Inference of the Demographic Histories and Selective Effects of Human Gut Commensal Microbiota Over the Course of Human History
Open accessPublished version of a preprint
Abstract
Despite the importance of gut commensal microbiota to human health, there is little knowledge about their evolutionary histories, including their demographic histories and distributions of fitness effects (DFEs) of mutations. Here, we infer the demographic histories and DFEs for amino acid-changing mutations of 39 of the most prevalent and abundant commensal gut microbial species found in Westernized individuals over timescales exceeding human generations. Some species display contractions in population size and others expansions, with several of these events coinciding with several key historical moments in human history. DFEs across species vary from highly to mildly deleterious, with differences between accessory and core gene DFEs largely driven by genetic drift. Within genera, DFEs tend to be more congruent, reflective of underlying phylogenetic relationships. Together, these findings suggest that gut microbes have distinct demographic and selective histories.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The higher biodiversity observed in non-Westernized settings is consistent with more heterogeneous dietary and environmental exposures allowing a broader range of accessory gene content to persist than in industrialized populations.
“This characteristic is consistent with the higher biodiversity observed in non-Westernized settings, where more heterogeneous dietary and environmental exposures may allow a broader range of accessory gene content to persist than is usually observed in genomes from industrialized populations [73-75] .”
From Genome-scale insights into the metabolic landscape and evolutionary development of Bifidobacterium bifidum (2026) · cites this paper as [75]
The Introduction (page unavailable) reports greater species-, gene-, and nucleotide-level diversity in rural African than urban Western microbiomes and identifies shifts in diet as a possible contributor. The Results (page unavailable) also find lower nucleotide diversity in North American than rural African microbiomes. The paper does not establish that heterogeneous dietary and environmental exposures allow broader accessory-gene content to persist in non-Westernized populations. (LLM, conf=0.85)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400 · see citing works
A human gut microbial gene catalogue established by metagenomic sequencing
MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature · doi:10.1038/nature08821 · Cited by 11,624 · see citing works
ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R
Paradis, E., & Schliep, K. P. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty633 · Cited by 9,224 · see citing works
Human gut microbiome viewed across age and geography
Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R. N., Anokhin, A. P., et al. (2012) · Nature · doi:10.1038/nature11053 · Cited by 7,815 · see citing works
Linking long-term dietary patterns with gut microbial enterotypes
Wu, G. D., Chen, J., Hoffmann, C., Bittinger, K., Chen, Y.-Y., Keilbaugh, S. A., Bewtra, M., Knights, D., Walters, W. A., Knight, R., et al. (2011) · Science · doi:10.1126/science.1208344 · Cited by 6,513 · see citing works
Turnbaugh, P. J., Ley, R. E., Hamady, M., Fraser-Liggett, C. M., Knight, R., & Gordon, J. I. (2007) · Nature · doi:10.1038/nature06244 · Cited by 6,091 · see citing works
De Filippo, C., Cavalieri, D., Di Paola, M., Ramazzotti, M., Poullet, J. B., Massart, S., Collini, S., Pieraccini, G., & Lionetti, P. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1005963107 · Cited by 5,579 · see citing works
A framework for human microbiome research
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11209 · Cited by 2,650 · see citing works
Opportunities and challenges in long-read sequencing data analysis
Amarasinghe, S. L., Su, S., Dong, X., Zappia, L., Ritchie, M. E., & Gouil, Q. (2020) · Genome Biology · doi:10.1186/s13059-020-1935-5 · Cited by 2,530 · see citing works
Adaptation, Plasticity, and Extinction in a Changing Environment: Towards a Predictive Theory
Chevin, L., Lande, R., & Mace, G. M. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000357 · Cited by 1,968 · see citing works
Gutenkunst, R. N., Hernandez, R. D., Williamson, S. H., & Bustamante, C. D. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000695 · Cited by 1,906 · see citing works
Hitchhiking Under Positive Darwinian Selection
Fay, J. C., & Wu, C.-I. (2000) · Genetics · doi:10.1093/genetics/155.3.1405 · Cited by 1,819 · see citing works
Smith, J. M., Smith, N. H., O'Rourke, M., & Spratt, B. G. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.10.4384 · Cited by 1,802 · see citing works
Diet-induced extinctions in the gut microbiota compound over generations
Sonnenburg, E. D., Smits, S. A., Tikhonov, M., Higginbottom, S. K., Wingreen, N. S., & Sonnenburg, J. L. (2016) · Nature · doi:10.1038/nature16504 · Cited by 1,730 · see citing works
Pasolli, E., Asnicar, F., Manara, S., Zolfo, M., Karcher, N., Armanini, F., Beghini, F., Manghi, P., Tett, A., Ghensi, P., et al. (2019) · Cell · doi:10.1016/j.cell.2019.01.001 · Cited by 1,591 · see citing works
The distribution of fitness effects of new mutations
Eyre‐Walker, A., & Keightley, P. D. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2146 · Cited by 1,444 · see citing works
Gut microbiome of the Hadza hunter-gatherers
Schnorr, S. L., Candela, M., Rampelli, S., Centanni, M., Consolandi, C., Basaglia, G., Turroni, S., Biagi, E., Peano, C., Severgnini, M., et al. (2014) · Nature Communications · doi:10.1038/ncomms4654 · Cited by 1,317 · see citing works
Strains, functions and dynamics in the expanded Human Microbiome Project
Lloyd-Price, J., Mahurkar, A., Rahnavard, G., Crabtree, J., Orvis, J., Hall, A. B., Brady, A., Creasy, H. H., McCracken, C., Giglio, M. G., et al. (2017) · Nature · doi:10.1038/nature23889 · Cited by 1,267 · see citing works
A constant rate of spontaneous mutation in DNA-based microbes.
Drake, J. W. (1991) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.88.16.7160 · Cited by 1,199 · see citing works
Traces of Human Migrations in Helicobacter pylori Populations
Falush, D., Wirth, T., Linz, B., Pritchard, J. K., Stephens, M., Kidd, M. S., Blaser, M. J., Graham, D. Y., Vacher, S., Perez-Perez, G. I., et al. (2003) · Science · doi:10.1126/science.1080857 · Cited by 1,019 · see citing works
Genomic variation landscape of the human gut microbiome
Schloissnig, S., Arumugam, M., Sunagawa, S., Mitreva, M., Tap, J., Zhu, A., Waller, A., Mende, D. R., Kultima, J. R., Martin, J., et al. (2013) · Nature · doi:10.1038/nature11711 · Cited by 907 · see citing works
The microbiome of uncontacted Amerindians
Clemente, J. C., Pehrsson, E. C., Blaser, M. J., Sandhu, K., Gao, Z., Wang, B., Magris, M., Hidalgo, G., Contreras, M., Noya-Alarcón, Ó., et al. (2015) · Science Advances · doi:10.1126/sciadv.1500183 · Cited by 851 · see citing works
Microbial strain-level population structure and genetic diversity from metagenomes
Truong, D. T., Tett, A., Pasolli, E., Huttenhower, C., & Segata, N. (2017) · Genome Research · doi:10.1101/gr.216242.116 · Cited by 839 · see citing works
Assessing the evolutionary impact of amino acid mutations in the human genome.
Boyko, A. R., Williamson, S. H., Indap, A. R., Degenhardt, J. D., Hernandez, R. D., Lohmueller, K. E., Adams, M. D., Schmidt, S., Sninsky, J. J., Sunyaev, S. R., et al. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000083 · Cited by 628 · see citing works
Self-citationGenome dynamics during experimental evolution
Barrick, J. E., & Lenski, R. E. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3564 · Cited by 619 · see citing works
The hitchhiking effect on the site frequency spectrum of DNA polymorphisms
Braverman, J. M., Hudson, R. R., Kaplan, N. L., Langley, C. H., & Stephan, W. (1995) · Genetics · doi:10.1093/genetics/140.2.783 · Cited by 601 · see citing works
Subsistence strategies in traditional societies distinguish gut microbiomes
Obregon-Tito, A. J., Tito, R. Y., Metcalf, J., Sankaranarayanan, K., Clemente, J. C., Ursell, L. K., Zech Xu, Z., Van Treuren, W., Knight, R., Gaffney, P. M., et al. (2015) · Nature Communications · doi:10.1038/ncomms7505 · Cited by 587 · see citing works
Cospeciation of gut microbiota with hominids
Moeller, A. H., Caro‐Quintero, A., Mjungu, D. C., Georgiev, A. V., Lonsdorf, E. V., Muller, M. N., Pusey, A. E., Peeters, M., Hahn, B. H., & Ochman, H. (2016) · Science · doi:10.1126/science.aaf3951 · Cited by 570 · see citing works
A comparison of homologous recombination rates in bacteria and archaea
Vos, M., & Didelot, X. (2008) · The ISME Journal · doi:10.1038/ismej.2008.93 · Cited by 541 · see citing works
Olm, M. R., Crits-Christoph, A., Bouma-Gregson, K., Firek, B. A., Morowitz, M. J., & Banfield, J. F. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-00797-0 · Cited by 537 · see citing works
phylosignal: an R package to measure, test, and explore the phylogenetic signal
Keck, F., Rimet, F., Bouchez, A., & Franc, A. (2016) · Ecology and Evolution · doi:10.1002/ece3.2051 · Cited by 499 · see citing works
Tett, A., Huang, K. D., Asnicar, F., Fehlner-Peach, H., Pasolli, E., Karcher, N., Armanini, F., Manghi, P., Bonham, K., Zolfo, M., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.08.018 · Cited by 476 · see citing works
Nayfach, S., Rodriguez-Mueller, B., Garud, N., & Pollard, K. S. (2016) · Genome Research · doi:10.1101/gr.201863.115 · Cited by 470 · see citing works
Self-citationAdaptive Evolution within Gut Microbiomes of Healthy People
Zhao, S., Lieberman, T. D., Poyet, M., Kauffman, K. M., Gibbons, S. M., Groussin, M., Xavier, R. J., & Alm, E. J. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.03.007 · Cited by 434 · see citing works
Estimating Ancestral Population Parameters
Wakeley, J., & Hey, J. (1997) · Genetics · doi:10.1093/genetics/145.3.847 · Cited by 393 · see citing works
The distribution of fitness effects of new deleterious amino acid mutations in humans.
Eyre-Walker, A., Woolfit, M., & Phelps, T. (2006) · Genetics · doi:10.1534/genetics.106.057570 · Cited by 377 · see citing works
Gillespie, J. (2004) · doi:10.56021/9780801880087 · Cited by 366 · see citing works
Estimation of Population Parameters and Recombination Rates From Single Nucleotide Polymorphisms
Nielsen, R. (2000) · Genetics · doi:10.1093/genetics/154.2.931 · Cited by 359 · see citing works
Keightley, P. D., & Eyre‐Walker, A. (2007) · Genetics · doi:10.1534/genetics.107.080663 · Cited by 358 · see citing works
Evolutionary dynamics of bacteria in the gut microbiome within and across hosts
Garud, N. R., Good, B. H., Hallatschek, O., & Pollard, K. S. (2019) · PLoS Biology · doi:10.1371/journal.pbio.3000102 · Cited by 347 · see citing works
Self-citationXie, H., Guo, R., Zhong, H., Feng, Q., Lan, Z., Qin, B., Ward, K. J., Jackson, M. A., Xia, Y., Chen, X., et al. (2016) · Cell Systems · doi:10.1016/j.cels.2016.10.004 · Cited by 341 · see citing works
Rapid changes in the gut microbiome during human evolution
Moeller, A. H., Li, Y., Ngole, E. M., Ahuka‐Mundeke, S., Lonsdorf, E. V., Pusey, A. E., Peeters, M., Hahn, B. H., & Ochman, H. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1419136111 · Cited by 336 · see citing works
Vulnerability of the industrialized microbiota
Sonnenburg, J. L., & Sonnenburg, E. D. (2019) · Science · doi:10.1126/science.aaw9255 · Cited by 331 · see citing works
Williamson, S., Hernandez, R. D., Fledel-Alon, A., Zhu, L., Nielsen, R., & Bustamante, C. D. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0502300102 · Cited by 325 · see citing works
Selective maternal seeding and environment shape the human gut microbiomePreprint
Korpela, K., Costea, P. I., Coelho, L. P., Kandels-Lewis, S. E., Willemsen, G. A. H. M., Boomsma, D. I., Segata, N., & Bork, P. (2018) · Genome Research · doi:10.1101/gr.233940.117 · Cited by 325 · see citing works
Escherichia coli Habitats, Cell Types, and Molecular Mechanisms of Gene Control
Savageau, M. A. (1983) · The American Naturalist · doi:10.1086/284168 · Cited by 315 · see citing works
Directional Selection and the Site-Frequency Spectrum
Bustamante, C. D., Wakeley, J., Sawyer, S. A., & Hartl, D. L. (2001) · Genetics · doi:10.1093/genetics/159.4.1779 · Cited by 227 · see citing works
Confounding from Cryptic Relatedness in Case-Control Association Studies
Voight, B. F., & Pritchard, J. K. (2005) · PLoS Genetics · doi:10.1371/journal.pgen.0010032 · Cited by 216 · see citing works
Städler, T., Haubold, B., Merino, C., Stephan, W., & Pfaffelhuber, P. (2009) · Genetics · doi:10.1534/genetics.108.094904 · Cited by 214 · see citing works
Codiversification of gut microbiota with humans
Suzuki, T. A., Fitzstevens, J. L., Schmidt, V. T., Enav, H., Huus, K. E., Mbong Ngwese, M., Grießhammer, A., Pfleiderer, A., Adegbite, B. R., Zinsou, J. F., et al. (2022) · Science · doi:10.1126/science.abm7759 · Cited by 210 · see citing works
Using Genomic Data to Infer Historic Population Dynamics of Nonmodel Organisms
Beichman, A. C., Huerta‐Sánchez, E., & Lohmueller, K. E. (2018) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev-ecolsys-110617-062431 · Cited by 207 · see citing works
Self-citationEvolutionary and Population Genomics of the Cavity Causing Bacteria Streptococcus mutans
Cornejo, O. E., Lefébure, T., Pavinski Bitar, P. D., Lang, P., Richards, V. P., Eilertson, K., Do, T., Beighton, D., Zeng, L., Ahn, S.-J., et al. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mss278 · Cited by 198 · see citing works
Kim, B. Y., Huber, C. D., & Lohmueller, K. E. (2017) · Genetics · doi:10.1534/genetics.116.197145 · Cited by 194 · see citing works
Self-citationGenetic Diversity and the Efficacy of Purifying Selection across Plant and Animal Species
Chen, J., Glémin, S., & Lascoux, M. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx088 · Cited by 190 · see citing works
Factors driving effective population size and pan-genome evolution in bacteria
Bobay, L., & Ochman, H. (2018) · BMC Evolutionary Biology · doi:10.1186/s12862-018-1272-4 · Cited by 150 · see citing works
Subspecies in the global human gut microbiome
Costea, P. I., Coelho, L. P., Sunagawa, S., Munch, R., Huerta‐Cepas, J., Forslund, S. K., Hildebrand, F., Kushugulova, A. R., Zeller, G., & Bork, P. (2017) · Molecular Systems Biology · doi:10.15252/msb.20177589 · Cited by 141 · see citing works
Determining the factors driving selective effects of new nonsynonymous mutations
Huber, C. D., Kim, B. Y., Marsden, C. D., & Lohmueller, K. E. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1619508114 · Cited by 140 · see citing works
Self-citationPopulation Genetics in the Human Microbiome
Garud, N. R., & Pollard, K. S. (2019) · Trends in Genetics · doi:10.1016/j.tig.2019.10.010 · Cited by 137 · see citing works
Self-citationThe Role of Selection in Shaping Diversity of Natural M. tuberculosis Populations
Pepperell, C. S., Casto, A. M., Kitchen, A., Granka, J. M., Cornejo, O. E., Holmes, E. C., Birren, B. W., Galagan, J. E., & Feldman, M. W. (2013) · PLoS Pathogens · doi:10.1371/journal.ppat.1003543 · Cited by 127 · see citing works
Why Genes Evolve Faster on Secondary Chromosomes in Bacteria
Cooper, V. S., Vohr, S. H., Wrocklage, S. C., & Hatcher, P. J. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000732 · Cited by 116 · see citing works
Quantifying bias introduced by sample collection in relative and absolute microbiome measurements
Maghini, D. G., Dvorak, M., Dahlen, A., Roos, M., Doyle, B., Kuersten, S., & Bhatt, A. S. (2024) · Nature Biotechnology · doi:10.1038/s41587-023-01754-3 · Cited by 116 · see citing works
Karcher, N., Pasolli, E., Asnicar, F., Huang, K. D., Tett, A., Manara, S., Armanini, F., Bain, D., Duncan, S. H., Louis, P., et al. (2020) · Genome Biology · doi:10.1186/s13059-020-02042-y · Cited by 116 · see citing works
Johri, P., Riall, K., Becher, H., Excoffier, L., Charlesworth, B., & Jensen, J. D. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab050 · Cited by 115 · see citing works
Rocha, E. P. C., & Feil, E. J. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001104 · Cited by 103 · see citing works
Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species
Sakoparnig, T., Field, C. M., & van Nimwegen, E. (2021) · eLife · doi:10.7554/elife.65366 · Cited by 94 · see citing works
Evidence for Abundant Slightly Deleterious Polymorphisms in Bacterial Populations
Hughes, A. L. (2004) · Genetics · doi:10.1534/genetics.104.036939 · Cited by 91 · see citing works
Lapierre, M., Lambert, A., & Achaz, G. (2017) · Genetics · doi:10.1534/genetics.116.192708 · Cited by 91 · see citing works
Gibbons, R. J., & Kapsimalis, B. (1967) · Journal of Bacteriology · doi:10.1128/jb.93.1.510-512.1967 · Cited by 84 · see citing works
Inferring bacterial recombination rates from large-scale sequencing datasets
Lin, M., & Kussell, E. L. (2019) · Nature Methods · doi:10.1038/s41592-018-0293-7 · Cited by 82 · see citing works
Neutral genomic regions refine models of recent rapid human population growth
Gazave, É., Ma, L., Chang, D., Coventry, A., Gao, F., Muzny, D. M., Boerwinkle, E., Gibbs, R. A., Sing, C. F., Clark, A. G., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1310398110 · Cited by 79 · see citing works
The Past and Future Biology of the Human Microbiome in an Age of Extinctions
Blaser, M. J. (2018) · Cell · doi:10.1016/j.cell.2018.02.040 · Cited by 76 · see citing works
Murphy, D. A., Elyashiv, E., Amster, G., & Sella, G. (2022) · eLife · doi:10.7554/elife.76065 · Cited by 58 · see citing works
Comparative population genomics: power and principles for the inference of functionality
Lawrie, D. S., & Petrov, D. A. (2014) · Trends in Genetics · doi:10.1016/j.tig.2014.02.002 · Cited by 52 · see citing works
Microbiome of uncontacted Amerindians
Yèagle, P. L. (2015) · Science · doi:10.1126/science.348.6232.298-a · Cited by 42 · see citing works
Inferring Genome-Wide Correlations of Mutation Fitness Effects between Populations
Huang, X., Fortier, A. L., Coffman, A. J., Struck, T. J., Irby, M. N., James, J., León-Burguete, J. E., Ragsdale, A. P., & Gutenkunst, R. N. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab162 · Cited by 36 · see citing works
Ghosh, O. M., & Good, B. H. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2114931119 · Cited by 36 · see citing works
Within-host evolution of the gut microbiome
Đapa, T., Wong, D. P. G. H., Vasquez, K. S., Xavier, K. B., Huang, K. C., & Good, B. H. (2023) · Current Opinion in Microbiology · doi:10.1016/j.mib.2022.102258 · Cited by 36 · see citing works
Dynamics of bacterial recombination in the human gut microbiome
Liu, Z., & Good, B. H. (2024) · PLoS Biology · doi:10.1371/journal.pbio.3002472 · Cited by 34 · see citing works
Quantifying the adaptive landscape of commensal gut bacteria using high-resolution lineage tracking
Wong, D. P. G. H., & Good, B. H. (2024) · Nature Communications · doi:10.1038/s41467-024-45792-0 · Cited by 21 · see citing works
Murphy, D. A., Elyashiv, E., Amster, G., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.02.450762 · Cited by 20 · see citing works
A Method to Correct for the Effects of Purifying Selection on Genealogical Inference
O’Fallon, B. D. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq132 · Cited by 16 · see citing works
Nayfach, S., Rodriguez-Mueller, B., Garud, N. R., & Pollard, K. S. (2015) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/031757 · Cited by 14 · see citing works
Self-citationConfounding from Cryptic Relatedness in Case-Control Association Studies
Voight, B. F., & Pritchard, J. K. (2005) · PLoS Genetics · doi:10.1371/journal.pgen.0010032.eor · Cited by 13 · see citing works
Adaptation in a Fibronectin Binding Autolysin of Staphylococcus saprophyticus
Mortimer, T. D., Annis, D. S., O’Neill, M. B., Bohr, L. L., Smith, T. M., Poinar, H. N., Mosher, D. F., & Pepperell, C. S. (2017) · mSphere · doi:10.1128/msphere.00511-17 · Cited by 12 · see citing works
Shiver, A. L., Sun, J., Culver, R. N., Violette, A., Wynter, C., Nieckarz, M., Mattiello, S. P., Sekhon, P. K., Friess, L., Carlson, H. K., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.08.29.555234 · Cited by 12 · see citing works
N’Guessan, A., Brito, I., Serohijos, A. W. R., & Shapiro, B. J. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab142 · Cited by 10 · see citing works
Pervasive selective sweeps across human gut microbiomesPreprint
Wolff, R., & Garud, N. R. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.12.22.573162 · Cited by 8 · see citing works
Self-citationThe impact of non-neutral synonymous mutations when inferring selection on nonsynonymous mutations
Martinez, A. Z., Kyriazis, C. C., & Lohmueller, K. E. (2025) · Genetics · doi:10.1093/genetics/iyaf200 · Cited by 6 · see citing works
Self-citationLinkage equilibrium between rare mutations
Lyulina, A. S., Liu, Z., & Good, B. H. (2024) · Genetics · doi:10.1093/genetics/iyae145 · Cited by 5 · see citing works
Genomic Expansions in the Human Gut Microbiome
Moeller, A. H. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab156 · Cited by 4 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- Nayfach S., Pollard K.S., 2015. Population genetic analyses of metagenomes reveal extensive strain-level variation in prevalent human-associated bacteria. bioRxiv 031757.
Cited by
Sorted by citations
Selleri, E., Longhi, G., Tarracchini, C., Carolis, E. D., Petraro, S., Mancabelli, L., Milani, C., Turroni, F., Ventura, M., & Lugli, G. A. (2026) · Microbiome Research Reports · doi:10.20517/mrr.2026.19
- Authors
- Mah, J. C., Lohmueller, K. E., & Garud, N. R.
- Affiliations
- University of California, Los Angeles (US)
- Corresponding author
- Lohmueller, Kirk E
- Garud, Nandita R
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2025-01-22
- Volume
- 42
- Issue
- 2
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- PMC
- PMC10680615
- OpenAlex
- W4406708630
- Cited by
- 11
- References
- 90
- Citations by year
- 2026: 3 · 2025: 4 · 2024: 3 · 2023: 1
- FWCI
- 4.09
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Molecular Biology and Evolution (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- PubMed Central (submittedVersion, cc-by-nc-nd)
- Funders
- NIGMS NIH (T32 5T32GM008185, R35GM151023, R35GM119856, 2240098)
- Paul Allen Research Foundation
- UC Hellman Fellows
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- gut microbiota, demography, genetic drift, accessory genes, core genes, historical demography
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
