1
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Ravikanthachari N, Steward RA, Boggs CL. Patterns of genetic variation and local adaptation of a native herbivore to a lethal invasive plant. Mol Ecol 2024:e17326. [PMID: 38515231 DOI: 10.1111/mec.17326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 12/03/2023] [Accepted: 02/19/2024] [Indexed: 03/23/2024]
Abstract
Understanding the evolutionary processes that influence fitness is critical to predicting species' responses to selection. Interactions among evolutionary processes including gene flow, drift and the strength of selection can lead to either local adaptation or maladaptation, especially in heterogenous landscapes. Populations experiencing novel environments or resources are ideal for understanding the mechanisms underlying adaptation or maladaptation, specifically in locally co-evolved interactions. We used the interaction between a native herbivore that oviposits on a patchily distributed introduced plant that in turn causes significant mortality to the larvae to test for signatures of local adaptation in areas where the two co-occurred. We used whole-genome sequencing to explore population structure, patterns of gene flow and signatures of local adaptation. We found signatures of local adaptation in response to the introduced plant in the absence of strong population structure with no genetic differentiation and low genetic variation. Additionally, we found localized allele frequency differences within a single population between habitats with and without the lethal plant, highlighting the effects of strong selection. Finally, we identified that selection was acting on larval ability to feed on the plant rather than on females' ability to avoid oviposition, thus uncovering the specific ontogenetic target of selection. Our work highlights the potential for adaptation to occur in a fine-grained landscape in the presence of gene flow and low genetic variation.
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Affiliation(s)
- Nitin Ravikanthachari
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA
- Rocky Mountain Biological Laboratory, Crested Butte, Colorado, USA
| | - Rachel A Steward
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA
- Rocky Mountain Biological Laboratory, Crested Butte, Colorado, USA
- Department of Biology, Lund University, Lund, Sweden
| | - Carol L Boggs
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA
- Rocky Mountain Biological Laboratory, Crested Butte, Colorado, USA
- School of Earth, Ocean & Environment, University of South Carolina, Columbia, South Carolina, USA
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2
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Ravigné V, Rodrigues LR, Charlery de la Masselière M, Facon B, Kuczyński L, Radwan J, Skoracka A, Magalhães S. Understanding the joint evolution of dispersal and host specialisation using phytophagous arthropods as a model group. Biol Rev Camb Philos Soc 2024; 99:219-237. [PMID: 37724465 DOI: 10.1111/brv.13018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 09/20/2023]
Abstract
Theory generally predicts that host specialisation and dispersal should evolve jointly. Indeed, many models predict that specialists should be poor dispersers to avoid landing on unsuitable hosts while generalists will have high dispersal abilities. Phytophagous arthropods are an excellent group to test this prediction, given extensive variation in their host range and dispersal abilities. Here, we explore the degree to which the empirical literature on this group is in accordance with theoretical predictions. We first briefly outline the theoretical reasons to expect such a correlation. We then report empirical studies that measured both dispersal and the degree of specialisation in phytophagous arthropods. We find a correlation between dispersal and levels of specialisation in some studies, but with wide variation in this result. We then review theoretical attributes of species and environment that may blur this correlation, namely environmental grain, temporal heterogeneity, habitat selection, genetic architecture, and coevolution between plants and herbivores. We argue that theoretical models fail to account for important aspects, such as phenotypic plasticity and the impact of selective forces stemming from other biotic interactions, on both dispersal and specialisation. Next, we review empirical caveats in the study of this interplay. We find that studies use different measures of both dispersal and specialisation, hampering comparisons. Moreover, several studies do not provide independent measures of these two traits. Finally, variation in these traits may occur at scales that are not being considered. We conclude that this correlation is likely not to be expected from large-scale comparative analyses as it is highly context dependent and should not be considered in isolation from the factors that modulate it, such as environmental scale and heterogeneity, intrinsic traits or biotic interactions. A stronger crosstalk between theoretical and empirical studies is needed to understand better the prevalence and basis of the correlation between dispersal and specialisation.
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Affiliation(s)
- Virginie Ravigné
- CIRAD, UMR PHIM, - PHIM, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, TA A-120/K, Campus international de Baillarguet, avenue du Campus d'Agropolis, Montpellier Cedex 5, 34398, France
| | - Leonor R Rodrigues
- cE3c: Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, edifício C2, Lisboa, 1749-016, Portugal
| | - Maud Charlery de la Masselière
- cE3c: Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, edifício C2, Lisboa, 1749-016, Portugal
| | - Benoît Facon
- CBGP, INRAE, IRD, CIRAD, Institut Agro, University of Montpellier, 755 avenue du Campus Agropolis, CS 34988, Montferrier sur Lez cedex, 30016, France
| | - Lechosław Kuczyński
- Population Ecology Lab, Faculty of Biology, Institute of Environmental Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, Poznań, 61-614, Poland
| | - Jacek Radwan
- Evolutionary Biology Group, Faculty of Biology, Institute of Environmental Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, Poznań, 61-614, Poland
| | - Anna Skoracka
- Population Ecology Lab, Faculty of Biology, Institute of Environmental Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, Poznań, 61-614, Poland
| | - Sara Magalhães
- cE3c: Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, edifício C2, Lisboa, 1749-016, Portugal
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3
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Peláez JN, Gloss AD, Goldman-Huertas B, Kim B, Lapoint RT, Pimentel-Solorio G, Verster KI, Aguilar JM, Nelson Dittrich AC, Singhal M, Suzuki HC, Matsunaga T, Armstrong EE, Charboneau JLM, Groen SC, Hembry DH, Ochoa CJ, O’Connor TK, Prost S, Zaaijer S, Nabity PD, Wang J, Rodas E, Liang I, Whiteman NK. Evolution of chemosensory and detoxification gene families across herbivorous Drosophilidae. G3 (BETHESDA, MD.) 2023; 13:jkad133. [PMID: 37317982 PMCID: PMC10411586 DOI: 10.1093/g3journal/jkad133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 03/19/2023] [Accepted: 05/31/2023] [Indexed: 06/16/2023]
Abstract
Herbivorous insects are exceptionally diverse, accounting for a quarter of all known eukaryotic species, but the genomic basis of adaptations that enabled this dietary transition remains poorly understood. Many studies have suggested that expansions and contractions of chemosensory and detoxification gene families-genes directly mediating interactions with plant chemical defenses-underlie successful plant colonization. However, this hypothesis has been challenging to test because the origins of herbivory in many insect lineages are ancient (>150 million years ago (mya)), obscuring genomic evolutionary patterns. Here, we characterized chemosensory and detoxification gene family evolution across Scaptomyza, a genus nested within Drosophila that includes a recently derived (<15 mya) herbivore lineage of mustard (Brassicales) specialists and carnation (Caryophyllaceae) specialists, and several nonherbivorous species. Comparative genomic analyses revealed that herbivorous Scaptomyza has among the smallest chemosensory and detoxification gene repertoires across 12 drosophilid species surveyed. Rates of gene turnover averaged across the herbivore clade were significantly higher than background rates in over half of the surveyed gene families. However, gene turnover was more limited along the ancestral herbivore branch, with only gustatory receptors and odorant-binding proteins experiencing strong losses. The genes most significantly impacted by gene loss, duplication, or changes in selective constraint were those involved in detecting compounds associated with feeding on living plants (bitter or electrophilic phytotoxins) or their ancestral diet (fermenting plant volatiles). These results provide insight into the molecular and evolutionary mechanisms of plant-feeding adaptations and highlight gene candidates that have also been linked to other dietary transitions in Drosophila.
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Affiliation(s)
- Julianne N Peláez
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Andrew D Gloss
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Benjamin Goldman-Huertas
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Bernard Kim
- Department of Biology, Stanford University, Palo Alto, CA 94305, USA
| | - Richard T Lapoint
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | | | - Kirsten I Verster
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Biology, Stanford University, Palo Alto, CA 94305, USA
| | - Jessica M Aguilar
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Anna C Nelson Dittrich
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Malvika Singhal
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Chemistry & Biochemistry, University of Oregon, Eugene, OR 97403, USA
| | - Hiromu C Suzuki
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Teruyuki Matsunaga
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Ellie E Armstrong
- Department of Biology, Stanford University, Palo Alto, CA 94305, USA
| | - Joseph L M Charboneau
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Simon C Groen
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
- Department of Nematology, University of California Riverside, Riverside, CA 92521, USA
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA
- Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA 92521, USA
| | - David H Hembry
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Department of Biology, University of Texas Permian Basin, Odessa, TX 79762, USA
| | - Christopher J Ochoa
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Timothy K O’Connor
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Stefan Prost
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Biology, Stanford University, Palo Alto, CA 94305, USA
| | - Sophie Zaaijer
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Jacobs Institute, Cornell Tech, New York, NY 10044, USA
- FIND Genomics, New York, NY 10044, USA
| | - Paul D Nabity
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA
| | - Jiarui Wang
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90007, USA
| | - Esteban Rodas
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Irene Liang
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Noah K Whiteman
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
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4
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Pelaez JN, Gloss AD, Goldman-Huertas B, Kim B, Lapoint RT, Pimentel-Solorio G, Verster KI, Aguilar JM, Dittrich ACN, Singhal M, Suzuki HC, Matsunaga T, Armstrong EE, Charboneau JL, Groen SC, Hembry DH, Ochoa CJ, O’Connor TK, Prost S, Zaaijer S, Nabity PD, Wang J, Rodas E, Liang I, Whiteman NK. Evolution of chemosensory and detoxification gene families across herbivorous Drosophilidae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.532987. [PMID: 36993186 PMCID: PMC10055167 DOI: 10.1101/2023.03.16.532987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Herbivorous insects are exceptionally diverse, accounting for a quarter of all known eukaryotic species, but the genetic basis of adaptations that enabled this dietary transition remains poorly understood. Many studies have suggested that expansions and contractions of chemosensory and detoxification gene families - genes directly mediating interactions with plant chemical defenses - underlie successful plant colonization. However, this hypothesis has been challenging to test because the origins of herbivory in many lineages are ancient (>150 million years ago [mya]), obscuring genomic evolutionary patterns. Here, we characterized chemosensory and detoxification gene family evolution across Scaptomyza, a genus nested within Drosophila that includes a recently derived (<15 mya) herbivore lineage of mustard (Brassicales) specialists and carnation (Caryophyllaceae) specialists, and several non-herbivorous species. Comparative genomic analyses revealed that herbivorous Scaptomyza have among the smallest chemosensory and detoxification gene repertoires across 12 drosophilid species surveyed. Rates of gene turnover averaged across the herbivore clade were significantly higher than background rates in over half of the surveyed gene families. However, gene turnover was more limited along the ancestral herbivore branch, with only gustatory receptors and odorant binding proteins experiencing strong losses. The genes most significantly impacted by gene loss, duplication, or changes in selective constraint were those involved in detecting compounds associated with feeding on plants (bitter or electrophilic phytotoxins) or their ancestral diet (yeast and fruit volatiles). These results provide insight into the molecular and evolutionary mechanisms of plant-feeding adaptations and highlight strong gene candidates that have also been linked to other dietary transitions in Drosophila .
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Affiliation(s)
- Julianne N. Pelaez
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Andrew D. Gloss
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Benjamin Goldman-Huertas
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Bernard Kim
- Department of Biology, Stanford University, Palo Alto, CA 94305, USA
| | - Richard T. Lapoint
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- National Center for Biotechnology Information, Bethesda, MD 20894, USA
| | | | - Kirsten I. Verster
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Department of Biology, Stanford University, Palo Alto, CA 94305, USA
| | - Jessica M. Aguilar
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Anna C. Nelson Dittrich
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Boyce Thompson Institute, Ithaca NY 14853 USA
| | - Malvika Singhal
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Department of Chemistry & Biochemistry, University of Oregon, OR, CA 97403, USA
| | - Hiromu C. Suzuki
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Teruyuki Matsunaga
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | | | - Joseph L.M. Charboneau
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Simon C. Groen
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
- Department of Nematology, University of California-Riverside, Riverside, CA 92521, USA
- Department of Botany and Plant Sciences, University of California-Riverside, Riverside, CA 92521, USA
- Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California-Riverside, Riverside, CA 92521, USA
| | - David H. Hembry
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Department of Biology, University of Texas Permian Basin, Odessa, TX 79762, USA
| | - Christopher J. Ochoa
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Molecular Biology Institute, University of California-Los Angeles, Los Angeles, CA 90095, USA
| | - Timothy K. O’Connor
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Stefan Prost
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Department of Biology, Stanford University, Palo Alto, CA 94305, USA
| | - Sophie Zaaijer
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Jacobs Institute, Cornell Tech, New York, NY 10044, USA
- FIND Genomics, New York, NY 10044, USA
| | - Paul D. Nabity
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Department of Botany and Plant Sciences, University of California-Riverside, Riverside, CA 92521, USA
| | - Jiarui Wang
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90007, USA
| | - Esteban Rodas
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Irene Liang
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Noah K. Whiteman
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA 94720, USA
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5
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Hardy NB, Forister ML. Niche Specificity, Polygeny, and Pleiotropy in Herbivorous Insects. Am Nat 2023; 201:376-388. [PMID: 36848511 DOI: 10.1086/722568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractWhat causes host use specificity in herbivorous insects? Population genetic models predict specialization when habitat preference can evolve and there is antagonistic pleiotropy at a performance-affecting locus. But empirically for herbivorous insects, host use performance is governed by many genetic loci, and antagonistic pleiotropy seems to be rare. Here, we use individual-based quantitative genetic simulation models to investigate the role of pleiotropy in the evolution of sympatric host use specialization when performance and preference are quantitative traits. We look first at pleiotropies affecting only host use performance. We find that when the host environment changes slowly, the evolution of host use specialization requires levels of antagonistic pleiotropy much higher than what has been observed in nature. On the other hand, with rapid environmental change or pronounced asymmetries in productivity across host species, the evolution of host use specialization readily occurs without pleiotropy. When pleiotropies affect preference as well as performance, even with slow environmental change and host species of equal productivity, we observe fluctuations in host use breadth, with mean specificity increasing with the pervasiveness of antagonistic pleiotropy. Thus, our simulations show that pleiotropy is not necessary for specialization, although it can be sufficient, provided it is extensive or multifarious.
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6
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Reisenman CE, Wong J, Vedagarbha N, Livelo C, Scott K. Taste adaptations associated with host specialization in the specialist Drosophila sechellia. J Exp Biol 2023; 226:jeb244641. [PMID: 36637369 PMCID: PMC10088416 DOI: 10.1242/jeb.244641] [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: 06/08/2022] [Accepted: 01/09/2023] [Indexed: 01/14/2023]
Abstract
Chemosensory-driven host plant specialization is a major force mediating insect ecological adaptation and speciation. Drosophila sechellia, a species endemic to the Seychelles islands, feeds and oviposits on Morinda citrifolia almost exclusively. This fruit is harmless to D. sechellia but toxic to other Drosophilidae, including the closely related generalists D. simulans and D. melanogaster, because of its high content of fatty acids. While several olfactory adaptations mediating D. sechellia's preference for its host have been uncovered, the role of taste has been much less examined. We found that D. sechellia has reduced taste and feeding aversion to bitter compounds and host fatty acids that are aversive to D. melanogaster and D. simulans. The loss of aversion to canavanine, coumarin and fatty acids arose in the D. sechellia lineage, as its sister species D. simulans showed responses akin to those of D. melanogaster. Drosophila sechellia has increased taste and feeding responses towards M. citrifolia. These results are in line with D. sechellia's loss of genes that encode bitter gustatory receptors (GRs) in D. melanogaster. We found that two GR genes which are lost in D. sechellia, GR39a.a and GR28b.a, influence the reduction of aversive responses to some bitter compounds. Also, D. sechellia has increased appetite for a prominent host fatty acid compound that is toxic to its relatives. Our results support the hypothesis that changes in the taste system, specifically a reduction of sensitivity to bitter compounds that deter generalist ancestors, contribute to the specialization of D. sechellia for its host.
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Affiliation(s)
- Carolina E. Reisenman
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
- Essig Museum of Entomology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Joshua Wong
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Namrata Vedagarbha
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | | | - Kristin Scott
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
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7
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MacDonald ZG, Snape KL, Roe AD, Sperling FAH. Host association, environment, and geography underlie genomic differentiation in a major forest pest. Evol Appl 2022; 15:1749-1765. [PMID: 36426133 PMCID: PMC9679251 DOI: 10.1111/eva.13466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/29/2022] [Indexed: 11/30/2022] Open
Abstract
Diverse geographic, environmental, and ecological factors affect gene flow and adaptive genomic variation within species. With recent advances in landscape ecological modelling and high‐throughput DNA sequencing, it is now possible to effectively quantify and partition their relative contributions. Here, we use landscape genomics to identify determinants of genomic differentiation in the forest tent caterpillar, Malacosoma disstria, a widespread and irruptive pest of numerous deciduous tree species in North America. We collected larvae from multiple populations across Eastern Canada, where the species experiences a diversity of environmental gradients and feeds on a number of different host tree species, including trembling aspen (Populus tremuloides), sugar maple (Acer saccharum), red oak (Quercus rubra), and white birch (Betula papyrifera). Using a combination of reciprocal causal modelling (RCM) and distance‐based redundancy analyses (dbRDA), we show that differentiation of thousands of genome‐wide single nucleotide polymorphisms (SNPs) among individuals is best explained by a combination of isolation by distance, isolation by environment (spatial variation in summer temperatures and length of the growing season), and differences in host association. Configuration of suitable habitat inferred from ecological niche models was not significantly related to genomic differentiation, suggesting that M. disstria dispersal is agnostic with respect to habitat quality. Although population structure was not discretely related to host association, our modelling framework provides the first molecular evidence of host‐associated differentiation in M. disstria, congruent with previous documentation of reduced growth and survival of larvae moved between natal host species. We conclude that ecologically mediated selection is contributing to variation within M. disstria, and that divergent adaptation related to both environmental conditions and host association should be considered in ongoing research and management of this important forest pest.
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Affiliation(s)
- Zachary G. MacDonald
- Department of Biological Sciences University of Alberta Edmonton Alberta Canada
- UCLA La Kretz Center for California Conservation Science University of California Los Angeles Los Angeles CA USA
- Institute of the Environmental and Sustainability University of California Los Angeles Los Angeles CA USA
| | - Kyle L. Snape
- Department of Biological Sciences University of Alberta Edmonton Alberta Canada
| | - Amanda D. Roe
- Great Lakes Forestry Centre, Canadian Forest Service, Natural Resources Canada Sault Ste. Marie ON Canada
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8
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De-la-Cruz IM, Batsleer F, Bonte D, Diller C, Hytönen T, Muola A, Osorio S, Posé D, Vandegehuchte ML, Stenberg JA. Evolutionary Ecology of Plant-Arthropod Interactions in Light of the "Omics" Sciences: A Broad Guide. FRONTIERS IN PLANT SCIENCE 2022; 13:808427. [PMID: 35548276 PMCID: PMC9084618 DOI: 10.3389/fpls.2022.808427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 04/01/2022] [Indexed: 06/15/2023]
Abstract
Aboveground plant-arthropod interactions are typically complex, involving herbivores, predators, pollinators, and various other guilds that can strongly affect plant fitness, directly or indirectly, and individually, synergistically, or antagonistically. However, little is known about how ongoing natural selection by these interacting guilds shapes the evolution of plants, i.e., how they affect the differential survival and reproduction of genotypes due to differences in phenotypes in an environment. Recent technological advances, including next-generation sequencing, metabolomics, and gene-editing technologies along with traditional experimental approaches (e.g., quantitative genetics experiments), have enabled far more comprehensive exploration of the genes and traits involved in complex ecological interactions. Connecting different levels of biological organization (genes to communities) will enhance the understanding of evolutionary interactions in complex communities, but this requires a multidisciplinary approach. Here, we review traditional and modern methods and concepts, then highlight future avenues for studying the evolution of plant-arthropod interactions (e.g., plant-herbivore-pollinator interactions). Besides promoting a fundamental understanding of plant-associated arthropod communities' genetic background and evolution, such knowledge can also help address many current global environmental challenges.
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Affiliation(s)
- Ivan M. De-la-Cruz
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Femke Batsleer
- Terrestrial Ecology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Dries Bonte
- Terrestrial Ecology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Carolina Diller
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Timo Hytönen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
- NIAB EMR, West Malling, United Kingdom
| | - Anne Muola
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
- Biodiversity Unit, University of Turku, Finland
| | - Sonia Osorio
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos, Málaga, Spain
| | - David Posé
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos, Málaga, Spain
| | - Martijn L. Vandegehuchte
- Terrestrial Ecology Unit, Department of Biology, Ghent University, Ghent, Belgium
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Johan A. Stenberg
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
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9
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Herrig DK, Vertacnik KL, Kohrs AR, Linnen CR. Support for the adaptive decoupling hypothesis from whole-transcriptome profiles of a hypermetamorphic and sexually dimorphic insect, Neodiprion lecontei. Mol Ecol 2021; 30:4551-4566. [PMID: 34174126 DOI: 10.1111/mec.16041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/31/2022]
Abstract
Though seemingly bizarre, the dramatic morphological and ecological transformation that occurs when immature life stages metamorphose into reproductive adults is one of the most successful developmental strategies on the planet. The adaptive decoupling hypothesis (ADH) proposes that metamorphosis is an adaptation for breaking developmental links between traits expressed in different life stages, thereby facilitating their independent evolution when exposed to opposing selection pressures. Here, we draw inspiration from the ADH to develop a conceptual framework for understanding changes in gene expression across ontogeny. We hypothesized that patterns of stage-biased and sex-biased gene expression are the product of both decoupling mechanisms and selection history. To test this hypothesis, we characterized transcriptome-wide patterns of gene-expression traits for three ecologically distinct larval stages (all male) and adult males and females of a hypermetamorphic insect (Neodiprion lecontei). We found that stage-biased gene expression was most pronounced between larval and adult males, which is consistent with the ADH. However, even in the absence of a metamorphic transition, considerable stage-biased expression was observed among morphologically and behaviourally distinct larval stages. Stage-biased expression was also observed across ecologically relevant Gene Ontology categories and genes, highlighting the role of ecology in shaping patterns of gene expression. We also found that the magnitude and prevalence of stage-biased expression far exceeded adult sex-biased expression. Overall, our results highlight how the ADH can shed light on transcriptome-wide patterns of gene expression in organisms with complex life cycles. For maximal insight, detailed knowledge of organismal ecology is also essential.
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Affiliation(s)
- Danielle K Herrig
- Department of Biology, University of Kentucky, Lexington, Kentucky, USA
| | - Kim L Vertacnik
- Department of Biology, University of Kentucky, Lexington, Kentucky, USA
| | - Anna R Kohrs
- Department of Biology, University of Kentucky, Lexington, Kentucky, USA
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10
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Jermy T, Szentesi Á. Why are there not more herbivorous insect species? ACTA ZOOL ACAD SCI H 2021. [DOI: 10.17109/azh.67.2.119.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Insect species richness is estimated to exceed three million species, of which roughly half is herbivorous. Despite the vast number of species and varied life histories, the proportion of herbivorous species among plant-consuming organisms is lower than it could be due to constraints that impose limits to their diversification. These include ecological factors, such as vague interspecific competition; anatomical and physiological limits, such as neural limits and inability of handling a wide range of plant allelochemicals; phylogenetic constraints, like niche conservatism; and most importantly, a low level of concerted genetic variation necessary to a phyletic conversion. It is suggested that diversification ultimately depends on what we call the intrinsic trend of diversification of the insect genome. In support of the above, we survey the major types of host-specificity, the mechanisms and constraints of host specialization, possible pathways of speciation, and hypotheses concerning insect diversification.
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11
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Ferreira EA, Lambert S, Verrier T, Marion-Poll F, Yassin A. Soft Selective Sweep on Chemosensory Genes Correlates with Ancestral Preference for Toxic Noni in a Specialist Drosophila Population. Genes (Basel) 2020; 12:genes12010032. [PMID: 33383708 PMCID: PMC7824377 DOI: 10.3390/genes12010032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/17/2020] [Accepted: 12/22/2020] [Indexed: 12/14/2022] Open
Abstract
Understanding how organisms adapt to environmental changes is a major question in evolution and ecology. In particular, the role of ancestral variation in rapid adaptation remains unclear because its trace on genetic variation, known as soft selective sweep, is often hardly recognizable from genome-wide selection scans. Here, we investigate the evolution of chemosensory genes in Drosophila yakuba mayottensis, a specialist subspecies on toxic noni (Morinda citrifolia) fruits on the island of Mayotte. We combine population genomics analyses and behavioral assays to evaluate the level of divergence in chemosensory genes and perception of noni chemicals between specialist and generalist subspecies of D. yakuba. We identify a signal of soft selective sweep on a handful of genes, with the most diverging ones involving a cluster of gustatory receptors expressed in bitter-sensing neurons. Our results highlight the potential role of ancestral genetic variation in promoting host plant specialization in herbivorous insects and identify a number of candidate genes underlying behavioral adaptation.
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Affiliation(s)
- Erina A. Ferreira
- Laboratoire Évolution, Génomes, Comportement et Écologie, CNRS, IRD, Université Paris-Saclay, 91198 Gif-sur-Yvette, France; (E.A.F.); (F.M.-P.)
- Institut Systématique Evolution Biodiversité (ISYEB) Centre National de la Recherche Scientifique, MNHN, Sorbonne Université, EPHE 57 rue Cuvier, CP 50, 75005 Paris, France; (S.L.); (T.V.)
| | - Sophia Lambert
- Institut Systématique Evolution Biodiversité (ISYEB) Centre National de la Recherche Scientifique, MNHN, Sorbonne Université, EPHE 57 rue Cuvier, CP 50, 75005 Paris, France; (S.L.); (T.V.)
| | - Thibault Verrier
- Institut Systématique Evolution Biodiversité (ISYEB) Centre National de la Recherche Scientifique, MNHN, Sorbonne Université, EPHE 57 rue Cuvier, CP 50, 75005 Paris, France; (S.L.); (T.V.)
| | - Frédéric Marion-Poll
- Laboratoire Évolution, Génomes, Comportement et Écologie, CNRS, IRD, Université Paris-Saclay, 91198 Gif-sur-Yvette, France; (E.A.F.); (F.M.-P.)
- AgroParisTech, Université Paris-Saclay, 75231 Paris, France
| | - Amir Yassin
- Laboratoire Évolution, Génomes, Comportement et Écologie, CNRS, IRD, Université Paris-Saclay, 91198 Gif-sur-Yvette, France; (E.A.F.); (F.M.-P.)
- Institut Systématique Evolution Biodiversité (ISYEB) Centre National de la Recherche Scientifique, MNHN, Sorbonne Université, EPHE 57 rue Cuvier, CP 50, 75005 Paris, France; (S.L.); (T.V.)
- Correspondence:
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12
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de Medeiros BAS, Farrell BD. Evaluating insect-host interactions as a driver of species divergence in palm flower weevils. Commun Biol 2020; 3:749. [PMID: 33299067 PMCID: PMC7726107 DOI: 10.1038/s42003-020-01482-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 11/10/2020] [Indexed: 01/01/2023] Open
Abstract
Plants and their specialized flower visitors provide valuable insights into the evolutionary consequences of species interactions. In particular, antagonistic interactions between insects and plants have often been invoked as a major driver of diversification. Here we use a tropical community of palms and their specialized insect flower visitors to test whether antagonisms lead to higher population divergence. Interactions between palms and the insects visiting their flowers range from brood pollination to florivory and commensalism, with the latter being species that feed on decaying-and presumably undefended-plant tissues. We test the role of insect-host interactions in the early stages of diversification of nine species of beetles sharing host plants and geographical ranges by first delimiting cryptic species and then using models of genetic isolation by environment. The degree to which insect populations are structured by the genetic divergence of plant populations varies. A hierarchical model reveals that this variation is largely uncorrelated with the kind of interaction, showing that antagonistic interactions are not associated with higher genetic differentiation. Other aspects of host use that affect plant-associated insects regardless of the outcomes of their interactions, such as sensory biases, are likely more general drivers of insect population divergence.
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Affiliation(s)
- Bruno A S de Medeiros
- Smithsonian Tropical Research Institute, Panama City, Panama.
- Museum of Comparative Zoology, Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Brian D Farrell
- Museum of Comparative Zoology, Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, MA, USA
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13
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Hardy NB, Kaczvinsky C, Bird G, Normark BB. What We Don't Know About Diet-Breadth Evolution in Herbivorous Insects. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-011720-023322] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Half a million species of herbivorous insects have been described. Most of them are diet specialists, using only a few plant species as hosts. Biologists suspect that their specificity is key to their diversity. But why do herbivorous insects tend to be diet specialists? In this review, we catalog a broad range of explanations. We review the evidence for each and suggest lines of research to obtain the evidence we lack. We then draw attention to a second major question, namely how changes in diet breadth affect the rest of a species’ biology. In particular, we know little about how changes in diet breadth feed back on genetic architecture, the population genetic environment, and other aspects of a species’ ecology. Knowing more about how generalists and specialists differ should go a long way toward sorting out potential explanations of specificity, and yield a deeper understanding of herbivorous insect diversity.
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Affiliation(s)
- Nate B. Hardy
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama 36849, USA
| | - Chloe Kaczvinsky
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama 36849, USA
| | - Gwendolyn Bird
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama 36849, USA
| | - Benjamin B. Normark
- Department of Biology and Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, Massachusetts 01003, USA
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14
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Singh KS, Troczka BJ, Duarte A, Balabanidou V, Trissi N, Carabajal Paladino LZ, Nguyen P, Zimmer CT, Papapostolou KM, Randall E, Lueke B, Marec F, Mazzoni E, Williamson MS, Hayward A, Nauen R, Vontas J, Bass C. The genetic architecture of a host shift: An adaptive walk protected an aphid and its endosymbiont from plant chemical defenses. SCIENCE ADVANCES 2020; 6:eaba1070. [PMID: 32494722 PMCID: PMC7202869 DOI: 10.1126/sciadv.aba1070] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 02/18/2020] [Indexed: 05/05/2023]
Abstract
Host shifts can lead to ecological speciation and the emergence of new pests and pathogens. However, the mutational events that facilitate the exploitation of novel hosts are poorly understood. Here, we characterize an adaptive walk underpinning the host shift of the aphid Myzus persicae to tobacco, including evolution of mechanisms that overcame tobacco chemical defenses. A series of mutational events added as many as 1.5 million nucleotides to the genome of the tobacco-adapted subspecies, M. p. nicotianae, and yielded profound increases in expression of an enzyme that efficiently detoxifies nicotine, both in aphid gut tissue and in the bacteriocytes housing the obligate aphid symbiont Buchnera aphidicola. This dual evolutionary solution overcame the challenge of preserving fitness of a mutualistic symbiosis during adaptation to a toxic novel host. Our results reveal the intricate processes by which genetic novelty can arise and drive the evolution of key innovations required for ecological adaptation.
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Affiliation(s)
- Kumar Saurabh Singh
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Bartlomiej J. Troczka
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Ana Duarte
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Vasileia Balabanidou
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, Crete, Greece
| | - Nasser Trissi
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | | | - Petr Nguyen
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05 České Budějovice, Czech Republic
- University of South Bohemia, Faculty of Science, 370 05 České Budějovice, Czech Republic
| | - Christoph T. Zimmer
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Kyriaki M. Papapostolou
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, Crete, Greece
| | - Emma Randall
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Bettina Lueke
- Bayer AG, Crop Science Division, R&D, Alfred Nobel-Strasse 50, 40789 Monheim, Germany
| | - Frantisek Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05 České Budějovice, Czech Republic
| | - Emanuele Mazzoni
- Department of Sustainable Crop Production, Section Sustainable Crop and Food Protection, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Martin S. Williamson
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Alex Hayward
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Ralf Nauen
- Bayer AG, Crop Science Division, R&D, Alfred Nobel-Strasse 50, 40789 Monheim, Germany
| | - John Vontas
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, Crete, Greece
- Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Chris Bass
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
- Corresponding author.
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15
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Avoidance and aggregation create consistent egg distribution patterns of congeneric caddisflies across spatially variable oviposition landscapes. Oecologia 2020; 192:375-389. [PMID: 31938883 DOI: 10.1007/s00442-019-04587-7] [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: 04/13/2019] [Accepted: 12/26/2019] [Indexed: 10/25/2022]
Abstract
Amongst oviparous animals, the spatial distribution of individuals is often set initially by where females lay eggs, with potential implications for populations and species coexistence. Do the spatial arrangements of oviposition sites or female behaviours determine spatial patterns of eggs? The consequences of spatial patterns may be context independent if strong behaviours drive patterns; context dependent if the local environment dominates. We tested these ideas using a guild of stream-dwelling caddisflies that oviposit on emergent rocks, focussing on genera with contrasting behaviours. In naturally occurring oviposition landscapes (riffles with emergent rocks), we surveyed the spatial arrangement and environmental characteristics of all emergent rocks, identified and enumerated egg masses on each. Multiple riffles were surveyed to test for spatially invariant patterns and behaviours. In landscapes, we tested for spatial clumping of oviposition sites exploited by each species and for segregation of congeneric species. At oviposition sites, we characterised the frequency distributions of egg masses and tested for species associations. Genus-specific behaviours produced different spatial patterns of egg masses in the same landscapes. Congregative behaviour of Ulmerochorema spp. at landscape scales and an aggregative response at preferred oviposition sites led to clumped patterns, local aggregation and species overlap. In contrast, avoidance behaviours by congeners of Apsilochorema resulted in no or weak clumping, and species segregation in some landscapes. Spatial patterns were consistent across riffles that varied in area and oviposition site density. These results suggest that quite different oviposition behaviours may be context independent, and the consequences of spatial patterns may be spatially invariant also.
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16
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Etges WJ. Evolutionary genomics of host plant adaptation: insights from Drosophila. CURRENT OPINION IN INSECT SCIENCE 2019; 36:96-102. [PMID: 31542627 DOI: 10.1016/j.cois.2019.08.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/13/2019] [Accepted: 08/19/2019] [Indexed: 06/10/2023]
Abstract
Variation in gene expression in response to the use of alternate host plants can reveal genetic and physiological mechanisms explaining why insect-host relationships vary from host specialism to generalism. Interpreting transcriptome variation relies on well-annotated genomes, making drosophilids valuable model systems, particularly those species with tractable ecological associations. Patterns of whole genome expression and alternate gene splicing in response to growth on different hosts have revealed expression of gene networks of known detoxification genes as well as novel functionally enriched genes of diverse metabolic and structural functions. Integrating trancriptomic responses with fitness differences and levels of phenotypic plasticity in response to alternate hosts will help to reveal the general nature of genotype-phenotype relationships.
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Affiliation(s)
- William J Etges
- Ecology, Evolution and Organismal Biology, Department of Biological Sciences, SCEN 632, 1 University of Arkansas, Fayetteville, AR 72701, USA.
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17
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Gene Expression and Diet Breadth in Plant-Feeding Insects: Summarizing Trends. Trends Ecol Evol 2019; 35:259-277. [PMID: 31791830 DOI: 10.1016/j.tree.2019.10.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 10/18/2019] [Accepted: 10/29/2019] [Indexed: 11/20/2022]
Abstract
Transcriptomic studies lend insights into the role of transcriptional plasticity in adaptation and specialization. Recently, there has been growing interest in understanding the relationship between variation in herbivorous insect gene expression and the evolution of diet breadth. We review the studies that have emerged on insect gene expression and host plant use, and outline the questions and approaches in the field. Many candidate genes underlying herbivory and specialization have been identified, and a few key studies demonstrate increased transcriptional plasticity associated with generalist compared with specialist species. Addressing the roles that transcriptional variation plays in insect diet breadth will have important implications for our understanding of the evolution of specialization and the genetic and environmental factors that govern insect-plant interactions.
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18
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Bakovic V, Schuler H, Schebeck M, Feder JL, Stauffer C, Ragland GJ. Host plant-related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi. Mol Ecol 2019; 28:4648-4666. [PMID: 31495015 PMCID: PMC6899720 DOI: 10.1111/mec.15239] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 08/29/2019] [Accepted: 08/30/2019] [Indexed: 12/13/2022]
Abstract
Elucidating the mechanisms and conditions facilitating the formation of biodiversity are central topics in evolutionary biology. A growing number of studies imply that divergent ecological selection may often play a critical role in speciation by counteracting the homogenising effects of gene flow. Several examples involve phytophagous insects, where divergent selection pressures associated with host plant shifts may generate reproductive isolation, promoting speciation. Here, we use ddRADseq to assess the population structure and to test for host‐related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi (L., 1758) (Diptera: Tephritidae). This tephritid is distributed throughout Europe and western Asia, and has adapted to two different genera of host plants, Prunus spp. (cherries) and Lonicera spp. (honeysuckle). Our data imply that geographic distance and geomorphic barriers serve as the primary factors shaping genetic population structure across the species range. Locally, however, flies genetically cluster according to host plant, with consistent allele frequency differences displayed by a subset of loci between Prunus and Lonicera flies across four sites surveyed in Germany and Norway. These 17 loci display significantly higher FST values between host plants than others. They also showed high levels of linkage disequilibrium within and between Prunus and Lonicera flies, supporting host‐related selection and reduced gene flow. Our findings support the existence of sympatric host races in R. cerasi embedded within broader patterns of geographic variation in the fly, similar to the related apple maggot, Rhagoletis pomonella, in North America.
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Affiliation(s)
- Vid Bakovic
- Department of Forest and Soil Sciences, BOKU, University of Natural Resources and Life Sciences Vienna, Vienna, Austria.,Department of Biology, IFM, University of Linköping, Linköping, Sweden
| | - Hannes Schuler
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Bolzano, Italy
| | - Martin Schebeck
- Department of Forest and Soil Sciences, BOKU, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Christian Stauffer
- Department of Forest and Soil Sciences, BOKU, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Gregory J Ragland
- Department of Integrative Biology, University of Colorado-Denver, Denver, CO, USA
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19
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Linnen CR. Predicting evolutionary predictability. Mol Ecol 2019; 27:2647-2650. [PMID: 29894580 DOI: 10.1111/mec.14716] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 04/23/2018] [Indexed: 11/28/2022]
Abstract
The observation that phenotypic convergence and genetic convergence are widespread in nature implies that evolution is at least somewhat predictable. But to what extent and under what circumstances? In other words, how predictable is evolutionary predictability? Answering this question requires going beyond documenting examples of repeated evolution to actually quantifying predictability at different hierarchical levels. At present, few such studies exist. In this issue of Molecular Ecology, Chaturvedi et al. () quantify the predictability of genomewide changes that accompany shifts to an introduced host plant (alfalfa) in populations of the Melissa blue butterfly (Lycaeides melissa). They evaluate predictability in two contexts: (i) overlap in host-associated loci among populations that have independently colonized alfalfa, and (ii) overlap between host-associated loci in nature and loci associated with host performance in laboratory experiments. Overall, they find that the genomic changes that accompany host shifts in this system are indeed somewhat predictable. However, the degree of predictability depends on the type of comparison (among natural populations vs. between natural and experimental populations), type of convergence (specific genomic locations vs. direction of allele frequency change), geographic scale (rangewide vs. specific population pairs) and location in the genome (autosomes vs. sex chromosomes). Together with a handful of comparable data sets, Chaturvedi et al.'s () work suggests that the relative contribution of stochastic and deterministic processes to genomewide responses to novel selection pressures may be highly variable, but possibly predictably so.
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20
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Doellman MM, Feder JL. Genomic transitions during host race and species formation. CURRENT OPINION IN INSECT SCIENCE 2019; 31:84-92. [PMID: 31109679 DOI: 10.1016/j.cois.2018.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 11/19/2018] [Accepted: 11/20/2018] [Indexed: 06/09/2023]
Abstract
Darwin recognized species as discontinuous, yet considered them to be formed by an incremental process of natural selection. Recent theoretical work on 'genome-wide congealing' is bridging this gap between the gradualism of divergent selection and rapid genome-wide divergence, particularly during ecological speciation-with-gene-flow. Host races and species of phytophagous insects, displaying a spectrum of divergence and gene flow among member taxa, provide model systems for testing predicted non-linear transitions from 'genic' divergence at a few uncoupled loci to 'genomic' divergence with genome-wide coupling of selected loci and strong reproductive isolation. Integrating across natural history, genomics, and evolutionary theory, emerging research suggests a tipping point from 'genic' to 'genomic' divergence between host races and species, during both sympatric speciation and secondary contact.
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Affiliation(s)
- Meredith M Doellman
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
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21
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Diaz F, Allan CW, Matzkin LM. Positive selection at sites of chemosensory genes is associated with the recent divergence and local ecological adaptation in cactophilic Drosophila. BMC Evol Biol 2018; 18:144. [PMID: 30236055 PMCID: PMC6148956 DOI: 10.1186/s12862-018-1250-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 08/20/2018] [Indexed: 11/25/2022] Open
Abstract
Background Adaptation to new hosts in phytophagous insects often involves mechanisms of host recognition by genes of sensory pathways. Most often the molecular evolution of sensory genes has been explained in the context of the birth-and-death model. The role of positive selection is less understood, especially associated with host adaptation and specialization. Here we aim to contribute evidence for this latter hypothesis by considering the case of Drosophila mojavensis, a species with an evolutionary history shaped by multiple host shifts in a relatively short time scale, and its generalist sister species, D. arizonae. Results We used a phylogenetic and population genetic analysis framework to test for positive selection in a subset of four chemoreceptor genes, one gustatory receptor (Gr) and three odorant receptors (Or), for which their expression has been previously associated with host shifts. We found strong evidence of positive selection at several amino acid sites in all genes investigated, most of which exhibited changes predicted to cause functional effects in these transmembrane proteins. A significant portion of the sites identified as evolving positively were largely found in the cytoplasmic region, although a few were also present in the extracellular domains. Conclusions The pattern of substitution observed suggests that some of these changes likely had an effect on signal transduction as well as odorant recognition and protein-protein interactions. These findings support the role of positive selection in shaping the pattern of variation at chemosensory receptors, both during the specialization onto one or a few related hosts, but as well as during the evolution and adaptation of generalist species into utilizing several hosts. Electronic supplementary material The online version of this article (10.1186/s12862-018-1250-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fernando Diaz
- Department of Entomology, University of Arizona, Tucson, AZ, 85721, USA
| | - Carson W Allan
- Department of Entomology, University of Arizona, Tucson, AZ, 85721, USA
| | - Luciano M Matzkin
- Department of Entomology, University of Arizona, Tucson, AZ, 85721, USA. .,Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA. .,BIO5 Institute, University of Arizona, Tucson, AZ, 85721, USA.
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22
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Chaturvedi S, Lucas LK, Nice CC, Fordyce JA, Forister ML, Gompert Z. The predictability of genomic changes underlying a recent host shift in Melissa blue butterflies. Mol Ecol 2018; 27:2651-2666. [DOI: 10.1111/mec.14578] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 02/05/2018] [Accepted: 02/09/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Samridhi Chaturvedi
- Department of Biology Utah State University Logan Utah
- Ecology Center Utah State University Logan Utah
| | | | | | | | | | - Zachariah Gompert
- Department of Biology Utah State University Logan Utah
- Ecology Center Utah State University Logan Utah
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