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Divergence and Redundancy of 16S rRNA Sequences in Genomes with Multiple rrn Operons
TLDR
An upper bound of roughly threefold overestimation of bacterial diversity resulting from cloning and sequencing of 16S rRNA genes from the environment is suggested, however, the inclusion of genomes with a single rrn operon may lower this correction factor to approximately 2.5.
Bias in Template-to-Product Ratios in Multitemplate PCR
ABSTRACT Bias introduced by the simultaneous amplification of specific genes from complex mixtures of templates remains poorly understood. To explore potential causes and the extent of bias in PCR
Triploblastic relationships with emphasis on the acoelomates and the position of Gnathostomulida, Cycliophora, Plathelminthes, and Chaetognatha: a combined approach of 18S rDNA sequences and
TLDR
For the first time, a data analysis recognizes a clade of acoelomates, the Platyzoa, which is expanded to include the enigmatic phylum Cycliophora, as sister group to Syndermata.
Resource Partitioning and Sympatric Differentiation Among Closely Related Bacterioplankton
TLDR
Spatial and temporal resource partitioning among Vibrionaceae strains coexisting in coastal bacterioplankton is described and environmental specialization may be an important correlate or even trigger of speciation among sympatric microbes.
Population Genomics of Early Events in the Ecological Differentiation of Bacteria
TLDR
It is shown that in two recently diverged populations of ocean bacteria, ecological differentiation has occurred akin to a sexual mechanism: A few genome regions have swept through subpopulations in a habitat-specific manner, accompanied by gradual separation of gene pools as evidenced by increased habitat specificity of the most recent recombinations.
Fine-scale phylogenetic architecture of a complex bacterial community
TLDR
It is proposed that such microdiverse clusters arise by selective sweeps and persist because competitive mechanisms are too weak to purge diversity from within them, indicating a large predominance of closely related taxa in this community.
Diversity and Dynamics of a North Atlantic Coastal Vibrio Community
TLDR
Temperature is a good predictor of the occurrence of closely related vibrios but that considerable microdiversity of unknown significance coexists within this trend, suggesting distinct warm-water and year-round populations.
Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'.
TLDR
A method to eliminate heteroduplexes from mixed- template PCR products by subjecting them to 'reconditioning PCR', a low cycle number re-amplification of a 10-fold diluted mixed-template PCR product is developed.
PCR-Induced Sequence Artifacts and Bias: Insights from Comparison of Two 16S rRNA Clone Libraries Constructed from the Same Sample
TLDR
Taq DNA polymerase errors were found to be the dominant sequence artifact but could be constrained by clustering the sequences into 99% sequence similarity groups, and no skew in sequence types was detected in the two libraries constructed from PCR products amplified for different numbers of cycles.
Genotypic Diversity Within a Natural Coastal Bacterioplankton Population
TLDR
This work shows that this group of coastal bacterioplankton consists of at least a thousand distinct genotypes, each occurring at extremely low environmental concentrations (on average less than one cell per milliliter), and shows extensive allelic diversity and size variation.
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