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Bendall EE, Mattingly KM, Moehring AJ, Linnen CR. A Test of Haldane's Rule in Neodiprion Sawflies and Implications for the Evolution of Postzygotic Isolation in Haplodiploids. Am Nat 2023; 202:40-54. [PMID: 37384768 DOI: 10.1086/724820] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2023]
Abstract
AbstractHaldane's rule-a pattern in which hybrid sterility or inviability is observed in the heterogametic sex of an interspecific cross-is one of the most widely obeyed rules in nature. Because inheritance patterns are similar for sex chromosomes and haplodiploid genomes, Haldane's rule may apply to haplodiploid taxa, predicting that haploid male hybrids will evolve sterility or inviability before diploid female hybrids. However, there are several genetic and evolutionary mechanisms that may reduce the tendency of haplodiploids to obey Haldane's rule. Currently, there are insufficient data from haplodiploids to determine how frequently they adhere to Haldane's rule. To help fill this gap, we crossed a pair of haplodiploid hymenopteran species (Neodiprion lecontei and Neodiprion pinetum) and evaluated the viability and fertility of female and male hybrids. Despite considerable divergence, we found no evidence of reduced fertility in hybrids of either sex, consistent with the hypothesis that hybrid sterility evolves slowly in haplodiploids. For viability, we found a pattern opposite to that of Haldane's rule: hybrid females, but not males, had reduced viability. This reduction was most pronounced in one direction of the cross, possibly due to a cytoplasmic-nuclear incompatibility. We also found evidence of extrinsic postzygotic isolation in hybrids of both sexes, raising the possibility that this form or reproductive isolation tends to emerge early in speciation in host-specialized insects. Our work emphasizes the need for more studies on reproductive isolation in haplodiploids, which are abundant in nature but underrepresented in the speciation literature.
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Olney KC, Gibson JD, Natri HM, Underwood A, Gadau J, Wilson MA. Lack of parent-of-origin effects in Nasonia jewel wasp: A replication and extension study. PLoS One 2021; 16:e0252457. [PMID: 34111141 PMCID: PMC8191985 DOI: 10.1371/journal.pone.0252457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/16/2021] [Indexed: 11/28/2022] Open
Abstract
In diploid cells, the paternal and maternal alleles are, on average, equally expressed. There are exceptions from this: a small number of genes express the maternal or paternal allele copy exclusively. This phenomenon, known as genomic imprinting, is common among eutherian mammals and some plant species; however, genomic imprinting in species with haplodiploid sex determination is not well characterized. Previous work reported no parent-of-origin effects in the hybrids of closely related haplodiploid Nasonia vitripennis and Nasonia giraulti jewel wasps, suggesting a lack of epigenetic reprogramming during embryogenesis in these species. Here, we replicate the gene expression dataset and observations using different individuals and sequencing technology, as well as reproduce these findings using the previously published RNA sequence data following our data analysis strategy. The major difference from the previous dataset is that they used an introgression strain as one of the parents and we found several loci that resisted introgression in that strain. Our results from both datasets demonstrate a species-of-origin effect, rather than a parent-of-origin effect. We present a reproducible workflow that others may use for replicating the results. Overall, we reproduced the original report of no parent-of-origin effects in the haplodiploid Nasonia using the original data with our new processing and analysis pipeline and replicated these results with our newly generated data.
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Affiliation(s)
- Kimberly C. Olney
- School of Life Sciences, Arizona State University, Tempe, AZ, United States of America
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, United States of America
| | - Joshua D. Gibson
- Department of Biology, Georgia Southern University, Statesboro, GA, United States of America
| | - Heini M. Natri
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, United States of America
| | - Avery Underwood
- School of Life Sciences, Arizona State University, Tempe, AZ, United States of America
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, United States of America
| | - Juergen Gadau
- Institut fuer Evolution and Biodiversity, University of Muenster, Muenster, Germany
| | - Melissa A. Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ, United States of America
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, United States of America
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, AZ, United States of America
- * E-mail:
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Zhou Y, Huang D, Xin Z, Xiao J. Evolution of Oxidative Phosphorylation (OXPHOS) Genes Reflecting the Evolutionary and Life Histories of Fig Wasps (Hymenoptera, Chalcidoidea). Genes (Basel) 2020; 11:genes11111353. [PMID: 33203150 PMCID: PMC7697784 DOI: 10.3390/genes11111353] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 11/06/2020] [Accepted: 11/13/2020] [Indexed: 11/23/2022] Open
Abstract
Fig wasps are a peculiar group of insects which, for millions of years, have inhabited the enclosed syconia of fig trees. Considering the relatively closed and dark environment of fig syconia, we hypothesize that the fig wasps’ oxidative phosphorylation (OXPHOS) pathway, which is the main oxygen consumption and adenosine triphosphate (ATP) production system, may have adaptively evolved. In this study, we manually annotated the OXPHOS genes of 11 species of fig wasps, and compared the evolutionary patterns of OXPHOS genes for six pollinators and five non-pollinators. Thirteen mitochondrial protein-coding genes and 30 nuclear-coding single-copy orthologous genes were used to analyze the amino acid substitution rate and natural selection. The results showed high amino acid substitution rates of both mitochondrial and nuclear OXPHOS genes in fig wasps, implying the co-evolution of mitochondrial and nuclear genes. Our results further revealed that the OXPHOS-related genes evolved significantly faster in pollinators than in non-pollinators, and five genes had significant positive selection signals in the pollinator lineage, indicating that OXPHOS genes play an important role in the adaptation of pollinators. This study can help us understand the relationship between gene evolution and environmental adaptation.
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Dennis AB, Ballesteros GI, Robin S, Schrader L, Bast J, Berghöfer J, Beukeboom LW, Belghazi M, Bretaudeau A, Buellesbach J, Cash E, Colinet D, Dumas Z, Errbii M, Falabella P, Gatti JL, Geuverink E, Gibson JD, Hertaeg C, Hartmann S, Jacquin-Joly E, Lammers M, Lavandero BI, Lindenbaum I, Massardier-Galata L, Meslin C, Montagné N, Pak N, Poirié M, Salvia R, Smith CR, Tagu D, Tares S, Vogel H, Schwander T, Simon JC, Figueroa CC, Vorburger C, Legeai F, Gadau J. Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum. BMC Genomics 2020; 21:376. [PMID: 32471448 PMCID: PMC7257214 DOI: 10.1186/s12864-020-6764-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/30/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Parasitoid wasps have fascinating life cycles and play an important role in trophic networks, yet little is known about their genome content and function. Parasitoids that infect aphids are an important group with the potential for biological control. Their success depends on adapting to develop inside aphids and overcoming both host aphid defenses and their protective endosymbionts. RESULTS We present the de novo genome assemblies, detailed annotation, and comparative analysis of two closely related parasitoid wasps that target pest aphids: Aphidius ervi and Lysiphlebus fabarum (Hymenoptera: Braconidae: Aphidiinae). The genomes are small (139 and 141 Mbp) and the most AT-rich reported thus far for any arthropod (GC content: 25.8 and 23.8%). This nucleotide bias is accompanied by skewed codon usage and is stronger in genes with adult-biased expression. AT-richness may be the consequence of reduced genome size, a near absence of DNA methylation, and energy efficiency. We identify missing desaturase genes, whose absence may underlie mimicry in the cuticular hydrocarbon profile of L. fabarum. We highlight key gene groups including those underlying venom composition, chemosensory perception, and sex determination, as well as potential losses in immune pathway genes. CONCLUSIONS These findings are of fundamental interest for insect evolution and biological control applications. They provide a strong foundation for further functional studies into coevolution between parasitoids and their hosts. Both genomes are available at https://bipaa.genouest.org.
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Affiliation(s)
- Alice B Dennis
- Department of Aquatic Ecology, Eawag, 8600, Dübendorf, Switzerland.
- Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland.
- Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany.
| | - Gabriel I Ballesteros
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- Centre for Molecular and Functional Ecology in Agroecosystems, Universidad de Talca, Talca, Chile
- Laboratorio de Control Biológico, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Stéphanie Robin
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
- Université de Rennes 1, INRIA, CNRS, IRISA, 35000, Rennes, France
| | - Lukas Schrader
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Jens Bast
- Department of Ecology and Evolution, Université de Lausanne, 1015, Lausanne, Switzerland
- Institute of Zoology, Universität zu Köln, 50674, Köln, Germany
| | - Jan Berghöfer
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Leo W Beukeboom
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Maya Belghazi
- Aix-Marseille Univ, CNRS, INP, Inst Neurophysiopathol, PINT, PFNT, Marseille, France
| | - Anthony Bretaudeau
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
- Université de Rennes 1, INRIA, CNRS, IRISA, 35000, Rennes, France
| | - Jan Buellesbach
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Elizabeth Cash
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, Berkeley, CA, 94720, USA
| | | | - Zoé Dumas
- Department of Ecology and Evolution, Université de Lausanne, 1015, Lausanne, Switzerland
| | - Mohammed Errbii
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | | | - Jean-Luc Gatti
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Elzemiek Geuverink
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Joshua D Gibson
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, Berkeley, CA, 94720, USA
- Department of Biology, Georgia Southern University, Statesboro, GA, 30460, USA
| | - Corinne Hertaeg
- Department of Aquatic Ecology, Eawag, 8600, Dübendorf, Switzerland
- Department of Environmental Systems Sciences, D-USYS, ETH Zürich, Zürich, Switzerland
| | - Stefanie Hartmann
- Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Emmanuelle Jacquin-Joly
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université Paris Diderot, Institute of Ecology and Environmental Sciences of Paris, iEES-Paris, F-78000, Versailles, France
| | - Mark Lammers
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Blas I Lavandero
- Laboratorio de Control Biológico, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Ina Lindenbaum
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | | | - Camille Meslin
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université Paris Diderot, Institute of Ecology and Environmental Sciences of Paris, iEES-Paris, F-78000, Versailles, France
| | - Nicolas Montagné
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université Paris Diderot, Institute of Ecology and Environmental Sciences of Paris, iEES-Paris, F-78000, Versailles, France
| | - Nina Pak
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Marylène Poirié
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Rosanna Salvia
- Department of Sciences, University of Basilicata, 85100, Potenza, Italy
| | - Chris R Smith
- Department of Biology, Earlham College, Richmond, IN, 47374, USA
| | - Denis Tagu
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
| | - Sophie Tares
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Tanja Schwander
- Department of Ecology and Evolution, Université de Lausanne, 1015, Lausanne, Switzerland
| | | | - Christian C Figueroa
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- Centre for Molecular and Functional Ecology in Agroecosystems, Universidad de Talca, Talca, Chile
| | - Christoph Vorburger
- Department of Aquatic Ecology, Eawag, 8600, Dübendorf, Switzerland
- Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland
| | - Fabrice Legeai
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
- Université de Rennes 1, INRIA, CNRS, IRISA, 35000, Rennes, France
| | - Jürgen Gadau
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany.
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Iannello M, Puccio G, Piccinini G, Passamonti M, Ghiselli F. The dynamics of mito-nuclear coevolution: A perspective from bivalve species with two different mechanisms of mitochondrial inheritance. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12271] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Mariangela Iannello
- Department of Biological, Geological, and Environmental Sciences; University of Bologna; Bologna Italy
| | - Guglielmo Puccio
- Department of Biological, Geological, and Environmental Sciences; University of Bologna; Bologna Italy
| | - Giovanni Piccinini
- Department of Biological, Geological, and Environmental Sciences; University of Bologna; Bologna Italy
| | - Marco Passamonti
- Department of Biological, Geological, and Environmental Sciences; University of Bologna; Bologna Italy
| | - Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental Sciences; University of Bologna; Bologna Italy
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Li Y, Zhang R, Liu S, Donath A, Peters RS, Ware J, Misof B, Niehuis O, Pfrender ME, Zhou X. The molecular evolutionary dynamics of oxidative phosphorylation (OXPHOS) genes in Hymenoptera. BMC Evol Biol 2017; 17:269. [PMID: 29281964 PMCID: PMC5745899 DOI: 10.1186/s12862-017-1111-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 12/08/2017] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND The primary energy-producing pathway in eukaryotic cells, the oxidative phosphorylation (OXPHOS) system, comprises proteins encoded by both mitochondrial and nuclear genes. To maintain the function of the OXPHOS system, the pattern of substitutions in mitochondrial and nuclear genes may not be completely independent. It has been suggested that slightly deleterious substitutions in mitochondrial genes are compensated by substitutions in the interacting nuclear genes due to positive selection. Among the four largest insect orders, Coleoptera (beetles), Hymenoptera (sawflies, wasps, ants, and bees), Diptera (midges, mosquitoes, and flies) and Lepidoptera (moths and butterflies), the mitochondrial genes of Hymenoptera exhibit an exceptionally high amino acid substitution rate while the evolution of nuclear OXPHOS genes is largely unknown. Therefore, Hymenoptera is an excellent model group for testing the hypothesis of positive selection driving the substitution rate of nuclear OXPHOS genes. In this study, we report the evolutionary rate of OXPHOS genes in Hymenoptera and test for evidence of positive selection in nuclear OXPHOS genes of Hymenoptera. RESULTS Our analyses revealed that the amino acid substitution rate of mitochondrial and nuclear OXPHOS genes in Hymenoptera is higher than that in other studied insect orders. In contrast, the amino acid substitution rate of non-OXPHOS genes in Hymenoptera is lower than the rate in other insect orders. Overall, we found the dN/dS ratio of the nuclear OXPHOS genes to be higher in Hymenoptera than in other insect orders. However, nuclear OXPHOS genes with high dN/dS ratio did not always exhibit a high amino acid substitution rate. Using branch-site and site model tests, we identified various codon sites that evolved under positive selection in nuclear OXPHOS genes. CONCLUSIONS Our results showed that nuclear OXPHOS genes in Hymenoptera are evolving faster than the genes in other three insect orders. The branch test suggested that while some nuclear OXPHOS genes in Hymenoptera show a signature of positive selection, the pattern is not consistent across all nuclear OXPHOS genes. As only few codon sites were under positive selection, we suggested that positive selection might not be the only factor contributing to the rapid evolution of nuclear OXPHOS genes in Hymenoptera.
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Affiliation(s)
- Yiyuan Li
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN USA
- Environmental Change Initiative, Notre Dame, IN USA
| | - Rui Zhang
- China National GeneBank, BGI-Shenzhen, Guangdong Province, Shenzhen, China
| | - Shanlin Liu
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Alexander Donath
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung (zmb), Bonn, Germany
| | - Ralph S. Peters
- Zoologisches Forschungsmuseum Alexander Koenig, Abteilung Arthropoda, Bonn, Germany
| | - Jessica Ware
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102 USA
| | - Bernhard Misof
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Oliver Niehuis
- Evolutionary Biology and Animal Ecology, Institute of Biology I (Zoology), Albert Ludwig University of Freiburg, Hauptstr. 1, 79104 Freiburg, Germany
| | - Michael E. Pfrender
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN USA
- Environmental Change Initiative, Notre Dame, IN USA
| | - Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, 100193 China
- Department of Entomology, China Agricultural University, Beijing, 100193 China
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Temporal transcriptomic profiling of the ant-feeding assassin bug Acanthaspis cincticrus reveals a biased expression of genes associated with predation in nymphs. Sci Rep 2017; 7:12691. [PMID: 28978945 PMCID: PMC5627237 DOI: 10.1038/s41598-017-12978-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 09/13/2017] [Indexed: 12/22/2022] Open
Abstract
Acanthaspis cincticrus (Stål) is an assassin bug with a specialized camouflaging behavior to ambush ants in the nymphal stages. In this study, we comprehensively sequenced all the life stages of A. cincticrus, including the eggs, five nymph instars, female and male adults using Illumina HiSeq technology. We obtained 176 million clean sequence reads. The assembled 84,055 unigenes were annotated and classified functionally based on protein databases. Among the unigenes, 29.03% were annotated by one or more databases, suggesting their well-conserved functions. Comparison of the gene expression profiles in the egg, nymph and adult stages revealed certain bias. Functional enrichment analysis of significantly differentially expressed genes (SDEGs) showed positive correlation with specific physiological processes within each stage, including venom, aggression, olfactory recognition as well as growth and development. Relative expression of ten SDEGs involved in predation process was validated using quantitative real-time PCR (qRT-PCR).
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Saunier A, Garcia P, Becquet V, Marsaud N, Escudié F, Pante E. Mitochondrial genomes of the Baltic clam Macoma balthica (Bivalvia: Tellinidae): setting the stage for studying mito-nuclear incompatibilities. BMC Evol Biol 2014; 14:259. [PMID: 25527898 PMCID: PMC4302422 DOI: 10.1186/s12862-014-0259-z] [Citation(s) in RCA: 15] [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: 12/01/2014] [Accepted: 12/05/2014] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Allopatric divergence across lineages can lead to post-zygotic reproductive isolation upon secondary contact and disrupt coevolution between mitochondrial and nuclear genomes, promoting emergence of genetic incompatibilities. A previous F ST scan on the transcriptome of the Baltic clam Macoma balthica highlighted several genes potentially involved in mito-nuclear incompatibilities (MNIs). As proteins involved in the mitochondrial oxidative phosphorylation (OXPHO) chain are prone to MNIs and can contribute to the maintenance of genetic barriers, the mitochondrial genomes of six Ma. balthica individuals spanning two secondary contact zones were sequenced using the Illumina MiSeq plateform. RESULTS The mitogenome has an approximate length of 16,806 bp and encodes 13 protein-coding genes, 2 rRNAs and 22 tRNAs, all located on the same strand. atp8, a gene long reported as rare in bivalves, was detected. It encodes 42 amino acids and is putatively expressed and functional. A large unassigned region was identified between rrnS and tRNA (Met) and could likely correspond to the Control Region. Replacement and synonymous mutations were mapped on the inferred secondary structure of all protein-coding genes of the OXPHO chain. The atp6 and atp8 genes were characterized by background levels of replacement mutations, relative to synonymous mutations. However, most nad genes (notably nad2 and nad5) were characterized by an elevated proportion of replacement mutations. CONCLUSIONS Six nearly complete mitochondrial genomes were successfully assembled and annotated, providing the necessary roadmap to study MNIs at OXPHO loci. Few replacement mutations were mapped on mitochondrial-encoded ATP synthase subunits, which is in contrast with previous data on nuclear-encoded subunits. Conversely, the high population divergence and the prevalence of non-synonymous mutations at nad genes are congruent with previous observations from the nuclear transcriptome. This further suggest that MNIs between subunits of Complex I of the OXPHO chain, coding for NADH dehydrogenase, may play a role in maintaining barriers to gene flow in Ma. balthica.
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Affiliation(s)
- Alice Saunier
- Littoral, Environnement et Sociétés, UMR 7266 CNRS, Université de La Rochelle, 2 rue Olympe de Gouges, La Rochelle, 17000, France.
| | - Pascale Garcia
- Littoral, Environnement et Sociétés, UMR 7266 CNRS, Université de La Rochelle, 2 rue Olympe de Gouges, La Rochelle, 17000, France.
| | - Vanessa Becquet
- Littoral, Environnement et Sociétés, UMR 7266 CNRS, Université de La Rochelle, 2 rue Olympe de Gouges, La Rochelle, 17000, France.
| | - Nathalie Marsaud
- GeT-PlaGe, Genotoul, INRA Auzeville, Castanet-Tolosan, 31326, France.
| | - Frédéric Escudié
- GeT-PlaGe, Genotoul, INRA Auzeville, Castanet-Tolosan, 31326, France.
| | - Eric Pante
- Littoral, Environnement et Sociétés, UMR 7266 CNRS, Université de La Rochelle, 2 rue Olympe de Gouges, La Rochelle, 17000, France.
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9
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Brucker RM, Bordenstein SR. The hologenomic basis of speciation: gut bacteria cause hybrid lethality in the genus Nasonia. Science 2013; 341:667-9. [PMID: 23868918 DOI: 10.1126/science.1240659] [Citation(s) in RCA: 250] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Although the gut microbiome influences numerous aspects of organismal fitness, its role in animal evolution and the origin of new species is largely unknown. Here we present evidence that beneficial bacterial communities in the guts of closely related species of the genus Nasonia form species-specific phylosymbiotic assemblages that cause lethality in interspecific hybrids. Bacterial constituents and abundance are irregular in hybrids relative to parental controls, and antibiotic curing of the gut bacteria significantly rescues hybrid survival. Moreover, feeding bacteria to germ-free hybrids reinstates lethality and recapitulates the expression of innate immune genes observed in conventionally reared hybrids. We conclude that in this animal complex, the gut microbiome and host genome represent a coadapted "hologenome" that breaks down during hybridization, promoting hybrid lethality and assisting speciation.
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Affiliation(s)
- Robert M Brucker
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA.
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Gibson JD, Niehuis O, Peirson BRE, Cash EI, Gadau J. GENETIC AND DEVELOPMENTAL BASIS OF F2HYBRID BREAKDOWN INNASONIAPARASITOID WASPS. Evolution 2013; 67:2124-32. [DOI: 10.1111/evo.12080] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 01/24/2013] [Indexed: 01/14/2023]
Affiliation(s)
- J. D. Gibson
- School of Life Sciences, Arizona State University; PO Box 874501 Tempe Arizona 85287
| | - O. Niehuis
- Center for Molecular Biodiversity Research; Zoological Research Museum Alexander Koenig; Adenauerallee 160 53113 Bonn Germany
| | - B. R. E. Peirson
- School of Life Sciences, Arizona State University; PO Box 874501 Tempe Arizona 85287
| | - E. I. Cash
- School of Life Sciences, Arizona State University; PO Box 874501 Tempe Arizona 85287
| | - J. Gadau
- School of Life Sciences, Arizona State University; PO Box 874501 Tempe Arizona 85287
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11
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Fine-scale mapping of the Nasonia genome to chromosomes using a high-density genotyping microarray. G3-GENES GENOMES GENETICS 2013; 3:205-15. [PMID: 23390597 PMCID: PMC3564981 DOI: 10.1534/g3.112.004739] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 11/30/2012] [Indexed: 01/16/2023]
Abstract
Nasonia, a genus of four closely related parasitoid insect species, is a model system for genetic research. Their haplodiploid genetics (haploid males and diploid females) and interfertile species are advantageous for the genetic analysis of complex traits and the genetic basis of species differences. A fine-scale genomic map is an important tool for advancing genetic studies in this system. We developed and used a hybrid genotyping microarray to generate a high-resolution genetic map that covers 79% of the sequenced genome of Nasonia vitripennis. The microarray is based on differential hybridization of species-specific oligos between N. vitripennis and Nasonia giraulti at more than 20,000 markers spanning the Nasonia genome. The map places 729 scaffolds onto the five linkage groups of Nasonia, including locating many smaller scaffolds that would be difficult to map by other means. The microarray was used to characterize 26 segmental introgression lines containing chromosomal regions from one species in the genetic background of another. These segmental introgression lines have been used for rapid screening and mapping of quantitative trait loci involved in species differences. Finally, the microarray is extended to bulk-segregant analysis and genotyping of other Nasonia species combinations. These resources should further expand the usefulness of Nasonia for studies of the genetic basis and architecture of complex traits and speciation.
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Nabholz B, Ellegren H, Wolf JBW. High Levels of Gene Expression Explain the Strong Evolutionary Constraint of Mitochondrial Protein-Coding Genes. Mol Biol Evol 2012; 30:272-84. [DOI: 10.1093/molbev/mss238] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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13
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Koevoets T, Niehuis O, van de Zande L, Beukeboom LW. Hybrid incompatibilities in the parasitic wasp genus Nasonia: negative effects of hemizygosity and the identification of transmission ratio distortion loci. Heredity (Edinb) 2012; 108:302-11. [PMID: 21878985 PMCID: PMC3282399 DOI: 10.1038/hdy.2011.75] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 05/10/2011] [Accepted: 05/12/2011] [Indexed: 01/01/2023] Open
Abstract
The occurrence of hybrid incompatibilities forms an important stage during the evolution of reproductive isolation. In early stages of speciation, males and females often respond differently to hybridization. Haldane's rule states that the heterogametic sex suffers more from hybridization than the homogametic sex. Although haplodiploid reproduction (haploid males, diploid females) does not involve sex chromosomes, sex-specific incompatibilities are predicted to be prevalent in haplodiploid species. Here, we evaluate the effect of sex/ploidy level on hybrid incompatibilities and locate genomic regions that cause increased mortality rates in hybrid males of the haplodiploid wasps Nasonia vitripennis and Nasonia longicornis. Our data show that diploid F(1) hybrid females suffer less from hybridization than haploid F(2) hybrid males. The latter not only suffer from an increased mortality rate, but also from behavioural and spermatogenic sterility. Genetic mapping in recombinant F(2) male hybrids revealed that the observed hybrid mortality is most likely due to a disruption of cytonuclear interactions. As these sex-specific hybrid incompatibilities follow predictions based on Haldane's rule, our data accentuate the need to broaden the view of Haldane's rule to include species with haplodiploid sex determination, consistent with Haldane's original definition.
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Affiliation(s)
- T Koevoets
- Evolutionary Genetics, Centre for Ecological and Evolutionary Studies, University of Groningen, Groningen, The Netherlands.
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Gagnaire PA, Normandeau E, Bernatchez L. Comparative Genomics Reveals Adaptive Protein Evolution and a Possible Cytonuclear Incompatibility between European and American Eels. Mol Biol Evol 2012; 29:2909-19. [DOI: 10.1093/molbev/mss076] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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15
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KOEVOETS T, Van De ZANDE L, BEUKEBOOM LW. Temperature stress increases hybrid incompatibilities in the parasitic wasp genus Nasonia. J Evol Biol 2011; 25:304-16. [DOI: 10.1111/j.1420-9101.2011.02424.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Butlin R, Debelle A, Kerth C, Snook RR, Beukeboom LW, Castillo Cajas RF, Diao W, Maan ME, Paolucci S, Weissing FJ, van de Zande L, Hoikkala A, Geuverink E, Jennings J, Kankare M, Knott KE, Tyukmaeva VI, Zoumadakis C, Ritchie MG, Barker D, Immonen E, Kirkpatrick M, Noor M, Macias Garcia C, Schmitt T, Schilthuizen M. What do we need to know about speciation? Trends Ecol Evol 2011; 27:27-39. [PMID: 21978464 DOI: 10.1016/j.tree.2011.09.002] [Citation(s) in RCA: 256] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 08/31/2011] [Accepted: 09/01/2011] [Indexed: 11/27/2022]
Abstract
Speciation has been a major focus of evolutionary biology research in recent years, with many important advances. However, some of the traditional organising principles of the subject area no longer provide a satisfactory framework, such as the classification of speciation mechanisms by geographical context into allopatric, parapatric and sympatry classes. Therefore, we have asked where speciation research should be directed in the coming years. Here, we present a distillation of questions about the mechanisms of speciation, the genetic basis of speciation and the relationship between speciation and diversity. Our list of topics is not exhaustive; rather we aim to promote discussion on research priorities and on the common themes that underlie disparate speciation processes.
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Montooth KL, Meiklejohn CD, Abt DN, Rand DM. Mitochondrial-nuclear epistasis affects fitness within species but does not contribute to fixed incompatibilities between species of Drosophila. Evolution 2010; 64:3364-79. [PMID: 20624176 PMCID: PMC2997886 DOI: 10.1111/j.1558-5646.2010.01077.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Efficient mitochondrial function requires physical interactions between the proteins encoded by the mitochondrial and nuclear genomes. Coevolution between these genomes may result in the accumulation of incompatibilities between divergent lineages. We test whether mitochondrial-nuclear incompatibilities have accumulated within the Drosophila melanogaster species subgroup by combining divergent mitochondrial and nuclear lineages and quantifying the effects on relative fitness. Precise placement of nine mtDNAs from D. melanogaster, D. simulans, and D. mauritiana into two D. melanogaster nuclear genetic backgrounds reveals significant mitochondrial-nuclear epistasis affecting fitness in females. Combining the mitochondrial genomes with three different D. melanogaster X chromosomes reveals significant epistasis for male fitness between X-linked and mitochondrial variation. However, we find no evidence that the more than 500 fixed differences between the mitochondrial genomes of D. melanogaster and the D. simulans species complex are incompatible with the D. melanogaster nuclear genome. Rather, the interactions of largest effect occur between mitochondrial and nuclear polymorphisms that segregate within species of the D. melanogaster species subgroup. We propose that a low mitochondrial substitution rate, resulting from a low mutation rate and/or efficient purifying selection, precludes the accumulation of mitochondrial-nuclear incompatibilities among these Drosophila species.
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Affiliation(s)
- Kristi L Montooth
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912, USA.
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Pannebakker BA, Niehuis O, Hedley A, Gadau J, Shuker DM. The distribution of microsatellites in the Nasonia parasitoid wasp genome. INSECT MOLECULAR BIOLOGY 2010; 19 Suppl 1:91-8. [PMID: 20167020 DOI: 10.1111/j.1365-2583.2009.00915.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Microsatellites are important molecular markers used in numerous genetic contexts. Despite this widespread use, the evolutionary processes governing microsatellite distribution and diversity remain controversial. Here, we present results on the distribution of microsatellites of three species in the parasitic wasp genus Nasonia generated by an in silico data-mining approach. Our results show that the overall microsatellite density in Nasonia is comparable to that of the honey bee, but much higher than in eight non-Hymenopteran arthropods. Across the Nasonia vitripennis genome, microsatellite density varied both within and amongst chromosomes. In contrast to other taxa, dinucleotides are the most abundant repeat type in all four species of Hymenoptera studied. Whether the differences between the Hymenoptera and other taxa are of functional significance remains to be determined.
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Affiliation(s)
- B A Pannebakker
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
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Kim J, Cunningham R, James B, Wyder S, Gibson JD, Niehuis O, Zdobnov EM, Robertson HM, Robinson GE, Werren JH, Sinha S. Functional characterization of transcription factor motifs using cross-species comparison across large evolutionary distances. PLoS Comput Biol 2010; 6:e1000652. [PMID: 20126523 PMCID: PMC2813253 DOI: 10.1371/journal.pcbi.1000652] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Accepted: 12/18/2009] [Indexed: 11/19/2022] Open
Abstract
We address the problem of finding statistically significant associations between cis-regulatory motifs and functional gene sets, in order to understand the biological roles of transcription factors. We develop a computational framework for this task, whose features include a new statistical score for motif scanning, the use of different scores for predicting targets of different motifs, and new ways to deal with redundancies among significant motif–function associations. This framework is applied to the recently sequenced genome of the jewel wasp, Nasonia vitripennis, making use of the existing knowledge of motifs and gene annotations in another insect genome, that of the fruitfly. The framework uses cross-species comparison to improve the specificity of its predictions, and does so without relying upon non-coding sequence alignment. It is therefore well suited for comparative genomics across large evolutionary divergences, where existing alignment-based methods are not applicable. We also apply the framework to find motifs associated with socially regulated gene sets in the honeybee, Apis mellifera, using comparisons with Nasonia, a solitary species, to identify honeybee-specific associations. We develop a computational pipeline for predicting the functions of transcription factor motifs, through DNA sequence analysis. The pipeline is applied to the newly sequenced genome of the jewel wasp, Nasonia vitripennis. It exploits the wealth of molecular data available in another insect species, the fruitfly Drosophila melanogaster, and uses cross-species comparison to its advantage. Our main contribution is to show how this can be done despite the large evolutionary divergence between the two species. The methodology presented here may be applied more generally to other scenarios (genomes) where comparative regulatory genomics must deal with large evolutionary divergences.
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Affiliation(s)
- Jaebum Kim
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Ryan Cunningham
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Brian James
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Stefan Wyder
- Department of Genetic Medicine and Development, University of Geneva Medical School, and Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Joshua D. Gibson
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Oliver Niehuis
- Department of Biology, University of Osnabrück, Osnabrück, Germany
| | - Evgeny M. Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School, and Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Hugh M. Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Gene E. Robinson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - John H. Werren
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - Saurabh Sinha
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail:
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Niehuis O, Gibson JD, Rosenberg MS, Pannebakker BA, Koevoets T, Judson AK, Desjardins CA, Kennedy K, Duggan D, Beukeboom LW, van de Zande L, Shuker DM, Werren JH, Gadau J. Recombination and its impact on the genome of the haplodiploid parasitoid wasp Nasonia. PLoS One 2010; 5:e8597. [PMID: 20087411 PMCID: PMC2799529 DOI: 10.1371/journal.pone.0008597] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2009] [Accepted: 06/14/2009] [Indexed: 12/17/2022] Open
Abstract
Homologous meiotic recombination occurs in most sexually reproducing organisms, yet its evolutionary advantages are elusive. Previous research explored recombination in the honeybee, a eusocial hymenopteran with an exceptionally high genome-wide recombination rate. A comparable study in a non-social member of the Hymenoptera that would disentangle the impact of sociality from Hymenoptera-specific features such as haplodiploidy on the evolution of the high genome-wide recombination rate in social Hymenoptera is missing. Utilizing single-nucleotide polymorphisms (SNPs) between two Nasonia parasitoid wasp genomes, we developed a SNP genotyping microarray to infer a high-density linkage map for Nasonia. The map comprises 1,255 markers with an average distance of 0.3 cM. The mapped markers enabled us to arrange 265 scaffolds of the Nasonia genome assembly 1.0 on the linkage map, representing 63.6% of the assembled N. vitripennis genome. We estimated a genome-wide recombination rate of 1.4-1.5 cM/Mb for Nasonia, which is less than one tenth of the rate reported for the honeybee. The local recombination rate in Nasonia is positively correlated with the distance to the center of the linkage groups, GC content, and the proportion of simple repeats. In contrast to the honeybee genome, gene density in the parasitoid wasp genome is positively associated with the recombination rate; regions of low recombination are characterized by fewer genes with larger introns and by a greater distance between genes. Finally, we found that genes in regions of the genome with a low recombination frequency tend to have a higher ratio of non-synonymous to synonymous substitutions, likely due to the accumulation of slightly deleterious non-synonymous substitutions. These findings are consistent with the hypothesis that recombination reduces interference between linked sites and thereby facilitates adaptive evolution and the purging of deleterious mutations. Our results imply that the genomes of haplodiploid and of diploid higher eukaryotes do not differ systematically in their recombination rates and associated parameters.
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Affiliation(s)
- Oliver Niehuis
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA.
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