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I am no expert but I think this pre-print may answer your second question! www.biorxiv.org/content/10.6...

Parallel evolution of industrial melanism in the peppered moth: one locus, many allelesThe extent to which adaptation to environmental change occurs via single or multiple advantageous mutations remains an open question, which we examined by studying the spread of melanic forms of the p...www.biorxiv.org

Congrats Devon! 🎉

A special shout-out to @zzzhiru.bsky.social and @benjaminhgood.bsky.social, whose work on recombination in the human gut has been hugely influential. It directly informed our simulations + stochastic model with empirical rates of recombination estimated for each species. journals.plos.org/p... n/n

Dynamics of bacterial recombination in the human gut microbiomeRecombination is a ubiquitous force in bacterial evolution, but its dynamics are poorly characterized in many natural populations. This study presents a metagenomic approach for quantifying the landsc...journals.plos.org

Check out all of this and more in our preprint! We welcome comments, questions and thoughts. www.biorxiv.org/co... 11/n

Complex adaptive architectures constrain the pace of adaptations sweeping across human gut microbiomesRecent work has shown that commensal gut bacteria can evolve rapidly within hosts on short timescales of days to months, fueled by the enormous mutational input generated daily in the microbiome. Yet ...www.biorxiv.org

Many questions have yet to be answered. "Complex architecture" is a broad category, but we're excited at the prospect that mobile or epistatic elements drive sweeps, potentially across species boundaries. The potential for global widespread parallelism at single sites is also intriguing. 10/n

Overall, we show that adaptation in the gut spans timescales from rapid to gradual, contingent on the complexity of the adaptive allele. Importantly, the potential for your gut to adapt may critically depend on the reservoir of adaptive material your fellow community members provide. 9/n

Genomic signatures in sweep regions support this idea, and hint at particular mechanisms such as adaptive introgression and gene-length epistasis. For example, we observe elevated nucleotide diversity (pi) at sweeps, in contrast to an expected decrease in pi from simple architectures. 8/n

Such low adaptive mutation rates are possible if sweeps arise from complex genetic architectures, such as epistasis or structural variation. These adaptations are difficult to mutate de novo, and may arise only once or rarely over the timescales adaptations spread across host microbiomes. 7/n

How do we square this with previous results? We show in a stochastic model that despite recombination seeding adaptation in the vast majority of hosts, only widespread parallelism is expected in the empirically-estimated range... Sweeps arise from orders-of-magnitude lower mutation rates 6/n

Confirming our previous findings, we recapitulate signals of widespread selective sweeps. However, to our surprise, hard sweeps were common! As one example, check out the region below, where a single adaptive genetic fragment (+ slight derivative) has spread to ~70% of A. finegoldii strains. 5/n

We highlight three signatures of rapidity: hard sweeps (slow, arising from one strain/gut), soft sweeps (rapid, arising from multiple strains/guts), and widespread parallelism, where adaptations arise so rapidly, no sweep is detected. We hypothesized that sweeps would undoubtedly be soft. 4/n

However, mutation is not the only game in town! Recombination is extensive in the gut, and work from our group (led by @rwolff.bsky.social) shows recombination can spread adaptations globally across gut populations. We first ask: how rapidly do these sweeps arise? www.nature.com/article... 3/n

Gene-specific selective sweeps are pervasive across human gut microbiomes - NatureDevelopment and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...www.nature.com

Commensal gut bacteria are capable of rapid adaptation fueled by enormous mutational input. Independent de novo adaptations can therefore arise quickly in individual hosts. @contaminatedsci.bsky.social and group have been influential in driving this line of thinking. www.cell.com/cell-h... 2/n

Adaptive Evolution within Gut Microbiomes of Healthy PeopleBacteria acquire adaptive mutations during infections, but the role of mutations in the gut microbiome is unknown. Zhao and Lieberman et al. report that Bacteroides fragilis adapts via mutation within...www.cell.com

Congrats Diana!!