1
|
Kocher AA, Dutrow EV, Uebbing S, Yim KM, Rosales Larios MF, Baumgartner M, Nottoli T, Noonan JP. CpG island turnover events predict evolutionary changes in enhancer activity. Genome Biol 2024; 25:156. [PMID: 38872220 PMCID: PMC11170920 DOI: 10.1186/s13059-024-03300-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 06/04/2024] [Indexed: 06/15/2024] Open
Abstract
BACKGROUND Genetic changes that modify the function of transcriptional enhancers have been linked to the evolution of biological diversity across species. Multiple studies have focused on the role of nucleotide substitutions, transposition, and insertions and deletions in altering enhancer function. CpG islands (CGIs) have recently been shown to influence enhancer activity, and here we test how their turnover across species contributes to enhancer evolution. RESULTS We integrate maps of CGIs and enhancer activity-associated histone modifications obtained from multiple tissues in nine mammalian species and find that CGI content in enhancers is strongly associated with increased histone modification levels. CGIs show widespread turnover across species and species-specific CGIs are strongly enriched for enhancers exhibiting species-specific activity across all tissues and species. Genes associated with enhancers with species-specific CGIs show concordant biases in their expression, supporting that CGI turnover contributes to gene regulatory innovation. Our results also implicate CGI turnover in the evolution of Human Gain Enhancers (HGEs), which show increased activity in human embryonic development and may have contributed to the evolution of uniquely human traits. Using a humanized mouse model, we show that a highly conserved HGE with a large CGI absent from the mouse ortholog shows increased activity at the human CGI in the humanized mouse diencephalon. CONCLUSIONS Collectively, our results point to CGI turnover as a mechanism driving gene regulatory changes potentially underlying trait evolution in mammals.
Collapse
Affiliation(s)
- Acadia A Kocher
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
- Division of Molecular Genetics and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Emily V Dutrow
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
- Zoetis, Inc, 333 Portage St, Kalamazoo, MI, 49007, USA
| | - Severin Uebbing
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
- Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Kristina M Yim
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
| | | | | | - Timothy Nottoli
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT, 06510, USA
- Yale Genome Editing Center, Yale School of Medicine, New Haven, CT, 06510, USA
| | - James P Noonan
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA.
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA.
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, 06510, USA.
- Wu Tsai Institute, Yale University, New Haven, CT, 06510, USA.
| |
Collapse
|
2
|
Sakamoto F, Kanamori S, Díaz LM, Cádiz A, Ishii Y, Yamaguchi K, Shigenobu S, Nakayama T, Makino T, Kawata M. Detection of evolutionary conserved and accelerated genomic regions related to adaptation to thermal niches in Anolis lizards. Ecol Evol 2024; 14:e11117. [PMID: 38455144 PMCID: PMC10920033 DOI: 10.1002/ece3.11117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 02/18/2024] [Accepted: 02/22/2024] [Indexed: 03/09/2024] Open
Abstract
Understanding the genetic basis for adapting to thermal environments is important due to serious effects of global warming on ectothermic species. Various genes associated with thermal adaptation in lizards have been identified mainly focusing on changes in gene expression or the detection of positively selected genes using coding regions. Only a few comprehensive genome-wide analyses have included noncoding regions. This study aimed to identify evolutionarily conserved and accelerated genomic regions using whole genomes of eight Anolis lizard species that have repeatedly adapted to similar thermal environments in multiple lineages. Evolutionarily conserved genomic regions were extracted as regions with overall sequence conservation (regions with fewer base substitutions) across all lineages compared with the neutral model. Genomic regions that underwent accelerated evolution in the lineage of interest were identified as those with more base substitutions in the target branch than in the entire background branch. Conserved elements across all branches were relatively abundant in "intergenic" genomic regions among noncoding regions. Accelerated regions (ARs) of each lineage contained a significantly greater proportion of noncoding RNA genes than the entire multiple alignment. Common genes containing ARs within 5 kb of their vicinity in lineages with similar thermal habitats were identified. Many genes associated with circadian rhythms and behavior were found in hot-open and cool-shaded habitat lineages. These genes might play a role in contributing to thermal adaptation and assist future studies examining the function of genes involved in thermal adaptation via genome editing.
Collapse
Affiliation(s)
- Fuku Sakamoto
- Graduate School of Life SciencesTohoku UniversitySendaiJapan
| | | | - Luis M. Díaz
- National Museum of Natural History of CubaHavanaCuba
| | - Antonio Cádiz
- Faculty of BiologyUniversity of HavanaHavanaCuba
- Present address:
Department of BiologyUniversity of MiamiCoral GablesFloridaUSA
| | - Yuu Ishii
- Graduate School of Life SciencesTohoku UniversitySendaiJapan
| | | | - Shuji Shigenobu
- Trans‐Omics FacilityNational Institute for Basic BiologyOkazakiJapan
- Department of Basic Biology, School of Life ScienceThe Graduate University for Advanced Studies, SOKENDAIOkazakiJapan
| | - Takuro Nakayama
- Division of Life Sciences, Center for Computational SciencesUniversity of TsukubaTsukubaJapan
| | - Takashi Makino
- Graduate School of Life SciencesTohoku UniversitySendaiJapan
| | - Masakado Kawata
- Graduate School of Life SciencesTohoku UniversitySendaiJapan
| |
Collapse
|
3
|
Jorstad NL, Song JH, Exposito-Alonso D, Suresh H, Castro-Pacheco N, Krienen FM, Yanny AM, Close J, Gelfand E, Long B, Seeman SC, Travaglini KJ, Basu S, Beaudin M, Bertagnolli D, Crow M, Ding SL, Eggermont J, Glandon A, Goldy J, Kiick K, Kroes T, McMillen D, Pham T, Rimorin C, Siletti K, Somasundaram S, Tieu M, Torkelson A, Feng G, Hopkins WD, Höllt T, Keene CD, Linnarsson S, McCarroll SA, Lelieveldt BP, Sherwood CC, Smith K, Walsh CA, Dobin A, Gillis J, Lein ES, Hodge RD, Bakken TE. Comparative transcriptomics reveals human-specific cortical features. Science 2023; 382:eade9516. [PMID: 37824638 PMCID: PMC10659116 DOI: 10.1126/science.ade9516] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 09/13/2023] [Indexed: 10/14/2023]
Abstract
The cognitive abilities of humans are distinctive among primates, but their molecular and cellular substrates are poorly understood. We used comparative single-nucleus transcriptomics to analyze samples of the middle temporal gyrus (MTG) from adult humans, chimpanzees, gorillas, rhesus macaques, and common marmosets to understand human-specific features of the neocortex. Human, chimpanzee, and gorilla MTG showed highly similar cell-type composition and laminar organization as well as a large shift in proportions of deep-layer intratelencephalic-projecting neurons compared with macaque and marmoset MTG. Microglia, astrocytes, and oligodendrocytes had more-divergent expression across species compared with neurons or oligodendrocyte precursor cells, and neuronal expression diverged more rapidly on the human lineage. Only a few hundred genes showed human-specific patterning, suggesting that relatively few cellular and molecular changes distinctively define adult human cortical structure.
Collapse
Affiliation(s)
| | - Janet H.T. Song
- Allen Discovery Center for Human Brain Evolution, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA 02115, USA
| | - David Exposito-Alonso
- Allen Discovery Center for Human Brain Evolution, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Hamsini Suresh
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Fenna M. Krienen
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | | - Jennie Close
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Emily Gelfand
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Brian Long
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | | | | | - Soumyadeep Basu
- LKEB, Dept of Radiology, Leiden University Medical Center; Leiden, The Netherlands
- Computer Graphics and Visualization Group, Delft University of Technology, Delft, Netherlands
| | - Marc Beaudin
- Allen Discovery Center for Human Brain Evolution, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA 02115, USA
| | | | - Megan Crow
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Song-Lin Ding
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Jeroen Eggermont
- LKEB, Dept of Radiology, Leiden University Medical Center; Leiden, The Netherlands
| | | | - Jeff Goldy
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Katelyn Kiick
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Thomas Kroes
- LKEB, Dept of Radiology, Leiden University Medical Center; Leiden, The Netherlands
| | | | | | | | - Kimberly Siletti
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | - Michael Tieu
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Amy Torkelson
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Guoping Feng
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - William D. Hopkins
- Keeling Center for Comparative Medicine and Research, University of Texas, MD Anderson Cancer Center, Houston, TX 78602, USA
| | - Thomas Höllt
- Computer Graphics and Visualization Group, Delft University of Technology, Delft, Netherlands
| | - C. Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 981915, USA
| | - Sten Linnarsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Steven A. McCarroll
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Boudewijn P. Lelieveldt
- LKEB, Dept of Radiology, Leiden University Medical Center; Leiden, The Netherlands
- Pattern Recognition and Bioinformatics group, Delft University of Technology, Delft, Netherlands
| | - Chet C. Sherwood
- Department of Anthropology, The George Washington University, Washington, DC 20037, USA
| | - Kimberly Smith
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | - Christopher A. Walsh
- Allen Discovery Center for Human Brain Evolution, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Alexander Dobin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jesse Gillis
- Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Ed S. Lein
- Allen Institute for Brain Science; Seattle, WA, 98109, USA
| | | | | |
Collapse
|
4
|
Bi X, Zhou L, Zhang JJ, Feng S, Hu M, Cooper DN, Lin J, Li J, Wu DD, Zhang G. Lineage-specific accelerated sequences underlying primate evolution. SCIENCE ADVANCES 2023; 9:eadc9507. [PMID: 37262186 PMCID: PMC10413682 DOI: 10.1126/sciadv.adc9507] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 05/05/2023] [Indexed: 06/03/2023]
Abstract
Understanding the mechanisms underlying phenotypic innovation is a key goal of comparative genomic studies. Here, we investigated the evolutionary landscape of lineage-specific accelerated regions (LinARs) across 49 primate species. Genomic comparison with dense taxa sampling of primate species significantly improved LinAR detection accuracy and revealed many novel human LinARs associated with brain development or disease. Our study also yielded detailed maps of LinARs in other primate lineages that may have influenced lineage-specific phenotypic innovation and adaptation. Functional experimentation identified gibbon LinARs, which could have participated in the developmental regulation of their unique limb structures, whereas some LinARs in the Colobinae were associated with metabolite detoxification which may have been adaptive in relation to their leaf-eating diet. Overall, our study broadens knowledge of the functional roles of LinARs in primate evolution.
Collapse
Affiliation(s)
- Xupeng Bi
- Centre for Evolutionary & Organismal Biology, and Women’s Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Long Zhou
- Centre for Evolutionary & Organismal Biology, and Women’s Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jin-Jin Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Shaohong Feng
- Centre for Evolutionary & Organismal Biology, and Women’s Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
| | - Mei Hu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - David N. Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Jiangwei Lin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Jiali Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming 650223, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Guojie Zhang
- Centre for Evolutionary & Organismal Biology, and Women’s Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
5
|
Kocher AA, Dutrow EV, Uebbing S, Yim KM, Larios MFR, Baumgartner M, Nottoli T, Noonan JP. CpG island turnover events predict evolutionary changes in enhancer activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.540063. [PMID: 37214934 PMCID: PMC10197647 DOI: 10.1101/2023.05.09.540063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Genetic changes that modify the function of transcriptional enhancers have been linked to the evolution of biological diversity across species. Multiple studies have focused on the role of nucleotide substitutions, transposition, and insertions and deletions in altering enhancer function. Here we show that turnover of CpG islands (CGIs), which contribute to enhancer activation, is broadly associated with changes in enhancer activity across mammals, including humans. We integrated maps of CGIs and enhancer activity-associated histone modifications obtained from multiple tissues in nine mammalian species and found that CGI content in enhancers was strongly associated with increased histone modification levels. CGIs showed widespread turnover across species and species-specific CGIs were strongly enriched for enhancers exhibiting species-specific activity across all tissues and species we examined. Genes associated with enhancers with species-specific CGIs showed concordant biases in their expression, supporting that CGI turnover contributes to gene regulatory innovation. Our results also implicate CGI turnover in the evolution of Human Gain Enhancers (HGEs), which show increased activity in human embryonic development and may have contributed to the evolution of uniquely human traits. Using a humanized mouse model, we show that a highly conserved HGE with a large CGI absent from the mouse ortholog shows increased activity at the human CGI in the humanized mouse diencephalon. Collectively, our results point to CGI turnover as a mechanism driving gene regulatory changes potentially underlying trait evolution in mammals.
Collapse
Affiliation(s)
- Acadia A. Kocher
- Department of Genetics, Yale School of Medicine, New Haven CT 06510, USA
| | - Emily V. Dutrow
- Department of Genetics, Yale School of Medicine, New Haven CT 06510, USA
- Present address: Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Severin Uebbing
- Department of Genetics, Yale School of Medicine, New Haven CT 06510, USA
| | - Kristina M. Yim
- Department of Genetics, Yale School of Medicine, New Haven CT 06510, USA
| | | | | | - Timothy Nottoli
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT 06510, USA
- Yale Genome Editing Center, Yale School of Medicine, New Haven, CT 06510, USA
| | - James P. Noonan
- Department of Genetics, Yale School of Medicine, New Haven CT 06510, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
- Wu Tsai Institute, Yale University, New Haven, CT 06510, USA
| |
Collapse
|
6
|
Keough KC, Whalen S, Inoue F, Przytycki PF, Fair T, Deng C, Steyert M, Ryu H, Lindblad-Toh K, Karlsson E, Nowakowski T, Ahituv N, Pollen A, Pollard KS. Three-dimensional genome rewiring in loci with human accelerated regions. Science 2023; 380:eabm1696. [PMID: 37104607 PMCID: PMC10999243 DOI: 10.1126/science.abm1696] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 03/01/2023] [Indexed: 04/29/2023]
Abstract
Human accelerated regions (HARs) are conserved genomic loci that evolved at an accelerated rate in the human lineage and may underlie human-specific traits. We generated HARs and chimpanzee accelerated regions with an automated pipeline and an alignment of 241 mammalian genomes. Combining deep learning with chromatin capture experiments in human and chimpanzee neural progenitor cells, we discovered a significant enrichment of HARs in topologically associating domains containing human-specific genomic variants that change three-dimensional (3D) genome organization. Differential gene expression between humans and chimpanzees at these loci suggests rewiring of regulatory interactions between HARs and neurodevelopmental genes. Thus, comparative genomics together with models of 3D genome folding revealed enhancer hijacking as an explanation for the rapid evolution of HARs.
Collapse
Affiliation(s)
- Kathleen C Keough
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Sean Whalen
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Fumitaka Inoue
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Pawel F Przytycki
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Tyler Fair
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Chengyu Deng
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Marilyn Steyert
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Hane Ryu
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Elinor Karlsson
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA, USA
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA, USA
| | - Tomasz Nowakowski
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Alex Pollen
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Katherine S Pollard
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics and Bakar Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| |
Collapse
|
7
|
Human and African ape myosin heavy chain content and the evolution of hominin skeletal muscle. Comp Biochem Physiol A Mol Integr Physiol 2023; 281:111415. [PMID: 36931425 DOI: 10.1016/j.cbpa.2023.111415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/13/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023]
Abstract
Humans are unique among terrestrial mammals in our manner of walking and running, reflecting 7 to 8 Ma of musculoskeletal evolution since diverging with the genus Pan. One component of this is a shift in our skeletal muscle biology towards a predominance of myosin heavy chain (MyHC) I isoforms (i.e. slow fibers) across our pelvis and lower limbs, which distinguishes us from chimpanzees. Here, new MyHC data from 35 pelvis and hind limb muscles of a Western gorilla (Gorilla gorilla) are presented. These data are combined with a similar chimpanzee dataset to assess the MyHC I content of humans in comparison to African apes (chimpanzees and gorillas) and other terrestrial mammals. The responsiveness of human skeletal muscle to behavioral interventions is also compared to the human-African ape differential. Humans are distinct from African apes and among a small group of terrestrial mammals whose pelvis and hind/lower limb muscle is slow fiber dominant, on average. Behavioral interventions, including immobilization, bed rest, spaceflight and exercise, can induce modest decreases and increases in human MyHC I content (i.e. -9.3% to 2.3%, n = 2033 subjects), but these shifts are much smaller than the mean human-African ape differential (i.e. 31%). Taken together, these results indicate muscle fiber content is likely an evolvable trait under selection in the hominin lineage. As such, we highlight potential targets of selection in the genome (e.g. regions that regulate MyHC content) that may play an important role in hominin skeletal muscle evolution.
Collapse
|
8
|
Zhang X, Fang B, Huang YF. Transcription factor binding sites are frequently under accelerated evolution in primates. Nat Commun 2023; 14:783. [PMID: 36774380 PMCID: PMC9922303 DOI: 10.1038/s41467-023-36421-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 01/31/2023] [Indexed: 02/13/2023] Open
Abstract
Recent comparative genomic studies have identified many human accelerated elements (HARs) with elevated substitution rates in the human lineage. However, it remains unknown to what extent transcription factor binding sites (TFBSs) are under accelerated evolution in humans and other primates. Here, we introduce two pooling-based phylogenetic methods with dramatically enhanced sensitivity to examine accelerated evolution in TFBSs. Using these new methods, we show that more than 6000 TFBSs annotated in the human genome have experienced accelerated evolution in Hominini, apes, and Old World monkeys. Although these TFBSs individually show relatively weak signals of accelerated evolution, they collectively are more abundant than HARs. Also, we show that accelerated evolution in Pol III binding sites may be driven by lineage-specific positive selection, whereas accelerated evolution in other TFBSs might be driven by nonadaptive evolutionary forces. Finally, the accelerated TFBSs are enriched around developmental genes, suggesting that accelerated evolution in TFBSs may drive the divergence of developmental processes between primates.
Collapse
Affiliation(s)
- Xinru Zhang
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA. .,Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA. .,Bioinformatics and Genomics Graduate Program, Pennsylvania State University, University Park, PA, 16802, USA.
| | - Bohao Fang
- Department of Organismic and Evolutionary Biology and the Museum of Comparative Zoology, Harvard University, Boston, MA, 02135, USA
| | - Yi-Fei Huang
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA. .,Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA.
| |
Collapse
|
9
|
Abstract
Human accelerated regions (HARs) are the fastest-evolving sequences in the human genome. When HARs were discovered in 2006, their function was mysterious due to scant annotation of the noncoding genome. Diverse technologies, from transgenic animals to machine learning, have consistently shown that HARs function as gene regulatory enhancers with significant enrichment in neurodevelopment. It is now possible to quantitatively measure the enhancer activity of thousands of HARs in parallel and model how each nucleotide contributes to gene expression. These strategies have revealed that many human HAR sequences function differently than their chimpanzee orthologs, though individual nucleotide changes in the same HAR may have opposite effects, consistent with compensatory substitutions. To fully evaluate the role of HARs in human evolution, it will be necessary to experimentally and computationally dissect them across more cell types and developmental stages.
Collapse
Affiliation(s)
- Sean Whalen
- Gladstone Institute of Data Science and Biotechnology, San Francisco, California, USA; ,
| | - Katherine S Pollard
- Gladstone Institute of Data Science and Biotechnology, San Francisco, California, USA; ,
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| |
Collapse
|
10
|
Ferrández-Peral L, Zhan X, Alvarez-Estape M, Chiva C, Esteller-Cucala P, García-Pérez R, Julià E, Lizano E, Fornas Ò, Sabidó E, Li Q, Marquès-Bonet T, Juan D, Zhang G. Transcriptome innovations in primates revealed by single-molecule long-read sequencing. Genome Res 2022; 32:gr.276395.121. [PMID: 35840341 PMCID: PMC9435740 DOI: 10.1101/gr.276395.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 07/12/2022] [Indexed: 11/24/2022]
Abstract
Transcriptomic diversity greatly contributes to the fundamentals of disease, lineage-specific biology, and environmental adaptation. However, much of the actual isoform repertoire contributing to shaping primate evolution remains unknown. Here, we combined deep long- and short-read sequencing complemented with mass spectrometry proteomics in a panel of lymphoblastoid cell lines (LCLs) from human, three other great apes, and rhesus macaque, producing the largest full-length isoform catalog in primates to date. Around half of the captured isoforms are not annotated in their reference genomes, significantly expanding the gene models in primates. Furthermore, our comparative analyses unveil hundreds of transcriptomic innovations and isoform usage changes related to immune function and immunological disorders. The confluence of these evolutionary innovations with signals of positive selection and their limited impact in the proteome points to changes in alternative splicing in genes involved in immune response as an important target of recent regulatory divergence in primates.
Collapse
Affiliation(s)
| | | | | | - Cristina Chiva
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | | | | | - Eva Julià
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
| | - Esther Lizano
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Òscar Fornas
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Eduard Sabidó
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Qiye Li
- BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
- CNAG-CRG, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - David Juan
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen 2200, Denmark
- Evolutionary and Organismal Biology Research Center, School of Medicine, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
11
|
Blaxter M, Archibald JM, Childers AK, Coddington JA, Crandall KA, Di Palma F, Durbin R, Edwards SV, Graves JAM, Hackett KJ, Hall N, Jarvis ED, Johnson RN, Karlsson EK, Kress WJ, Kuraku S, Lawniczak MKN, Lindblad-Toh K, Lopez JV, Moran NA, Robinson GE, Ryder OA, Shapiro B, Soltis PS, Warnow T, Zhang G, Lewin HA. Why sequence all eukaryotes? Proc Natl Acad Sci U S A 2022; 119:e2115636118. [PMID: 35042801 PMCID: PMC8795522 DOI: 10.1073/pnas.2115636118] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there on the origins of novelty and the continuing maintenance of biodiversity on Earth? The history of life and the code for the working parts of cells and systems are written in the genome. The Earth BioGenome Project has proposed that the genomes of all extant, named eukaryotes-about 2 million species-should be sequenced to high quality to produce a digital library of life on Earth, beginning with strategic phylogenetic, ecological, and high-impact priorities. Here we discuss why we should sequence all eukaryotic species, not just a representative few scattered across the many branches of the tree of life. We suggest that many questions of evolutionary and ecological significance will only be addressable when whole-genome data representing divergences at all of the branchings in the tree of life or all species in natural ecosystems are available. We envisage that a genomic tree of life will foster understanding of the ongoing processes of speciation, adaptation, and organismal dependencies within entire ecosystems. These explorations will resolve long-standing problems in phylogenetics, evolution, ecology, conservation, agriculture, bioindustry, and medicine.
Collapse
Affiliation(s)
- Mark Blaxter
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4H7, Canada
| | - Anna K Childers
- Bee Research Laboratory, Agricultural Research Service, US Department of Agriculture (USDA), Beltsville, MD 20705
| | - Jonathan A Coddington
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Keith A Crandall
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, George Washington University, Washington, DC 20052
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC 20013
| | - Federica Di Palma
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Richard Durbin
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Jennifer A M Graves
- School of Life Sciences, La Trobe University, Bundoora, VIC 751 23, Australia
- University of Canberra, Bruce, ACT 2617, Australia
| | - Kevin J Hackett
- Crop Production and Protection, Office of National Programs, Agricultural Research Service, USDA, Beltsville, MD 20705
| | - Neil Hall
- Earlham Institute, Norwich, Norfolk NR4 7UZ, United Kingdom
| | - Erich D Jarvis
- Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY 10065
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - Rebecca N Johnson
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Elinor K Karlsson
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - W John Kress
- Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012
| | - Shigehiro Kuraku
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
| | | | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 751 23, Sweden
| | - Jose V Lopez
- Department of Biological Sciences, Halmos College of Arts and Sciences, Nova Southeastern University, Dania Beach, FL 33004
- Guy Harvey Oceanographic Center, Dania Beach, FL 33004
| | - Nancy A Moran
- Integrative Biology, University of Texas at Austin, Austin, TX 78712
| | - Gene E Robinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Oliver A Ryder
- Conservation Genetics, Division of Biology, San Diego Zoo Wildlife Alliance, Escondido, CA 92027
- Department of Evolution, Behavior and Ecology, University of California, San Diego, La Jolla, CA 92039
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611
- Biodiversity Institute, University of Florida, Gainesville, FL 32611
| | - Tandy Warnow
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61301
| | - Guojie Zhang
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
- China National Genebank, Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China
| | - Harris A Lewin
- Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, CA 95616
- Department of Population Health and Reproduction, University of California, Davis, CA 95616
| |
Collapse
|
12
|
Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans. Genome Res 2021; 31:2035-2049. [PMID: 34667117 PMCID: PMC8559704 DOI: 10.1101/gr.275989.121] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/17/2021] [Indexed: 11/25/2022]
Abstract
Vocal learning, the ability to imitate sounds from conspecifics and the environment, is a key component of human spoken language and learned song in three independently evolved avian groups—oscine songbirds, parrots, and hummingbirds. Humans and each of these three bird clades exhibit specialized behavioral, neuroanatomical, and brain gene expression convergence related to vocal learning, speech, and song. To understand the evolutionary basis of vocal learning gene specializations and convergence, we searched for and identified accelerated genomic regions (ARs), a marker of positive selection, specific to vocal learning birds. We found avian vocal learner-specific ARs, and they were enriched in noncoding regions near genes with known speech functions or brain gene expression specializations in humans and vocal learning birds, including FOXP2, NEUROD6, ZEB2, and MEF2C, and near genes with major neurodevelopmental functions, including NR2F1, NRP2, and BCL11B. We also found enrichment near the SFARI class S genes associated with syndromic vocal communication forms of autism spectrum disorders. These findings reveal strong candidate noncoding regions near genes for the evolutionary adaptations that distinguish vocal learning species from their close vocal nonlearning relatives and provide further evidence of molecular convergence between birdsong and human spoken language.
Collapse
|
13
|
Lewis EMA, Kaushik K, Sandoval LA, Antony I, Dietmann S, Kroll KL. Epigenetic regulation during human cortical development: Seq-ing answers from the brain to the organoid. Neurochem Int 2021; 147:105039. [PMID: 33915225 PMCID: PMC8387070 DOI: 10.1016/j.neuint.2021.105039] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 03/23/2021] [Accepted: 03/27/2021] [Indexed: 01/22/2023]
Abstract
Epigenetic regulation plays an important role in controlling gene expression during complex processes, such as development of the human brain. Mutations in genes encoding chromatin modifying proteins and in the non-protein coding sequences of the genome can potentially alter transcription factor binding or chromatin accessibility. Such mutations can frequently cause neurodevelopmental disorders, therefore understanding how epigenetic regulation shapes brain development is of particular interest. While epigenetic regulation of neural development has been extensively studied in murine models, significant species-specific differences in both the genome sequence and in brain development necessitate human models. However, access to human fetal material is limited and these tissues cannot be grown or experimentally manipulated ex vivo. Therefore, models that recapitulate particular aspects of human fetal brain development, such as the in vitro differentiation of human pluripotent stem cells (hPSCs), are instrumental for studying the epigenetic regulation of human neural development. Here, we examine recent studies that have defined changes in the epigenomic landscape during fetal brain development. We compare these studies with analogous data derived by in vitro differentiation of hPSCs into specific neuronal cell types or as three-dimensional cerebral organoids. Such comparisons can be informative regarding which aspects of fetal brain development are faithfully recapitulated by in vitro differentiation models and provide a foundation for using experimentally tractable in vitro models of human brain development to study neural gene regulation and the basis of its disruption to cause neurodevelopmental disorders.
Collapse
Affiliation(s)
- Emily M A Lewis
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue St, Louis, MO, 63110, USA.
| | - Komal Kaushik
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue St, Louis, MO, 63110, USA.
| | - Luke A Sandoval
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue St, Louis, MO, 63110, USA.
| | - Irene Antony
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue St, Louis, MO, 63110, USA.
| | - Sabine Dietmann
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue St, Louis, MO, 63110, USA.
| | - Kristen L Kroll
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue St, Louis, MO, 63110, USA.
| |
Collapse
|
14
|
Human-chimpanzee fused cells reveal cis-regulatory divergence underlying skeletal evolution. Nat Genet 2021; 53:467-476. [PMID: 33731941 PMCID: PMC8038968 DOI: 10.1038/s41588-021-00804-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/26/2021] [Indexed: 01/06/2023]
Abstract
Gene regulatory divergence is thought to play a central role in determining human-specific traits. However, our ability to link divergent regulation to divergent phenotypes is limited. Here, we utilized human-chimpanzee hybrid induced pluripotent stem cells to study gene expression separating these species. The tetraploid hybrid cells allowed us to separate cis- from trans-regulatory effects, and to control for non-genetic confounding factors. We differentiated these cells into cranial neural crest cells (CNCCs), the primary cell type giving rise to the face. We discovered evidence of lineage-specific selection on the hedgehog signaling pathway, including a human-specific 6-fold down-regulation of EVC2 (LIMBIN), a key hedgehog gene. Inducing a similar down-regulation of EVC2 substantially reduced hedgehog signaling output. Mice and humans lacking functional EVC2 show striking phenotypic parallels to human-chimpanzee craniofacial differences, suggesting that the regulatory divergence of hedgehog signaling may have contributed to the unique craniofacial morphology of humans.
Collapse
|
15
|
Walker CR, Scally A, De Maio N, Goldman N. Short-range template switching in great ape genomes explored using pair hidden Markov models. PLoS Genet 2021; 17:e1009221. [PMID: 33651813 PMCID: PMC7954356 DOI: 10.1371/journal.pgen.1009221] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 03/12/2021] [Accepted: 02/10/2021] [Indexed: 12/14/2022] Open
Abstract
Many complex genomic rearrangements arise through template switch errors, which occur in DNA replication when there is a transient polymerase switch to an alternate template nearby in three-dimensional space. While typically investigated at kilobase-to-megabase scales, the genomic and evolutionary consequences of this mutational process are not well characterised at smaller scales, where they are often interpreted as clusters of independent substitutions, insertions and deletions. Here we present an improved statistical approach using pair hidden Markov models, and use it to detect and describe short-range template switches underlying clusters of mutations in the multi-way alignment of hominid genomes. Using robust statistics derived from evolutionary genomic simulations, we show that template switch events have been widespread in the evolution of the great apes’ genomes and provide a parsimonious explanation for the presence of many complex mutation clusters in their phylogenetic context. Larger-scale mechanisms of genome rearrangement are typically associated with structural features around breakpoints, and accordingly we show that atypical patterns of secondary structure formation and DNA bending are present at the initial template switch loci. Our methods improve on previous non-probabilistic approaches for computational detection of template switch mutations, allowing the statistical significance of events to be assessed. By specifying realistic evolutionary parameters based on the genomes and taxa involved, our methods can be readily adapted to other intra- or inter-species comparisons. DNA replication is an imperfect process which causes the mutations that give rise to genetic diversity during the evolution of genomes. While many mutations are independent, single-nucleotide substitutions or small insertions and deletions, some mutations arise as nonindependent clusters of substitutions and larger scale chromosomal rearrangements. Large-scale rearrangements (also called structural variants) in particular can have a profound impact on genome evolution and contribute to both germline and somatic disease in humans. The replication-based mechanisms underlying structural variation typically involve a polymerase switch event in which a large segment of DNA is copied using a template from an alternate location in the genome. Methods for identifying these template switch mutations lack the power to detect smaller scale rearrangements which can arise through the same replication-based pathways. Here we outline a model which can detect and assess the statistical significance of such small-scale template switches within their evolutionary context. We show that these events are widespread in the evolution of great apes and that the genomic features associated with these small-scale rearrangements are similar to those of large-scale structural variants.
Collapse
Affiliation(s)
- Conor R. Walker
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Aylwyn Scally
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Nicola De Maio
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom
| | - Nick Goldman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom
- * E-mail:
| |
Collapse
|
16
|
Caporale AL, Gonda CM, Franchini LF. Transcriptional Enhancers in the FOXP2 Locus Underwent Accelerated Evolution in the Human Lineage. Mol Biol Evol 2019; 36:2432-2450. [PMID: 31359064 DOI: 10.1093/molbev/msz173] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 04/26/2019] [Accepted: 07/16/2019] [Indexed: 12/11/2022] Open
Abstract
Unique human features such as complex language are the result of molecular evolutionary changes that modified developmental programs of our brain. The human-specific evolution of the forkhead box P2 (FOXP2) gene coding region has been linked to the emergence of speech and language in the human kind. However, little is known about how the expression of FOXP2 is regulated and if its regulatory machinery evolved in a lineage-specific manner in humans. In order to identify FOXP2 regulatory regions containing human-specific changes we used databases of human accelerated non-coding sequences or HARs. We found that the topologically associating domain (TAD) determined using developing human cerebral cortex containing the FOXP2 locus includes two clusters of 12 HARs, placing the locus occupied by FOXP2 among the top regions showing fast acceleration rates in non-coding regions in the human genome. Using in vivo enhancer assays in zebrafish, we found that at least five FOXP2-HARs behave as transcriptional enhancers throughout different developmental stages. In addition, we found that at least two FOXP2-HARs direct the expression of the reporter gene EGFP to foxP2 expressing regions and cells. Moreover, we uncovered two FOXP2-HARs showing reporter expression gain of function in the nervous system when compared with the chimpanzee ortholog sequences. Our results indicate that regulatory sequences in the FOXP2 locus underwent a human-specific evolutionary process suggesting that the transcriptional machinery controlling this gene could have also evolved differentially in the human lineage.
Collapse
Affiliation(s)
- Alfredo Leandro Caporale
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Catalina M Gonda
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Lucía Florencia Franchini
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| |
Collapse
|
17
|
Lamichhaney S, Card DC, Grayson P, Tonini JFR, Bravo GA, Näpflin K, Termignoni-Garcia F, Torres C, Burbrink F, Clarke JA, Sackton TB, Edwards SV. Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180248. [PMID: 31154982 PMCID: PMC6560268 DOI: 10.1098/rstb.2018.0248] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2019] [Indexed: 12/20/2022] Open
Abstract
Evolutionary convergence has been long considered primary evidence of adaptation driven by natural selection and provides opportunities to explore evolutionary repeatability and predictability. In recent years, there has been increased interest in exploring the genetic mechanisms underlying convergent evolution, in part, owing to the advent of genomic techniques. However, the current 'genomics gold rush' in studies of convergence has overshadowed the reality that most trait classifications are quite broadly defined, resulting in incomplete or potentially biased interpretations of results. Genomic studies of convergence would be greatly improved by integrating deep 'vertical', natural history knowledge with 'horizontal' knowledge focusing on the breadth of taxonomic diversity. Natural history collections have and continue to be best positioned for increasing our comprehensive understanding of phenotypic diversity, with modern practices of digitization and databasing of morphological traits providing exciting improvements in our ability to evaluate the degree of morphological convergence. Combining more detailed phenotypic data with the well-established field of genomics will enable scientists to make progress on an important goal in biology: to understand the degree to which genetic or molecular convergence is associated with phenotypic convergence. Although the fields of comparative biology or comparative genomics alone can separately reveal important insights into convergent evolution, here we suggest that the synergistic and complementary roles of natural history collection-derived phenomic data and comparative genomics methods can be particularly powerful in together elucidating the genomic basis of convergent evolution among higher taxa. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.
Collapse
Affiliation(s)
- Sangeet Lamichhaney
- 1 Department of Organismic and Evolutionary Biology, Harvard University , Cambridge, MA 02138 , USA
- 2 Museum of Comparative Zoology, Harvard University , Cambridge, MA 02138 , USA
| | - Daren C Card
- 1 Department of Organismic and Evolutionary Biology, Harvard University , Cambridge, MA 02138 , USA
- 2 Museum of Comparative Zoology, Harvard University , Cambridge, MA 02138 , USA
- 4 Department of Biology, University of Texas Arlington , Arlington, TX 76019 , USA
| | - Phil Grayson
- 1 Department of Organismic and Evolutionary Biology, Harvard University , Cambridge, MA 02138 , USA
- 2 Museum of Comparative Zoology, Harvard University , Cambridge, MA 02138 , USA
| | - João F R Tonini
- 1 Department of Organismic and Evolutionary Biology, Harvard University , Cambridge, MA 02138 , USA
- 2 Museum of Comparative Zoology, Harvard University , Cambridge, MA 02138 , USA
| | - Gustavo A Bravo
- 1 Department of Organismic and Evolutionary Biology, Harvard University , Cambridge, MA 02138 , USA
- 2 Museum of Comparative Zoology, Harvard University , Cambridge, MA 02138 , USA
| | - Kathrin Näpflin
- 1 Department of Organismic and Evolutionary Biology, Harvard University , Cambridge, MA 02138 , USA
- 2 Museum of Comparative Zoology, Harvard University , Cambridge, MA 02138 , USA
| | - Flavia Termignoni-Garcia
- 1 Department of Organismic and Evolutionary Biology, Harvard University , Cambridge, MA 02138 , USA
- 2 Museum of Comparative Zoology, Harvard University , Cambridge, MA 02138 , USA
| | - Christopher Torres
- 5 Department of Biology, The University of Texas at Austin , Austin, MA 78712 , USA
- 6 Department of Geological Sciences, The University of Texas at Austin , Austin, MA 78712 , USA
| | - Frank Burbrink
- 7 Department of Herpetology, The American Museum of Natural History , New York, NY 10024 , USA
| | - Julia A Clarke
- 5 Department of Biology, The University of Texas at Austin , Austin, MA 78712 , USA
- 6 Department of Geological Sciences, The University of Texas at Austin , Austin, MA 78712 , USA
| | | | - Scott V Edwards
- 1 Department of Organismic and Evolutionary Biology, Harvard University , Cambridge, MA 02138 , USA
- 2 Museum of Comparative Zoology, Harvard University , Cambridge, MA 02138 , USA
| |
Collapse
|
18
|
Hu Z, Sackton TB, Edwards SV, Liu JS. Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees. Mol Biol Evol 2019; 36:1086-1100. [PMID: 30851112 PMCID: PMC6501877 DOI: 10.1093/molbev/msz049] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Conservation of DNA sequence over evolutionary time is a strong indicator of function, and gain or loss of sequence conservation can be used to infer changes in function across a phylogeny. Changes in evolutionary rates on particular lineages in a phylogeny can indicate shared functional shifts, and thus can be used to detect genomic correlates of phenotypic convergence. However, existing methods do not allow easy detection of patterns of rate variation, which causes challenges for detecting convergent rate shifts or other complex evolutionary scenarios. Here we introduce PhyloAcc, a new Bayesian method to model substitution rate changes in conserved elements across a phylogeny. The method assumes several categories of substitution rate for each branch on the phylogenetic tree, estimates substitution rates per category, and detects changes of substitution rate as the posterior probability of a category switch. Simulations show that PhyloAcc can detect genomic regions with rate shifts in multiple target species better than previous methods and has a higher accuracy of reconstructing complex patterns of substitution rate changes than prevalent Bayesian relaxed clock models. We demonstrate the utility of PhyloAcc in two classic examples of convergent phenotypes: loss of flight in birds and the transition to marine life in mammals. In each case, our approach reveals numerous examples of conserved nonexonic elements with accelerations specific to the phenotypically convergent lineages. Our method is widely applicable to any set of conserved elements where multiple rate changes are expected on a phylogeny.
Collapse
Affiliation(s)
- Zhirui Hu
- Department of Statistics, Harvard University, Cambridge, MA
| | | | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA.,Museum of Comparative Zoology, Harvard University, Cambridge, MA
| | - Jun S Liu
- Department of Statistics, Harvard University, Cambridge, MA
| |
Collapse
|
19
|
Sackton TB, Grayson P, Cloutier A, Hu Z, Liu JS, Wheeler NE, Gardner PP, Clarke JA, Baker AJ, Clamp M, Edwards SV. Convergent regulatory evolution and loss of flight in paleognathous birds. Science 2019; 364:74-78. [DOI: 10.1126/science.aat7244] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 02/27/2019] [Indexed: 01/05/2023]
Abstract
A core question in evolutionary biology is whether convergent phenotypic evolution is driven by convergent molecular changes in proteins or regulatory regions. We combined phylogenomic, developmental, and epigenomic analysis of 11 new genomes of paleognathous birds, including an extinct moa, to show that convergent evolution of regulatory regions, more so than protein-coding genes, is prevalent among developmental pathways associated with independent losses of flight. A Bayesian analysis of 284,001 conserved noncoding elements, 60,665 of which are corroborated as enhancers by open chromatin states during development, identified 2355 independent accelerations along lineages of flightless paleognaths, with functional consequences for driving gene expression in the developing forelimb. Our results suggest that the genomic landscape associated with morphological convergence in ratites has a substantial shared regulatory component.
Collapse
|