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Molecular ecology

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https://www.readbyqxmd.com/read/28817224/a-novel-post-hoc-method-for-detecting-index-switching-finds-no-evidence-for-increased-switching-on-the-illumina-hiseq-x
#1
Gregory L Owens, Marco Todesco, Emily B M Drummond, Sam Yeaman, Loren H Rieseberg
High throughput sequencing using the Illumina HiSeq platform is a pervasive and critical molecular ecology resource, and has provided the data underlying many recent advances. A recent study has suggested that 'index switching', where reads are misattributed to the wrong sample, may be higher in new versions of the HiSeq platform. This has the potential to invalidate both published and in-progress work across the field. Here, we test for evidence of index switching in an exemplar whole genome shotgun dataset sequenced on both the Illumina HiSeq 2500, which should not have the problem, and the Illumina HiSeq X, which may...
August 17, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28817121/meganuclease-assisted-generation-of-stable-transgenics-in-the-sea-anemone-nematostella-vectensis
#2
Eduard Renfer, Ulrich Technau
The sea anemone Nematostella vectensis is a model system used by a rapidly growing research community for comparative genomics, developmental biology and ecology. Here, we describe a microinjection procedure for creating stable transgenic lines in Nematostella based on meganuclease (I-SceI)-assisted integration of a transgenic cassette into the genome. The procedure describes the preparation of the reagents, microinjection of the transgenesis vector and the husbandry of transgenic animals. The microinjection setup differs from those of previously published protocols by the use of a holding capillary mounted on an inverted fluorescence microscope...
September 2017: Nature Protocols
https://www.readbyqxmd.com/read/28816638/high-prevalence-of-multidrug-resistant-community-acquired-methicillin-resistant-staphylococcus-aureus-at-the-largest-veterinary-teaching-hospital-in-costa-rica
#3
Irene Rojas, Elías Barquero-Calvo, Joany C van Balen, Norman Rojas, Lohendy Muñoz-Vargas, Armando E Hoet
Methicillin-resistant Staphylococcus aureus (MRSA) is a pathogen associated with severe infections in companion animals present in the community, and it is diagnosed in animals admitted to veterinary hospitals. However, reports that describe the circulation of MRSA in animal populations and veterinary settings in Latin America are scarce. Therefore, the objective of this study was to determine the prevalence and investigate the molecular epidemiology of MRSA in the environment of the largest veterinary teaching hospital in Costa Rica...
August 17, 2017: Vector Borne and Zoonotic Diseases
https://www.readbyqxmd.com/read/28814516/baculovirus-molecular-evolution-via-gene-turnover-and-recurrent-positive-selection-of-key-genes
#4
Tom Hill, Robert L Unckless
Hosts and viruses are locked in an evolutionary arms race. Hosts are constantly evolving to suppress virulence and replication, while viruses, reliant on host machinery for survival and reproduction, develop counter-strategies to escape this immune defense. Viruses must also adapt to novel conditions when establishing themselves in a host species. Both processes provide strong selection for viral adaptation. Understanding adaptive evolution in insect viruses can help us better understand adaptive evolution in general, and is important due to their use as biocontrol agents, and for protecting ecologically or economically important species from outbreaks...
August 16, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28813463/genetic-diversity-of-bemisia-tabaci-species-colonizing-cassava-in-central-african-republic-characterized-by-analysis-of-cytochrome-c-oxidase-subunit-i
#5
Brice Kette Tocko-Marabena, Semballa Silla, Christophe Simiand, Innocent Zinga, James Legg, Bernard Reynaud, Helene Delatte
After 2007, upsurges of whiteflies on cassava plants and high incidences of cassava diseases were observed in Central African Republic. This recent upsurge in the abundance of Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) was directly linked to serious damage to cassava crops resulting from spread of whitefly-borne cassava mosaic geminiviruses (CMGs). There is currently very little information describing whitefly populations on cassava and associated crops in Central African Republic. The current study aimed to address this gap, and to determine whether the increasing damage associated with B...
2017: PloS One
https://www.readbyqxmd.com/read/28813409/the-rise-of-algae-in-cryogenian-oceans-and-the-emergence-of-animals
#6
Jochen J Brocks, Amber J M Jarrett, Eva Sirantoine, Christian Hallmann, Yosuke Hoshino, Tharika Liyanage
The transition from dominant bacterial to eukaryotic marine primary productivity was one of the most profound ecological revolutions in the Earth's history, reorganizing the distribution of carbon and nutrients in the water column and increasing energy flow to higher trophic levels. But the causes and geological timing of this transition, as well as possible links with rising atmospheric oxygen levels and the evolution of animals, remain obscure. Here we present a molecular fossil record of eukaryotic steroids demonstrating that bacteria were the only notable primary producers in the oceans before the Cryogenian period (720-635 million years ago)...
August 16, 2017: Nature
https://www.readbyqxmd.com/read/28812605/experimental-test-and-refutation-of-a-classic-case-of-molecular-adaptation-in-drosophila-melanogaster
#7
Mohammad A Siddiq, David W Loehlin, Kristi L Montooth, Joseph W Thornton
Identifying the genetic basis for adaptive differences between species requires explicit tests of historical hypotheses concerning the effects of past changes in gene sequence on molecular function, organismal phenotype and fitness. We address this challenge by combining ancestral protein reconstruction with biochemical experiments and physiological analysis of transgenic animals that carry ancestral genes. We tested a widely held hypothesis of molecular adaptation-that changes in the alcohol dehydrogenase protein (ADH) along the lineage leading to Drosophila melanogaster increased the catalytic activity of the enzyme and thereby contributed to the ethanol tolerance and adaptation of the species to its ethanol-rich ecological niche...
January 13, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812568/gene-expression-plasticity-as-a-mechanism-of-coral-adaptation-to-a-variable-environment
#8
Carly D Kenkel, Mikhail V Matz
Local adaptation is ubiquitous, but the molecular mechanisms that give rise to this ecological phenomenon remain largely unknown. A year-long reciprocal transplant of mustard hill coral (Porites astreoides) between a highly environmentally variable inshore habitat and a more stable offshore habitat demonstrated that populations exhibit phenotypic signatures that are consistent with local adaptation. We characterized the genomic basis of this adaptation in both coral hosts and their intracellular symbionts (Symbiodinium sp...
November 7, 2016: Nature ecology & evolution
https://www.readbyqxmd.com/read/28810907/schr%C3%A3-dinger-s-microbes-tools-for-distinguishing-the-living-from-the-dead-in-microbial-ecosystems
#9
REVIEW
Joanne B Emerson, Rachel I Adams, Clarisse M Betancourt Román, Brandon Brooks, David A Coil, Katherine Dahlhausen, Holly H Ganz, Erica M Hartmann, Tiffany Hsu, Nicholas B Justice, Ivan G Paulino-Lima, Julia C Luongo, Despoina S Lymperopoulou, Cinta Gomez-Silvan, Brooke Rothschild-Mancinelli, Melike Balk, Curtis Huttenhower, Andreas Nocker, Parag Vaishampayan, Lynn J Rothschild
While often obvious for macroscopic organisms, determining whether a microbe is dead or alive is fraught with complications. Fields such as microbial ecology, environmental health, and medical microbiology each determine how best to assess which members of the microbial community are alive, according to their respective scientific and/or regulatory needs. Many of these fields have gone from studying communities on a bulk level to the fine-scale resolution of microbial populations within consortia. For example, advances in nucleic acid sequencing technologies and downstream bioinformatic analyses have allowed for high-resolution insight into microbial community composition and metabolic potential, yet we know very little about whether such community DNA sequences represent viable microorganisms...
August 16, 2017: Microbiome
https://www.readbyqxmd.com/read/28810710/testing-convergent-evolution-in-auditory-processing-genes-between-echolocating-mammals-and-the-aye-aye-a-percussive-foraging-primate
#10
Richard J Bankoff, Michael Jerjos, Baily Hohman, M Elise Lauterbur, Logan Kistler, George H Perry
Several taxonomically distinct mammalian groups-certain microbats and cetaceans (e.g., dolphins)-share both morphological adaptations related to echolocation behavior and strong signatures of convergent evolution at the amino acid level across seven genes related to auditory processing. Aye-ayes (Daubentonia madagascariensis) are nocturnal lemurs with a specialized auditory processing system. Aye-ayes tap rapidly along the surfaces of trees, listening to reverberations to identify the mines of wood-boring insect larvae; this behavior has been hypothesized to functionally mimic echolocation...
July 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28808130/meeting-report-on-the-asm-conference-on-mechanisms-of-interbacterial-cooperation-and-competition
#11
Bram Lories, Ilse Parijs, Kevin R Foster, Hans P Steenackers
The ASM Conference on Mechanisms of Interbacterial Cooperation and Competition was held in Washington DC, from 1 to 4 March 2017. The conference provided an international forum for sociomicrobiologists from different disciplines to present and discuss new findings. The meeting covered a wide range of topics, spanning molecular mechanisms, ecology, evolution, computation and manipulation of interbacterial interactions, and encompassed social communities in medicine, the natural environment, and industry. This report summarizes the presentations and emerging themes...
August 14, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28806923/historical-biogeography-and-ecological-niche-modelling-of-the-asimina-disepalum-clade-annonaceae-role-of-ecological-differentiation-in-neotropical-asian-disjunctions-and-diversification-in-asia
#12
Pui-Sze Li, Daniel C Thomas, Richard M K Saunders
BACKGROUND: The Asimina-Disepalum clade (Annonaceae subfam. Annonoideae tribe Annoneae) includes a major Neotropical-Asian biogeographical disjunction. We evaluate whether this disjunction can be explained by the Eocene boreotropics hypothesis, which relies on the existence of extensive boreotropical forests during the Late Palaeocene-Early Eocene thermal maximum (52-50 Ma), followed by disruption of boreotropical vegetation during post-Eocene cooling. Molecular dating using an uncorrelated relaxed molecular clock (UCLD) model with two fossil calibrations, ancestral range estimation, and ecological niche modelling across evolutionary time were performed...
August 14, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28803904/complete-mitochondrial-genomes-of-triodontophorus-serratus-and-triodontophorus-nipponicus-and-their-comparison-with-triodontophorus-brevicauda
#13
Jun-Feng Gao, Guo-Hua Liu, Hong Duan, Yuan Gao, Yan Zhang, Qiao-Cheng Chang, Ming Fang, Chun-Ren Wang
Triodontophorus serratus and Triodontophorus nipponicus are two of the most common nematodes inhabiting in the large intestine of horse. In the present study, the complete mitochondrial (mt) genome sequences of T. serratus and T. nipponicus have been determined. The mt genomes of T. serratus and T. nipponicus are circular molecules with 13,794 bp and 13,701 bp in size, respectively. These circular mt genomes encode 36 genes, including 12 protein-coding genes, two rRNA genes and 22 tRNA genes. All of these genes are transcribed in the same direction and gene arrangements are consistent with that of gene arrangement 3 (GA3-type)...
August 10, 2017: Experimental Parasitology
https://www.readbyqxmd.com/read/28800486/the-influence-of-e-waste-recycling-on-the-molecular-ecological-network-of-soil-microbial-communities-in-pakistan-and-china
#14
Longfei Jiang, Zhineng Cheng, Dayi Zhang, Mengke Song, Yujie Wang, Chunling Luo, Hua Yin, Jun Li, Gan Zhang
Primitive electronic waste (e-waste) recycling releases large amounts of organic pollutants and heavy metals into the environment. As crucial moderators of geochemical cycling processes and pollutant remediation, soil microbes may be affected by these contaminants. We collected soil samples heavily contaminated by e-waste recycling in China and Pakistan, and analyzed the indigenous microbial communities. The results of this work revealed that the microbial community composition and diversity, at both whole and core community levels, were affected significantly by polycyclic aromatic hydrocarbons (PAHs), polybrominated diphenyl ethers (PBDEs) and heavy metals (e...
August 8, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28797634/ecological-distribution-of-extremely-thermophilic-bacteria-belonging-to-the-genus-calditerricola-using-the-novel-enrichment-mpn-pcr-method
#15
Kathrina Mae Bienes, Minoru Ito, Kota Shiotsuka, Sachi Yamaguchi, Taiki Fujioka, Yukihiro Tashiro, Kenji Sakai
A unique compost called Satsuma soil is produced from sewage sludge by a hyperthermal composting process in Kagoshima City, Japan. The composting process is carried out at a controlled temperature of at least 80°C and the resulting compost might be useful for recycling sustainable agricultural products. The extremely thermophilic bacterial genus Calditerricola was initially isolated from the high-temperature compost. Likewise, the bacteria were previously isolated from material sludge. It is believed that bacteria in this genus might be involved in the hyperthermal composting process...
August 7, 2017: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/28797302/development-and-characterization-of-microsatellite-markers-for-diploid-populations-of-the-wind-pollinated-herb-mercurialis-annua
#16
Ana Paula Machado, John R Pannell, Jeanne Tonnabel
OBJECTIVE: Mercurialis annua is a wind-pollinated annual plant that has long been used as a model for the study of ploidy and sexual-systems evolution. However, no molecular markers are yet available for genetic studies of its diploid populations. Here, we develop and characterize a set of eight polymorphic microsatellite markers for diploid dioecious M. annua. RESULTS: Following an SSR-enrichment protocol, 13 microsatellite markers were proposed, eight of which yielded successful amplification and polymorphism...
August 10, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28796830/dynamic-changes-of-nutrient-composition-throughout-the-entire-life-cycle-of-black-soldier-fly
#17
Xiu Liu, Xuan Chen, Hui Wang, Qinqin Yang, Kashif Ur Rehman, Wu Li, Minmin Cai, Qing Li, Lorenzo Mazza, Jibin Zhang, Ziniu Yu, Longyu Zheng
Black soldier fly (BSF) larvae, Hermetia illucens L., develops on organic wastes, reducing ecological pollution and converting waste biomass into protein and fat rich insect biomass. BSF can replace increasingly expensive protein sources used in poultry, aquaculture and livestock compound diet formulation, such as fish meal and soybean meal, which holds the potential to alleviate future food and feed insecurity. The fate of nutritional spectra in BSF during its life cycle phases is still poorly understood. This study assessed metabolic changes in nutrition composition of BSF from egg to adult...
2017: PloS One
https://www.readbyqxmd.com/read/28792680/transcriptomic-basis-of-genome-by-genome-variation-in-a-legume-rhizobia-mutualism
#18
Liana T Burghardt, Joseph Guhlin, Chan Lan Chun, Junqi Liu, Michael J Sadowsky, Robert M Stupar, Nevin D Young, Peter Tiffin
In the legume-rhizobia mutualism, the benefit each partner derives from the other depends on the genetic identity of both host and rhizobial symbiont. To gain insight into the extent of genome x genome interactions on hosts at the molecular level and to identify potential mechanisms responsible for the variation, we examined host gene expression within nodules (the plant organ where the symbiosis occurs) of four genotypes of Medicago truncatula grown with either Ensifer meliloti or E. medicae symbionts. These host x symbiont combinations show significant variation in nodule and biomass phenotypes...
August 9, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28792676/the-messenger-matters-pollinator-functional-group-influences-mating-system-dynamics
#19
Jennifer J Weber
The incredible diversity of plant mating systems has fuelled research in evolutionary biology for over a century. Currently, there is broad concern about the impact of rapidly changing pollinator communities on plant populations. Very few studies, however, examine patterns and mechanisms associated with multiple paternity from cross-pollen loads. Often, foraging pollinators collect a mixed pollen load that may result in the deposition of pollen from different sires to receptive stigmas. Coincident deposition of self- and cross-pollen leads to interesting mating system dynamics and has been investigated in numerous species...
August 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28792654/euchlorocystis-gen-nov-and-densicystis-gen-nov-two-new-genera-of-oocystaceae-algae-from-high-altitude-semi-saline-habitat-trebouxiophyceae-chlorophyta
#20
Xudong Liu, Huan Zhu, Huiyin Song, Qinghua Wang, Xiong Xiong, Chenxi Wu, Guoxiang Liu, Zhengyu Hu
The Oocystaceae family is generally considered to contain common freshwater eukaryotic microalgae, and few are reported living in semi-saline habitats. Our latest ecological survey in Qinghai Lake and Angzicuo Lake, both large, closed, high-altitude, semi-saline lakes located on the Qinghai-Tibet plateau in China, revealed Oocystaceae species as a dominant group among plankton. Since limited knowledge exists about semi-saline species in the Oocystaceae family, a taxonomical study was carried out using morphological and phylogenetic methods...
August 9, 2017: Journal of Eukaryotic Microbiology
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