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Palacios C, Wang P, Wang N, Brown MA, Capatosto L, Du J, Jiang J, Zhang Q, Dahal N, Lamichhaney S. Genomic Variation, Population History, and Long-Term Genetic Adaptation to High Altitudes in Tibetan Partridge (Perdix hodgsoniae). Mol Biol Evol 2023; 40:msad214. [PMID: 37768198 PMCID: PMC10583571 DOI: 10.1093/molbev/msad214] [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: 01/24/2023] [Revised: 09/09/2023] [Accepted: 09/25/2023] [Indexed: 09/29/2023] Open
Abstract
Species residing across elevational gradients display adaptations in response to environmental changes such as oxygen availability, ultraviolet radiation, and temperature. Here, we study genomic variation, gene expression, and long-term adaptation in Tibetan Partridge (Perdix hodgsoniae) populations residing across the elevational gradient of the Tibetan Plateau. We generated a high-quality draft genome and used it to carry out downstream population genomic and transcriptomic analysis. The P. hodgsoniae populations residing across various elevations were genetically distinct, and their phylogenetic clustering was consistent with their geographic distribution. We identified possible evidence of gene flow between populations residing in <3,000 and >4,200 m elevation that is consistent with known habitat expansion of high-altitude populations of P. hodgsoniae to a lower elevation. We identified a 60 kb haplotype encompassing the Estrogen Receptor 1 (ESR1) gene, showing strong genetic divergence between populations of P. hodgsoniae. We identified six single nucleotide polymorphisms within the ESR1 gene fixed for derived alleles in high-altitude populations that are strongly conserved across vertebrates. We also compared blood transcriptome profiles and identified differentially expressed genes (such as GAPDH, LDHA, and ALDOC) that correlated with differences in altitude among populations of P. hodgsoniae. These candidate genes from population genomics and transcriptomics analysis were enriched for neutrophil degranulation and glycolysis pathways, which are known to respond to hypoxia and hence may contribute to long-term adaptation to high altitudes in P. hodgsoniae. Our results highlight Tibetan Partridges as a useful model to study molecular mechanisms underlying long-term adaptation to high altitudes.
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Affiliation(s)
- Catalina Palacios
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
| | - Pengcheng Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, P. R. China
| | - Nan Wang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, P. R. China
| | - Megan A Brown
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
| | - Lukas Capatosto
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
| | - Juan Du
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Jiahu Jiang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, P. R. China
| | - Qingze Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, P. R. China
| | - Nishma Dahal
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, HP 176061, India
| | - Sangeet Lamichhaney
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
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2
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Cano AV, Gitschlag BL, Rozhoňová H, Stoltzfus A, McCandlish DM, Payne JL. Mutation bias and the predictability of evolution. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220055. [PMID: 37004719 PMCID: PMC10067271 DOI: 10.1098/rstb.2022.0055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023] Open
Abstract
Predicting evolutionary outcomes is an important research goal in a diversity of contexts. The focus of evolutionary forecasting is usually on adaptive processes, and efforts to improve prediction typically focus on selection. However, adaptive processes often rely on new mutations, which can be strongly influenced by predictable biases in mutation. Here, we provide an overview of existing theory and evidence for such mutation-biased adaptation and consider the implications of these results for the problem of prediction, in regard to topics such as the evolution of infectious diseases, resistance to biochemical agents, as well as cancer and other kinds of somatic evolution. We argue that empirical knowledge of mutational biases is likely to improve in the near future, and that this knowledge is readily applicable to the challenges of short-term prediction. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.
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Affiliation(s)
- Alejandro V Cano
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Bryan L Gitschlag
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Hana Rozhoňová
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Arlin Stoltzfus
- Office of Data and Informatics, Material Measurement Laboratory, National Institute of Standards and Technology, Rockville, MD 20899, USA
- Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - David M McCandlish
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Joshua L Payne
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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3
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Moreira LR, Smith BT. Convergent genomic signatures of local adaptation across a continental-scale environmental gradient. SCIENCE ADVANCES 2023; 9:eadd0560. [PMID: 37205757 PMCID: PMC10198635 DOI: 10.1126/sciadv.add0560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 04/17/2023] [Indexed: 05/21/2023]
Abstract
Convergent local adaptation offers a glimpse into the role of constraint and stochasticity in adaptive evolution, in particular the extent to which similar genetic mechanisms drive adaptation to common selective forces. Here, we investigated the genomics of local adaptation in two nonsister woodpeckers that are codistributed across an entire continent and exhibit remarkably convergent patterns of geographic variation. We sequenced the genomes of 140 individuals of Downy (Dryobates pubescens) and Hairy (Dryobates villosus) woodpeckers and used a suite of genomic approaches to identify loci under selection. We showed evidence that convergent genes have been targeted by selection in response to shared environmental pressures, such as temperature and precipitation. Among candidates, we found multiple genes putatively linked to key phenotypic adaptations to climate, including differences in body size (e.g., IGFPB) and plumage (e.g., MREG). These results are consistent with genetic constraints limiting the pathways of adaptation to broad climatic gradients, even after genetic backgrounds diverge.
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Affiliation(s)
- Lucas R. Moreira
- Department of Ecology, Evolution and Environmental Biology, Columbia University, NY, USA
- Department of Ornithology, American Museum of Natural History, New York City, NY, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, New York City, NY, USA
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4
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Wang G, Vasquez KM. Dynamic alternative DNA structures in biology and disease. Nat Rev Genet 2023; 24:211-234. [PMID: 36316397 DOI: 10.1038/s41576-022-00539-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
Abstract
Repetitive elements in the human genome, once considered 'junk DNA', are now known to adopt more than a dozen alternative (that is, non-B) DNA structures, such as self-annealed hairpins, left-handed Z-DNA, three-stranded triplexes (H-DNA) or four-stranded guanine quadruplex structures (G4 DNA). These dynamic conformations can act as functional genomic elements involved in DNA replication and transcription, chromatin organization and genome stability. In addition, recent studies have revealed a role for these alternative structures in triggering error-generating DNA repair processes, thereby actively enabling genome plasticity. As a driving force for genetic variation, non-B DNA structures thus contribute to both disease aetiology and evolution.
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Affiliation(s)
- Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Paediatric Research Institute, Austin, TX, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Paediatric Research Institute, Austin, TX, USA.
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5
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Vogt G. Environmental Adaptation of Genetically Uniform Organisms with the Help of Epigenetic Mechanisms-An Insightful Perspective on Ecoepigenetics. EPIGENOMES 2022; 7:1. [PMID: 36648862 PMCID: PMC9844400 DOI: 10.3390/epigenomes7010001] [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: 11/21/2022] [Revised: 12/11/2022] [Accepted: 12/15/2022] [Indexed: 12/28/2022] Open
Abstract
Organisms adapt to different environments by selection of the most suitable phenotypes from the standing genetic variation or by phenotypic plasticity, the ability of single genotypes to produce different phenotypes in different environments. Because of near genetic identity, asexually reproducing populations are particularly suitable for the investigation of the potential and molecular underpinning of the latter alternative in depth. Recent analyses on the whole-genome scale of differently adapted clonal animals and plants demonstrated that epigenetic mechanisms such as DNA methylation, histone modifications and non-coding RNAs are among the molecular pathways supporting phenotypic plasticity and that epigenetic variation is used to stably adapt to different environments. Case studies revealed habitat-specific epigenetic fingerprints that were maintained over subsequent years pointing at the existence of epigenetic ecotypes. Environmentally induced epimutations and corresponding gene expression changes provide an ideal means for fast and directional adaptation to changing or new conditions, because they can synchronously alter phenotypes in many population members. Because microorganisms inclusive of human pathogens also exploit epigenetically mediated phenotypic variation for environmental adaptation, this phenomenon is considered a universal biological principle. The production of different phenotypes from the same DNA sequence in response to environmental cues by epigenetic mechanisms also provides a mechanistic explanation for the "general-purpose genotype hypothesis" and the "genetic paradox of invasions".
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Affiliation(s)
- Günter Vogt
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany
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6
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Liang C, Liu D, Song P, Zhou Y, Yu H, Sun G, Ma X, Yan J. Transcriptomic Analyses Suggest the Adaptation of Bumblebees to High Altitudes. INSECTS 2022; 13:1173. [PMID: 36555083 PMCID: PMC9783775 DOI: 10.3390/insects13121173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/15/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
Determining the adaptive mechanisms by which bumblebees adapt to high altitudes can help us to better understand their distribution, providing a basis for the future protection and utilization of bumblebee resources. For this study, the adaptive mechanisms of two dominant bumblebee species in the northeastern Qinghai-Tibet Plateau-Bombus kashmirensis and B. waltoni-were studied through transcriptomics methods. For each species, enrichment analysis of the differentially expressed genes and gene set enrichment analysis were carried out between samples collected at different altitudes (4000 m, 4500 m, and 5000 m). The results indicate that these bumblebees tend to up-regulate energy metabolism-related genes when facing extremely high-altitude environments. Of the enriched pathways up-regulated in higher altitudes, the pentose and glucuronate interconversions pathway presented the most severe up-regulation in multiple comparisons of different altitudes for B. kashmirensis, as well as the AMPK signaling pathway, which was found to be up-regulated in both species. Notably, limited by the extreme hypoxic conditions in this study, oxidative phosphorylation was found to be down-regulated with increasing altitude, which is uncommon in studies on bumblebee adaptation to high altitudes.
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Affiliation(s)
- Chengbo Liang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Daoxin Liu
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- Kunlun College, Qinghai University, Xining 810016, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, China
| | - Pengfei Song
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, China
| | - Yuantao Zhou
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Hongyan Yu
- Qinghai Service Guarantee Center of Qilian Mountain National Park, Xining 810001, China
| | - Guo Sun
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Xiaoxuan Ma
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Jingyan Yan
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
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7
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The Mutagenic Consequences of DNA Methylation within and across Generations. EPIGENOMES 2022; 6:epigenomes6040033. [PMID: 36278679 PMCID: PMC9624357 DOI: 10.3390/epigenomes6040033] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/20/2022] [Accepted: 09/28/2022] [Indexed: 12/28/2022] Open
Abstract
DNA methylation is an epigenetic modification with wide-ranging consequences across the life of an organism. This modification can be stable, persisting through development despite changing environmental conditions. However, in other contexts, DNA methylation can also be flexible, underlying organismal phenotypic plasticity. One underappreciated aspect of DNA methylation is that it is a potent mutagen; methylated cytosines mutate at a much faster rate than other genetic motifs. This mutagenic property of DNA methylation has been largely ignored in eco-evolutionary literature, despite its prevalence. Here, we explore how DNA methylation induced by environmental and other factors could promote mutation and lead to evolutionary change at a more rapid rate and in a more directed manner than through stochastic genetic mutations alone. We argue for future research on the evolutionary implications of DNA methylation driven mutations both within the lifetime of organisms, as well as across timescales.
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8
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A homotetrameric hemoglobin expressed in alveolar epithelial cells increases blood oxygenation in high-altitude plateau pika (Ochotona curzoniae). Cell Rep 2022; 41:111446. [DOI: 10.1016/j.celrep.2022.111446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 06/28/2022] [Accepted: 09/12/2022] [Indexed: 11/23/2022] Open
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9
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Majic P, Erten EY, Payne JL. The adaptive potential of nonheritable somatic mutations. Am Nat 2022; 200:755-772. [DOI: 10.1086/721766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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10
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Lele A, Garrod HM, Ferguson E, Azahara Prieto Gil C, Ellis M. Variation in avian morphology along a short tropical elevational gradient. Biotropica 2022. [DOI: 10.1111/btp.13110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Abhimanyu Lele
- Committee on Evolutionary Biology University of Chicago Chicago Illinois USA
- Negaunee Integrative Research Center The Field Museum Chicago Illinois USA
- Third Millennium Alliance Quito Pichincha Ecuador
| | | | | | | | - Mike Ellis
- Third Millennium Alliance Quito Pichincha Ecuador
- Department of Ecology & Evolutionary Biology Tulane University Louisiana USA
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11
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Li J, An Z, Wei L, Xu B, Wang Z, Gao C, Wei L, Qi D, Shi P, Zhang T, Wei D. A New Homotetramer Hemoglobin in the Pulmonary Surfactant of Plateau Zokors (Myospalax Baileyi). Front Genet 2022; 13:824049. [PMID: 35368669 PMCID: PMC8967358 DOI: 10.3389/fgene.2022.824049] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/27/2022] [Indexed: 11/13/2022] Open
Abstract
The plateau zokor (Myospalax baileyi) is a native species to the Qinghai-Tibetan Plateau, inhabiting hypoxia and hypercapnia sealed subterranean burrows that pose several unique physiological challenges. In this study, we observed a novel heme-containing protein in the pulmonary surfactant (PS) of plateau zokor, identified the encoding gene of the protein, predicted its origination and structure, verified its expression in alveolar epithelial cells, and determined the protein’s affinity to oxygen and its effect on the oxygen-dissolving capability in the PS of plateau zokors. The protein is an unusual homotetramer hemoglobin consisting of four γ-like subunits, and the subunit is encoded by a paralog gene of γ, that is γ-like. The divergence time of γ-like from γ is estimated by the molecular clock to be about 2.45 Mya. The generation of γ-like in plateau zokors might well relate to long-time stress of the high land hypoxia. Unlike γ, the γ-like has a hypoxia response element (HRE) and a lung tissue-specific enhancer in its upstream region, and it is expressed specifically in lung tissues and up-regulated by hypoxia. The protein is named as γ4-like which is expressed specifically in Alveolar epithelial type II (ATII) cells and secreted into the alveolar cavities through the osmiophilic multilamellar body (LBs). The γ4-like has a higher affinity to oxygen, and that increases significantly oxygen-dissolving capability in the PS of plateau zokors by its oxygenation function, which might be beneficial for the plateau zokors to obtain oxygen from the severe hypoxia environments by facilitating oxygen diffusion from alveoli to blood.
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Affiliation(s)
- Jimei Li
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
- Research Center for High Altitude Medicine, Qinghai University, Xining, China
| | - Zhifang An
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Linna Wei
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Bo Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Zhijie Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Conghui Gao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Lian Wei
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Delin Qi
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Peng Shi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- *Correspondence: Dengbang Wei, ; Tongzuo Zhang, ; Peng Shi,
| | - Tongzuo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- *Correspondence: Dengbang Wei, ; Tongzuo Zhang, ; Peng Shi,
| | - Dengbang Wei
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
- Research Center for High Altitude Medicine, Qinghai University, Xining, China
- *Correspondence: Dengbang Wei, ; Tongzuo Zhang, ; Peng Shi,
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12
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Ivy CM, Wearing OH, Natarajan C, Schweizer RM, Gutiérrez-Pinto N, Velotta JP, Campbell-Staton SC, Petersen EE, Fago A, Cheviron ZA, Storz JF, Scott GR. Genetic variation in haemoglobin is associated with evolved changes in breathing in high-altitude deer mice. J Exp Biol 2022; 225:273749. [PMID: 34913467 PMCID: PMC8917448 DOI: 10.1242/jeb.243595] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/09/2021] [Indexed: 01/21/2023]
Abstract
Physiological systems often have emergent properties but the effects of genetic variation on physiology are often unknown, which presents a major challenge to understanding the mechanisms of phenotypic evolution. We investigated whether genetic variants in haemoglobin (Hb) that contribute to high-altitude adaptation in deer mice (Peromyscus maniculatus) are associated with evolved changes in the control of breathing. We created F2 inter-population hybrids of highland and lowland deer mice to test for phenotypic associations of α- and β-globin variants on a mixed genetic background. Hb genotype had expected effects on Hb-O2 affinity that were associated with differences in arterial O2 saturation in hypoxia. However, high-altitude genotypes were also associated with breathing phenotypes that should contribute to enhancing O2 uptake in hypoxia. Mice with highland α-globin exhibited a more effective breathing pattern, with highland homozygotes breathing deeper but less frequently across a range of inspired O2, and this difference was comparable to the evolved changes in breathing pattern in deer mouse populations native to high altitude. The ventilatory response to hypoxia was augmented in mice that were homozygous for highland β-globin. The association of globin variants with variation in breathing phenotypes could not be recapitulated by acute manipulation of Hb-O2 affinity, because treatment with efaproxiral (a synthetic drug that acutely reduces Hb-O2 affinity) had no effect on breathing in normoxia or hypoxia. Therefore, adaptive variation in Hb may have unexpected effects on physiology in addition to the canonical function of this protein in circulatory O2 transport.
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Affiliation(s)
- Catherine M. Ivy
- Department of Biology, McMaster University, Hamilton, ON, Canada, L8S 4K1,Author for correspondence ()
| | - Oliver H. Wearing
- Department of Biology, McMaster University, Hamilton, ON, Canada, L8S 4K1
| | | | - Rena M. Schweizer
- Divison of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | | | - Jonathan P. Velotta
- Divison of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Shane C. Campbell-Staton
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Elin E. Petersen
- Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Angela Fago
- Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Zachary A. Cheviron
- Divison of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Jay F. Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
| | - Graham R. Scott
- Department of Biology, McMaster University, Hamilton, ON, Canada, L8S 4K1
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13
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Protein innovation through template switching in the Saccharomyces cerevisiae lineage. Sci Rep 2021; 11:22558. [PMID: 34799587 PMCID: PMC8604942 DOI: 10.1038/s41598-021-01736-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 10/27/2021] [Indexed: 11/08/2022] Open
Abstract
DNA polymerase template switching between short, non-identical inverted repeats (IRs) is a genetic mechanism that leads to the homogenization of IR arms and to IR spacer inversion, which cause multinucleotide mutations (MNMs). It is unknown if and how template switching affects gene evolution. In this study, we performed a phylogenetic analysis to determine the effect of template switching between IR arms on coding DNA of Saccharomyces cerevisiae. To achieve this, perfect IRs that co-occurred with MNMs between a strain and its parental node were identified in S. cerevisiae strains. We determined that template switching introduced MNMs into 39 protein-coding genes through S. cerevisiae evolution, resulting in both arm homogenization and inversion of the IR spacer. These events in turn resulted in nonsynonymous substitutions and up to five neighboring amino acid replacements in a single gene. The study demonstrates that template switching is a powerful generator of multiple substitutions within codons. Additionally, some template switching events occurred more than once during S. cerevisiae evolution. Our findings suggest that template switching constitutes a general mutagenic mechanism that results in both nonsynonymous substitutions and parallel evolution, which are traditionally considered as evidence for positive selection, without the need for adaptive explanations.
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14
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Horton JS, Flanagan LM, Jackson RW, Priest NK, Taylor TB. A mutational hotspot that determines highly repeatable evolution can be built and broken by silent genetic changes. Nat Commun 2021; 12:6092. [PMID: 34667151 PMCID: PMC8526746 DOI: 10.1038/s41467-021-26286-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 09/28/2021] [Indexed: 11/08/2022] Open
Abstract
Mutational hotspots can determine evolutionary outcomes and make evolution repeatable. Hotspots are products of multiple evolutionary forces including mutation rate heterogeneity, but this variable is often hard to identify. In this work, we reveal that a near-deterministic genetic hotspot can be built and broken by a handful of silent mutations. We observe this when studying homologous immotile variants of the bacteria Pseudomonas fluorescens, AR2 and Pf0-2x. AR2 resurrects motility through highly repeatable de novo mutation of the same nucleotide in >95% lines in minimal media (ntrB A289C). Pf0-2x, however, evolves via a number of mutations meaning the two strains diverge significantly during adaptation. We determine that this evolutionary disparity is owed to just 6 synonymous variations within the ntrB locus, which we demonstrate by swapping the sites and observing that we are able to both break (>95% to 0%) and build (0% to 80%) a deterministic mutational hotspot. Our work reveals a key role for silent genetic variation in determining adaptive outcomes.
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Affiliation(s)
- James S Horton
- Milner Centre for Evolution, Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
| | - Louise M Flanagan
- Milner Centre for Evolution, Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Robert W Jackson
- School of Biosciences and Birmingham Institute of Forest Research (BIFoR), University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Nicholas K Priest
- Milner Centre for Evolution, Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Tiffany B Taylor
- Milner Centre for Evolution, Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
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15
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Graham AM, Peters JL, Wilson RE, Muñoz-Fuentes V, Green AJ, Dorfsman DA, Valqui TH, Winker K, McCracken KG. Adaptive introgression of the beta-globin cluster in two Andean waterfowl. Heredity (Edinb) 2021; 127:107-123. [PMID: 33903741 PMCID: PMC8249413 DOI: 10.1038/s41437-021-00437-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 04/04/2021] [Accepted: 04/08/2021] [Indexed: 11/09/2022] Open
Abstract
Introgression of beneficial alleles has emerged as an important avenue for genetic adaptation in both plant and animal populations. In vertebrates, adaptation to hypoxic high-altitude environments involves the coordination of multiple molecular and cellular mechanisms, including selection on the hypoxia-inducible factor (HIF) pathway and the blood-O2 transport protein hemoglobin (Hb). In two Andean duck species, a striking DNA sequence similarity reflecting identity by descent is present across the ~20 kb β-globin cluster including both embryonic (HBE) and adult (HBB) paralogs, though it was yet untested whether this is due to independent parallel evolution or adaptive introgression. In this study, we find that identical amino acid substitutions in the β-globin cluster that increase Hb-O2 affinity have likely resulted from historical interbreeding between high-altitude populations of two different distantly-related species. We examined the direction of introgression and discovered that the species with a deeper mtDNA divergence that colonized high altitude earlier in history (Anas flavirostris) transferred adaptive genetic variation to the species with a shallower divergence (A. georgica) that likely colonized high altitude more recently possibly following a range shift into a novel environment. As a consequence, the species that received these β-globin variants through hybridization might have adapted to hypoxic conditions in the high-altitude environment more quickly through acquiring beneficial alleles from the standing, hybrid-origin variation, leading to faster evolution.
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Affiliation(s)
- Allie M Graham
- Eccles Institute for Human Genetics, University of Utah, Salt Lake City, UT, USA.
| | - Jeffrey L Peters
- Department of Biological Sciences, Wright State University, Dayton, OH, USA
| | - Robert E Wilson
- School of Natural Resources, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Violeta Muñoz-Fuentes
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK
| | - Andy J Green
- Department of Wetland Ecology, Estación Biológica de Doñana, EBD-CSIC, Sevilla, Spain
| | - Daniel A Dorfsman
- Human Genetics and Genomics, Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Thomas H Valqui
- Centro de Ornitología y Biodiversidad (CORBIDI), Surco, Lima, Perú
- Universidad Nacional Agraria, La Molina, Perú
| | - Kevin Winker
- University of Alaska Museum and Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Kevin G McCracken
- Human Genetics and Genomics, Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.
- Centro de Ornitología y Biodiversidad (CORBIDI), Surco, Lima, Perú.
- University of Alaska Museum and Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, USA.
- Department of Biology, University of Miami, Coral Gables, FL, USA.
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Miami, FL, USA.
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16
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Storz JF, Signore AV. Introgressive Hybridization and Hypoxia Adaptation in High-Altitude Vertebrates. Front Genet 2021; 12:696484. [PMID: 34239546 PMCID: PMC8258166 DOI: 10.3389/fgene.2021.696484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
In natural populations of animals, a growing body of evidence suggests that introgressive hybridization may often serve as an important source of adaptive genetic variation. Population genomic studies of high-altitude vertebrates have provided strong evidence of positive selection on introgressed allelic variants, typically involving a long-term highland species as the donor and a more recently arrived colonizing species as the recipient. In high-altitude humans and canids from the Tibetan Plateau, case studies of adaptive introgression involving the HIF transcription factor, EPAS1, have provided insights into complex histories of ancient introgression, including examples of admixture from now-extinct source populations. In Tibetan canids and Andean waterfowl, directed mutagenesis experiments involving introgressed hemoglobin variants successfully identified causative amino acid mutations and characterized their phenotypic effects, thereby providing insights into the functional properties of selectively introgressed alleles. We review case studies of adaptive introgression in high-altitude vertebrates and we highlight findings that may be of general significance for understanding mechanisms of environmental adaptation involving different sources of genetic variation.
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Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE, United States
| | - Anthony V Signore
- School of Biological Sciences, University of Nebraska, Lincoln, NE, United States
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17
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Evolved increases in hemoglobin-oxygen affinity and the Bohr effect coincided with the aquatic specialization of penguins. Proc Natl Acad Sci U S A 2021; 118:2023936118. [PMID: 33753505 PMCID: PMC8020755 DOI: 10.1073/pnas.2023936118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In diving birds like penguins, physiologic considerations suggest that increased hemoglobin (Hb)-O2 affinity may improve pulmonary O2 extraction and enhance dive capacity. We integrated experimental tests on whole-blood and native Hbs of penguins with protein engineering experiments on reconstructed ancestral Hbs. The experiments involving ancestral protein resurrection enabled us to test for evolved changes in Hb function in the stem lineage of penguins after divergence from their closest nondiving relatives. We demonstrate that penguins evolved an increased Hb-O2 affinity in conjunction with a greatly augmented Bohr effect (i.e., reduction in Hb-O2 affinity at low pH) that should maximize pulmonary O2 extraction without compromising O2 delivery at systemic capillaries. Dive capacities of air-breathing vertebrates are dictated by onboard O2 stores, suggesting that physiologic specialization of diving birds such as penguins may have involved adaptive changes in convective O2 transport. It has been hypothesized that increased hemoglobin (Hb)-O2 affinity improves pulmonary O2 extraction and enhances the capacity for breath-hold diving. To investigate evolved changes in Hb function associated with the aquatic specialization of penguins, we integrated comparative measurements of whole-blood and purified native Hb with protein engineering experiments based on site-directed mutagenesis. We reconstructed and resurrected ancestral Hb representing the common ancestor of penguins and the more ancient ancestor shared by penguins and their closest nondiving relatives (order Procellariiformes, which includes albatrosses, shearwaters, petrels, and storm petrels). These two ancestors bracket the phylogenetic interval in which penguin-specific changes in Hb function would have evolved. The experiments revealed that penguins evolved a derived increase in Hb-O2 affinity and a greatly augmented Bohr effect (i.e., reduced Hb-O2 affinity at low pH). Although an increased Hb-O2 affinity reduces the gradient for O2 diffusion from systemic capillaries to metabolizing cells, this can be compensated by a concomitant enhancement of the Bohr effect, thereby promoting O2 unloading in acidified tissues. We suggest that the evolved increase in Hb-O2 affinity in combination with the augmented Bohr effect maximizes both O2 extraction from the lungs and O2 unloading from the blood, allowing penguins to fully utilize their onboard O2 stores and maximize underwater foraging time.
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18
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Storz JF. High-Altitude Adaptation: Mechanistic Insights from Integrated Genomics and Physiology. Mol Biol Evol 2021; 38:2677-2691. [PMID: 33751123 PMCID: PMC8233491 DOI: 10.1093/molbev/msab064] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Population genomic analyses of high-altitude humans and other vertebrates have identified numerous candidate genes for hypoxia adaptation, and the physiological pathways implicated by such analyses suggest testable hypotheses about underlying mechanisms. Studies of highland natives that integrate genomic data with experimental measures of physiological performance capacities and subordinate traits are revealing associations between genotypes (e.g., hypoxia-inducible factor gene variants) and hypoxia-responsive phenotypes. The subsequent search for causal mechanisms is complicated by the fact that observed genotypic associations with hypoxia-induced phenotypes may reflect second-order consequences of selection-mediated changes in other (unmeasured) traits that are coupled with the focal trait via feedback regulation. Manipulative experiments to decipher circuits of feedback control and patterns of phenotypic integration can help identify causal relationships that underlie observed genotype–phenotype associations. Such experiments are critical for correct inferences about phenotypic targets of selection and mechanisms of adaptation.
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Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
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19
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Lim MCW, Bi K, Witt CC, Graham CH, Dávalos LM. Pervasive Genomic Signatures of Local Adaptation to Altitude Across Highland Specialist Andean Hummingbird Populations. J Hered 2021; 112:229-240. [PMID: 33631009 DOI: 10.1093/jhered/esab008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 02/23/2021] [Indexed: 01/28/2023] Open
Abstract
Populations along steep environmental gradients are subject to differentiating selection that can result in local adaptation, despite countervailing gene flow, and genetic drift. In montane systems, where species are often restricted to narrow ranges of elevation, it is unclear whether the selection is strong enough to influence functional differentiation of subpopulations differing by a few hundred meters in elevation. We used targeted capture of 12 501 exons from across the genome, including 271 genes previously implicated in altitude adaptation, to test for adaptation to local elevations for 2 highland hummingbird species, Coeligena violifer (n = 62) and Colibri coruscans (n = 101). For each species, we described population genetic structure across the complex geography of the Peruvian Andes and, while accounting for this structure, we tested whether elevational allele frequency clines in single nucleotide polymorphisms (SNPs) showed evidence for local adaptation to elevation. Although the 2 species exhibited contrasting population genetic structures, we found signatures of clinal genetic variation with shifts in elevation in both. The genes with SNP-elevation associations included candidate genes previously discovered for high-elevation adaptation as well as others not previously identified, with cellular functions related to hypoxia response, energy metabolism, and immune function, among others. Despite the homogenizing effects of gene flow and genetic drift, natural selection on parts of the genome evidently optimizes elevation-specific cellular function even within elevation range-restricted montane populations. Consequently, our results suggest local adaptation occurring in narrow elevation bands in tropical mountains, such as the Andes, may effectively make them "taller" biogeographic barriers.
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Affiliation(s)
- Marisa C W Lim
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY
| | - Ke Bi
- Museum of Vertebrate Zoology, University of California, Berkeley, CA.,California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA (Bi)
| | - Christopher C Witt
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM
| | - Catherine H Graham
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY.,Swiss Federal Research Institute (WSL), Birmensdorf, Switzerland
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY.,Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY
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20
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Effect of NH2-terminal acetylation on the oxygenation properties of vertebrate haemoglobin. Biochem J 2021; 477:3839-3850. [PMID: 32936244 DOI: 10.1042/bcj20200623] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 09/08/2020] [Accepted: 09/15/2020] [Indexed: 01/07/2023]
Abstract
In vertebrate haemoglobin (Hb), the NH2-terminal residues of the α- and β-chain subunits are thought to play an important role in the allosteric binding of protons (Bohr effect), CO2 (as carbamino derivatives), chloride ions, and organic phosphates. Accordingly, acetylation of the α- and/or β-chain NH2-termini may have significant effects on the oxygenation properties of Hb. Here we investigate the effect of NH2-terminal acetylation by using a newly developed expression plasmid system that enables us to compare recombinantly expressed Hbs that are structurally identical except for the presence or absence of NH2-terminal acetyl groups. Experiments with native and recombinant Hbs of representative vertebrates reveal that NH2-terminal acetylation does not impair the Bohr effect, nor does it significantly diminish responsiveness to allosteric cofactors, such as chloride ions or organic phosphates. These results suggest that observed variation in the oxygenation properties of vertebrate Hbs is principally explained by amino acid divergence in the constituent globin chains rather than post-translational modifications of the globin chain NH2-termini.
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21
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Abstract
Population genomic studies of humans and other animals at high altitude have generated many hypotheses about the genes and pathways that may have contributed to hypoxia adaptation. Future advances require experimental tests of such hypotheses to identify causal mechanisms. Studies to date illustrate the challenge of moving from lists of candidate genes to the identification of phenotypic targets of selection, as it can be difficult to determine whether observed genotype-phenotype associations reflect causal effects or secondary consequences of changes in other traits that are linked via homeostatic regulation. Recent work on high-altitude models such as deer mice has revealed both plastic and evolved changes in respiratory, cardiovascular, and metabolic traits that contribute to aerobic performance capacity in hypoxia, and analyses of tissue-specific transcriptomes have identified changes in regulatory networks that mediate adaptive changes in physiological phenotype. Here we synthesize recent results and discuss lessons learned from studies of high-altitude adaptation that lie at the intersection of genomics and physiology.
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Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588, USA;
| | - Zachary A Cheviron
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA;
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22
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Ivy CM, Scott GR. Life-long exposure to hypoxia affects metabolism and respiratory physiology across life stages in high-altitude deer mice ( Peromyscus maniculatus). ACTA ACUST UNITED AC 2021; 224:jeb.237024. [PMID: 33268530 DOI: 10.1242/jeb.237024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/24/2020] [Indexed: 12/12/2022]
Abstract
Hypoxia exposure can have distinct physiological effects between early developmental and adult life stages, but it is unclear how the effects of hypoxia may progress during continuous exposure throughout life. We examined this issue in deer mice (Peromyscus maniculatus) from a population native to high altitude. Mice were bred in captivity in one of three treatment groups: normoxia (controls), life-long hypoxia (∼12 kPa O2 from conception to adulthood) and parental hypoxia (normoxia from conception to adulthood, but parents previously exposed to hypoxia). Metabolic, thermoregulatory and ventilatory responses to progressive stepwise hypoxia and haematology were then measured at post-natal day (P) 14 and 30 and/or in adulthood. Life-long hypoxia had consistent effects across ages on metabolism, attenuating the declines in O2 consumption rate (V̇ O2 ) and body temperature during progressive hypoxia compared with control mice. However, life-long hypoxia had age-specific effects on breathing, blunting the hypoxia-induced increases in air convection requirement (quotient of total ventilation and V̇ O2 ) at P14 and P30 only, but then shifting breathing pattern towards deeper and/or less frequent breaths at P30 and adulthood. Hypoxia exposure also increased blood-O2 affinity at P14 and P30, in association with an increase in arterial O2 saturation in hypoxia at P30. In contrast, parental hypoxia had no effects on metabolism or breathing, but it increased blood-O2 affinity and decreased red cell haemoglobin content at P14 (but not P30). Therefore, hypoxia exposure has some consistent effects across early life and adulthood, and some other effects that are unique to specific life stages.
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Affiliation(s)
- Catherine M Ivy
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Graham R Scott
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
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23
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Pejo M, Tomasco IH. Adaptive evolution of β-globin gene in subterranean in South America octodontid rodents. Gene 2020; 772:145352. [PMID: 33359035 DOI: 10.1016/j.gene.2020.145352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 11/15/2020] [Accepted: 12/01/2020] [Indexed: 11/17/2022]
Abstract
The convergent evolution of subterranean rodents is an excellent model to study how natural selection operates and the genetic bases of these adaptations, but the study on the different taxa has been very uneven and still insufficient. In the octodontoid caviomorph rodent superfamily there are two independent lineages where they have recently evolved into totally underground lifestyles: the genera Ctenomys (tuco-tucos) and Spalacopus (coruro). The underground habitat is characterized by an hypoxic and hypercapnic atmosphere, thus gas exchange is one of the most important challenges for these animals. The invasion of the underground niche could have modified the selective regimes of proteins involved in the respiration and transport of O2 of these rodents, positively selecting mutations of higher affinity for O2. Here we examine the sequence variation in the beta globin gene in these two lineages, within a robust phylogenetic context. Using different approaches (classical and Bayesian maximum likelihood (PAML/Datamonkey) and alternatives methods (TreeSAAP)) we found at least three sites with evidence of positive selection in underground lineages, especially the basal branch that leads to the Octodontidae family and the branch that leads to the coruro, suggesting some adaptive changes to the underground life. We also found a convergence with another underground rodent, which cannot be identified by the above methods.
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Affiliation(s)
- Mariana Pejo
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Ivanna H Tomasco
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.
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24
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Xiong Y, Fan L, Hao Y, Cheng Y, Chang Y, Wang J, Lin H, Song G, Qu Y, Lei F. Physiological and genetic convergence supports hypoxia resistance in high-altitude songbirds. PLoS Genet 2020; 16:e1009270. [PMID: 33370292 PMCID: PMC7793309 DOI: 10.1371/journal.pgen.1009270] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 01/08/2021] [Accepted: 11/02/2020] [Indexed: 02/06/2023] Open
Abstract
Skeletal muscle plays a central role in regulating glucose uptake and body metabolism; however, highland hypoxia is a severe challenge to aerobic metabolism in small endotherms. Therefore, understanding the physiological and genetic convergence of muscle hypoxia tolerance has a potential broad range of medical implications. Here we report and experimentally validate a common physiological mechanism across multiple high-altitude songbirds that improvement in insulin sensitivity contributes to glucose homeostasis, low oxygen consumption, and relative activity, and thus increases body weight. By contrast, low-altitude songbirds exhibit muscle loss, glucose intolerance, and increase energy expenditures under hypoxia. This adaptive mechanism is attributable to convergent missense mutations in the BNIP3L gene, and METTL8 gene that activates MEF2C expression in highlanders, which in turn increases hypoxia tolerance. Together, our findings from wild high-altitude songbirds suggest convergent physiological and genetic mechanisms of skeletal muscle in hypoxia resistance, which highlights the potentially medical implications of hypoxia-related metabolic diseases.
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Affiliation(s)
- Ying Xiong
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Liqing Fan
- National Forest Ecosystem Observation & Research Station of Nyingchi Tibet, Institute of Plateau Ecology, Tibet Agriculture & Animal Husbandry University, Linzhi City, China
- Key Laboratory of Forest Ecology in Tibet Plateau (Tibet Agriculture & Animal Husbandry University), Ministry of Education, Linzhi City, China
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yongbin Chang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haiyan Lin
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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25
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Dawson NJ, Alza L, Nandal G, Scott GR, McCracken KG. Convergent changes in muscle metabolism depend on duration of high-altitude ancestry across Andean waterfowl. eLife 2020; 9:e56259. [PMID: 32729830 PMCID: PMC7494360 DOI: 10.7554/elife.56259] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 07/23/2020] [Indexed: 01/07/2023] Open
Abstract
High-altitude environments require that animals meet the metabolic O2 demands for locomotion and thermogenesis in O2-thin air, but the degree to which convergent metabolic changes have arisen across independent high-altitude lineages or the speed at which such changes arise is unclear. We examined seven high-altitude waterfowl that have inhabited the Andes (3812-4806 m elevation) over varying evolutionary time scales, to elucidate changes in biochemical pathways of energy metabolism in flight muscle relative to low-altitude sister taxa. Convergent changes across high-altitude taxa included increased hydroxyacyl-coA dehydrogenase and succinate dehydrogenase activities, decreased lactate dehydrogenase, pyruvate kinase, creatine kinase, and cytochrome c oxidase activities, and increased myoglobin content. ATP synthase activity increased in only the longest established high-altitude taxa, whereas hexokinase activity increased in only newly established taxa. Therefore, changes in pathways of lipid oxidation, glycolysis, and mitochondrial oxidative phosphorylation are common strategies to cope with high-altitude hypoxia, but some changes require longer evolutionary time to arise.
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Affiliation(s)
- Neal J Dawson
- Department of Biology, McMaster UniversityHamiltonCanada
- Department of Biology University of MiamiCoral GablesUnited States
| | - Luis Alza
- Department of Biology University of MiamiCoral GablesUnited States
- University of Alaska Museum and Institute of Arctic Biology, University of Alaska FairbanksFairbanksUnited States
- Centro de Ornitología y Biodiversidad - CORBIDILimaPeru
| | | | - Graham R Scott
- Department of Biology, McMaster UniversityHamiltonCanada
| | - Kevin G McCracken
- Department of Biology University of MiamiCoral GablesUnited States
- University of Alaska Museum and Institute of Arctic Biology, University of Alaska FairbanksFairbanksUnited States
- Centro de Ornitología y Biodiversidad - CORBIDILimaPeru
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of MiamiMiamiUnited States
- Human Genetics and Genomics, Hussman Institute for Human Genomics, University of Miami Miller School of MedicineMiamiUnited States
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26
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Natarajan C, Signore AV, Kumar V, Storz JF. Synthesis of Recombinant Human Hemoglobin With NH 2 -Terminal Acetylation in Escherichia coli. ACTA ACUST UNITED AC 2020; 101:e112. [PMID: 32687676 DOI: 10.1002/cpps.112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The development of new technologies for the efficient expression of recombinant hemoglobin (rHb) is of interest for experimental studies of protein biochemistry and the development of cell-free blood substitutes in transfusion medicine. Expression of rHb in Escherichia coli host cells has numerous advantages, but one disadvantage of using prokaryotic systems to express eukaryotic proteins is that they are incapable of performing post-translational modifications such as NH2 -terminal acetylation. One possible solution is to coexpress additional enzymes that can perform the necessary modifications in the host cells. Here, we report a new method for synthesizing human rHb with proper NH2 -terminal acetylation. Mass spectrometry experiments involving native and recombinant human Hb confirmed the efficacy of the new technique in producing correctly acetylated globin chains. Finally, functional experiments provided insights into the effects of NH2 -terminal acetylation on O2 binding properties. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Gene synthesis and cloning the cassette to the expression plasmid Basic Protocol 2: Selection of E. coli expression strains for coexpression Basic Protocol 3: Large-scale recombinant hemoglobin expression and purification Support Protocol 1: Measuring O2 equilibration curves Support Protocol 2: Mass spectrometry to confirm NH2 -terminal acetylation.
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Affiliation(s)
| | - Anthony V Signore
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska
| | - Vikas Kumar
- Mass Spectrometry and Proteomics Core Facility, University of Nebraska Medical Center, Omaha, Nebraska
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska
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27
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Signore AV, Storz JF. Biochemical pedomorphosis and genetic assimilation in the hypoxia adaptation of Tibetan antelope. SCIENCE ADVANCES 2020; 6:eabb5447. [PMID: 32596473 PMCID: PMC7299627 DOI: 10.1126/sciadv.abb5447] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/11/2020] [Indexed: 05/17/2023]
Abstract
Developmental shifts in stage-specific gene expression can provide a ready mechanism of phenotypic change by altering the rate or timing of ontogenetic events. We found that the high-altitude Tibetan antelope (Panthelops hodgsonii) has evolved an adaptive increase in blood-O2 affinity by truncating the ancestral ontogeny of globin gene expression such that a high-affinity juvenile hemoglobin isoform (isoHb) completely supplants the lower-affinity isoHb that is expressed in the adult red blood cells of other bovids. This juvenilization of blood properties represents a canalization of an acclimatization response to hypoxia that has been well documented in adult goats and sheep. We also found the genomic mechanism underlying this regulatory isoHb switch, revealing how a reversible acclimatization response became genetically assimilated as an irreversible adaptation to chronic hypoxia.
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Affiliation(s)
- Anthony V. Signore
- University of Nebraska, School of Biological Sciences, Lincoln, NE 68588, USA
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28
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The Role of Mutation Bias in Adaptive Evolution. Trends Ecol Evol 2019; 34:422-434. [PMID: 31003616 DOI: 10.1016/j.tree.2019.01.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 01/27/2019] [Accepted: 01/30/2019] [Indexed: 11/24/2022]
Abstract
Mutational input is the ultimate source of genetic variation, but mutations are not thought to affect the direction of adaptive evolution. Recently, critics of standard evolutionary theory have questioned the random and non-directional nature of mutations, claiming that the mutational process can be adaptive in its own right. We discuss here mutation bias in adaptive evolution. We find little support for mutation bias as an independent force in adaptive evolution, although it can interact with selection under conditions of small population size and when standing genetic variation is limited, entirely consistent with standard evolutionary theory. We further emphasize that natural selection can shape the phenotypic effects of mutations, giving the false impression that directed mutations are driving adaptive evolution.
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29
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Storz JF, Scott GR. Life Ascending: Mechanism and Process in Physiological Adaptation to High-Altitude Hypoxia. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2019; 50:503-526. [PMID: 33033467 DOI: 10.1146/annurev-ecolsys-110218-025014] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
To cope with the reduced availability of O2 at high altitude, air-breathing vertebrates have evolved myriad adjustments in the cardiorespiratory system to match tissue O2 delivery with metabolic O2 demand. We explain how changes at interacting steps of the O2 transport pathway contribute to plastic and evolved changes in whole-animal aerobic performance under hypoxia. In vertebrates native to high altitude, enhancements of aerobic performance under hypoxia are attributable to a combination of environmentally induced and evolved changes in multiple steps of the pathway. Additionally, evidence suggests that many high-altitude natives have evolved mechanisms for attenuating maladaptive acclimatization responses to hypoxia, resulting in counter-gradient patterns of altitudinal variation for key physiological phenotypes. For traits that exhibit counteracting environmental and genetic effects, evolved changes in phenotype may be cryptic under field conditions and can only be revealed by rearing representatives of high-and low-altitude populations under standardized environmental conditions to control for plasticity.
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Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588, USA
| | - Graham R Scott
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
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30
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Storz JF, Natarajan C, Signore AV, Witt CC, McCandlish DM, Stoltzfus A. The role of mutation bias in adaptive molecular evolution: insights from convergent changes in protein function. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180238. [PMID: 31154983 DOI: 10.1098/rstb.2018.0238] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
An underexplored question in evolutionary genetics concerns the extent to which mutational bias in the production of genetic variation influences outcomes and pathways of adaptive molecular evolution. In the genomes of at least some vertebrate taxa, an important form of mutation bias involves changes at CpG dinucleotides: if the DNA nucleotide cytosine (C) is immediately 5' to guanine (G) on the same coding strand, then-depending on methylation status-point mutations at both sites occur at an elevated rate relative to mutations at non-CpG sites. Here, we examine experimental data from case studies in which it has been possible to identify the causative substitutions that are responsible for adaptive changes in the functional properties of vertebrate haemoglobin (Hb). Specifically, we examine the molecular basis of convergent increases in Hb-O2 affinity in high-altitude birds. Using a dataset of experimentally verified, affinity-enhancing mutations in the Hbs of highland avian taxa, we tested whether causative changes are enriched for mutations at CpG dinucleotides relative to the frequency of CpG mutations among all possible missense mutations. The tests revealed that a disproportionate number of causative amino acid replacements were attributable to CpG mutations, suggesting that mutation bias can influence outcomes of molecular adaptation. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.
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Affiliation(s)
- Jay F Storz
- 1 School of Biological Sciences, University of Nebraska , Lincoln, NE 68588 , USA
| | | | - Anthony V Signore
- 1 School of Biological Sciences, University of Nebraska , Lincoln, NE 68588 , USA
| | - Christopher C Witt
- 2 Department of Biology, University of New Mexico , Albuquerque, NM 87131 , USA.,3 Museum of Southwestern Biology, University of New Mexico , Albuquerque, NM 87131 , USA
| | | | - Arlin Stoltzfus
- 5 Office of Data and Informatics, Material Measurement Laboratory, NIST, and Institute for Bioscience and Biotechnology Research , Rockville, MD 20850 , USA
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31
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Storz JF, Cheviron ZA, McClelland GB, Scott GR. Evolution of physiological performance capacities and environmental adaptation: insights from high-elevation deer mice ( Peromyscus maniculatus). J Mammal 2019; 100:910-922. [PMID: 31138949 DOI: 10.1093/jmammal/gyy173] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 12/14/2018] [Indexed: 12/14/2022] Open
Abstract
Analysis of variation in whole-animal performance can shed light on causal connections between specific traits, integrated physiological capacities, and Darwinian fitness. Here, we review and synthesize information on naturally occurring variation in physiological performance capacities and how it relates to environmental adaptation in deer mice (Peromyscus maniculatus). We discuss how evolved changes in aerobic exercise capacity and thermogenic capacity have contributed to adaptation to high elevations. Comparative work on deer mice at high and low elevations has revealed evolved differences in aerobic performance capacities in hypoxia. Highland deer mice have consistently higher aerobic performance capacities under hypoxia relative to lowland natives, consistent with the idea that it is beneficial to have a higher maximal metabolic rate (as measured by the maximal rate of O2 consumption, VO2max) in an environment characterized by lower air temperatures and lower O2 availability. Observed differences in aerobic performance capacities between highland and lowland deer mice stem from changes in numerous subordinate traits that alter the flux capacity of the O2-transport system, the oxidative capacity of tissue mitochondria, and the relationship between O2 consumption and ATP synthesis. Many such changes in physiological phenotype are associated with hypoxia-induced changes in gene expression. Research on natural variation in whole-animal performance forms a nexus between physiological ecology and evolutionary biology that requires insight into the natural history of the study species.
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Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Zachary A Cheviron
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | | | - Graham R Scott
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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32
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Payne JL, Menardo F, Trauner A, Borrell S, Gygli SM, Loiseau C, Gagneux S, Hall AR. Transition bias influences the evolution of antibiotic resistance in Mycobacterium tuberculosis. PLoS Biol 2019; 17:e3000265. [PMID: 31083647 PMCID: PMC6532934 DOI: 10.1371/journal.pbio.3000265] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 05/23/2019] [Accepted: 04/26/2019] [Indexed: 11/21/2022] Open
Abstract
Transition bias, an overabundance of transitions relative to transversions, has been widely reported among studies of the rates and spectra of spontaneous mutations. However, demonstrating the role of transition bias in adaptive evolution remains challenging. In particular, it is unclear whether such biases direct the evolution of bacterial pathogens adapting to treatment. We addressed this challenge by analyzing adaptive antibiotic-resistance mutations in the major human pathogen Mycobacterium tuberculosis (MTB). We found strong evidence for transition bias in two independently curated data sets comprising 152 and 208 antibiotic-resistance mutations. This was true at the level of mutational paths (distinct adaptive DNA sequence changes) and events (individual instances of the adaptive DNA sequence changes) and across different genes and gene promoters conferring resistance to a diversity of antibiotics. It was also true for mutations that do not code for amino acid changes (in gene promoters and the 16S ribosomal RNA gene rrs) and for mutations that are synonymous to each other and are therefore likely to have similar fitness effects, suggesting that transition bias can be caused by a bias in mutation supply. These results point to a central role for transition bias in determining which mutations drive adaptive antibiotic resistance evolution in a key pathogen. Some types of mutations occur more frequently than expected. This study shows that such bias —an excess of transitions over transversions—influences the evolution of antibiotic resistance in a key global pathogen, Mycobacterium tuberculosis.
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Affiliation(s)
- Joshua L. Payne
- Institute of Integrative Biology, ETH Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- * E-mail:
| | - Fabrizio Menardo
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Andrej Trauner
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sebastian M. Gygli
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Chloe Loiseau
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Alex R. Hall
- Institute of Integrative Biology, ETH Zurich, Switzerland
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33
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Lind PA, Libby E, Herzog J, Rainey PB. Predicting mutational routes to new adaptive phenotypes. eLife 2019; 8:e38822. [PMID: 30616716 PMCID: PMC6324874 DOI: 10.7554/elife.38822] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 11/27/2018] [Indexed: 12/21/2022] Open
Abstract
Predicting evolutionary change poses numerous challenges. Here we take advantage of the model bacterium Pseudomonas fluorescens in which the genotype-to-phenotype map determining evolution of the adaptive 'wrinkly spreader' (WS) type is known. We present mathematical descriptions of three necessary regulatory pathways and use these to predict both the rate at which each mutational route is used and the expected mutational targets. To test predictions, mutation rates and targets were determined for each pathway. Unanticipated mutational hotspots caused experimental observations to depart from predictions but additional data led to refined models. A mismatch was observed between the spectra of WS-causing mutations obtained with and without selection due to low fitness of previously undetected WS-causing mutations. Our findings contribute toward the development of mechanistic models for forecasting evolution, highlight current limitations, and draw attention to challenges in predicting locus-specific mutational biases and fitness effects.
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Affiliation(s)
- Peter A Lind
- New Zealand Institute for Advanced StudyMassey University at AlbanyAucklandNew Zealand
- Department of Molecular BiologyUmeå UniversityUmeåSweden
| | - Eric Libby
- New Zealand Institute for Advanced StudyMassey University at AlbanyAucklandNew Zealand
- Santa Fe InstituteNew MexicoUnited States
- Department of MathematicsUmeå UniversityUmeåSweden
| | - Jenny Herzog
- New Zealand Institute for Advanced StudyMassey University at AlbanyAucklandNew Zealand
| | - Paul B Rainey
- New Zealand Institute for Advanced StudyMassey University at AlbanyAucklandNew Zealand
- Department of Microbial Population BiologyMax Planck Institute for Evolutionary BiologyPlönGermany
- Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris, ESPCI Paris-TechCNRS UMR 8231, PSL Research UniversityParisFrance
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34
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Xie KT, Wang G, Thompson AC, Wucherpfennig JI, Reimchen TE, MacColl ADC, Schluter D, Bell MA, Vasquez KM, Kingsley DM. DNA fragility in the parallel evolution of pelvic reduction in stickleback fish. Science 2019; 363:81-84. [PMID: 30606845 DOI: 10.1126/science.aan1425] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 04/18/2018] [Accepted: 11/28/2018] [Indexed: 01/22/2023]
Abstract
Evolution generates a remarkable breadth of living forms, but many traits evolve repeatedly, by mechanisms that are still poorly understood. A classic example of repeated evolution is the loss of pelvic hindfins in stickleback fish (Gasterosteus aculeatus). Repeated pelvic loss maps to recurrent deletions of a pelvic enhancer of the Pitx1 gene. Here, we identify molecular features contributing to these recurrent deletions. Pitx1 enhancer sequences form alternative DNA structures in vitro and increase double-strand breaks and deletions in vivo. Enhancer mutability depends on DNA replication direction and is caused by TG-dinucleotide repeats. Modeling shows that elevated mutation rates can influence evolution under demographic conditions relevant for sticklebacks and humans. DNA fragility may thus help explain why the same loci are often used repeatedly during parallel adaptive evolution.
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Affiliation(s)
- Kathleen T Xie
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Guliang Wang
- Division of Pharmacology and Toxicology, University of Texas at Austin, Austin, TX, USA
| | - Abbey C Thompson
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia I Wucherpfennig
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Dolph Schluter
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Michael A Bell
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA.
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, University of Texas at Austin, Austin, TX, USA
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA. .,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
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35
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Abstract
During infection, bacteria must steal metals, including iron, from the host tissue. Therefore, pathogenic bacteria have evolved metal acquisition systems to overcome the elaborate processes mammals use to withhold metal from pathogens. Staphylococcus aureus uses IsdB, a hemoglobin receptor, to thieve iron-containing heme from hemoglobin within human blood. We find evidence that primate hemoglobin has undergone rapid evolution at protein surfaces contacted by IsdB. Additionally, variation in the hemoglobin sequences among primates, or variation in IsdB of related staphylococci, reduces bacterial hemoglobin capture. Together, these data suggest that S. aureus has evolved to recognize human hemoglobin in the face of rapid evolution at the IsdB binding interface, consistent with repeated evolutionary conflicts in the battle for iron during host-pathogen interactions. Metals are a limiting resource for pathogenic bacteria and must be scavenged from host proteins. Hemoglobin provides the most abundant source of iron in the human body and is required by several pathogens to cause invasive disease. However, the consequences of hemoglobin evolution for bacterial nutrient acquisition remain unclear. Here we show that the α- and β-globin genes exhibit strikingly parallel signatures of adaptive evolution across simian primates. Rapidly evolving sites in hemoglobin correspond to binding interfaces of IsdB, a bacterial hemoglobin receptor harbored by pathogenic Staphylococcus aureus. Using an evolution-guided experimental approach, we demonstrate that the divergence between primates and staphylococcal isolates governs hemoglobin recognition and bacterial growth. The reintroduction of putative adaptive mutations in α- or β-globin proteins was sufficient to impair S. aureus binding, providing a mechanism for the evolution of disease resistance. These findings suggest that bacterial hemoprotein capture has driven repeated evolutionary conflicts with hemoglobin during primate descent.
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36
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Hoffmann FG, Vandewege MW, Storz JF, Opazo JC. Gene Turnover and Diversification of the α- and β-Globin Gene Families in Sauropsid Vertebrates. Genome Biol Evol 2018; 10:344-358. [PMID: 29340581 PMCID: PMC5786229 DOI: 10.1093/gbe/evy001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2018] [Indexed: 11/24/2022] Open
Abstract
The genes that encode the α- and β-chain subunits of vertebrate hemoglobin have served as a model system for elucidating general principles of gene family evolution, but little is known about patterns of evolution in amniotes other than mammals and birds. Here, we report a comparative genomic analysis of the α- and β-globin gene clusters in sauropsids (archosaurs and nonavian reptiles). The objectives were to characterize changes in the size and membership composition of the α- and β-globin gene families within and among the major sauropsid lineages, to reconstruct the evolutionary history of the sauropsid α- and β-globin genes, to resolve orthologous relationships, and to reconstruct evolutionary changes in the developmental regulation of gene expression. Our comparisons revealed contrasting patterns of evolution in the unlinked α- and β-globin gene clusters. In the α-globin gene cluster, which has remained in the ancestral chromosomal location, evolutionary changes in gene content are attributable to the differential retention of paralogous gene copies that were present in the common ancestor of tetrapods. In the β-globin gene cluster, which was translocated to a new chromosomal location, evolutionary changes in gene content are attributable to differential gene gains (via lineage-specific duplication events) and gene losses (via lineage-specific deletions and inactivations). Consequently, all major groups of amniotes possess unique repertoires of embryonic and postnatally expressed β-type globin genes that diversified independently in each lineage. These independently derived β-type globins descend from a pair of tandemly linked paralogs in the most recent common ancestor of sauropsids.
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Affiliation(s)
- Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University.,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University
| | | | - Jay F Storz
- School of Biological Sciences, University of Nebraska
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
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37
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Jendroszek A, Malte H, Overgaard CB, Beedholm K, Natarajan C, Weber RE, Storz JF, Fago A. Allosteric mechanisms underlying the adaptive increase in hemoglobin-oxygen affinity of the bar-headed goose. J Exp Biol 2018; 221:jeb185470. [PMID: 30026237 PMCID: PMC6176913 DOI: 10.1242/jeb.185470] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 07/16/2018] [Indexed: 01/07/2023]
Abstract
The high blood-O2 affinity of the bar-headed goose (Anser indicus) is an integral component of the biochemical and physiological adaptations that allow this hypoxia-tolerant species to undertake migratory flights over the Himalayas. The high blood-O2 affinity of this species was originally attributed to a single amino acid substitution of the major hemoglobin (Hb) isoform, HbA, which was thought to destabilize the low-affinity T state, thereby shifting the T-R allosteric equilibrium towards the high-affinity R state. Surprisingly, this mechanistic hypothesis has never been addressed using native proteins purified from blood. Here, we report a detailed analysis of O2 equilibria and kinetics of native major HbA and minor HbD isoforms from bar-headed goose and greylag goose (Anser anser), a strictly lowland species, to identify and characterize the mechanistic basis for the adaptive change in Hb function. We find that HbA and HbD of bar-headed goose have consistently higher O2 affinities than those of the greylag goose. The corresponding Hb isoforms of the two species are equally responsive to physiological allosteric cofactors and have similar Bohr effects. Thermodynamic analyses of O2 equilibrium curves according to the two-state Monod-Wyman-Changeaux model revealed higher R-state O2 affinities in the bar-headed goose Hbs, associated with lower O2 dissociation rates, compared with the greylag goose. Conversely, the T state was not destabilized and the T-R allosteric equilibrium was unaltered in bar-headed goose Hbs. The physiological implication of these results is that increased R-state affinity allows for enhanced O2 saturation in the lungs during hypoxia, but without impairing O2 delivery to tissues.
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Affiliation(s)
| | - Hans Malte
- Department of Bioscience, Aarhus University, DK-8000 Aarhus C, Denmark
| | | | - Kristian Beedholm
- Department of Bioscience, Aarhus University, DK-8000 Aarhus C, Denmark
| | | | - Roy E Weber
- Department of Bioscience, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
| | - Angela Fago
- Department of Bioscience, Aarhus University, DK-8000 Aarhus C, Denmark
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38
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Botero-Castro F, Tilak MK, Justy F, Catzeflis F, Delsuc F, Douzery EJP. In Cold Blood: Compositional Bias and Positive Selection Drive the High Evolutionary Rate of Vampire Bats Mitochondrial Genomes. Genome Biol Evol 2018; 10:2218-2239. [PMID: 29931241 PMCID: PMC6127110 DOI: 10.1093/gbe/evy120] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2018] [Indexed: 12/24/2022] Open
Abstract
Mitochondrial genomes of animals have long been considered to evolve under the action of purifying selection. Nevertheless, there is increasing evidence that they can also undergo episodes of positive selection in response to shifts in physiological or environmental demands. Vampire bats experienced such a shift, as they are the only mammals feeding exclusively on blood and possessing anatomical adaptations to deal with the associated physiological requirements (e.g., ingestion of high amounts of liquid water and iron). We sequenced eight new chiropteran mitogenomes including two species of vampire bats, five representatives of other lineages of phyllostomids and one close outgroup. Conducting detailed comparative mitogenomic analyses, we found evidence for accelerated evolutionary rates at the nucleotide and amino acid levels in vampires. Moreover, the mitogenomes of vampire bats are characterized by an increased cytosine (C) content mirrored by a decrease in thymine (T) compared with other chiropterans. Proteins encoded by the vampire bat mitogenomes also exhibit a significant increase in threonine (Thr) and slight reductions in frequency of the hydrophobic residues isoleucine (Ile), valine (Val), methionine (Met), and phenylalanine (Phe). We show that these peculiar substitution patterns can be explained by the co-occurrence of both neutral (mutational bias) and adaptive (positive selection) processes. We propose that vampire bat mitogenomes may have been impacted by selection on mitochondrial proteins to accommodate the metabolism and nutritional qualities of blood meals.
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Affiliation(s)
- Fidel Botero-Castro
- Institut des Sciences de l'Evolution (ISEM), Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France.,Division of Evolutionary Biology, Faculty of Biology II, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Marie-Ka Tilak
- Institut des Sciences de l'Evolution (ISEM), Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Fabienne Justy
- Institut des Sciences de l'Evolution (ISEM), Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - François Catzeflis
- Institut des Sciences de l'Evolution (ISEM), Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Frédéric Delsuc
- Institut des Sciences de l'Evolution (ISEM), Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Emmanuel J P Douzery
- Institut des Sciences de l'Evolution (ISEM), Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
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39
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ZHu X, Guan Y, Qu Y, David G, Song G, Lei F. Elevational divergence in the great tit complex revealed by major hemoglobin genes. Curr Zool 2018; 64:455-464. [PMID: 30108626 PMCID: PMC6084574 DOI: 10.1093/cz/zox042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/14/2017] [Indexed: 01/19/2023] Open
Abstract
Gene flow and demographic history can play important roles in the adaptive genetic differentiation of species, which is rarely understood in the high-altitude adaptive evolution of birds. To elucidate genetic divergence of populations in the great tit complex (Parus major, P. minor and P. cinereus) at different elevations, we compared the genetic structure and gene flow in hemoglobin genes with neutral loci. Our results revealed the elevationally divergent structure of αA-globin gene, distinctive from that of the βA-globin gene and neutral loci. We further investigated gene flow patterns among the populations in the central-northern (> 1,000 m a.s.l.), south-eastern (< 1,000 m a.s.l.) regions and the Southwest Mountains (> 2,000 m a.s.l.) in China. The high-altitude (> 1,000 m a.s.l.) diverged αA-globin genetic structure coincided with higher αA-globin gene flow between highland populations, in contrast to restricted neutral gene flow concordant with the phylogeny. The higher αA-globin gene flow suggests the possibility of adaptive evolution during population divergence, contrary to the lower αA-globin gene flow homogenized by neutral loci during population expansion. In concordance with patterns of historical gene flow, genotypic and allelic profiles provide distinctive patterns of fixation in different high-altitude populations. The fixation of alleles at contrasting elevations may primarily due to highland standing variants αA49Asn/72Asn/108Ala originating from the south-western population. Our findings demonstrate a pattern of genetic divergence with gene flow in major hemoglobin genes depending on population demographic history.
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Affiliation(s)
- Xiaojia ZHu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuyan Guan
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yanhua Qu
- University of Chinese Academy of Sciences, Beijing, China
| | - Gabriel David
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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40
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Sackman AM, McGee LW, Morrison AJ, Pierce J, Anisman J, Hamilton H, Sanderbeck S, Newman C, Rokyta DR. Mutation-Driven Parallel Evolution during Viral Adaptation. Mol Biol Evol 2018; 34:3243-3253. [PMID: 29029274 DOI: 10.1093/molbev/msx257] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Convergent evolution has been demonstrated across all levels of biological organization, from parallel nucleotide substitutions to convergent evolution of complex phenotypes, but whether instances of convergence are the result of selection repeatedly finding the same optimal solution to a recurring problem or are the product of mutational biases remains unsettled. We generated 20 replicate lineages allowed to fix a single mutation from each of four bacteriophage genotypes under identical selective regimes to test for parallel changes within and across genotypes at the levels of mutational effect distributions and gene, protein, amino acid, and nucleotide changes. All four genotypes shared a distribution of beneficial mutational effects best approximated by a distribution with a finite upper bound. Parallel adaptation was high at the protein, gene, amino acid, and nucleotide levels, both within and among phage genotypes, with the most common first-step mutation in each background fixing on an average in 7 of 20 replicates and half of the substitutions in two of the four genotypes occurring at shared sites. Remarkably, the mutation of largest beneficial effect that fixed for each genotype was never the most common, as would be expected if parallelism were driven by selection. In fact, the mutation of smallest benefit for each genotype fixed in a total of 7 of 80 lineages, equally as often as the mutation of largest benefit, leading us to conclude that adaptation was largely mutation-driven, such that mutational biases led to frequent parallel fixation of mutations of suboptimal effect.
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Affiliation(s)
- Andrew M Sackman
- Department of Biological Science, Florida State University, Tallahassee, FL
| | - Lindsey W McGee
- Department of Biological Science, Florida State University, Tallahassee, FL
| | | | - Jessica Pierce
- Department of Biological Science, Florida State University, Tallahassee, FL
| | - Jeremy Anisman
- Department of Biological Science, Florida State University, Tallahassee, FL
| | - Hunter Hamilton
- Department of Biological Science, Florida State University, Tallahassee, FL
| | | | - Cayla Newman
- Department of Biological Science, Florida State University, Tallahassee, FL
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL
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41
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Lozano‐Jaramillo M, McCracken KG, Cadena CD. Neutral and functionally important genes shed light on phylogeography and the history of high-altitude colonization in a widespread New World duck. Ecol Evol 2018; 8:6515-6528. [PMID: 30038753 PMCID: PMC6053577 DOI: 10.1002/ece3.4108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 03/05/2018] [Accepted: 03/15/2018] [Indexed: 12/16/2022] Open
Abstract
Phylogeographic studies often infer historical demographic processes underlying species distributions based on patterns of neutral genetic variation, but spatial variation in functionally important genes can provide additional insights about biogeographic history allowing for inferences about the potential role of adaptation in geographic range evolution. Integrating data from neutral markers and genes involved in oxygen (O2)-transport physiology, we test historical hypotheses about colonization and gene flow across low- and high-altitude regions in the Ruddy Duck (Oxyura jamaicensis), a widely distributed species in the New World. Using multilocus analyses that for the first time include populations from the Colombian Andes, we also examined the hypothesis that Ruddy Duck populations from northern South America are of hybrid origin. We found that neutral and functional genes appear to have moved into the Colombian Andes from both North America and southern South America, and that high-altitude Colombian populations do not exhibit evidence of adaptation to hypoxia in hemoglobin genes. Therefore, the biogeographic history of Ruddy Ducks is likely more complex than previously inferred. Our new data raise questions about the hypothesis that adaptation via natural selection to high-altitude conditions through amino acid replacements in the hemoglobin protein allowed Ruddy Ducks to disperse south along the high Andes into southern South America. The existence of shared genetic variation with populations from both North America and southern South America as well as private alleles suggests that the Colombian population of Ruddy Ducks may be of old hybrid origin. This study illustrates the breadth of inferences one can make by combining data from nuclear and functionally important loci in phylogeography, and underscores the importance of complete range-wide sampling to study species history in complex landscapes.
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Affiliation(s)
- Maria Lozano‐Jaramillo
- Laboratorio de Biología Evolutiva de VertebradosDepartamento de Ciencias BiológicasUniversidad de Los AndesBogotáColombia
- Wageningen University & Research Animal Breeding and GenomicsWageningenThe Netherlands
| | - Kevin G. McCracken
- Department of BiologyUniversity of MiamiCoral GablesFlorida
- Rosenstiel School of Marine and Atmospheric SciencesUniversity of MiamiMiamiFlorida
- Human Genetics and GenomicsHussman Institute for Human GenomicsUniversity of Miami Miller School of MedicineMiamiFlorida
- Institute of Arctic Biology and University of Alaska MuseumUniversity of Alaska FairbanksFairbanksAlaska
| | - Carlos Daniel Cadena
- Laboratorio de Biología Evolutiva de VertebradosDepartamento de Ciencias BiológicasUniversidad de Los AndesBogotáColombia
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Molecular basis of hemoglobin adaptation in the high-flying bar-headed goose. PLoS Genet 2018; 14:e1007331. [PMID: 29608560 PMCID: PMC5903655 DOI: 10.1371/journal.pgen.1007331] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 04/17/2018] [Accepted: 03/23/2018] [Indexed: 01/14/2023] Open
Abstract
During the adaptive evolution of a particular trait, some selectively fixed mutations may be directly causative and others may be purely compensatory. The relative contribution of these two classes of mutation to adaptive phenotypic evolution depends on the form and prevalence of mutational pleiotropy. To investigate the nature of adaptive substitutions and their pleiotropic effects, we used a protein engineering approach to characterize the molecular basis of hemoglobin (Hb) adaptation in the high-flying bar-headed goose (Anser indicus), a hypoxia-tolerant species renowned for its trans-Himalayan migratory flights. To test the effects of observed substitutions on evolutionarily relevant genetic backgrounds, we synthesized all possible genotypic intermediates in the line of descent connecting the wildtype bar-headed goose genotype with the most recent common ancestor of bar-headed goose and its lowland relatives. Site-directed mutagenesis experiments revealed one major-effect mutation that significantly increased Hb-O2 affinity on all possible genetic backgrounds. Two other mutations exhibited smaller average effect sizes and less additivity across backgrounds. One of the latter mutations produced a concomitant increase in the autoxidation rate, a deleterious side-effect that was fully compensated by a second-site mutation at a spatially proximal residue. The experiments revealed three key insights: (i) subtle, localized structural changes can produce large functional effects; (ii) relative effect sizes of function-altering mutations may depend on the sequential order in which they occur; and (iii) compensation of deleterious pleiotropic effects may play an important role in the adaptive evolution of protein function.
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Divergent and parallel routes of biochemical adaptation in high-altitude passerine birds from the Qinghai-Tibet Plateau. Proc Natl Acad Sci U S A 2018; 115:1865-1870. [PMID: 29432191 DOI: 10.1073/pnas.1720487115] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
When different species experience similar selection pressures, the probability of evolving similar adaptive solutions may be influenced by legacies of evolutionary history, such as lineage-specific changes in genetic background. Here we test for adaptive convergence in hemoglobin (Hb) function among high-altitude passerine birds that are native to the Qinghai-Tibet Plateau, and we examine whether convergent increases in Hb-O2 affinity have a similar molecular basis in different species. We documented that high-altitude parid and aegithalid species from the Qinghai-Tibet Plateau have evolved derived increases in Hb-O2 affinity in comparison with their closest lowland relatives in East Asia. However, convergent increases in Hb-O2 affinity and convergence in underlying functional mechanisms were seldom attributable to the same amino acid substitutions in different species. Using ancestral protein resurrection and site-directed mutagenesis, we experimentally confirmed two cases in which parallel substitutions contributed to convergent increases in Hb-O2 affinity in codistributed high-altitude species. In one case involving the ground tit (Parus humilis) and gray-crested tit (Lophophanes dichrous), parallel amino acid replacements with affinity-enhancing effects were attributable to nonsynonymous substitutions at a CpG dinucleotide, suggesting a possible role for mutation bias in promoting recurrent changes at the same site. Overall, most altitude-related changes in Hb function were caused by divergent amino acid substitutions, and a select few were caused by parallel substitutions that produced similar phenotypic effects on the divergent genetic backgrounds of different species.
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.Rainey PB, Remigi P, Farr AD, Lind PA. Darwin was right: where now for experimental evolution? Curr Opin Genet Dev 2017; 47:102-109. [DOI: 10.1016/j.gde.2017.09.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/13/2017] [Accepted: 09/14/2017] [Indexed: 01/02/2023]
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Gadek CR, Newsome SD, Beckman EJ, Chavez AN, Galen SC, Bautista E, Witt CC. Why are tropical mountain passes “low” for some species? Genetic and stable-isotope tests for differentiation, migration and expansion in elevational generalist songbirds. J Anim Ecol 2017; 87:741-753. [DOI: 10.1111/1365-2656.12779] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 10/23/2017] [Indexed: 11/26/2022]
Affiliation(s)
- Chauncey R. Gadek
- Department of Biology; University of New Mexico; Albuquerque NM USA
- Museum of Southwestern Biology; University of New Mexico; Albuquerque NM USA
| | - Seth D. Newsome
- Department of Biology; University of New Mexico; Albuquerque NM USA
| | - Elizabeth J. Beckman
- Department of Biology; University of New Mexico; Albuquerque NM USA
- Museum of Southwestern Biology; University of New Mexico; Albuquerque NM USA
- Division of Biological Sciences; University of Montana; Missoula MT USA
| | - Andrea N. Chavez
- Department of Biology; University of New Mexico; Albuquerque NM USA
- Museum of Southwestern Biology; University of New Mexico; Albuquerque NM USA
- Bureau of Land Management; Rio Puerco District Office; Albuquerque NM USA
| | - Spencer C. Galen
- Sackler Institute for Comparative Genomics; American Museum of Natural History; New York NY USA
| | - Emil Bautista
- Centro de Ornitología y Biodiversidad (CORBIDI); Urbanización Huertos de San Antonio; Surco Lima Perú
| | - Christopher C. Witt
- Department of Biology; University of New Mexico; Albuquerque NM USA
- Museum of Southwestern Biology; University of New Mexico; Albuquerque NM USA
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46
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Abstract
While mutational biases strongly influence neutral molecular evolution, the role of mutational biases in shaping the course of adaptation is less clear. Here we consider the frequency of transitions relative to transversions among adaptive substitutions. Because mutation rates for transitions are higher than those for transversions, if mutational biases influence the dynamics of adaptation, then transitions should be overrepresented among documented adaptive substitutions. To test this hypothesis, we assembled two sets of data on putatively adaptive amino acid replacements that have occurred in parallel during evolution, either in nature or in the laboratory. We find that the frequency of transitions in these data sets is much higher than would be predicted under a null model where mutation has no effect. Our results are qualitatively similar even if we restrict ourself to changes that have occurred, not merely twice, but three or more times. These results suggest that the course of adaptation is biased by mutation.
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Affiliation(s)
- Arlin Stoltzfus
- Genome-scale Measurements Group, Material Measurement Laboratory, NIST, and Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - David M McCandlish
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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47
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McGuigan K, Aw E. How does mutation affect the distribution of phenotypes? Evolution 2017; 71:2445-2456. [PMID: 28884791 DOI: 10.1111/evo.13358] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 08/27/2017] [Accepted: 08/29/2017] [Indexed: 12/14/2022]
Abstract
The potential for mutational processes to influence patterns of neutral or adaptive phenotypic evolution is not well understood. If mutations are directionally biased, shifting trait means in a particular direction, or if mutation generates more variance in some directions of multivariate trait space than others, mutation itself might be a source of bias in phenotypic evolution. Here, we use mutagenesis to investigate the affect of mutation on trait mean and (co)variances in zebrafish, Danio rerio. Mutation altered the relationship between age and both prolonged swimming speed and body shape. These observations suggest that mutational effects on ontogeny or aging have the potential to generate variance across the phenome. Mutations had a far greater effect in males than females, although whether this is a reflection of sex-specific ontogeny or aging remains to be determined. In males, mutations generated positive covariance between swimming speed, size, and body shape suggesting the potential for mutation to affect the evolutionary covariation of these traits. Overall, our observations suggest that mutation does not generate equal variance in all directions of phenotypic space or in each sex, and that pervasive variation in ontogeny or aging within a cohort could affect the variation available to evolution.
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Affiliation(s)
- Katrina McGuigan
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland 4072
| | - Ernest Aw
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland 4072
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48
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Kumar A, Natarajan C, Moriyama H, Witt CC, Weber RE, Fago A, Storz JF. Stability-Mediated Epistasis Restricts Accessible Mutational Pathways in the Functional Evolution of Avian Hemoglobin. Mol Biol Evol 2017; 34:1240-1251. [PMID: 28201714 PMCID: PMC5400398 DOI: 10.1093/molbev/msx085] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
If the fitness effects of amino acid mutations are conditional on genetic background, then mutations can have different effects depending on the sequential order in which they occur during evolutionary transitions in protein function. A key question concerns the fraction of possible mutational pathways connecting alternative functional states that involve transient reductions in fitness. Here we examine the functional effects of multiple amino acid substitutions that contributed to an evolutionary transition in the oxygenation properties of avian hemoglobin (Hb). The set of causative changes included mutations at intradimer interfaces of the Hb tetramer. Replacements at such sites may be especially likely to have epistatic effects on Hb function since residues at intersubunit interfaces are enmeshed in networks of salt bridges and hydrogen bonds between like and unlike subunits; mutational reconfigurations of these atomic contacts can affect allosteric transitions in quaternary structure and the propensity for tetramer-dimer dissociation. We used ancestral protein resurrection in conjunction with a combinatorial protein engineering approach to synthesize genotypes representing the complete set of mutational intermediates in all possible forward pathways that connect functionally distinct ancestral and descendent genotypes. The experiments revealed that 1/2 of all possible forward pathways included mutational intermediates with aberrant functional properties because particular combinations of mutations promoted tetramer-dimer dissociation. The subset of mutational pathways with unstable intermediates may be selectively inaccessible, representing evolutionary roads not taken. The experimental results also demonstrate how epistasis for particular functional properties of proteins may be mediated indirectly by mutational effects on quaternary structural stability.
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Affiliation(s)
- Amit Kumar
- School of Biological Sciences, University of Nebraska, Lincoln, NE
| | | | - Hideaki Moriyama
- School of Biological Sciences, University of Nebraska, Lincoln, NE
| | - Christopher C. Witt
- Department of Biology, University of New Mexico, Albuquerque, NM
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM
| | - Roy E. Weber
- Zoophysiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Angela Fago
- Zoophysiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Jay F. Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE
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49
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Natarajan C, Hoffmann FG, Weber RE, Fago A, Witt CC, Storz JF. Predictable convergence in hemoglobin function has unpredictable molecular underpinnings. Science 2017; 354:336-339. [PMID: 27846568 DOI: 10.1126/science.aaf9070] [Citation(s) in RCA: 160] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 07/20/2016] [Indexed: 12/28/2022]
Abstract
To investigate the predictability of genetic adaptation, we examined the molecular basis of convergence in hemoglobin function in comparisons involving 56 avian taxa that have contrasting altitudinal range limits. Convergent increases in hemoglobin-oxygen affinity were pervasive among high-altitude taxa, but few such changes were attributable to parallel amino acid substitutions at key residues. Thus, predictable changes in biochemical phenotype do not have a predictable molecular basis. Experiments involving resurrected ancestral proteins revealed that historical substitutions have context-dependent effects, indicating that possible adaptive solutions are contingent on prior history. Mutations that produce an adaptive change in one species may represent precluded possibilities in other species because of differences in genetic background.
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Affiliation(s)
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology and Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Roy E Weber
- Zoophysiology, Department of Bioscience, Aarhus University, DK-8000 Aarhus, Denmark
| | - Angela Fago
- Zoophysiology, Department of Bioscience, Aarhus University, DK-8000 Aarhus, Denmark
| | - Christopher C Witt
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
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50
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Storz JF. Gene Duplication and Evolutionary Innovations in Hemoglobin-Oxygen Transport. Physiology (Bethesda) 2017; 31:223-32. [PMID: 27053736 DOI: 10.1152/physiol.00060.2015] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
During vertebrate evolution, duplicated hemoglobin (Hb) genes diverged with respect to functional properties as well as the developmental timing of expression. For example, the subfamilies of genes that encode the different subunit chains of Hb are ontogenetically regulated such that functionally distinct Hb isoforms are expressed during different developmental stages. In some vertebrate taxa, functional differentiation between co-expressed Hb isoforms may also contribute to physiologically important divisions of labor.
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Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska
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