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Benowitz KM, Allan CW, Jaworski CC, Sanderson MJ, Diaz F, Chen X, Matzkin LM. Fundamental Patterns of Structural Evolution Revealed by Chromosome-Length Genomes of Cactophilic Drosophila. Genome Biol Evol 2024; 16:evae191. [PMID: 39228294 PMCID: PMC11411373 DOI: 10.1093/gbe/evae191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/22/2024] [Accepted: 08/26/2024] [Indexed: 09/05/2024] Open
Abstract
A thorough understanding of adaptation and speciation requires model organisms with both a history of ecological and phenotypic study as well as a complete set of genomic resources. In particular, high-quality genome assemblies of ecological model organisms are needed to assess the evolution of genome structure and its role in adaptation and speciation. Here, we generate new genomes of cactophilic Drosophila, a crucial model clade for understanding speciation and ecological adaptation in xeric environments. We generated chromosome-level genome assemblies and complete annotations for seven populations across Drosophila mojavensis, Drosophila arizonae, and Drosophila navojoa. We use these data first to establish the most robust phylogeny for this clade to date, and to assess patterns of molecular evolution across the phylogeny, showing concordance with a priori hypotheses regarding adaptive genes in this system. We then show that structural evolution occurs at constant rate across the phylogeny, varies by chromosome, and is correlated with molecular evolution. These results advance the understanding of the D. mojavensis clade by demonstrating core evolutionary genetic patterns and integrating those patterns to generate new gene-level hypotheses regarding adaptation. Our data are presented in a new public database (cactusflybase.arizona.edu), providing one of the most in-depth resources for the analysis of inter- and intraspecific evolutionary genomic data. Furthermore, we anticipate that the patterns of structural evolution identified here will serve as a baseline for future comparative studies to identify the factors that influence the evolution of genome structure across taxa.
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Affiliation(s)
- Kyle M Benowitz
- Department of Entomology, University of Arizona, Tucson, AZ, USA
| | - Carson W Allan
- Department of Entomology, University of Arizona, Tucson, AZ, USA
| | | | - Michael J Sanderson
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Fernando Diaz
- Department of Entomology, University of Arizona, Tucson, AZ, USA
| | - Xingsen Chen
- Department of Entomology, University of Arizona, Tucson, AZ, USA
| | - Luciano M Matzkin
- Department of Entomology, University of Arizona, Tucson, AZ, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
- BIO5 Institute, University of Arizona, Tucson, AZ, USA
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2
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Gonçalves C, Harrison MC, Steenwyk JL, Opulente DA, LaBella AL, Wolters JF, Zhou X, Shen XX, Groenewald M, Hittinger CT, Rokas A. Diverse signatures of convergent evolution in cactus-associated yeasts. PLoS Biol 2024; 22:e3002832. [PMID: 39312572 DOI: 10.1371/journal.pbio.3002832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Revised: 10/03/2024] [Accepted: 09/05/2024] [Indexed: 09/25/2024] Open
Abstract
Many distantly related organisms have convergently evolved traits and lifestyles that enable them to live in similar ecological environments. However, the extent of phenotypic convergence evolving through the same or distinct genetic trajectories remains an open question. Here, we leverage a comprehensive dataset of genomic and phenotypic data from 1,049 yeast species in the subphylum Saccharomycotina (Kingdom Fungi, Phylum Ascomycota) to explore signatures of convergent evolution in cactophilic yeasts, ecological specialists associated with cacti. We inferred that the ecological association of yeasts with cacti arose independently approximately 17 times. Using a machine learning-based approach, we further found that cactophily can be predicted with 76% accuracy from both functional genomic and phenotypic data. The most informative feature for predicting cactophily was thermotolerance, which we found to be likely associated with altered evolutionary rates of genes impacting the cell envelope in several cactophilic lineages. We also identified horizontal gene transfer and duplication events of plant cell wall-degrading enzymes in distantly related cactophilic clades, suggesting that putatively adaptive traits evolved independently through disparate molecular mechanisms. Notably, we found that multiple cactophilic species and their close relatives have been reported as emerging human opportunistic pathogens, suggesting that the cactophilic lifestyle-and perhaps more generally lifestyles favoring thermotolerance-might preadapt yeasts to cause human disease. This work underscores the potential of a multifaceted approach involving high-throughput genomic and phenotypic data to shed light onto ecological adaptation and highlights how convergent evolution to wild environments could facilitate the transition to human pathogenicity.
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Affiliation(s)
- Carla Gonçalves
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, United States of America
- Associate Laboratory i4HB-Institute for Health and Bioeconomy and UCIBIO-Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO-i4HB, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Marie-Claire Harrison
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Jacob L Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, United States of America
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Dana A Opulente
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Biology Department, Villanova University, Villanova, Pennsylvania, United States of America
| | - Abigail L LaBella
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - John F Wolters
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Xiaofan Zhou
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, United States of America
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China
| | - Xing-Xing Shen
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, United States of America
- College of Agriculture and Biotechnology and Centre for Evolutionary & Organismal Biology, Zhejiang University, Hangzhou, China
| | | | - Chris Todd Hittinger
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, United States of America
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3
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Fonseca PM, Robe LJ, Carvalho TL, Loreto ELS. Characterization of the chemoreceptor repertoire of a highly specialized fly with comparisons to other Drosophila species. Genet Mol Biol 2024; 47:e20220383. [PMID: 38885260 PMCID: PMC11182316 DOI: 10.1590/1678-4685-gmb-2022-0383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/07/2024] [Indexed: 06/20/2024] Open
Abstract
To explore the diversity of scenarios in nature, animals have evolved tools to interact with different environmental conditions. Chemoreceptors are an important interface component and among them, olfactory receptors (ORs) and gustatory receptors (GRs) can be used to find food and detect healthy resources. Drosophila is a model organism in many scientific fields, in part due to the diversity of species and niches they occupy. The contrast between generalists and specialists Drosophila species provides an important model for studying the evolution of chemoreception. Here, we compare the repertoire of chemoreceptors of different species of Drosophila with that of D. incompta, a highly specialized species whose ecology is restricted to Cestrum flowers, after reporting the preferences of D. incompta to the odor of Cestrum flowers in olfactory tests. We found evidence that the chemoreceptor repertoire in D. incompta is smaller than that presented by species in the Sophophora subgenus. Similar patterns were found in other non-Sophophora species, suggesting the presence of underlying phylogenetic trends. Nevertheless, we also found autapomorphic gene losses and detected some genes that appear to be under positive selection in D. incompta, suggesting that the specific lifestyle of these flies may have shaped the evolution of individual genes in each of these gene families.
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Affiliation(s)
- Pedro Mesquita Fonseca
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Lizandra Jaqueline Robe
- Universidade Federal de Santa Maria, Centro de Ciências Naturais e Exatas, Programa de Pós-Graduação em Biodiversidade Animal, Santa Maria, RS, Brazil
| | - Tuane Letícia Carvalho
- Universidade Federal de Santa Maria, Centro de Ciências Naturais e Exatas, Programa de Pós-Graduação em Biodiversidade Animal, Santa Maria, RS, Brazil
| | - Elgion Lucio Silva Loreto
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Universidade Federal de Santa Maria, Centro de Ciências Naturais e Exatas, Departamento de Bioquímica e Biologia Molecular, Santa Maria, RS, Brazil
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4
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Yano J, Nave C, Larratt K, Honey P, Roberts M, Jingco C, Fung ML, Trotter D, He X, Elezi G, Whitelegge JP, Wasserman S, Donlea JM. Elevated sleep quota in a stress-resilient Drosophila species. Curr Biol 2024; 34:2487-2501.e3. [PMID: 38772361 PMCID: PMC11163955 DOI: 10.1016/j.cub.2024.04.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/09/2024] [Accepted: 04/25/2024] [Indexed: 05/23/2024]
Abstract
Sleep is broadly conserved across the animal kingdom but can vary widely between species. It is currently unclear which selective pressures and regulatory mechanisms influence differences in sleep between species. The fruit fly Drosophila melanogaster has become a successful model system for examining sleep regulation and function, but little is known about the sleep patterns in many related fly species. Here, we find that fly species with adaptations to extreme desert environments, including D. mojavensis, exhibit strong increases in baseline sleep compared with D. melanogaster. Long-sleeping D. mojavensis show intact homeostasis, indicating that desert flies carry an elevated drive for sleep. In addition, D. mojavensis exhibit altered abundance or distribution of several sleep/wake-related neuromodulators and neuropeptides that are consistent with their reduced locomotor activity and increased sleep. Finally, we find that in a nutrient-deprived environment, the sleep patterns of individual D. mojavensis are strongly correlated with their survival time and that disrupting sleep via constant light stimulation renders D. mojavensis more sensitive to starvation. Our results demonstrate that D. mojavensis is a novel model for studying organisms with high sleep drive and for exploring sleep strategies that provide resilience in extreme environments.
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Affiliation(s)
- Jessica Yano
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; Molecular, Cellular & Integrative Physiology Interdepartmental PhD Program, UCLA, Los Angeles, CA 90095, USA
| | - Ceazar Nave
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Katherine Larratt
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Phia Honey
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; Department of Neuroscience, Wellesley College, Wellesley, MA 02481, USA
| | - Makayla Roberts
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Cassandra Jingco
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Melanie L Fung
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Damion Trotter
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; Molecular, Cellular & Integrative Physiology Interdepartmental PhD Program, UCLA, Los Angeles, CA 90095, USA
| | - Xin He
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Gazmend Elezi
- Pasarow Mass Spectrometry Laboratory, Jane & Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; Cotsen Institute of Archaeology, UCLA, Los Angeles, CA 90095, USA
| | - Julian P Whitelegge
- Pasarow Mass Spectrometry Laboratory, Jane & Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Sara Wasserman
- Department of Neuroscience, Wellesley College, Wellesley, MA 02481, USA
| | - Jeffrey M Donlea
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA.
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5
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Ravigné V, Rodrigues LR, Charlery de la Masselière M, Facon B, Kuczyński L, Radwan J, Skoracka A, Magalhães S. Understanding the joint evolution of dispersal and host specialisation using phytophagous arthropods as a model group. Biol Rev Camb Philos Soc 2024; 99:219-237. [PMID: 37724465 DOI: 10.1111/brv.13018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 09/20/2023]
Abstract
Theory generally predicts that host specialisation and dispersal should evolve jointly. Indeed, many models predict that specialists should be poor dispersers to avoid landing on unsuitable hosts while generalists will have high dispersal abilities. Phytophagous arthropods are an excellent group to test this prediction, given extensive variation in their host range and dispersal abilities. Here, we explore the degree to which the empirical literature on this group is in accordance with theoretical predictions. We first briefly outline the theoretical reasons to expect such a correlation. We then report empirical studies that measured both dispersal and the degree of specialisation in phytophagous arthropods. We find a correlation between dispersal and levels of specialisation in some studies, but with wide variation in this result. We then review theoretical attributes of species and environment that may blur this correlation, namely environmental grain, temporal heterogeneity, habitat selection, genetic architecture, and coevolution between plants and herbivores. We argue that theoretical models fail to account for important aspects, such as phenotypic plasticity and the impact of selective forces stemming from other biotic interactions, on both dispersal and specialisation. Next, we review empirical caveats in the study of this interplay. We find that studies use different measures of both dispersal and specialisation, hampering comparisons. Moreover, several studies do not provide independent measures of these two traits. Finally, variation in these traits may occur at scales that are not being considered. We conclude that this correlation is likely not to be expected from large-scale comparative analyses as it is highly context dependent and should not be considered in isolation from the factors that modulate it, such as environmental scale and heterogeneity, intrinsic traits or biotic interactions. A stronger crosstalk between theoretical and empirical studies is needed to understand better the prevalence and basis of the correlation between dispersal and specialisation.
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Affiliation(s)
- Virginie Ravigné
- CIRAD, UMR PHIM, - PHIM, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, TA A-120/K, Campus international de Baillarguet, avenue du Campus d'Agropolis, Montpellier Cedex 5, 34398, France
| | - Leonor R Rodrigues
- cE3c: Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, edifício C2, Lisboa, 1749-016, Portugal
| | - Maud Charlery de la Masselière
- cE3c: Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, edifício C2, Lisboa, 1749-016, Portugal
| | - Benoît Facon
- CBGP, INRAE, IRD, CIRAD, Institut Agro, University of Montpellier, 755 avenue du Campus Agropolis, CS 34988, Montferrier sur Lez cedex, 30016, France
| | - Lechosław Kuczyński
- Population Ecology Lab, Faculty of Biology, Institute of Environmental Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, Poznań, 61-614, Poland
| | - Jacek Radwan
- Evolutionary Biology Group, Faculty of Biology, Institute of Environmental Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, Poznań, 61-614, Poland
| | - Anna Skoracka
- Population Ecology Lab, Faculty of Biology, Institute of Environmental Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, Poznań, 61-614, Poland
| | - Sara Magalhães
- cE3c: Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, edifício C2, Lisboa, 1749-016, Portugal
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6
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Erlenbach T, Haynes L, Fish O, Beveridge J, Giambrone S, Reed LK, Dyer KA, Scott Chialvo CH. Investigating the phylogenetic history of toxin tolerance in mushroom-feeding Drosophila. Ecol Evol 2023; 13:e10736. [PMID: 38099137 PMCID: PMC10719611 DOI: 10.1002/ece3.10736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/01/2023] [Accepted: 11/02/2023] [Indexed: 12/17/2023] Open
Abstract
Understanding how and when key novel adaptations evolved is a central goal of evolutionary biology. Within the immigrans-tripunctata radiation of Drosophila, many mushroom-feeding species are tolerant of host toxins, such as cyclopeptides, that are lethal to nearly all other eukaryotes. In this study, we used phylogenetic and functional approaches to investigate the evolution of cyclopeptide tolerance in the immigrans-tripunctata radiation of Drosophila. First, we inferred the evolutionary relationships among 48 species in this radiation using 978 single copy orthologs. Our results resolved previous incongruities within species groups across the phylogeny. Second, we expanded on previous studies of toxin tolerance by assaying 16 of these species for tolerance to α-amanitin and found that six of them could develop on diet with toxin. Finally, we asked how α-amanitin tolerance might have evolved across the immigrans-tripunctata radiation, and inferred that toxin tolerance was ancestral in mushroom-feeding Drosophila and subsequently lost multiple times. Our findings expand our understanding of toxin tolerance across the immigrans-tripunctata radiation and emphasize the uniqueness of toxin tolerance in this adaptive radiation and the complexity of biochemical adaptations.
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Affiliation(s)
| | - Lauren Haynes
- Department of Biological SciencesUniversity of AlabamaTuscaloosaAlabamaUSA
| | - Olivia Fish
- Department of Biological SciencesUniversity of AlabamaTuscaloosaAlabamaUSA
| | - Jordan Beveridge
- Department of Biological SciencesUniversity of AlabamaTuscaloosaAlabamaUSA
| | | | - Laura K. Reed
- Department of Biological SciencesUniversity of AlabamaTuscaloosaAlabamaUSA
| | - Kelly A. Dyer
- Department of GeneticsUniversity of GeorgiaAthensGeorgiaUSA
| | - Clare H. Scott Chialvo
- Department of Biological SciencesUniversity of AlabamaTuscaloosaAlabamaUSA
- Department of BiologyAppalachian State UniversityBooneNorth CarolinaUSA
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7
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Gonçalves C, Harrison MC, Steenwyk JL, Opulente DA, LaBella AL, Wolters JF, Zhou X, Shen XX, Groenewald M, Hittinger CT, Rokas A. Diverse signatures of convergent evolution in cacti-associated yeasts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.14.557833. [PMID: 37745407 PMCID: PMC10515907 DOI: 10.1101/2023.09.14.557833] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Many distantly related organisms have convergently evolved traits and lifestyles that enable them to live in similar ecological environments. However, the extent of phenotypic convergence evolving through the same or distinct genetic trajectories remains an open question. Here, we leverage a comprehensive dataset of genomic and phenotypic data from 1,049 yeast species in the subphylum Saccharomycotina (Kingdom Fungi, Phylum Ascomycota) to explore signatures of convergent evolution in cactophilic yeasts, ecological specialists associated with cacti. We inferred that the ecological association of yeasts with cacti arose independently ~17 times. Using machine-learning, we further found that cactophily can be predicted with 76% accuracy from functional genomic and phenotypic data. The most informative feature for predicting cactophily was thermotolerance, which is likely associated with duplication and altered evolutionary rates of genes impacting the cell envelope in several cactophilic lineages. We also identified horizontal gene transfer and duplication events of plant cell wall-degrading enzymes in distantly related cactophilic clades, suggesting that putatively adaptive traits evolved through disparate molecular mechanisms. Remarkably, multiple cactophilic lineages and their close relatives are emerging human opportunistic pathogens, suggesting that the cactophilic lifestyle-and perhaps more generally lifestyles favoring thermotolerance-may preadapt yeasts to cause human disease. This work underscores the potential of a multifaceted approach involving high throughput genomic and phenotypic data to shed light onto ecological adaptation and highlights how convergent evolution to wild environments could facilitate the transition to human pathogenicity.
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Affiliation(s)
- Carla Gonçalves
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- Present address: Associate Laboratory i4HB—Institute for Health and Bioeconomy and UCIBIO—Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Present address: UCIBIO-i4HB, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Marie-Claire Harrison
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Jacob L. Steenwyk
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Dana A. Opulente
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institu te, University of Wisconsin-Madison, Madison, WI 53726, USA
- Biology Department, Villanova University, Villanova, PA 19085, USA
| | - Abigail L. LaBella
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte NC 28223
| | - John F. Wolters
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institu te, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Xiaofan Zhou
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Xing-Xing Shen
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- College of Agriculture and Biotechnology and Centre for Evolutionary & Organismal Biology, Zhejiang University, Hangzhou 310058, China
| | | | - Chris Todd Hittinger
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institu te, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Antonis Rokas
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
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8
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Yano J, Nave C, Larratt K, Honey P, Jingco C, Roberts M, Trotter D, He X, Elezi G, Whitelegge JP, Wasserman S, Donlea JM. Elevated sleep need in a stress-resilient Drosophila species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.27.542279. [PMID: 37292829 PMCID: PMC10245952 DOI: 10.1101/2023.05.27.542279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Sleep is broadly conserved across the animal kingdom, but can vary widely between species. It is currently unclear which types of selective pressures and sleep regulatory mechanisms influence differences in sleep between species. The fruit fly Drosophila melanogaster has become a successful model system for examining sleep regulation and function, but little is known about the sleep patterns and need for sleep in many related fly species. Here, we find that Drosophila mojavensis, a fly species that has adapted to extreme desert environments, exhibits strong increases in sleep compared to D. melanogaster. Long-sleeping D. mojavensis show intact sleep homeostasis, indicating that these flies carry an elevated need for sleep. In addition, D. mojavensis exhibit altered abundance or distribution of several sleep/wake related neuromodulators and neuropeptides that are consistent with their reduced locomotor activity, and increased sleep. Finally, we find that in a nutrient-deprived environment, the sleep responses of individual D. mojavensis are correlated with their survival time. Our results demonstrate that D. mojavensis is a novel model for studying organisms with high sleep need, and for exploring sleep strategies that provide resilience in extreme environments.
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Affiliation(s)
- Jessica Yano
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- Molecular, Cellular & Integrative Physiology Interdepartmental PhD Program, UCLA, Los Angeles, CA 90095, USA
| | - Ceazar Nave
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Katherine Larratt
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Phia Honey
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- Department of Neuroscience, Wellesley College, Wellesley, MA 02481, USA
| | - Cassandra Jingco
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Makayla Roberts
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Damion Trotter
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- Molecular, Cellular & Integrative Physiology Interdepartmental PhD Program, UCLA, Los Angeles, CA 90095, USA
| | - Xin He
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Gazmend Elezi
- Pasarow Mass Spectrometry Laboratory, Jane & Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- Cotsen Institute of Archaeology, UCLA, Los Angeles, CA 90095, USA
| | - Julian P. Whitelegge
- Pasarow Mass Spectrometry Laboratory, Jane & Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Sara Wasserman
- Department of Neuroscience, Wellesley College, Wellesley, MA 02481, USA
| | - Jeffrey M. Donlea
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
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9
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Ribeiro LB, Proença CEB, Tidon R. Host Preferences Shown by Drosophilids (Diptera) in a Commercial Fruit and Vegetable Distribution Center Follow the Wild Neotropical Pattern. INSECTS 2023; 14:375. [PMID: 37103190 PMCID: PMC10141734 DOI: 10.3390/insects14040375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/04/2023] [Accepted: 04/08/2023] [Indexed: 06/19/2023]
Abstract
Although drosophilids have been extensively studied in laboratories worldwide, their ecology is still relatively poorly understood. This is unfortunate because some species are currently expanding their geographic distribution and infesting fruit crops. Here, we investigated the relationship between drosophilids and potential plant hosts in a commercial fruit and vegetable distribution center in the Neotropical region. We collected discarded fruits and vegetables from this commercial center during two time periods (2007-2008 and 2017-2018). Resources were weighted and individually monitored in the laboratory. The drosophilids that emerged were identified, and the relationship between them and their resources was explored. From the 99,478 kg of potential hosts collected, we identified 48 plant taxa, from which 48,894 drosophilids of 16 species emerged. On both collecting occasions, drosophilid assemblages were strongly dominated by basically the same exotic species, which explore a broader range of resources, especially those of exotic origin, when compared to neotropical drosophilids. These results are concerning because the studied site, Along with other urban markets around the world, might be acting as sources of generalist widespread species that disperse to surrounding natural vegetation and contribute to biotic homogenization.
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Affiliation(s)
- Laís Barbosa Ribeiro
- Graduate Program in Ecology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil;
| | | | - Rosana Tidon
- Graduate Program in Ecology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil;
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília, Brasilia 70910-900, Brazil
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10
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Rondón JJ, Moreyra NN, Pisarenco VA, Rozas J, Hurtado J, Hasson E. Evolution of the odorant-binding protein gene family in Drosophila. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.957247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Odorant-binding proteins (OBPs) are encoded by a gene family involved in the perception of olfactory signals in insects. This chemosensory gene family has been advocated as a candidate to mediate host preference and host shifts in insects, although it also participates in other physiological processes. Remarkable differences in the OBP gene repertoire have been described across insect groups, suggesting an accelerated gene turnover rate. The genus Drosophila, is a valuable resource for ecological genomics studies since it comprises groups of ecologically diverse species and there are genome data for many of them. Here, we investigate the molecular evolution of this chemosensory gene family across 19 Drosophila genomes, including the melanogaster and repleta species groups, which are mostly associated with rotting fruit and cacti, respectively. We also compared the OBP repertoire among the closely related species of the repleta group, associated with different subfamilies of Cactaceae that represent disparate chemical challenges for the flies. We found that the gene family size varies widely between species, ranging from 39 to 54 candidate OBPs. Indeed, more than 54% of these genes are organized in clusters and located on chromosomes X, 2, and 5, with a distribution conserved throughout the genus. The family sizes in the repleta group and D. virilis (virilis-repleta radiation) were smaller than in the melanogaster group. We tested alternative evolutionary models for OBP family size and turnover rates based on different ecological scenarios. We found heterogeneous gene turnover rates (GR) in comparisons involving columnar cactus specialists, prickly pear specialists, and fruit dwellers lineages, and signals of rapid molecular evolution compatible with positive selection in specific OBP genes. Taking ours and previous results together, we propose that this chemosensory gene family is involved in host adaptation and hypothesize that the adoption of the cactophilic lifestyle in the repleta group accelerated the evolution of members of the family.
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11
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Padró J, De Panis DN, Luisi P, Dopazo H, Szajnman S, Hasson E, Soto IM. Ortholog genes from cactophilic Drosophila provide insight into human adaptation to hallucinogenic cacti. Sci Rep 2022; 12:13180. [PMID: 35915153 PMCID: PMC9343604 DOI: 10.1038/s41598-022-17118-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 07/20/2022] [Indexed: 11/18/2022] Open
Abstract
Cultural transformations of lifestyles and dietary practices have been key drivers of human evolution. However, while most of the evidence of genomic adaptations is related to the hunter-gatherer transition to agricultural societies, little is known on the influence of other major cultural manifestations. Shamanism is considered the oldest religion that predominated throughout most of human prehistory and still prevails in many indigenous populations. Several lines of evidence from ethno-archeological studies have demonstrated the continuity and importance of psychoactive plants in South American cultures. However, despite the well-known importance of secondary metabolites in human health, little is known about its role in the evolution of ethnic differences. Herein, we identified candidate genes of adaptation to hallucinogenic cactus in Native Andean populations with a long history of shamanic practices. We used genome-wide expression data from the cactophilic fly Drosophila buzzatii exposed to a hallucinogenic columnar cactus, also consumed by humans, to identify ortholog genes exhibiting adaptive footprints of alkaloid tolerance. Genomic analyses in human populations revealed a suite of ortholog genes evolving under recent positive selection in indigenous populations of the Central Andes. Our results provide evidence of selection in genetic variants related to alkaloids toxicity, xenobiotic metabolism, and neuronal plasticity in Aymara and Quechua populations, suggesting a possible process of gene-culture coevolution driven by religious practices.
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Affiliation(s)
- Julian Padró
- INIBIOMA-CONICET, Universidad Nacional del Comahue, Quintral 1250, R8400FRF, San Carlos de Bariloche, Argentina.
| | - Diego N De Panis
- IEGEBA-CONICET, Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Intendente Güiraldes 2160, C1428EHA, Buenos Aires, Argentina
| | - Pierre Luisi
- Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba (FFyH-UNC), Córdoba, Argentina.,Microbial Paleogenomics Unit, Institut Pasteur, 25-28 Rue du Dr Roux, 75015, Paris, France
| | - Hernan Dopazo
- IEGEBA-CONICET, Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Intendente Güiraldes 2160, C1428EHA, Buenos Aires, Argentina
| | - Sergio Szajnman
- Departamento de Química Orgánica and UMYMFOR (CONICET-FCEyN), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Intendente Güiraldes 2160, C1428EHA, Buenos Aires, Argentina
| | - Esteban Hasson
- IEGEBA-CONICET, Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Intendente Güiraldes 2160, C1428EHA, Buenos Aires, Argentina
| | - Ignacio M Soto
- IEGEBA-CONICET, Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Intendente Güiraldes 2160, C1428EHA, Buenos Aires, Argentina
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12
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De Panis D, Dopazo H, Bongcam-Rudloff E, Conesa A, Hasson E. Transcriptional responses are oriented towards different components of the rearing environment in two Drosophila sibling species. BMC Genomics 2022; 23:515. [PMID: 35840900 PMCID: PMC9288027 DOI: 10.1186/s12864-022-08745-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/01/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND The chance to compare patterns of differential gene expression in related ecologically distinct species can be particularly fruitful to investigate the genetics of adaptation and phenotypic plasticity. In this regard, a powerful technique such as RNA-Seq applied to ecologically amenable taxa allows to address issues that are not possible in classic model species. Here, we study gene expression profiles and larval performance of the cactophilic siblings Drosophila buzzatii and D. koepferae reared in media that approximate natural conditions and evaluate both chemical and nutritional components of the diet. These closely related species are complementary in terms of host-plant use since the primary host of one is the secondary of the other. D. koepferae is mainly a columnar cactus dweller while D. buzzatii prefers Opuntia hosts. RESULTS Our comparative study shows that D. buzzatii and D. koepferae have different transcriptional strategies to face the challenges posed by their natural resources. The former has greater transcriptional plasticity, and its response is mainly modulated by alkaloids of its secondary host, while the latter has a more canalized genetic response, and its transcriptional plasticity is associated with the cactus species. CONCLUSIONS Our study unveils a complex pleiotropic genetic landscape in both species, with functional links that relate detox responses and redox mechanisms with developmental and neurobiological processes. These results contribute to deepen our understanding of the role of host plant shifts and natural stress driving ecological specialization.
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Affiliation(s)
- D De Panis
- Instituto de Ecología, Genética y Evolución de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - H Dopazo
- Instituto de Ecología, Genética y Evolución de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - E Bongcam-Rudloff
- SLU-Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - A Conesa
- Microbiology and Cell Science Department, University of Florida, Gainesville, Florida, USA
| | - E Hasson
- Instituto de Ecología, Genética y Evolución de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina.
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
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13
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Ferreira EA, Lambert S, Verrier T, Marion-Poll F, Yassin A. Soft Selective Sweep on Chemosensory Genes Correlates with Ancestral Preference for Toxic Noni in a Specialist Drosophila Population. Genes (Basel) 2020; 12:genes12010032. [PMID: 33383708 PMCID: PMC7824377 DOI: 10.3390/genes12010032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/17/2020] [Accepted: 12/22/2020] [Indexed: 12/14/2022] Open
Abstract
Understanding how organisms adapt to environmental changes is a major question in evolution and ecology. In particular, the role of ancestral variation in rapid adaptation remains unclear because its trace on genetic variation, known as soft selective sweep, is often hardly recognizable from genome-wide selection scans. Here, we investigate the evolution of chemosensory genes in Drosophila yakuba mayottensis, a specialist subspecies on toxic noni (Morinda citrifolia) fruits on the island of Mayotte. We combine population genomics analyses and behavioral assays to evaluate the level of divergence in chemosensory genes and perception of noni chemicals between specialist and generalist subspecies of D. yakuba. We identify a signal of soft selective sweep on a handful of genes, with the most diverging ones involving a cluster of gustatory receptors expressed in bitter-sensing neurons. Our results highlight the potential role of ancestral genetic variation in promoting host plant specialization in herbivorous insects and identify a number of candidate genes underlying behavioral adaptation.
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Affiliation(s)
- Erina A. Ferreira
- Laboratoire Évolution, Génomes, Comportement et Écologie, CNRS, IRD, Université Paris-Saclay, 91198 Gif-sur-Yvette, France; (E.A.F.); (F.M.-P.)
- Institut Systématique Evolution Biodiversité (ISYEB) Centre National de la Recherche Scientifique, MNHN, Sorbonne Université, EPHE 57 rue Cuvier, CP 50, 75005 Paris, France; (S.L.); (T.V.)
| | - Sophia Lambert
- Institut Systématique Evolution Biodiversité (ISYEB) Centre National de la Recherche Scientifique, MNHN, Sorbonne Université, EPHE 57 rue Cuvier, CP 50, 75005 Paris, France; (S.L.); (T.V.)
| | - Thibault Verrier
- Institut Systématique Evolution Biodiversité (ISYEB) Centre National de la Recherche Scientifique, MNHN, Sorbonne Université, EPHE 57 rue Cuvier, CP 50, 75005 Paris, France; (S.L.); (T.V.)
| | - Frédéric Marion-Poll
- Laboratoire Évolution, Génomes, Comportement et Écologie, CNRS, IRD, Université Paris-Saclay, 91198 Gif-sur-Yvette, France; (E.A.F.); (F.M.-P.)
- AgroParisTech, Université Paris-Saclay, 75231 Paris, France
| | - Amir Yassin
- Laboratoire Évolution, Génomes, Comportement et Écologie, CNRS, IRD, Université Paris-Saclay, 91198 Gif-sur-Yvette, France; (E.A.F.); (F.M.-P.)
- Institut Systématique Evolution Biodiversité (ISYEB) Centre National de la Recherche Scientifique, MNHN, Sorbonne Université, EPHE 57 rue Cuvier, CP 50, 75005 Paris, France; (S.L.); (T.V.)
- Correspondence:
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14
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Khallaf MA, Auer TO, Grabe V, Depetris-Chauvin A, Ammagarahalli B, Zhang DD, Lavista-Llanos S, Kaftan F, Weißflog J, Matzkin LM, Rollmann SM, Löfstedt C, Svatoš A, Dweck HKM, Sachse S, Benton R, Hansson BS, Knaden M. Mate discrimination among subspecies through a conserved olfactory pathway. SCIENCE ADVANCES 2020; 6:eaba5279. [PMID: 32704542 PMCID: PMC7360436 DOI: 10.1126/sciadv.aba5279] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 05/07/2020] [Indexed: 05/22/2023]
Abstract
Communication mechanisms underlying the sexual isolation of species are poorly understood. Using four subspecies of Drosophila mojavensis as a model, we identify two behaviorally active, male-specific pheromones. One functions as a conserved male antiaphrodisiac in all subspecies and acts via gustation. The second induces female receptivity via olfaction exclusively in the two subspecies that produce it. Genetic analysis of the cognate receptor for the olfactory pheromone indicates an important role for this sensory pathway in promoting sexual isolation of subspecies, in combination with auditory signals. Unexpectedly, the peripheral sensory pathway detecting this pheromone is conserved molecularly, physiologically, and anatomically across subspecies. These observations imply that subspecies-specific behaviors arise from differential interpretation of the same peripheral cue, reminiscent of sexually conserved detection but dimorphic interpretation of male pheromones in Drosophila melanogaster. Our results reveal that, during incipient speciation, pheromone production, detection, and interpretation do not necessarily evolve in a coordinated manner.
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Affiliation(s)
- Mohammed A. Khallaf
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Thomas O. Auer
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Veit Grabe
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Ana Depetris-Chauvin
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Byrappa Ammagarahalli
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Dan-Dan Zhang
- Department of Biology, Lund University, SE-22362 Lund, Sweden
| | - Sofía Lavista-Llanos
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Filip Kaftan
- Group of Mass Spectrometry and Proteomics, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Jerrit Weißflog
- Group of Mass Spectrometry and Proteomics, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Luciano M. Matzkin
- Department of Entomology, University of Arizona, 1140 E. South Campus Drive, Tucson, AZ 85721, USA
| | - Stephanie M. Rollmann
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | | | - Aleš Svatoš
- Group of Mass Spectrometry and Proteomics, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Hany K. M. Dweck
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Silke Sachse
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Richard Benton
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Bill S. Hansson
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Markus Knaden
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
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15
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Rêgo A, Chaturvedi S, Springer A, Lish AM, Barton CL, Kapheim KM, Messina FJ, Gompert Z. Combining Experimental Evolution and Genomics to Understand How Seed Beetles Adapt to a Marginal Host Plant. Genes (Basel) 2020; 11:genes11040400. [PMID: 32276323 PMCID: PMC7230198 DOI: 10.3390/genes11040400] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 04/01/2020] [Accepted: 04/01/2020] [Indexed: 12/21/2022] Open
Abstract
Genes that affect adaptive traits have been identified, but our knowledge of the genetic basis of adaptation in a more general sense (across multiple traits) remains limited. We combined population-genomic analyses of evolve-and-resequence experiments, genome-wide association mapping of performance traits, and analyses of gene expression to fill this knowledge gap and shed light on the genomics of adaptation to a marginal host (lentil) by the seed beetle Callosobruchus maculatus. Using population-genomic approaches, we detected modest parallelism in allele frequency change across replicate lines during adaptation to lentil. Mapping populations derived from each lentil-adapted line revealed a polygenic basis for two host-specific performance traits (weight and development time), which had low to modest heritabilities. We found less evidence of parallelism in genotype-phenotype associations across these lines than in allele frequency changes during the experiments. Differential gene expression caused by differences in recent evolutionary history exceeded that caused by immediate rearing host. Together, the three genomic datasets suggest that genes affecting traits other than weight and development time are likely to be the main causes of parallel evolution and that detoxification genes (especially cytochrome P450s and beta-glucosidase) could be especially important for colonization of lentil by C. maculatus.
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Affiliation(s)
- Alexandre Rêgo
- Department of Biology, Utah State University, Logan, UT 84322, USA; (A.R.); (A.S.); (A.M.L.); (C.L.B.); (K.M.K.); (F.J.M.)
- Department of Zoology, Stockholm University, 114 19 Stockholm, Sweden
| | - Samridhi Chaturvedi
- Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA;
| | - Amy Springer
- Department of Biology, Utah State University, Logan, UT 84322, USA; (A.R.); (A.S.); (A.M.L.); (C.L.B.); (K.M.K.); (F.J.M.)
| | - Alexandra M. Lish
- Department of Biology, Utah State University, Logan, UT 84322, USA; (A.R.); (A.S.); (A.M.L.); (C.L.B.); (K.M.K.); (F.J.M.)
| | - Caroline L. Barton
- Department of Biology, Utah State University, Logan, UT 84322, USA; (A.R.); (A.S.); (A.M.L.); (C.L.B.); (K.M.K.); (F.J.M.)
| | - Karen M. Kapheim
- Department of Biology, Utah State University, Logan, UT 84322, USA; (A.R.); (A.S.); (A.M.L.); (C.L.B.); (K.M.K.); (F.J.M.)
| | - Frank J. Messina
- Department of Biology, Utah State University, Logan, UT 84322, USA; (A.R.); (A.S.); (A.M.L.); (C.L.B.); (K.M.K.); (F.J.M.)
| | - Zachariah Gompert
- Department of Biology, Utah State University, Logan, UT 84322, USA; (A.R.); (A.S.); (A.M.L.); (C.L.B.); (K.M.K.); (F.J.M.)
- Correspondence:
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16
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Clark RM, Ragland GJ. Editorial overview: Tapping arthropod diversity to elaborate the genotype-to-phenotype map. CURRENT OPINION IN INSECT SCIENCE 2019; 36:v-viii. [PMID: 31732447 DOI: 10.1016/j.cois.2019.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
- Richard M Clark
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA.
| | - Gregory J Ragland
- Department of Integrative Biology, University of Colorado Denver, Denver, CO 80217, USA
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