Genome-wide sweeps create ecological units in the human gut microbiome - Nature

Genome-wide selective sweeps commonly occur in the human gut microbiome and can spread across the world within decades to produce epidemic-like population structures.

nature.com

The president speaks genocide

The words, the law, the future

snyder.substack.com

Kurzgesagt – In a Nutshell

Animation videos explaining things with optimistic nihilism since 12,013. We’re a team of illustrators, animators, number crunchers and one dog who aim to spark curiosity about science and the world ...

youtube.com

(EPSRC DTP) How do the interactions between temperate and lytic phages shape microbial communities? at The University of Manchester on FindAPhD.com

PhD Project - (EPSRC DTP) How do the interactions between temperate and lytic phages shape microbial communities? at The University of Manchester, listed on FindAPhD.com

findaphd.com

Genome duplication in a long-term multicellularity evolution experiment - Nature

In the Multicellularity Long Term Evolution Experiment, diploid yeast evolve to be tetraploid under selection for larger multicellular size, revealing how whole-genome duplication can arise due to its...

nature.com

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my.corehr.com

Order of amino acid recruitment into the genetic code resolved by last universal common ancestor’s protein domains | PNAS

The current “consensus” order in which amino acids were added to the genetic code is based on potentially biased criteria, such as the absence of s...

pnas.org

PNAS

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

pnas.org

Dispersal stabilizes coupled ecological and evolutionary dynamics in a host-parasitoid system

Experiments and simulations show that dispersal maintains host genetic diversity and promotes host-parasitoid coexistence.

doi.org

Obsession with methods in microbial ecology

Striving towards bare minimum technique awesomeness

open.substack.com

Bacterial ecology and evolution converge on seasonal and decadal scales

Ecology and evolution are distinct theories, but the short lifespans and large population sizes of microbes allow evolution to unfold along contemporary ecological time scales. To document this in a natural system, we collected a two-decade, 471-metagenome time series from a single site in a freshwater lake, which we refer to as the TYMEFLIES dataset. This massive sampling and sequencing effort resulted in the reconstruction of 30,389 metagenomic-assembled genomes (MAGs) over 50% complete, which dereplicated into 2,855 distinct genomes (>96% nucleotide sequence identity). We found both ecological and evolutionary processes occurred at seasonal time scales. There were recurring annual patterns at the species level in abundances, nucleotide diversities (π), and single nucleotide variant (SNV) profiles for the majority of all taxa. During annual blooms, we observed both higher and lower nucleotide diversity, indicating that both ecological differentiation and competition drove evolutionary dynamics. Overlayed upon seasonal patterns, we observed long-term change in 20% of the species' SNV profiles including gradual changes, step changes, and disturbances followed by resilience. Most abrupt changes occurred in a single species, suggesting evolutionary drivers are highly specific. Nevertheless, seven members of the abundant Nanopelagicaceae family experienced abrupt change in 2012, an unusually hot and dry year. This shift coincided with increased numbers of genes under selection involved in amino acid and nucleic acid metabolism, suggesting fundamental organic nitrogen compounds drive strain differentiation in the most globally abundant freshwater family. Overall, we observed seasonal and decadal trends in both interspecific ecological and intraspecific evolutionary processes. The convergence of microbial ecology and evolution on the same time scales demonstrates that understanding microbiomes requires a new unified approach that views ecology and evolution as a single continuum. ### Competing Interest Statement The authors have declared no competing interest.

biorxiv.org

Large-scale duplication events underpin population-level flexibility in tRNA gene copy number in Pse...

Abstract. The complement of tRNA genes within a genome is typically considered to be a (relatively) stable characteristic of an organism. Here, we demonstrate t

academic.oup.com

Invading a New Host: Importance of the bacterial accessory genetic material in host colonization –...

southcoastbiosciencesdtp.ac.uk

What makes a temperate phage an effective bacterial weapon?

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

biorxiv.org