Population Genetics in the Microbiome — Review for Trends in Genetics

We are very happy that our review on Population Genetics in the Microbiome has been recently accepted to Trends in Genetics! The review will be officially published in January, but in the meanwhile, a copy is available here. Below is one of our figures illustrating modes of horizontal gene transfer, incorporation of DNA into the receipient’s genome, and statistical signatures of recombination.

Welcome Leah, Spencer, and Sara!

We are excited to have Leah, Spencer, and Sara join us in the  lab. Leah is a 3rd year PhD student working on developing new statistical methods to quanitfy ecological and evolutionary dynamics in microbial communities and is co-advised by Dr. Eran Halperin at UCLA. Sara is an MS student in EEB and Spencer is a 3rd year undergraduate student majoring in CS.

Recombination in bacteria

This quarter, Nandita will be teaching an EEB 297 course on Recombination in Bacteria. Please check out the syllabus with the list of readings and feel free to join us on Mondays from 2-4pm in 120 La Kretz Hall.

Welcome BIG Summer Students

This summer, Daisy Chen and Sara Thornburgh join the lab! Sara and Daisy are  undergaduates from UCLA majoring in Ecology and Evolutionary Biology and CS, respectively. Both are a part of the Bruins in Genomics (BIG) summer research program on campus. We are excited to be working together!

Sara and Daisy with their colleagues from BIG, Jon and Miguel!

Breakdancing + evolution of gut microbiota?!

Really excited to be collaborating with the breakdancing group, We Break, this Sunday to ‘perform’ my paper on the evolutionary dynamics of gut microbiota! This event is free and open to the public, so please come!

Paper published!

I’m thrilled to share that our paper on the Evolutionary dynamics of bacteria in the gut microbiome within and across hosts is now published in PLoS Biology!

What is the paper about?

The human gut microbiome is comprised of a complex ecosystem of microbes that reside inside of us and play an important role in our health. With as many as a billion new mutations entering our microbiomes per day, bacterial genomes inside us have a great opportunity to evolve rapidly, unlike our own genomes, which change very little throughout our lifetimes. For us humans, this genetic dynamism is both an opportunity (e.g., enabling digestion of new foods) and a challenge (e.g. the evolution of drug resistance). Despite the potential importance of these effects, we currently know very little about if and how bacteria living in us evolve. In our recent work, we quantify the evolutionary dynamics of ~40 prevalent species of gut bacteria. We find that gut bacteria can evolve within humans on short timescales (~6 months), but over our lifetimes resident bacteria are typically replaced by distantly related strains. These results suggest that gut bacteria can evolve on human-relevant timescales, but that there are limits to the extent of local adaptation.

Isabel Gordo wrote a very nice perspective featuring our work.

Eco-Evo symposium at the Gulbenkian

I had the pleasure of presenting my work on the evolutionary dynamics of bacteria in the human gut at the IGC symposium at the Gulbenkian near Lisbon. Here is a sketch of the me and the other speakers in my session by the talented @CireniaSketches!

Evolutionary dynamics of bacteria in the gut microbiome — revision posted!

Happy to share that I have revised my manuscript on the Evolutionary dynamics of bacteria in the gut microbiome within and across hosts with my colleagues Benjamin Good, Oskar Hallatschek, and Katherine Pollard. Please see the latest on bioRxiv.

My talented colleague, Alison Feder, drew a graphical abstract of my paper!


Detection and classification of hard and soft sweeps from unphased genotypes by multilocus genotype identity

I am excited to share a new bioRxiv preprint on detecting and classifying hard and soft sweeps from unphased population genomic data, co-authored with Alexandre Harris and Michael DeGiorgio from Penn State University. One challenge with working with non-model eukaryotic organisms is that genomic data is often unphased, and therefore it is difficult to apply statistics intended for phased data. Here, we introduce the G12 and G123 statistics for detecting hard and soft sweeps from unphased data. These statistics are analogs to the H12 statistic for phased data (Garud et al. 2015). We also introduce G2/G1 to classify hard and soft sweeps analogously to H2/H1, conditional on a genomic region having high G12 and G123 values.

Please visit my github repository for code to compute H12, H123, H2/H1, G12, G123, and G2/G1:

Below: A visual depiction of H12 and G123.

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New York Area Population Genomics Meeting

I will be presenting my latest paper on the evolution of bacteria in the gut microbiome at the New York Area Population Genomics Meeting at Cold Spring Harbor.

Bacteria in the microbiome can potentially respond to selective pressures in many ways. One possible mechanism could be via a change in the relative abundances of species. Alternatively, a better fit strain could invade the population. Or, a pre-existing strain could evolve an adaptive mutation. Although differences in species abundances and the genetic composition between samples has been well-studied, little is known about whether lineages within a healthy host can evolve. Here is a preview of the hypotheses I will be addressing in my talk!

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