Abstract：
:The post-genomic era is characterized by the direct acquisition and analysis of genomic data with many applications, including the enhancement of the understanding of microbial epidemiology and pathology. However, there are a number of molecular approaches to survey pathogen diversity, and the impact of these different approaches on parameter estimation and inference are not entirely clear. We sequenced whole genomes of bacterial pathogens, Burkholderia pseudomallei, Yersinia pestis, and Brucella spp. (60 new genomes), and combined them with 55 genomes from GenBank to address how different molecular survey approaches (whole genomes, SNPs, and MLST) impact downstream inferences on molecular evolutionary parameters, evolutionary relationships, and trait character associations. We selected isolates for sequencing to represent temporal, geographic origin, and host range variability. We found that substitution rate estimates vary widely among approaches, and that SNP and genomic datasets yielded different but strongly supported phylogenies. MLST yielded poorly supported phylogenies, especially in our low diversity dataset, i.e., Y. pestis. Trait associations showed that B. pseudomallei and Y. pestis phylogenies are significantly associated with geography, irrespective of the molecular survey approach used, while Brucella spp. phylogeny appears to be strongly associated with geography and host origin. We contrast inferences made among monomorphic (clonal) and non-monomorphic bacteria, and between intra- and inter-specific datasets. We also discuss our results in light of underlying assumptions of different approaches.
journal_name
PeerJjournal_title
PeerJauthors
Castro-Nallar E,Hasan NA,Cebula TA,Colwell RR,Robison RA,Johnson WE,Crandall KAdoi
10.7717/peerj.761subject
Has Abstractpub_date
2015-02-17 00:00:00pages
e761issn
2167-8359pii
761journal_volume
3pub_type
杂志文章相关文献
PeerJ文献大全abstract：:Four species of true crocodile (genus Crocodylus) have been described from the Americas. Three of these crocodile species exhibit non-overlapping distributions-Crocodylus intermedius in South America, C. moreletii along the Caribbean coast of Mesoamerica, and C. rhombifer confined to Cuba. The fourth, C. acutus, is na...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.5836
更新日期：2018-11-12 00:00:00
abstract：:Caloric restriction (CR) can trigger gorging behavior. We examined macronutrient choice and behavior in mice that gorged during restriction compared to restricted non-gorgers and controls. Fifty MF1 male mice were restricted to 75% of ad-libitum food intake (FI), while ten controls were fed ad-lib. Body mass (BM) and ...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.1091
更新日期：2015-07-02 00:00:00
abstract：:The structural complexity of coral reefs plays a major role in the biodiversity, productivity, and overall functionality of reef ecosystems. Conventional metrics with 2-dimensional properties are inadequate for characterization of reef structural complexity. A 3-dimensional (3D) approach can better quantify topography...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.1077
更新日期：2015-07-07 00:00:00
abstract：:Outbreaks of the processionary moth Thaumetopoea pityocampa (Denis & Schiffermüller, 1775), a forest pest from the Palearctic, are thought to induce a behavioral response of bats, but up to now the moth has been seldom identified as bats' prey. Studies on bat diets suggest moths with cyclical outbreaks attract a wide ...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.7169
更新日期：2019-07-05 00:00:00
abstract：:Grand Staircase-Escalante National Monument is a federally protected area found in central southern Utah. Designated in 1996 by President William J. Clinton, it was recently reduced in size by President Donald J. Trump in a proclamation that turned the one large monument into three smaller ones. A long-term, standardi...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.6057
更新日期：2018-12-04 00:00:00
abstract：:Supertree methods enable the reconstruction of large phylogenies. The supertree problem can be formalized in different ways in order to cope with contradictory information in the input. Some supertree methods are based on encoding the input trees in a matrix; other methods try to find minimum cuts in some graph. Recen...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.4987
更新日期：2018-06-08 00:00:00
abstract：:Background. A "cafeteria" diet is a self-selected high-fat diet, providing an excess of energy, which can induce obesity. Excess of lipids in the diet hampers glucose utilization eliciting insulin resistance, which, further limits amino acid oxidation for energy. Methods. Male Wistar rats were exposed for a month to "...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.2302
更新日期：2016-08-03 00:00:00
abstract：Background:Leucojum aestivum L. is an important medicinal plant which produces Amaryllidaceae alkaloids, especially galanthamine and lycorine. Research is currently exploring the possibility of producing these alkaloids using biotechnological methods, including in vitro cultures. The biosynthesis of alkaloids may be af...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.8688
更新日期：2020-03-16 00:00:00
abstract：Background:Begomoviruses are widely distributed and causing devastating diseases in many crops. According to the number of genomic components, a begomovirus is known as either monopartite or bipartite begomovirus. Both the monopartite and bipartite begomoviruses have the DNA-A component which encodes all essential prot...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.9625
更新日期：2020-08-03 00:00:00
abstract：:Deposits spanning the Radotruncana calcarata Taxon Range Zone at the Postalm section, Northern Calcareous Alps (Austria) are examined quantitatively for foraminiferal assemblages, especially the planktonic group. This study focuses on establishing a high resolution record spanning an 800 ka long stratigraphic interval...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.1757
更新日期：2016-03-08 00:00:00
abstract：:Neem (Azadirachta indica A. Juss) is one of the most versatile tropical evergreen tree species known in India since the Vedic period (1500 BC-600 BC). Neem tree is a rich source of limonoids, having a wide spectrum of activity against insect pests and microbial pathogens. Complex tetranortriterpenoids such as azadirac...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.1066
更新日期：2015-08-06 00:00:00
abstract：:Reliable abundance estimates for species are fundamental in ecology, fisheries, and conservation. Consequently, predictive models able to provide reliable estimates for un- or poorly-surveyed locations would prove a valuable tool for management. Based on commonly used environmental and physical predictors, we develope...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.4566
更新日期：2018-04-17 00:00:00
abstract：:Avoidance behavior involves learning responses that prevent upcoming aversive events; these responses typically extinguish when the aversive events stop materializing. Stimuli that signal safety from aversive events can paradoxically inhibit extinction of avoidance behavior. In animals, males and females process safet...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.1081
更新日期：2015-07-14 00:00:00
abstract：:The number of people suffering from eye fatigue induced by visual display terminal (VDT) viewing is expected to increase in the modern world. Eye dysfunction is suggested to induce a decrease in cognitive function, at least in the long term. Furthermore, considering other previous findings, it may be reasonable to thi...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.7978
更新日期：2019-10-29 00:00:00
abstract：:Individual movement influences the spatial and social structuring of a population. Animals regularly use the same paths to move efficiently to familiar places, or to patrol and mark home ranges. We found that Australian sleepy lizards (Tiliqua rugosa), a monogamous species with stable pair-bonds, repeatedly used the s...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.1844
更新日期：2016-03-22 00:00:00
abstract：:Background. Despite massive immigration towards Southern Europe in the last two decades, data on mortality by cause among immigrants in Italy are scarce. The aim of this study was to investigate mortality from all and from specific causes of death among immigrants residing in the Veneto Region (Northeastern Italy). Me...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.975
更新日期：2015-05-21 00:00:00
abstract：:The ε subunit from ATP synthases acts as an ATP sensor in the bacterial cell to prevent ATP hydrolysis and thus the waste of ATP under conditions of low ATP concentration. However, the ATP binding affinities from various bacterial organisms differ markedly, over several orders of magnitude. For example, the ATP syntha...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.5505
更新日期：2018-09-05 00:00:00
abstract：Background:Sepsis represents a significant healthcare problem worldwide and causes a high number of deaths every year but remains to be fully understood. During and after sepsis, the host immune response is complex and involves an initial excessive host inflammatory response to infection that is closely related to tiss...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.7116
更新日期：2019-06-17 00:00:00
abstract：:In recent years, the use of lectins for screening of potential biomarkers has gained increased importance in cancer research, given the development in glycobiology that highlights altered structural changes of glycans in cancer associated processes. Lectins, having the properties of recognizing specific carbohydrate m...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.3784
更新日期：2017-09-07 00:00:00
abstract：Background:WRKY proteins play a vital role in the plants response to different stresses, growth and development. Studies of WRKY proteins have been mainly focused on model plant Arabidopsis and a few other vegetable plants. However, the systematical study of eggplant WRKY transcription factor superfamily is scarce. Me...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.8777
更新日期：2020-03-17 00:00:00
abstract：:We demonstrated that the 3-substituted benzothiophene-1,1-dioxide class of compounds are effective inhibitors of Mycobacterium tuberculosis growth under aerobic conditions. We examined substitution at the C-3 position of the benzothiophene-1,1-dioxide series systematically to delineate structure-activity relationships...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.612
更新日期：2014-10-07 00:00:00
abstract：:Knowledge on the precise identification of fish resources is critical for sustainable fisheries management. This study employs the DNA barcoding approach to generate a molecular taxonomic catalogue of commercially important reef fishes in the waters of Weh Island (Aceh Province), the most northerly inhabited island in...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.9641
更新日期：2020-08-05 00:00:00
abstract：:Hypocotyl elongation is a critical sign of seed germination and seedling growth, and it is regulated by multi-environmental factors. Light, temperature, and water potential are the major environmental stimuli, and their regulatory mechanism on hypocotyl growth has been extensively studied at molecular level. However, ...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.9106
更新日期：2020-05-26 00:00:00
abstract：Background:In the absence of highly effective antiviral therapies against SARS-CoV-2, it is crucial to counter the known pathophysiological causes of severe COVID-19. Evaluating the efficacy existing drugs may expedite the development of such therapeutics. Severe COVID-19 is largely the result of a dysregulated immune ...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.10322
更新日期：2020-11-02 00:00:00
abstract：:The role of glial cells in pain modulation has recently gathered attention. The objective of this study was to determine healthy spinal microglia and astrocyte morphology and disposition in equine spinal cord dorsal horns using Iba-1 and GFAP/Cx-43 immunofluorescence labeling, respectively. Five adult horses without v...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.3965
更新日期：2017-10-27 00:00:00
abstract：:The study of material collected during routine monitoring surveys dealing with oil extraction and aquaculture in waters off Myanmar (North Andaman Sea) and in the Gulf of Thailand, respectively, allowed us to analyse the taxonomy and diversity of the polychaete genus Terebellides (Annelida). Three species were found, ...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.2313
更新日期：2016-08-16 00:00:00
abstract：Background:Using wearable inertial sensors to accurately estimate energy expenditure (EE) during an athletic training process is important. Due to the characteristics of inertial sensors, however, the positions in which they are worn can produce signals of different natures. To understand and solve this issue, this stu...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.7973
更新日期：2019-11-04 00:00:00
abstract：Background:Herpesviral hematopoietic necrosis disease, caused by cyprinid herpesvirus-2 (CyHV-2), is responsible for massive mortalities in the aquaculture of goldfish, Carassius auratus. Permissive cell lines for the isolation and propagation of CyHV-2 have been established from various goldfish tissues by sacrificing...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.9373
更新日期：2020-07-14 00:00:00
abstract：:Ichthyosaur fossils are abundant in Lower Jurassic sediments with nine genera found in the UK. In this paper, we describe the partial skeleton of a large ichthyosaur from the Lower Jurassic (lower Sinemurian) of Warwickshire, England, which was conserved and rearticulated to form the centrepiece of a new permanent gal...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.6112
更新日期：2019-01-08 00:00:00
abstract：:In this study, we sequenced the genome of Pandoraea pnomenusa RB38 using Pacific Biosciences RSII (PacBio) Single Molecule Real Time (SMRT) sequencing technology. A pair of cognate luxI/R homologs was identified where the luxI homolog, ppnI, was found adjacent to a luxR homolog, ppnR1. An additional orphan luxR homolo...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.1225
更新日期：2015-08-27 00:00:00
