Reposted by Nandita GarudDmitri Petrov @petrovadmitri.bsky.social · 15/07/2026Cannot be more excited about the lineup for the inaugural Function of Evolving Systems GRC conference I am co-organizing with the amazing Joy Bergelson. Less than a month away: August 9 - 14, 2026. Still a few spots left! And do check out the amazing list of speakers: www.grc.org/function-of-...grc.org2026 Function of Evolving Systems Conference GRCThe 2026 Gordon Research Conference on Function of Evolving Systems will be held in Waterville Valley, New Hampshire. Apply today to reserve your spot. 44026
Nandita Garud @nanditagarud.bsky.social · 30/06/2026We are very excited to share our latest. We thought that soft sweeps would be the only type of sweep spreading across human gut microbiomes. Turns out many are hard! Reach @peterlaurin.bsky.social 's thread on why! And tomorrow at #SMBE2026 I will share this work and more! 14017
Nandita Garud @nanditagarud.bsky.social · 17/06/2026UCLA is so lucky to have this amazing course by @clsong.com ! 1100
Nandita Garud @nanditagarud.bsky.social · 06/05/2026In sum, the number, modalities and dynamics of selective sweeps over human history still remains to be fully understood. Our approach with the DANN provides a new lens on the prevalence and resilience of hard sweeps over the past 7000 years. We hope you enjoy the paper! (5/5) 050
Nandita Garud @nanditagarud.bsky.social · 06/05/2026Moreover, we found that while some ancient sweeps were lost in more recent epochs, several persisted from the earliest to the most recent time periods, highlighting potentially important traits resilient to the effects of strong admixture. (4/n) 120
Nandita Garud @nanditagarud.bsky.social · 06/05/2026That hard sweeps were common is consistent with the historically low effective population size in humans. (3/n) 110
Nandita Garud @nanditagarud.bsky.social · 06/05/2026In this paper we applied a Domain Adaptive Neural Network to discover ~50 sweeps from 7000 years of Eurasian aDNA, correcting for any simulation model misspecification. We found that hard sweeps, as opposed to soft sweeps, were the dominant mode of evolution throughout human history. (2/n) 110
Nandita Garud @nanditagarud.bsky.social · 06/05/2026Our paper entitled "The persistence and loss of hard selective sweeps amid admixture in ancient Eurasians" is now out in PNAS! www.pnas.org/doi/abs/10.1.... A really fun and informative collaboration with @mharris.bsky.social, Ziyi Mo and Adam Siepel. (1/n)pnas.orgThe persistence and loss of hard selective sweeps amid admixture in ancient Eurasians | PNASThe extent to which human adaptations have persisted throughout history despite strong eroding demographic events such as admixture, genetic drift,... 17026
Nandita Garud @nanditagarud.bsky.social · 31/03/2026Finally, if interested, please check out @michaelwasney.bsky.social 's talk on this work, broadcasted by MVIF (and won best talk prize in his session!) www.youtube.com/watch?v=vAzH... (6/6)youtube.comMichael Wasney - Uniform bacterial genetic diversity of mice inoculated with human stool |MVIF40 S04YouTube video by Microbiome Virtual International Forum 041
Nandita Garud @nanditagarud.bsky.social · 31/03/2026This work was led by @michaelwasney.bsky.social and @leahbriscoe.bsky.social and was a fun collaboration with @ctropini.bsky.social's lab! Many thanks to @rwolff.bsky.social and Hans Gezzi for their hard work and insights as well in making this work possible. (5/n) 111
Nandita Garud @nanditagarud.bsky.social · 31/03/2026More work is needed in the future to understand if there is spatial segregation at finer scales as well as in the mucosa. But, for now, we start to obtain a picture of uniform diversity along the gut at the strain and evolutionary level. (4/n) 111
Nandita Garud @nanditagarud.bsky.social · 31/03/2026We found that these results replicate in both mice as well as humans. These results indicate that spatial segregation is not a requisite for strain coexistence in the gut microbiome (at least in the lumen) and that evolutionary changes do not face barriers in their spread. (3/n) 111
Nandita Garud @nanditagarud.bsky.social · 31/03/2026In this work we sought to understand how strains and their evolutionary adaptations are distributed along the lumen of the mouse gut. We found a surprising amount of uniformity despite there being extensive species-level heterogeneity along the gut. (2/n) 121
Nandita Garud @nanditagarud.bsky.social · 31/03/2026I am excited to share our latest paper, Uniform bacterial genetic diversity along the gut, now out in Nature Communications! www.nature.com/articles/s41.... (1/n) 27032
Nandita Garud @nanditagarud.bsky.social · 12/02/2026I am seeking a postdoc to join my group at UCLA -- ideally the candidate would have some experience in either population genetics or microbes/microbiome (computational background needed). We have a range of projects and are happy to tailer to your interests. Please dm/email me if interested. 05796
Nandita Garud @nanditagarud.bsky.social · 17/12/2025If you are interested in this work and are looking for a postdoc position, please get in touch -- we are actively looking for someone to join our group at UCLA! 0148
Nandita Garud @nanditagarud.bsky.social · 17/12/2025Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible. www.nature.com/articles/s41...nature.comGene-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 ... 1014969
Reposted by Nandita GarudGenetics Society of America @genetics-gsa.bsky.social · 05/12/2025New research in #GENETICS from @azurita.bsky.social, Christopher Kyriazis, and @klohmueller.bsky.social demonstrates how unmodeled selection on synonymous mutations may affect downstream inferences of the distribution of fitness effects. buff.ly/IDY87W1 053
Reposted by Nandita GarudZamin Iqbal @zaminiqbal.bsky.social · 25/09/2025Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols. Thread 1/n 14300154
Reposted by Nandita GarudBen Good @benjaminhgood.bsky.social · 16/08/2025Excited to share a new preprint w/ the Sonnenberg lab, led by Matt Carter, @zzzhiru.bsky.social & @mattolm.bsky.social. We analyzed the microbiomes of two non-industrialized populations from opposite sides of the globe to try to reconstruct the recent evolutionary history of our gut microbiota.biorxiv.orgPrehistoric Global Migration of Vanishing Gut Microbes With HumansThe gut microbiome is crucial for health and greatly affected by lifestyle. Many microbes common in non-industrialized populations are disappearing or extinct in industrialized populations. Understand... 26521
Nandita Garud @nanditagarud.bsky.social · 22/07/2025I am seeking a postdoc for my group at UCLA. We work at the intersection of population genetics x microbiome (garud.eeb.ucla.edu). If interested, please message me!garud.eeb.ucla.eduGarud Lab 18598
Reposted by Nandita GarudKatherine Xue @ksxue.bsky.social · 17/07/2025The Xue lab at UC Irvine is looking for a staff scientist to support our work investigating how microbes interact and evolve in the gut microbiome! Open to a wide range of previous experience levels, see ad for more. recruit.ap.uci.edu/JPF09601recruit.ap.uci.eduJunior, Assistant, or Associate Specialist – Xue LabUniversity of California, Irvine is hiring. Apply now! 0117112
Nandita Garud @nanditagarud.bsky.social · 19/06/2025So excited to see @alisonfeder.bsky.social among the winners of the freeman hrabowski award!! www.hhmi.org/programs/fre...hhmi.orgThe 2025 Freeman Hrabowski Scholars | HHMIFreeman Hrabowski Scholars are outstanding early career faculty who have the potential to become leaders in their research fields. 3287
Reposted by Nandita GarudXinjun Zhang @zhanglabpopgen.bsky.social · 08/05/2025Super excited to share my latest preprint with @klohmueller.bsky.social! Here we leverage the unique signature that recessive deleterious variants can lead to an increase in archaic ancestry to tackle a classic question - the dominance distribution on the human genome www.biorxiv.org/content/10.1...biorxiv.orgNeanderthal introgressed ancestry reveals human genomic regions enriched with recessive deleterious mutationsNegative natural selection on deleterious mutations plays a key role in shaping human genetic variation. Understanding the dominance of deleterious mutations is critical as it can fundamentally impact... 23217
Nandita Garud @nanditagarud.bsky.social · 24/01/2025This work provides an unprecedented inference of the demographic histories and DFEs of ~25 common gut commensals. Inferring so many models was not an easy task, but was gamely taken on by the talented @jonmah.bsky.social. Many thanks also to @klohmueller.bsky.social for such a fun collaboration! 060
Nandita Garud @nanditagarud.bsky.social · 24/01/2025We are thrilled to share that our paper entitled "Inference of the demographic histories and selective effects of human gut commensal microbiota over the course of human history" is officially out in MBE! academic.oup.com/mbe/advance-...academic.oup.comInference of the demographic histories and selective effects of human gut commensal microbiota over the course of human historyAbstract. Despite the importance of gut commensal microbiota to human health, there is little knowledge about their evolutionary histories, including their 26124
Reposted by Nandita GarudChuliang Song @clsong.com · 14/01/2025Thrilled to share my Perspective piece "Assembly Graph as the Rosetta Stone of Ecological Assembly" in Environmental Microbiology! Huge thanks to @asanchezlab.bsky.social for the invite & reviewers for insightful feedback.enviromicro-journals.onlinelibrary.wiley.comAssembly Graph as the Rosetta Stone of Ecological AssemblyThis paper introduces the assembly graph as an integrative lens to unify ecological assembly theories across dynamical, informational, and probabilistic approaches. In addition to theory, it also pre... 33310
Nandita Garud @nanditagarud.bsky.social · 06/01/2025UCLA QCBIO is looking for its next director! Please consider applying! recruit.apo.ucla.edu/JPF10007recruit.apo.ucla.eduDirector, Institute for Quantitative and Computational BiosciencesUniversity of California, Los Angeles is hiring. Apply now! 02129
Reposted by Nandita GarudKarina Gutiérrez García @karinagtz.bsky.social · 23/12/2024Finally, our paper, "A Conserved Bacterial Genetic Basis for Commensal-Host Specificity," has been officially published in Science. www.science.org/doi/10.1126/...science.orgA conserved bacterial genetic basis for commensal-host specificityAnimals selectively acquire specific symbiotic gut bacteria from their environments that aid host fitness. To colonize, a symbiont must locate its niche and sustain growth within the gut. Adhesins are... 27924
Nandita Garud @nanditagarud.bsky.social · 20/11/2024Apply to work with Katherine! A fantastic opportunity! 030
Reposted by Nandita GarudKatherine Xue @ksxue.bsky.social · 19/11/2024Hi friends new and old! I study how microbes interact and evolve in complex communities like the human gut microbiome.🦠🧬💩 I'm thrilled to share that I'm starting a lab at UC Irvine in April 2025 and am recruiting at all levels - please spread the word! kxuelab.com More about my work below...🧵1/nkxuelab.comXue lab at UC IrvineEcology and evolution in the human gut microbiome 24390115
Nandita Garud @nanditagarud.bsky.social · 13/11/2024Delighted to share that our paper on discovering selective sweeps with haplotype statistics in aDNA is now out in Nat. Comm! www.nature.com/articles/s41... Wonderful collaboration with Vagheesh Narasimhan, Devansh Pandey, and @mharris.bsky.socialnature.comLeveraging ancient DNA to uncover signals of natural selection in Europe lost due to admixture or drift - Nature CommunicationsLarge-scale ancient DNA (aDNA) studies offer the chance to examine genomic changes over time, providing direct insights into human evolution. Here the authors use aDNA from 708 European samples to ide... 06127
Reposted by Nandita GarudKirk Lohmueller @klohmueller.bsky.social · 12/11/2024Hi all! I'm excited to announce a tenure track faculty position in conservation genomics in EEB at UCLA! We're looking for candidates who use genomic tools to study evolutionary processes related to conservation. Note, the actual application deadline is Nov 29. recruit.apo.ucla.edu/JPF09875recruit.apo.ucla.eduConservation Genomics Faculty PositionUniversity of California, Los Angeles is hiring. Apply now! 08599
Nandita Garud @nanditagarud.bsky.social · 23/10/2024Job alert! We are searching for a faculty member to join us @UCLAEEB in the area of Conservation Genomics. I have had very positive experiences here at UCLA and would be happy to chat with you if you are interested! Please apply and be my colleague! recruit.apo.ucla.edu/JPF09875recruit.apo.ucla.eduConservation Genomics Faculty PositionUniversity of California, Los Angeles is hiring. Apply now! 0417
Nandita Garud @nanditagarud.bsky.social · 16/04/2024The UCLA Goodman-Luskin Endowed Postdoctoral Fellowship in Microbiome Research ($100K in salary + supplies) deadline is June 1. Get in touch if you would like to write a proposal together! And, get in touch even if your timeline is different - I am looking for a postdoc! 022
Reposted by Nandita GarudZhiru Liu @zzzhiru.bsky.social · 14/02/2024Excited (and relieved!) to share that my 1st paper in grad school finally came out in PLOS Biology! We were motivated by a very basic question: how fast, really, do bacteria exchange DNA in the human gut? (1/n)t.coDynamics 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... 37631
Nandita Garud @nanditagarud.bsky.social · 10/01/2024Really proud of this work with Richard Wolff on detecting selective sweeps that have spread across host microbiomes. I leave for you an animation we made featuring the highlights of our paper. Ricky has done a great job sharing some highlights of the paper below. garud.eeb.ucla.edu/pervasive-se... 0121
Nandita Garud @nanditagarud.bsky.social · 14/11/2023This was an extremely fun collaboration with first author @jonmah.bsky.social and co-senior author @klohmueller.bsky.social. It has been a dream of mine to learn from Kirk’s deep wisdom on demographic and DFE inference, and I am grateful that the three of us could make paper happen. 010
Nandita Garud @nanditagarud.bsky.social · 14/11/2023We are delighted to share our work on “Inference of the demographic histories and selective effects of human gut commensal microbiota over the course of human history”! www.biorxiv.org/content/10.1... Please check out the full tweet thread and GIF here: twitter.com/nanditagarud... 21510
Nandita Garud @nanditagarud.bsky.social · 19/10/2023I am looking for a graduate student and a postdoc to join my group! We are a computational group working on understanding evolution in natural populations with a large emphasis on the microbiome. Please get in touch by dm or email! garud.eeb.ucla.edu 05376
Nandita Garud @nanditagarud.bsky.social · 17/09/2023Very cool work Paul Torrillo and @contaminatedsci.bsky.social!! We saw some empirical evidence of reversions at 1D sites in infant microbiome evolution: genome.cshlp.org/content/32/6... 140
