scholarly journals Environmental Sequence Data from the Sargasso Sea Reveal That the Characteristics of Genome Reduction in Prochlorococcus Are Not a Harbinger for an Escalation in Genetic Drift

2008 ◽  
Vol 26 (1) ◽  
pp. 5-13 ◽  
Author(s):  
J. Hu ◽  
J. L. Blanchard
Keyword(s):  
Genetic Drift ◽  
Sequence Data ◽  
Genome Reduction ◽  
Sargasso Sea ◽  
Environmental Sequence

scholarly journals Advantages and limits of metagenomic assembly and binning of a giant virus

2020 ◽  
Author(s):  
Frederik Schulz ◽  
Julien Andreani ◽  
Rania Francis ◽  
Jacques Yaacoub Bou Khalil ◽  
Janey Lee ◽  
...  
Keyword(s):  
Size Range ◽  
Sequence Data ◽  
Giant Virus ◽  
Sample Matrix ◽  
Environmental Sequence ◽  
Successful Recovery ◽  
Metagenome Assembly ◽  
Giant Viruses ◽  
Metagenomic Assembly ◽  
Virus Genomes

AbstractGiant viruses have large genomes, often within the size range of cellular organisms. This distinguishes them from most other viruses and demands additional effort for the successful recovery of their genomes from environmental sequence data. Here we tested the performance of genome-resolved metagenomics on a recently isolated giant virus, Fadolivirus, by spiking it into an environmental sample from which two other giant viruses were isolated. At high spike-in levels, metagenome assembly and binning led to the successful genomic recovery of Fadolivirus from the sample. A complementary survey of viral hallmark genes indicated the presence of other giant viruses in the sample matrix, but did not detect the two isolated from this sample. Our results indicate that genome-resolved metagenomics is a valid approach for the recovery of near-complete giant virus genomes given that sufficient clonal particles are present. Our data also underline that a vast majority of giant viruses remain currently undetected, even in an era of terabase-scale metagenomics.

scholarly journals A Need for Improved Cellulase Identification from Metagenomic Sequence Data

2020 ◽  
Vol 87 (1) ◽  
Author(s):  
Rebecca Co ◽  
Laura A. Hug
Keyword(s):  
Sequence Data ◽  
Industrial Applications ◽  
Data Sets ◽  
Metagenomic Sequence ◽  
Environmental Sequence ◽  
Sequencing Technologies ◽  
Current Classification ◽  
Applied Microbiology ◽  
Environmental Surveys ◽  
Metagenomic Sequence Data

ABSTRACT Improved sequencing technologies and the maturation of metagenomic approaches allow the identification of gene variants with potential industrial applications, including cellulases. Cellulase identification from metagenomic environmental surveys is complicated by inconsistent nomenclature and multiple categorization systems. Here, we summarize the current classification and nomenclature systems, with recommendations for improvements to these systems. Addressing the issues described will strengthen the annotation of cellulose-active enzymes from environmental sequence data sets—a rapidly growing resource in environmental and applied microbiology.

scholarly journals Ancient genomes from Iceland reveal the making of a human population

Science ◽  
2018 ◽  
Vol 360 (6392) ◽  
pp. 1028-1032 ◽  
Author(s):  
S. Sunna Ebenesersdóttir ◽  
Marcela Sandoval-Velasco ◽  
Ellen D. Gunnarsdóttir ◽  
Anuradha Jagadeesan ◽  
Valdís B. Guðmundsdóttir ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genetic Drift ◽  
Gene Pool ◽  
Human Population ◽  
Evolutionary History ◽  
Sequence Data ◽  
Genome Sequence Data ◽  
Source Populations

Opportunities to directly study the founding of a human population and its subsequent evolutionary history are rare. Using genome sequence data from 27 ancient Icelanders, we demonstrate that they are a combination of Norse, Gaelic, and admixed individuals. We further show that these ancient Icelanders are markedly more similar to their source populations in Scandinavia and the British-Irish Isles than to contemporary Icelanders, who have been shaped by 1100 years of extensive genetic drift. Finally, we report evidence of unequal contributions from the ancient founders to the contemporary Icelandic gene pool. These results provide detailed insights into the making of a human population that has proven extraordinarily useful for the discovery of genotype-phenotype associations.

scholarly journals Quantifying within-host diversity of H5N1 influenza viruses in humans and poultry in Cambodia

2019 ◽  
Author(s):  
Louise H. Moncla ◽  
Trevor Bedford ◽  
Philippe Dussart ◽  
Srey Viseth Horm ◽  
Sareth Rith ◽  
...  
Keyword(s):  
Genetic Drift ◽  
H5n1 Virus ◽  
Sequence Data ◽  
Natural Infection ◽  
Purifying Selection ◽  
Influenza Viruses ◽  
Single Infection ◽  
Domestic Ducks ◽  
Human Infections ◽  
Human Receptor

AbstractAvian influenza viruses (AIVs) periodically cross species barriers and infect humans. The likelihood that an AIV will evolve mammalian transmissibility depends on acquiring and selecting mutations during spillover, but data from natural infection is limited. We analyze deep sequencing data from infected humans and domestic ducks in Cambodia to examine how H5N1 viruses evolve during spillover. Overall, viral populations in both species are predominated by low-frequency (<10%) variation shaped by purifying selection and genetic drift, and half of the variants detected within-host are never detected on the H5N1 virus phylogeny. However, we do detect a subset of mutations linked to human receptor binding and replication (PB2 E627K, HA A150V, and HA Q238L) that arose in multiple, independent humans. PB2 E627K and HA A150V were also enriched along phylogenetic branches leading to human infections, suggesting that they are likely human-adaptive. Our data show that H5N1 viruses generate putative human-adapting mutations during natural spillover infection, many of which are detected at >5% frequency within-host. However, short infection times, genetic drift, and purifying selection likely restrict their ability to evolve extensively during a single infection. Applying evolutionary methods to sequence data, we reveal a detailed view of H5N1 virus adaptive potential, and develop a foundation for studying host-adaptation in other zoonotic viruses.Author summaryH5N1 avian influenza viruses can cross species barriers and cause severe disease in humans. H5N1 viruses currently cannot replicate and transmit efficiently among humans, but animal infection studies and modeling experiments have suggested that human adaptation may require only a few mutations. However, data from natural spillover infection has been limited, posing a challenge for risk assessment. Here, we analyze a unique dataset of deep sequence data from H5N1 virus-infected humans and domestic ducks in Cambodia. We find that well-known markers of human receptor binding and replication arise in multiple, independent humans. We also find that 3 mutations detected within-host are enriched along phylogenetic branches leading to human infections, suggesting that they are likely human-adapting. However, we also show that within-host evolution in both humans and ducks are shaped heavily by purifying selection and genetic drift, and that a large fraction of within-host variation is never detected on the H5N1 phylogeny. Taken together, our data show that H5N1 viruses do generate human-adapting mutations during natural infection. However, short infection times, purifying selection, and genetic drift may severely limit how much H5N1 viruses can evolve during the course of a single infection.

Modeling Taxa-Abundance Distributions in Microbial Communities using Environmental Sequence Data

2006 ◽  
Vol 53 (3) ◽  
pp. 443-455 ◽  
Author(s):  
William T. Sloan ◽  
Stephen Woodcock ◽  
Mary Lunn ◽  
Ian M. Head ◽  
Thomas P. Curtis
Keyword(s):  
Microbial Communities ◽  
Sequence Data ◽  
Environmental Sequence

scholarly journals Constraints on Allele Size at Microsatellite Loci: Implications for Genetic Differentiation

Genetics ◽  
1996 ◽  
Vol 143 (2) ◽  
pp. 1021-1032 ◽  
Author(s):  
Maarten J Nauta ◽  
Franz J Weissing
Keyword(s):  
Genetic Drift ◽  
Time Perspective ◽  
Sequence Data ◽  
Distance Measures ◽  
Population Divergence ◽  
Small Populations ◽  
Random Genetic Drift ◽  
Microsatellite Data ◽  
Mutation Pressure ◽  
History Of

Abstract Microsatellites are promising genetic markers for studying the demographic structure and phylogenetic history of populations. We present theoretical arguments indicating that the usefulness of microsatellite data for these purposes may be limited to a short time perspective and to relatively small populations. The evolution of selectively neutral markers is governed by the interaction of mutation and random genetic drift. Mutation pressure has the inherent tendency to shift different populations to the same distribution of alleles. Hence, mutation pressure is a homogenizing force, and population divergence is caused by random genetic drift. In case of allozymes or sequence data, the diversifying effect of drift is typically orders of magnitude larger than the homogenizing effect of mutation pressure. By a simple model, we demonstrate that the situation may be different for microsatellites where mutation rates are high and the range of alleles is limited. With the help of computer simulations, we investigate to what extent genetic distance measures applied to microsatellite data can nevertheless yield useful estimators for phylogenetic relationships or demographic parameters. We show that predictions based on microsatellite data are quite reliable in small populations, but that already in moderately sized populations the danger of misinterpretation is substantial.

Diversification of the North American Doellingeria-Eucephalus Clade (Astereae: Asteraceae) Inferred from Molecular and Morphological Evidence

2019 ◽  
Vol 44 (4) ◽  
pp. 930-942
Author(s):  
Geraldine A. Allen ◽  
Luc Brouillet ◽  
John C. Semple ◽  
Heidi J. Guest ◽  
Robert Underhill
Keyword(s):  
North American ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Morphological Evidence ◽  
South American ◽  
New Combinations ◽  
The North ◽  
Hybridization Event ◽  
Ancient Hybridization

Abstract—Doellingeria and Eucephalus form the earliest-diverging clade of the North American Astereae lineage. Phylogenetic analyses of both nuclear and plastid sequence data show that the Doellingeria-Eucephalus clade consists of two main subclades that differ from current circumscriptions of the two genera. Doellingeria is the sister group to E. elegans, and the Doellingeria + E. elegans subclade in turn is sister to the subclade containing all remaining species of Eucephalus. In the plastid phylogeny, the two subclades are deeply divergent, a pattern that is consistent with an ancient hybridization event involving ancestral species of the Doellingeria-Eucephalus clade and an ancestral taxon of a related North American or South American group. Divergence of the two Doellingeria-Eucephalus subclades may have occurred in association with northward migration from South American ancestors. We combine these two genera under the older of the two names, Doellingeria, and propose 12 new combinations (10 species and two varieties) for all species of Eucephalus.

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