scholarly journals Quantitative evolutionary dynamics using high-resolution lineage tracking

Nature ◽  
2015 ◽  
Vol 519 (7542) ◽  
pp. 181-186 ◽  
Author(s):  
Sasha F. Levy ◽  
Jamie R. Blundell ◽  
Sandeep Venkataram ◽  
Dmitri A. Petrov ◽  
Daniel S. Fisher ◽  
...  
Keyword(s):  
High Resolution ◽  
Evolutionary Dynamics ◽  
Lineage Tracking

scholarly journals Quantifying the interplay between rapid bacterial evolution within the mouse intestine and transmission between hosts

2020 ◽  
Author(s):  
Kimberly S. Vasquez ◽  
Lisa Willis ◽  
Nate Cira ◽  
Katharine M. Ng ◽  
Miguel F. Pedro ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Population Genetics ◽  
High Resolution ◽  
Evolutionary Dynamics ◽  
Day Treatment ◽  
Whole Genome ◽  
Germ Free ◽  
Selection Dynamics ◽  
Mouse Intestine ◽  
Ciprofloxacin Resistance

SummaryDue to limitations on high-resolution strain tracking, selection dynamics during gut-microbiota colonization and transmission between hosts remain mostly mysterious. Here, we introduced hundreds of barcoded Escherichia coli strains into germ-free mice and quantified strain-level dynamics and metagenomic changes. Mutants involved in motility and utilization of abundant metabolites were reproducibly selected within days. Even with rapid selection, coprophagy enforced similar barcode distributions across co-housed mice. Whole-genome sequencing of hundreds of isolates quantified evolutionary dynamics and revealed linked alleles. A population-genetics model predicted substantial fitness advantages for certain mutants and that migration accounted for ~10% of the resident microbiota each day. Treatment with ciprofloxacin demonstrated the interplay between selection and transmission. While initial colonization was mostly uniform, in two mice a bottleneck reduced diversity and selected for ciprofloxacin resistance in the absence of drug. These findings highlight the interplay between environmental transmission and rapid, deterministic selection during evolution of the intestinal microbiota.

scholarly journals High-resolution lineage tracking reveals travelling wave of adaptation in laboratory yeast

Nature ◽  
2019 ◽  
Vol 575 (7783) ◽  
pp. 494-499 ◽  
Author(s):  
Alex N. Nguyen Ba ◽  
Ivana Cvijović ◽  
José I. Rojas Echenique ◽  
Katherine R. Lawrence ◽  
Artur Rego-Costa ◽  
...  
Keyword(s):  
High Resolution ◽  
Travelling Wave ◽  
Lineage Tracking

Geomorphology of the lakebed and sediment deposition during the Holocene in Lake Visovac

2021 ◽  
Author(s):  
Nikolina Ilijanić ◽  
Slobodan Miko ◽  
Ozren Hasan ◽  
Dea Brunović ◽  
Martina Šparica Miko ◽  
...  
Keyword(s):  
High Resolution ◽  
Lake Sediment ◽  
National Park ◽  
Lake Level ◽  
Evolutionary Dynamics ◽  
Environmental Changes ◽  
Sediment Cores ◽  
Depositional Environments ◽  
Lake Levels ◽  
The Holocene

<p>Lake Visovac is a tufa barrier lake on the Krka River between Roški slap (60 m asl) and Skradinski buk (46 m absl) waterfalls, included in the Krka national park as primarily unaltered area of exceptional natural value. Paleolimnological research was conceived to address a lake evolution and depositional environments through the geophysical survey and collection of the lake sediment cores. A high-resolution bathymetric map was obtained using a multibeam sonar. The average lake depth varies between 20 and 25 m. Sediment cores were investigated to extract physical properties, sedimentological, mineralogical, geochemical and paleoecological records constrained by the radiocarbon chronology, to understand what was happening to both the landscapes and lakescapes of Lake Visovac during the last 2.000 cal yr.</p><p>Significant findings of the project are geomorphological features on the lake bottom: submerged sinkholes of various sizes (up to 40 m deep); submerged tufa barriers in the area of Kalički kuk (southern part of Lake Visovac) at the depths of 15 and 17 m, followed by a series of buried cascade tufa barriers at the depth of 25 m covered with up to 10 m of Holocene lake sediments; submerged vertical tufa barrier up to 32 m-high near the mouth of Čikola River; submerged landslides, small (river) fan structures characterized by sediment waves. Ground-penetrating-radar (GPR) data have been acquired due to the presence of gas-saturated sediments over a large area of the lake, that limited the use of high-resolution acoustic profiling. A total thickness of sediments is up to 40 m. High resolution paleoenvironmental record through the Late Holocene gives evidence of high sedimentation rates in Lake Visovac, variable soil erosion impact on lake sediment composition and carbonate authigenic sedimentation. Higher organic carbon is observed in the last 50 years due to changes in land cover and reforestation. Pleistocene lake sediment outcrops occur up to 20 m above the present lake levels indicating higher lake levels as a consequence of higher elevation of tuffa barriers. Kalički kuk, which lies up to 20 m above present lake level, is a remnant of these barriers which have been dated to MIS5. Results allow us to interpret the environmental and evolutionary dynamics of Lake Visovac in the following way: lake level more than 20 m higher than today in mid-Pleistocene with significantly larger lake volume in Lake Visovac, with active Kalički kuk and Skradinski buk waterfalls; lower lake-level at the beginning of the Holocene when several small lakes existed in isolated basins in the area of Lake Visovac. The tufa barrier at Skradinski buk started to grow faster than the Kalički kuk barriers and waterfalls resulting in their flooding and submergence during the Holocene. The tufa barrier at Skradinski buk has grown 15 m since then. This study demonstrates the role of geomorphological lakebed characteristics in reshaping our understanding of the environmental changes and the future of Lake Visovac.</p><p>The research was conducted as part of the project funded by the Krka National Park and CSF funded QMAD project (IP-04-2019-8505).</p>

scholarly journals Chromosomal barcoding of E. coli populations reveals lineage diversity dynamics at high resolution

2019 ◽  
Author(s):  
Jesse Lerner ◽  
Michael Manhart ◽  
Weronika Jasinska ◽  
Louis Gauthier ◽  
Adrian W.R. Serohijos ◽  
...  
Keyword(s):  
High Resolution ◽  
Evolutionary Dynamics ◽  
Frequency Resolution ◽  
Low Frequencies ◽  
Bacterial Populations ◽  
E Coli ◽  
Asexual Populations ◽  
Diversity Dynamics ◽  
Lineage Diversity ◽  
New Mutations

Evolutionary dynamics in large asexual populations is strongly influenced by multiple competing beneficial lineages, most of which segregate at very low frequencies. However, technical barriers to tracking a large number of these rare lineages have so far prevented a detailed elucidation of evolutionary dynamics in large bacterial populations. Here, we overcome this hurdle by developing a chromosomal barcoding technique that allows simultaneous tracking of ∼450,000 distinct lineages in E. coli. We used this technique to gather insights into the evolutionary dynamics of large (>107 cells) E. coli populations propagated for ∼420 generations in the presence of sub-inhibitory concentrations of common antibiotics. By deep sequencing the barcodes, we reconstructed trajectories of individual lineages at high frequency resolution (< 10−5). Using quantitative tools from ecology, we found that populations lost lineage diversity at distinct rates corresponding to their antibiotic regimen. Additionally, by quantifying the reproducibility of these dynamics across replicate populations, we found that some lineages had similar fates over independent experiments. Combined with an analysis of individual lineage trajectories, these results suggest how standing genetic variation and new mutations may contribute to adaptation to sub-inhibitory antibiotic levels. Altogether, our results demonstrate the power of high-resolution barcoding in studying the dynamics of bacterial evolution.

scholarly journals Changes in the distribution of fitness effects and adaptive mutational spectra following a single first step towards adaptation

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Dimitra Aggeli ◽  
Yuping Li ◽  
Gavin Sherlock
Keyword(s):  
Evolutionary Dynamics ◽  
Second Step ◽  
Historical Contingency ◽  
Loss Of Function ◽  
Mutational Spectra ◽  
Fitness Effects ◽  
Mutational Step ◽  
Diminishing Returns ◽  
Lineage Tracking ◽  
Adaptive Step

AbstractHistorical contingency and diminishing returns epistasis have been typically studied for relatively divergent genotypes and/or over long evolutionary timescales. Here, we use Saccharomyces cerevisiae to study the extent of diminishing returns and the changes in the adaptive mutational spectra following a single first adaptive mutational step. We further evolve three clones that arose under identical conditions from a common ancestor. We follow their evolutionary dynamics by lineage tracking and determine adaptive outcomes using fitness assays and whole genome sequencing. We find that diminishing returns manifests as smaller fitness gains during the 2nd step of adaptation compared to the 1st step, mainly due to a compressed distribution of fitness effects. We also find that the beneficial mutational spectra for the 2nd adaptive step are contingent on the 1st step, as we see both shared and diverging adaptive strategies. Finally, we find that adaptive loss-of-function mutations, such as nonsense and frameshift mutations, are less common in the second step of adaptation than in the first step.

scholarly journals Early adaptation in a microbial community is dominated by mutualism-enhancing mutations

2021 ◽  
Author(s):  
Sandeep Venkataram ◽  
Huan-Yu Kuo ◽  
Erik F. Y. Hom ◽  
Sergey Kryazhimskiy
Keyword(s):  
Species Interactions ◽  
Evolutionary Dynamics ◽  
Ecological Communities ◽  
Ecological Interactions ◽  
Biological Organization ◽  
Adaptive Mutations ◽  
Fitness Effects ◽  
Multiple Levels ◽  
Lineage Tracking ◽  
Different Levels

Evolutionary dynamics in ecological communities are often repeatable, but how species interactions affect the distribution of evolutionary outcomes at different levels of biological organization is unclear. Here, we use barcode lineage tracking to experimentally address this gap in a facultatively mutualistic community formed by the alga Chlamydomonas reinhardtii and the yeast Saccharomyces cerevisiae. We find that interactions with the alga alter the magnitude but not the sign of the fitness effects of adaptive mutations in yeast, changing the distribution of mutants contending for fixation. In the presence of alga, most contending mutants reinforce the mutualism and make evolution more repeatable at the community level. Thus, ecological interactions not only alter the trajectory of evolution but also dictate its repeatability at multiple levels of biological organization.

scholarly journals Efficient Bayesian inference of phylogenetic trees from large scale, low-depth genome-wide single-cell data

2020 ◽  
Author(s):  
Fatemeh Dorri ◽  
Sohrab Salehi ◽  
Kevin Chern ◽  
Tyler Funnell ◽  
Marc Williams ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
High Resolution ◽  
Phylogenetic Tree ◽  
Single Cell ◽  
Copy Number ◽  
Phylogenetic Trees ◽  
Evolutionary Dynamics ◽  
Phylogenetic Inference ◽  
Copy Number Data ◽  
Polynomial Size

A new generation of scalable single cell whole genome sequencing (scWGS) methods, allows unprecedented high resolution measurement of the evolutionary dynamics of cancer cells populations. Phylogenetic reconstruction is central to identifying sub-populations and distinguishing mutational processes. The ability to sequence tens of thousands of single genomes at high resolution per experiment is challenging the assumptions and scalability of existing phylogenetic tree building methods and calls for tailored phylogenetic models and scalable inference algorithms. We propose a phylogenetic model and associated Bayesian inference procedure which exploits the specifics of scWGS data. A first highlight of our approach is a novel phylogenetic encoding of copy-number data providing an attractive statistical-computational trade-off by simplifying the site dependencies induced by rearrangements while still forming a sound foundation to phylogenetic inference. A second highlight is an innovative phylogenetic tree exploration move which makes the cost of MCMC iterations bounded by O(|C| + |L|), where |C| is the number of cells and |L| is the number of loci. In contrast, existing off-the-shelf likelihood-based methods incur iteration cost of O(|C| |L|). Moreover, the novel move considers an exponential number of neighbouring trees whereas off-the-shelf moves consider a polynomial size set of neighbours. The third highlight is a novel mutation calling method that incorporates the copy-number data and the underlying phylogenetic tree to overcome the missing data issue. This framework allows us to realistically consider routine Bayesian phylogenetic inference at the scale of scWGS data.

scholarly journals High resolution evolutionary analysis of within-host hepatitis C virus infection

2018 ◽  
Author(s):  
Jayna Raghwani ◽  
Chieh-Hsi Wu ◽  
Cynthia K. Y. Ho ◽  
Menno de Jong ◽  
Richard Molenkamp ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Population Structure ◽  
High Resolution ◽  
Evolutionary Dynamics ◽  
Hcv Infection ◽  
Envelope Gene ◽  
Evolutionary Analysis ◽  
Nucleotide Substitution Rate ◽  
Virus Diversity ◽  
Population Scale

ABSTRACTDespite the breakthroughs in the treatment of HCV infection in recent years, we have a limited understanding of how virus diversity generated within individuals impacts the evolution and spread of HCV variants at the population scale. Addressing this gap will be important for building models for molecular epidemiology, which can identify main sources of disease transmission and evaluate the risks of drug-resistance mutations emerging and disseminating in a population. Here, we have undertaken a high-resolution analysis of HCV within-host evolution from four individuals co-infected with HIV. Specifically, we used long-read, deep-sequenced data of the full-length HCV envelope glycoprotein, longitudinally sampled from acute to chronic HCV infection to investigate the underlying viral evolutionary dynamics. In three individuals we found strong statistical support for population structure maintaining within-host HCV genetic diversity. Furthermore, we found significant variation in rates of molecular evolution among different regions of the HCV envelope region, both within and between individuals. Lastly, we report the first estimate of the within-host population genetic rate of recombination for HCV (0.28 x 10-7 recombinations per site per day; interquartile range: 0.13-1.05 x 10-7), which is two orders of magnitude lower than that estimated for HIV-1, and four orders of magnitude lower than the nucleotide substitution rate of the HCV envelope gene. Together, these observations indicate that population structure and strong genetic linkage shapes within-host HCV evolutionary dynamics. These results will guide the future investigation of potential HCV drug resistance adaptation during infection, and at the population scale.

Observations of the spatial structure of interstellar hydrogen

1967 ◽  
Vol 31 ◽  
pp. 45-46
Author(s):  
Carl Heiles
Keyword(s):  
High Resolution ◽  
Spatial Structure ◽  
Velocity Dispersion ◽  
Temperature Variations

High-resolution 21-cm line observations in a region aroundlII= 120°,b11= +15°, have revealed four types of structure in the interstellar hydrogen: a smooth background, large sheets of density 2 atoms cm-3, clouds occurring mostly in groups, and ‘Cloudlets’ of a few solar masses and a few parsecs in size; the velocity dispersion in the Cloudlets is only 1 km/sec. Strong temperature variations in the gas are in evidence.

Combining integrated systems-biology approaches with intervention-based experimental design provides a higher-resolution path forward for microbiome research

2019 ◽  
Vol 42 ◽  
Author(s):  
J. Alfredo Blakeley-Ruiz ◽  
Carlee S. McClintock ◽  
Ralph Lydic ◽  
Helen A. Baghdoyan ◽  
James J. Choo ◽  
...  
Keyword(s):  
Systems Biology ◽  
High Resolution ◽  
Experimental Design ◽  
Integrated Systems ◽  
Microbiome Research ◽  
Constructive Criticism

Abstract The Hooks et al. review of microbiota-gut-brain (MGB) literature provides a constructive criticism of the general approaches encompassing MGB research. This commentary extends their review by: (a) highlighting capabilities of advanced systems-biology “-omics” techniques for microbiome research and (b) recommending that combining these high-resolution techniques with intervention-based experimental design may be the path forward for future MGB research.

Sign in / Sign up

Export Citation Format

Share Document