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Bontonou G, Saint-Leandre B, Kafle T, Baticle T, Hassan A, Sánchez-Alcañiz JA, Arguello JR. Evolution of chemosensory tissues and cells across ecologically diverse Drosophilids. Nat Commun 2024; 15:1047. [PMID: 38316749 PMCID: PMC10844241 DOI: 10.1038/s41467-023-44558-4] [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: 05/10/2023] [Accepted: 12/19/2023] [Indexed: 02/07/2024] Open
Abstract
Chemosensory tissues exhibit significant between-species variability, yet the evolution of gene expression and cell types underlying this diversity remain poorly understood. To address these questions, we conducted transcriptomic analyses of five chemosensory tissues from six Drosophila species and integrated the findings with single-cell datasets. While stabilizing selection predominantly shapes chemosensory transcriptomes, thousands of genes in each tissue have evolved expression differences. Genes that have changed expression in one tissue have often changed in multiple other tissues but at different past epochs and are more likely to be cell type-specific than unchanged genes. Notably, chemosensory-related genes have undergone widespread expression changes, with numerous species-specific gains/losses including novel chemoreceptors expression patterns. Sex differences are also pervasive, including a D. melanogaster-specific excess of male-biased expression in sensory and muscle cells in its forelegs. Together, our analyses provide new insights for understanding evolutionary changes in chemosensory tissues at both global and individual gene levels.
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Affiliation(s)
- Gwénaëlle Bontonou
- Department of Ecology & Evolution, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Bastien Saint-Leandre
- Department of Ecology & Evolution, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Tane Kafle
- Department of Ecology & Evolution, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tess Baticle
- Department of Ecology & Evolution, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Afrah Hassan
- Department of Ecology & Evolution, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | | | - J Roman Arguello
- Department of Ecology & Evolution, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.
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2
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Vertacnik KL, Herrig DK, Godfrey RK, Hill T, Geib SM, Unckless RL, Nelson DR, Linnen CR. Evolution of five environmentally responsive gene families in a pine-feeding sawfly, Neodiprion lecontei (Hymenoptera: Diprionidae). Ecol Evol 2023; 13:e10506. [PMID: 37791292 PMCID: PMC10542623 DOI: 10.1002/ece3.10506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 10/05/2023] Open
Abstract
A central goal in evolutionary biology is to determine the predictability of adaptive genetic changes. Despite many documented cases of convergent evolution at individual loci, little is known about the repeatability of gene family expansions and contractions. To address this void, we examined gene family evolution in the redheaded pine sawfly Neodiprion lecontei, a noneusocial hymenopteran and exemplar of a pine-specialized lineage evolved from angiosperm-feeding ancestors. After assembling and annotating a draft genome, we manually annotated multiple gene families with chemosensory, detoxification, or immunity functions before characterizing their genomic distributions and molecular evolution. We find evidence of recent expansions of bitter gustatory receptor, clan 3 cytochrome P450, olfactory receptor, and antimicrobial peptide subfamilies, with strong evidence of positive selection among paralogs in a clade of gustatory receptors possibly involved in the detection of bitter compounds. In contrast, these gene families had little evidence of recent contraction via pseudogenization. Overall, our results are consistent with the hypothesis that in response to novel selection pressures, gene families that mediate ecological interactions may expand and contract predictably. Testing this hypothesis will require the comparative analysis of high-quality annotation data from phylogenetically and ecologically diverse insect species and functionally diverse gene families. To this end, increasing sampling in under-sampled hymenopteran lineages and environmentally responsive gene families and standardizing manual annotation methods should be prioritized.
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Affiliation(s)
- Kim L. Vertacnik
- Department of EntomologyUniversity of KentuckyLexingtonKentuckyUSA
| | | | - R. Keating Godfrey
- McGuire Center for Lepidoptera and Biodiversity, University of FloridaGainesvilleFloridaUSA
| | - Tom Hill
- National Institute of Allergy and Infectious DiseasesBethesdaMarylandUSA
| | - Scott M. Geib
- Tropical Crop and Commodity Protection Research UnitUnited States Department of Agriculture: Agriculture Research Service Pacific Basin Agricultural Research CenterHiloHawaiiUSA
| | - Robert L. Unckless
- Department of Molecular BiosciencesUniversity of KansasLawrenceKansasUSA
| | - David R. Nelson
- Department of Microbiology, Immunology and BiochemistryUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
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3
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De Novo Assembly and Characterization of the Transcriptome of an Omnivorous Camel Cricket ( Tachycines meditationis). Int J Mol Sci 2023; 24:ijms24044005. [PMID: 36835417 PMCID: PMC9966759 DOI: 10.3390/ijms24044005] [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: 01/02/2023] [Revised: 01/12/2023] [Accepted: 01/16/2023] [Indexed: 02/18/2023] Open
Abstract
Tachycines meditationis (Orthoptera: Rhaphidophoridae: Tachycines) is a widely distributed insect in eastern Asia. This species is common in urban environments, and its unique omnivorous diet may contribute to its success in various habitats. However, molecular studies on the species are scarce. Here, we obtained the first transcriptome sequence of T. meditationis and performed preliminary analyses to test whether the evolution of coding sequences fits the expectations based on the species' ecology. We retrieved 476,495 effective transcripts and annotated 46,593 coding sequences (CDS). We analysed the codon usage and found that directional mutation pressure was the leading cause of codon usage bias in this species. This genome-wide relaxed codon usage pattern in T. meditationis is surprising, given the potentially large population size of this species. Moreover, despite the omnivorous diet, the chemosensory genes of this species do not exhibit codon usage deviating significantly from the genome-level pattern. They also do not seem to experience more gene family expansion than other cave cricket species do. A thorough search for rapidly evolved genes using the dN/dS value showed that genes associated with substance synthesis and metabolic pathways, such as retinol metabolism, aminoacyl-tRNA biosynthesis, and fatty acid metabolism, underwent species-specific positive selection. While some results seem to contradict the species ecology, our transcriptome assembly provides a valuable molecular resource for future studies on camel cricket evolution and molecular genetics for feeding ecology in insects, in general.
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4
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Johny J, Diallo S, Lukšan O, Shewale M, Kalinová B, Hanus R, Große-Wilde E. Conserved orthology in termite chemosensory gene families. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.1065947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Termites are eusocial insects known to use a variety of pheromones in tasks necessary for maintenance of their societies. As such, olfaction and pheromone communication in termites has been an object of intense study; trail-following pheromones (TFPs) and sex-pairing pheromones (SPPs), for example, have been identified in many termite species. In contrast, the molecular basis of olfactory detection is understudied in the group. Here, we present chemosensory genes of three species of termites belonging to three distinct lineages, Neotermes cubanus (Kalotermitidae), Prorhinotermes simplex (Rhinotermitidae), and Inquilinitermes inquilinus (Termitidae). Using antennal transcriptome screening of termite workers, we identified the chemosensory genes, which allowed us to perform phylogenetic analysis. We found a comparatively large repertoires of odorant receptors (ORs), gustatory receptors (GRs), ionotropic receptors (IRs), odorant binding proteins (OBPs), chemosensory proteins (CSPs), and sensory neuron membrane proteins (SNMPs). The evolutionary analysis of termite chemosensory genes revealed Isoptera-specific expansions with a 1:1 orthologous pattern, indicating the existence of conserved olfactory functions. Our findings on basal eusocial insects will further enhance our understanding of the molecular underpinnings of eusociality and the evolution of olfactory communication in termites.
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Abstract
Among the many wonders of nature, the sense of smell of the fly Drosophila melanogaster might seem, at first glance, of esoteric interest. Nevertheless, for over a century, the 'nose' of this insect has been an extraordinary system to explore questions in animal behaviour, ecology and evolution, neuroscience, physiology and molecular genetics. The insights gained are relevant for our understanding of the sensory biology of vertebrates, including humans, and other insect species, encompassing those detrimental to human health. Here, I present an overview of our current knowledge of D. melanogaster olfaction, from molecules to behaviours, with an emphasis on the historical motivations of studies and illustration of how technical innovations have enabled advances. I also highlight some of the pressing and long-term questions.
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Affiliation(s)
- Richard Benton
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
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6
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Dornburg A, Mallik R, Wang Z, Bernal MA, Thompson B, Bruford EA, Nebert DW, Vasiliou V, Yohe LR, Yoder JA, Townsend JP. Placing human gene families into their evolutionary context. Hum Genomics 2022; 16:56. [PMID: 36369063 PMCID: PMC9652883 DOI: 10.1186/s40246-022-00429-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/12/2022] [Indexed: 11/13/2022] Open
Abstract
Following the draft sequence of the first human genome over 20 years ago, we have achieved unprecedented insights into the rules governing its evolution, often with direct translational relevance to specific diseases. However, staggering sequence complexity has also challenged the development of a more comprehensive understanding of human genome biology. In this context, interspecific genomic studies between humans and other animals have played a critical role in our efforts to decode human gene families. In this review, we focus on how the rapid surge of genome sequencing of both model and non-model organisms now provides a broader comparative framework poised to empower novel discoveries. We begin with a general overview of how comparative approaches are essential for understanding gene family evolution in the human genome, followed by a discussion of analyses of gene expression. We show how homology can provide insights into the genes and gene families associated with immune response, cancer biology, vision, chemosensation, and metabolism, by revealing similarity in processes among distant species. We then explain methodological tools that provide critical advances and show the limitations of common approaches. We conclude with a discussion of how these investigations position us to gain fundamental insights into the evolution of gene families among living organisms in general. We hope that our review catalyzes additional excitement and research on the emerging field of comparative genomics, while aiding the placement of the human genome into its existentially evolutionary context.
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Affiliation(s)
- Alex Dornburg
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA.
| | - Rittika Mallik
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA
| | - Zheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Moisés A Bernal
- Department of Biological Sciences, College of Science and Mathematics, Auburn University, Auburn, AL, USA
| | - Brian Thompson
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Elspeth A Bruford
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Daniel W Nebert
- Department of Environmental Health, Center for Environmental Genetics, University of Cincinnati Medical Center, P.O. Box 670056, Cincinnati, OH, 45267, USA
- Department of Pediatrics and Molecular Developmental Biology, Division of Human Genetics, Cincinnati Children's Hospital, Cincinnati, OH, 45229, USA
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Laurel R Yohe
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Jeffrey P Townsend
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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7
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Roberts RJV, Pop S, Prieto-Godino LL. Evolution of central neural circuits: state of the art and perspectives. Nat Rev Neurosci 2022; 23:725-743. [DOI: 10.1038/s41583-022-00644-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2022] [Indexed: 11/09/2022]
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8
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Yohe LR, Fabbri M, Lee D, Davies KTJ, Yohe TP, Sánchez MKR, Rengifo EM, Hall RP, Mutumi G, Hedrick BP, Sadier A, Simmons NB, Sears KE, Dumont E, Rossiter SJ, Bhullar BAS, Dávalos LM. Ecological constraints on highly evolvable olfactory receptor genes and morphology in neotropical bats. Evolution 2022; 76:2347-2360. [PMID: 35904467 DOI: 10.1111/evo.14591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 05/06/2022] [Accepted: 05/13/2022] [Indexed: 01/22/2023]
Abstract
Although evolvability of genes and traits may promote specialization during species diversification, how ecology subsequently restricts such variation remains unclear. Chemosensation requires animals to decipher a complex chemical background to locate fitness-related resources, and thus the underlying genomic architecture and morphology must cope with constant exposure to a changing odorant landscape; detecting adaptation amidst extensive chemosensory diversity is an open challenge. In phyllostomid bats, an ecologically diverse clade that evolved plant visiting from a presumed insectivorous ancestor, the evolution of novel food detection mechanisms is suggested to be a key innovation, as plant-visiting species rely strongly on olfaction, supplementarily using echolocation. If this is true, exceptional variation in underlying olfactory genes and phenotypes may have preceded dietary diversification. We compared olfactory receptor (OR) genes sequenced from olfactory epithelium transcriptomes and olfactory epithelium surface area of bats with differing diets. Surprisingly, although OR evolution rates were quite variable and generally high, they are largely independent of diet. Olfactory epithelial surface area, however, is relatively larger in plant-visiting bats and there is an inverse relationship between OR evolution rates and surface area. Relatively larger surface areas suggest greater reliance on olfactory detection and stronger constraint on maintaining an already diverse OR repertoire. Instead of the typical case in which specialization and elaboration are coupled with rapid diversification of associated genes, here the relevant genes are already evolving so quickly that increased reliance on smell has led to stabilizing selection, presumably to maintain the ability to consistently discriminate among specific odorants-a potential ecological constraint on sensory evolution.
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Affiliation(s)
- Laurel R Yohe
- Department of Earth and Planetary Sciences, Yale University, New Haven, Connecticut, 06511, USA.,Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, 11794, USA.,Deaprtment of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, 28223, USA.,North Carolina Research Campus, Kannapolis, North Carolina, 28081, USA
| | - Matteo Fabbri
- Department of Earth and Planetary Sciences, Yale University, New Haven, Connecticut, 06511, USA.,Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, 60605, USA
| | - Daniela Lee
- Department of Earth and Planetary Sciences, Yale University, New Haven, Connecticut, 06511, USA.,Harvard School of Medicine, Cambridge, Massachusetts, 02115, USA
| | - Kalina T J Davies
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, E1 4NS, United Kingdom
| | | | - Miluska K R Sánchez
- Escuela Profesional de Ciencias Biológicas, Universidad Nacional de Piura, Piura, 20004, Peru
| | - Edgardo M Rengifo
- Programa de Pós-Graduação Interunidades em Ecologia Aplicada, Escola Superior de Agricultura 'Luiz de Queiroz', Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, 13416-970, Brazil.,Centro de Investigación Biodiversidad Sostenible (BioS), Lima, 15073, Peru
| | - Ronald P Hall
- School of Natural Sciences, University of California, Merced, Merced, California, 95344, USA
| | - Gregory Mutumi
- School of Natural Sciences, University of California, Merced, Merced, California, 95344, USA
| | - Brandon P Hedrick
- Department of Biomedical Sciences, Cornell University, Ithaca, New York, 14853, USA
| | - Alexa Sadier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, 90095, USA
| | - Nancy B Simmons
- Department of Mammalogy, American Museum of Natural History, New York, New York, 10024, USA
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, 90095, USA
| | - Elizabeth Dumont
- School of Natural Sciences, University of California, Merced, Merced, California, 95344, USA
| | - Stephen J Rossiter
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, E1 4NS, United Kingdom
| | - Bhart-Anjan S Bhullar
- Department of Earth and Planetary Sciences, Yale University, New Haven, Connecticut, 06511, USA.,Yale Peabody Museum of Natural History, Yale University, New Haven, Connecticut, 06511, USA
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, 11794, USA.,Center for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, New York, 11794, USA
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9
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Feitzinger AA, Le A, Thompson A, Haseeb M, Murugesan MK, Tang AM, Lott SE. Natural variation in the maternal and zygotic mRNA complements of the early embryo in Drosophila melanogaster. BMC Genomics 2022; 23:641. [PMID: 36076188 PMCID: PMC9461177 DOI: 10.1186/s12864-022-08839-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 08/10/2022] [Indexed: 11/23/2022] Open
Abstract
Background Maternal gene products supplied to the egg during oogenesis drive the earliest events of development in all metazoans. After the initial stages of embryogenesis, maternal transcripts are degraded as zygotic transcription is activated; this is known as the maternal to zygotic transition (MZT). Recently, it has been shown that the expression of maternal and zygotic transcripts have evolved in the Drosophila genus over the course of 50 million years. However, the extent of natural variation of maternal and zygotic transcripts within a species has yet to be determined. We asked how the maternal and zygotic pools of mRNA vary within and between populations of D. melanogaster. In order to maximize sampling of genetic diversity, African lines of D. melanogaster originating from Zambia as well as DGRP lines originating from North America were chosen for transcriptomic analysis. Results Generally, we find that maternal transcripts are more highly conserved, and zygotic transcripts evolve at a higher rate. We find that there is more within-population variation in transcript abundance than between populations and that expression variation is highest post- MZT between African lines. Conclusions Determining the natural variation of gene expression surrounding the MZT in natural populations of D. melanogaster gives insight into the extent of how a tightly regulated process may vary within a species, the extent of developmental constraint at both stages and on both the maternal and zygotic genomes, and reveals expression changes allowing this species to adapt as it spread across the world. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08839-4.
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Affiliation(s)
- Anna A Feitzinger
- Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA.
| | - Anthony Le
- Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA
| | - Ammon Thompson
- Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA
| | - Mehnoor Haseeb
- Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA
| | | | - Austin M Tang
- Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA
| | - Susan E Lott
- Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA
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10
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Copy number changes in co-expressed odorant receptor genes enable selection for sensory differences in drosophilid species. Nat Ecol Evol 2022; 6:1343-1353. [PMID: 35864227 DOI: 10.1038/s41559-022-01830-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 06/15/2022] [Indexed: 11/09/2022]
Abstract
Despite numerous examples of chemoreceptor gene family expansions and contractions, how these relate to modifications in the sensory neuron populations in which they are expressed remains unclear. Drosophila melanogaster's odorant receptor (Or) family is ideal for addressing this question because most Ors are expressed in distinct olfactory sensory neuron (OSN) types. Between-species changes in Or copy number may therefore indicate increases or reductions in the number of OSN populations. Here we investigated the Or67a subfamily, which exhibits copy number variation in D. melanogaster and its closest relatives: D. simulans, D. sechellia and D. mauritiana. These species' common ancestor had three Or67a paralogues that had already diverged adaptively. Following speciation, two Or67a paralogues were lost independently in D. melanogaster and D. sechellia, with ongoing positive selection shaping the intact genes. Unexpectedly, the functionally diverged Or67a paralogues in D. simulans are co-expressed in a single neuron population, which projects to a glomerulus homologous to that innervated by Or67a neurons in D. melanogaster. Thus, while sensory pathway neuroanatomy is conserved, independent selection on co-expressed receptors has contributed to species-specific peripheral coding. This work reveals a type of adaptive change largely overlooked for olfactory evolution, raising the possibility that similar processes influence other cases of insect Or co-expression.
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11
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Jiang F, Liang L, Wang J, Zhu S. Chromosome-level genome assembly of Bactrocera dorsalis reveals its adaptation and invasion mechanisms. Commun Biol 2022; 5:25. [PMID: 35017661 PMCID: PMC8752857 DOI: 10.1038/s42003-021-02966-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 12/13/2021] [Indexed: 12/14/2022] Open
Abstract
Bactrocera dorsalis is an invasive polyphagous pest causing considerable ecological and economic damage worldwide. We report a high-quality chromosome-level genome assembly and combine various transcriptome data to explore the molecular mechanisms of its rapid adaptation to new environments. The expansions of the DDE transposase superfamily and key gene families related to environmental adaptation and enrichment of the expanded and unique gene families in metabolism and defence response pathways explain its environmental adaptability. The relatively high but not significantly different expression of heat-shock proteins, regardless of the environmental conditions, suggests an intrinsic mechanism underlying its adaptation to high temperatures. The mitogen-activated protein kinase pathway plays a key role in adaptation to new environments. The prevalence of duplicated genes in its genome explains the diversity in the B. dorsalis complex. These findings provide insights into the genetic basis of the invasiveness and diversity of B. dorsalis, explaining its rapid adaptation and expansion. Jiang et al. sequence the genome of Bactrocera dorsalis, a destructive and invasive agricultural pest. Insights from this chromosome-level assembly shed light on molecular adaptations that allow for the global invasion and expansion of this pest.
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Affiliation(s)
- Fan Jiang
- Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Liang Liang
- Academy of Agricultural Planning and Engineering, MARA, Beijing, 100125, China
| | - Jing Wang
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Shuifang Zhu
- Chinese Academy of Inspection and Quarantine, Beijing, 100176, China. .,Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Hainan, 572025, China.
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12
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Wang Y, Fang G, Chen X, Cao Y, Wu N, Cui Q, Zhu C, Qian L, Huang Y, Zhan S. The genome of the black cutworm Agrotis ipsilon. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 139:103665. [PMID: 34624466 DOI: 10.1016/j.ibmb.2021.103665] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 09/29/2021] [Accepted: 09/29/2021] [Indexed: 06/13/2023]
Abstract
The black cutworm (BCW), Agrotis ipsilon, is a worldwide polyphagous and underground pest that causes a high level of economic loss to a wide range of crops through the damage of roots. This species performs non-directed migration throughout East and Southeast Asia seasonally. Lack of a genome information has limited further studies on its unique biology and the development of novel management approaches. In this study, we present a 476 Mb de novo assembly of BCW, along with a consensus gene set of 14,801 protein-coding gene models. Quality controls show that both genome assembly and annotations are high-quality and mostly complete. We focus manual annotation and comparative genomics on gene families that related to the unique attributes of this species, such as nocturnality, long-distance migration, and host adaptation. We find that the BCW genome encodes a similar gene repertoire in various migration-related gene families to the diural migratory butterfly Danaus plexiipus, with additional copies of long wavelength opsin and two eye development-related genes. On the other hand, we find that the genomes of BCW and many other polyphagous lepidopterans encode many more gustatory receptor genes, particularly the lineage-specific expanded bitter receptor genes, than the mono- or oligo-phagous species, suggesting a common role of gustatory receptors (GRs) expansion in host range expansion. The availability of a BCW genome provides valuable resources to study the molecular mechanisms of non-directed migration in lepidopteran pests and to develop novel strategies to control migratory nocturnal pests.
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Affiliation(s)
- Yaohui Wang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Gangqi Fang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Xi'en Chen
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yanghui Cao
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ningning Wu
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qian Cui
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Chenxu Zhu
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lansa Qian
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yongping Huang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China.
| | - Shuai Zhan
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China.
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13
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Prieto-Godino LL, Schmidt HR, Benton R. Molecular reconstruction of recurrent evolutionary switching in olfactory receptor specificity. eLife 2021; 10:69732. [PMID: 34677122 PMCID: PMC8575457 DOI: 10.7554/elife.69732] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 10/21/2021] [Indexed: 11/13/2022] Open
Abstract
Olfactory receptor repertoires exhibit remarkable functional diversity, but how these proteins have evolved is poorly understood. Through analysis of extant and ancestrally reconstructed drosophilid olfactory receptors from the Ionotropic receptor (Ir) family, we investigated evolution of two organic acid-sensing receptors, Ir75a and Ir75b. Despite their low amino acid identity, we identify a common ‘hotspot’ in their ligand-binding pocket that has a major effect on changing the specificity of both Irs, as well as at least two distinct functional transitions in Ir75a during evolution. Moreover, we show that odor specificity is refined by changes in additional, receptor-specific sites, including those outside the ligand-binding pocket. Our work reveals how a core, common determinant of ligand-tuning acts within epistatic and allosteric networks of substitutions to lead to functional evolution of olfactory receptors.
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Affiliation(s)
- Lucia L Prieto-Godino
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.,The Francis Crick Institute, London, United Kingdom
| | - Hayden R Schmidt
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Richard Benton
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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14
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Yue L, Cao LJ, Chen JC, Gong YJ, Lin YH, Hoffmann AA, Wei SJ. Low levels of genetic differentiation with isolation by geography and environment in populations of Drosophila melanogaster from across China. Heredity (Edinb) 2021; 126:942-954. [PMID: 33686193 PMCID: PMC8178374 DOI: 10.1038/s41437-021-00419-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 01/31/2023] Open
Abstract
The fruit fly, Drosophila melanogaster, is a model species in evolutionary studies. However, population processes of this species in East Asia are poorly studied. Here we examined the population genetic structure of D. melanogaster across China. There were 14 mitochondrial haplotypes with 10 unique ones out of 23 known from around the globe. Pairwise FST values estimated from 15 novel microsatellites ranged from 0 to 0.11, with geographically isolated populations showing the highest level of genetic uniqueness. STRUCTURE analysis identified high levels of admixture at both the individual and population levels. Mantel tests indicated a strong association between genetic distance and geographical distance as well as environmental distance. Full redundancy analysis (RDA) showed that independent effects of environmental conditions and geography accounted for 62.10% and 31.58% of the total explained genetic variance, respectively. When geographic variables were constrained in a partial RDA analysis, the environmental variables bio2 (mean diurnal air temperature range), bio13 (precipitation of the wettest month), and bio15 (precipitation seasonality) were correlated with genetic distance. Our study suggests that demographic history, geographical isolation, and environmental factors have together shaped the population genetic structure of D. melanogaster after its introduction into China.
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Affiliation(s)
- Lei Yue
- grid.418260.90000 0004 0646 9053Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Li-Jun Cao
- grid.418260.90000 0004 0646 9053Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jin-Cui Chen
- grid.418260.90000 0004 0646 9053Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ya-Jun Gong
- grid.418260.90000 0004 0646 9053Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yan-Hao Lin
- grid.418260.90000 0004 0646 9053Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China ,International Department of Beijing No. 80 High School, Beijing, China
| | - Ary Anthony Hoffmann
- grid.1008.90000 0001 2179 088XBio21 Institute, School of BioSciences, The University of Melbourne, Victoria, Australia
| | - Shu-Jun Wei
- grid.418260.90000 0004 0646 9053Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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15
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Xiao J, Wei X, Zhou Y, Xin Z, Miao Y, Hou H, Li J, Zhao D, Liu J, Chen R, Niu L, Ma G, Zhen W, He S, Wang J, Wei X, Dou W, Sui Z, Zhang H, Xing S, Shi M, Huang D. Genomes of 12 fig wasps provide insights into the adaptation of pollinators to fig syconia. J Genet Genomics 2021; 48:225-236. [PMID: 34011484 DOI: 10.1016/j.jgg.2021.02.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/14/2021] [Accepted: 02/28/2021] [Indexed: 10/21/2022]
Abstract
Figs and fig pollinators are one of the few classic textbook examples of obligate pollination mutualism. The specific dependence of fig pollinators on the relatively safe living environment with sufficient food sources in the enclosed fig syconia implies that they are vulnerable to habitat changes. However, there is still no extensive genomic evidence to reveal the evolutionary footprint of this long-term mutually beneficial symbiosis in fig pollinators. In fig syconia, there are also non-pollinator species. The non-pollinator species differ in their evolutionary and life histories from pollinators. We conducted comparative analyses on 11 newly sequenced fig wasp genomes and one previously published genome. The pollinators colonized the figs approximately 66.9 million years ago, consistent with the origin of host figs. Compared with non-pollinators, many more genes in pollinators were subject to relaxed selection. Seven genes were absent in pollinators in response to environmental stress and immune activation. Pollinators had more streamlined gene repertoires in the innate immune system, chemosensory toolbox, and detoxification system. Our results provide genomic evidence for the differentiation between pollinators and nonpollinators. The data suggest that owing to the long-term adaptation to the fig, some genes related to functions no longer required are absent in pollinators.
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Affiliation(s)
- Jinhua Xiao
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Xianqin Wei
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yi Zhou
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zhaozhe Xin
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yunheng Miao
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hongxia Hou
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jiaxing Li
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Dan Zhao
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jing Liu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Rui Chen
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Liming Niu
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Guangchang Ma
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Wenquan Zhen
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou 535011, China
| | - Shunmin He
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxia Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Xunfan Wei
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Weihao Dou
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zhuoxiao Sui
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | | | - Shilai Xing
- Berry Genomics Corporation, Beijing 102206, China
| | - Miao Shi
- Berry Genomics Corporation, Beijing 102206, China
| | - Dawei Huang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China; Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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16
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Wang Y, Ferveur JF, Moussian B. Eco-genetics of desiccation resistance in Drosophila. Biol Rev Camb Philos Soc 2021; 96:1421-1440. [PMID: 33754475 DOI: 10.1111/brv.12709] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 12/18/2022]
Abstract
Climate change globally perturbs water circulation thereby influencing ecosystems including cultivated land. Both harmful and beneficial species of insects are likely to be vulnerable to such changes in climate. As small animals with a disadvantageous surface area to body mass ratio, they face a risk of desiccation. A number of behavioural, physiological and genetic strategies are deployed to solve these problems during adaptation in various Drosophila species. Over 100 desiccation-related genes have been identified in laboratory and wild populations of the cosmopolitan fruit fly Drosophila melanogaster and its sister species in large-scale and single-gene approaches. These genes are involved in water sensing and homeostasis, and barrier formation and function via the production and composition of surface lipids and via pigmentation. Interestingly, the genetic strategy implemented in a given population appears to be unpredictable. In part, this may be due to different experimental approaches in different studies. The observed variability may also reflect a rich standing genetic variation in Drosophila allowing a quasi-random choice of response strategies through soft-sweep events, although further studies are needed to unravel any underlying principles. These findings underline that D. melanogaster is a robust species well adapted to resist climate change-related desiccation. The rich data obtained in Drosophila research provide a framework to address and understand desiccation resistance in other insects. Through the application of powerful genetic tools in the model organism D. melanogaster, the functions of desiccation-related genes revealed by correlative studies can be tested and the underlying molecular mechanisms of desiccation tolerance understood. The combination of the wealth of available data and its genetic accessibility makes Drosophila an ideal bioindicator. Accumulation of data on desiccation resistance in Drosophila may allow us to create a world map of genetic evolution in response to climate change in an insect genome. Ultimately these efforts may provide guidelines for dealing with the effects of climate-related perturbations on insect population dynamics in the future.
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Affiliation(s)
- Yiwen Wang
- Interfaculty Institute of Cell Biology, Section Animal Genetics, University of Tübingen, Auf der Morgenstelle 15, Tübingen, 72076, Germany.,School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Jean-François Ferveur
- Centre des Sciences du Goût et de l'Alimentation, UMR-CNRS 6265, Université de Bourgogne, 6, Bd Gabriel, Dijon, 21000, France
| | - Bernard Moussian
- Interfaculty Institute of Cell Biology, Section Animal Genetics, University of Tübingen, Auf der Morgenstelle 15, Tübingen, 72076, Germany.,Institute of Biology Valrose, Université Côte d'Azur, CNRS, Inserm, Parc Valrose, Nice CEDEX 2, 06108, France
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17
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Wang X, Verschut TA, Billeter JC, Maan ME. Seven Questions on the Chemical Ecology and Neurogenetics of Resource-Mediated Speciation. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.640486] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Adaptation to different environments can result in reproductive isolation between populations and the formation of new species. Food resources are among the most important environmental factors shaping local adaptation. The chemosensory system, the most ubiquitous sensory channel in the animal kingdom, not only detects food resources and their chemical composition, but also mediates sexual communication and reproductive isolation in many taxa. Chemosensory divergence may thus play a crucial role in resource-mediated adaptation and speciation. Understanding how the chemosensory system can facilitate resource-mediated ecological speciation requires integrating mechanistic studies of the chemosensory system with ecological studies, to link the genetics and physiology of chemosensory properties to divergent adaptation. In this review, we use examples of insect research to present seven key questions that can be used to understand how the chemosensory system can facilitate resource-mediated ecological speciation in consumer populations.
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18
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Gonzalez F, Borrero‐Echeverry F, Jósvai JK, Strandh M, Unelius CR, Tóth M, Witzgall P, Bengtsson M, Walker WB. Odorant receptor phylogeny confirms conserved channels for sex pheromone and host plant signals in tortricid moths. Ecol Evol 2020; 10:7334-7348. [PMID: 32760532 PMCID: PMC7391548 DOI: 10.1002/ece3.6458] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/08/2020] [Accepted: 05/12/2020] [Indexed: 11/09/2022] Open
Abstract
The search for mates and food is mediated by volatile chemicals. Insects sense food odorants and sex pheromones through odorant receptors (ORs) and pheromone receptors (PRs), which are expressed in olfactory sensory neurons. Molecular phylogenetics of ORs, informed by behavioral and functional data, generates sound hypotheses for the identification of semiochemicals driving olfactory behavior. Studying orthologous receptors and their ligands across taxa affords insights into the role of chemical communication in reproductive isolation and phylogenetic divergence. The female sex pheromone of green budworm moth Hedya nubiferana (Lepidoptera, Totricidae) is a blend of two unsaturated acetates, only a blend of both elicits male attraction. Females produce in addition codlemone, which is the sex pheromone of another tortricid, codling moth Cydia pomonella. Codlemone also attracts green budworm moth males. Concomitantly, green budworm and codling moth males are attracted to the host plant volatile pear ester. A congruent behavioral response to the same pheromone and plant volatile in two tortricid species suggests co-occurrence of dedicated olfactory channels. In codling moth, one PR is tuned to both compounds, the sex pheromone codlemone and the plant volatile pear ester. Our phylogenetic analysis finds that green budworm moth expresses an orthologous PR gene. Shared ancestry, and high levels of amino acid identity and sequence similarity, in codling and green budworm moth PRs offer an explanation for parallel attraction of both species to the same compounds. A conserved olfactory channel for a sex pheromone and a host plant volatile substantiates the alliance of social and habitat signals in insect chemical communication. Field attraction assays confirm that in silico investigations of ORs afford powerful predictions for an efficient identification of behavior-modifying semiochemicals, for an improved understanding of the mechanisms of host plant attraction in insect herbivores and for the further development of sustainable insect control.
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Affiliation(s)
- Francisco Gonzalez
- Department to Plant Protection BiologySwedish University of Agricultural SciencesAlnarpSweden
- ChemTica InternacionalHerediaCosta Rica
| | - Felipe Borrero‐Echeverry
- Department to Plant Protection BiologySwedish University of Agricultural SciencesAlnarpSweden
- Corporación Colombiana de Investgación AgropecuariaAgrosaviaMosqueraColombia
| | | | - Maria Strandh
- Department to Plant Protection BiologySwedish University of Agricultural SciencesAlnarpSweden
- Molecular Ecology and Evolution LabDepartment of BiologyLund UniversityLundSweden
| | | | - Miklós Tóth
- Plant Protection Institute CARBudapestHungary
| | - Peter Witzgall
- Department to Plant Protection BiologySwedish University of Agricultural SciencesAlnarpSweden
| | - Marie Bengtsson
- Department to Plant Protection BiologySwedish University of Agricultural SciencesAlnarpSweden
| | - William B. Walker
- Department to Plant Protection BiologySwedish University of Agricultural SciencesAlnarpSweden
- Faculty of Forestry and Wood SciencesCzech University of Life SciencesPragueCzech Republic
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19
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Price N, Lopez L, Platts AE, Lasky JR. In the presence of population structure: From genomics to candidate genes underlying local adaptation. Ecol Evol 2020; 10:1889-1904. [PMID: 32128123 DOI: 10.1101/642306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 05/26/2023] Open
Abstract
Understanding the genomic signatures, genes, and traits underlying local adaptation of organisms to heterogeneous environments is of central importance to the field evolutionary biology. To identify loci underlying local adaptation, models that combine allelic and environmental variation while controlling for the effects of population structure have emerged as the method of choice. Despite being evaluated in simulation studies, there has not been a thorough investigation of empirical evidence supporting local adaptation across these alleles. To evaluate these methods, we use 875 Arabidopsis thaliana Eurasian accessions and two mixed models (GEMMA and LFMM) to identify candidate SNPs underlying local adaptation to climate. Subsequently, to assess evidence of local adaptation and function among significant SNPs, we examine allele frequency differentiation and recent selection across Eurasian populations, in addition to their distribution along quantitative trait loci (QTL) explaining fitness variation between Italy and Sweden populations and cis-regulatory/nonsynonymous sites showing significant selective constraint. Our results indicate that significant LFMM/GEMMA SNPs show low allele frequency differentiation and linkage disequilibrium across locally adapted Italy and Sweden populations, in addition to a poor association with fitness QTL peaks (highest logarithm of odds score). Furthermore, when examining derived allele frequencies across the Eurasian range, we find that these SNPs are enriched in low-frequency variants that show very large climatic differentiation but low levels of linkage disequilibrium. These results suggest that their enrichment along putative functional sites most likely represents deleterious variation that is independent of local adaptation. Among all the genomic signatures examined, only SNPs showing high absolute allele frequency differentiation (AFD) and linkage disequilibrium (LD) between Italy and Sweden populations showed a strong association with fitness QTL peaks and were enriched along selectively constrained cis-regulatory/nonsynonymous sites. Using these SNPs, we find strong evidence linking flowering time, freezing tolerance, and the abscisic-acid pathway to local adaptation.
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Affiliation(s)
- Nicholas Price
- Department of Bioagricultural Sciences & Pest Management Colorado State University Fort Collins CO USA
- Department of Biological Sciences University of Cyprus Nicosia Cyprus
| | - Lua Lopez
- Department of Biology Binghamton University (State University of New York) Binghamton NY USA
| | - Adrian E Platts
- Simons Center for Quantitative Biology Cold Spring Harbor Laboratory Cold Spring Harbor NY USA
- Department of Biology Center for Genomics and Systems Biology New York University New York NY USA
| | - Jesse R Lasky
- Department of Biology Pennsylvania State University University Park PA USA
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20
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Price N, Lopez L, Platts AE, Lasky JR. In the presence of population structure: From genomics to candidate genes underlying local adaptation. Ecol Evol 2020; 10:1889-1904. [PMID: 32128123 PMCID: PMC7042746 DOI: 10.1002/ece3.6002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 12/25/2022] Open
Abstract
Understanding the genomic signatures, genes, and traits underlying local adaptation of organisms to heterogeneous environments is of central importance to the field evolutionary biology. To identify loci underlying local adaptation, models that combine allelic and environmental variation while controlling for the effects of population structure have emerged as the method of choice. Despite being evaluated in simulation studies, there has not been a thorough investigation of empirical evidence supporting local adaptation across these alleles. To evaluate these methods, we use 875 Arabidopsis thaliana Eurasian accessions and two mixed models (GEMMA and LFMM) to identify candidate SNPs underlying local adaptation to climate. Subsequently, to assess evidence of local adaptation and function among significant SNPs, we examine allele frequency differentiation and recent selection across Eurasian populations, in addition to their distribution along quantitative trait loci (QTL) explaining fitness variation between Italy and Sweden populations and cis-regulatory/nonsynonymous sites showing significant selective constraint. Our results indicate that significant LFMM/GEMMA SNPs show low allele frequency differentiation and linkage disequilibrium across locally adapted Italy and Sweden populations, in addition to a poor association with fitness QTL peaks (highest logarithm of odds score). Furthermore, when examining derived allele frequencies across the Eurasian range, we find that these SNPs are enriched in low-frequency variants that show very large climatic differentiation but low levels of linkage disequilibrium. These results suggest that their enrichment along putative functional sites most likely represents deleterious variation that is independent of local adaptation. Among all the genomic signatures examined, only SNPs showing high absolute allele frequency differentiation (AFD) and linkage disequilibrium (LD) between Italy and Sweden populations showed a strong association with fitness QTL peaks and were enriched along selectively constrained cis-regulatory/nonsynonymous sites. Using these SNPs, we find strong evidence linking flowering time, freezing tolerance, and the abscisic-acid pathway to local adaptation.
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Affiliation(s)
- Nicholas Price
- Department of Bioagricultural Sciences & Pest ManagementColorado State UniversityFort CollinsCOUSA
- Department of Biological SciencesUniversity of CyprusNicosiaCyprus
| | - Lua Lopez
- Department of BiologyBinghamton University (State University of New York)BinghamtonNYUSA
| | - Adrian E. Platts
- Simons Center for Quantitative BiologyCold Spring Harbor LaboratoryCold Spring HarborNYUSA
- Department of BiologyCenter for Genomics and Systems BiologyNew York UniversityNew YorkNYUSA
| | - Jesse R. Lasky
- Department of BiologyPennsylvania State UniversityUniversity ParkPAUSA
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21
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Thomas GWC, Dohmen E, Hughes DST, Murali SC, Poelchau M, Glastad K, Anstead CA, Ayoub NA, Batterham P, Bellair M, Binford GJ, Chao H, Chen YH, Childers C, Dinh H, Doddapaneni HV, Duan JJ, Dugan S, Esposito LA, Friedrich M, Garb J, Gasser RB, Goodisman MAD, Gundersen-Rindal DE, Han Y, Handler AM, Hatakeyama M, Hering L, Hunter WB, Ioannidis P, Jayaseelan JC, Kalra D, Khila A, Korhonen PK, Lee CE, Lee SL, Li Y, Lindsey ARI, Mayer G, McGregor AP, McKenna DD, Misof B, Munidasa M, Munoz-Torres M, Muzny DM, Niehuis O, Osuji-Lacy N, Palli SR, Panfilio KA, Pechmann M, Perry T, Peters RS, Poynton HC, Prpic NM, Qu J, Rotenberg D, Schal C, Schoville SD, Scully ED, Skinner E, Sloan DB, Stouthamer R, Strand MR, Szucsich NU, Wijeratne A, Young ND, Zattara EE, Benoit JB, Zdobnov EM, Pfrender ME, Hackett KJ, Werren JH, Worley KC, Gibbs RA, Chipman AD, Waterhouse RM, Bornberg-Bauer E, Hahn MW, Richards S. Gene content evolution in the arthropods. Genome Biol 2020; 21:15. [PMID: 31969194 PMCID: PMC6977273 DOI: 10.1186/s13059-019-1925-7] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/26/2019] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods. RESULTS Using 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality, and chemoperception. CONCLUSIONS These analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity.
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Affiliation(s)
- Gregg W. C. Thomas
- 0000 0001 0790 959Xgrid.411377.7Department of Biology and Department of Computer Science, Indiana University, Bloomington, IN USA
| | - Elias Dohmen
- Institute for Evolution and Biodiversity, University of Münsterss, 48149 Münster, Germany ,0000 0001 2287 2617grid.9026.dInstitute for Bioinformatics and Chemoinformatics, University of Hamburg, Hamburg, Germany ,Westphalian University of Applied Sciences, 45665 Recklinghausen, Germany
| | - Daniel S. T. Hughes
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,0000000419368729grid.21729.3fPresent Address: Institute for Genomic Medicine, Columbia University, New York, NY 10032 USA
| | - Shwetha C. Murali
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,0000000122986657grid.34477.33Present Address: Howard Hughes Medical Institute, Department of Genome Sciences, University of Washington, Seattle, WA 98195 USA
| | - Monica Poelchau
- 0000 0001 2113 2895grid.483014.aNational Agricultural Library, USDA, Beltsville, MD 20705 USA
| | - Karl Glastad
- 0000 0001 2097 4943grid.213917.fSchool of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332 USA ,0000 0004 1936 8972grid.25879.31Present Address: Penn Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104 USA
| | - Clare A. Anstead
- 0000 0001 2179 088Xgrid.1008.9Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Nadia A. Ayoub
- grid.268042.aDepartment of Biology, Washington and Lee University, 204 West Washington Street, Lexington, VA 24450 USA
| | - Phillip Batterham
- 0000 0001 2179 088Xgrid.1008.9School of BioSciences Science Faculty, The University of Melbourne, Melbourne, VIC 3010 Australia
| | - Michelle Bellair
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,Present Address: CooperGenomics, Houston, TX USA
| | - Greta J. Binford
- 0000 0004 1936 9043grid.259053.8Department of Biology, Lewis & Clark College, Portland, OR 97219 USA
| | - Hsu Chao
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Yolanda H. Chen
- 0000 0004 1936 7689grid.59062.38Department of Plant and Soil Sciences, University of Vermont, Burlington, USA
| | - Christopher Childers
- 0000 0001 2113 2895grid.483014.aNational Agricultural Library, USDA, Beltsville, MD 20705 USA
| | - Huyen Dinh
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Harsha Vardhan Doddapaneni
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Jian J. Duan
- 0000 0004 0404 0958grid.463419.dBeneficial Insects Introduction Research Unit, United States Department of Agriculture, Agricultural Research Service, Newark, DE USA
| | - Shannon Dugan
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Lauren A. Esposito
- 0000 0004 0461 6769grid.242287.9Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118 USA
| | - Markus Friedrich
- 0000 0001 1456 7807grid.254444.7Department of Biological Sciences, Wayne State University, Detroit, MI 48202 USA
| | - Jessica Garb
- 0000 0000 9620 1122grid.225262.3Department of Biological Sciences, University of Massachusetts Lowell, 198 Riverside Street, Lowell, MA 01854 USA
| | - Robin B. Gasser
- 0000 0001 2179 088Xgrid.1008.9Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Michael A. D. Goodisman
- 0000 0001 2097 4943grid.213917.fSchool of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332 USA
| | - Dawn E. Gundersen-Rindal
- 0000 0004 0404 0958grid.463419.dUSDA-ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, MD USA
| | - Yi Han
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Alfred M. Handler
- 0000 0004 0404 0958grid.463419.dUSDA-ARS, Center for Medical, Agricultural, and Veterinary Entomology, 1700 S.W. 23rd Drive, Gainesville, FL 32608 USA
| | - Masatsugu Hatakeyama
- 0000 0001 0699 0373grid.410590.9Division of Insect Sciences, National Institute of Agrobiological Sciences, Owashi, Tsukuba, 305-8634 Japan
| | - Lars Hering
- 0000 0001 1089 1036grid.5155.4Department of Zoology, Institute of Biology, University of Kassel, 34132 Kassel, Germany
| | - Wayne B. Hunter
- 0000 0004 0404 0958grid.463419.dUSDA ARS, U. S. Horticultural Research Laboratory, Ft. Pierce, FL 34945 USA
| | - Panagiotis Ioannidis
- 0000 0001 2322 4988grid.8591.5Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211 Geneva, Switzerland ,0000 0004 0635 685Xgrid.4834.bPresent Address: Foundation for Research and Technology Hellas, Institute of Molecular Biology and Biotechnology, Vassilika Vouton, 70013 Heraklion, Greece
| | - Joy C. Jayaseelan
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Divya Kalra
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Abderrahman Khila
- 0000 0001 2150 7757grid.7849.2Université de Lyon, Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d’Italie, 69364 Lyon, France
| | - Pasi K. Korhonen
- 0000 0001 2179 088Xgrid.1008.9Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Carol Eunmi Lee
- 0000 0001 0701 8607grid.28803.31Department of Integrative Biology, University of Wisconsin, Madison, WI 53706 USA
| | - Sandra L. Lee
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Yiyuan Li
- 0000 0001 2168 0066grid.131063.6Department of Biological Sciences, University of Notre Dame, 109B Galvin Life Sciences, Notre Dame, IN 46556 USA
| | - Amelia R. I. Lindsey
- 0000 0001 2222 1582grid.266097.cDepartment of Entomology, University of California Riverside, Riverside, CA USA ,0000 0001 0790 959Xgrid.411377.7Present Address: Department of Biology, Indiana University, Bloomington, IN USA
| | - Georg Mayer
- 0000 0001 1089 1036grid.5155.4Department of Zoology, Institute of Biology, University of Kassel, 34132 Kassel, Germany
| | - Alistair P. McGregor
- 0000 0001 0726 8331grid.7628.bDepartment of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP UK
| | - Duane D. McKenna
- 0000 0000 9560 654Xgrid.56061.34Department of Biological Sciences, University of Memphis, 3700 Walker Ave, Memphis, TN 38152 USA
| | - Bernhard Misof
- 0000 0001 2216 5875grid.452935.cCenter for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Mala Munidasa
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Monica Munoz-Torres
- 0000 0001 2231 4551grid.184769.5Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, USA ,0000 0004 4665 2899grid.497331.bPresent Address: Phoenix Bioinformatics, 39221 Paseo Padre Parkway, Ste. J., Fremont, CA 94538 USA
| | - Donna M. Muzny
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Oliver Niehuis
- grid.5963.9Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University of Freiburg, 79104 Freiburg (Brsg.), Germany
| | - Nkechinyere Osuji-Lacy
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Subba R. Palli
- 0000 0004 1936 8438grid.266539.dDepartment of Entomology, University of Kentucky, Lexington, KY 40546 USA
| | - Kristen A. Panfilio
- 0000 0000 8809 1613grid.7372.1School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL UK
| | - Matthias Pechmann
- 0000 0000 8580 3777grid.6190.eCologne Biocenter, Zoological Institute, Department of Developmental Biology, University of Cologne, 50674 Cologne, Germany
| | - Trent Perry
- 0000 0001 2179 088Xgrid.1008.9School of BioSciences Science Faculty, The University of Melbourne, Melbourne, VIC 3010 Australia
| | - Ralph S. Peters
- 0000 0001 2216 5875grid.452935.cCentre of Taxonomy and Evolutionary Research, Arthropoda Department, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Helen C. Poynton
- 0000 0004 0386 3207grid.266685.9School for the Environment, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Nikola-Michael Prpic
- 0000 0001 2364 4210grid.7450.6Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Abteilung für Entwicklungsbiologie, Georg-August-Universität Göttingen, Göttingen, Germany ,0000 0001 2364 4210grid.7450.6Göttingen Center for Molecular Biosciences (GZMB), Georg-August-Universität Göttingen, Göttingen, Germany
| | - Jiaxin Qu
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Dorith Rotenberg
- 0000 0001 2173 6074grid.40803.3fDepartment of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27606 USA
| | - Coby Schal
- 0000 0001 2173 6074grid.40803.3fDepartment of Entomology and W.M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695 USA
| | - Sean D. Schoville
- 0000 0001 2167 3675grid.14003.36Department of Entomology, University of Wisconsin-Madison, Madison, USA
| | - Erin D. Scully
- Stored Product Insect and Engineering Research Unit, USDA-ARS Center for Grain and Animal Health Research, Manhattan, KS 66502 USA
| | - Evette Skinner
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Daniel B. Sloan
- 0000 0004 1936 8083grid.47894.36Department of Biology, Colorado State University, Ft. Collins, CO USA
| | - Richard Stouthamer
- 0000 0001 2222 1582grid.266097.cDepartment of Entomology, University of California Riverside, Riverside, CA USA
| | - Michael R. Strand
- 0000 0004 1936 738Xgrid.213876.9Department of Entomology, University of Georgia, Athens, GA USA
| | - Nikolaus U. Szucsich
- 0000 0001 2169 5989grid.252381.fPresent Address: Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR USA
| | - Asela Wijeratne
- 0000 0000 9560 654Xgrid.56061.34Department of Biological Sciences, University of Memphis, 3700 Walker Ave, Memphis, TN 38152 USA ,0000 0001 2112 4115grid.425585.bNatural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
| | - Neil D. Young
- 0000 0001 2179 088Xgrid.1008.9Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Eduardo E. Zattara
- 0000 0001 2112 473Xgrid.412234.2INIBIOMA, Univ. Nacional del Comahue – CONICET, Bariloche, Argentina
| | - Joshua B. Benoit
- 0000 0001 2179 9593grid.24827.3bDepartment of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221 USA
| | - Evgeny M. Zdobnov
- 0000 0001 2322 4988grid.8591.5Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211 Geneva, Switzerland
| | - Michael E. Pfrender
- 0000 0001 2168 0066grid.131063.6Department of Biological Sciences, University of Notre Dame, 109B Galvin Life Sciences, Notre Dame, IN 46556 USA
| | - Kevin J. Hackett
- 0000 0004 0404 0958grid.463419.dCrop Production and Protection, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD 20705 USA
| | - John H. Werren
- 0000 0004 1936 9174grid.16416.34Department of Biology, University of Rochester, Rochester, NY 14627 USA
| | - Kim C. Worley
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Richard A. Gibbs
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Ariel D. Chipman
- 0000 0004 1937 0538grid.9619.7Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904 Jerusalem, Israel
| | - Robert M. Waterhouse
- 0000 0001 2165 4204grid.9851.5Department of Ecology & Evolution and Swiss Institute of Bioinformatics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münsterss, 48149 Münster, Germany ,0000 0001 2287 2617grid.9026.dInstitute for Bioinformatics and Chemoinformatics, University of Hamburg, Hamburg, Germany ,0000 0001 1014 8330grid.419495.4Department Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Matthew W. Hahn
- 0000 0001 0790 959Xgrid.411377.7Department of Biology and Department of Computer Science, Indiana University, Bloomington, IN USA
| | - Stephen Richards
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,0000 0004 1936 9684grid.27860.3bPresent Address: UC Davis Genome Center, University of California, Davis, CA 95616 USA
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22
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Koropoulis A, Alachiotis N, Pavlidis P. Detecting Positive Selection in Populations Using Genetic Data. Methods Mol Biol 2020; 2090:87-123. [PMID: 31975165 DOI: 10.1007/978-1-0716-0199-0_5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
High-throughput genomic sequencing allows to disentangle the evolutionary forces acting in populations. Among evolutionary forces, positive selection has received a lot of attention because it is related to the adaptation of populations in their environments, both biotic and abiotic. Positive selection, also known as Darwinian selection, occurs when an allele is favored by natural selection. The frequency of the favored allele increases in the population and, due to genetic hitchhiking, neighboring linked variation diminishes, creating so-called selective sweeps. Such a process leaves traces in genomes that can be detected in a future time point. Detecting traces of positive selection in genomes is achieved by searching for signatures introduced by selective sweeps, such as regions of reduced variation, a specific shift of the site frequency spectrum, and particular linkage disequilibrium (LD) patterns in the region. A variety of approaches can be used for detecting selective sweeps, ranging from simple implementations that compute summary statistics to more advanced statistical approaches, e.g., Bayesian approaches, maximum-likelihood-based methods, and machine learning methods. In this chapter, we discuss selective sweep detection methodologies on the basis of their capacity to analyze whole genomes or just subgenomic regions, and on the specific polymorphism patterns they exploit as selective sweep signatures. We also summarize the results of comparisons among five open-source software releases (SweeD, SweepFinder, SweepFinder2, OmegaPlus, and RAiSD) regarding sensitivity, specificity, and execution times. Furthermore, we test and discuss machine learning methods and present a thorough performance analysis. In equilibrium neutral models or mild bottlenecks, most methods are able to detect selective sweeps accurately. Methods and tools that rely on linkage disequilibrium (LD) rather than single SNPs exhibit higher true positive rates than the site frequency spectrum (SFS)-based methods under the model of a single sweep or recurrent hitchhiking. However, their false positive rate is elevated when a misspecified demographic model is used to build the distribution of the statistic under the null hypothesis. Both LD and SFS-based approaches suffer from decreased accuracy on localizing the true target of selection in bottleneck scenarios. Furthermore, we present an extensive analysis of the effects of gene flow on selective sweep detection, a problem that has been understudied in selective sweep literature.
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Affiliation(s)
- Angelos Koropoulis
- Institute of Computer Science, Foundation for Research and Technology Hellas, Heraklion, Greece
- Computer Science Department, University of Crete, Crete, Heraklion, Greece
| | - Nikolaos Alachiotis
- Institute of Computer Science, Foundation for Research and Technology Hellas, Heraklion, Greece
| | - Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology Hellas, Heraklion, Greece.
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23
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Allan CW, Matzkin LM. Genomic analysis of the four ecologically distinct cactus host populations of Drosophila mojavensis. BMC Genomics 2019; 20:732. [PMID: 31606030 PMCID: PMC6790045 DOI: 10.1186/s12864-019-6097-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 09/11/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Relationships between an organism and its environment can be fundamental in the understanding how populations change over time and species arise. Local ecological conditions can shape variation at multiple levels, among these are the evolutionary history and trajectories of coding genes. This study examines the rate of molecular evolution at protein-coding genes throughout the genome in response to host adaptation in the cactophilic Drosophila mojavensis. These insects are intimately associated with cactus necroses, developing as larvae and feeding as adults in these necrotic tissues. Drosophila mojavensis is composed of four isolated populations across the deserts of western North America and each population has adapted to utilize different cacti that are chemically, nutritionally, and structurally distinct. RESULTS High coverage Illumina sequencing was performed on three previously unsequenced populations of D. mojavensis. Genomes were assembled using the previously sequenced genome of D. mojavensis from Santa Catalina Island (USA) as a template. Protein coding genes were aligned across all four populations and rates of protein evolution were determined for all loci using a several approaches. CONCLUSIONS Loci that exhibited elevated rates of molecular evolution tend to be shorter, have fewer exons, low expression, be transcriptionally responsive to cactus host use and have fixed expression differences across the four cactus host populations. Fast evolving genes were involved with metabolism, detoxification, chemosensory reception, reproduction and behavior. Results of this study give insight into the process and the genomic consequences of local ecological adaptation.
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Affiliation(s)
- Carson W Allan
- Department of Biological Sciences, University of Alabama in Huntsville, 301 Sparkman Drive, Huntsville, AL, 35899, USA
- Department of Entomology, University of Arizona, 1140 E. South Campus Drive, Tucson, AZ, 85721, USA
| | - Luciano M Matzkin
- Department of Biological Sciences, University of Alabama in Huntsville, 301 Sparkman Drive, Huntsville, AL, 35899, USA.
- Department of Entomology, University of Arizona, 1140 E. South Campus Drive, Tucson, AZ, 85721, USA.
- BIO5 Institute, University of Arizona, 1657 East Helen Street, Tucson, AZ, 85721, USA.
- Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E. Lowell St., Tucson, AZ, 85721, USA.
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24
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Experimental Introgression To Evaluate the Impact of Sex Specific Traits on Drosophila melanogaster Incipient Speciation. G3-GENES GENOMES GENETICS 2019; 9:2561-2572. [PMID: 31167833 PMCID: PMC6686937 DOI: 10.1534/g3.119.400385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Sex specific traits are involved in speciation but it is difficult to determine whether their variation initiates or reinforces sexual isolation. In some insects, speciation depends of the rapid change of expression in desaturase genes coding for sex pheromones. Two closely related desaturase genes are involved in Drosophila melanogaster pheromonal communication: desat1 affects both the production and the reception of sex pheromones while desat2 is involved in their production in flies of Zimbabwe populations. There is a strong asymmetric sexual isolation between Zimbabwe populations and all other "Cosmopolitan" populations: Zimbabwe females rarely copulate with Cosmopolitan males whereas Zimbabwe males readily copulate with all females. All populations express desat1 but only Zimbabwe strains show high desat2 expression. To evaluate the impact of sex pheromones, female receptivity and desat expression on the incipient speciation process between Zimbabwe and Cosmopolitan populations, we introgressed the Zimbabwe genome into a Cosmopolitan genome labeled with the white mutation, using a multi-generation procedure. The association between these sex-specific traits was determined during the procedure. The production of pheromones was largely dissociated between the sexes. The copulation frequency (but not latency) was highly correlated with the female-but not with the male-principal pheromones. We finally obtained two stable white lines showing Zimbabwe-like sex pheromones, copulation discrimination and desat expression. Our study indicates that the variation of sex pheromones and mating discrimination depend of distinct-yet overlapping-sets of genes in each sex suggesting that their cumulated effects participate to reinforce the speciation process.
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25
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Arguello JR, Laurent S, Clark AG. Demographic History of the Human Commensal Drosophila melanogaster. Genome Biol Evol 2019; 11:844-854. [PMID: 30715331 PMCID: PMC6430986 DOI: 10.1093/gbe/evz022] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2019] [Indexed: 12/14/2022] Open
Abstract
The cohabitation of Drosophila melanogaster with humans is nearly ubiquitous. Though it has been well established that this fly species originated in sub-Saharan Africa, and only recently has spread globally, many details of its swift expansion remain unclear. Elucidating the demographic history of D. melanogaster provides a unique opportunity to investigate how human movement might have impacted patterns of genetic diversity in a commensal species, as well as providing neutral null models for studies aimed at identifying genomic signatures of local adaptation. Here, we use whole-genome data from five populations (Africa, North America, Europe, Central Asia, and the South Pacific) to carry out demographic inferences, with particular attention to the inclusion of migration and admixture. We demonstrate the importance of these parameters for model fitting and show that how previous estimates of divergence times are likely to be significantly underestimated as a result of not including them. Finally, we discuss how human movement along early shipping routes might have shaped the present-day population structure of D. melanogaster.
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Affiliation(s)
- J Roman Arguello
- Department of Ecology and Evolution, University of Lausanne, Switzerland
| | - Stefan Laurent
- Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University.,Department of Biological Statistics and Computational Biology, Cornell University
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26
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Zhou C, Wang G, Yu H, Geng Y, Wu W, Tu H, Price M, Fan Z, Meng Y, Yue B. Genome-wide analysis reveals the genomic features of the turkey vulture (Cathartes aura) as a scavenger. Mol Genet Genomics 2019; 294:679-692. [DOI: 10.1007/s00438-019-01541-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 02/23/2019] [Indexed: 12/24/2022]
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27
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Gomez-Diaz C, Martin F, Garcia-Fernandez JM, Alcorta E. The Two Main Olfactory Receptor Families in Drosophila, ORs and IRs: A Comparative Approach. Front Cell Neurosci 2018; 12:253. [PMID: 30214396 PMCID: PMC6125307 DOI: 10.3389/fncel.2018.00253] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 07/23/2018] [Indexed: 12/20/2022] Open
Abstract
Most insect species rely on the detection of olfactory cues for critical behaviors for the survival of the species, e.g., finding food, suitable mates and appropriate egg-laying sites. Although insects show a diverse array of molecular receptors dedicated to the detection of sensory cues, two main types of molecular receptors have been described as responsible for olfactory reception in Drosophila, the odorant receptors (ORs) and the ionotropic receptors (IRs). Although both receptor families share the role of being the first chemosensors in the insect olfactory system, they show distinct evolutionary origins and several distinct structural and functional characteristics. While ORs are seven-transmembrane-domain receptor proteins, IRs are related to the ionotropic glutamate receptor (iGluR) family. Both types of receptors are expressed on the olfactory sensory neurons (OSNs) of the main olfactory organ, the antenna, but they are housed in different types of sensilla, IRs in coeloconic sensilla and ORs in basiconic and trichoid sensilla. More importantly, from the functional point of view, they display different odorant specificity profiles. Research advances in the last decade have improved our understanding of the molecular basis, evolution and functional roles of these two families, but there are still controversies and unsolved key questions that remain to be answered. Here, we present an updated review on the advances of the genetic basis, evolution, structure, functional response and regulation of both types of chemosensory receptors. We use a comparative approach to highlight the similarities and differences among them. Moreover, we will discuss major open questions in the field of olfactory reception in insects. A comprehensive analysis of the structural and functional convergence and divergence of both types of receptors will help in elucidating the molecular basis of the function and regulation of chemoreception in insects.
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Affiliation(s)
- Carolina Gomez-Diaz
- Department of Functional Biology, Faculty of Medicine, University of Oviedo, Oviedo, Spain
| | - Fernando Martin
- Department of Functional Biology, Faculty of Medicine, University of Oviedo, Oviedo, Spain
| | | | - Esther Alcorta
- Department of Functional Biology, Faculty of Medicine, University of Oviedo, Oviedo, Spain
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28
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Grillet M, Ferveur JF, Everaerts C. Behavioural elements and sensory cues involved in sexual isolation between Drosophila melanogaster strains. ROYAL SOCIETY OPEN SCIENCE 2018; 5:172060. [PMID: 29892393 PMCID: PMC5990781 DOI: 10.1098/rsos.172060] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 04/03/2018] [Indexed: 06/08/2023]
Abstract
Sensory cues exchanged during courtship are crucial for mate choice: if they show intraspecific divergence, this may cause or reinforce sexual isolation between strains, ultimately leading to speciation. There is a strong asymmetric sexual isolation between Drosophila melanogaster females from Zimbabwe (Z) and males from all other populations (M). While M and Z flies of both sexes show different cuticular pheromones, this variation is only partly responsible for the intraspecific isolation effect. Male acoustic signals are also partly involved in sexual isolation. We examined strain-specific courtship behaviour sequences to determine which body parts and sensory appendages may be involved in sexual isolation. Using two strains representative of the Z- and M-types, we manipulated sensory cues and the social context; we then measured the consequence of these manipulations on courtship and copulation. Our data suggest that Z females mated best with males whose sensory characteristics matched those of Z males in both quantity and quality. M females were less choosy and much less influenced by the sensory and social contexts. Differences in emission and reception of sensory signals seen between Z and M flies may lead to the concerted evolution of multiple sensory channel, thereby shaping a population-specific mate recognition system.
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Affiliation(s)
| | | | - Claude Everaerts
- Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, CNRS, INRA, University Bourgogne Franche-Comté, 21000 Dijon, France
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29
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Weigand H, Leese F. Detecting signatures of positive selection in non-model species using genomic data. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly007] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Hannah Weigand
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
| | - Florian Leese
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße, Essen, Germany
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30
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Becher PG, Lebreton S, Wallin EA, Hedenström E, Borrero F, Bengtsson M, Joerger V, Witzgall P. The Scent of the Fly. J Chem Ecol 2018; 44:431-435. [PMID: 29611073 DOI: 10.1007/s10886-018-0950-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 03/13/2018] [Accepted: 03/19/2018] [Indexed: 11/30/2022]
Abstract
(Z)-4-undecenal (Z4-11Al) is the volatile pheromone produced by females of the vinegar fly Drosophila melanogaster. Female flies emit Z4-11Al for species-specific communication and mate-finding. A sensory panel finds that synthetic Z4-11Al has a characteristic flavour, which can be perceived even at the small amounts produced by a single female fly. Since only females produce Z4-11Al, and not males, we can reliably distinguish between single D. melanogaster males and females, according to their scent. Females release Z4-11Al at 2.4 ng/h and we readily sense 1 ng synthetic Z4-11Al in a glass of wine (0.03 nmol/L), while a tenfold concentration is perceived as a loud off-flavour. This corroborates the observation that a glass of wine is spoilt by a single D. melanogaster fly falling into it, which we here show is caused by Z4-11Al. The biological role of Z4-11Al or structurally related aldehydes in humans and the basis for this semiochemical convergence remains yet unclear.
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Affiliation(s)
- Paul G Becher
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Box 102, 23053, Alnarp, Sweden
| | - Sebastien Lebreton
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Box 102, 23053, Alnarp, Sweden
| | - Erika A Wallin
- Department of Chemical Engineering, Mid Sweden University, Holmgatan 10, 85170, Sundsvall, Sweden
| | - Erik Hedenström
- Department of Chemical Engineering, Mid Sweden University, Holmgatan 10, 85170, Sundsvall, Sweden
| | - Felipe Borrero
- Biological Control Laboratory, Colombian Corporation of Agricultural Research, AA 240142 Las Palmas, Bogota, Colombia
| | - Marie Bengtsson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Box 102, 23053, Alnarp, Sweden
| | - Volker Joerger
- Staatliches Weinbauinstitut, Merzhauserstr. 119, 79100, Freiburg, Germany
| | - Peter Witzgall
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Box 102, 23053, Alnarp, Sweden. .,SLU, Box 102, 23053, Alnarp, Sweden.
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31
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The genomic and functional landscapes of developmental plasticity in the American cockroach. Nat Commun 2018; 9:1008. [PMID: 29559629 PMCID: PMC5861062 DOI: 10.1038/s41467-018-03281-1] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 02/02/2018] [Indexed: 11/08/2022] Open
Abstract
Many cockroach species have adapted to urban environments, and some have been serious pests of public health in the tropics and subtropics. Here, we present the 3.38-Gb genome and a consensus gene set of the American cockroach, Periplaneta americana. We report insights from both genomic and functional investigations into the underlying basis of its adaptation to urban environments and developmental plasticity. In comparison with other insects, expansions of gene families in P. americana exist for most core gene families likely associated with environmental adaptation, such as chemoreception and detoxification. Multiple pathways regulating metamorphic development are well conserved, and RNAi experiments inform on key roles of 20-hydroxyecdysone, juvenile hormone, insulin, and decapentaplegic signals in regulating plasticity. Our analyses reveal a high level of sequence identity in genes between the American cockroach and two termite species, advancing it as a valuable model to study the evolutionary relationships between cockroaches and termites.
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Sánchez-Gracia A, Guirao-Rico S, Hinojosa-Alvarez S, Rozas J. Computational prediction of the phenotypic effects of genetic variants: basic concepts and some application examples in Drosophila nervous system genes. J Neurogenet 2017; 31:307-319. [DOI: 10.1080/01677063.2017.1398241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Alejandro Sánchez-Gracia
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Sara Guirao-Rico
- Center for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Bellaterra, Spain
| | - Silvia Hinojosa-Alvarez
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
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Pavlidis P, Alachiotis N. A survey of methods and tools to detect recent and strong positive selection. ACTA ACUST UNITED AC 2017; 24:7. [PMID: 28405579 PMCID: PMC5385031 DOI: 10.1186/s40709-017-0064-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 03/29/2017] [Indexed: 01/25/2023]
Abstract
Positive selection occurs when an allele is favored by natural selection. The frequency of the favored allele increases in the population and due to genetic hitchhiking the neighboring linked variation diminishes, creating so-called selective sweeps. Detecting traces of positive selection in genomes is achieved by searching for signatures introduced by selective sweeps, such as regions of reduced variation, a specific shift of the site frequency spectrum, and particular LD patterns in the region. A variety of methods and tools can be used for detecting sweeps, ranging from simple implementations that compute summary statistics such as Tajima's D, to more advanced statistical approaches that use combinations of statistics, maximum likelihood, machine learning etc. In this survey, we present and discuss summary statistics and software tools, and classify them based on the selective sweep signature they detect, i.e., SFS-based vs. LD-based, as well as their capacity to analyze whole genomes or just subgenomic regions. Additionally, we summarize the results of comparisons among four open-source software releases (SweeD, SweepFinder, SweepFinder2, and OmegaPlus) regarding sensitivity, specificity, and execution times. In equilibrium neutral models or mild bottlenecks, both SFS- and LD-based methods are able to detect selective sweeps accurately. Methods and tools that rely on LD exhibit higher true positive rates than SFS-based ones under the model of a single sweep or recurrent hitchhiking. However, their false positive rate is elevated when a misspecified demographic model is used to represent the null hypothesis. When the correct (or similar to the correct) demographic model is used instead, the false positive rates are considerably reduced. The accuracy of detecting the true target of selection is decreased in bottleneck scenarios. In terms of execution time, LD-based methods are typically faster than SFS-based methods, due to the nature of required arithmetic.
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Affiliation(s)
- Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, 70013 Crete, Greece
| | - Nikolaos Alachiotis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, 70013 Crete, Greece
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Benton R. The neurobiology of gustation in insect disease vectors: progress and potential. CURRENT OPINION IN INSECT SCIENCE 2017; 20:19-27. [PMID: 28602232 DOI: 10.1016/j.cois.2017.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/06/2017] [Accepted: 02/17/2017] [Indexed: 06/07/2023]
Abstract
For insect vectors of human diseases, mealtimes are a key moment of infection. Understanding how and when such species decide on what to feed is both an interesting problem in sensory neurobiology and a source of information for intervention of these behaviors to control spread of infectious agents. Here I review the current knowledge of the molecular and cellular mechanisms of gustation in insect disease vectors, covering blood-feeders as well as scavengers that spread pathogens indirectly. I also consider how these behaviors are modulated over short and long timescales, and describe efforts to artificially modulate them. Though a relatively nascent field, gustatory neurobiology in insect vectors has much promise for future fundamental discoveries and practical applications.
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Affiliation(s)
- Richard Benton
- Center for Integrative Genomics, Faculty of Biology and Medicine, Génopode Building, University of Lausanne, CH-1015 Lausanne, Switzerland.
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Antennal transcriptomes of three tortricid moths reveal putative conserved chemosensory receptors for social and habitat olfactory cues. Sci Rep 2017; 7:41829. [PMID: 28150741 PMCID: PMC5288797 DOI: 10.1038/srep41829] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 12/28/2016] [Indexed: 11/30/2022] Open
Abstract
Insects use chemical signals to find mates, food and oviposition sites. The main chemoreceptor gene families comprise odorant receptors (ORs), ionotropic receptors (IRs) and gustatory receptors (GRs). Understanding the evolution of these receptors as well as their function will assist in advancing our knowledge of how chemical stimuli are perceived and may consequently lead to the development of new insect management strategies. Tortricid moths are important pests in horticulture, forestry and agriculture around the globe. Here, we characterize chemoreceptors from the three main gene families of three economically important tortricids, based on male antennal transcriptomes using an RNA-Seq approach. We identified 49 ORs, 11 GRs and 23 IRs in the green budworm moth, Hedya nubiferana; 49 ORs, 12 GRs and 19 IRs in the beech moth, Cydia fagiglandana; and 48 ORs, 11 GRs and 19 IRs in the pea moth, Cydia nigricana. Transcript abundance estimation, phylogenetic relationships and molecular evolution rate comparisons with deorphanized receptors of Cydia pomonella allow us to hypothesize conserved functions and therefore candidate receptors for pheromones and kairomones.
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Evolutionary Insights into Taste Perception of the Invasive Pest Drosophila suzukii. G3-GENES GENOMES GENETICS 2016; 6:4185-4196. [PMID: 27760794 PMCID: PMC5144986 DOI: 10.1534/g3.116.036467] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Chemosensory perception allows insects to interact with the environment by perceiving odorant or tastant molecules; genes encoding chemoreceptors are the molecular interface between the environment and the insect, and play a central role in mediating its chemosensory behavior. Here, we explore how the evolution of these genes in the emerging pest Drosophila suzukii correlates with the peculiar ecology of this species. We annotated approximately 130 genes coding for gustatory receptors (GRs) and divergent ionotropic receptors (dIRs) in D. suzukii and in its close relative D. biarmipes. We then analyzed the evolution, in terms of size, of each gene family as well of the molecular evolution of the genes in a 14 Drosophila species phylogenetic framework. We show that the overall evolution of GRs parallels that of dIRs not only in D. suzukii, but also in all other analyzed Drosophila. Our results reveal an unprecedented burst of gene family size in the lineage leading to the suzukii subgroup, as well as genomic changes that characterize D. suzukii, particularly duplications and strong signs of positive selection in the putative bitter-taste receptor GR59d. Expression studies of duplicate genes in D. suzukii support a spatio-temporal subfunctionalization of the duplicate isoforms. Our results suggest that D. suzukii is not characterized by gene loss, as observed in other specialist Drosophila species, but rather by a dramatic acceleration of gene gains, compatible with a highly generalist feeding behavior. Overall, our analyses provide candidate taste receptors specific for D. suzukii that may correlate with its specific behavior, and which may be tested in functional studies to ultimately enhance its control in the field.
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Abstract
Pseudogenes are generally considered to be non-functional DNA sequences that arise from protein-coding genes through nonsense or frame-shift mutations1. Although certain pseudogene-derived RNAs have regulatory roles2, and some pseudogene fragments are translated3, no clear functions for pseudogene-derived proteins are known. Olfactory receptor families contain many pseudogenes, reflecting low selection pressures to maintain receptors that are either functionally redundant or detect odours no longer relevant for a species’ fitness4. Here we have characterised a pseudogene in the chemosensory variant ionotropic glutamate receptor (IR) repertoire5,6 of Drosophila sechellia, an insect endemic to the Seychelles that feeds only on ripe fruit of Morinda citrifolia7. This locus, DsecIr75a, bears a premature termination codon (PTC) that appears to be fixed in the population. Unexpectedly, DsecIr75a encodes a functional receptor, due to efficient translational readthrough of the PTC. Readthrough occurs only in neurons, and is independent of the type of termination codon but dependent upon the sequence downstream of the PTC. Furthermore, while the intact D. melanogaster IR75a orthologue detects acetic acid – a chemical cue important for this species to locate fermenting food8,9 but at trace levels in Morinda fruit10 – DsecIR75a has evolved distinct odour-tuning properties, through amino acid changes in its ligand-binding domain. We identify functional PTC-containing loci within different olfactory receptor repertoires and species, suggesting that such “pseudo-pseudogenes” represent a widespread phenomenon.
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Andersson MN, Corcoran JA, Zhang DD, Hillbur Y, Newcomb RD, Löfstedt C. A Sex Pheromone Receptor in the Hessian Fly Mayetiola destructor (Diptera, Cecidomyiidae). Front Cell Neurosci 2016; 10:212. [PMID: 27656130 PMCID: PMC5013046 DOI: 10.3389/fncel.2016.00212] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 08/24/2016] [Indexed: 11/13/2022] Open
Abstract
The Hessian fly, Mayetiola destructor Say (Diptera, Cecidomyiidae), is a pest of wheat and belongs to a group of gall-inducing herbivores. This species has a unique life history and several ecological features that differentiate it from other Diptera such as Drosophila melanogaster and blood-feeding mosquitoes. These features include a short, non-feeding adult life stage (1-2 days) and the use of a long-range sex pheromone produced and released by adult females. Sex pheromones are detected by members of the odorant receptor (OR) family within the Lepidoptera, but no receptors for similar long-range sex pheromones have been characterized from the Diptera. Previously, 122 OR genes have been annotated from the Hessian fly genome, with many of them showing sex-biased expression in the antennae. Here we have expressed, in HEK293 cells, five MdesORs that display male-biased expression in antennae, and we have identified MdesOR115 as a Hessian fly sex pheromone receptor. MdesOR115 responds primarily to the sex pheromone component (2S,8E,10E)-8,10-tridecadien-2-yl acetate, and secondarily to the corresponding Z,E-isomer. Certain sensory neuron membrane proteins (i.e., SNMP1) are important for responses of pheromone receptors in flies and moths. The Hessian fly genome is unusual in that it encodes six SNMP1 paralogs, of which five are expressed in antennae. We co-expressed each of the five antennal SNMP1 paralogs together with each of the five candidate sex pheromone receptors from the Hessian fly and found that they do not influence the response of MdesOR115, nor do they confer responsiveness in any of the non-responsive ORs to any of the sex pheromone components identified to date in the Hessian fly. Using Western blots, we detected protein expression of MdesOrco, all MdesSNMPs, and all MdesORs except for MdesOR113, potentially explaining the lack of response from this OR. In conclusion, we report the first functional characterization of an OR from the Cecidomyiidae, extending the role of ORs as long-range sex pheromone detectors from the Lepidoptera into the Diptera.
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Affiliation(s)
| | | | | | - Ylva Hillbur
- International Institute of Tropical Agriculture Ibadan, Nigeria
| | - Richard D Newcomb
- The New Zealand Institute for Plant and Food Research Ltd Auckland, New Zealand
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Librado P, Rozas J. Weak Polygenic Selection Drives the Rapid Adaptation of the Chemosensory System: Lessons from the Upstream Regions of the Major Gene Families. Genome Biol Evol 2016; 8:2493-504. [PMID: 27503297 PMCID: PMC5010915 DOI: 10.1093/gbe/evw191] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2016] [Indexed: 12/12/2022] Open
Abstract
The animal chemosensory system is involved in essential biological processes, most of them mediated by proteins encoded in multigene families. These multigene families have been fundamental for the adaptation to new environments, significantly contributing to phenotypic variation. This adaptive potential contrasts, however, with the lack of studies at their upstream regions, especially taking into account the evidence linking their transcriptional changes to certain phenotypic effects. Here, we explicitly characterize the contribution of the upstream sequences of the major chemosensory gene families to rapid adaptive processes. For that, we analyze the genome sequences of 158 lines from a population of Drosophila melanogaster that recently colonized North America, and integrate functional and transcriptional data available for this species. We find that both, strong negative and strong positive selection, shape transcriptional evolution at the genome-wide level. The chemosensory upstream regions, however, exhibit a distinctive adaptive landscape, including multiple mutations of small beneficial effect and a reduced number of cis-regulatory elements. Together, our results suggest that the promiscuous and partially redundant transcription and function of the chemosensory genes provide evolutionarily opportunities for rapid adaptive episodes through weak polygenic selection.
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Affiliation(s)
- Pablo Librado
- Departament de Genètica, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Julio Rozas
- Departament de Genètica, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
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