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Berles P, Wölfer J, Alfieri F, Botton-Divet L, Guéry JP, Nyakatura JA. Linking morphology, performance, and habitat utilization: adaptation across biologically relevant 'levels' in tamarins. BMC Ecol Evol 2024; 24:22. [PMID: 38355429 PMCID: PMC10865561 DOI: 10.1186/s12862-023-02193-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 12/19/2023] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Biological adaptation manifests itself at the interface of different biologically relevant 'levels', such as ecology, performance, and morphology. Integrated studies at this interface are scarce due to practical difficulties in study design. We present a multilevel analysis, in which we combine evidence from habitat utilization, leaping performance and limb bone morphology of four species of tamarins to elucidate correlations between these 'levels'. RESULTS We conducted studies of leaping behavior in the field and in a naturalistic park and found significant differences in support use and leaping performance. Leontocebus nigrifrons leaps primarily on vertical, inflexible supports, with vertical body postures, and covers greater leaping distances on average. In contrast, Saguinus midas and S. imperator use vertical and horizontal supports for leaping with a relatively similar frequency. S. mystax is similar to S. midas and S. imperator in the use of supports, but covers greater leaping distances on average, which are nevertheless shorter than those of L. nigrifrons. We assumed these differences to be reflected in the locomotor morphology, too, and compared various morphological features of the long bones of the limbs. According to our performance and habitat utilization data, we expected the long bone morphology of L. nigrifrons to reflect the largest potential for joint torque generation and stress resistance, because we assume longer leaps on vertical supports to exert larger forces on the bones. For S. mystax, based on our performance data, we expected the potential for torque generation to be intermediate between L. nigrifrons and the other two Saguinus species. Surprisingly, we found S. midas and S. imperator having relatively more robust morphological structures as well as relatively larger muscle in-levers, and thus appearing better adapted to the stresses involved in leaping than the other two. CONCLUSION This study demonstrates the complex ways in which behavioral and morphological 'levels' map onto each other, cautioning against oversimplification of ecological profiles when using large interspecific eco-morphological studies to make adaptive evolutionary inferences.
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Affiliation(s)
- Patricia Berles
- AG Vergleichende Zoologie, Institut für Biologie, Humboldt-Universität zu Berlin, Philippstr. 12/13, 10115, Berlin, Germany.
| | - Jan Wölfer
- AG Vergleichende Zoologie, Institut für Biologie, Humboldt-Universität zu Berlin, Philippstr. 12/13, 10115, Berlin, Germany
| | - Fabio Alfieri
- AG Vergleichende Zoologie, Institut für Biologie, Humboldt-Universität zu Berlin, Philippstr. 12/13, 10115, Berlin, Germany
- Institute of Ecology and Evolution, University of Bern, Bern, 3012, Switzerland
- Department of Earth Sciences, University of Cambridge, Cambridge, UK
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
| | - Léo Botton-Divet
- AG Vergleichende Zoologie, Institut für Biologie, Humboldt-Universität zu Berlin, Philippstr. 12/13, 10115, Berlin, Germany
| | | | - John A Nyakatura
- AG Vergleichende Zoologie, Institut für Biologie, Humboldt-Universität zu Berlin, Philippstr. 12/13, 10115, Berlin, Germany
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Ramirez JM, Restrepo J, Lucarini V, Weston D. Probabilistic measures for biological adaptation and resilience. Phys Rev E 2024; 109:024413. [PMID: 38491626 DOI: 10.1103/physreve.109.024413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/10/2024] [Indexed: 03/18/2024]
Abstract
This paper introduces an approach to quantifying ecological resilience in biological systems, particularly focusing on noisy systems responding to episodic disturbances with sudden adaptations. Incorporating concepts from nonequilibrium statistical mechanics, we propose a measure termed "ecological resilience through adaptation," specifically tailored to noisy, forced systems that undergo physiological adaptation in the face of stressful environmental changes. Randomness plays a key role, accounting for model uncertainty and the inherent variability in the dynamical response among components of biological systems. Our measure of resilience is rooted in the probabilistic description of states within these systems and is defined in terms of the dynamics of the ensemble average of a model-specific observable quantifying success or well-being. Our approach utilizes stochastic linear response theory to compute how the expected success of a system, originally in statistical equilibrium, dynamically changes in response to a environmental perturbation and a subsequent adaptation. The resulting mathematical derivations allow for the estimation of resilience in terms of ensemble averages of simulated or experimental data. Finally, through a simple but clear conceptual example, we illustrate how our resilience measure can be interpreted and compared to other existing frameworks in the literature. The methodology is general but inspired by applications in plant systems, with the potential for broader application to complex biological processes.
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Affiliation(s)
- Jorge M Ramirez
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Juan Restrepo
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Valerio Lucarini
- School of Computing and Mathematical Sciences, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - David Weston
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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Huang Y, Maurer A, Giehl RFH, Zhao S, Golan G, Thirulogachandar V, Li G, Zhao Y, Trautewig C, Himmelbach A, Börner A, Jayakodi M, Stein N, Mascher M, Pillen K, Schnurbusch T. Dynamic Phytomeric Growth Contributes to Local Adaptation in Barley. Mol Biol Evol 2024; 41:msae011. [PMID: 38243866 PMCID: PMC10837018 DOI: 10.1093/molbev/msae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/03/2023] [Accepted: 01/10/2024] [Indexed: 01/22/2024] Open
Abstract
Vascular plants have segmented body axes with iterative nodes and internodes. Appropriate node initiation and internode elongation are fundamental to plant fitness and crop yield; however, how these events are spatiotemporally coordinated remains elusive. We show that in barley (Hordeum vulgare L.), selections during domestication have extended the apical meristematic phase to promote node initiation, but constrained subsequent internode elongation. In both vegetative and reproductive phases, internode elongation displays a dynamic proximal-distal gradient, and among subpopulations of domesticated barleys worldwide, node initiation and proximal internode elongation are associated with latitudinal and longitudinal gradients, respectively. Genetic and functional analyses suggest that, in addition to their converging roles in node initiation, flowering-time genes have been repurposed to specify the timing and duration of internode elongation. Our study provides an integrated view of barley node initiation and internode elongation and suggests that plant architecture should be recognized as a collection of dynamic phytomeric units in the context of crop adaptive evolution.
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Affiliation(s)
- Yongyu Huang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Andreas Maurer
- Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, 06120 Halle, Germany
| | - Ricardo F H Giehl
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Shuangshuang Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Guy Golan
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | | | - Guoliang Li
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Corinna Trautewig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Murukarthick Jayakodi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
- Center for Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Klaus Pillen
- Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, 06120 Halle, Germany
| | - Thorsten Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
- Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, 06120 Halle, Germany
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Bhattacharya P, Raman K, Tangirala AK. Design Principles for Biological Adaptation: A Systems and Control-Theoretic Treatment. Methods Mol Biol 2024; 2760:35-56. [PMID: 38468081 DOI: 10.1007/978-1-0716-3658-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Establishing a mapping between (from and to) the functionality of interest and the underlying network structure (design principles) remains a crucial step toward understanding and design of bio-systems. Perfect adaptation is one such crucial functionality that enables every living organism to regulate its essential activities in the presence of external disturbances. Previous approaches to deducing the design principles for adaptation have either relied on computationally burdensome brute-force methods or rule-based design strategies detecting only a subset of all possible adaptive network structures. This chapter outlines a scalable and generalizable method inspired by systems theory that unravels an exhaustive set of adaptation-capable structures. We first use the well-known performance parameters to characterize perfect adaptation. These performance parameters are then mapped back to a few parameters (poles, zeros, gain) characteristic of the underlying dynamical system constituted by the rate equations. Therefore, the performance parameters evaluated for the scenario of perfect adaptation can be expressed as a set of precise mathematical conditions involving the system parameters. Finally, we use algebraic graph theory to translate these abstract mathematical conditions to certain structural requirements for adaptation. The proposed algorithm does not assume any particular dynamics and is applicable to networks of any size. Moreover, the results offer a significant advancement in the realm of understanding and designing complex biochemical networks.
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Affiliation(s)
- Priyan Bhattacharya
- Department of Chemical Engineering, Indian Institute of Technology, Madras (IIT Madras), Chennai, India
- Robert Bosch Centre of Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai, India
- Initiative for Biological Science and Systems mEdicine (IBSE), IIT Madras, Chennai, India
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, IIT Madras, Chennai, India.
- Robert Bosch Centre of Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai, India.
- Initiative for Biological Science and Systems mEdicine (IBSE), IIT Madras, Chennai, India.
| | - Arun K Tangirala
- Robert Bosch Centre of Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai, India.
- Initiative for Biological Science and Systems mEdicine (IBSE), IIT Madras, Chennai, India.
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Pisor A, Lansing JS, Magargal K. Climate change adaptation needs a science of culture. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220390. [PMID: 37718608 PMCID: PMC10505856 DOI: 10.1098/rstb.2022.0390] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 08/07/2023] [Indexed: 09/19/2023] Open
Abstract
There is global consensus that we must immediately prioritize climate change adaptation-change in response to or anticipation of risks from climate change. Some researchers and policymakers urge 'transformative change', a complete break from past practices, yet report having little data on whether new practices reduce the risks communities face, even over the short term. However, researchers have some leads: human communities have long generated solutions to changing climate, and scientists who study culture have examples of effective and persistent solutions. This theme issue discusses cultural adaptation to climate change, and in this paper, we review how processes of biological adaptation, including innovation, modification, selective retention and transmission, shape the landscapes decision-makers care about-from which solutions emerge in communities, to the spread of effective adaptations, to regional or global collective action. We introduce a comprehensive portal of data and models on cultural adaptation to climate change, and we outline ways forward. This article is part of the theme issue 'Climate change adaptation needs a science of culture'.
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Affiliation(s)
- Anne Pisor
- Department of Anthropology, Washington State University, Pullman, WA 99164-1009, USA
- Department of Human Behavior, Ecology and Culture, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Sachsen, Germany
| | - J. Stephen Lansing
- Santa Fe Institute, NM87506, USA
- Complexity Science Hub, 1080 Vienna, Austria
| | - Kate Magargal
- Environmental and Sustainability Studies, University of Utah Health, Salt Lake City, UT84112, USA
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6
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Enbody ED, Sendell-Price AT, Sprehn CG, Rubin CJ, Visscher PM, Grant BR, Grant PR, Andersson L. Community-wide genome sequencing reveals 30 years of Darwin's finch evolution. Science 2023; 381:eadf6218. [PMID: 37769091 DOI: 10.1126/science.adf6218] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 08/22/2023] [Indexed: 09/30/2023]
Abstract
A fundamental goal in evolutionary biology is to understand the genetic architecture of adaptive traits. Using whole-genome data of 3955 of Darwin's finches on the Galápagos Island of Daphne Major, we identified six loci of large effect that explain 45% of the variation in the highly heritable beak size of Geospiza fortis, a key ecological trait. The major locus is a supergene comprising four genes. Abrupt changes in allele frequencies at the loci accompanied a strong change in beak size caused by natural selection during a drought. A gradual change in Geospiza scandens occurred across 30 years as a result of introgressive hybridization with G. fortis. This study shows how a few loci with large effect on a fitness-related trait contribute to the genetic potential for rapid adaptive radiation.
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Affiliation(s)
- Erik D Enbody
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 751 23 Uppsala, Sweden
| | - Ashley T Sendell-Price
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 751 23 Uppsala, Sweden
| | - C Grace Sprehn
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 751 23 Uppsala, Sweden
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 751 23 Uppsala, Sweden
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Rd., St. Lucia QLD 4072, Australia
| | - B Rosemary Grant
- Department of Ecology and Evolutionary Biology, Princeton University, 106A Guyot Hall, Princeton, NJ 08544, USA
| | - Peter R Grant
- Department of Ecology and Evolutionary Biology, Princeton University, 106A Guyot Hall, Princeton, NJ 08544, USA
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 751 23 Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, Texas A&M University, 402 Raymond Stotzer Pkwy Building 2, College Station, TX 77843, USA
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7
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Meier JI, McGee MD, Marques DA, Mwaiko S, Kishe M, Wandera S, Neumann D, Mrosso H, Chapman LJ, Chapman CA, Kaufman L, Taabu-Munyaho A, Wagner CE, Bruggmann R, Excoffier L, Seehausen O. Cycles of fusion and fission enabled rapid parallel adaptive radiations in African cichlids. Science 2023; 381:eade2833. [PMID: 37769075 DOI: 10.1126/science.ade2833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 08/21/2023] [Indexed: 09/30/2023]
Abstract
Although some lineages of animals and plants have made impressive adaptive radiations when provided with ecological opportunity, the propensities to radiate vary profoundly among lineages for unknown reasons. In Africa's Lake Victoria region, one cichlid lineage radiated in every lake, with the largest radiation taking place in a lake less than 16,000 years old. We show that all of its ecological guilds evolved in situ. Cycles of lineage fusion through admixture and lineage fission through speciation characterize the history of the radiation. It was jump-started when several swamp-dwelling refugial populations, each of which were of older hybrid descent, met in the newly forming lake, where they fused into a single population, resuspending old admixture variation. Each population contributed a different set of ancient alleles from which a new adaptive radiation assembled in record time, involving additional fusion-fission cycles. We argue that repeated fusion-fission cycles in the history of a lineage make adaptive radiation fast and predictable.
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Affiliation(s)
- Joana I Meier
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
- Department of Zoology, University of Cambridge, Cambridge, UK
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Matthew D McGee
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - David A Marques
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
- Natural History Museum Basel, Basel, Switzerland
| | - Salome Mwaiko
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
| | - Mary Kishe
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
| | - Sylvester Wandera
- National Fisheries Resources Research Institute (NAFIRRI), Jinja, Uganda
| | - Dirk Neumann
- Leipniz Institute for Biodiversity Change, Hamburg, Germany
| | - Hilary Mrosso
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
| | - Lauren J Chapman
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Colin A Chapman
- Wilson Center, Washington, DC, USA
- Biology Department, Vancouver Island University, Nanaimo, British Columbia, Canada
- School of Life Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi'an, China
- Biology Department, Vancouver Island University, Nanaimo, British Columbia, Canada
| | - Les Kaufman
- Boston University Marine Program, Department of Biology, Boston University, Boston, MA, USA
| | | | | | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Laurent Excoffier
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ole Seehausen
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
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Abstract
Experiments on worms suggest that a statistical measure called the G matrix can accurately predict how phenotypes will adapt to a novel environment over multiple generations.
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Affiliation(s)
- Greg M Walter
- School of Biological Sciences, Monash UniversityMelbourneAustralia
| | - Katrina McGuigan
- School of the Environment, University of QueenslandBrisbaneAustralia
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9
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Fabbri G, Molinaro L, Mucci N, Pagani L, Scandura M. Anthropogenic hybridization and its influence on the adaptive potential of the Sardinian wild boar (Sus scrofa meridionalis). J Appl Genet 2023; 64:521-530. [PMID: 37369962 PMCID: PMC10457222 DOI: 10.1007/s13353-023-00763-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 05/06/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023]
Abstract
The wild boar (Sus scrofa meridionalis) arrived in Sardinia with the first human settlers in the early Neolithic with the potential to hybridize with the domestic pig (S. s. domesticus) throughout its evolution on the island. In this paper, we investigated the possible microevolutionary effects of such introgressive hybridization on the present wild boar population, comparing Sardinian wild specimens with several commercial pig breeds and Sardinian local pigs, along with a putatively unadmixed wild boar population from Central Italy, all genotyped with a medium density SNP chip. We first aimed at identifying hybrids in the population using different approaches, then examined genomic regions enriched for domestic alleles in the hybrid group, and finally we applied two methods to find regions under positive selection to possibly highlight instances of domestic adaptive introgression into a wild population. We found three hybrids within the Sardinian sample (3.1% out of the whole dataset). We reported 11 significant windows under positive selection with a method that looks for overly differentiated loci in the target population, compared with other two populations. We also identified 82 genomic regions with signs of selection in the domestic pig but not in the wild boar, two of which overlapped with genomic regions enriched for domestic alleles in the hybrid pool. Genes in these regions can be linked with reproductive success. Given our results, domestic introgression does not seem to be pervasive in the Sardinian wild boar. Nevertheless, we suggest monitoring the possible spread of advantageous domestic alleles in the coming years.
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Affiliation(s)
- Giulia Fabbri
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2A, 07100, Sassari, Italy.
| | - Ludovica Molinaro
- Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Nadia Mucci
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell'Emilia, Bologna, Italy
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Biology, University of Padua, Viale G. Colombo 3, 35131, Padua, Italy
| | - Massimo Scandura
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2A, 07100, Sassari, Italy
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Linder RA, Zabanavar B, Majumder A, Hoang HCS, Delgado VG, Tran R, La VT, Leemans SW, Long AD. Adaptation in Outbred Sexual Yeast is Repeatable, Polygenic and Favors Rare Haplotypes. Mol Biol Evol 2022; 39:msac248. [PMID: 36366952 PMCID: PMC9728589 DOI: 10.1093/molbev/msac248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We carried out a 200 generation Evolve and Resequence (E&R) experiment initiated from an outbred diploid recombined 18-way synthetic base population. Replicate populations were evolved at large effective population sizes (>105 individuals), exposed to several different chemical challenges over 12 weeks of evolution, and whole-genome resequenced. Weekly forced outcrossing resulted in an average between adjacent-gene per cell division recombination rate of ∼0.0008. Despite attempts to force weekly sex, roughly half of our populations evolved cheaters and appear to be evolving asexually. Focusing on seven chemical stressors and 55 total evolved populations that remained sexual we observed large fitness gains and highly repeatable patterns of genome-wide haplotype change within chemical challenges, with limited levels of repeatability across chemical treatments. Adaptation appears highly polygenic with almost the entire genome showing significant and consistent patterns of haplotype change with little evidence for long-range linkage disequilibrium in a subset of populations for which we sequenced haploid clones. That is, almost the entire genome is under selection or drafting with selected sites. At any given locus adaptation was almost always dominated by one of the 18 founder's alleles, with that allele varying spatially and between treatments, suggesting that selection acts primarily on rare variants private to a founder or haplotype blocks harboring multiple mutations.
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Affiliation(s)
- Robert A Linder
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
| | - Behzad Zabanavar
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
| | - Arundhati Majumder
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
| | - Hannah Chiao-Shyan Hoang
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
| | - Vanessa Genesaret Delgado
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
| | - Ryan Tran
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
| | - Vy Thoai La
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
| | - Simon William Leemans
- Department of Biomedical Engineering, School of Engineering, University of California, Irvine
| | - Anthony D Long
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
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Kahl BC, Moreau K. Editorial: Co-Infection and Consequences in Cystic Fibrosis. Front Cell Infect Microbiol 2022; 12:924527. [PMID: 35719342 PMCID: PMC9199434 DOI: 10.3389/fcimb.2022.924527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/05/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Barbara C. Kahl
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Karen Moreau
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Lyon, France
- *Correspondence: Karen Moreau,
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12
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Guo R, Zhang YH, Zhang HJ, Landis JB, Zhang X, Wang HC, Yao XH. Molecular phylogeography and species distribution modelling evidence of 'oceanic' adaptation for Actinidia eriantha with a refugium along the oceanic-continental gradient in a biodiversity hotspot. BMC Plant Biol 2022; 22:89. [PMID: 35227218 PMCID: PMC8883688 DOI: 10.1186/s12870-022-03464-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Refugia is considered to be critical for maintaining biodiversity; while discerning the type and pattern of refugia is pivotal for our understanding of evolutionary processes in the context of conservation. Interglacial and glacial refugia have been studied throughout subtropical China. However, studies on refugia along the oceanic-continental gradient have largely been ignored. We used a liana Actinidia eriantha, which occurs across the eastern moist evergreen broad-leaved forests of subtropical China, as a case study to test hypotheses of refugia along the oceanic-continental gradient and 'oceanic' adaptation. RESULTS The phylogeographic pattern of A. eriantha was explored using a combination of three cpDNA markers and 38 nuclear microsatellite loci, Species distribution modelling and dispersal corridors analysis. Our data showed intermediate levels of genetic diversity [haplotype diversity (hT) = 0.498; unbiased expected heterozygosity (UHE) = 0.510] both at the species and population level. Microsatellite loci revealed five clusters largely corresponding to geographic regions. Coalescent time of cpDNA lineages was dated to the middle Pliocene (ca. 4.03 Ma). Both geographic distance and climate difference have important roles for intraspecific divergence of the species. The Zhejiang-Fujian Hilly Region was demonstrated to be a refugium along the oceanic-continental gradient of the species and fit the 'refugia in refugia' pattern. Species distribution modelling analysis indicated that Precipitation of Coldest Quarter (importance of 44%), Temperature Seasonality (29%) and Mean Temperature of Wettest Quarter (25%) contributed the most to model development. By checking the isolines in the three climate layers, we found that A. eriantha prefer higher precipitation during the coldest quarter, lower seasonal temperature difference and lower mean temperature during the wettest quarter, which correspond to 'oceanic' adaptation. Actinidia eriantha expanded to its western distribution range along the dispersal corridor repeatedly during the glacial periods. CONCLUSIONS Overall, our results provide integrated evidence demonstrating that the Zhejiang-Fujian Hilly Region is a refugium along the oceanic-continental gradient of Actinidia eriantha in subtropical China and that speciation is attributed to 'oceanic' adaptation. This study gives a deeper understanding of the refugia in subtropical China and will contribute to the conservation and utilization of kiwifruit wild resources in the context of climate change.
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Affiliation(s)
- Rui Guo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Department of Plant Sciences, University of Cambridge, Tennis Court Road, Cambridge, CB2 3EA, UK
| | - Yong-Hua Zhang
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou, 325035, China
| | - Hua-Jie Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, 14853, USA
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Heng-Chang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Xiao-Hong Yao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
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13
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Mukhia S, Kumar A, Kumari P, Kumar R, Kumar S. Multilocus sequence based identification and adaptational strategies of Pseudomonas sp. from the supraglacial site of Sikkim Himalaya. PLoS One 2022; 17:e0261178. [PMID: 35073328 PMCID: PMC8786180 DOI: 10.1371/journal.pone.0261178] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 11/26/2021] [Indexed: 11/18/2022] Open
Abstract
Microorganisms inhabiting the supraglacial ice are biotechnologically significant as they are equipped with unique adaptive features in response to extreme environmental conditions of high ultraviolet radiations and frequent freeze-thaw. In the current study, we obtained eleven strains of Pseudomonas from the East Rathong supraglacial site in Sikkim Himalaya that showed taxonomic ambiguity in terms of species affiliation. Being one of the most complex and diverse genera, deciphering the correct taxonomy of Pseudomonas species has always been challenging. So, we conducted multilocus sequence analysis (MLSA) using five housekeeping genes, which concluded the taxonomic assignment of these strains to Pseudomonas antarctica. This was further supported by the lesser mean genetic distances with P. antarctica (0.73%) compared to P. fluorescens (3.65%), and highest ANI value of ~99 and dDDH value of 91.2 of the representative strains with P. antarctica PAMC 27494. We examined the multi-tolerance abilities of these eleven Pseudomonas strains. Indeed the studied strains displayed significant tolerance to freezing for 96 hours compared to the mesophilic control strain, while except for four strains, seven strains exhibited noteworthy tolerance to UV-C radiations. The genome-based findings revealed many cold and radiation resistance-associated genes that supported the physiological findings. Further, the bacterial strains produced two or more cold-active enzymes in plate-based assays. Owing to the polyadaptational attributes, the strains ERGC3:01 and ERGC3:05 could be most promising for bioprospection.
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Affiliation(s)
- Srijana Mukhia
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
- Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Anil Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR- Human Resource Development Centre (CSIR-HRDC), Ghaziabad, Uttar Pradesh, India
| | - Poonam Kumari
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Rakshak Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
- * E-mail:
| | - Sanjay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
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14
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Hüdig M, Tronconi MA, Zubimendi JP, Sage TL, Poschmann G, Bickel D, Gohlke H, Maurino VG. Respiratory and C4-photosynthetic NAD-malic enzyme coexist in bundle sheath cell mitochondria and evolved via association of differentially adapted subunits. Plant Cell 2022; 34:597-615. [PMID: 34734993 PMCID: PMC8773993 DOI: 10.1093/plcell/koab265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/26/2021] [Indexed: 05/29/2023]
Abstract
In plant mitochondria, nicotinamide adenine dinucleotide-malic enzyme (NAD-ME) has a housekeeping function in malate respiration. In different plant lineages, NAD-ME was independently co-opted in C4 photosynthesis. In the C4 Cleome species, Gynandropsis gynandra and Cleome angustifolia, all NAD-ME genes (NAD-MEα, NAD-MEβ1, and NAD-MEβ2) were affected by C4 evolution and are expressed at higher levels than their orthologs in the C3 species Tarenaya hassleriana. In T. hassleriana, the NAD-ME housekeeping function is performed by two heteromers, NAD-MEα/β1 and NAD-MEα/β2, with similar biochemical properties. In both C4 species, this role is restricted to NAD-MEα/β2. In the C4 species, NAD-MEα/β1 is exclusively present in the leaves, where it accounts for most of the enzymatic activity. Gynandropsis gynandra NAD-MEα/β1 (GgNAD-MEα/β1) exhibits high catalytic efficiency and is differentially activated by the C4 intermediate aspartate, confirming its role as the C4-decarboxylase. During C4 evolution, NAD-MEβ1 lost its catalytic activity; its contribution to the enzymatic activity results from a stabilizing effect on the associated α-subunit and the acquisition of regulatory properties. We conclude that in bundle sheath cell mitochondria of C4 species, the functions of NAD-ME as C4 photosynthetic decarboxylase and as a housekeeping enzyme coexist and are performed by isoforms that combine the same α-subunit with differentially adapted β-subunits.
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Affiliation(s)
- Meike Hüdig
- Molekulare Pflanzenphysiologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Kirschallee, Bonn 53115, Germany
| | - Marcos A Tronconi
- Centro de Estudios Fotosintéticos y Bioquímicos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina
| | - Juan P Zubimendi
- Centro de Estudios Fotosintéticos y Bioquímicos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina
| | - Tammy L Sage
- Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Gereon Poschmann
- Molecular Proteomics Laboratory, Biomedical Research Centre (BMFZ) & Institute of Molecular Medicine, Proteome Research, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Universitätsstraße 1, Düsseldorf 40225, Germany
| | - David Bickel
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, Düsseldorf 40225, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, Düsseldorf 40225, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry) & Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Veronica G Maurino
- Molekulare Pflanzenphysiologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Kirschallee, Bonn 53115, Germany
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15
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Irfan J, Febrianto MR, Sharma A, Rose T, Mahmudzade Y, Di Giovanni S, Nagy I, Torres-Perez JV. DNA Methylation and Non-Coding RNAs during Tissue-Injury Associated Pain. Int J Mol Sci 2022; 23:ijms23020752. [PMID: 35054943 PMCID: PMC8775747 DOI: 10.3390/ijms23020752] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/04/2022] [Accepted: 01/07/2022] [Indexed: 02/01/2023] Open
Abstract
While about half of the population experience persistent pain associated with tissue damages during their lifetime, current symptom-based approaches often fail to reduce such pain to a satisfactory level. To provide better patient care, mechanism-based analgesic approaches must be developed, which necessitates a comprehensive understanding of the nociceptive mechanism leading to tissue injury-associated persistent pain. Epigenetic events leading the altered transcription in the nervous system are pivotal in the maintenance of pain in tissue injury. However, the mechanisms through which those events contribute to the persistence of pain are not fully understood. This review provides a summary and critical evaluation of two epigenetic mechanisms, DNA methylation and non-coding RNA expression, on transcriptional modulation in nociceptive pathways during the development of tissue injury-associated pain. We assess the pre-clinical data and their translational implication and evaluate the potential of controlling DNA methylation and non-coding RNA expression as novel analgesic approaches and/or biomarkers of persistent pain.
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Affiliation(s)
- Jahanzaib Irfan
- Nociception Group, Department of Surgery and Cancer, Division of Anaesthetics, Pain Medicine and Intensive Care, Chelsea and Westminster Hospital Campus, Imperial College London, 369 Fulham Road, London SW10 9FJ, UK; (J.I.); (M.R.F.); (A.S.); (T.R.); (Y.M.)
| | - Muhammad Rizki Febrianto
- Nociception Group, Department of Surgery and Cancer, Division of Anaesthetics, Pain Medicine and Intensive Care, Chelsea and Westminster Hospital Campus, Imperial College London, 369 Fulham Road, London SW10 9FJ, UK; (J.I.); (M.R.F.); (A.S.); (T.R.); (Y.M.)
| | - Anju Sharma
- Nociception Group, Department of Surgery and Cancer, Division of Anaesthetics, Pain Medicine and Intensive Care, Chelsea and Westminster Hospital Campus, Imperial College London, 369 Fulham Road, London SW10 9FJ, UK; (J.I.); (M.R.F.); (A.S.); (T.R.); (Y.M.)
| | - Thomas Rose
- Nociception Group, Department of Surgery and Cancer, Division of Anaesthetics, Pain Medicine and Intensive Care, Chelsea and Westminster Hospital Campus, Imperial College London, 369 Fulham Road, London SW10 9FJ, UK; (J.I.); (M.R.F.); (A.S.); (T.R.); (Y.M.)
| | - Yasamin Mahmudzade
- Nociception Group, Department of Surgery and Cancer, Division of Anaesthetics, Pain Medicine and Intensive Care, Chelsea and Westminster Hospital Campus, Imperial College London, 369 Fulham Road, London SW10 9FJ, UK; (J.I.); (M.R.F.); (A.S.); (T.R.); (Y.M.)
| | - Simone Di Giovanni
- Department of Brain Sciences, Division of Neuroscience, Imperial College London, E505, Burlington Danes, Du Cane Road, London W12 ONN, UK;
| | - Istvan Nagy
- Nociception Group, Department of Surgery and Cancer, Division of Anaesthetics, Pain Medicine and Intensive Care, Chelsea and Westminster Hospital Campus, Imperial College London, 369 Fulham Road, London SW10 9FJ, UK; (J.I.); (M.R.F.); (A.S.); (T.R.); (Y.M.)
- Correspondence: (I.N.); (J.V.T.-P.)
| | - Jose Vicente Torres-Perez
- Department of Brain Sciences, Dementia Research Institute, Imperial College London, 86 Wood Ln, London W12 0BZ, UK
- Departament de Biologia Cellular, Biologia Funcional i Antropologia Física, Facultat de Ciències Biològiques, Universitat de València, C/Dr. Moliner 50, 46100 Burjassot, Spain
- Correspondence: (I.N.); (J.V.T.-P.)
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16
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Bai J, Li L, Li Y, Zhang L. Genetic and immune changes in Tibetan high-altitude populations contribute to biological adaptation to hypoxia. Environ Health Prev Med 2022; 27:39. [PMID: 36244759 PMCID: PMC9640738 DOI: 10.1265/ehpm.22-00040] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 08/19/2022] [Indexed: 07/27/2023] Open
Abstract
BACKGROUND Tibetans have lived at very high altitudes for thousands of years, and have a distinctive suite of physiological traits that enable them to tolerate environmental hypoxia. Expanding awareness and knowledge of the differences in hematology, hypoxia-associated genes, immune system of people living at different altitudes and from different ethnic groups may provide evidence for the prevention of mountain sickness. METHOD Ninety-five Han people at mid-altitude, ninety-five Tibetan people at high-altitude and ninety-eight Han people at high-altitude were recruited. Red blood cell parameters, immune cells, the contents of cytokines, hypoxia-associated gene single nucleotide polymorphisms (SNPs) were measured. RESULTS The values of Hematocrit (HCT), Mean cell volume (MCV) and Mean cell hemoglobin (MCH) in red blood cell, immune cell CD19+ B cell number, the levels of cytokines Erb-B2 receptor tyrosine kinase 3 (ErbB3) and Tumor necrosis factor receptor II (TNF-RII) and the levels of hypoxia-associated factors Hypoxia inducible factor-1α (HIF-1α), Hypoxia inducible factor-2α (HIF-2α) and HIF prolyl 4-hydroxylase 2 (PHD2) were decreased, while the frequencies of SNPs in twenty-six Endothelial PAS domain protein 1 (EPAS1) and Egl-9 family hypoxia inducible factor 1 (EGLN1) were increased in Tibetan people at high-altitude compared with that of Han peoples at high-altitude. Furthermore, compared with mid-altitude individuals, high-altitude individuals showed lower blood cell parameters including Hemoglobin concentration (HGB), HCT, MCV and MCH, higher Mean cell hemoglobin concentration (MCHC), lower immune cells including CD19+ B cells, CD4+ T cells and CD4/CD8 ratio, higher immune cells containing CD8+ T cells and CD16/56NK cells, decreased Growth regulated oncogene alpha (GROa), Macrophage inflammatory protein 1 beta (MIP-1b), Interleukin-8 (IL-8), and increased Thrombomodulin, downregulated hypoxia-associated factors including HIF1α, HIF2α and PHD2, and higher frequency of EGLN1 rs2275279. CONCLUSIONS These results indicated that biological adaption to hypoxia at high altitude might have been mediated by changes in immune cells, cytokines, and hypoxia-associated genes during the evolutionary history of Tibetan populations. Furthermore, different responses to high altitude were observed in different ethnic groups, which may provide a useful knowledge to improve the protection of high-altitude populations from mountain sickness.
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Affiliation(s)
- Jun Bai
- Institute of Hematology, Lanzhou University Second Hospital, Lanzhou 730000, China
- Gansu Key Laboratory of Hematology, Lanzhou 730000, China
| | - Lijuan Li
- Institute of Hematology, Lanzhou University Second Hospital, Lanzhou 730000, China
- Gansu Key Laboratory of Hematology, Lanzhou 730000, China
| | - Yanhong Li
- Institute of Hematology, Lanzhou University Second Hospital, Lanzhou 730000, China
- Gansu Key Laboratory of Hematology, Lanzhou 730000, China
| | - Liansheng Zhang
- Institute of Hematology, Lanzhou University Second Hospital, Lanzhou 730000, China
- Gansu Key Laboratory of Hematology, Lanzhou 730000, China
- Dingxi People’s Hospital, Dingxi 730500, China
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Kravtsov A, Kozin S, Basov A, Butina E, Baryshev M, Malyshko V, Moiseev A, Elkina A, Dzhimak S. Reduction of Deuterium Level Supports Resistance of Neurons to Glucose Deprivation and Hypoxia: Study in Cultures of Neurons and on Animals. Molecules 2021; 27:243. [PMID: 35011474 PMCID: PMC8746303 DOI: 10.3390/molecules27010243] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/29/2021] [Accepted: 12/29/2021] [Indexed: 11/17/2022] Open
Abstract
The effect of a reduced deuterium (D) content in the incubation medium on the survival of cultured neurons in vitro and under glucose deprivation was studied. In addition, we studied the effect of a decrease in the deuterium content in the rat brain on oxidative processes in the nervous tissue, its antioxidant protection, and training of rats in the T-shaped maze test under hypoxic conditions. For experiments with cultures of neurons, 7-8-day cultures of cerebellar neurons were used. Determination of the rate of neuronal death in cultures was carried out using propidium iodide. Acute hypoxia with hypercapnia was simulated in rats by placing them in sealed vessels with a capacity of 1 L. The effect on oxidative processes in brain tissues was assessed by changes in the level of free radical oxidation and malondialdehyde. The effect on the antioxidant system of the brain was assessed by the activity of catalase. The study in the T-maze was carried out in accordance with the generally accepted methodology, the skill of alternating right-sided and left-sided loops on positive reinforcement was developed. This work has shown that a decrease in the deuterium content in the incubation medium to a level of -357‱ has a neuroprotective effect, increasing the survival rate of cultured neurons under glucose deprivation. When exposed to hypoxia, a preliminary decrease in the deuterium content in the rat brain to -261‱ prevents the development of oxidative stress in their nervous tissue and preserves the learning ability of animals in the T-shaped maze test at the level of the control group. A similar protective effect during the modification of the 2H/1H internal environment of the body by the consumption of DDW can potentially be used for the prevention of pathological conditions associated with the development of oxidative stress with damage to the central nervous system.
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Affiliation(s)
- Alexandr Kravtsov
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, 350040 Krasnodar, Russia; (A.K.); (S.K.); (A.B.); (M.B.); (A.E.)
- South Scientific Center of the Russian Academy of Sciences, Laboratory of Problems of Stable Isotope Spreading in Living Systems, 344006 Rostov-on-Don, Russia;
| | - Stanislav Kozin
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, 350040 Krasnodar, Russia; (A.K.); (S.K.); (A.B.); (M.B.); (A.E.)
- South Scientific Center of the Russian Academy of Sciences, Laboratory of Problems of Stable Isotope Spreading in Living Systems, 344006 Rostov-on-Don, Russia;
| | - Alexandr Basov
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, 350040 Krasnodar, Russia; (A.K.); (S.K.); (A.B.); (M.B.); (A.E.)
- Department of Fundamental and Clinical Biochemistry, Kuban State Medical University, 350063 Krasnodar, Russia
| | - Elena Butina
- Department of Technology of Fats, Cosmetics, Commodity Science, Processes and Devices, Kuban State Technological University, 350072 Krasnodar, Russia;
| | - Mikhail Baryshev
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, 350040 Krasnodar, Russia; (A.K.); (S.K.); (A.B.); (M.B.); (A.E.)
- South Scientific Center of the Russian Academy of Sciences, Laboratory of Problems of Stable Isotope Spreading in Living Systems, 344006 Rostov-on-Don, Russia;
- Department of Technology of Fats, Cosmetics, Commodity Science, Processes and Devices, Kuban State Technological University, 350072 Krasnodar, Russia;
| | - Vadim Malyshko
- South Scientific Center of the Russian Academy of Sciences, Laboratory of Problems of Stable Isotope Spreading in Living Systems, 344006 Rostov-on-Don, Russia;
- Department of Fundamental and Clinical Biochemistry, Kuban State Medical University, 350063 Krasnodar, Russia
| | - Arkady Moiseev
- Department of Organization and Support of Scientific Activities, Kuban State Agrarian University, 350044 Krasnodar, Russia;
| | - Anna Elkina
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, 350040 Krasnodar, Russia; (A.K.); (S.K.); (A.B.); (M.B.); (A.E.)
- South Scientific Center of the Russian Academy of Sciences, Laboratory of Problems of Stable Isotope Spreading in Living Systems, 344006 Rostov-on-Don, Russia;
- Department of Physics, K.G. Razumovsky Moscow State University of Technologies and Management (The First Cossack University), 109004 Moscow, Russia
| | - Stepan Dzhimak
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, 350040 Krasnodar, Russia; (A.K.); (S.K.); (A.B.); (M.B.); (A.E.)
- South Scientific Center of the Russian Academy of Sciences, Laboratory of Problems of Stable Isotope Spreading in Living Systems, 344006 Rostov-on-Don, Russia;
- The V.M. Gorbatov Federal Research Center for Food Systems of the Russian Academy of Sciences, Experimental Clinic—Laboratory of Biologically Active Substances of Animal Origin, 109316 Moscow, Russia
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Abstract
The most frequently mutated metabolic genes in human cancer are those encoding the enzymes isocitrate dehydrogenase 1 (IDH1) and IDH2; these mutations have so far been identified in more than 20 tumor types. Since IDH mutations were first reported in glioma over a decade ago, extensive research has revealed their association with altered cellular processes. Mutations in IDH lead to a change in enzyme function, enabling efficient conversion of 2-oxoglutarate to R-2-hydroxyglutarate (R-2-HG). It is proposed that elevated cellular R-2-HG inhibits enzymes that regulate transcription and metabolism, subsequently affecting nuclear, cytoplasmic, and mitochondrial biochemistry. The significance of these biochemical changes for tumorigenesis and potential for therapeutic exploitation remains unclear. Here we comprehensively review reported direct and indirect metabolic changes linked to IDH mutations and discuss their clinical significance. We also review the metabolic effects of first-generation mutant IDH inhibitors and highlight the potential for combination treatment strategies and new metabolic targets.
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Affiliation(s)
- Ingvild Comfort Hvinden
- Chemistry Research Laboratory, 12 Mansfield Road, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Tom Cadoux-Hudson
- Chemistry Research Laboratory, 12 Mansfield Road, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Christopher J. Schofield
- Chemistry Research Laboratory, 12 Mansfield Road, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
- Ineos Oxford Institute for Antimicrobial Research, 12 Mansfield Road, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - James S.O. McCullagh
- Chemistry Research Laboratory, 12 Mansfield Road, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
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Abstract
With accelerating global warming, understanding the evolutionary dynamics of plant adaptation to environmental change is increasingly urgent. Here, we reveal the enigmatic history of the genus Cochlearia (Brassicaceae), a Pleistocene relic that originated from a drought-adapted Mediterranean sister genus during the Miocene. Cochlearia rapidly diversified and adapted to circum-Arctic regions and other cold-characterized habitat types during the Pleistocene. This sudden change in ecological preferences was accompanied by a highly complex, reticulate polyploid evolution, which was apparently triggered by the impact of repeated Pleistocene glaciation cycles. Our results illustrate that two early diversified Arctic-alpine diploid gene pools contributed differently to the evolution of this young polyploid genus now captured in a cold-adapted niche. Metabolomics revealed central carbon metabolism responses to cold in diverse species and ecotypes, likely due to continuous connections to cold habitats that may have facilitated widespread adaptation to alpine and subalpine habitats, and which we speculate were coopted from existing drought adaptations. Given the growing scientific interest in the adaptive evolution of temperature-related traits, our results provide much-needed taxonomic and phylogenomic resolution of a model system as well as first insights into the origins of its adaptation to cold.
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Affiliation(s)
- Eva Wolf
- Centre for Organismal Studies, University of HeidelbergHeidelbergGermany
| | - Emmanuel Gaquerel
- Centre for Organismal Studies, University of HeidelbergHeidelbergGermany
| | - Mathias Scharmann
- Department of Ecology and Evolution, University of LausanneLausanneSwitzerland
| | - Levi Yant
- Future Food Beacon and School of Life Sciences, the University of NottinghamNottinghamUnited Kingdom
| | - Marcus A Koch
- Centre for Organismal Studies, University of HeidelbergHeidelbergGermany
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Salehipourshirazi G, Bruinsma K, Ratlamwala H, Dixit S, Arbona V, Widemann E, Milojevic M, Jin P, Bensoussan N, Gómez-Cadenas A, Zhurov V, Grbic M, Grbic V. Rapid specialization of counter defenses enables two-spotted spider mite to adapt to novel plant hosts. Plant Physiol 2021; 187:2608-2622. [PMID: 34618096 PMCID: PMC8644343 DOI: 10.1093/plphys/kiab412] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/05/2021] [Indexed: 05/06/2023]
Abstract
Genetic adaptation, occurring over a long evolutionary time, enables host-specialized herbivores to develop novel resistance traits and to efficiently counteract the defenses of a narrow range of host plants. In contrast, physiological acclimation, leading to the suppression and/or detoxification of host defenses, is hypothesized to enable broad generalists to shift between plant hosts. However, the host adaptation mechanisms used by generalists composed of host-adapted populations are not known. Two-spotted spider mite (TSSM; Tetranychus urticae) is an extreme generalist herbivore whose individual populations perform well only on a subset of potential hosts. We combined experimental evolution, Arabidopsis thaliana genetics, mite reverse genetics, and pharmacological approaches to examine mite host adaptation upon the shift of a bean (Phaseolus vulgaris)-adapted population to Arabidopsis. We showed that cytochrome P450 monooxygenases are required for mite adaptation to Arabidopsis. We identified activities of two tiers of P450s: general xenobiotic-responsive P450s that have a limited contribution to mite adaptation to Arabidopsis and adaptation-associated P450s that efficiently counteract Arabidopsis defenses. In approximately 25 generations of mite selection on Arabidopsis plants, mites evolved highly efficient detoxification-based adaptation, characteristic of specialist herbivores. This demonstrates that specialization to plant resistance traits can occur within the ecological timescale, enabling the TSSM to shift to novel plant hosts.
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Affiliation(s)
| | - Kristie Bruinsma
- Department of Biology, The University of Western Ontario, London, Ontario N6A 5B8, Canada
| | - Huzefa Ratlamwala
- Department of Biology, The University of Western Ontario, London, Ontario N6A 5B8, Canada
| | - Sameer Dixit
- Department of Biology, The University of Western Ontario, London, Ontario N6A 5B8, Canada
| | - Vicent Arbona
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castelló de la Plana, E-12071, Spain
| | - Emilie Widemann
- Department of Biology, The University of Western Ontario, London, Ontario N6A 5B8, Canada
| | - Maja Milojevic
- Department of Biology, The University of Western Ontario, London, Ontario N6A 5B8, Canada
| | - Pengyu Jin
- Department of Biology, The University of Western Ontario, London, Ontario N6A 5B8, Canada
| | - Nicolas Bensoussan
- Department of Biology, The University of Western Ontario, London, Ontario N6A 5B8, Canada
| | - Aurelio Gómez-Cadenas
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castelló de la Plana, E-12071, Spain
| | - Vladimir Zhurov
- Department of Biology, The University of Western Ontario, London, Ontario N6A 5B8, Canada
| | - Miodrag Grbic
- Department of Biology, The University of Western Ontario, London, Ontario N6A 5B8, Canada
- Instituto de Ciencias de la Vid y el Vino (CSIC, UR, Gobiernode La Rioja), Logrono 26006, Spain
- Department of Biology, University of Belgrade, Belgrade, Serbia
| | - Vojislava Grbic
- Department of Biology, The University of Western Ontario, London, Ontario N6A 5B8, Canada
- Author for communication:
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21
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Fink G, Venkataramani AS, Zanolini A. Early life adversity, biological adaptation, and human capital: evidence from an interrupted malaria control program in Zambia. J Health Econ 2021; 80:102532. [PMID: 34600186 DOI: 10.1016/j.jhealeco.2021.102532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/25/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
Growing evidence from evolutionary biology demonstrates how early life shocks trigger physiological changes designed to be adaptive in challenging environments. We examine the implications of one type of physiological adaptation - immunity formation - for human capital accumulation. Using variation in early life malaria risk generated by an interrupted disease control program in Zambia, we show that exposure to infectious diseases during the first two years of life can reduce the harmful effects of malaria exposure on cognitive development during the preschool years. These findings suggest a non-linear and trajectory-dependent relationship between early life adversity and human capital formation.
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Affiliation(s)
- Günther Fink
- Swiss Tropical and Public Health Institute and University of Basel, Basel, Switzerland.
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22
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Ding Y, Gardiner DM, Powell JJ, Colgrave ML, Park RF, Kazan K. Adaptive defence and sensing responses of host plant roots to fungal pathogen attack revealed by transcriptome and metabolome analyses. Plant Cell Environ 2021; 44:3526-3544. [PMID: 34591319 DOI: 10.1111/pce.14195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 09/15/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Plant root-produced constitutive and inducible defences inhibit pathogenic microorganisms within roots and in the rhizosphere. However, regulatory mechanisms underlying host responses during root-pathogen interactions are largely unexplored. Using the model species Brachypodium distachyon (Bd), we studied transcriptional and metabolic responses altered in Bd roots following challenge with Fusarium graminearum (Fg), a fungal pathogen that causes diseases in diverse organs of cereal crops. Shared gene expression patterns were found between Bd roots and spikes during Fg infection associated with the mycotoxin deoxynivalenol (DON). Overexpression of BdMYB78, an up-regulated transcription factor, significantly increased root resistance during Fg infection. We show that Bd roots recognize encroaching Fg prior to physical contact by altering transcription of genes associated with multiple cellular processes such as reactive oxygen species and cell development. These changes coincide with altered levels of secreted host metabolites detected by an untargeted metabolomic approach. The secretion of Bd metabolites was suppressed by Fg as enhanced levels of defence-associated metabolites were found in roots during pre-contact with a Fg mutant defective in host perception and the ability to cause disease. Our results help to understand root defence strategies employed by plants, with potential implications for improving the resistance of cereal crops to soil pathogens.
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Affiliation(s)
- Yi Ding
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, St Lucia, Queensland, Australia
- The Plant Breeding Institute, School of Life & Environmental Sciences, Faculty of Science, The University of Sydney, Cobbitty, New South Wales, Australia
| | - Donald M Gardiner
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, St Lucia, Queensland, Australia
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, St Lucia, Queensland, Australia
| | - Jonathan J Powell
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, St Lucia, Queensland, Australia
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, St Lucia, Queensland, Australia
| | - Michelle L Colgrave
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, St Lucia, Queensland, Australia
- Australian Research Council, Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Robert F Park
- The Plant Breeding Institute, School of Life & Environmental Sciences, Faculty of Science, The University of Sydney, Cobbitty, New South Wales, Australia
| | - Kemal Kazan
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, St Lucia, Queensland, Australia
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, St Lucia, Queensland, Australia
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23
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Zhang Z, Guo F, Roy A, Yang J, Luo W, Shen X, Irwin DM, Chen RA, Shen Y. Evolutionary perspectives and adaptation dynamics of human seasonal influenza viruses from 2009 to 2019: An insight from codon usage. Infect Genet Evol 2021; 96:105067. [PMID: 34487866 DOI: 10.1016/j.meegid.2021.105067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/28/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
The annually recurrent seasonal influenza viruses, namely, influenza A viruses (H1N1/pdm2009 and H3N2) and influenza B viruses, contribute substantially to human disease burden. Elucidation of host adaptation, population dynamics and evolutionary patterns of these viruses contribute to better control of current epidemic situation and bolster efforts towards pandemic preparedness. Present study has been addressed at unraveling the signatures of codon usage and dinucleotide distribution of these seasonal influenza viruses associating with their fitness and ongoing adaptive evolution in human population. Thorough analysis of codon usage adaptation revealed that H3N2 has been exhibited best adapted to human cellular system, which correlate with its highest epidemic intensity as compared with the other seasonal influenza viruses. CpG dinucleotide was found to be strongly avoided among the seasonal influenza viruses with more restraint among influenza B viruses than influenza A viruses, and might be accounted to the strategy of the viral pathogens in evading human immune signals. Dynamic scenes of ongoing evolution in codon usage and elimination of CpG motif among the viruses, which correlate with their distinct host adaption state, signifying the marked impact of selective force operational on the viral genomes, aimed at proficient circulation, enhanced fitness and successful infective manifestations in humans.
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Affiliation(s)
- Zhipeng Zhang
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China; Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Fucheng Guo
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Ayan Roy
- Department of Biotechnology, Lovely Professional University, Punjab, India
| | - Jinjin Yang
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Wen Luo
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Xuejuan Shen
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China; Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto M5S 1A8, Canada; Banting and Best Diabetes Centre, University of Toronto, Toronto M5S 1A8, Canada
| | - Rui-Ai Chen
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China; Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Zhaoqing Institute of Biotechnology, Zhaoqing 526238, China.
| | - Yongyi Shen
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China; Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; Zhaoqing Institute of Biotechnology, Zhaoqing 526238, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China.
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Abstract
Sexual selection is considered the major driver for the evolution of sex differences. However, the eco-evolutionary dynamics of sexual selection and their role for a population's adaptive potential to respond to environmental change have only recently been explored. Theory predicts that sexual selection promotes adaptation at a low demographic cost only if sexual selection is aligned with natural selection and if net selection is stronger on males compared to females. We used a comparative approach to show that net selection is indeed stronger in males and provide preliminary support that this sex bias is associated with sexual selection. Given that both sexes share the vast majority of their genes, our findings corroborate the notion that the genome is often confronted with a more stressful environment when expressed in males. Collectively, our study supports one of the long-standing key assumptions required for sexual selection to bolster adaptation, and sexual selection may therefore enable some species to track environmental change more efficiently.
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Affiliation(s)
| | - Maria Moiron
- CEFE, CNRS, Univ Montpellier, EPHE, IRDMontpellierFrance
| | - Edward H Morrow
- Department for Environmental and Life Sciences, Karlstad UniversityKarlstadSweden
| | - Tim Janicke
- Applied Zoology, Technical University DresdenDresdenGermany
- CEFE, CNRS, Univ Montpellier, EPHE, IRDMontpellierFrance
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25
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Fang G, Zhang Q, Chen X, Cao Y, Wang Y, Qi M, Wu N, Qian L, Zhu C, Huang Y, Zhan S. The draft genome of the Asian corn borer yields insights into ecological adaptation of a devastating maize pest. Insect Biochem Mol Biol 2021; 138:103638. [PMID: 34428581 DOI: 10.1016/j.ibmb.2021.103638] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/13/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
The Asian corn borer (ACB) is the most devastating pest on maize in the western Pacific region of Asia. Despite broad interests in insecticide resistance, seasonal adaptation, and larval color mimicry regarding the ACB system, lacking of reference genomic information and a powerful gene editing approach have hindered the in-depth studies of these aspects. Here we present a 455.7 Mb draft genome of ACB with 98.4% completeness. Comparative genomics analysis showed an evident expansion in gene families of gustatory receptors (105), which is related to polyphagous characteristics. Based on the comparative transcriptome analysis of resistant and susceptible ACB against Bt Cry1Ab toxin, we identified 26 genes related to Cry1Ab resistance. Additionally, transcriptomics of insects exposed to conditions of low temperature and diapause (LT) vs. room temperature and diapause (RT) provided insights into the genetic mechanisms of cold adaptation. We also successfully developed an efficient CRISPR/Cas9-based genome editing system and applied it to explore the role of color pattern genes in the ecological adaptation of ACB. Taken together, our study provides a fully annotated high-quality reference genome and efficient gene editing system to realize the potential of ACB as a study system to address important biological questions such as insecticide resistance, seasonal adaptation, and coloration. These valuable genomic resources will also benefit the development of novel strategies for maize pest management.
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Affiliation(s)
- Gangqi Fang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China; CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Qi Zhang
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xi'en Chen
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yanghui Cao
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yaohui Wang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Mengmeng Qi
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China; CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Ningning Wu
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Lansa Qian
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Chenxu Zhu
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yongping Huang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China; CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, 100049, China.
| | - Shuai Zhan
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China; CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, 100049, China.
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26
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Zhou X, Mikaeloff F, Curbo S, Zhao Q, Kuiper R, Végvári Á, Neogi U, Karlsson A. Coordinated pyruvate kinase activity is crucial for metabolic adaptation and cell survival during mitochondrial dysfunction. Hum Mol Genet 2021; 30:2012-2026. [PMID: 34169315 PMCID: PMC8522632 DOI: 10.1093/hmg/ddab168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/26/2021] [Accepted: 06/17/2021] [Indexed: 12/21/2022] Open
Abstract
Deoxyguanosine kinase (DGUOK) deficiency causes mtDNA depletion and mitochondrial dysfunction. We reported long survival of DGUOK knockout (Dguok-/-) mice despite low (<5%) mtDNA content in liver tissue. However, the molecular mechanisms enabling the extended survival remain unknown. Using transcriptomics, proteomics and metabolomics followed by in vitro assays, we aimed to identify the molecular pathways involved in the extended survival of the Dguok-/- mice. At the early stage, the serine synthesis and folate cycle were activated but declined later. Increased activity of the mitochondrial citric acid cycle (TCA cycle) and the urea cycle and degradation of branched chain amino acids were hallmarks of the extended lifespan in DGUOK deficiency. Furthermore, the increased synthesis of TCA cycle intermediates was supported by coordination of two pyruvate kinase genes, PKLR and PKM, indicating a central coordinating role of pyruvate kinases to support the long-term survival in mitochondrial dysfunction.
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Affiliation(s)
- Xiaoshan Zhou
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Karolinska University Hospital, Stockholm 141 86, Sweden
| | - Flora Mikaeloff
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Karolinska University Hospital, Stockholm 141 86, Sweden
| | - Sophie Curbo
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Karolinska University Hospital, Stockholm 141 86, Sweden
| | - Qian Zhao
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Karolinska University Hospital, Stockholm 141 86, Sweden
| | - Raoul Kuiper
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institute, Karolinska University Hospital, Stockholm 141 86, Sweden
| | - Ákos Végvári
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm SE-171 65, Sweden
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Karolinska University Hospital, Stockholm 141 86, Sweden
| | - Anna Karlsson
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Karolinska University Hospital, Stockholm 141 86, Sweden
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27
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Abstract
The human capacity to synchronize movements to an auditory beat is central to musical behaviour and to debates over the evolution of human musicality. Have humans evolved any neural specializations for music processing, or does music rely entirely on brain circuits that evolved for other reasons? The vocal learning and rhythmic synchronization hypothesis proposes that our ability to move in time with an auditory beat in a precise, predictive and tempo-flexible manner originated in the neural circuitry for complex vocal learning. In the 15 years, since the hypothesis was proposed a variety of studies have supported it. However, one study has provided a significant challenge to the hypothesis. Furthermore, it is increasingly clear that vocal learning is not a binary trait animals have or lack, but varies more continuously across species. In the light of these developments and of recent progress in the neurobiology of beat processing and of vocal learning, the current paper revises the vocal learning hypothesis. It argues that an advanced form of vocal learning acts as a preadaptation for sporadic beat perception and synchronization (BPS), providing intrinsic rewards for predicting the temporal structure of complex acoustic sequences. It further proposes that in humans, mechanisms of gene-culture coevolution transformed this preadaptation into a genuine neural adaptation for sustained BPS. The larger significance of this proposal is that it outlines a hypothesis of cognitive gene-culture coevolution which makes testable predictions for neuroscience, cross-species studies and genetics. This article is part of the theme issue 'Synchrony and rhythm interaction: from the brain to behavioural ecology'.
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Affiliation(s)
- Aniruddh D. Patel
- Department of Psychology, Tufts University, Medford, MA, USA
- Program in Brain, Mind, and Consciousness, Canadian Institute for Advanced Research, Toronto, Canada
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28
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Burton NO, Willis A, Fisher K, Braukmann F, Price J, Stevens L, Baugh LR, Reinke A, Miska EA. Intergenerational adaptations to stress are evolutionarily conserved, stress-specific, and have deleterious trade-offs. eLife 2021; 10:e73425. [PMID: 34622777 PMCID: PMC8570697 DOI: 10.7554/elife.73425] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 09/27/2021] [Indexed: 12/24/2022] Open
Abstract
Despite reports of parental exposure to stress promoting physiological adaptations in progeny in diverse organisms, there remains considerable debate over the significance and evolutionary conservation of such multigenerational effects. Here, we investigate four independent models of intergenerational adaptations to stress in Caenorhabditis elegans - bacterial infection, eukaryotic infection, osmotic stress, and nutrient stress - across multiple species. We found that all four intergenerational physiological adaptations are conserved in at least one other species, that they are stress -specific, and that they have deleterious tradeoffs in mismatched environments. By profiling the effects of parental bacterial infection and osmotic stress exposure on progeny gene expression across species, we established a core set of 587 genes that exhibited a greater than twofold intergenerational change in expression in response to stress in C. elegans and at least one other species, as well as a set of 37 highly conserved genes that exhibited a greater than twofold intergenerational change in expression in all four species tested. Furthermore, we provide evidence suggesting that presumed adaptive and deleterious intergenerational effects are molecularly related at the gene expression level. Lastly, we found that none of the effects we detected of these stresses on C. elegans F1 progeny gene expression persisted transgenerationally three generations after stress exposure. We conclude that intergenerational responses to stress play a substantial and evolutionarily conserved role in regulating animal physiology and that the vast majority of the effects of parental stress on progeny gene expression are reversible and not maintained transgenerationally.
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Affiliation(s)
- Nicholas O Burton
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of CambridgeCambridgeUnited Kingdom
- Gurdon Institute, University of CambridgeCambridgeUnited Kingdom
- Van Andel InstituteGrand RapidsUnited States
| | - Alexandra Willis
- Department of Molecular Genetics, University of TorontoTorontoCanada
| | - Kinsey Fisher
- Department of Biology, Duke UniversityDurhamUnited States
| | - Fabian Braukmann
- Gurdon Institute, University of CambridgeCambridgeUnited Kingdom
| | - Jonathan Price
- Gurdon Institute, University of CambridgeCambridgeUnited Kingdom
| | - Lewis Stevens
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
- Wellcome Sanger Institute, Wellcome Genome CampusCambridgeUnited Kingdom
| | - L Ryan Baugh
- Department of Biology, Duke UniversityDurhamUnited States
- Center for Genomic and Computational Biology, Duke UniversityDurhamUnited States
| | - Aaron Reinke
- Department of Molecular Genetics, University of TorontoTorontoCanada
| | - Eric A Miska
- Gurdon Institute, University of CambridgeCambridgeUnited Kingdom
- Wellcome Sanger Institute, Wellcome Genome CampusCambridgeUnited Kingdom
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
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29
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Walker B, Segovia Martín J, Tamariz M, Fay N. Maintenance of prior behaviour can enhance cultural selection. Sci Rep 2021; 11:19897. [PMID: 34615959 PMCID: PMC8494921 DOI: 10.1038/s41598-021-99340-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/21/2021] [Indexed: 11/25/2022] Open
Abstract
Many cultural phenomena evolve through a Darwinian process whereby adaptive variants are selected and spread at the expense of competing variants. While cultural evolutionary theory emphasises the importance of social learning to this process, experimental studies indicate that people's dominant response is to maintain their prior behaviour. In addition, while payoff-biased learning is crucial to Darwinian cultural evolution, learner behaviour is not always guided by variant payoffs. Here, we use agent-based modelling to investigate the role of maintenance in Darwinian cultural evolution. We vary the degree to which learner behaviour is payoff-biased (i.e., based on critical evaluation of variant payoffs), and compare three uncritical (non-payoff-biased) strategies that are used alongside payoff-biased learning: copying others, innovating new variants, and maintaining prior variants. In line with previous research, we show that some level of payoff-biased learning is crucial for populations to converge on adaptive cultural variants. Importantly, when combined with payoff-biased learning, uncritical maintenance leads to stronger population-level adaptation than uncritical copying or innovation, highlighting the importance of maintenance to cultural selection. This advantage of maintenance as a default learning strategy may help explain why it is a common human behaviour.
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Affiliation(s)
- Bradley Walker
- School of Psychological Science, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - José Segovia Martín
- Centre National de la Recherche Scientifique (CNRS), Institut des Systèmes Complexes Paris Île-de-France (ISC-PIF), Paris, France
| | - Monica Tamariz
- Department of Psychology, Heriot-Watt University, Edinburgh, UK
| | - Nicolas Fay
- School of Psychological Science, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
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30
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Mertens D, Fernández de Bobadilla M, Rusman Q, Bloem J, Douma JC, Poelman EH. Plant defence to sequential attack is adapted to prevalent herbivores. Nat Plants 2021; 7:1347-1353. [PMID: 34650263 DOI: 10.1038/s41477-021-00999-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/02/2021] [Indexed: 05/21/2023]
Abstract
Plants have evolved plastic defence strategies to deal with the uncertainty of when, by which species and in which order attack by herbivores will take place1-3. However, the responses to current herbivore attack may come with a cost of compromising resistance to other, later arriving herbivores. Due to antagonistic cross-talk between physiological regulation of plant resistance to phloem-feeding and leaf-chewing herbivores4-8, the feeding guild of the initial herbivore is considered to be the primary factor determining whether resistance to subsequent attack is compromised. We show that, by investigating 90 pairwise insect-herbivore interactions among ten different herbivore species, resistance of the annual plant Brassica nigra to a later arriving herbivore species is not explained by feeding guild of the initial attacker. Instead, the prevalence of herbivore species that arrive on induced plants as approximated by three years of season-long insect community assessments in the field explained cross-resistance. Plants maintained resistance to prevalent herbivores in common patterns of herbivore arrival and compromises in resistance especially occurred for rare patterns of herbivore attack. We conclude that plants tailor induced defence strategies to deal with common patterns of sequential herbivore attack and anticipate arrival of the most prevalent herbivores.
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Affiliation(s)
- Daan Mertens
- Laboratory of Entomology, Wageningen University, Wageningen, the Netherlands
| | | | - Quint Rusman
- Laboratory of Entomology, Wageningen University, Wageningen, the Netherlands
| | - Janneke Bloem
- Laboratory of Entomology, Wageningen University, Wageningen, the Netherlands
| | - Jacob C Douma
- Centre for Crop Systems Analysis, Wageningen University, Wageningen, the Netherlands
| | - Erik H Poelman
- Laboratory of Entomology, Wageningen University, Wageningen, the Netherlands.
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Artur MAS, Kajala K. Convergent evolution of gene regulatory networks underlying plant adaptations to dry environments. Plant Cell Environ 2021; 44:3211-3222. [PMID: 34196969 PMCID: PMC8518057 DOI: 10.1111/pce.14143] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 06/25/2021] [Indexed: 05/21/2023]
Abstract
Plants transitioned from an aquatic to a terrestrial lifestyle during their evolution. On land, fluctuations on water availability in the environment became one of the major problems they encountered. The appearance of morpho-physiological adaptations to cope with and tolerate water loss from the cells was undeniably useful to survive on dry land. Some of these adaptations, such as carbon concentrating mechanisms (CCMs), desiccation tolerance (DT) and root impermeabilization, appeared in multiple plant lineages. Despite being crucial for evolution on land, it has been unclear how these adaptations convergently evolved in the various plant lineages. Recent advances on whole genome and transcriptome sequencing are revealing that co-option of genes and gene regulatory networks (GRNs) is a common feature underlying the convergent evolution of these adaptations. In this review, we address how the study of CCMs and DT has provided insight into convergent evolution of GRNs underlying plant adaptation to dry environments, and how these insights could be applied to currently emerging understanding of evolution of root impermeabilization through different barrier cell types. We discuss examples of co-option, conservation and innovation of genes and GRNs at the cell, tissue and organ levels revealed by recent phylogenomic (comparative genomic) and comparative transcriptomic studies.
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Affiliation(s)
- Mariana A. S. Artur
- Laboratory of Plant PhysiologyWageningen UniversityWageningenThe Netherlands
- Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrechtThe Netherlands
| | - Kaisa Kajala
- Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrechtThe Netherlands
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32
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Gericke O, Fowler RM, Heskes AM, Bayly MJ, Semple SJ, Ndi CP, Stærk D, Løland CJ, Murphy DJ, Buirchell BJ, Møller BL. Navigating through chemical space and evolutionary time across the Australian continent in plant genus Eremophila. Plant J 2021; 108:555-578. [PMID: 34324744 PMCID: PMC9292440 DOI: 10.1111/tpj.15448] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/07/2021] [Accepted: 07/22/2021] [Indexed: 05/13/2023]
Abstract
Eremophila is the largest genus in the plant tribe Myoporeae (Scrophulariaceae) and exhibits incredible morphological diversity across the Australian continent. The Australian Aboriginal Peoples recognize many Eremophila species as important sources of traditional medicine, the most frequently used plant parts being the leaves. Recent phylogenetic studies have revealed complex evolutionary relationships between Eremophila and related genera in the tribe. Unique and structurally diverse metabolites, particularly diterpenoids, are also a feature of plants in this group. To assess the full dimension of the chemical space of the tribe Myoporeae, we investigated the metabolite diversity in a chemo-evolutionary framework applying a combination of molecular phylogenetic and state-of-the-art computational metabolomics tools to build a dataset involving leaf samples from a total of 291 specimens of Eremophila and allied genera. The chemo-evolutionary relationships are expounded into a systematic context by integration of information about leaf morphology (resin and hairiness), environmental factors (pollination and geographical distribution), and medicinal properties (traditional medicinal uses and antibacterial studies), augmenting our understanding of complex interactions in biological systems.
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Affiliation(s)
- Oliver Gericke
- Plant Biochemistry LaboratoryDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDK‐1871Denmark
| | - Rachael M. Fowler
- School of BioSciencesThe University of MelbourneParkvilleVic.3010Australia
| | - Allison M. Heskes
- Plant Biochemistry LaboratoryDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDK‐1871Denmark
| | - Michael J. Bayly
- School of BioSciencesThe University of MelbourneParkvilleVic.3010Australia
| | - Susan J. Semple
- Quality Use of Medicines and Pharmacy Research CentreSchool of Pharmacy and Medical SciencesUniversity of South AustraliaAdelaideSA5000Australia
| | - Chi P. Ndi
- Quality Use of Medicines and Pharmacy Research CentreSchool of Pharmacy and Medical SciencesUniversity of South AustraliaAdelaideSA5000Australia
| | - Dan Stærk
- Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDK‐2100Denmark
| | - Claus J. Løland
- Department of NeuroscienceFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDK‐2100Denmark
| | | | | | - Birger Lindberg Møller
- Plant Biochemistry LaboratoryDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDK‐1871Denmark
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Bakerlee CW, Phillips AM, Nguyen Ba AN, Desai MM. Dynamics and variability in the pleiotropic effects of adaptation in laboratory budding yeast populations. eLife 2021; 10:e70918. [PMID: 34596043 PMCID: PMC8579951 DOI: 10.7554/elife.70918] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/29/2021] [Indexed: 12/15/2022] Open
Abstract
Evolutionary adaptation to a constant environment is driven by the accumulation of mutations which can have a range of unrealized pleiotropic effects in other environments. These pleiotropic consequences of adaptation can influence the emergence of specialists or generalists, and are critical for evolution in temporally or spatially fluctuating environments. While many experiments have examined the pleiotropic effects of adaptation at a snapshot in time, very few have observed the dynamics by which these effects emerge and evolve. Here, we propagated hundreds of diploid and haploid laboratory budding yeast populations in each of three environments, and then assayed their fitness in multiple environments over 1000 generations of evolution. We find that replicate populations evolved in the same condition share common patterns of pleiotropic effects across other environments, which emerge within the first several hundred generations of evolution. However, we also find dynamic and environment-specific variability within these trends: variability in pleiotropic effects tends to increase over time, with the extent of variability depending on the evolution environment. These results suggest shifting and overlapping contributions of chance and contingency to the pleiotropic effects of adaptation, which could influence evolutionary trajectories in complex environments that fluctuate across space and time.
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Affiliation(s)
- Christopher W Bakerlee
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Angela M Phillips
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Alex N Nguyen Ba
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Department of Cell and Systems Biology, University of TorontoTorontoCanada
| | - Michael M Desai
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Department of Physics, Harvard University, CambridgeCambridgeUnited States
- NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard UniversityCambridgeUnited States
- Quantitative Biology Initiative, Harvard University, CambridgeCambridgeUnited States
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34
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Wang Y, Xu C, Sun J, Dong L, Li M, Liu Y, Wang J, Zhang X, Li D, Sun J, Zhang Y, Shan J, Li W, Zhao L. GmRAV confers ecological adaptation through photoperiod control of flowering time and maturity in soybean. Plant Physiol 2021; 187:361-377. [PMID: 34618136 PMCID: PMC8418415 DOI: 10.1093/plphys/kiab255] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/12/2021] [Indexed: 05/31/2023]
Abstract
Photoperiod strictly controls vegetative and reproductive growth stages in soybean (Glycine max). A soybean GmRAV (Related to ABI3/VP1) transcription factor containing both AP2 and B3 domains was shown to be a key component of this process. We identified six polymorphisms in the GmRAV promoter that showed significant association with flowering time and maturity of soybean in one or multiple environments. Soybean varieties with minor polymorphism exhibited a longer growth period contributing to soybean adaptation to lower latitudes. The cis-acting element GT1CONSENSUS motif of the GmRAV promoter controlled the growth period, and the major allele in this motif shortened duration of late reproductive stages by reducing GmRAV expression levels. Three GmRAV-overexpressing (GmRAV-ox) transgenic lines displayed later flowering time and maturity, shorter height and fewer numbers of leaves compared with control plants, whereas transgenic inhibition of GmRAV expression resulted in earlier flowering time and maturity and increased plant height. Combining DNA affinity purification sequencing and RNA sequencing analyses revealed 154 putative target genes directly bound and transcriptionally regulated by GmRAV. Two GmRAV binding motifs [C(A/G)AACAA(G/T)A(C/T)A(G/T)] and [C(T/A)A(C)C(T/G)CTG] were identified, and acting downstream of E3E4, GmRAV repressed GmFT5a transcriptional activity through binding a CAACA motif, thereby delaying soybean growth and extending both vegetative and reproductive phases.
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Affiliation(s)
- Yuhe Wang
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Chongjing Xu
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Jiafan Sun
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Lidong Dong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Minmin Li
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Ying Liu
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Jianhui Wang
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Xiaoming Zhang
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Dongmei Li
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Jingzhe Sun
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Yuntong Zhang
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Jinming Shan
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Wenbin Li
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Lin Zhao
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
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Blumstein M, Hopkins R. Adaptive variation and plasticity in non-structural carbohydrate storage in a temperate tree species. Plant Cell Environ 2021; 44:2494-2505. [PMID: 33244757 DOI: 10.1111/pce.13959] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 11/16/2020] [Accepted: 11/20/2020] [Indexed: 06/11/2023]
Abstract
Trees' total amount of non-structural carbohydrate (NSC) stores and the proportion of these stores residing as insoluble starch are vital traits for individuals living in variable environments. However, our understanding of how stores vary in response to environmental stress is poorly understood as the genetic component of storage is rarely accounted for in studies. Here, we quantified variation in NSC traits in branch samples taken from over 600 clonally transplanted black cottonwood (Populus trichocarpa) trees grown in two common gardens. We found heritable variation in both total NSC stores and the proportion of stores in starch (H2TNC = 0.19, H2PropStarch = 0.31), indicating a substantial genetic component of variation. In addition, we found high amounts of plasticity in both traits in response to cold temperatures and significant genotype-by-environment (GxE) interactions in the total amount of NSC stored (54% of P is GxE). This finding of high GxE indicates extensive variation across trees in their response to environment, which may explain why previous studies of carbohydrate stores' responses to stress have failed to converge on a consistent pattern. Overall, we found high amounts of environmental and genetic variation in NSC storage concentrations, which may bolster species against future climate change.
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Affiliation(s)
- Meghan Blumstein
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Robin Hopkins
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- The Arnold Arboretum, Boston, Massachusetts, USA
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36
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Bhattacharya T, Rice DW, Crawford JM, Hardy RW, Newton ILG. Evidence of Adaptive Evolution in Wolbachia-Regulated Gene DNMT2 and Its Role in the Dipteran Immune Response and Pathogen Blocking. Viruses 2021; 13:1464. [PMID: 34452330 PMCID: PMC8402854 DOI: 10.3390/v13081464] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/09/2021] [Accepted: 07/09/2021] [Indexed: 12/23/2022] Open
Abstract
Eukaryotic nucleic acid methyltransferase (MTase) proteins are essential mediators of epigenetic and epitranscriptomic regulation. DNMT2 belongs to a large, conserved family of DNA MTases found in many organisms, including holometabolous insects such as fruit flies and mosquitoes, where it is the lone MTase. Interestingly, despite its nomenclature, DNMT2 is not a DNA MTase, but instead targets and methylates RNA species. A growing body of literature suggests that DNMT2 mediates the host immune response against a wide range of pathogens, including RNA viruses. Curiously, although DNMT2 is antiviral in Drosophila, its expression promotes virus replication in mosquito species. We, therefore, sought to understand the divergent regulation, function, and evolution of these orthologs. We describe the role of the Drosophila-specific host protein IPOD in regulating the expression and function of fruit fly DNMT2. Heterologous expression of these orthologs suggests that DNMT2's role as an antiviral is host-dependent, indicating a requirement for additional host-specific factors. Finally, we identify and describe potential evidence of positive selection at different times throughout DNMT2 evolution within dipteran insects. We identify specific codons within each ortholog that are under positive selection and find that they are restricted to four distinct protein domains, which likely influence substrate binding, target recognition, and adaptation of unique intermolecular interactions. Collectively, our findings highlight the evolution of DNMT2 in Dipteran insects and point to structural, regulatory, and functional differences between mosquito and fruit fly homologs.
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Affiliation(s)
- Tamanash Bhattacharya
- Department of Biology, Indiana University Bloomington, Bloomington, IN 47405, USA; (T.B.); (D.W.R.); (J.M.C.)
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Danny W. Rice
- Department of Biology, Indiana University Bloomington, Bloomington, IN 47405, USA; (T.B.); (D.W.R.); (J.M.C.)
| | - John M. Crawford
- Department of Biology, Indiana University Bloomington, Bloomington, IN 47405, USA; (T.B.); (D.W.R.); (J.M.C.)
| | - Richard W. Hardy
- Department of Biology, Indiana University Bloomington, Bloomington, IN 47405, USA; (T.B.); (D.W.R.); (J.M.C.)
| | - Irene L. G. Newton
- Department of Biology, Indiana University Bloomington, Bloomington, IN 47405, USA; (T.B.); (D.W.R.); (J.M.C.)
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37
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Machado HE, Bergland AO, Taylor R, Tilk S, Behrman E, Dyer K, Fabian DK, Flatt T, González J, Karasov TL, Kim B, Kozeretska I, Lazzaro BP, Merritt TJS, Pool JE, O'Brien K, Rajpurohit S, Roy PR, Schaeffer SW, Serga S, Schmidt P, Petrov DA. Broad geographic sampling reveals the shared basis and environmental correlates of seasonal adaptation in Drosophila. eLife 2021; 10:e67577. [PMID: 34155971 PMCID: PMC8248982 DOI: 10.7554/elife.67577] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/21/2021] [Indexed: 11/16/2022] Open
Abstract
To advance our understanding of adaptation to temporally varying selection pressures, we identified signatures of seasonal adaptation occurring in parallel among Drosophila melanogaster populations. Specifically, we estimated allele frequencies genome-wide from flies sampled early and late in the growing season from 20 widely dispersed populations. We identified parallel seasonal allele frequency shifts across North America and Europe, demonstrating that seasonal adaptation is a general phenomenon of temperate fly populations. Seasonally fluctuating polymorphisms are enriched in large chromosomal inversions, and we find a broad concordance between seasonal and spatial allele frequency change. The direction of allele frequency change at seasonally variable polymorphisms can be predicted by weather conditions in the weeks prior to sampling, linking the environment and the genomic response to selection. Our results suggest that fluctuating selection is an important evolutionary force affecting patterns of genetic variation in Drosophila.
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Affiliation(s)
- Heather E Machado
- Department of Biology, Stanford UniversityStanfordUnited States
- Wellcome Sanger InstituteHinxtonUnited Kingdom
| | - Alan O Bergland
- Department of Biology, Stanford UniversityStanfordUnited States
- Department of Biology, University of VirginiaCharlottesvilleUnited States
| | - Ryan Taylor
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Susanne Tilk
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Emily Behrman
- Department of Biology, University of PennsylvaniaPhiladelphiaUnited States
| | - Kelly Dyer
- Department of Genetics, University of GeorgiaAthensUnited States
| | - Daniel K Fabian
- Institute of Population Genetics, Vetmeduni ViennaViennaAustria
- Centre for Pathogen Evolution, Department of Zoology, University of CambridgeCambridgeUnited Kingdom
| | - Thomas Flatt
- Institute of Population Genetics, Vetmeduni ViennaViennaAustria
- Department of Biology, University of FribourgFribourgSwitzerland
| | - Josefa González
- Institute of Evolutionary Biology, CSIC- Universitat Pompeu FabraBarcelonaSpain
| | - Talia L Karasov
- Department of Biology, University of UtahSalt Lake CityUnited States
| | - Bernard Kim
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Iryna Kozeretska
- Taras Shevchenko National University of KyivKyivUkraine
- National Antarctic Scientific Centre of Ukraine, Taras Shevchenko Blvd.KyivUkraine
| | - Brian P Lazzaro
- Department of Entomology, Cornell UniversityIthacaUnited States
| | - Thomas JS Merritt
- Department of Chemistry & Biochemistry, Laurentian UniversitySudburyCanada
| | - John E Pool
- Laboratory of Genetics, University of Wisconsin-MadisonMadisonUnited States
| | - Katherine O'Brien
- Department of Biology, University of PennsylvaniaPhiladelphiaUnited States
| | - Subhash Rajpurohit
- Department of Biology, University of PennsylvaniaPhiladelphiaUnited States
| | - Paula R Roy
- Department of Ecology and Evolutionary Biology, University of KansasLawrenceUnited States
| | - Stephen W Schaeffer
- Department of Biology, The Pennsylvania State UniversityUniversity ParkUnited States
| | - Svitlana Serga
- Taras Shevchenko National University of KyivKyivUkraine
- National Antarctic Scientific Centre of Ukraine, Taras Shevchenko Blvd.KyivUkraine
| | - Paul Schmidt
- Department of Biology, University of PennsylvaniaPhiladelphiaUnited States
| | - Dmitri A Petrov
- Department of Biology, Stanford UniversityStanfordUnited States
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Abstract
Epigenetics is the study of changes in gene activity that can be transmitted through cell divisions but cannot be explained by changes in the DNA sequence. Epigenetic mechanisms are central to gene regulation, phenotypic plasticity, development and the preservation of genome integrity. Epigenetic mechanisms are often held to make a minor contribution to evolutionary change because epigenetic states are typically erased and reset at every generation, and are therefore, not heritable. Nonetheless, there is growing appreciation that epigenetic variation makes direct and indirect contributions to evolutionary processes. First, some epigenetic states are transmitted intergenerationally and affect the phenotype of offspring. Moreover, bona fide heritable 'epialleles' exist and are quite common in plants. Such epialleles could, therefore, be subject to natural selection in the same way as conventional DNA sequence-based alleles. Second, epigenetic variation enhances phenotypic plasticity and phenotypic variance and thus can modulate the effect of natural selection on sequence-based genetic variation. Third, given that phenotypic plasticity is central to the adaptability of organisms, epigenetic mechanisms that generate plasticity and acclimation are important to consider in evolutionary theory. Fourth, some genes are under selection to be 'imprinted' identifying the sex of the parent from which they were derived, leading to parent-of-origin-dependent gene expression and effects. These effects can generate hybrid disfunction and contribute to speciation. Finally, epigenetic processes, particularly DNA methylation, contribute directly to DNA sequence evolution, because they act as mutagens on the one hand and modulate genome stability on the other by keeping transposable elements in check. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Alyson Ashe
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Vincent Colot
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Ecole Normale Supérieure, PSL Research University, 75005 Paris, France
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Abstract
The aim of this article is to put the growing interest in epigenetics in the field of evolutionary theory into a historical context. First, I assess the view that epigenetic inheritance could be seen as vindicating a revival of (neo)Lamarckism. Drawing on Jablonka's and Lamb's considerable output, I identify several differences between modern epigenetics and what Lamarckism was in the history of science. Even if Lamarckism is not back, epigenetic inheritance might be appealing for evolutionary biologists because it could potentiate two neglected mechanisms: the Baldwin effect and genetic assimilation. Second, I go back to the first ideas about the Baldwin effect developed in the late nineteenth century to show that the efficiency of this mechanism was already linked with a form of non-genetic inheritance. The opposition to all forms of non-genetic inheritance that prevailed at the time of the rise of the Modern Synthesis helps to explain why the Baldwin effect was understood as an insignificant mechanism during the second half of the twentieth century. Based on this historical reconstruction, in §4, I examine what modern epigenetics can bring to the picture and under what conditions epigenetic inheritance might be seen as strengthening the causal relationship between adaptability and adaptation. Throughout I support the view that the Baldwin effect and genetic assimilation, even if they are quite close, should not be conflated, and that drawing a line between these concepts is helpful in order to better understand where epigenetic inheritance might endorse a new causal role. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Laurent Loison
- Institut d'Histoire et de Philsophie des Sciences et des Techniques (CNRS, Université Paris 1 Panthéon-Sorbonne), 13 rue du Four, 75006 Paris, France
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Rittschof CC, Nieh JC. Honey robbing: could human changes to the environment transform a rare foraging tactic into a maladaptive behavior? Curr Opin Insect Sci 2021; 45:84-90. [PMID: 33601060 DOI: 10.1016/j.cois.2021.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/22/2021] [Accepted: 02/05/2021] [Indexed: 06/12/2023]
Abstract
Human environmental modifications have outpaced honey bees' ability to evolve adaptive regulation of foraging tactics, possibly including a tactic associated with extreme food shortage, honey robbing. Honey robbing is a high risk, high reward, and understudied honey bee tactic whereby workers attack and often kill neighboring colonies to steal honey. Humans have exacerbated the conditions that provoke such robbing and its consequences. We describe robbing as an individual-level and colony-level behavioral syndrome, implicating worker bees specialized for foraging, food processing, and defense. We discuss how colony signaling mechanisms could regulate this syndrome and then explore the ecological underpinnings of robbing-highlighting its unusual prevalence in the commonly managed Apis mellifera and outlining the conditions that provoke robbing. We advocate for studies that identify the cues that modulate this robbing syndrome. Additionally, studies that apply behavioral ecology modeling approaches to generate testable predictions about robbing could clarify basic bee biology and have practical implications for colony management.
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Affiliation(s)
- Clare C Rittschof
- University of Kentucky, Department of Entomology, S-225 Agriculture Science Center North Lexington, KY, 40546, United States.
| | - James C Nieh
- University of California, San Diego, Division of Biological Sciences, 9500 Gilman Drive, MC 0116, La Jolla, CA 92093-0116, United States
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41
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Zheng X, Zhu L, He G. Genetic and molecular understanding of host rice resistance and Nilaparvata lugens adaptation. Curr Opin Insect Sci 2021; 45:14-20. [PMID: 33227482 DOI: 10.1016/j.cois.2020.11.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/08/2020] [Accepted: 11/11/2020] [Indexed: 06/11/2023]
Abstract
The variability of brown planthopper (BPH) populations and diversity of the host rice germplasm provide an ideal model for exploring the genetic and molecular basis of insect-plant interactions. During the long-term evolutionary arms race, complicated feeding and defense strategies have developed in BPH and rice. Nine major BPH resistance genes have been cloned and the exploration of BPH resistance genes medicated mechanism against BPH shed a light on the molecular basis of the rice-BPH interaction. This short review provides an update on our current understanding of the genetic and molecular mechanism for rice resistance and BPH adaptation. Understanding the interactions between BPH and rice will provide novel insights for sustainable control of this pest.
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Affiliation(s)
- Xiaohong Zheng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Lili Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Guangcun He
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China.
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Leith NT, Macchiano A, Moore MP, Fowler-Finn KD. Temperature impacts all behavioral interactions during insect and arachnid reproduction. Curr Opin Insect Sci 2021; 45:106-114. [PMID: 33831604 DOI: 10.1016/j.cois.2021.03.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/17/2021] [Accepted: 03/23/2021] [Indexed: 05/26/2023]
Abstract
Temperature shapes the processes and outcomes of behaviors that occur throughout the progression of insect and arachnid mating interactions and reproduction. Here, we highlight how temperature impacts precopulatory activity levels, competition among rivals, communication with potential mates, and the relative costs and benefits of mating. We review how both the prevailing temperature conditions during reproductive activity and the temperatures experienced early in life influence mating-related behavior. To effectively predict the consequences of global warming for insect and arachnid mating behavior, we advocate for future work that universally integrates a function-valued approach to measuring thermal sensitivity. A function-valued approach will be especially useful for understanding how fine-scale temperature variation shapes current and future selection on mating interactions.
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Affiliation(s)
- Noah T Leith
- Department of Biology, Saint Louis University, United States.
| | | | - Michael P Moore
- Living Earth Collaborative, Washington University in St. Louis, United States
| | - Kasey D Fowler-Finn
- Department of Biology, Saint Louis University, United States; Living Earth Collaborative, Washington University in St. Louis, United States
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43
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Haynes KJ, Robertson BA. A transdisciplinary research agenda for understanding insect responses to ecological light pollution informed by evolutionary trap theory. Curr Opin Insect Sci 2021; 45:91-96. [PMID: 33601058 DOI: 10.1016/j.cois.2021.02.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/18/2020] [Accepted: 02/04/2021] [Indexed: 06/12/2023]
Abstract
Evolutionary traps are phenomena in which rapid environmental change causes environmental cues that historically guided adaptive behavioral or life-history decisions to become poor predictors of the consequences of such decisions for an organism's fitness. Evolutionary trap theory offers an ideal framework for understanding and mitigating the effects of ecological light pollution (ELP) on insects. We emphasize the utility of an evolutionary trap perspective in demonstrating the importance of an integrated understanding of the sensory, behavioral, evolutionary, and demographic mechanisms underlying insect responses to ELP. We also highlight neglected areas of research where greater focus can help enhance understanding of how ELP affects the persistence, evolutionary trajectory, and population dynamics of insects across space and time.
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Affiliation(s)
- Kyle J Haynes
- Blandy Experimental Farm, University of Virginia, 400 Blandy Farm Lane, Boyce, VA, 22620, USA.
| | - Bruce A Robertson
- Division of Science, Mathematics and Computing, Bard College, Annandale-on-Hudson, New York 12504, USA
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Schmitt L, Burghardt KT. Urbanization as a disrupter and facilitator of insect herbivore behaviors and life cycles. Curr Opin Insect Sci 2021; 45:97-105. [PMID: 33676055 DOI: 10.1016/j.cois.2021.02.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/18/2021] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
Insect herbivores require a variety of habitats across their life cycle, with behavior often mediating transitions between life stages or habitats. Human management strongly alters urban habitats, yet herbivore behavior is rarely examined in cities. We review the existing literature on several key behaviors: host finding, feeding, egg placement and pupation location, and antipredator defense. We emphasize that unapparent portions of the life cycle, such as the habitat of the overwintering stage, may influence if urbanized areas act as population sources or sinks. Here, management of the soil surface and aboveground biomass are two areas with especially pressing research gaps. Lastly, high variability in urban environments may select for more plastic behaviors or greater generalism. We encourage future research that assesses both behavior and less apparent portions of insect life cycles to determine best practices for conservation and management.
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Affiliation(s)
- Lauren Schmitt
- Department of Entomology, University of Maryland, College Park, MD 20742, USA
| | - Karin T Burghardt
- Department of Entomology, University of Maryland, College Park, MD 20742, USA.
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Szewczyk-Golec K, Pawłowska M, Wesołowski R, Wróblewski M, Mila-Kierzenkowska C. Oxidative Stress as a Possible Target in the Treatment of Toxoplasmosis: Perspectives and Ambiguities. Int J Mol Sci 2021; 22:ijms22115705. [PMID: 34071892 PMCID: PMC8198901 DOI: 10.3390/ijms22115705] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 12/16/2022] Open
Abstract
Toxoplasma gondii is an apicomplexan parasite causing toxoplasmosis, a common disease, which is most typically asymptomatic. However, toxoplasmosis can be severe and even fatal in immunocompromised patients and fetuses. Available treatment options are limited, so there is a strong impetus to develop novel therapeutics. This review focuses on the role of oxidative stress in the pathophysiology and treatment of T. gondii infection. Chemical compounds that modify redox status can reduce the parasite viability and thus be potential anti-Toxoplasma drugs. On the other hand, oxidative stress caused by the activation of the inflammatory response may have some deleterious consequences in host cells. In this respect, the potential use of natural antioxidants is worth considering, including melatonin and some vitamins, as possible novel anti-Toxoplasma therapeutics. Results of in vitro and animal studies are promising. However, supplementation with some antioxidants was found to promote the increase in parasitemia, and the disease was then characterized by a milder course. Undoubtedly, research in this area may have a significant impact on the future prospects of toxoplasmosis therapy.
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Calcino AD, Kenny NJ, Gerdol M. Single individual structural variant detection uncovers widespread hemizygosity in molluscs. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200153. [PMID: 33813894 PMCID: PMC8059565 DOI: 10.1098/rstb.2020.0153] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2021] [Indexed: 11/12/2022] Open
Abstract
The advent of complete genomic sequencing has opened a window into genomic phenomena obscured by fragmented assemblies. A good example of these is the existence of hemizygous regions of autosomal chromosomes, which can result in marked differences in gene content between individuals within species. While these hemizygous regions, and presence/absence variation of genes that can result, are well known in plants, firm evidence has only recently emerged for their existence in metazoans. Here, we use recently published, complete genomes from wild-caught molluscs to investigate the prevalence of hemizygosity across a well-known and ecologically important clade. We show that hemizygous regions are widespread in mollusc genomes, not clustered in individual chromosomes, and often contain genes linked to transposition, DNA repair and stress response. With targeted investigations of HSP70-12 and C1qDC, we also show how individual gene families are distributed within pan-genomes. This work suggests that extensive pan-genomes are widespread across the conchiferan Mollusca, and represent useful tools for genomic evolution, allowing the maintenance of additional genetic diversity within the population. As genomic sequencing and re-sequencing becomes more routine, the prevalence of hemizygosity, and its impact on selection and adaptation, are key targets for research across the tree of life. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
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Affiliation(s)
- Andrew D. Calcino
- Department of Evolutionary Biology, Integrative Zoology, University of Vienna, Althanstrasse 14, Vienna 1090, Austria
| | - Nathan J. Kenny
- Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
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Gonzalez BC, Martínez A, Worsaae K, Osborn KJ. Morphological convergence and adaptation in cave and pelagic scale worms (Polynoidae, Annelida). Sci Rep 2021; 11:10718. [PMID: 34021174 PMCID: PMC8139957 DOI: 10.1038/s41598-021-89459-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/27/2021] [Indexed: 02/07/2023] Open
Abstract
Across Annelida, accessing the water column drives morphological and lifestyle modifications-yet in the primarily "benthic" scale worms, the ecological significance of swimming has largely been ignored. We investigated genetic, morphological and behavioural adaptations associated with swimming across Polynoidae, using mitogenomics and comparative methods. Mitochondrial genomes from cave and pelagic polynoids were highly similar, with non-significant rearrangements only present in cave Gesiella. Gene orders of the new mitogenomes were highly similar to shallow water species, suggestive of an underlying polynoid ground pattern. Being the first phylogenetic analyses to include the holopelagic Drieschia, we recovered this species nested among shallow water terminals, suggesting a shallow water ancestry. Based on these results, our phylogenetic reconstructions showed that swimming evolved independently three times in Polynoidae, involving convergent adaptations in morphology and motility patterns across the deep sea (Branchipolynoe), midwater (Drieschia) and anchialine caves (Pelagomacellicephala and Gesiella). Phylogenetic generalized least-squares (PGLS) analyses showed that holopelagic and anchialine cave species exhibit hypertrophy of the dorsal cirri, yet, these morphological modifications are achieved along different evolutionary pathways, i.e., elongation of the cirrophore versus style. Together, these findings suggest that a water column lifestyle elicits similar morphological adaptations, favouring bodies designed for drifting and sensing.
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Affiliation(s)
- Brett C Gonzalez
- Department of Invertebrate Zoology, Smithsonian Institution, National Museum of Natural History, P.O. Box 37012, Washington, DC, USA.
| | - Alejandro Martínez
- Molecular Ecology Group (MEG), Water Research Institute (IRSA), National Research Council of Italy (CNR), Largo Tonolli, 50, Pallanza, Italy
| | - Katrine Worsaae
- Marine Biological Section, Department of Biology, University of Copenhagen, Universitetsparken 4, Copenhagen Ø, Denmark
| | - Karen J Osborn
- Department of Invertebrate Zoology, Smithsonian Institution, National Museum of Natural History, P.O. Box 37012, Washington, DC, USA
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA, USA
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Durkin SM, Chakraborty M, Abrieux A, Lewald KM, Gadau A, Svetec N, Peng J, Kopyto M, Langer CB, Chiu JC, Emerson JJ, Zhao L. Behavioral and Genomic Sensory Adaptations Underlying the Pest Activity of Drosophila suzukii. Mol Biol Evol 2021; 38:2532-2546. [PMID: 33586767 PMCID: PMC8136512 DOI: 10.1093/molbev/msab048] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Studying how novel phenotypes originate and evolve is fundamental to the field of evolutionary biology as it allows us to understand how organismal diversity is generated and maintained. However, determining the basis of novel phenotypes is challenging as it involves orchestrated changes at multiple biological levels. Here, we aim to overcome this challenge by using a comparative species framework combining behavioral, gene expression, and genomic analyses to understand the evolutionary novel egg-laying substrate-choice behavior of the invasive pest species Drosophila suzukii. First, we used egg-laying behavioral assays to understand the evolution of ripe fruit oviposition preference in D. suzukii compared with closely related species D. subpulchrella and D. biarmipes as well as D. melanogaster. We show that D. subpulchrella and D. biarmipes lay eggs on both ripe and rotten fruits, suggesting that the transition to ripe fruit preference was gradual. Second, using two-choice oviposition assays, we studied how D. suzukii, D. subpulchrella, D. biarmipes, and D. melanogaster differentially process key sensory cues distinguishing ripe from rotten fruit during egg-laying. We found that D. suzukii's preference for ripe fruit is in part mediated through a species-specific preference for stiff substrates. Last, we sequenced and annotated a high-quality genome for D. subpulchrella. Using comparative genomic approaches, we identified candidate genes involved in D. suzukii's ability to seek out and target ripe fruits. Our results provide detail to the stepwise evolution of pest activity in D. suzukii, indicating important cues used by this species when finding a host, and the molecular mechanisms potentially underlying their adaptation to a new ecological niche.
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Affiliation(s)
- Sylvia M Durkin
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, USA
| | - Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Antoine Abrieux
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, USA
| | - Kyle M Lewald
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, USA
| | - Alice Gadau
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Nicolas Svetec
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Junhui Peng
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Miriam Kopyto
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Christopher B Langer
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Joanna C Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, USA
| | - J J Emerson
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Li Zhao
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
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Lander N, Chiurillo MA, Docampo R. Signaling pathways involved in environmental sensing in Trypanosoma cruzi. Mol Microbiol 2021; 115:819-828. [PMID: 33034088 PMCID: PMC8032824 DOI: 10.1111/mmi.14621] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 09/28/2020] [Accepted: 09/30/2020] [Indexed: 12/18/2022]
Abstract
Trypanosoma cruzi is a unicellular parasite and the etiologic agent of Chagas disease. The parasite has a digenetic life cycle alternating between mammalian and insect hosts, where it faces a variety of environmental conditions to which it must adapt in order to survive. The adaptation to these changes is mediated by signaling pathways that coordinate the cellular responses to the new environmental settings. Major environmental changes include temperature, nutrient availability, ionic composition, pH, osmolarity, oxidative stress, contact with host cells and tissues, host immune response, and intracellular life. Some of the signaling pathways and second messengers potentially involved in the response to these changes have been elucidated in recent years and will be the subject of this review.
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Affiliation(s)
- Noelia Lander
- Center for Tropical and Emerging Global Diseases, and Department of Cellular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Miguel A. Chiurillo
- Center for Tropical and Emerging Global Diseases, and Department of Cellular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Roberto Docampo
- Center for Tropical and Emerging Global Diseases, and Department of Cellular Biology, University of Georgia, Athens, GA, 30602, USA
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Chen T, Zeineldin M, Johnson BA, Dong Y, Narkar A, Li T, Zhu J, Li R, Larman TC. Colonic epithelial adaptation to EGFR-independent growth induces chromosomal instability and is accelerated by prior injury. Neoplasia 2021; 23:488-501. [PMID: 33906087 PMCID: PMC8099723 DOI: 10.1016/j.neo.2021.03.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/26/2021] [Accepted: 03/29/2021] [Indexed: 11/17/2022]
Abstract
Although much is known about the gene mutations required to drive colorectal cancer (CRC) initiation, the tissue-specific selective microenvironments in which neoplasia arises remains less characterized. Here, we determined whether modulation of intestinal stem cell niche morphogens alone can exert a neoplasia-relevant selective pressure on normal colonic epithelium. Using adult stem cell-derived murine colonic epithelial organoids (colonoids), we employed a strategy of sustained withdrawal of epidermal growth factor (EGF) and epidermal growth factor receptor (EGFR) inhibition to select for and expand survivors. EGFR-signaling-independent (iEGFR) colonoids emerged over rounds of selection and expansion. Colonoids derived from a mouse model of chronic mucosal injury showed an enhanced ability to adapt to EGFR inhibition. Whole-exome and transcriptomic analyses of iEGFR colonoids demonstrated acquisition of deleterious mutations and altered expression of genes implicated in EGF signaling, pyroptosis, and CRC. iEGFR colonoids acquired dysplasia-associated cytomorphologic changes, an increased proliferative rate, and the ability to survive independently of other required niche factors. These changes were accompanied by emergence of aneuploidy and chromosomal instability; further, the observed mitotic segregation errors were significantly associated with loss of interkinetic nuclear migration, a fundamental and dynamic process underlying intestinal epithelial homeostasis. This study provides key evidence that chromosomal instability and other phenotypes associated with neoplasia can be induced ex vivo via adaptation to EGF withdrawal in normal and stably euploid colonic epithelium, without introducing cancer-associated driver mutations. In addition, prior mucosal injury accelerates this evolutionary process.
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Affiliation(s)
- Tiane Chen
- Department of Pathology, Division of GI/Liver Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA; Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Maged Zeineldin
- Department of Pathology, Division of GI/Liver Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA; Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Blake A Johnson
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD USA; Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD USA; Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Yi Dong
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD USA; Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Akshay Narkar
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD USA; Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Taibo Li
- Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Jin Zhu
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD USA; Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Rong Li
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD USA; Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD USA; Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore
| | - Tatianna C Larman
- Department of Pathology, Division of GI/Liver Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA; Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD USA.
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