danielfalush.bsky.social @danielfalush.bsky.social · 30/06/2025We 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. 110
danielfalush.bsky.social @danielfalush.bsky.social · 30/06/2025Upregulated genes provide clues about the ecological advantage of fast swimming in viscous liquids. A Type 6 secretion system and nutrient uptake genes are upregulated, allowing the bacteria to kill and devour bacterial prey. 100
danielfalush.bsky.social @danielfalush.bsky.social · 30/06/2025We use TNseq and RNA seq to show that 2/3 of ecospecies loci are either essential for this enhanced swimming or are unregulated along with it. 110
danielfalush.bsky.social @danielfalush.bsky.social · 30/06/2025Bacterial ecospecies are powerful tools for molecular biological, evolutionary and ecological investigation because all of the differentiated genes are working together. Molassodon have abandoned swarming on surfaces and instead use their lateral flagella to swim faster in viscous liquids. 100
danielfalush.bsky.social @danielfalush.bsky.social · 30/06/2025Bacterial ecospecies are complex adaptations on an otherwise freely recombining background. Molassodon has evolved via introgression of accessory genes and a few core genes from other Vibrio species, as well as point mutation. 100
danielfalush.bsky.social @danielfalush.bsky.social · 30/06/2025Molassodon! 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 @campy-bara.bsky.social www.biorxiv.org/content/10.1... 186
danielfalush.bsky.social @danielfalush.bsky.social · 28/02/2025Fascinatingly, their convergence in ecospecies differentiation between the two streptococcus species, involving the same genes and gene categories (cell division related), despite independent origins. Different genera find different but predictable paths for adaptive differentiation. 100
danielfalush.bsky.social @danielfalush.bsky.social · 28/02/2025And the first bacterial ecospecies threesome, in Streptococcus oralis. 100
danielfalush.bsky.social @danielfalush.bsky.social · 28/02/2025We illustrate this concretely by discovering a third bacterial ecospecies pair in Streptococcus mitis. 100
danielfalush.bsky.social @danielfalush.bsky.social · 28/02/2025Why? 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. 120
danielfalush.bsky.social @danielfalush.bsky.social · 28/02/2025Last and not least, 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. 100
danielfalush.bsky.social @danielfalush.bsky.social · 28/02/2025And 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! 100
danielfalush.bsky.social @danielfalush.bsky.social · 28/02/2025We are able to use the population genetic data to address classic questions such as what determines the number of genes? It seems to be a balance between deletion bias and selection favoring increasing genome complexity. 110
danielfalush.bsky.social @danielfalush.bsky.social · 28/02/2025Why has it taken us so long to update it? Like fine wine, it has matured. Unlike fine wine, it has also grown in scale. We now analyze population genetic data from nearly 800 species, instead of twenty something and genomic data from 15000. Figure 1 presents an overview of genomic parameters. 100
danielfalush.bsky.social @danielfalush.bsky.social · 27/01/2025So the million dollar question, what is the trait? Is there a trait? We don't know. The top loading genes provide some hints (number 1 is a fimbria locus). Really interested to hear your thoughts and suggestions, thanks for reading and reposting :). 000
danielfalush.bsky.social @danielfalush.bsky.social · 27/01/2025We propose instead that the structure is due to diversifying selection on a quantitative trait. The trait is influenced by many genes, and the most extreme genotypes have a small advantage. For low recombination rates, the species splits into two. For intermediate rates get an ecocline. 100
danielfalush.bsky.social @danielfalush.bsky.social · 27/01/2025Another way to visualize this is by looking at pairwise Linkage Disequilibrium (LD) between the most differentiated genes. This shows that PC1 captures the structure of association with PC1 values explaining pairwise LD between genes well. 110
danielfalush.bsky.social @danielfalush.bsky.social · 27/01/2025We think that this structure is due to a genome-wide component of variation, which can be captured for example using Principal Components Analysis (PCA). A handful of loci in the genome contribute disproportionately to PC1 values, these loci are the most different between different ends of the tree. 100
danielfalush.bsky.social @danielfalush.bsky.social · 27/01/2025Have you never noticed the "backbone" in a tree of Klebsiella pneumoniae genomes? Did you ever wonder what might be causing it? If so, very interested to hear what you thought. 100
