daniel falush

Our paper "An Ancient ecospecies of Helicobacter pylori" was published yesterday in Nature. Thanks to Elise, Roberto, Sarah and our collaborators in Oita, Gothenburg and elsewhere for their hard work. nature.com/articles/s4158…

We are hiring a postdoc studying the ecological niche of bacterial ecospecies. This interdisciplinary project combines genomics, molecular microbiology and fieldwork on an island near Shanghai. Please forward :). simm.cas.cn/web/rcdw/rczp/…

What's left to discover: What are the viscous liquids in which Molassodon hunts, kills and devours bacterial prey? We now have many more tools to help us find out, and to understand the trade offs for different bacterial strategies. All comments welcome, thank you for reading.

We also identify a convergent intermediate form and are also able to provide details about the molecular and evolutionary assembly of the Molassodon genotype, revealing a key role for lateral flagella glycosylation.

Molassodon! Excited to post my research group's first laboratory project. We identify a phenotype and a putative ecological strategy for the Molassodon ecospecies of Vibrio parahamolyticus, thanks to the hard work of our lab team led by Sarah biorxiv.org/content/10.110…

Postdoc position in my group in Tokyo! Please get in touch if you are interested. And happy to discuss projects - ranging from developing new methods to analysis of new genomes that we are now sequencing in the lab. riken.jp/en/careers/res… Lab page: speidellab.github.io

@luispedrocoelho the main issue about Trump is he is just exhausting, all this attention he manages to capture..

In a certain light, isn't the trade war exciting?

@gbradburd maybe coming to this a bit late but do look at our hoary old classic of this genre journals.plos.org/plosgenetics/a…

10/10 Really excited for feedback on this - please reach out w/ thoughts/suggestions!

8/n We think the method offers a big step forward for how to think about ancestry (particularly in humans): best defined with *explicit* reference to a point in space AND time.

@millanek1 Cool! although not very applicable to bacteria.

Want a to make genetic maps from sperm/pollen/gametes? Now there is an easy way, based on Hi-C sequencing. Thanks to Richard Durbin and Ed Green for the idea and a great group of co-authors for contributions.

Thank you for reading our thread, please read the preprint too! your comments on all aspects are extremely welcome.

So in summary our atlas provides a new way of systematizing prokaryotic life, suggesting that diverse species form ecologically selected clusters.

The convergence in ecospecies differentiation between the two streptococcus species, involving the same genes and gene categories (cell division related), suggest that particular genera find predictable paths for adaptive differentiation.

The first two bacterial ecospecies, in Heliocobacter pylori and vibrio parahaemolyticus are characterized by high differentiation restricted to a small fraction of the genome. The streptococcal ones have progressed further, consistent with the older age of the species.

Delighted to present our Macrogenetics atlas of prokaryotes. biorxiv.org/content/10.1... This is a herculean effort from Chao Yang, which has a previous existence as a preprint first posted in 2018 "why panmictic bacteria are rare?" biorxiv.org/content/10.110…

And the first bacterial ecospecies threesome, in Streptococcus oralis.

We illustrate this concretely by discovering a third bacterial ecospecies pair in Streptococcus mitis.

Why? Well what happens is that for species which maintain large population sizes for long time periods, natural selection becomes increasingly important in structuring diversity and this generates long range LD.

Finally, we provide an answer to the question of why panmictic bacterial species are rare. A well-mixed bacterial species should have low LD at all genetic distances, but there are no such species. Instead we find that the most diverse species have intermediate long-range LD.

And there are curious findings too, like the fact that the genome fluidity of rod shaped bacteria is more than double that of spherical ones. What can you see in the data? Or what would you like to see? Let us know!