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Rigano L, Schmitz M, Linnemann V, Krauss M, Hollert H, Pfenninger M. Exposure to complex mixtures of urban sediments containing Tyre and Road Wear Particles (TRWPs) increases the germ-line mutation rate in Chironomus riparius. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2025; 281:107292. [PMID: 39985910 DOI: 10.1016/j.aquatox.2025.107292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2024] [Revised: 01/16/2025] [Accepted: 02/15/2025] [Indexed: 02/24/2025]
Abstract
Tyre and road wear particles (TRWPs) are a significant yet often underestimated source of environmental pollution, contributing to the accumulation of microplastics and a complex mixture of contaminants in both terrestrial and aquatic ecosystems. Despite their prevalence, the long-term evolutionary effects of TRWPs, beyond their immediate toxicity, remain largely unknown. In this study, we assessed mutagenicity in the non-biting midge Chironomus riparius, upon exposure to urban sediment collected from a runoff sedimentation basin. To assess the extent of mutagenic effects over multiple generations, we combined the urban sediment exposure model with short-term mutation accumulation lines (MALs) and subsequent whole genome sequencing (WGS). The study was conducted over five generations, with urban sediment concentrations of 0.5 % and 10 %. Our results reveal that the exposure to urban sediment significantly increases mutation rates compared to control groups by 50 %, independent of concentration (0.5 % and 10 %). To infer potential causal processes, we conducted a comparative analysis using known mutational spectra from previous studies. This comparison showed that the mutation profiles induced by urban sediment clearly clustered with those caused by Benzo[a]Pyrene (BaP), a known Polycyclic Aromatic Hydrocarbon (PAH). A comprehensive chemical characterization of the sediment confirmed a considerable impact of road runoff and traffic-related contamination, including PAHs of primarily petrogenic origin. This suggests that PAH-like compounds present in urban sediments may play a significant role in the observed mutagenic effects. Our study shows that urban sediments influence mutation rates and alter mutational spectra in exposed organisms, potentially compromising genomic stability and shaping evolutionary trajectories. These genetic changes can have profound long-term effects on population dynamics and ecosystem health, underlining the importance of understanding the evolutionary consequences of environmental pollution. Additionally, we show that comparatively analysing of mutational spectra may provide valuable insights into mutational processes.
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Affiliation(s)
- Lorenzo Rigano
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany; LOEWE Centre of Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany.
| | - Markus Schmitz
- Department of Evolutionary Ecology & Environmental Toxicology (E3T), Institute for Ecology, Evolution and Diversity, Faculty 15 Biological Sciences, Goethe University Frankfurt am Main, Germany
| | - Volker Linnemann
- Institute for Environmental Engineering, RWTH Aachen University, Germany
| | - Martin Krauss
- Department of Exposure Science, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Germany
| | - Henner Hollert
- LOEWE Centre of Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany; Department of Evolutionary Ecology & Environmental Toxicology (E3T), Institute for Ecology, Evolution and Diversity, Faculty 15 Biological Sciences, Goethe University Frankfurt am Main, Germany; Department Environmental Media Related Ecotoxicology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany
| | - Markus Pfenninger
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany; LOEWE Centre of Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany; Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Johann-Joachim-Becker-Weg 7, D-55128, Mainz, Germany
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2
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Shakya SB, Edwards SV, Sackton TB. Convergent evolution of noncoding elements associated with short tarsus length in birds. BMC Biol 2025; 23:52. [PMID: 39984930 PMCID: PMC11846207 DOI: 10.1186/s12915-025-02156-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2024] [Accepted: 02/12/2025] [Indexed: 02/23/2025] Open
Abstract
BACKGROUND Convergent evolution is the independent evolution of similar traits in unrelated lineages across the Tree of Life. Various genomic signatures can help identify cases of convergent evolution at the molecular level, including changes in substitution rate in the same genes or gene networks. In this study, utilizing tarsus measurements of ~ 5400 species of birds, we identify independent shifts in tarsus length and use both comparative genomic and population genetic data to identify convergent evolutionary changes among focal clades with shifts to shorter optimal tarsus length. RESULTS Using a newly generated, comprehensive and broadly accessible set of 932,467 avian conserved non-exonic elements (CNEEs) and a whole-genome alignment of 79 birds, we find strong evidence for convergent acceleration in short-tarsus clades among 14,422 elements. Analysis of 9854 protein-coding genes, however, yielded no evidence of convergent patterns of positive selection. Accelerated elements in short-tarsus clades are concentrated near genes with functions in development, with the strongest enrichment associated with skeletal system development. Analysis of gene networks supports convergent changes in regulation of broadly homologous limb developmental genes and pathways. CONCLUSIONS Our results highlight the important role of regulatory elements undergoing convergent acceleration in convergent skeletal traits and are consistent with previous studies showing the roles of regulatory elements and skeletal phenotypes.
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Affiliation(s)
- Subir B Shakya
- Informatics Group, Harvard University, Cambridge, MA, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Timothy B Sackton
- Informatics Group, Harvard University, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
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3
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Uebbing S, Kocher AA, Baumgartner M, Ji Y, Bai S, Xing X, Nottoli T, Noonan JP. Evolutionary Innovations in Conserved Regulatory Elements Associate With Developmental Genes in Mammals. Mol Biol Evol 2024; 41:msae199. [PMID: 39302728 PMCID: PMC11465374 DOI: 10.1093/molbev/msae199] [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: 04/09/2024] [Revised: 08/26/2024] [Accepted: 09/17/2024] [Indexed: 09/22/2024] Open
Abstract
Transcriptional enhancers orchestrate cell type- and time point-specific gene expression programs. Genetic variation within enhancer sequences is an important contributor to phenotypic variation including evolutionary adaptations and human disease. Certain genes and pathways may be more prone to regulatory evolution than others, with different patterns across diverse organisms, but whether such patterns exist has not been investigated at a sufficient scale. To address this question, we identified signatures of accelerated sequence evolution in conserved enhancer elements throughout the mammalian phylogeny at an unprecedented scale. While different genes and pathways were enriched for regulatory evolution in different parts of the tree, we found a striking overall pattern of pleiotropic genes involved in gene regulatory and developmental processes being enriched for accelerated enhancer evolution. These genes were connected to more enhancers than other genes, which was the basis for having an increased amount of sequence acceleration over all their enhancers combined. We provide evidence that sequence acceleration is associated with turnover of regulatory function. Detailed study of one acceleration event in an enhancer of HES1 revealed that sequence evolution led to a new activity domain in the developing limb that emerged concurrently with the evolution of digit reduction in hoofed mammals. Our results provide evidence that enhancer evolution has been a frequent contributor to regulatory innovation at conserved developmental signaling genes in mammals.
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Affiliation(s)
- Severin Uebbing
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Department of Biology, Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Utrecht University, Utrecht, The Netherlands
| | - Acadia A Kocher
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | | | - Yu Ji
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Suxia Bai
- Yale Genome Editing Center, Yale School of Medicine, New Haven, CT, USA
| | - Xiaojun Xing
- Yale Genome Editing Center, Yale School of Medicine, New Haven, CT, USA
| | - Timothy Nottoli
- Yale Genome Editing Center, Yale School of Medicine, New Haven, CT, USA
| | - James P Noonan
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Wu Tsai Institute, Yale University, New Haven, CT, USA
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4
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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.
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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.
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5
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Galtier N. Half a Century of Controversy: The Neutralist/Selectionist Debate in Molecular Evolution. Genome Biol Evol 2024; 16:evae003. [PMID: 38311843 PMCID: PMC10839204 DOI: 10.1093/gbe/evae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/01/2024] [Indexed: 02/06/2024] Open
Abstract
The neutral and nearly neutral theories, introduced more than 50 yr ago, have raised and still raise passionate discussion regarding the forces governing molecular evolution and their relative importance. The debate, initially focused on the amount of within-species polymorphism and constancy of the substitution rate, has spread, matured, and now underlies a wide range of topics and questions. The neutralist/selectionist controversy has structured the field and influences the way molecular evolutionary scientists conceive their research.
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Affiliation(s)
- Nicolas Galtier
- ISEM, CNRS, IRD, Université de Montpellier, Montpellier, France
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6
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Uebbing S, Kocher AA, Baumgartner M, Ji Y, Bai S, Xing X, Nottoli T, Noonan JP. Evolutionary innovation in conserved regulatory elements across the mammalian tree of life. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578197. [PMID: 38352419 PMCID: PMC10862883 DOI: 10.1101/2024.01.31.578197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Transcriptional enhancers orchestrate cell type- and time point-specific gene expression programs. Evolution of enhancer sequences can alter target gene expression without causing detrimental misexpression in other contexts. It has long been thought that this modularity allows evolutionary changes in enhancers to escape pleiotropic constraints, which is especially important for evolutionary constrained developmental patterning genes. However, there is still little data supporting this hypothesis. Here we identified signatures of accelerated evolution in conserved enhancer elements across the mammalian phylogeny. We found that pleiotropic genes involved in gene regulatory and developmental processes were enriched for accelerated sequence evolution within their enhancer elements. These genes were associated with an excess number of enhancers compared to other genes, and due to this they exhibit a substantial degree of sequence acceleration over all their enhancers combined. We provide evidence that sequence acceleration is associated with turnover of regulatory function. We studied one acceleration event in depth and found that its sequence evolution led to the emergence of a new enhancer activity domain that may be involved in the evolution of digit reduction in hoofed mammals. Our results provide tangible evidence that enhancer evolution has been a frequent contributor to modifications involving constrained developmental signaling genes in mammals.
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Affiliation(s)
- Severin Uebbing
- Department of Genetics, Yale School of Medicine, New Haven CT, USA
- Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Acadia A Kocher
- Department of Genetics, Yale School of Medicine, New Haven CT, USA
- Present address: Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Yu Ji
- Department of Genetics, Yale School of Medicine, New Haven CT, USA
| | - Suxia Bai
- Yale Genome Editing Center, Yale School of Medicine, New Haven CT, USA
| | - Xiaojun Xing
- Yale Genome Editing Center, Yale School of Medicine, New Haven CT, USA
| | - Timothy Nottoli
- Yale Genome Editing Center, Yale School of Medicine, New Haven CT, USA
| | - James P Noonan
- Department of Genetics, Yale School of Medicine, New Haven CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven CT, USA
- Department of Neuroscience, Yale School of Medicine, New Haven CT, USA
- Wu Tsai Institute, Yale University, New Haven CT, USA
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7
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Liu A, Wang N, Xie G, Li Y, Yan X, Li X, Zhu Z, Li Z, Yang J, Meng F, Dou M, Chen W, Ma N, Jiang Y, Gao Y, Wang Y. GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes. Genome Res 2023; 33:1673-1689. [PMID: 37884342 PMCID: PMC10691551 DOI: 10.1101/gr.277784.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/23/2023] [Indexed: 10/28/2023]
Abstract
Ultraconserved elements (UCEs) are the most conserved regions among the genomes of evolutionarily distant species and are thought to play critical biological functions. However, some UCEs rapidly evolved in specific lineages, and whether they contributed to adaptive evolution is still controversial. Here, using an increased number of sequenced genomes with high taxonomic coverage, we identified 2191 mammalian UCEs and 5938 avian UCEs from 95 mammal and 94 bird genomes, respectively. Our results show that these UCEs are functionally constrained and that their adjacent genes are prone to widespread expression with low expression diversity across tissues. Functional enrichment of mammalian and avian UCEs shows different trends indicating that UCEs may contribute to adaptive evolution of taxa. Focusing on lineage-specific accelerated evolution, we discover that the proportion of fast-evolving UCEs in nine mammalian and 10 avian test lineages range from 0.19% to 13.2%. Notably, up to 62.1% of fast-evolving UCEs in test lineages are much more likely to result from GC-biased gene conversion (gBGC). A single cervid-specific gBGC region embracing the uc.359 allele significantly alters the expression of Nova1 and other neural-related genes in the rat brain. Combined with the altered regulatory activity of ancient gBGC-induced fast-evolving UCEs in eutherians, our results provide evidence that synergy between gBGC and selection shaped lineage-specific substitution patterns, even in the most constrained regulatory elements. In summary, our results show that gBGC played an important role in facilitating lineage-specific accelerated evolution of UCEs, and further support the idea that a combination of multiple evolutionary forces shapes adaptive evolution.
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Affiliation(s)
- Anguo Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Nini Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Faculty of Mathematics and Natural Sciences, University of Cologne, and Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University Hospital Cologne, Cologne 50931, Germany
| | - Guoxiang Xie
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yang Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xixi Yan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xinmei Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhenliang Zhu
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhuohui Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jing Yang
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fanxin Meng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingle Dou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Weihuang Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Nange Ma
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Center for Functional Genomics, Institute of Future Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuanpeng Gao
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China;
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China;
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
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8
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Brovkina MV, Chapman MA, Holding ML, Clowney EJ. Emergence and influence of sequence bias in evolutionarily malleable, mammalian tandem arrays. BMC Biol 2023; 21:179. [PMID: 37612705 PMCID: PMC10463633 DOI: 10.1186/s12915-023-01673-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/01/2023] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND The radiation of mammals at the extinction of the dinosaurs produced a plethora of new forms-as diverse as bats, dolphins, and elephants-in only 10-20 million years. Behind the scenes, adaptation to new niches is accompanied by extensive innovation in large families of genes that allow animals to contact the environment, including chemosensors, xenobiotic enzymes, and immune and barrier proteins. Genes in these "outward-looking" families are allelically diverse among humans and exhibit tissue-specific and sometimes stochastic expression. RESULTS Here, we show that these tandem arrays of outward-looking genes occupy AT-biased isochores and comprise the "tissue-specific" gene class that lack CpG islands in their promoters. Models of mammalian genome evolution have not incorporated the sharply different functions and transcriptional patterns of genes in AT- versus GC-biased regions. To examine the relationship between gene family expansion, sequence content, and allelic diversity, we use population genetic data and comparative analysis. First, we find that AT bias can emerge during evolutionary expansion of gene families in cis. Second, human genes in AT-biased isochores or with GC-poor promoters experience relatively low rates of de novo point mutation today but are enriched for non-synonymous variants. Finally, we find that isochores containing gene clusters exhibit low rates of recombination. CONCLUSIONS Our analyses suggest that tolerance of non-synonymous variation and low recombination are two forces that have produced the depletion of GC bases in outward-facing gene arrays. In turn, high AT content exerts a profound effect on their chromatin organization and transcriptional regulation.
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Affiliation(s)
- Margarita V Brovkina
- Graduate Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Margaret A Chapman
- Neurosciences Graduate Program, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - E Josephine Clowney
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA.
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9
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Li J, Li N, Roellig DM, Zhao W, Guo Y, Feng Y, Xiao L. High subtelomeric GC content in the genome of a zoonotic Cryptosporidium species. Microb Genom 2023; 9:mgen001052. [PMID: 37399068 PMCID: PMC10438818 DOI: 10.1099/mgen.0.001052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 05/24/2023] [Indexed: 07/04/2023] Open
Abstract
Cryptosporidium canis is a zoonotic species causing cryptosporidiosis in humans in addition to its natural hosts dogs and other fur animals. To understand the genetic basis for host adaptation, we sequenced the genomes of C. canis from dogs, minks, and foxes and conducted a comparative genomics analysis. While the genomes of C. canis have similar gene contents and organisations, they (~41.0 %) and C. felis (39.6 %) have GC content much higher than other Cryptosporidium spp. (24.3-32.9 %) sequenced to date. The high GC content is mostly restricted to subtelomeric regions of the eight chromosomes. Most of these GC-balanced genes encode Cryptosporidium-specific proteins that have intrinsically disordered regions and are involved in host-parasite interactions. Natural selection appears to play a more important role in the evolution of codon usage in GC-balanced C. canis, and most of the GC-balanced genes have undergone positive selection. While the identity in whole genome sequences between the mink- and dog-derived isolates is 99.9 % (9365 SNVs), it is only 96.0 % (362 894 SNVs) between them and the fox-derived isolate. In agreement with this, the fox-derived isolate possesses more subtelomeric genes encoding invasion-related protein families. Therefore, the change in subtelomeric GC content appears to be responsible for the more GC-balanced C. canis genomes, and the fox-derived isolate could represent a new Cryptosporidium species.
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Affiliation(s)
- Jiayu Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Na Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Dawn M. Roellig
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Wentao Zhao
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Yaqiong Guo
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Yaoyu Feng
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Lihua Xiao
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
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10
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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.
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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
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11
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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.
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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.
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12
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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: 17] [Impact Index Per Article: 4.3] [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.
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13
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Bergman J, Schierup MH. Population dynamics of GC-changing mutations in humans and great apes. Genetics 2021; 218:6291657. [PMID: 34081117 DOI: 10.1093/genetics/iyab083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/27/2021] [Indexed: 11/14/2022] Open
Abstract
The nucleotide composition of the genome is a balance between origin and fixation rates of different mutations. For example, it is well-known that transitions occur more frequently than transversions, particularly at CpG sites. Differences in fixation rates of mutation types are less explored. Specifically, recombination-associated GC-biased gene conversion (gBGC) may differentially impact GC-changing mutations, due to differences in their genomic distributions and efficiency of mismatch repair mechanisms. Given that recombination evolves rapidly across species, we explore gBGC of different mutation types across human populations and great ape species. We report a stronger correlation between segregating GC frequency and recombination for transitions than for transversions. Notably, CpG transitions are most strongly affected by gBGC in humans and chimpanzees. We show that the overall strength of gBGC is generally correlated with effective population sizes in humans, with some notable exceptions, such as a stronger effect of gBGC on non-CpG transitions in populations of European descent. Furthermore, species of the Gorilla and Pongo genus have a greatly reduced gBGC effect on CpG sites. We also study the dependence of gBGC dynamics on flanking nucleotides and show that some mutation types evolve in opposition to the gBGC expectation, likely due to hypermutability of specific nucleotide contexts. Our results highlight the importance of different gBGC dynamics experienced by GC-changing mutations and their impact on nucleotide composition evolution.
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Affiliation(s)
- Juraj Bergman
- Bioinformatics Research Institute, Aarhus University, DK-8000 Aarhus C, Denmark
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14
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García-Pérez R, Esteller-Cucala P, Mas G, Lobón I, Di Carlo V, Riera M, Kuhlwilm M, Navarro A, Blancher A, Di Croce L, Gómez-Skarmeta JL, Juan D, Marquès-Bonet T. Epigenomic profiling of primate lymphoblastoid cell lines reveals the evolutionary patterns of epigenetic activities in gene regulatory architectures. Nat Commun 2021; 12:3116. [PMID: 34035253 PMCID: PMC8149829 DOI: 10.1038/s41467-021-23397-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 04/21/2021] [Indexed: 02/04/2023] Open
Abstract
Changes in the epigenetic regulation of gene expression have a central role in evolution. Here, we extensively profiled a panel of human, chimpanzee, gorilla, orangutan, and macaque lymphoblastoid cell lines (LCLs), using ChIP-seq for five histone marks, ATAC-seq and RNA-seq, further complemented with whole genome sequencing (WGS) and whole genome bisulfite sequencing (WGBS). We annotated regulatory elements (RE) and integrated chromatin contact maps to define gene regulatory architectures, creating the largest catalog of RE in primates to date. We report that epigenetic conservation and its correlation with sequence conservation in primates depends on the activity state of the regulatory element. Our gene regulatory architectures reveal the coordination of different types of components and highlight the role of promoters and intragenic enhancers (gE) in the regulation of gene expression. We observe that most regulatory changes occur in weakly active gE. Remarkably, novel human-specific gE with weak activities are enriched in human-specific nucleotide changes. These elements appear in genes with signals of positive selection and human acceleration, tissue-specific expression, and particular functional enrichments, suggesting that the regulatory evolution of these genes may have contributed to human adaptation.
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Affiliation(s)
| | | | - Glòria Mas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Irene Lobón
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
| | - Valerio Di Carlo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Meritxell Riera
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
| | - Martin Kuhlwilm
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
| | - Arcadi Navarro
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
- National Institute for Bioinformatics (INB), PRBB, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Antoine Blancher
- Laboratoire d'immunologie, CHU de Toulouse, Institut Fédératif de Biologie, hôpital Purpan, Toulouse, France
- Centre de Physiopathologie Toulouse-Purpan (CPTP), Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (Inserm), Université Paul Sabatier (UPS), Toulouse, France
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - David Juan
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain.
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain.
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15
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Abstract
Recombination increases the local GC-content in genomic regions through GC-biased gene conversion (gBGC). The recent discovery of a large genomic region with extreme GC-content in the fat sand rat Psammomys obesus provides a model to study the effects of gBGC on chromosome evolution. Here, we compare the GC-content and GC-to-AT substitution patterns across protein-coding genes of four gerbil species and two murine rodents (mouse and rat). We find that the known high-GC region is present in all the gerbils, and is characterized by high substitution rates for all mutational categories (AT-to-GC, GC-to-AT, and GC-conservative) both at synonymous and nonsynonymous sites. A higher AT-to-GC than GC-to-AT rate is consistent with the high GC-content. Additionally, we find more than 300 genes outside the known region with outlying values of AT-to-GC synonymous substitution rates in gerbils. Of these, over 30% are organized into at least 17 large clusters observable at the megabase-scale. The unusual GC-skewed substitution pattern suggests the evolution of genomic regions with very high recombination rates in the gerbil lineage, which can lead to a runaway increase in GC-content. Our results imply that rapid evolution of GC-content is possible in mammals, with gerbil species providing a powerful model to study the mechanisms of gBGC.
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Affiliation(s)
- Rodrigo Pracana
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - John F Mulley
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
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16
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Dai Y, Pracana R, Holland PWH. Divergent genes in gerbils: prevalence, relation to GC-biased substitution, and phenotypic relevance. BMC Evol Biol 2020; 20:134. [PMID: 33076817 PMCID: PMC7574485 DOI: 10.1186/s12862-020-01696-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/29/2020] [Indexed: 11/25/2022] Open
Abstract
Background Two gerbil species, sand rat (Psammomys obesus) and Mongolian jird (Meriones unguiculatus), can become obese and show signs of metabolic dysregulation when maintained on standard laboratory diets. The genetic basis of this phenotype is unknown. Recently, genome sequencing has uncovered very unusual regions of high guanine and cytosine (GC) content scattered across the sand rat genome, most likely generated by extreme and localized biased gene conversion. A key pancreatic transcription factor PDX1 is encoded by a gene in the most extreme GC-rich region, is remarkably divergent and exhibits altered biochemical properties. Here, we ask if gerbils have proteins in addition to PDX1 that are aberrantly divergent in amino acid sequence, whether they have also become divergent due to GC-biased nucleotide changes, and whether these proteins could plausibly be connected to metabolic dysfunction exhibited by gerbils. Results We analyzed ~ 10,000 proteins with 1-to-1 orthologues in human and rodents and identified 50 proteins that accumulated unusually high levels of amino acid change in the sand rat and 41 in Mongolian jird. We show that more than half of the aberrantly divergent proteins are associated with GC biased nucleotide change and many are in previously defined high GC regions. We highlight four aberrantly divergent gerbil proteins, PDX1, INSR, MEDAG and SPP1, that may plausibly be associated with dietary metabolism. Conclusions We show that through the course of gerbil evolution, many aberrantly divergent proteins have accumulated in the gerbil lineage, and GC-biased nucleotide substitution rather than positive selection is the likely cause of extreme divergence in more than half of these. Some proteins carry putatively deleterious changes that could be associated with metabolic and physiological phenotypes observed in some gerbil species. We propose that these animals provide a useful model to study the ‘tug-of-war’ between natural selection and the excessive accumulation of deleterious substitutions mutations through biased gene conversion.
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Affiliation(s)
- Yichen Dai
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Rodrigo Pracana
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Peter W H Holland
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
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17
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Sackton TB. Studying Natural Selection in the Era of Ubiquitous Genomes. Trends Genet 2020; 36:792-803. [DOI: 10.1016/j.tig.2020.07.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 01/15/2023]
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18
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Haag KL, Pombert JF, Sun Y, de Albuquerque NRM, Batliner B, Fields P, Lopes TF, Ebert D. Microsporidia with Vertical Transmission Were Likely Shaped by Nonadaptive Processes. Genome Biol Evol 2020; 12:3599-3614. [PMID: 31825473 PMCID: PMC6944219 DOI: 10.1093/gbe/evz270] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2019] [Indexed: 12/14/2022] Open
Abstract
Microsporidia have the leanest genomes among eukaryotes, and their physiological and genomic simplicity has been attributed to their intracellular, obligate parasitic life-style. However, not all microsporidia genomes are small or lean, with the largest dwarfing the smallest ones by at least an order of magnitude. To better understand the evolutionary mechanisms behind this genomic diversification, we explore here two clades of microsporidia with distinct life histories, Ordospora and Hamiltosporidium, parasitizing the same host species, Daphnia magna. Based on seven newly assembled genomes, we show that mixed-mode transmission (the combination of horizontal and vertical transmission), which occurs in Hamiltosporidium, is found to be associated with larger and AT-biased genomes, more genes, and longer intergenic regions, as compared with the exclusively horizontally transmitted Ordospora. Furthermore, the Hamiltosporidium genome assemblies contain a variety of repetitive elements and long segmental duplications. We show that there is an excess of nonsynonymous substitutions in the microsporidia with mixed-mode transmission, which cannot be solely attributed to the lack of recombination, suggesting that bursts of genome size in these microsporidia result primarily from genetic drift. Overall, these findings suggest that the switch from a horizontal-only to a mixed mode of transmission likely produces population bottlenecks in Hamiltosporidium species, therefore reducing the effectiveness of natural selection, and allowing their genomic features to be largely shaped by nonadaptive processes.
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Affiliation(s)
- Karen L Haag
- Department of Genetics and Post-Graduation Program of Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Yukun Sun
- Department of Biology, Illinois Institute of Technology
| | - Nathalia Rammé M de Albuquerque
- Department of Genetics and Post-Graduation Program of Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Peter Fields
- Department of Environmental Sciences, Zoology, Basel University, Switzerland
| | - Tiago Falcon Lopes
- Department of Genetics and Post-Graduation Program of Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, Basel University, Switzerland
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19
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Analyses of RAG1 and RAG2 genes suggest different evolutionary rates in the Cetacea lineage. Mol Immunol 2019; 117:131-138. [PMID: 31770676 DOI: 10.1016/j.molimm.2019.10.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 10/14/2019] [Accepted: 10/23/2019] [Indexed: 01/01/2023]
Abstract
V(D)J recombination is a process of somatic recombination catalyzed by proteins encoded by RAG1 and RAG2 genes, both restricted to the genome of jawed vertebrates. Their proteins constitute the enzymatic core of V(D)J recombination machinery and are crucial for jawed vertebrate adaptive immunity. Mammals possess great ecological diversity, and their complex evolutionary history associated with radiation to different environments presented many distinct pathogenic challenges from these different habitats. Cetaceans comprise a mammalian order of fully aquatic mammals that have arisen from a complete terrestrial ancestor and, accordingly, was confronted with challenges from changing environmental pathogens while they transitioned from land to sea. In this study we undertook molecular evolutionary analyses of RAG1 and RAG2 genes, exploring the possible role of natural selection acting on these genes focusing on the cetacean lineage. We performed phylogenetic reconstructions on IQ-TREE, together with selection analyses in the codeml program of the PAML package, and in the FITMODEL program for codon evolution and switching on both the RAG1 and RAG2 genes. Our findings demonstrate that RAG1 and RAG2 remained fairly conserved among tetrapods, with purifying selection acting on both genes, with evidence for a few punctuated shifts in nucleotide substitution rates of both genes along tetrapod evolution. We demonstrate differential evolution in the closely linked genes RAG1 and RAG2 specifically in cetaceans.
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20
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Feigin CY, Newton AH, Pask AJ. Widespread cis-regulatory convergence between the extinct Tasmanian tiger and gray wolf. Genome Res 2019; 29:1648-1658. [PMID: 31533979 PMCID: PMC6771401 DOI: 10.1101/gr.244251.118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 08/19/2019] [Indexed: 12/18/2022]
Abstract
The extinct marsupial Tasmanian tiger, or thylacine, and the eutherian gray wolf are among the most widely recognized examples of convergent evolution in mammals. Despite being distantly related, these large predators independently evolved extremely similar craniofacial morphologies, and evidence suggests that they filled similar ecological niches. Previous analyses revealed little evidence of adaptive convergence between their protein-coding genes. Thus, the genetic basis of their convergence is still unclear. Here, we identified candidate craniofacial cis-regulatory elements across vertebrates and compared their evolutionary rates in the thylacine and wolf, revealing abundant signatures of convergent positive selection. Craniofacial thylacine-wolf accelerated regions were enriched near genes involved in TGF beta (TGFB) and BMP signaling, both of which are key morphological signaling pathways with critical roles in establishing the identities and boundaries between craniofacial tissues. Similarly, enhancers of genes involved in craniofacial nerve development showed convergent selection and involvement in these pathways. Taken together, these results suggest that adaptation in cis-regulators of TGF beta and BMP signaling may provide a mechanism to explain the coevolution of developmentally and functionally integrated craniofacial structures in these species. We also found that despite major structural differences in marsupial and eutherian brains, accelerated regions in both species were common near genes with roles in brain development. Our findings support the hypothesis that, relative to protein-coding genes, positive selection on cis-regulatory elements is likely to be an essential driver of adaptive convergent evolution and may underpin thylacine-wolf phenotypic similarities.
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Affiliation(s)
- Charles Y Feigin
- School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia.,Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Axel H Newton
- School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia.,Museums Victoria, Melbourne, Victoria 3053, Australia
| | - Andrew J Pask
- School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia.,Museums Victoria, Melbourne, Victoria 3053, Australia
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21
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Borges R, Szöllősi GJ, Kosiol C. Quantifying GC-Biased Gene Conversion in Great Ape Genomes Using Polymorphism-Aware Models. Genetics 2019; 212:1321-1336. [PMID: 31147380 PMCID: PMC6707462 DOI: 10.1534/genetics.119.302074] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 05/20/2019] [Indexed: 11/18/2022] Open
Abstract
As multi-individual population-scale data become available, more complex modeling strategies are needed to quantify genome-wide patterns of nucleotide usage and associated mechanisms of evolution. Recently, the multivariate neutral Moran model was proposed. However, it was shown insufficient to explain the distribution of alleles in great apes. Here, we propose a new model that includes allelic selection. Our theoretical results constitute the basis of a new Bayesian framework to estimate mutation rates and selection coefficients from population data. We apply the new framework to a great ape dataset, where we found patterns of allelic selection that match those of genome-wide GC-biased gene conversion (gBGC). In particular, we show that great apes have patterns of allelic selection that vary in intensity-a feature that we correlated with great apes' distinct demographies. We also demonstrate that the AT/GC toggling effect decreases the probability of a substitution, promoting more polymorphisms in the base composition of great ape genomes. We further assess the impact of GC-bias in molecular analysis, and find that mutation rates and genetic distances are estimated under bias when gBGC is not properly accounted for. Our results contribute to the discussion on the tempo and mode of gBGC evolution, while stressing the need for gBGC-aware models in population genetics and phylogenetics.
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Affiliation(s)
- Rui Borges
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Wien, Wien, Austria
| | - Gergely J Szöllősi
- Department of Biological Physics, MTA-ELTE "Lendulet" Evolutionary Genomics Research Group, Eötvös University, Pázmány P. stny. 1A, Budapest 1117, Hungary
| | - Carolin Kosiol
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Wien, Wien, Austria
- Centre for Biological Diversity, School of Biology, University of St Andrews, Fife KY16 9TH, UK
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22
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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: 39] [Impact Index Per Article: 6.5] [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.
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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
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23
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Litterman AJ, Kageyama R, Le Tonqueze O, Zhao W, Gagnon JD, Goodarzi H, Erle DJ, Ansel KM. A massively parallel 3' UTR reporter assay reveals relationships between nucleotide content, sequence conservation, and mRNA destabilization. Genome Res 2019; 29:896-906. [PMID: 31152051 PMCID: PMC6581050 DOI: 10.1101/gr.242552.118] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 05/02/2019] [Indexed: 01/02/2023]
Abstract
Compared to coding sequences, untranslated regions of the transcriptome are not well conserved, and functional annotation of these sequences is challenging. Global relationships between nucleotide composition of 3′ UTR sequences and their sequence conservation have been appreciated since mammalian genomes were first sequenced, but the functional relevance of these patterns remain unknown. We systematically measured the effect on gene expression of the sequences of more than 25,000 RNA-binding protein (RBP) binding sites in primary mouse T cells using a massively parallel reporter assay. GC-rich sequences were destabilizing of reporter mRNAs and come from more rapidly evolving regions of the genome. These sequences were more likely to be folded in vivo and contain a number of structural motifs that reduced accumulation of a heterologous reporter protein. Comparison of full-length 3′ UTR sequences across vertebrate phylogeny revealed that strictly conserved 3′ UTRs were GC-poor and enriched in genes associated with organismal development. In contrast, rapidly evolving 3′ UTRs tended to be GC-rich and derived from genes involved in metabolism and immune responses. Cell-essential genes had lower GC content in their 3′ UTRs, suggesting a connection between unstructured mRNA noncoding sequences and optimal protein production. By reducing gene expression, GC-rich RBP-occupied sequences act as a rapidly evolving substrate for gene regulatory interactions.
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Affiliation(s)
- Adam J Litterman
- Department of Microbiology and Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, California 94143, USA
| | - Robin Kageyama
- Department of Microbiology and Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, California 94143, USA
| | - Olivier Le Tonqueze
- Department of Medicine and Lung Biology Center, University of California San Francisco, San Francisco, California 94143, USA
| | - Wenxue Zhao
- Department of Medicine and Lung Biology Center, University of California San Francisco, San Francisco, California 94143, USA.,School of Medicine, Sun Yat-Sen University, Guangzhou, People's Republic of China, 510245
| | - John D Gagnon
- Department of Microbiology and Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, California 94143, USA
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, Department of Urology, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94143, USA
| | - David J Erle
- Department of Medicine and Lung Biology Center, University of California San Francisco, San Francisco, California 94143, USA
| | - K Mark Ansel
- Department of Microbiology and Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, California 94143, USA
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24
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Transposable Elements: Classification, Identification, and Their Use As a Tool For Comparative Genomics. Methods Mol Biol 2019; 1910:177-207. [PMID: 31278665 DOI: 10.1007/978-1-4939-9074-0_6] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Most genomes are populated by hundreds of thousands of sequences originated from mobile elements. On the one hand, these sequences present a real challenge in the process of genome analysis and annotation. On the other hand, they are very interesting biological subjects involved in many cellular processes. Here we present an overview of transposable elements biodiversity, and we discuss different approaches to transposable elements detection and analyses.
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25
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Hey J, Chung Y, Sethuraman A, Lachance J, Tishkoff S, Sousa VC, Wang Y. Phylogeny Estimation by Integration over Isolation with Migration Models. Mol Biol Evol 2018; 35:2805-2818. [PMID: 30137463 PMCID: PMC6231491 DOI: 10.1093/molbev/msy162] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Phylogeny estimation is difficult for closely related populations and species, especially if they have been exchanging genes. We present a hierarchical Bayesian, Markov-chain Monte Carlo method with a state space that includes all possible phylogenies in a full Isolation-with-Migration model framework. The method is based on a new type of genealogy augmentation called a "hidden genealogy" that enables efficient updating of the phylogeny. This is the first likelihood-based method to fully incorporate directional gene flow and genetic drift for estimation of a species or population phylogeny. Application to human hunter-gatherer populations from Africa revealed a clear phylogenetic history, with strong support for gene exchange with an unsampled ghost population, and relatively ancient divergence between a ghost population and modern human populations, consistent with human/archaic divergence. In contrast, a study of five chimpanzee populations reveals a clear phylogeny with several pairs of populations having exchanged DNA, but does not support a history with an unsampled ghost population.
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Affiliation(s)
- Jody Hey
- Department of Biology, Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA
| | - Yujin Chung
- Department of Biology, Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA
- The Department of Applied Statistics, Kyonggi University, Suwon, South Korea
| | - Arun Sethuraman
- Department of Biology, Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA
| | - Joseph Lachance
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Georgia Institute of Technology, Atlanta, GA
| | - Sarah Tishkoff
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Vitor C Sousa
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, NJ
- University of Lisbon, Lisboa, Portugal
| | - Yong Wang
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, NJ
- Ancestry, San Francisco, CA
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26
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Patel R, Scheinfeldt LB, Sanderford MD, Lanham TR, Tamura K, Platt A, Glicksberg BS, Xu K, Dudley JT, Kumar S. Adaptive Landscape of Protein Variation in Human Exomes. Mol Biol Evol 2018; 35:2015-2025. [PMID: 29846678 PMCID: PMC6063297 DOI: 10.1093/molbev/msy107] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The human genome contains hundreds of thousands of missense mutations. However, only a handful of these variants are known to be adaptive, which implies that adaptation through protein sequence change is an extremely rare phenomenon in human evolution. Alternatively, existing methods may lack the power to pinpoint adaptive variation. We have developed and applied an Evolutionary Probability Approach (EPA) to discover candidate adaptive polymorphisms (CAPs) through the discordance between allelic evolutionary probabilities and their observed frequencies in human populations. EPA reveals thousands of missense CAPs, which suggest that a large number of previously optimal alleles experienced a reversal of fortune in the human lineage. We explored nonadaptive mechanisms to explain CAPs, including the effects of demography, mutation rate variability, and negative and positive selective pressures in modern humans. Many nonadaptive hypotheses were tested, but failed to explain the data, which suggests that a large proportion of CAP alleles have increased in frequency due to beneficial selection. This suggestion is supported by the fact that a vast majority of adaptive missense variants discovered previously in humans are CAPs, and hundreds of CAP alleles are protective in genotype-phenotype association data. Our integrated phylogenomic and population genetic EPA approach predicts the existence of thousands of nonneutral candidate variants in the human proteome. We expect this collection to be enriched in beneficial variation. The EPA approach can be applied to discover candidate adaptive variation in any protein, population, or species for which allele frequency data and reliable multispecies alignments are available.
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Affiliation(s)
- Ravi Patel
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
- Department of Biology, Temple University, Philadelphia, PA
| | - Laura B Scheinfeldt
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
- Department of Biology, Temple University, Philadelphia, PA
- Coriell Institute for Medical Research, Camden, NJ
| | - Maxwell D Sanderford
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
| | - Tamera R Lanham
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
| | - Koichiro Tamura
- Department of Biology, Tokyo Metropolitan University, Tokyo, Japan
| | - Alexander Platt
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
- Department of Biology, Temple University, Philadelphia, PA
- Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA
| | - Benjamin S Glicksberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ke Xu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Joel T Dudley
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
- Department of Biology, Temple University, Philadelphia, PA
- Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
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27
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Torres R, Szpiech ZA, Hernandez RD. Human demographic history has amplified the effects of background selection across the genome. PLoS Genet 2018; 14:e1007387. [PMID: 29912945 PMCID: PMC6056204 DOI: 10.1371/journal.pgen.1007387] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 07/23/2018] [Accepted: 04/30/2018] [Indexed: 01/22/2023] Open
Abstract
Natural populations often grow, shrink, and migrate over time. Such demographic processes can affect genome-wide levels of genetic diversity. Additionally, genetic variation in functional regions of the genome can be altered by natural selection, which drives adaptive mutations to higher frequencies or purges deleterious ones. Such selective processes affect not only the sites directly under selection but also nearby neutral variation through genetic linkage via processes referred to as genetic hitchhiking in the context of positive selection and background selection (BGS) in the context of purifying selection. While there is extensive literature examining the consequences of selection at linked sites at demographic equilibrium, less is known about how non-equilibrium demographic processes influence the effects of hitchhiking and BGS. Utilizing a global sample of human whole-genome sequences from the Thousand Genomes Project and extensive simulations, we investigate how non-equilibrium demographic processes magnify and dampen the consequences of selection at linked sites across the human genome. When binning the genome by inferred strength of BGS, we observe that, compared to Africans, non-African populations have experienced larger proportional decreases in neutral genetic diversity in strong BGS regions. We replicate these findings in admixed populations by showing that non-African ancestral components of the genome have also been affected more severely in these regions. We attribute these differences to the strong, sustained/recurrent population bottlenecks that non-Africans experienced as they migrated out of Africa and throughout the globe. Furthermore, we observe a strong correlation between FST and the inferred strength of BGS, suggesting a stronger rate of genetic drift. Forward simulations of human demographic history with a model of BGS support these observations. Our results show that non-equilibrium demography significantly alters the consequences of selection at linked sites and support the need for more work investigating the dynamic process of multiple evolutionary forces operating in concert.
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Affiliation(s)
- Raul Torres
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, United States of America
| | - Zachary A. Szpiech
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, United States of America
| | - Ryan D. Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, United States of America
- Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA, United States of America
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, United States of America
- * E-mail:
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28
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Dutta R, Saha-Mandal A, Cheng X, Qiu S, Serpen J, Fedorova L, Fedorov A. 1000 human genomes carry widespread signatures of GC biased gene conversion. BMC Genomics 2018; 19:256. [PMID: 29661137 PMCID: PMC5902838 DOI: 10.1186/s12864-018-4593-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 03/12/2018] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND GC-Biased Gene Conversion (gBGC) is one of the important theories put forward to explain profound long-range non-randomness in nucleotide compositions along mammalian chromosomes. Nucleotide changes due to gBGC are hard to distinguish from regular mutations. Here, we present an algorithm for analysis of millions of known SNPs that detects a subset of so-called "SNP flip-over" events representing recent gBGC nucleotide changes, which occurred in previous generations via non-crossover meiotic recombination. RESULTS This algorithm has been applied in a large-scale analysis of 1092 sequenced human genomes. Altogether, 56,328 regions on all autosomes have been examined, which revealed 223,955 putative gBGC cases leading to SNP flip-overs. We detected a strong bias (11.7% ± 0.2% excess) in AT- > GC over GC- > AT base pair changes within the entire set of putative gBGC cases. CONCLUSIONS On average, a human gamete acquires 7 SNP flip-over events, in which one allele is replaced by its complementary allele during the process of meiotic non-crossover recombination. In each meiosis event, on average, gBGC results in replacement of 7 AT base pairs by GC base pairs, while only 6 GC pairs are replaced by AT pairs. Therefore, every human gamete is enriched by one GC pair. Happening over millions of years of evolution, this bias may be a noticeable force in changing the nucleotide composition landscape along chromosomes.
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Affiliation(s)
- Rajib Dutta
- Program in Biomedical Sciences, University of Toledo, Health Science Campus, Toledo, OH 43614 USA
- Department of Medicine, University of Toledo, Health Science Campus, Toledo, OH 43614 USA
- Present Address: Center for Cardiovascular and Pulmonary Research, Nationwide Children’s Hospital, 700 Children’s Dr, Columbus, OH USA
| | - Arnab Saha-Mandal
- Program in Bioinformatics and Proteomics/Genomics, University of Toledo, Health Science Campus, Toledo, OH 43614 USA
- Present Address: Biochemistry and Molecular Biology Graduate Program, Cumming School of Medicine, University of Calgary, Calgary, AB T2N4N1 Canada
| | - Xi Cheng
- Program in Biomedical Sciences, University of Toledo, Health Science Campus, Toledo, OH 43614 USA
| | - Shuhao Qiu
- Program in Biomedical Sciences, University of Toledo, Health Science Campus, Toledo, OH 43614 USA
- Department of Medicine, University of Toledo, Health Science Campus, Toledo, OH 43614 USA
| | - Jasmine Serpen
- SURF Program, University of Toledo, Health Science Campus, Toledo, OH 43614 USA
- College of Arts and Sciences, Washington University in St. Louis, 1 Brookings Dr, St. Louis, MO 63130 USA
| | | | - Alexei Fedorov
- Department of Medicine, University of Toledo, Health Science Campus, Toledo, OH 43614 USA
- Program in Bioinformatics and Proteomics/Genomics, University of Toledo, Health Science Campus, Toledo, OH 43614 USA
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29
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van der Lee R, Wiel L, van Dam TJP, Huynen MA. Genome-scale detection of positive selection in nine primates predicts human-virus evolutionary conflicts. Nucleic Acids Res 2017; 45:10634-10648. [PMID: 28977405 PMCID: PMC5737536 DOI: 10.1093/nar/gkx704] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/02/2017] [Indexed: 12/17/2022] Open
Abstract
Hotspots of rapid genome evolution hold clues about human adaptation. We present a comparative analysis of nine whole-genome sequenced primates to identify high-confidence targets of positive selection. We find strong statistical evidence for positive selection in 331 protein-coding genes (3%), pinpointing 934 adaptively evolving codons (0.014%). Our new procedure is stringent and reveals substantial artefacts (20% of initial predictions) that have inflated previous estimates. The final 331 positively selected genes (PSG) are strongly enriched for innate and adaptive immunity, secreted and cell membrane proteins (e.g. pattern recognition, complement, cytokines, immune receptors, MHC, Siglecs). We also find evidence for positive selection in reproduction and chromosome segregation (e.g. centromere-associated CENPO, CENPT), apolipoproteins, smell/taste receptors and mitochondrial proteins. Focusing on the virus–host interaction, we retrieve most evolutionary conflicts known to influence antiviral activity (e.g. TRIM5, MAVS, SAMHD1, tetherin) and predict 70 novel cases through integration with virus–human interaction data. Protein structure analysis further identifies positive selection in the interaction interfaces between viruses and their cellular receptors (CD4-HIV; CD46-measles, adenoviruses; CD55-picornaviruses). Finally, primate PSG consistently show high sequence variation in human exomes, suggesting ongoing evolution. Our curated dataset of positive selection is a rich source for studying the genetics underlying human (antiviral) phenotypes. Procedures and data are available at https://github.com/robinvanderlee/positive-selection.
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Affiliation(s)
- Robin van der Lee
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Laurens Wiel
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Teunis J P van Dam
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Martijn A Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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30
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Johnston SE, Huisman J, Ellis PA, Pemberton JM. A High-Density Linkage Map Reveals Sexual Dimorphism in Recombination Landscapes in Red Deer ( Cervus elaphus). G3 (BETHESDA, MD.) 2017; 7:2859-2870. [PMID: 28667018 PMCID: PMC5555489 DOI: 10.1534/g3.117.044198] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/27/2017] [Indexed: 11/29/2022]
Abstract
High-density linkage maps are an important tool to gain insight into the genetic architecture of traits of evolutionary and economic interest, and provide a resource to characterize variation in recombination landscapes. Here, we used information from the cattle genome and the 50 K Cervine Illumina BeadChip to inform and refine a high-density linkage map in a wild population of red deer (Cervus elaphus). We constructed a predicted linkage map of 38,038 SNPs and a skeleton map of 10,835 SNPs across 34 linkage groups. We identified several chromosomal rearrangements in the deer lineage relative to sheep and cattle, including six chromosome fissions, one fusion, and two large inversions. Otherwise, our findings showed strong concordance with map orders in the cattle genome. The sex-averaged linkage map length was 2739.7 cM and the genome-wide autosomal recombination rate was 1.04 cM/Mb. The female autosomal map length was 1.21 longer than that of males (2767.4 cM vs. 2280.8 cM, respectively). Sex differences in map length were driven by high female recombination rates in peri-centromeric regions, a pattern that is unusual relative to other mammal species. This effect was more pronounced in fission chromosomes that would have had to produce new centromeres. We propose two hypotheses to explain this effect: (1) that this mechanism may have evolved to counteract centromeric drive associated with meiotic asymmetry in oocyte production; and/or (2) that sequence and structural characteristics suppressing recombination in close proximity to the centromere may not have evolved at neo-centromeres. Our study provides insight into how recombination landscapes vary and evolve in mammals, and will provide a valuable resource for studies of evolution, genetic improvement, and population management in red deer and related species.
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Affiliation(s)
- Susan E Johnston
- Institute of Evolutionary Biology, University of Edinburgh, EH9 3FL, United Kingdom
| | - Jisca Huisman
- Institute of Evolutionary Biology, University of Edinburgh, EH9 3FL, United Kingdom
| | - Philip A Ellis
- Institute of Evolutionary Biology, University of Edinburgh, EH9 3FL, United Kingdom
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31
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Terekhanova NV, Seplyarskiy VB, Soldatov RA, Bazykin GA. Evolution of Local Mutation Rate and Its Determinants. Mol Biol Evol 2017; 34:1100-1109. [PMID: 28138076 PMCID: PMC5850301 DOI: 10.1093/molbev/msx060] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Mutation rate varies along the human genome, and part of this variation is explainable by measurable local properties of the DNA molecule. Moreover, mutation rates differ between orthologous genomic regions of different species, but the drivers of this change are unclear. Here, we use data on human divergence from chimpanzee, human rare polymorphism, and human de novo mutations to predict the substitution rate at orthologous regions of non-human mammals. We show that the local mutation rates are very similar between human and apes, implying that their variation has a strong underlying cryptic component not explainable by the known genomic features. Mutation rates become progressively less similar in more distant species, and these changes are partially explainable by changes in the local genomic features of orthologous regions, most importantly, in the recombination rate. However, they are much more rapid, implying that the cryptic component underlying the mutation rate is more ephemeral than the known genomic features. These findings shed light on the determinants of mutation rate evolution. Key words local mutation rate, molecular evolution, recombination rate.
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Affiliation(s)
- Nadezhda V. Terekhanova
- Sector for Molecular Evolution, Institute for Information Transmission Problems of the RAS (Kharkevich Institute), Moscow, Russia
- M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Vladimir B. Seplyarskiy
- Sector for Molecular Evolution, Institute for Information Transmission Problems of the RAS (Kharkevich Institute), Moscow, Russia
| | - Ruslan A. Soldatov
- Sector for Molecular Evolution, Institute for Information Transmission Problems of the RAS (Kharkevich Institute), Moscow, Russia
- M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Georgii A. Bazykin
- Sector for Molecular Evolution, Institute for Information Transmission Problems of the RAS (Kharkevich Institute), Moscow, Russia
- M. V. Lomonosov Moscow State University, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
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32
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Romiguier J, Roux C. Analytical Biases Associated with GC-Content in Molecular Evolution. Front Genet 2017; 8:16. [PMID: 28261263 PMCID: PMC5309256 DOI: 10.3389/fgene.2017.00016] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 02/06/2017] [Indexed: 12/19/2022] Open
Abstract
Molecular evolution is being revolutionized by high-throughput sequencing allowing an increased amount of genome-wide data available for multiple species. While base composition summarized by GC-content is one of the first metrics measured in genomes, its genomic distribution is a frequently neglected feature in downstream analyses based on DNA sequence comparisons. Here, we show how base composition heterogeneity among loci and taxa can bias common molecular evolution analyses such as phylogenetic tree reconstruction, detection of natural selection and estimation of codon usage. We then discuss the biological, technical and methodological causes of these GC-associated biases and suggest approaches to overcome them.
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Affiliation(s)
- Jonathan Romiguier
- Department of Ecology and Evolution, University of Lausanne Lausanne, Switzerland
| | - Camille Roux
- Department of Ecology and Evolution, University of Lausanne Lausanne, Switzerland
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33
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Abstract
Events in primate evolution are often dated by assuming a constant rate of substitution per unit time, but the validity of this assumption remains unclear. Among mammals, it is well known that there exists substantial variation in yearly substitution rates. Such variation is to be expected from differences in life history traits, suggesting it should also be found among primates. Motivated by these considerations, we analyze whole genomes from 10 primate species, including Old World Monkeys (OWMs), New World Monkeys (NWMs), and apes, focusing on putatively neutral autosomal sites and controlling for possible effects of biased gene conversion and methylation at CpG sites. We find that substitution rates are up to 64% higher in lineages leading from the hominoid-NWM ancestor to NWMs than to apes. Within apes, rates are ∼2% higher in chimpanzees and ∼7% higher in the gorilla than in humans. Substitution types subject to biased gene conversion show no more variation among species than those not subject to it. Not all mutation types behave similarly, however; in particular, transitions at CpG sites exhibit a more clocklike behavior than do other types, presumably because of their nonreplicative origin. Thus, not only the total rate, but also the mutational spectrum, varies among primates. This finding suggests that events in primate evolution are most reliably dated using CpG transitions. Taking this approach, we estimate the human and chimpanzee divergence time is 12.1 million years, and the human and gorilla divergence time is 15.1 million years.
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34
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Kenigsberg E, Yehuda Y, Marjavaara L, Keszthelyi A, Chabes A, Tanay A, Simon I. The mutation spectrum in genomic late replication domains shapes mammalian GC content. Nucleic Acids Res 2016; 44:4222-32. [PMID: 27085808 PMCID: PMC4872117 DOI: 10.1093/nar/gkw268] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 03/10/2016] [Accepted: 03/30/2016] [Indexed: 11/14/2022] Open
Abstract
Genome sequence compositions and epigenetic organizations are correlated extensively across multiple length scales. Replication dynamics, in particular, is highly correlated with GC content. We combine genome-wide time of replication (ToR) data, topological domains maps and detailed functional epigenetic annotations to study the correlations between replication timing and GC content at multiple scales. We find that the decrease in genomic GC content at large scale late replicating regions can be explained by mutation bias favoring A/T nucleotide, without selection or biased gene conversion. Quantification of the free dNTP pool during the cell cycle is consistent with a mechanism involving replication-coupled mutation spectrum that favors AT nucleotides at late S-phase. We suggest that mammalian GC content composition is shaped by independent forces, globally modulating mutation bias and locally selecting on functional element. Deconvoluting these forces and analyzing them on their native scales is important for proper characterization of complex genomic correlations.
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Affiliation(s)
- Ephraim Kenigsberg
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Yishai Yehuda
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Lisette Marjavaara
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Andrea Keszthelyi
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Itamar Simon
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
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35
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Abstract
Cellular processes mediated through nuclear DNA must contend with chromatin. Chromatin structural assays can efficiently integrate information across diverse regulatory elements, revealing the functional noncoding genome. In this study, we use a differential nuclease sensitivity assay based on micrococcal nuclease (MNase) digestion to discover open chromatin regions in the maize genome. We find that maize MNase-hypersensitive (MNase HS) regions localize around active genes and within recombination hotspots, focusing biased gene conversion at their flanks. Although MNase HS regions map to less than 1% of the genome, they consistently explain a remarkably large amount (∼40%) of heritable phenotypic variance in diverse complex traits. MNase HS regions are therefore on par with coding sequences as annotations that demarcate the functional parts of the maize genome. These results imply that less than 3% of the maize genome (coding and MNase HS regions) may give rise to the overwhelming majority of phenotypic variation, greatly narrowing the scope of the functional genome.
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36
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Abstract
As a species, we possess unique biological features that distinguish us from other primates. Here, we review recent efforts to identify changes in gene regulation that drove the evolution of novel human phenotypes. We discuss genotype-directed comparisons of human and nonhuman primate genomes to identify human-specific genetic changes that may encode new regulatory functions. We also review phenotype-directed approaches, which use comparisons of gene expression or regulatory function in homologous human and nonhuman primate cells and tissues to identify changes in expression levels or regulatory activity that may be due to genetic changes in humans. Together, these studies are beginning to reveal the landscape of regulatory innovation in human evolution and point to specific regulatory changes for further study. Finally, we highlight two novel strategies to model human-specific regulatory functions in vivo: primate induced pluripotent stem cells and the generation of humanized mice by genome editing.
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Affiliation(s)
- Steven K Reilly
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06510;
| | - James P Noonan
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06510; .,Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511.,Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, Connecticut 06510
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37
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Hara Y. Tempo and mode of genomic mutations unveil human evolutionary history. Genes Genet Syst 2015; 90:123-31. [PMID: 26510567 DOI: 10.1266/ggs.90.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Mutations that have occurred in human genomes provide insight into various aspects of evolutionary history such as speciation events and degrees of natural selection. Comparing genome sequences between human and great apes or among humans is a feasible approach for inferring human evolutionary history. Recent advances in high-throughput or so-called 'next-generation' DNA sequencing technologies have enabled the sequencing of thousands of individual human genomes, as well as a variety of reference genomes of hominids, many of which are publicly available. These sequence data can help to unveil the detailed demographic history of the lineage leading to humans as well as the explosion of modern human population size in the last several thousand years. In addition, high-throughput sequencing illustrates the tempo and mode of de novo mutations, which are producing human genetic variation at this moment. Pedigree-based human genome sequencing has shown that mutation rates vary significantly across the human genome. These studies have also provided an improved timescale of human evolution, because the mutation rate estimated from pedigree analysis is half that estimated from traditional analyses based on molecular phylogeny. Because of the dramatic reduction in sequencing cost, sequencing on-demand samples designed for specific studies is now also becoming popular. To produce data of sufficient quality to meet the requirements of the study, it is necessary to set an explicit sequencing plan that includes the choice of sample collection methods, sequencing platforms, and number of sequence reads.
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Affiliation(s)
- Yuichiro Hara
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies
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38
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Mugal CF, Weber CC, Ellegren H. GC-biased gene conversion links the recombination landscape and demography to genomic base composition. Bioessays 2015; 37:1317-26. [DOI: 10.1002/bies.201500058] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Carina F. Mugal
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| | - Claudia C. Weber
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
- Department of Biology; Center for Computational Genetics and Genomics; Temple University; Philadelphia PA USA
| | - Hans Ellegren
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
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39
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Bolívar P, Mugal CF, Nater A, Ellegren H. Recombination Rate Variation Modulates Gene Sequence Evolution Mainly via GC-Biased Gene Conversion, Not Hill-Robertson Interference, in an Avian System. Mol Biol Evol 2015; 33:216-27. [PMID: 26446902 PMCID: PMC4693978 DOI: 10.1093/molbev/msv214] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The ratio of nonsynonymous to synonymous substitution rates (ω) is often used to measure the strength of natural selection. However, ω may be influenced by linkage among different targets of selection, that is, Hill–Robertson interference (HRI), which reduces the efficacy of selection. Recombination modulates the extent of HRI but may also affect ω by means of GC-biased gene conversion (gBGC), a process leading to a preferential fixation of G:C (“strong,” S) over A:T (“weak,” W) alleles. As HRI and gBGC can have opposing effects on ω, it is essential to understand their relative impact to make proper inferences of ω. We used a model that separately estimated S-to-S, S-to-W, W-to-S, and W-to-W substitution rates in 8,423 avian genes in the Ficedula flycatcher lineage. We found that the W-to-S substitution rate was positively, and the S-to-W rate negatively, correlated with recombination rate, in accordance with gBGC but not predicted by HRI. The W-to-S rate further showed the strongest impact on both dN and dS. However, since the effects were stronger at 4-fold than at 0-fold degenerated sites, likely because the GC content of these sites is farther away from its equilibrium, ω slightly decreases with increasing recombination rate, which could falsely be interpreted as a consequence of HRI. We corroborated this hypothesis analytically and demonstrate that under particular conditions, ω can decrease with increasing recombination rate. Analyses of the site-frequency spectrum showed that W-to-S mutations were skewed toward high, and S-to-W mutations toward low, frequencies, consistent with a prevalent gBGC-driven fixation bias.
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Affiliation(s)
- Paulina Bolívar
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Carina F Mugal
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Alexander Nater
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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40
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Simonti CN, Capra JA. The evolution of the human genome. Curr Opin Genet Dev 2015; 35:9-15. [PMID: 26338498 DOI: 10.1016/j.gde.2015.08.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 08/08/2015] [Accepted: 08/12/2015] [Indexed: 02/05/2023]
Abstract
Human genomes hold a record of the evolutionary forces that have shaped our species. Advances in DNA sequencing, functional genomics, and population genetic modeling have deepened our understanding of human demographic history, natural selection, and many other long-studied topics. These advances have also revealed many previously underappreciated factors that influence the evolution of the human genome, including functional modifications to DNA and histones, conserved 3D topological chromatin domains, structural variation, and heterogeneous mutation patterns along the genome. Using evolutionary theory as a lens to study these phenomena will lead to significant breakthroughs in understanding what makes us human and why we get sick.
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Affiliation(s)
- Corinne N Simonti
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37235, USA
| | - John A Capra
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37235, USA; Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37235, USA.
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41
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Glémin S, Arndt PF, Messer PW, Petrov D, Galtier N, Duret L. Quantification of GC-biased gene conversion in the human genome. Genome Res 2015; 25:1215-28. [PMID: 25995268 PMCID: PMC4510005 DOI: 10.1101/gr.185488.114] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 05/18/2015] [Indexed: 11/25/2022]
Abstract
Much evidence indicates that GC-biased gene conversion (gBGC) has a major impact on the evolution of mammalian genomes. However, a detailed quantification of the process is still lacking. The strength of gBGC can be measured from the analysis of derived allele frequency spectra (DAF), but this approach is sensitive to a number of confounding factors. In particular, we show by simulations that the inference is pervasively affected by polymorphism polarization errors and by spatial heterogeneity in gBGC strength. We propose a new general method to quantify gBGC from DAF spectra, incorporating polarization errors, taking spatial heterogeneity into account, and jointly estimating mutation bias. Applying it to human polymorphism data from the 1000 Genomes Project, we show that the strength of gBGC does not differ between hypermutable CpG sites and non-CpG sites, suggesting that in humans gBGC is not caused by the base-excision repair machinery. Genome-wide, the intensity of gBGC is in the nearly neutral area. However, given that recombination occurs primarily within recombination hotspots, 1%–2% of the human genome is subject to strong gBGC. On average, gBGC is stronger in African than in non-African populations, reflecting differences in effective population sizes. However, due to more heterogeneous recombination landscapes, the fraction of the genome affected by strong gBGC is larger in non-African than in African populations. Given that the location of recombination hotspots evolves very rapidly, our analysis predicts that, in the long term, a large fraction of the genome is affected by short episodes of strong gBGC.
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Affiliation(s)
- Sylvain Glémin
- Institut des Sciences de l'Evolution (ISEM - UMR 5554 Université de Montpellier-CNRS-IRD-EPHE), 34095 Montpellier, France; Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Peter F Arndt
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Philipp W Messer
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
| | - Dmitri Petrov
- Department of Biology, Stanford University, Stanford, California 94305-5020, USA
| | - Nicolas Galtier
- Institut des Sciences de l'Evolution (ISEM - UMR 5554 Université de Montpellier-CNRS-IRD-EPHE), 34095 Montpellier, France
| | - Laurent Duret
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, 69622 Villeurbanne, France
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42
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Rodgers-Melnick E, Bradbury PJ, Elshire RJ, Glaubitz JC, Acharya CB, Mitchell SE, Li C, Li Y, Buckler ES. Recombination in diverse maize is stable, predictable, and associated with genetic load. Proc Natl Acad Sci U S A 2015; 112:3823-8. [PMID: 25775595 PMCID: PMC4378432 DOI: 10.1073/pnas.1413864112] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Among the fundamental evolutionary forces, recombination arguably has the largest impact on the practical work of plant breeders. Varying over 1,000-fold across the maize genome, the local meiotic recombination rate limits the resolving power of quantitative trait mapping and the precision of favorable allele introgression. The consequences of low recombination also theoretically extend to the species-wide scale by decreasing the power of selection relative to genetic drift, and thereby hindering the purging of deleterious mutations. In this study, we used genotyping-by-sequencing (GBS) to identify 136,000 recombination breakpoints at high resolution within US and Chinese maize nested association mapping populations. We find that the pattern of cross-overs is highly predictable on the broad scale, following the distribution of gene density and CpG methylation. Several large inversions also suppress recombination in distinct regions of several families. We also identify recombination hotspots ranging in size from 1 kb to 30 kb. We find these hotspots to be historically stable and, compared with similar regions with low recombination, to have strongly differentiated patterns of DNA methylation and GC content. We also provide evidence for the historical action of GC-biased gene conversion in recombination hotspots. Finally, using genomic evolutionary rate profiling (GERP) to identify putative deleterious polymorphisms, we find evidence for reduced genetic load in hotspot regions, a phenomenon that may have considerable practical importance for breeding programs worldwide.
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Affiliation(s)
| | - Peter J Bradbury
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853; US Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853; and
| | - Robert J Elshire
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853
| | | | | | - Sharon E Mitchell
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853
| | - Chunhui Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yongxiang Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853; US Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853; and
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43
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Pandya S, Struck TJ, Mannakee BK, Paniscus M, Gutenkunst RN. Testing whether metazoan tyrosine loss was driven by selection against promiscuous phosphorylation. Mol Biol Evol 2015; 32:144-52. [PMID: 25312910 PMCID: PMC4271526 DOI: 10.1093/molbev/msu284] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Protein tyrosine phosphorylation is a key regulatory modification in metazoans, and the corresponding kinase enzymes have diversified dramatically. This diversification is correlated with a genome-wide reduction in protein tyrosine content, and it was recently suggested that this reduction was driven by selection to avoid promiscuous phosphorylation that might be deleterious. We tested three predictions of this intriguing hypothesis. 1) Selection should be stronger on residues that are more likely to be phosphorylated due to local solvent accessibility or structural disorder. 2) Selection should be stronger on proteins that are more likely to be promiscuously phosphorylated because they are abundant. We tested these predictions by comparing distributions of tyrosine within and among human and yeast orthologous proteins. 3) Selection should be stronger against mutations that create tyrosine versus remove tyrosine. We tested this prediction using human population genomic variation data. We found that all three predicted effects are modest for tyrosine when compared with the other amino acids, suggesting that selection against deleterious phosphorylation was not dominant in driving metazoan tyrosine loss.
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Affiliation(s)
- Siddharth Pandya
- Department of Molecular and Cellular Biology, University of Arizona
| | - Travis J Struck
- Department of Molecular and Cellular Biology, University of Arizona
| | - Brian K Mannakee
- Department of Molecular and Cellular Biology, University of Arizona Division of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona
| | - Mary Paniscus
- Department of Molecular and Cellular Biology, University of Arizona Graduate Interdisciplinary Program in Genetics, University of Arizona
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44
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Figuet E, Ballenghien M, Romiguier J, Galtier N. Biased gene conversion and GC-content evolution in the coding sequences of reptiles and vertebrates. Genome Biol Evol 2014; 7:240-50. [PMID: 25527834 PMCID: PMC4316630 DOI: 10.1093/gbe/evu277] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Mammalian and avian genomes are characterized by a substantial spatial heterogeneity of GC-content, which is often interpreted as reflecting the effect of local GC-biased gene conversion (gBGC), a meiotic repair bias that favors G and C over A and T alleles in high-recombining genomic regions. Surprisingly, the first fully sequenced nonavian sauropsid (i.e., reptile), the green anole Anolis carolinensis, revealed a highly homogeneous genomic GC-content landscape, suggesting the possibility that gBGC might not be at work in this lineage. Here, we analyze GC-content evolution at third-codon positions (GC3) in 44 vertebrates species, including eight newly sequenced transcriptomes, with a specific focus on nonavian sauropsids. We report that reptiles, including the green anole, have a genome-wide distribution of GC3 similar to that of mammals and birds, and we infer a strong GC3-heterogeneity to be already present in the tetrapod ancestor. We further show that the dynamic of coding sequence GC-content is largely governed by karyotypic features in vertebrates, notably in the green anole, in agreement with the gBGC hypothesis. The discrepancy between third-codon positions and noncoding DNA regarding GC-content dynamics in the green anole could not be explained by the activity of transposable elements or selection on codon usage. This analysis highlights the unique value of third-codon positions as an insertion/deletion-free marker of nucleotide substitution biases that ultimately affect the evolution of proteins.
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Affiliation(s)
- Emeric Figuet
- CNRS, Université Montpellier 2, UMR 5554, Institut des Sciences de l'Evolution de Montpellier, France
| | - Marion Ballenghien
- CNRS, Université Montpellier 2, UMR 5554, Institut des Sciences de l'Evolution de Montpellier, France
| | - Jonathan Romiguier
- CNRS, Université Montpellier 2, UMR 5554, Institut des Sciences de l'Evolution de Montpellier, France Department of Ecology and Evolution, Biophore, University of Lausanne, Switzerland
| | - Nicolas Galtier
- CNRS, Université Montpellier 2, UMR 5554, Institut des Sciences de l'Evolution de Montpellier, France
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45
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Scala G, Affinito O, Miele G, Monticelli A, Cocozza S. Evidence for evolutionary and nonevolutionary forces shaping the distribution of human genetic variants near transcription start sites. PLoS One 2014; 9:e114432. [PMID: 25474578 PMCID: PMC4256220 DOI: 10.1371/journal.pone.0114432] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 11/09/2014] [Indexed: 11/19/2022] Open
Abstract
The regions surrounding transcription start sites (TSSs) of genes play a critical role in the regulation of gene expression. At the same time, current evidence indicates that these regions are particularly stressed by transcription-related mutagenic phenomena. In this work we performed a genome-wide analysis of the distribution of single nucleotide polymorphisms (SNPs) inside the 10 kb region flanking human TSSs by dividing SNPs into four classes according to their frequency (rare, two intermediate classes, and common). We found that, in this 10 kb region, the distribution of variants depends on their frequency and on their localization relative to the TSS. We found that the distribution of variants is generally different for TSSs located inside or outside of CpG islands. We found a significant relationship between the distribution of rare variants and nucleosome occupancy scores. Furthermore, our analysis suggests that evolutionary (purifying selection) and nonevolutionary (biased gene conversion) forces both play a role in determining the relative SNP frequency around TSSs. Finally, we analyzed the potential pathogenicity of each class of variant using the Combined Annotation Dependent Depletion score. In conclusion, this study provides a novel and detailed view of the distribution of genomic variants around TSSs, providing insight into the forces that instigate and maintain variability in such critical regions.
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Affiliation(s)
- Giovanni Scala
- Gruppo Interdipartimentale di Bioinformatica e Biologia Computazionale, Università degli Studi di Napoli “Federico II”, Naples, Italy
- Dipartimento di Fisica, Università degli Studi di Napoli “Federico II”, Naples, Italy
- Istituto Nazionale di Fisica Nucleare, Sezione di Napoli, Naples, Italy
- * E-mail:
| | - Ornella Affinito
- Gruppo Interdipartimentale di Bioinformatica e Biologia Computazionale, Università degli Studi di Napoli “Federico II”, Naples, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli “Federico II”, Naples, Italy
- Istituto di Endocrinologia ed Oncologia Sperimentale (IEOS), CNR, Naples, Italy
| | - Gennaro Miele
- Gruppo Interdipartimentale di Bioinformatica e Biologia Computazionale, Università degli Studi di Napoli “Federico II”, Naples, Italy
- Dipartimento di Fisica, Università degli Studi di Napoli “Federico II”, Naples, Italy
- Istituto Nazionale di Fisica Nucleare, Sezione di Napoli, Naples, Italy
| | - Antonella Monticelli
- Gruppo Interdipartimentale di Bioinformatica e Biologia Computazionale, Università degli Studi di Napoli “Federico II”, Naples, Italy
- Istituto di Endocrinologia ed Oncologia Sperimentale (IEOS), CNR, Naples, Italy
| | - Sergio Cocozza
- Gruppo Interdipartimentale di Bioinformatica e Biologia Computazionale, Università degli Studi di Napoli “Federico II”, Naples, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli “Federico II”, Naples, Italy
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46
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Enard W. Mouse models of human evolution. Curr Opin Genet Dev 2014; 29:75-80. [DOI: 10.1016/j.gde.2014.08.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 08/13/2014] [Accepted: 08/23/2014] [Indexed: 10/24/2022]
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47
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Rosenbloom KR, Armstrong J, Barber GP, Casper J, Clawson H, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hickey G, Hinrichs AS, Hubley R, Karolchik D, Learned K, Lee BT, Li CH, Miga KH, Nguyen N, Paten B, Raney BJ, Smit AFA, Speir ML, Zweig AS, Haussler D, Kuhn RM, Kent WJ. The UCSC Genome Browser database: 2015 update. Nucleic Acids Res 2014; 43:D670-81. [PMID: 25428374 PMCID: PMC4383971 DOI: 10.1093/nar/gku1177] [Citation(s) in RCA: 717] [Impact Index Per Article: 65.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Launched in 2001 to showcase the draft human genome assembly, the UCSC Genome Browser database (http://genome.ucsc.edu) and associated tools continue to grow, providing a comprehensive resource of genome assemblies and annotations to scientists and students worldwide. Highlights of the past year include the release of a browser for the first new human genome reference assembly in 4 years in December 2013 (GRCh38, UCSC hg38), a watershed comparative genomics annotation (100-species multiple alignment and conservation) and a novel distribution mechanism for the browser (GBiB: Genome Browser in a Box). We created browsers for new species (Chinese hamster, elephant shark, minke whale), 'mined the web' for DNA sequences and expanded the browser display with stacked color graphs and region highlighting. As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data hubs has tripled.
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Affiliation(s)
- Kate R Rosenbloom
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Joel Armstrong
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Galt P Barber
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Jonathan Casper
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Hiram Clawson
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Mark Diekhans
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Timothy R Dreszer
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Pauline A Fujita
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Luvina Guruvadoo
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Maximilian Haeussler
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Rachel A Harte
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Steve Heitner
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Glenn Hickey
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Angie S Hinrichs
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Robert Hubley
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Donna Karolchik
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Katrina Learned
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Brian T Lee
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Chin H Li
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Karen H Miga
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Ngan Nguyen
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Benedict Paten
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Brian J Raney
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | | | - Matthew L Speir
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Ann S Zweig
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - David Haussler
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Robert M Kuhn
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - W James Kent
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
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48
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Bell CG, Wilson GA, Beck S. Human-specific CpG 'beacons' identify human-specific prefrontal cortex H3K4me3 chromatin peaks. Epigenomics 2014; 6:21-31. [PMID: 24579944 DOI: 10.2217/epi.13.74] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Targeted recruitment of chromatin-modifying enzymes to clusters of CpG dinucleotides contributes toward the formation of accessible chromatin. By interprimate comparison we previously identified the set of nonpolymorphic human-specific CpGs (CpG 'beacons') and revealed that these loci were enriched for human disease traits. Due to their human-specific CpG density change, extreme CpG 'beacon' clusters (≥20 CpG beacons/kb) were predicted to identify permissive chromatin peaks within the human genome. AIM We set out to explore these sequence-defined regions for evidence of an active chromatin signature. RESULTS Using available comparative primate epigenomic data from neurons of the prefrontal cortex, we show that these CpG 'beacon' clusters are indeed enriched for being human-specific H3K4me3 peaks (χ(2): p < 2.2 × 10(-16)) and thus predictive of permissive chromatin states. These sequence regions had a higher predictive value than previous selective analyses. We also show that both human-specific H3K4me3 and CpG 'beacon' clusters are increased within current and ancestral telomeric regions, supporting an association with recombination, which is higher towards the distal ends of chromosomes. CONCLUSION Therefore, CpG-focused comparative sequence analysis can precisely pinpoint chromatin structures that contribute to the human-specific phenotype and further supports an integrated approach in genomic and epigenomic studies.
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Affiliation(s)
- Christopher G Bell
- Medical Genomics, UCL Cancer Institute, University College London, London, UK
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49
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Evidence for stabilizing selection on codon usage in chromosomal rearrangements of Drosophila pseudoobscura. G3-GENES GENOMES GENETICS 2014; 4:2433-49. [PMID: 25326424 PMCID: PMC4267939 DOI: 10.1534/g3.114.014860] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
There has been a renewed interest in investigating the role of stabilizing selection acting on genome-wide traits such as codon usage bias. Codon bias, when synonymous codons are used at unequal frequencies, occurs in a wide variety of taxa. Standard evolutionary models explain the maintenance of codon bias through a balance of genetic drift, mutation and weak purifying selection. The efficacy of selection is expected to be reduced in regions of suppressed recombination. Contrary to observations in Drosophila melanogaster, some recent studies have failed to detect a relationship between the recombination rate, intensity of selection acting at synonymous sites, and the magnitude of codon bias as predicted under these standard models. Here, we examined codon bias in 2798 protein coding loci on the third chromosome of D. pseudoobscura using whole-genome sequences of 47 individuals, representing five common third chromosome gene arrangements. Fine-scale recombination maps were constructed using more than 1 million segregating sites. As expected, recombination was demonstrated to be significantly suppressed between chromosome arrangements, allowing for a direct examination of the relationship between recombination, selection, and codon bias. As with other Drosophila species, we observe a strong mutational bias away from the most frequently used codons. We find the rate of synonymous and nonsynonymous polymorphism is variable between different amino acids. However, we do not observe a reduction in codon bias or the strength of selection in regions of suppressed recombination as expected. Instead, we find that the interaction between weak stabilizing selection and mutational bias likely plays a role in shaping the composition of synonymous codons across the third chromosome in D. pseudoobscura.
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Lachance J, Tishkoff SA. Biased gene conversion skews allele frequencies in human populations, increasing the disease burden of recessive alleles. Am J Hum Genet 2014; 95:408-20. [PMID: 25279983 PMCID: PMC4185123 DOI: 10.1016/j.ajhg.2014.09.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 08/21/2014] [Accepted: 09/10/2014] [Indexed: 10/25/2022] Open
Abstract
Gene conversion results in the nonreciprocal transfer of genetic information between two recombining sequences, and there is evidence that this process is biased toward G and C alleles. However, the strength of GC-biased gene conversion (gBGC) in human populations and its effects on hereditary disease have yet to be assessed on a genomic scale. Using high-coverage whole-genome sequences of African hunter-gatherers, agricultural populations, and primate outgroups, we quantified the effects of GC-biased gene conversion on population genomic data sets. We find that genetic distances (FST and population branch statistics) are modified by gBGC. In addition, the site frequency spectrum is left-shifted when ancestral alleles are favored by gBGC and right-shifted when derived alleles are favored by gBGC. Allele frequency shifts due to gBGC mimic the effects of natural selection. As expected, these effects are strongest in high-recombination regions of the human genome. By comparing the relative rates of fixation of unbiased and biased sites, the strength of gene conversion was estimated to be on the order of Nb ≈ 0.05 to 0.09. We also find that derived alleles favored by gBGC are much more likely to be homozygous than derived alleles at unbiased SNPs (+42.2% to 62.8%). This results in a curse of the converted, whereby gBGC causes substantial increases in hereditary disease risks. Taken together, our findings reveal that GC-biased gene conversion has important population genetic and public health implications.
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MESH Headings
- Bias
- Evolution, Molecular
- Gene Conversion
- Gene Frequency
- Genes, Recessive/genetics
- Genetic Diseases, Inborn/genetics
- Genetics, Population
- Genome, Human/genetics
- Humans
- Models, Genetic
- Models, Theoretical
- Polymorphism, Single Nucleotide/genetics
- Recombination, Genetic
- Selection, Genetic/genetics
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Affiliation(s)
- Joseph Lachance
- Departments of Biology and Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Sarah A Tishkoff
- Departments of Biology and Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA.
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