We are extremely grateful to the NIH for awarding our lab an R35 grant. We will be working on furthering our understanding the evolutionary dynamics of gut bacteria during gut colonization. Stay tuned for results on this work!
Lead by Mariana Harris and in collaboration with Bernard Kim, we recently posted a preprint showing that hard sweeps are enriched on the X chromosome of six Drosophila species, generalizing findings that we previously made in a single population of D. melanogaster.
Please check out our video on the paper!
We are thrilled to welcome Jooeun Jeon, Radha Ganesh, and Rahul Natarajan this summer to our lab for the Bruins in Genomics summer program!
The Garud lab attended the Southern California Evolution meeting (SCALE) this past weekend and had a strong showing of presenters!
PhD student Mariana Harris gave a talk at SMBE Everywhere this month on her work on enrichment of hard sweeps on the X chromosome relative to autosomes. Congrats Mariana!
We are excited to share that our lab has received an NSF CAREER award to study rapid, repeatable adaptation in the human gut microbiome! Please stay tuned for results on this work!
We are delighted to share that our paper entitled Ecological Stability Emerges at the Level of Strains in the Human Gut Microbiome is now accepted at mBio! This work is with the very talented first author and PhD student Richard Wolff and postdoc William Shoemaker.
In healthy hosts, species abundance fluctuations in the microbiome have been frequently described as stable, and these fluctuations can be described by macroecological laws. However, it is less clear how strain abundances change over time. An open question is whether individual strains behave like species themselves, exhibiting stability and following the macroecological relationships known to hold at the species level, or whether strains have different dynamics, perhaps due to the relatively close phylogenetic relatedness of co-colonizing lineages. Here, we analyze the daily dynamics of intra-specific genetic variation in the gut microbiomes of four healthy, densely longitudinally sampled hosts. First, we find that overall genetic diversity in a large majority of species is stationary over time, despite short-term fluctuations. Next, we show that fluctuations in abundances in approximately 80% of strains analyzed can be predicted with a stochastic logistic model (SLM)—an ecological model of a population experiencing environmental fluctuations around a fixed carrying capacity which has previously been shown to capture statistical properties of species abundance fluctuations. The success of this model indicates that strain abundances typically fluctuate around a fixed carrying capacity, suggesting that most strains are dynamically Finally, we find that the strain abundances follow several empirical macroecological laws known to hold at the species level. Together, our results suggest that macroecological properties of the human gut microbiome, including its stability, emerge at the level of strains.
We are thrilled to share that our recent manuscript on the Enrichment of hard sweeps on the X chromosome of Drosophila melanogaster has now been accepted at Molecular Biology and Evolution! This work is with the very talented first author and PhD student, Mariana Harris.
The X chromosome is hemizygous in males and has ¾ Ne compared to autosomes. How do these factors impact the tempo and mode of adaptation (e.g. prevalence of hard versus soft sweeps) on the X compared to autosomes? Previously we showed with haplotype statistics (H12 and H2/H1) that soft sweeps are pervasive on autosomes in Drosophila melanogaster. These statistics since have been used in numerous other organisms to detect both hard and soft sweeps. https://tinyurl.com/soft-sweeps.
In this paper, we quantify the incidence of hard versus soft sweeps on the X chromosome with H12 and H2/H1 in both simulations and data. In simulations under a wide range of evolutionary scenarios, hard sweeps are expected to be more common than soft sweeps on the X. This arises from hemizygosity resulting in more efficient purging of initially deleterious standing variation, but also from the lower Ne on the X. Hard sweeps are enriched in D. mel data too. To apply H12 and H2/H1 to the data, we wanted to make sure that haplotype window sizes are comparable to that of autosomes. The X has fascinatingly lower levels of diversity compared to the autosomes, making comparable SNP-based window sizes based a little tricky. However, Mariana did some really great work in making this happen and I encourage you to read the paper to learn more.
Here is a plot of the scan of H12 along all chromosomes – highlighted in blue are the inferred hard sweeps, and in red the inferred soft sweeps. The X has proportionally more hard sweeps than the auto! Also notice that we recovered a positive control, Fezzik, on the X with this scan, in addition to three positive controls on the auto at Ace, Cyp6g1, and CHKov1!
Finding that hard sweeps are more enriched the X in D. mel is the first step. How general is this phenomenon across diverse Drosophila species? This is an avenue for future work! Many thanks to our colleagues and anonymous reviewers for the very helpful feedback! We’d love to hear from you if you have any comments of questions about our paper. Also, Mariana will be at #Dros23!