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Pierron F, Daffe G, Daramy F, Heroin D, Barré A, Bouchez O, Clérendeau C, Romero-Ramirez A, Nikolski M. Transgenerational endocrine disruptor effects of cadmium in zebrafish and contribution of standing epigenetic variation to adaptation. J Hazard Mater 2023; 455:131579. [PMID: 37163897 DOI: 10.1016/j.jhazmat.2023.131579] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/20/2023] [Accepted: 05/03/2023] [Indexed: 05/12/2023]
Abstract
Evidence has emerged that environmentally-induced epigenetic changes can have long-lasting effects on gene transcription across generations. These recent findings highlight the need to investigate the transgenerational impacts of pollutants to assess their long term effects on populations. In this study, we investigated the transgenerational effect of cadmium on zebrafish across 4 generations. A first whole methylome approach carried out on fish of the first two generations led us to focus our investigations on the estradiol receptor alpha gene (esr1). We observed a sex-dependent transgenerational inheritance of Cd-induced DNA methylation changes up to the last generation. These changes were associated with single nucleotide polymorphisms (SNPs) that were themselves at the origin of the creation or deletion of methylation sites. Thus, Cd-induced genetic selection gave rise to DNA methylation changes. We also analyzed the transcription level of various sections of esr1 as well as estrogen responsive genes. While Cd triggered transgenerational disorders, Cd-induced epigenetic changes in esr1 contributed to the rapid transgenerational adaptation of fish to Cd. Our results provide insight into the processes underpinning rapid adaptation and highlight the need to maintain genetic diversity within natural populations to bolster the resilience of species faced with the global environmental changes.
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Affiliation(s)
- Fabien Pierron
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, F-33600 Pessac, France.
| | - Guillemine Daffe
- Univ. Bordeaux, CNRS, INRAE, La Rochelle Univ., UMS 2567 POREA, F-33615 Pessac, France
| | - Flore Daramy
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, F-33600 Pessac, France
| | - Débora Heroin
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, F-33600 Pessac, France
| | - Aurélien Barré
- Univ. Bordeaux, Bordeaux Bioinformatics Center, Bordeaux, France
| | - Olivier Bouchez
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, 31326, France
| | | | | | - Macha Nikolski
- Univ. Bordeaux, Bordeaux Bioinformatics Center, Bordeaux, France; Univ. Bordeaux, CNRS, IBGC, UMR 5095, Bordeaux 33077, France
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Cohen Y, Hershberg R. Rapid adaptation often occurs through mutations to the most highly conserved positions of the RNA polymerase core enzyme. Genome Biol Evol 2022; 14:6649522. [PMID: 35876137 PMCID: PMC9459352 DOI: 10.1093/gbe/evac105] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2022] [Indexed: 11/17/2022] Open
Abstract
Mutations to the genes encoding the RNA polymerase core enzyme (RNAPC) and additional housekeeping regulatory genes were found to be involved in adaptation, in the context of numerous evolutionary experiments, in which bacteria were exposed to diverse selective pressures. This provides a conundrum, as the housekeeping genes that were so often mutated in response to these diverse selective pressures tend to be among the genes that are most conserved in their sequences across the bacterial phylogeny. In order to further examine this apparent discrepancy, we characterized the precise positions of the RNAPC involved in adaptation to a large variety of selective pressures. We found that RNAPC lab adaptations tended to occur at positions displaying traits associated with higher selective constraint. Specifically, compared to other RNAPC positions, positions involved in adaptation tended to be more conserved in their sequences within bacteria, were more often located within defined protein domains, and were located closer to the complex’s active site. Higher sequence conservation was also found for resource exhaustion adaptations occurring within additional housekeeping genes. Combined, our results demonstrate that the positions that change most readily in response to well-defined selective pressures exerted in lab environments are often also those that evolve most slowly in nature.
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Affiliation(s)
- Yasmin Cohen
- Rachel & Menachem Mendelovitch Evolutionary Processes of Mutation & Natural Selection Research Laboratory, Department of Genetics and Developmental Biology, the Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Ruth Hershberg
- Rachel & Menachem Mendelovitch Evolutionary Processes of Mutation & Natural Selection Research Laboratory, Department of Genetics and Developmental Biology, the Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
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Isshiki M, Naka I, Kimura R, Nishida N, Furusawa T, Natsuhara K, Yamauchi T, Nakazawa M, Ishida T, Inaoka T, Matsumura Y, Ohtsuka R, Ohashi J. Admixture with indigenous people helps local adaptation: admixture-enabled selection in Polynesians. BMC Ecol Evol 2021; 21:179. [PMID: 34551727 PMCID: PMC8456657 DOI: 10.1186/s12862-021-01900-y] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 08/25/2021] [Indexed: 01/08/2023] Open
Abstract
Background Homo sapiens have experienced admixture many times in the last few thousand years. To examine how admixture affects local adaptation, we investigated genomes of modern Polynesians, who are shaped through admixture between Austronesian-speaking people from Southeast Asia (Asian-related ancestors) and indigenous people in Near Oceania (Papuan-related ancestors). Methods In this study local ancestry was estimated across the genome in Polynesians (23 Tongan subjects) to find the candidate regions of admixture-enabled selection contributed by Papuan-related ancestors. Results The mean proportion of Papuan-related ancestry across the Polynesian genome was estimated as 24.6% (SD = 8.63%), and two genomic regions, the extended major histocompatibility complex (xMHC) region on chromosome 6 and the ATP-binding cassette transporter sub-family C member 11 (ABCC11) gene on chromosome 16, showed proportions of Papuan-related ancestry more than 5 SD greater than the mean (> 67.8%). The coalescent simulation under the assumption of selective neutrality suggested that such signals of Papuan-related ancestry enrichment were caused by positive selection after admixture (false discovery rate = 0.045). The ABCC11 harbors a nonsynonymous SNP, rs17822931, which affects apocrine secretory cell function. The approximate Bayesian computation indicated that, in Polynesian ancestors, a strong positive selection (s = 0.0217) acted on the ancestral allele of rs17822931 derived from Papuan-related ancestors. Conclusions Our results suggest that admixture with Papuan-related ancestors contributed to the rapid local adaptation of Polynesian ancestors. Considering frequent admixture events in human evolution history, the acceleration of local adaptation through admixture should be a common event in humans. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01900-y.
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Affiliation(s)
- Mariko Isshiki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Izumi Naka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, 903-0125, Japan
| | - Nao Nishida
- Genome Medical Science Project, Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Chiba, 272-8516, Japan
| | - Takuro Furusawa
- Graduate School of Asian and African Area Studies, Kyoto University, Kyoto, 606-8501, Japan
| | - Kazumi Natsuhara
- Department of International Health and Nursing, Faculty of Nursing, Toho University, Tokyo, 143-0015, Japan
| | - Taro Yamauchi
- Faculty of Health Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Minato Nakazawa
- Graduate School of Health Sciences, Kobe University, Kobe, 654-0142, Japan
| | - Takafumi Ishida
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Tsukasa Inaoka
- Department of Human Ecology, Faculty of Agriculture, Saga University, Saga, 840-8502, Japan
| | - Yasuhiro Matsumura
- Faculty of Health and Nutrition, Bunkyo University, Chigasaki, 253-8550, Japan
| | | | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
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Wang X, Ju Z, Jiang Q, Zhong J, Liu C, Wang J, Hoff JL, Schnabel RD, Zhao H, Gao Y, Liu W, Wang L, Gao Y, Yang C, Hou M, Huang N, Regitano LCA, Porto-Neto LR, Decker JE, Taylor JF, Huang J. Introgression, admixture, and selection facilitate genetic adaptation to high-altitude environments in cattle. Genomics 2021; 113:1491-1503. [PMID: 33771637 DOI: 10.1016/j.ygeno.2021.03.023] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/17/2021] [Accepted: 03/21/2021] [Indexed: 12/30/2022]
Abstract
Domestication and subsequent selection of cattle to form breeds and biological types that can adapt to different environments partitioned ancestral genetic diversity into distinct modern lineages. Genome-wide selection particularly for adaptation to extreme environments left detectable signatures genome-wide. We used high-density genotype data for 42 cattle breeds and identified the influence of Bos grunniens and Bos javanicus on the formation of Chinese indicine breeds that led to their divergence from India-origin zebu. We also found evidence for introgression, admixture, and migration in most of the Chinese breeds. Selection signature analyses between high-altitude (≥1800 m) and low-altitude adapted breeds (<1500 m) revealed candidate genes (ACSS2, ALDOC, EPAS1, EGLN1, NUCB2) and pathways that are putatively involved in hypoxia adaptation. Immunohistochemical, real-time PCR and CRISPR/cas9 ACSS2-knockout analyses suggest that the up-regulation of ACSS2 expression in the liver promotes the metabolic adaptation of cells to hypoxia via the hypoxia-inducible factor pathway. High altitude adaptation involved the introgression of alleles from high-altitude adapted yaks into Chinese Bos taurus taurus prior to their formation into recognized breeds and followed by selection. In addition to selection, adaptation to high altitude environments has been facilitated by admixture and introgression with locally adapted cattle populations.
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Affiliation(s)
- Xiuge Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250131, China
| | - Zhihua Ju
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250131, China
| | - Qiang Jiang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250131, China
| | - Jifeng Zhong
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250131, China; Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Chengkun Liu
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250131, China
| | - Jinpeng Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250131, China
| | - Jesse L Hoff
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA; Informatics Institute, University of Missouri, Columbia, MO 65211, USA
| | - Han Zhao
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250131, China; College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014, China
| | - Yaping Gao
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250131, China
| | - Wenhao Liu
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250131, China
| | - Lingling Wang
- Shandong OX Livestock Breeding Co., Ltd., Jinan, Shandong 250131, China
| | - Yundong Gao
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250131, China; Shandong OX Livestock Breeding Co., Ltd., Jinan, Shandong 250131, China
| | - Chunhong Yang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250131, China
| | - Minghai Hou
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250131, China
| | - Ning Huang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | | | | | - Jared E Decker
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA.
| | - Jinming Huang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250131, China; College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014, China.
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Härer A, Torres-Dowdall J, Rometsch SJ, Yohannes E, Machado-Schiaffino G, Meyer A. Parallel and non-parallel changes of the gut microbiota during trophic diversification in repeated young adaptive radiations of sympatric cichlid fish. Microbiome 2020; 8:149. [PMID: 33121541 PMCID: PMC7597055 DOI: 10.1186/s40168-020-00897-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/21/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Recent increases in understanding the ecological and evolutionary roles of microbial communities have underscored the importance of their hosts' biology. Yet, little is known about gut microbiota dynamics during the early stages of ecological diversification and speciation. We sequenced the V4 region of the 16s rRNA gene to study the gut microbiota of Nicaraguan Midas cichlid fish (Amphilophus cf. citrinellus). Specifically, we tested the hypothesis that parallel divergence in trophic ecology in extremely young adaptive radiations from two crater lakes is associated with parallel changes of their gut microbiota. RESULTS Bacterial communities of fish guts and lake water were highly distinct, indicating that the gut microbiota is shaped by host-specific factors. Among individuals of the same crater lake, differentiation in trophic ecology was weakly associated with gut microbiota differentiation, suggesting that diet, to some extent, affects the gut microbiota. However, differences in trophic ecology were much more pronounced across than within species whereas similar patterns were not observed for taxonomic and functional differences of the gut microbiota. Across the two crater lakes, we could not detect conclusive evidence for parallel changes of the gut microbiota associated with trophic ecology. CONCLUSIONS A lack of clearly differentiated niches during the early stages of ecological diversification might result in non-parallel changes of gut microbial communities, as observed in our study system as well as in other recently diverged fish species. Video Abstract.
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Affiliation(s)
- Andreas Härer
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
- Current address: Division of Biological Sciences, Section of Ecology, Behavior, & Evolution, University of California San Diego, La Jolla, California USA
| | - Julián Torres-Dowdall
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Sina J. Rometsch
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Elizabeth Yohannes
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Gonzalo Machado-Schiaffino
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
- Current address: Department of Functional Biology, University of Oviedo, Oviedo, Spain
| | - Axel Meyer
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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Bohnert S, Antelo L, Grünewald C, Yemelin A, Andresen K, Jacob S. Rapid adaptation of signaling networks in the fungal pathogen Magnaporthe oryzae. BMC Genomics 2019; 20:763. [PMID: 31640564 PMCID: PMC6805500 DOI: 10.1186/s12864-019-6113-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 09/20/2019] [Indexed: 11/10/2022] Open
Abstract
Background One fundamental question in biology is how the evolution of eukaryotic signaling networks has taken place. “Loss of function” (lof) mutants from components of the high osmolarity glycerol (HOG) signaling pathway in the filamentous fungus Magnaporthe oryzae are viable, but impaired in osmoregulation. Results After long-term cultivation upon high osmolarity, stable individuals with reestablished osmoregulation capacity arise independently from each of the mutants with inactivated HOG pathway. This phenomenon is extremely reproducible and occurs only in osmosensitive mutants related to the HOG pathway – not in other osmosensitive Magnaporthe mutants. The major compatible solute produced by these adapted strains to cope with high osmolarity is glycerol, whereas it is arabitol in the wildtype strain. Genome and transcriptome analysis resulted in candidate genes related to glycerol metabolism, perhaps responsible for an epigenetic induced reestablishment of osmoregulation, since these genes do not show structural variations within the coding or promotor sequences. Conclusion This is the first report of a stable adaptation in eukaryotes by producing different metabolites and opens a door for the scientific community since the HOG pathway is worked on intensively in many eukaryotic model organisms.
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Affiliation(s)
- Stefan Bohnert
- Institut für Biotechnologie und Wirkstoff-Forschung gGmbH (IBWF), Erwin-Schrödinger-Str. 56, D-67663, Kaiserslautern, Germany
| | - Luis Antelo
- Institut für Biotechnologie und Wirkstoff-Forschung gGmbH (IBWF), Erwin-Schrödinger-Str. 56, D-67663, Kaiserslautern, Germany
| | - Christiane Grünewald
- Johannes Gutenberg-University Mainz, Mikrobiologie und Weinforschung am Institut für Molekulare Physiologie, Johann-Joachim-Becherweg 15, D-55128, Mainz, Germany
| | - Alexander Yemelin
- Institut für Biotechnologie und Wirkstoff-Forschung gGmbH (IBWF), Erwin-Schrödinger-Str. 56, D-67663, Kaiserslautern, Germany
| | - Karsten Andresen
- Johannes Gutenberg-University Mainz, Mikrobiologie und Weinforschung am Institut für Molekulare Physiologie, Johann-Joachim-Becherweg 15, D-55128, Mainz, Germany
| | - Stefan Jacob
- Institut für Biotechnologie und Wirkstoff-Forschung gGmbH (IBWF), Erwin-Schrödinger-Str. 56, D-67663, Kaiserslautern, Germany. .,Johannes Gutenberg-University Mainz, Mikrobiologie und Weinforschung am Institut für Molekulare Physiologie, Johann-Joachim-Becherweg 15, D-55128, Mainz, Germany.
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7
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Feder AF, Pennings PS, Hermisson J, Petrov DA. Evolutionary Dynamics in Structured Populations Under Strong Population Genetic Forces. G3 (Bethesda) 2019; 9:3395-3407. [PMID: 31462443 PMCID: PMC6778802 DOI: 10.1534/g3.119.400605] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/16/2019] [Indexed: 12/16/2022]
Abstract
In the long-term neutral equilibrium, high rates of migration between subpopulations result in little population differentiation. However, in the short-term, even very abundant migration may not be enough for subpopulations to equilibrate immediately. In this study, we investigate dynamical patterns of short-term population differentiation in adapting populations via stochastic and analytical modeling through time. We characterize a regime in which selection and migration interact to create non-monotonic patterns of population differentiation over time when migration is weaker than selection, but stronger than drift. We demonstrate how these patterns can be leveraged to estimate high migration rates using approximate Bayesian computation. We apply this approach to estimate fast migration in a rapidly adapting intra-host Simian-HIV population sampled from different anatomical locations. We find differences in estimated migration rates between different compartments, even though all are above [Formula: see text] = 1. This work demonstrates how studying demographic processes on the timescale of selective sweeps illuminates processes too fast to leave signatures on neutral timescales.
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Affiliation(s)
- Alison F Feder
- Department of Biology, Stanford University,
- Department of Integrative Biology, University of California Berkeley
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8
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Pafilis P, Herrel A, Kapsalas G, Vasilopoulou-Kampitsi M, Fabre AC, Foufopoulos J, Donihue CM. Habitat shapes the thermoregulation of Mediterranean lizards introduced to replicate experimental islets. J Therm Biol 2019; 84:368-374. [PMID: 31466776 DOI: 10.1016/j.jtherbio.2019.07.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/11/2019] [Accepted: 07/27/2019] [Indexed: 10/26/2022]
Abstract
Both environmental temperatures and spatial heterogeneity can profoundly affect the biology of ectotherms. In lizards, thermoregulation may show high plasticity and may respond to environmental shifts. In the context of global climate change, lizards showing plastic thermoregulatory responses may be favored. In this study, we designed an experiment to evaluate the extent to which lizard thermoregulation responds to introduction to a new environment in a snapshot of time. In 2014, we captured individuals of the Aegean Wall lizard (Podarcis erhardii) from Naxos Island (429.8 km2) and released them onto two small, lizard-free islets, Galiatsos (0.0073 km2) and Kampana (0.004 km2) (Aegean Sea, Greece). In 2017, we returned to the islets and estimated the effectiveness (E), accuracy and precision of thermoregulation measuring operative, preferred (Tpref) and body temperatures. We hypothesized that the three habitats would differ in thermal quality and investigated the extent to which lizards from Naxos demonstrate plasticity when introduced to the novel, islet habitats. Thermal parameters did not differ between Galiatsos and Naxos and this was reflected in the similar E and Tpref. However, lizards from Kampana deviated in all focal traits from Naxos, resulting in higher E and a preference for higher Tpref. In sum, Naxos lizards shifted their thermoregulatory profile due to the idiosyncratic features of their new islet habitat. Our results advocate a high plasticity in lizard thermoregulation and suggest that there is room for effective responses to environmental changes, at least for Podarcis lizards in insular habitats.
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Affiliation(s)
- Panayiotis Pafilis
- Dept. of Biology, National and Kapodistrian University of Athens, Greece; Zoological Museum, National and Kapodistrian University of Athens, Greece.
| | - Anthony Herrel
- Dept. Adaptation du Vivant, UMR 7179 CNRS/MNHN, Paris, France; Dept. of Biology, University of Antwerp, Belgium; Dept. of Biology, Ghent University, Belgium
| | - Grigoris Kapsalas
- Dept. of Biology, National and Kapodistrian University of Athens, Greece
| | | | - Anne-Claire Fabre
- Dept. of Life Sciences, The Natural History Museum, London, United Kingdom
| | | | - Colin M Donihue
- Dept. Adaptation du Vivant, UMR 7179 CNRS/MNHN, Paris, France; Dept. of Organismic and Evolutionary Biology, Harvard University, USA; Dept. of Biology, Washington University of St. Louis, USA
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Hawes NA, Tremblay LA, Pochon X, Dunphy B, Fidler AE, Smith KF. Effects of temperature and salinity stress on DNA methylation in a highly invasive marine invertebrate, the colonial ascidian Didemnum vexillum. PeerJ 2018; 6:e5003. [PMID: 29967721 PMCID: PMC6022722 DOI: 10.7717/peerj.5003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 05/29/2018] [Indexed: 12/27/2022] Open
Abstract
Environmentally induced epigenetic changes may contribute to phenotypic plasticity, increase adaptive potential in changing environments, and play a key role in the establishment and spread of invasive species in new habitats. In this study, we used methylation-sensitive amplified polymorphism (MSAP) to assess environmentally induced DNA methylation changes in a globally invasive clonal ascidian, Didemnum vexillum. We tested the effect of increasing temperature (19, 25 and 27 °C) and decreasing salinity (34, 32, 30, 28 and 26 practical salinity units (PSU)) on global DNA methylation, growth and survival rates. Exposure to 27 °C resulted in significant changes in DNA methylation over time. Growth also decreased in colonies exposed to high temperatures, suggesting they were under thermal stress. In contrast, no differences in growth nor DNA methylation patterns were observed in colonies exposed to a decreasing salinity gradient, potentially due to prior adaptation. The results of this study show that environmental stress can induce significant global DNA methylation changes in an invasive marine invertebrate on very rapid timescales, and that this response varies depending on the type, magnitude, and duration of the stressor. Changes in genomic DNA methylation and the rate of growth may act to ‘buy survival time’ under stressful conditions, expanding the distribution limits of this globally invasive species.
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Affiliation(s)
- Nicola A Hawes
- Institute of Marine Science, University of Auckland, Auckland, New Zealand.,Cawthron Institute, Nelson, New Zealand
| | - Louis A Tremblay
- Cawthron Institute, Nelson, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Xavier Pochon
- Institute of Marine Science, University of Auckland, Auckland, New Zealand.,Cawthron Institute, Nelson, New Zealand
| | - Brendon Dunphy
- Institute of Marine Science, University of Auckland, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Andrew E Fidler
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
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Kang L, Aggarwal DD, Rashkovetsky E, Korol AB, Michalak P. Rapid genomic changes in Drosophila melanogaster adapting to desiccation stress in an experimental evolution system. BMC Genomics 2016; 17:233. [PMID: 26979755 DOI: 10.1186/s12864-016-2556-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/29/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Experimental evolution studies, coupled with whole genome resequencing and advances in bioinformatics, have become a powerful tool for exploring how populations respond to selection at the genome-wide level, complementary to genome-wide association studies (GWASs) and linkage mapping experiments as strategies to connect genotype and phenotype. In this experiment, we analyzed genomes of Drosophila melanogaster from lines evolving under long-term directional selection for increased desiccation resistance in comparison with control (no-selection) lines. RESULTS We demonstrate that adaptive responses to desiccation stress have exerted extensive footprints on the genomes, manifested through a high degree of fixation of alleles in surrounding neighborhoods of eroded heterozygosity. These patterns were highly convergent across replicates, consistent with signatures of 'soft' selective sweeps, where multiple alleles present as standing genetic variation become beneficial and sweep through the replicate populations at the same time. Albeit much less frequent, we also observed line-unique sweep regions with zero or near-zero heterozygosity, consistent with classic, or 'hard', sweeps, where novel rather than pre-existing adaptive mutations may have been driven to fixation. Genes responsible for cuticle and protein deubiquitination seemed to be central to these selective sweeps. High divergence within coding sequences between selected and control lines was also reflected by significant results of the McDonald-Kreitman and Ka/Ks tests, showing that as many as 347 genes may have been under positive selection. CONCLUSIONS Desiccation stress, a common challenge to many organisms inhabiting dry environments, proves to be a very potent selecting factor having a big impact on genome diversity.
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