult to identify morphologically with considerable debate on the degree to which phenotypic plasticity, introgressive hybridization and incomplete lineage sorting obscure well-defined taxonomic lineages. Here, we used RAD-seq to resolve the phylogenetic relationships among seven species of Pocillopora represented by 15 coral holobiont metagenomic libraries. We found strong concordance between the coral holobiont datasets, reads that mapped to the Pocillopora damicornis (Linnaeus, 1758) transcriptome, nearly complete mitochondrial genomes, 430 unlinked high-quality SNPs shared across all Pocillopora taxa, and a conspecificity matrix of the holobiont dataset...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729611/cryptic-speciation-in-pan-tropical-sea-urchins-a-case-study-of-an-edge-of-range-population-of-tripneustes-from-the-kermadec-islands
#19
Omri Bronstein, Andreas Kroh, Barbara Tautscher, Libby Liggins, Elisabeth Haring
Tripneustes is one of the most abundant and ecologically significant tropical echinoids. Highly valued for its gonads, wild populations of Tripneustes are commercially exploited and cultivated stocks are a prime target for the fisheries and aquaculture industry. Here we examine Tripneustes from the Kermadec Islands, a remote chain of volcanic islands in the southwest Pacific Ocean that mark the boundary of the genus' range, by combining morphological and genetic analyses, using two mitochondrial (COI and the Control Region), and one nuclear (bindin) marker...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28728885/characterization-of-the-neuropeptidome-of-a-southern-ocean-decapod-the-antarctic-shrimp-chorismus-antarcticus-focusing-on-a-new-decapod-itp-like-peptide-belonging-to-the-chh-peptide-family
#20
Jean-Yves Toullec, Erwan Corre, Perrine Mandon, Marcelo Gonzalez-Aravena, Céline Ollivaux, Chi-Ying Lee
As part of the study of the resilience of Antarctic crustaceans to global warming, the shrimp Chorismus antarcticus was subjected to an analysis of global approach using the Next Generation Sequencing Illumina Hi-Seq platform. With this data a detailed study into the principal neuropeptides and neurohormones of this species have been undertaken. Total RNAs from whole animals were enriched with eyestalk extracts to ensure maximum sequencing depth of the different neurohormones and neuropeptides mainly expressed into the X organ-sinus gland complex, which is a major endocrine organ of their synthesis...
July 17, 2017: General and Comparative Endocrinology
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