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Woitowich NC, Hengel SR, Solis C, Vilgalys TP, Babdor J, Tyrrell DJ. Analysis of NIH K99/R00 awards and the career progression of awardees. eLife 2024; 12:RP88984. [PMID: 38240745 PMCID: PMC10945599 DOI: 10.7554/elife.88984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2024] Open
Abstract
Many postdoctoral fellows and scholars who hope to secure tenure-track faculty positions in the United States apply to the National Institutes of Health (NIH) for a Pathway to Independence Award. This award has two phases (K99 and R00) and provides funding for up to 5 years. Using NIH data for the period 2006-2022, we report that ~230 K99 awards were made every year, representing up to ~$250 million annual investment. About 40% of K99 awardees were women and ~89% of K99 awardees went on to receive an R00 award annually. Institutions with the most NIH funding produced the most recipients of K99 awards and recruited the most recipients of R00 awards. The time between a researcher starting an R00 award and receiving a major NIH award (such as an R01) ranged between 4.6 and 7.4 years, and was significantly longer for women, for those who remained at their home institution, and for those hired by an institution that was not one of the 25 institutions with the most NIH funding. Shockingly, there has yet to be a K99 awardee at a historically Black college or university. We go on to show how K99 awardees flow to faculty positions, and to identify various factors that influence the future success of individual researchers and, therefore, also influence the composition of biomedical faculty at universities in the United States.
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Affiliation(s)
- Nicole C Woitowich
- Department of Medical Social Sciences, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
| | - Sarah R Hengel
- Department of Biology, Tufts UniversityMedfordUnited States
| | - Christopher Solis
- Department of Health, Nutrition, and Food Sciences, Florida State UniversityTallahasseeUnited States
| | - Tauras P Vilgalys
- Section of Genetic Medicine, Department of Medicine, University of ChicagoChicagoUnited States
| | - Joel Babdor
- Department of Systems Pharmacology and Translational Therapeutics, University of PennsylvaniaPhiladelphiaUnited States
| | - Daniel J Tyrrell
- Division of Molecular and Cellular Pathology, Department of Pathology, Heersink School of Medicine, University of Alabama at BirminghamBirminghamUnited States
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2
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Woitowich NC, Hengel SR, Solis C, Vilgalys TP, Babdor J, Tyrrell DJ. Analysis of NIH K99/R00 Awards and the Career Progression of Awardees. bioRxiv 2023:2023.01.26.525751. [PMID: 37162873 PMCID: PMC10168267 DOI: 10.1101/2023.01.26.525751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Many postdoctoral fellows and scholars who hope to secure tenure-track faculty positions in the United States apply to the National Institutes of Health (NIH) for a Pathway to Independence Award. This award has two phases (K99 and R00) and provides funding for up to five years. Using NIH data for the period 2006-2022, we report that ~230 K99 awards were made every year, representing up to ~$250 million annual investment. About 40% of K99 awardees were women and ~89% of K99 awardees went on to receive an R00 award annually. Institutions with the most NIH funding produced the most recipients of K99 awards and recruited the most recipients of R00 awards. The time between a researcher starting an R00 award and receiving a major NIH award (such as an R01) ranged between 4.6 and 7.4 years, and was significantly longer for women, for those who remained at their home institution, and for those hired by an institution that was not one of the 25 institutions with the most NIH funding. Shockingly, there has yet to be a K99 awardee at a historically Black college or university. We go on to show how K99 awardees flow to faculty positions, and to identify various factors that influence the future success of individual researchers and, therefore, also influence the composition of biomedical faculty at universities in the US.
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Affiliation(s)
- Nicole C Woitowich
- Department of Medical Social Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Sarah R Hengel
- Department of Biology, Tufts University, Medford, MA, USA
| | - Christopher Solis
- Department of Health, Nutrition, and Food Sciences, Florida State University, Tallahassee, FL, USA
| | - Tauras P Vilgalys
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Joel Babdor
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel J Tyrrell
- Division of Molecular and Cellular Pathology, Department of Pathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
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Vilgalys TP, Klunk J, Demeure CE, Cheng X, Shiratori M, Madej J, Beau R, Elli D, Patino MI, Redfern R, DeWitte SN, Gamble JA, Boldsen JL, Carmichael A, Varlik N, Eaton K, Grenier JC, Golding GB, Devault A, Rouillard JM, Yotova V, Sindeaux R, Ye CJ, Bikaran M, Dumaine A, Brinkworth JF, Missiakas D, Rouleau GA, Steinrücken M, Pizarro-Cerdá J, Poinar HN, Barreiro LB. Reply to Barton et al: signatures of natural selection during the Black Death. bioRxiv 2023:2023.04.06.535944. [PMID: 37066254 PMCID: PMC10104142 DOI: 10.1101/2023.04.06.535944] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Barton et al.1 raise several statistical concerns regarding our original analyses2 that highlight the challenge of inferring natural selection using ancient genomic data. We show here that these concerns have limited impact on our original conclusions. Specifically, we recover the same signature of enrichment for high FST values at the immune loci relative to putatively neutral sites after switching the allele frequency estimation method to a maximum likelihood approach, filtering to only consider known human variants, and down-sampling our data to the same mean coverage across sites. Furthermore, using permutations, we show that the rs2549794 variant near ERAP2 continues to emerge as the strongest candidate for selection (p = 1.2×10-5), falling below the Bonferroni-corrected significance threshold recommended by Barton et al. Importantly, the evidence for selection on ERAP2 is further supported by functional data demonstrating the impact of the ERAP2 genotype on the immune response to Y. pestis and by epidemiological data from an independent group showing that the putatively selected allele during the Black Death protects against severe respiratory infection in contemporary populations.
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Affiliation(s)
- Tauras P Vilgalys
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Jennifer Klunk
- McMaster Ancient DNA Centre, Departments of Anthropology, Biology and Biochemistry, McMaster University, Hamilton, Ontario, Canada L8S4L9
- Daicel Arbor Biosciences, Ann Arbor, MI, USA
| | - Christian E Demeure
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Microbiology Department, F-75015 Paris, France
| | - Xiaoheng Cheng
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Mari Shiratori
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Julien Madej
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Microbiology Department, F-75015 Paris, France
| | - Rémi Beau
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Microbiology Department, F-75015 Paris, France
| | - Derek Elli
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Lemont, IL, USA
| | - Maria I Patino
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Rebecca Redfern
- Centre for Human Bioarchaeology, Museum of London, London, UK, EC2Y 5HN
| | - Sharon N DeWitte
- Department of Anthropology, University of South Carolina, Columbia, SC, USA
| | - Julia A Gamble
- Department of Anthropology, University of Manitoba, Winnipeg, Manitoba, R3T2N2
| | - Jesper L Boldsen
- Department of Forensic Medicine, Unit of Anthropology (ADBOU), University of Southern Denmark, Odense S, 5260, Denmark
| | - Ann Carmichael
- History Department, Indiana University, Bloomington, IN, USA
| | - Nükhet Varlik
- Department of History, Rutgers University-Newark, NJ, USA
| | - Katherine Eaton
- McMaster Ancient DNA Centre, Departments of Anthropology, Biology and Biochemistry, McMaster University, Hamilton, Ontario, Canada L8S4L9
| | - Jean-Christophe Grenier
- Montreal Heart Institute, Faculty of Medicine, Université de Montréal, Montréal, Quebec, Canada, H1T 1C7
| | - G Brian Golding
- McMaster Ancient DNA Centre, Departments of Anthropology, Biology and Biochemistry, McMaster University, Hamilton, Ontario, Canada L8S4L9
| | | | - Jean-Marie Rouillard
- Daicel Arbor Biosciences, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan Ann Arbor, Ann Arbor, MI, USA
| | - Vania Yotova
- Centre Hospitalier Universitaire Sainte-Justine, Montréal, Quebec, Canada, H3T 1C5
| | - Renata Sindeaux
- Centre Hospitalier Universitaire Sainte-Justine, Montréal, Quebec, Canada, H3T 1C5
| | - Chun Jimmie Ye
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Matin Bikaran
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Anne Dumaine
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Jessica F Brinkworth
- Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Dominique Missiakas
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Lemont, IL, USA
| | - Guy A Rouleau
- Montreal Neurological Institute-Hospital, McGill University, Montréal, Quebec, Canada, H3A 2B4
| | - Matthias Steinrücken
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Javier Pizarro-Cerdá
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Microbiology Department, F-75015 Paris, France
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, Departments of Anthropology, Biology and Biochemistry, McMaster University, Hamilton, Ontario, Canada L8S4L9
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Lemont, IL, USA
| | - Luis B Barreiro
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
- Centre for Human Bioarchaeology, Museum of London, London, UK, EC2Y 5HN
- Department of Anthropology, University of South Carolina, Columbia, SC, USA
- Department of Anthropology, University of Manitoba, Winnipeg, Manitoba, R3T2N2
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Klunk J, Vilgalys TP, Demeure CE, Cheng X, Shiratori M, Madej J, Beau R, Elli D, Patino MI, Redfern R, DeWitte SN, Gamble JA, Boldsen JL, Carmichael A, Varlik N, Eaton K, Grenier JC, Golding GB, Devault A, Rouillard JM, Yotova V, Sindeaux R, Ye CJ, Bikaran M, Dumaine A, Brinkworth JF, Missiakas D, Rouleau GA, Steinrücken M, Pizarro-Cerdá J, Poinar HN, Barreiro LB. Evolution of immune genes is associated with the Black Death. Nature 2022; 611:312-319. [PMID: 36261521 PMCID: PMC9580435 DOI: 10.1038/s41586-022-05349-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 09/14/2022] [Indexed: 01/10/2023]
Abstract
Infectious diseases are among the strongest selective pressures driving human evolution1,2. This includes the single greatest mortality event in recorded history, the first outbreak of the second pandemic of plague, commonly called the Black Death, which was caused by the bacterium Yersinia pestis3. This pandemic devastated Afro-Eurasia, killing up to 30-50% of the population4. To identify loci that may have been under selection during the Black Death, we characterized genetic variation around immune-related genes from 206 ancient DNA extracts, stemming from two different European populations before, during and after the Black Death. Immune loci are strongly enriched for highly differentiated sites relative to a set of non-immune loci, suggesting positive selection. We identify 245 variants that are highly differentiated within the London dataset, four of which were replicated in an independent cohort from Denmark, and represent the strongest candidates for positive selection. The selected allele for one of these variants, rs2549794, is associated with the production of a full-length (versus truncated) ERAP2 transcript, variation in cytokine response to Y. pestis and increased ability to control intracellular Y. pestis in macrophages. Finally, we show that protective variants overlap with alleles that are today associated with increased susceptibility to autoimmune diseases, providing empirical evidence for the role played by past pandemics in shaping present-day susceptibility to disease.
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Affiliation(s)
- Jennifer Klunk
- McMaster Ancient DNA Centre, Departments of Anthropology, Biology and Biochemistry, McMaster University, Hamilton, Ontario, Canada
- Daicel Arbor Biosciences, Ann Arbor, MI, USA
| | - Tauras P Vilgalys
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | | | - Xiaoheng Cheng
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Mari Shiratori
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Julien Madej
- Yersinia Research Unit, Institut Pasteur, Paris, France
| | - Rémi Beau
- Yersinia Research Unit, Institut Pasteur, Paris, France
| | - Derek Elli
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Lemont, IL, USA
| | - Maria I Patino
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Rebecca Redfern
- Centre for Human Bioarchaeology, Museum of London, London, UK
| | - Sharon N DeWitte
- Department of Anthropology, University of South Carolina, Columbia, SC, USA
| | - Julia A Gamble
- Department of Anthropology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jesper L Boldsen
- Department of Forensic Medicine, Unit of Anthropology (ADBOU), University of Southern Denmark, Odense S, Denmark
| | - Ann Carmichael
- History Department, Indiana University, Bloomington, IN, USA
| | - Nükhet Varlik
- Department of History, Rutgers University, Newark, NJ, USA
| | - Katherine Eaton
- McMaster Ancient DNA Centre, Departments of Anthropology, Biology and Biochemistry, McMaster University, Hamilton, Ontario, Canada
| | - Jean-Christophe Grenier
- Montreal Heart Institute, Faculty of Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - G Brian Golding
- McMaster Ancient DNA Centre, Departments of Anthropology, Biology and Biochemistry, McMaster University, Hamilton, Ontario, Canada
| | | | - Jean-Marie Rouillard
- Daicel Arbor Biosciences, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan - Ann Arbor, Ann Arbor, MI, USA
| | - Vania Yotova
- Centre Hospitalier Universitaire Sainte-Justine, Montréal, Quebec, Canada
| | - Renata Sindeaux
- Centre Hospitalier Universitaire Sainte-Justine, Montréal, Quebec, Canada
| | - Chun Jimmie Ye
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Matin Bikaran
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Anne Dumaine
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Jessica F Brinkworth
- Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Dominique Missiakas
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Lemont, IL, USA
| | - Guy A Rouleau
- Montreal Neurological Institute-Hospital, McGill University, Montréal, Quebec, Canada
| | - Matthias Steinrücken
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | | | - Hendrik N Poinar
- McMaster Ancient DNA Centre, Departments of Anthropology, Biology and Biochemistry, McMaster University, Hamilton, Ontario, Canada.
- Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada.
| | - Luis B Barreiro
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA.
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA.
- Committee on Immunology, University of Chicago, Chicago, IL, USA.
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5
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Vilgalys TP, Fogel AS, Anderson JA, Mututua RS, Warutere JK, Siodi IL, Kim SY, Voyles TN, Robinson JA, Wall JD, Archie EA, Alberts SC, Tung J. Selection against admixture and gene regulatory divergence in a long-term primate field study. Science 2022; 377:635-641. [PMID: 35926022 PMCID: PMC9682493 DOI: 10.1126/science.abm4917] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genetic admixture is central to primate evolution. We combined 50 years of field observations of immigration and group demography with genomic data from ~9 generations of hybrid baboons to investigate the consequences of admixture in the wild. Despite no obvious fitness costs to hybrids, we found signatures of selection against admixture similar to those described for archaic hominins. These patterns were concentrated near genes where ancestry is strongly associated with gene expression. Our analyses also show that introgression is partially predictable across the genome. This study demonstrates the value of integrating genomic and field data for revealing how "genomic signatures of selection" (e.g., reduced introgression in low-recombination regions) manifest in nature; moreover, it underscores the importance of other primates as living models for human evolution.
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Affiliation(s)
- Tauras P. Vilgalys
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA,Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - Arielle S. Fogel
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA,University Program in Genetics and Genomics, Duke University, Durham, NC, USA
| | - Jordan A. Anderson
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
| | | | | | | | - Sang Yoon Kim
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
| | - Tawni N. Voyles
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
| | | | - Jeffrey D. Wall
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Elizabeth A. Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Susan C. Alberts
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA,Department of Biology, Duke University, Durham, NC, USA,Duke University Population Research Institute, Duke University, Durham, NC, USA
| | - Jenny Tung
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA,Department of Biology, Duke University, Durham, NC, USA,Duke University Population Research Institute, Duke University, Durham, NC, USA,Canadian Institute for Advanced Research, Toronto, Canada,Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany,Corresponding author
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Batra SS, Levy-Sakin M, Robinson J, Guillory J, Durinck S, Vilgalys TP, Kwok PY, Cox LA, Seshagiri S, Song YS, Wall JD. Accurate assembly of the olive baboon (Papio anubis) genome using long-read and Hi-C data. Gigascience 2020; 9:giaa134. [PMID: 33283855 PMCID: PMC7719865 DOI: 10.1093/gigascience/giaa134] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 07/14/2020] [Accepted: 11/04/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Baboons are a widely used nonhuman primate model for biomedical, evolutionary, and basic genetics research. Despite this importance, the genomic resources for baboons are limited. In particular, the current baboon reference genome Panu_3.0 is a highly fragmented, reference-guided (i.e., not fully de novo) assembly, and its poor quality inhibits our ability to conduct downstream genomic analyses. FINDINGS Here we present a de novo genome assembly of the olive baboon (Papio anubis) that uses data from several recently developed single-molecule technologies. Our assembly, Panubis1.0, has an N50 contig size of ∼1.46 Mb (as opposed to 139 kb for Panu_3.0) and has single scaffolds that span each of the 20 autosomes and the X chromosome. CONCLUSIONS We highlight multiple lines of evidence (including Bionano Genomics data, pedigree linkage information, and linkage disequilibrium data) suggesting that there are several large assembly errors in Panu_3.0, which have been corrected in Panubis1.0.
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Affiliation(s)
- Sanjit Singh Batra
- Computer Science Division, University of California Berkeley, 2626 Hearst Avenue, Berkeley, CA 94720, USA
| | - Michal Levy-Sakin
- Cardiovascular Research Institute, University of California San Francisco, 555 Mission Bay Boulevard South, San Francisco, CA 94158, USA
| | - Jacqueline Robinson
- Institute for Human Genetics, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Joseph Guillory
- Department of Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Steffen Durinck
- Department of Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
- Bioinformatics and Computational Biology Department, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Tauras P Vilgalys
- Department of Evolutionary Anthropology, Duke University, 130 Science Drive, Durham, NC 27705, USA
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, University of California San Francisco, 555 Mission Bay Boulevard South, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Laura A Cox
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, 475 Vine Drive, Winston-Salem, NC 27101, USA
- Southwest National Primate Research Center, Texas Biomedical Research Institute, 8715 W. Military Drive, San Antonio, TX 78227, USA
| | - Somasekar Seshagiri
- Department of Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Yun S Song
- Computer Science Division, University of California Berkeley, 2626 Hearst Avenue, Berkeley, CA 94720, USA
- Department of Statistics, University of California Berkeley, 367 Evans Hall, Berkeley, CA 94720, USA
- Chan Zuckerberg Biohub, Mission Bay, San Francisco, CA 94158, USA
| | - Jeffrey D Wall
- Institute for Human Genetics, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
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Anderson JA, Vilgalys TP, Tung J. Broadening primate genomics: new insights into the ecology and evolution of primate gene regulation. Curr Opin Genet Dev 2020; 62:16-22. [PMID: 32569794 PMCID: PMC7483836 DOI: 10.1016/j.gde.2020.05.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 12/17/2022]
Abstract
Comparative analyses have played a key role in understanding how gene regulatory evolution contributes to primate phenotypic diversity. Recently, these studies have expanded to include a wider range of species, within-population as well as interspecific analyses, and research on wild as well as captive individuals. This expansion provides context for understanding genetic and environmental effects on gene regulation in humans, including the importance of the pathogen and social environments. Although taxonomic representation remains biased, inclusion of more species has also begun to reveal the evolutionary processes that explain whether and when gene regulation is conserved. Together, this work highlights how studies in other primates contribute to understanding evolution in our own lineage, and we conclude by identifying promising avenues for future work.
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Affiliation(s)
- Jordan A Anderson
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | - Tauras P Vilgalys
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA; Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Jenny Tung
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA; Department of Biology, Duke University, Durham, NC 27708, USA; Institute of Primate Research, National Museums of Kenya, Nairobi 00502, Kenya; Duke Population Research Institute, Duke University, Durham, NC 27708, USA.
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8
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Fan Y, Vilgalys TP, Sun S, Peng Q, Tung J, Zhou X. IMAGE: high-powered detection of genetic effects on DNA methylation using integrated methylation QTL mapping and allele-specific analysis. Genome Biol 2019; 20:220. [PMID: 31651351 PMCID: PMC6813132 DOI: 10.1186/s13059-019-1813-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 09/03/2019] [Indexed: 12/15/2022] Open
Abstract
Identifying genetic variants that are associated with methylation variation-an analysis commonly referred to as methylation quantitative trait locus (mQTL) mapping-is important for understanding the epigenetic mechanisms underlying genotype-trait associations. Here, we develop a statistical method, IMAGE, for mQTL mapping in sequencing-based methylation studies. IMAGE properly accounts for the count nature of bisulfite sequencing data and incorporates allele-specific methylation patterns from heterozygous individuals to enable more powerful mQTL discovery. We compare IMAGE with existing approaches through extensive simulation. We also apply IMAGE to analyze two bisulfite sequencing studies, in which IMAGE identifies more mQTL than existing approaches.
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Affiliation(s)
- Yue Fan
- Systems Engineering Institute, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, People's Republic of China
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Tauras P Vilgalys
- Departments of Evolutionary Anthropology and Biology, Duke University, Durham, NC, 27708, USA
| | - Shiquan Sun
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Qinke Peng
- Systems Engineering Institute, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, People's Republic of China
| | - Jenny Tung
- Departments of Evolutionary Anthropology and Biology, Duke University, Durham, NC, 27708, USA
- Duke University Population Research Institute, Duke University, Durham, NC, 27708, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA.
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.
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9
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Abstract
Changes in gene regulation have long been thought to play an important role in primate evolution. However, although a number of studies have compared genome-wide gene expression patterns across primate species, fewer have investigated the gene regulatory mechanisms that underlie such patterns, or the relative contribution of drift versus selection. Here, we profiled genome-scale DNA methylation levels in blood samples from five of the six extant species of the baboon genus Papio (4-14 individuals per species). This radiation presents the opportunity to investigate DNA methylation divergence at both shallow and deeper timescales (0.380-1.4 My). In contrast to studies in human populations, but similar to studies in great apes, DNA methylation profiles clearly mirror genetic and geographic structure. Divergence in DNA methylation proceeds fastest in unannotated regions of the genome and slowest in regions of the genome that are likely more constrained at the sequence level (e.g., gene exons). Both heuristic approaches and Ornstein-Uhlenbeck models suggest that DNA methylation levels at a small set of sites have been affected by positive selection, and that this class is enriched in functionally relevant contexts, including promoters, enhancers, and CpG islands. Our results thus indicate that the rate and distribution of DNA methylation changes across the genome largely mirror genetic structure. However, at some CpG sites, DNA methylation levels themselves may have been a target of positive selection, pointing to loci that could be important in connecting sequence variation to fitness-related traits.
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Affiliation(s)
- Tauras P Vilgalys
- Department of Evolutionary Anthropology, Duke University, Durham, NC
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Clifford J Jolly
- Department of Anthropology, New York University, New York, NY
- Center for the Study of Human Origins, New York University, New York, NY
- New York Consortium for Evolutionary Primatology, New York, NY
| | | | - Sayan Mukherjee
- Department of Statistical Science, Duke University, Durham, NC
- Department of Mathematics, Duke University, Durham, NC
- Department of Computer Science, Duke University, Durham, NC
| | - Jenny Tung
- Department of Evolutionary Anthropology, Duke University, Durham, NC
- Department of Biology, Duke University, Durham, NC
- Duke University Population Research Institute, Duke University, Durham, NC
- Institute of Primate Research, National Museums of Kenya, Karen, Nairobi, Kenya
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10
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Watts HE, Jimenez D, Pacheco V, Vilgalys TP. Effects of temperature on the timing of breeding and molt transitions in house finches. ACTA ACUST UNITED AC 2018; 221:jeb.185058. [PMID: 30104303 DOI: 10.1242/jeb.185058] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/02/2018] [Indexed: 11/20/2022]
Abstract
Temperature-correlated shifts in reproductive timing are now well documented in numerous bird species. However, whether temperature directly influences reproductive timing or whether its effects are mediated by an intermediate environmental cue, such as plant phenology, remains poorly understood. In this study, we investigated the direct effects of temperature on reproductive timing in house finches (Haemorhous mexicanus), which have a range and breeding diet not well represented in previous studies of temperature and reproductive timing. We conducted experiments with captive male house finches in which temperature was elevated within realistic ranges and the effects on the timing of preparations for reproduction, as well as on the termination of reproduction and the onset of prebasic feather molt, were examined. We found no adjustments in the timing of reproductive preparations of males in direct response to temperature. However, elevated temperature did advance the breeding-molt transition. Our results suggest that elevated temperatures in the range tested here do not directly impact physiological preparations for reproduction in male house finches, but may constrain the timing of the breeding-molt transition in this species.
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Affiliation(s)
- Heather E Watts
- School of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164, USA .,Department of Biology, Loyola Marymount University, Los Angeles, CA 90045, USA
| | - Daniela Jimenez
- Department of Biology, Loyola Marymount University, Los Angeles, CA 90045, USA
| | - Veronica Pacheco
- Department of Biology, Loyola Marymount University, Los Angeles, CA 90045, USA
| | - Tauras P Vilgalys
- Department of Biology, Loyola Marymount University, Los Angeles, CA 90045, USA
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11
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Abstract
Genome-scale bisulfite sequencing approaches have opened the door to ecological and evolutionary studies of DNA methylation in many organisms. These approaches can be powerful. However, they introduce new methodological and statistical considerations, some of which are particularly relevant to non-model systems. Here, we highlight how these considerations influence a study's power to link methylation variation with a predictor variable of interest. Relative to current practice, we argue that sample sizes will need to increase to provide robust insights. We also provide recommendations for overcoming common challenges and an R Shiny app to aid in study design.
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Affiliation(s)
- Amanda J Lea
- Department of Biology, Duke University, Durham, NC, 27708, USA.
- Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, Washington Road, Princeton University, Princeton, NJ, 08540, USA.
| | - Tauras P Vilgalys
- Department of Evolutionary Anthropology, Duke University, Durham, NC, 27708, USA
| | - Paul A P Durst
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jenny Tung
- Department of Biology, Duke University, Durham, NC, 27708, USA.
- Department of Evolutionary Anthropology, Duke University, Durham, NC, 27708, USA.
- Institute of Primate Research, National Museums of Kenya, Nairobi, 00502, Kenya.
- Duke University Population Research Institute, Duke University, Durham, NC, 27708, USA.
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