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Moreyra NN, Almeida FC, Allan C, Frankel N, Matzkin LM, Hasson E. Phylogenomics provides insights into the evolution of cactophily and host plant shifts in Drosophila. Mol Phylogenet Evol 2023; 178:107653. [PMID: 36404461 DOI: 10.1016/j.ympev.2022.107653] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/30/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022]
Abstract
Cactophilic species of the Drosophila buzzatii cluster (repleta group) comprise an excellent model group to investigate genomic changes underlying adaptation to extreme climate conditions and host plants. In particular, these species form a tractable system to study the transition from chemically simpler breeding sites (like prickly pears of the genus Opuntia) to chemically more complex hosts (columnar cacti). Here, we report four highly contiguous genome assemblies of three species of the buzzatii cluster. Based on this genomic data and inferred phylogenetic relationships, we identified candidate taxonomically restricted genes (TRGs) likely involved in the evolution of cactophily and cactus host specialization. Functional enrichment analyses of TRGs within the buzzatii cluster identified genes involved in detoxification, water preservation, immune system response, anatomical structure development, and morphogenesis. In contrast, processes that regulate responses to stress, as well as the metabolism of nitrogen compounds, transport, and secretion were found in the set of species that are columnar cacti dwellers. These findings are in line with the hypothesis that those genomic changes brought about key mechanisms underlying the adaptation of the buzzatii cluster species to arid regions in South America.
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Affiliation(s)
- Nicolás Nahuel Moreyra
- Departamento de Ecología, Genética y Evolución (EGE), Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA), Ciudad Autónoma de Buenos Aires C1428EGA, Argentina; Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1428EGA, Argentina.
| | - Francisca Cunha Almeida
- Departamento de Ecología, Genética y Evolución (EGE), Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA), Ciudad Autónoma de Buenos Aires C1428EGA, Argentina; Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1428EGA, Argentina.
| | - Carson Allan
- Department of Entomology, University of Arizona, Tucson, AZ 85719, USA.
| | - Nicolás Frankel
- Departamento de Ecología, Genética y Evolución (EGE), Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA), Ciudad Autónoma de Buenos Aires C1428EGA, Argentina; Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1428EGA, Argentina.
| | | | - Esteban Hasson
- Departamento de Ecología, Genética y Evolución (EGE), Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA), Ciudad Autónoma de Buenos Aires C1428EGA, Argentina; Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1428EGA, Argentina.
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Shaible TM, Matzkin LM. Physiological and life history changes associated with seasonal adaptation in the cactophilic Drosophila mojavensis. Biol Open 2022; 11:bio059610. [PMID: 36285699 PMCID: PMC9637388 DOI: 10.1242/bio.059610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023] Open
Abstract
Many insects inhabiting temperate climates are faced with changing environmental conditions throughout the year. Depending on the species, these environmental fluctuations can be experienced within a single generation or across multiple generations. Strategies for dealing with these seasonal changes vary across populations. Drosophila mojavensis is a cactophilic Drosophila species endemic to the Sonoran Desert. The Sonoran Desert regularly reaches temperatures of 50°C in the summer months. As individuals of this population are rare to collect in the summer months, we simulated the cycling temperatures experienced by D. mojavensis in the Sonoran Desert from April to July (four generations) in a temperature- and light-controlled chamber, to understand the physiological and life history changes that allow this population to withstand these conditions. In contrast to our hypothesis of a summer aestivation, we found that D. mojavensis continue to reproduce during the summer months, albeit with lower viability, but the adult survivorship of the population is highly reduced during this period. As expected, stress resistance increased during the summer months in both the adult and the larval stages. This study examines several strategies for withstanding the Sonoran Desert summer conditions which may be informative in the study of other desert endemic species.
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Affiliation(s)
| | - Luciano M. Matzkin
- Department of Entomology, University of Arizona, Tucson, AZ 85721, USA
- BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
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Diaz F, Allan CW, Chen X, Coleman JM, Bono JM, Matzkin LM. Divergent evolutionary trajectories shape the postmating transcriptional profiles of conspecifically and heterospecifically mated cactophilic Drosophila females. Commun Biol 2022; 5:842. [PMID: 35986208 PMCID: PMC9391497 DOI: 10.1038/s42003-022-03758-2] [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: 11/18/2021] [Accepted: 07/22/2022] [Indexed: 12/03/2022] Open
Abstract
Postmating-prezygotic (PMPZ) reproductive isolation is hypothesized to result from divergent coevolutionary trajectories of sexual selection and/or sexual conflict in isolated populations. However, the genetic basis of PMPZ incompatibilities between species is poorly understood. Here, we use a comparative framework to compare global gene expression in con- and heterospecifically mated Drosophila mojavensis and D. arizonae female reproductive tracts. We find striking divergence between the species in the female postmating transcriptional response to conspecific mating, including differences in differential expression (DE), alternative splicing (AS), and intron retention (IR). As predicted, heterospecific matings produce disrupted transcriptional profiles, but the overall patterns of misregulation are different between the reciprocal crosses. Moreover, we find a positive correlation between postmating transcriptional divergence between species and levels of transcriptional disruption in heterospecific crosses. This result indicates that mating responsive genes that have diverged more in expression also have more disrupted transcriptional profiles in heterospecifically mated females. Overall, our results provide insights into the evolution of PMPZ isolation and lay the foundation for future studies aimed at identifying specific genes involved in PMPZ incompatibilities and the evolutionary forces that have contributed to their divergence in closely related species. Comparison of global gene expression patterns in con- and heterospecifically mated Drosophila mojavensis and Drosophila arizonae suggest that mating-responsive genes with divergent expression also exhibit more disrupted transcriptional profiles in heterospecifically mated females, providing further insight into the evolution of postmating-prezygotic reproductive isolation.
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Rondón JJ, Moreyra NN, Pisarenco VA, Rozas J, Hurtado J, Hasson E. Evolution of the odorant-binding protein gene family in Drosophila. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.957247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Odorant-binding proteins (OBPs) are encoded by a gene family involved in the perception of olfactory signals in insects. This chemosensory gene family has been advocated as a candidate to mediate host preference and host shifts in insects, although it also participates in other physiological processes. Remarkable differences in the OBP gene repertoire have been described across insect groups, suggesting an accelerated gene turnover rate. The genus Drosophila, is a valuable resource for ecological genomics studies since it comprises groups of ecologically diverse species and there are genome data for many of them. Here, we investigate the molecular evolution of this chemosensory gene family across 19 Drosophila genomes, including the melanogaster and repleta species groups, which are mostly associated with rotting fruit and cacti, respectively. We also compared the OBP repertoire among the closely related species of the repleta group, associated with different subfamilies of Cactaceae that represent disparate chemical challenges for the flies. We found that the gene family size varies widely between species, ranging from 39 to 54 candidate OBPs. Indeed, more than 54% of these genes are organized in clusters and located on chromosomes X, 2, and 5, with a distribution conserved throughout the genus. The family sizes in the repleta group and D. virilis (virilis-repleta radiation) were smaller than in the melanogaster group. We tested alternative evolutionary models for OBP family size and turnover rates based on different ecological scenarios. We found heterogeneous gene turnover rates (GR) in comparisons involving columnar cactus specialists, prickly pear specialists, and fruit dwellers lineages, and signals of rapid molecular evolution compatible with positive selection in specific OBP genes. Taking ours and previous results together, we propose that this chemosensory gene family is involved in host adaptation and hypothesize that the adoption of the cactophilic lifestyle in the repleta group accelerated the evolution of members of the family.
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Bodelón A, Fablet M, Veber P, Vieira C, García Guerreiro MP. OUP accepted manuscript. Genome Biol Evol 2022; 14:6526395. [PMID: 35143649 PMCID: PMC8872975 DOI: 10.1093/gbe/evac024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2022] [Indexed: 11/21/2022] Open
Abstract
Interspecific hybridization is often seen as a genomic stress that may lead to new gene expression patterns and deregulation of transposable elements (TEs). The understanding of expression changes in hybrids compared with parental species is essential to disentangle their putative role in speciation processes. However, to date we ignore the detailed mechanisms involved in genomic deregulation in hybrids. We studied the ovarian transcriptome and epigenome of the Drosophila buzzatii and Drosophila koepferae species together with their F1 hybrid females. We found a trend toward underexpression of genes and TE families in hybrids. The epigenome in hybrids was highly similar to the parental epigenomes and showed intermediate histone enrichments between parental species in most cases. Differential gene expression in hybrids was often associated only with changes in H3K4me3 enrichments, whereas differential TE family expression in hybrids may be associated with changes in H3K4me3, H3K9me3, or H3K27me3 enrichments. We identified specific genes and TE families, which their differential expression in comparison with the parental species was explained by their differential chromatin mark combination enrichment. Finally, cis–trans compensatory regulation could also contribute in some way to the hybrid deregulation. This work provides the first study of histone content in Drosophila interspecific hybrids and their effect on gene and TE expression deregulation.
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Affiliation(s)
- Alejandra Bodelón
- Grup de Genòmica, Bioinformática i Biologia Evolutiva, Departament de Genètica i Microbiologia (Edifici C), Universitat Autònoma de Barcelona, Spain
| | - Marie Fablet
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Claude Bernard Lyon 1, Villeurbanne, France
- Institut universitaire de France, France
| | - Philippe Veber
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Maria Pilar García Guerreiro
- Grup de Genòmica, Bioinformática i Biologia Evolutiva, Departament de Genètica i Microbiologia (Edifici C), Universitat Autònoma de Barcelona, Spain
- Corresponding author: E-mail:
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Benowitz KM, Coleman JM, Allan CW, Matzkin LM. Contributions of cis- and trans-Regulatory Evolution to Transcriptomic Divergence across Populations in the Drosophila mojavensis Larval Brain. Genome Biol Evol 2021; 12:1407-1418. [PMID: 32653899 PMCID: PMC7495911 DOI: 10.1093/gbe/evaa145] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2020] [Indexed: 12/22/2022] Open
Abstract
Natural selection on gene expression was originally predicted to result primarily in cis- rather than trans-regulatory evolution, due to the expectation of reduced pleiotropy. Despite this, numerous studies have ascribed recent evolutionary divergence in gene expression predominantly to trans-regulation. Performing RNA-seq on single isofemale lines from genetically distinct populations of the cactophilic fly Drosophila mojavensis and their F1 hybrids, we recapitulated this pattern in both larval brains and whole bodies. However, we demonstrate that improving the measurement of brain expression divergence between populations by using seven additional genotypes considerably reduces the estimate of trans-regulatory contributions to expression evolution. We argue that the finding of trans-regulatory predominance can result from biases due to environmental variation in expression or other sources of noise, and that cis-regulation is likely a greater contributor to transcriptional evolution across D. mojavensis populations. Lastly, we merge these lines of data to identify several previously hypothesized and intriguing novel candidate genes, and suggest that the integration of regulatory and population-level transcriptomic data can provide useful filters for the identification of potentially adaptive genes.
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Affiliation(s)
| | - Joshua M Coleman
- Department of Entomology, University of Arizona.,Department of Biological Sciences, University of Alabama in Huntsville
| | | | - Luciano M Matzkin
- Department of Entomology, University of Arizona.,Department of Ecology and Evolutionary Biology, University of Arizona.,BIO5 Institute, University of Arizona
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Diaz F, Allan CW, Markow TA, Bono JM, Matzkin LM. Gene expression and alternative splicing dynamics are perturbed in female head transcriptomes following heterospecific copulation. BMC Genomics 2021; 22:359. [PMID: 34006224 PMCID: PMC8132402 DOI: 10.1186/s12864-021-07669-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 04/27/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Despite the growing interest in the female side of copulatory interactions, the roles played by differential expression and alternative splicing mechanisms of pre-RNA on tissues outside of the reproductive tract have remained largely unknown. Here we addressed these questions in the context of con- vs heterospecific matings between Drosophila mojavensis and its sister species, D. arizonae. We analyzed transcriptional responses in female heads using an integrated investigation of genome-wide patterns of gene expression, including differential expression (DE), alternative splicing (AS) and intron retention (IR). RESULTS Our results indicated that early transcriptional responses were largely congruent between con- and heterospecific matings but are substantially perturbed over time. Conspecific matings induced functional pathways related to amino acid balance previously associated with the brain's physiology and female postmating behavior. Heterospecific matings often failed to activate regulation of some of these genes and induced expression of additional genes when compared with those of conspecifically-mated females. These mechanisms showed functional specializations with DE genes mostly linked to pathways of proteolysis and nutrient homeostasis, while AS genes were more related to photoreception and muscle assembly pathways. IR seems to play a more general role in DE regulation during the female postmating response. CONCLUSIONS We provide evidence showing that AS genes substantially perturbed by heterospecific matings in female heads evolve at slower evolutionary rates than the genome background. However, DE genes evolve at evolutionary rates similar, or even higher, than those of male reproductive genes, which highlights their potential role in sexual selection and the evolution of reproductive barriers.
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Affiliation(s)
- Fernando Diaz
- Department of Entomology, University of Arizona, Tucson, AZ, USA.
| | - Carson W Allan
- Department of Entomology, University of Arizona, Tucson, AZ, USA
| | - Therese Ann Markow
- Cinvestav UGA-Langebio, Irapuato, Guanajuato, Mexico
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, California, USA
| | - Jeremy M Bono
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, USA.
| | - Luciano M Matzkin
- Department of Entomology, University of Arizona, Tucson, AZ, USA.
- BIO5 Institute, University of Arizona, Tucson, AZ, USA.
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.
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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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Jaworski CC, Allan CW, Matzkin LM. Chromosome‐level hybrid de novo genome assemblies as an attainable option for nonmodel insects. Mol Ecol Resour 2020; 20:1277-1293. [DOI: 10.1111/1755-0998.13176] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 03/31/2020] [Accepted: 04/16/2020] [Indexed: 11/27/2022]
Affiliation(s)
- Coline C. Jaworski
- Department of Entomology The University of Arizona Tucson AZ USA
- Univ Avignon CNRS IRD IMBE Aix Marseille Université Marseille France
- Department of Zoology University of Oxford Oxford UK
| | - Carson W. Allan
- Department of Entomology The University of Arizona Tucson AZ USA
| | - Luciano M. Matzkin
- Department of Entomology The University of Arizona Tucson AZ USA
- BIO5 Institute The University of Arizona Tucson AZ USA
- Department of Ecology and Evolutionary Biology The University of Arizona Tucson AZ USA
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Khallaf MA, Auer TO, Grabe V, Depetris-Chauvin A, Ammagarahalli B, Zhang DD, Lavista-Llanos S, Kaftan F, Weißflog J, Matzkin LM, Rollmann SM, Löfstedt C, Svatoš A, Dweck HKM, Sachse S, Benton R, Hansson BS, Knaden M. Mate discrimination among subspecies through a conserved olfactory pathway. SCIENCE ADVANCES 2020; 6:eaba5279. [PMID: 32704542 PMCID: PMC7360436 DOI: 10.1126/sciadv.aba5279] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 05/07/2020] [Indexed: 05/22/2023]
Abstract
Communication mechanisms underlying the sexual isolation of species are poorly understood. Using four subspecies of Drosophila mojavensis as a model, we identify two behaviorally active, male-specific pheromones. One functions as a conserved male antiaphrodisiac in all subspecies and acts via gustation. The second induces female receptivity via olfaction exclusively in the two subspecies that produce it. Genetic analysis of the cognate receptor for the olfactory pheromone indicates an important role for this sensory pathway in promoting sexual isolation of subspecies, in combination with auditory signals. Unexpectedly, the peripheral sensory pathway detecting this pheromone is conserved molecularly, physiologically, and anatomically across subspecies. These observations imply that subspecies-specific behaviors arise from differential interpretation of the same peripheral cue, reminiscent of sexually conserved detection but dimorphic interpretation of male pheromones in Drosophila melanogaster. Our results reveal that, during incipient speciation, pheromone production, detection, and interpretation do not necessarily evolve in a coordinated manner.
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Affiliation(s)
- Mohammed A. Khallaf
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Thomas O. Auer
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Veit Grabe
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Ana Depetris-Chauvin
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Byrappa Ammagarahalli
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Dan-Dan Zhang
- Department of Biology, Lund University, SE-22362 Lund, Sweden
| | - Sofía Lavista-Llanos
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Filip Kaftan
- Group of Mass Spectrometry and Proteomics, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Jerrit Weißflog
- Group of Mass Spectrometry and Proteomics, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Luciano M. Matzkin
- Department of Entomology, University of Arizona, 1140 E. South Campus Drive, Tucson, AZ 85721, USA
| | - Stephanie M. Rollmann
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | | | - Aleš Svatoš
- Group of Mass Spectrometry and Proteomics, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Hany K. M. Dweck
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Silke Sachse
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Richard Benton
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Bill S. Hansson
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Markus Knaden
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
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