Sophie Jean Walton
@sophiejwalton.bsky.social
Stanford Biophysics PhD Student with Dmitri Petrov and Ben Good. evolution, ecology, genomics, microbiomes, biophysics :) she/her
https://sophiejwalton.github.io
https://sophiejwalton.github.io
Reposted by Sophie Jean Walton
The first is from former PhD student Zhiru Liu @zzzhiru.bsky.social (now in @bengrbm.bsky.social's group @ MSK) examining the long-term patterns of selective constraint – measured by the classical ratio of nonsynonymous to synonymous mutations (dN/dS) – within recombining populations of bacteria.
Dynamics of dN/dS within recombining bacterial populations
The ratio of nonsynonymous to synonymous substitutions (dN/dS) encodes important information about the selection pressures acting on protein-coding genes. In bacterial populations, dN/dS often decline...
www.biorxiv.org
November 16, 2025 at 3:26 PM
The first is from former PhD student Zhiru Liu @zzzhiru.bsky.social (now in @bengrbm.bsky.social's group @ MSK) examining the long-term patterns of selective constraint – measured by the classical ratio of nonsynonymous to synonymous mutations (dN/dS) – within recombining populations of bacteria.
i will never stop laughing
November 12, 2025 at 10:24 PM
i will never stop laughing
And of course thank you to @benjaminhgood.bsky.social and @petrovadmitri.bsky.social for mentoring me through this adventure. n/n
November 11, 2025 at 5:15 PM
And of course thank you to @benjaminhgood.bsky.social and @petrovadmitri.bsky.social for mentoring me through this adventure. n/n
Thanks to all my amazing collaborators! @ksxue.bsky.social , Jonas and Richa were instrumental to setting up this project! Also, huge shout out to Qing, @hgellert.bsky.social and Chih-Fu who contributed to the analysis and experiments. (20/n)
November 11, 2025 at 5:15 PM
Thanks to all my amazing collaborators! @ksxue.bsky.social , Jonas and Richa were instrumental to setting up this project! Also, huge shout out to Qing, @hgellert.bsky.social and Chih-Fu who contributed to the analysis and experiments. (20/n)
This suggests that conspecific strains can behave more like ecological species when competing within larger communities, even when their genomes appear to evolve as a single biological species. (19/n)
November 11, 2025 at 5:15 PM
This suggests that conspecific strains can behave more like ecological species when competing within larger communities, even when their genomes appear to evolve as a single biological species. (19/n)
Together, our results illustrate that selection on conspecific strains in large communities is strong, but attenuates as communities stabilize in a manner reminiscent of negative frequency dependent selection. (18/n)
November 11, 2025 at 5:15 PM
Together, our results illustrate that selection on conspecific strains in large communities is strong, but attenuates as communities stabilize in a manner reminiscent of negative frequency dependent selection. (18/n)
There are additional analyses in the paper that I didn’t cover here, including looking at how selection shifts across nutrient environments! (17/n)
November 11, 2025 at 5:15 PM
There are additional analyses in the paper that I didn’t cover here, including looking at how selection shifts across nutrient environments! (17/n)
We also examined whether strain-level competition outcomes were correlated across species. Interestingly, we found little evidence for strain-level cohesion during coalescence, despite prior co-selection during community assembly and within each host. (16/n)
November 11, 2025 at 5:15 PM
We also examined whether strain-level competition outcomes were correlated across species. Interestingly, we found little evidence for strain-level cohesion during coalescence, despite prior co-selection during community assembly and within each host. (16/n)
However, these findings are consistent with recent ecological theory by my amazing labmate @johndmcenany.bsky.social which suggested that conspecific strains may coexist in saturated communities even when new strains displace other species. (15/n) www.nature.com/articles/s41...
Predicting the first steps of evolution in randomly assembled communities - Nature Communications
Evolution often occurs within complex communities, but the way this context controls the rate and impact of evolution is poorly understood. The authors employ a model of resource competition to study ...
www.nature.com
November 11, 2025 at 5:15 PM
However, these findings are consistent with recent ecological theory by my amazing labmate @johndmcenany.bsky.social which suggested that conspecific strains may coexist in saturated communities even when new strains displace other species. (15/n) www.nature.com/articles/s41...
Our observations of strain-level coexistence were surprising because community mixtures did not have elevated diversity compared to autologous controls! (14/n)
November 11, 2025 at 5:15 PM
Our observations of strain-level coexistence were surprising because community mixtures did not have elevated diversity compared to autologous controls! (14/n)
Since the abiotic environment was held constant, we attributed these shifts in selection to biotic interactions within the community. This suggests that conspecific strains can coexist through niche partitioning in species rich communities. (13/n)
November 11, 2025 at 5:15 PM
Since the abiotic environment was held constant, we attributed these shifts in selection to biotic interactions within the community. This suggests that conspecific strains can coexist through niche partitioning in species rich communities. (13/n)
However, selection shifted at later generations in many competitions! Moreover, these shifts also tended to be biased towards maintaining coexistence. (12/n)
November 11, 2025 at 5:15 PM
However, selection shifted at later generations in many competitions! Moreover, these shifts also tended to be biased towards maintaining coexistence. (12/n)
We then estimated the time-varying relative fitnesses of conspecific strains. We found that selection during earlier generations was quite strong and predicted that one strain would dominate in most competitions. (11/n)
November 11, 2025 at 5:15 PM
We then estimated the time-varying relative fitnesses of conspecific strains. We found that selection during earlier generations was quite strong and predicted that one strain would dominate in most competitions. (11/n)
We found that the dynamics of competing strains were characterized by large and deterministic shifts. These shifts exceeded what could be generated by measurement noise or drift, demonstrating that these dynamics were driven by strong selection. (10/n)
November 11, 2025 at 5:15 PM
We found that the dynamics of competing strains were characterized by large and deterministic shifts. These shifts exceeded what could be generated by measurement noise or drift, demonstrating that these dynamics were driven by strong selection. (10/n)
We then monitored the dynamics of competing conspecific strains from each host through the course of the coalescence through shotgun metagenomics. This approach allowed us to follow pairwise strain competitions across many species in parallel! (9/n)
November 11, 2025 at 5:15 PM
We then monitored the dynamics of competing conspecific strains from each host through the course of the coalescence through shotgun metagenomics. This approach allowed us to follow pairwise strain competitions across many species in parallel! (9/n)
We collected fecal samples from donors in the Bay Area and assembled in vitro gut communities from these samples in anaerobic conditions. Communities from different hosts shared some species, but harbored diverged strains of those species. (8/n)
November 11, 2025 at 5:15 PM
We collected fecal samples from donors in the Bay Area and assembled in vitro gut communities from these samples in anaerobic conditions. Communities from different hosts shared some species, but harbored diverged strains of those species. (8/n)
Microbial community coalescence experiments have been used to gain a lot of intuition on species-level selection. We were also inspired by strain level data that had been obtained from FMTs in therapeutic contexts (fig from DOI: 10.1126/science.aad8852). (7/n)
November 11, 2025 at 5:15 PM
Microbial community coalescence experiments have been used to gain a lot of intuition on species-level selection. We were also inspired by strain level data that had been obtained from FMTs in therapeutic contexts (fig from DOI: 10.1126/science.aad8852). (7/n)
It’s hard to distinguish between these models in natural microbiomes, so turned to lab systems to get some intuition. Specifically, we performed whole community competitions, or community coalescence, with in vitro gut communities derived from different human donors. (6/n)
November 11, 2025 at 5:15 PM
It’s hard to distinguish between these models in natural microbiomes, so turned to lab systems to get some intuition. Specifically, we performed whole community competitions, or community coalescence, with in vitro gut communities derived from different human donors. (6/n)
Others have proposed that conspecific strains may compete as ‘ecological species’ and coexist via niche partitioning because we see lots of examples of multiple conspecific strains persisting in the same microbiome. (5/n)
November 11, 2025 at 5:15 PM
Others have proposed that conspecific strains may compete as ‘ecological species’ and coexist via niche partitioning because we see lots of examples of multiple conspecific strains persisting in the same microbiome. (5/n)
However, some ecology theory suggests that diverse communities could select for suites of strains with small fitness differences within a community. DOI: 10.1016/j.tree.2006.08.003(4/n)
November 11, 2025 at 5:15 PM
However, some ecology theory suggests that diverse communities could select for suites of strains with small fitness differences within a community. DOI: 10.1016/j.tree.2006.08.003(4/n)