1
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Lavanchy G, Brandt A, Bastardot M, Dumas Z, Labédan M, Massy M, Toubiana W, Tran Van P, Luchetti A, Scali V, Mantovani B, Schwander T. Evolution of alternative reproductive systems in Bacillus stick insects. Evolution 2024:qpae045. [PMID: 38501929 DOI: 10.1093/evolut/qpae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Indexed: 03/20/2024]
Abstract
Reproduction is a key feature of all organisms, yet the way in which it is achieved varies greatly across the tree of life. One striking example of this variation is the stick insect genus Bacillus, in which five different reproductive modes have been described: sex, facultative and obligate parthenogenesis, and two highly unusual reproductive modes: hybridogenesis and androgenesis. Under hybridogenesis, the entire genome from the paternal species is eliminated, and replaced each generation by mating with the corresponding species. Under androgenesis, an egg is fertilized but the developing diploid offspring bear two paternal genomes, and no maternal genome, as a consequence of unknown mechanisms. Here, we re-evaluate previous descriptions of Bacillus lineages and the proposed F1 hybrid ancestries of the hybridogenetic and obligately parthenogenetic lineages (based on allozymes and karyotypes) from Sicily, where all these reproductive modes are found. We generate a chromosome-level genome assembly for a facultative parthenogenetic species (B. rossius) and combine extensive field sampling with RADseq and mtDNA data. We identify and genetically corroborate all previously described species and confirm the ancestry of hybrid lineages. All hybrid lineages have fully retained their F1 hybrid constitution throughout the genome, indicating that the elimination of the paternal genome in hybridogens is always complete and that obligate parthenogenesis in Bacillus hybrid species is not associated with an erosion of heterozygosity as known in other hybrid asexuals. Our results provide a stepping stone towards understanding the transitions between reproductive modes and the proximate mechanisms of genome elimination.
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Affiliation(s)
| | - Alexander Brandt
- Department of Ecology and Evolution, University of Lausanne, CH - 1015 Lausanne, Switzerland
| | - Marc Bastardot
- Department of Ecology and Evolution, University of Lausanne, CH - 1015 Lausanne, Switzerland
| | - Zoé Dumas
- Department of Ecology and Evolution, University of Lausanne, CH - 1015 Lausanne, Switzerland
| | - Marjorie Labédan
- Department of Ecology and Evolution, University of Lausanne, CH - 1015 Lausanne, Switzerland
| | - Morgane Massy
- Department of Ecology and Evolution, University of Lausanne, CH - 1015 Lausanne, Switzerland
| | - William Toubiana
- Department of Ecology and Evolution, University of Lausanne, CH - 1015 Lausanne, Switzerland
| | - Patrick Tran Van
- Department of Ecology and Evolution, University of Lausanne, CH - 1015 Lausanne, Switzerland
| | - Andrea Luchetti
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, University of Bologna, Bologna, Italy
| | - Valerio Scali
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, University of Bologna, Bologna, Italy
| | - Barbara Mantovani
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, University of Bologna, Bologna, Italy
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, CH - 1015 Lausanne, Switzerland
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2
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Freitas S, Parker DJ, Labédan M, Dumas Z, Schwander T. Evidence for cryptic sex in parthenogenetic stick insects of the genus Timema. Proc Biol Sci 2023; 290:20230404. [PMID: 37727092 PMCID: PMC10509586 DOI: 10.1098/rspb.2023.0404] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 08/23/2023] [Indexed: 09/21/2023] Open
Abstract
Obligately parthenogenetic species are expected to be short lived since the lack of sex and recombination should translate into a slower adaptation rate and increased accumulation of deleterious alleles. Some, however, are thought to have been reproducing without males for millions of years. It is not clear how these old parthenogens can escape the predicted long-term costs of parthenogenesis, but an obvious explanation is cryptic sex. In this study, we screen for signatures of cryptic sex in eight populations of four parthenogenetic species of Timema stick insects, some estimated to be older than 1 Myr. Low genotype diversity, homozygosity of individuals and high linkage disequilibrium (LD) unaffected by marker distances support exclusively parthenogenetic reproduction in six populations. However, in two populations (namely, of the species Timema douglasi and T. monikensis) we find strong evidence for cryptic sex, most likely mediated by rare males. These populations had comparatively high genotype diversities, lower LD, and a clear LD decay with genetic distance. Rare sex in species that are otherwise largely parthenogenetic could help explain the unusual success of parthenogenesis in the Timema genus and raises the question whether episodes of rare sex are in fact the simplest explanation for the persistence of many old parthenogens in nature.
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Affiliation(s)
- Susana Freitas
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Darren J. Parker
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- School of Natural Sciences, Bangor University, Bangor, UK
| | - Marjorie Labédan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Zoé Dumas
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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3
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Parker DJ, Jaron KS, Dumas Z, Robinson‐Rechavi M, Schwander T. X chromosomes show relaxed selection and complete somatic dosage compensation across
Timema
stick insect species. J Evol Biol 2022; 35:1734-1750. [PMID: 35933721 PMCID: PMC10087215 DOI: 10.1111/jeb.14075] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 05/06/2022] [Accepted: 07/14/2022] [Indexed: 11/29/2022]
Abstract
Sex chromosomes have evolved repeatedly across the tree of life. As they are present in different copy numbers in males and females, they are expected to experience different selection pressures than the autosomes, with consequences including a faster rate of evolution, increased accumulation of sexually antagonistic alleles and the evolution of dosage compensation. Whether these consequences are general or linked to idiosyncrasies of specific taxa is not clear as relatively few taxa have been studied thus far. Here, we use whole-genome sequencing to identify and characterize the evolution of the X chromosome in five species of Timema stick insects with XX:X0 sex determination. The X chromosome had a similar size (approximately 12% of the genome) and gene content across all five species, suggesting that the X chromosome originated prior to the diversification of the genus. Genes on the X showed evidence of relaxed selection (elevated dN/dS) and a slower evolutionary rate (dN + dS) than genes on the autosomes, likely due to sex-biased mutation rates. Genes on the X also showed almost complete dosage compensation in somatic tissues (heads and legs), but dosage compensation was absent in the reproductive tracts. Contrary to prediction, sex-biased genes showed little enrichment on the X, suggesting that the advantage X-linkage provides to the accumulation of sexually antagonistic alleles is weak. Overall, we found the consequences of X-linkage on gene sequences and expression to be similar across Timema species, showing the characteristics of the X chromosome are surprisingly consistent over 30 million years of evolution.
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Affiliation(s)
- Darren J. Parker
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
- School of Natural Sciences Bangor University Bangor UK
| | - Kamil S. Jaron
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
- School of Biological Sciences Institute of Evolutionary Biology University of Edinburgh Edinburgh UK
| | - Zoé Dumas
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
| | - Marc Robinson‐Rechavi
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
| | - Tanja Schwander
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
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4
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Jaron KS, Parker DJ, Anselmetti Y, Tran Van P, Bast J, Dumas Z, Figuet E, François CM, Hayward K, Rossier V, Simion P, Robinson-Rechavi M, Galtier N, Schwander T. Convergent consequences of parthenogenesis on stick insect genomes. Sci Adv 2022; 8:eabg3842. [PMID: 35196080 PMCID: PMC8865771 DOI: 10.1126/sciadv.abg3842] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The shift from sexual reproduction to parthenogenesis has occurred repeatedly in animals, but how the loss of sex affects genome evolution remains poorly understood. We generated reference genomes for five independently evolved parthenogenetic species in the stick insect genus Timema and their closest sexual relatives. Using these references and population genomic data, we show that parthenogenesis results in an extreme reduction of heterozygosity and often leads to genetically uniform populations. We also find evidence for less effective positive selection in parthenogenetic species, suggesting that sex is ubiquitous in natural populations because it facilitates fast rates of adaptation. Parthenogenetic species did not show increased transposable element (TE) accumulation, likely because there is little TE activity in the genus. By using replicated sexual-parthenogenetic comparisons, our study reveals how the absence of sex affects genome evolution in natural populations, providing empirical support for the negative consequences of parthenogenesis as predicted by theory.
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Affiliation(s)
- Kamil S. Jaron
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
- Corresponding author. (D.J.P.); (K.S.J.); (T.S.)
| | - Darren J. Parker
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Corresponding author. (D.J.P.); (K.S.J.); (T.S.)
| | | | - Patrick Tran Van
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jens Bast
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Zoé Dumas
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Emeric Figuet
- ISEM—Institut des Sciences de l’Evolution, Montpellier, France
| | | | - Keith Hayward
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Victor Rossier
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Paul Simion
- ISEM—Institut des Sciences de l’Evolution, Montpellier, France
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nicolas Galtier
- ISEM—Institut des Sciences de l’Evolution, Montpellier, France
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Corresponding author. (D.J.P.); (K.S.J.); (T.S.)
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5
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Brandt A, Tran Van P, Bluhm C, Anselmetti Y, Dumas Z, Figuet E, François CM, Galtier N, Heimburger B, Jaron KS, Labédan M, Maraun M, Parker DJ, Robinson-Rechavi M, Schaefer I, Simion P, Scheu S, Schwander T, Bast J. Haplotype divergence supports long-term asexuality in the oribatid mite Oppiella nova. Proc Natl Acad Sci U S A 2021; 118:e2101485118. [PMID: 34535550 PMCID: PMC8463897 DOI: 10.1073/pnas.2101485118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2021] [Indexed: 12/05/2022] Open
Abstract
Sex strongly impacts genome evolution via recombination and segregation. In the absence of these processes, haplotypes within lineages of diploid organisms are predicted to accumulate mutations independently of each other and diverge over time. This so-called "Meselson effect" is regarded as a strong indicator of the long-term evolution under obligate asexuality. Here, we present genomic and transcriptomic data of three populations of the asexual oribatid mite species Oppiella nova and its sexual relative Oppiella subpectinata We document strikingly different patterns of haplotype divergence between the two species, strongly supporting Meselson effect-like evolution and long-term asexuality in O. nova: I) variation within individuals exceeds variation between populations in O. nova but vice versa in O. subpectinata; II) two O. nova sublineages feature a high proportion of lineage-specific heterozygous single-nucleotide polymorphisms (SNPs), indicating that haplotypes continued to diverge after lineage separation; III) the deepest split in gene trees generally separates the two haplotypes in O. nova, but populations in O. subpectinata; and IV) the topologies of the two haplotype trees match each other. Our findings provide positive evidence for the absence of canonical sex over evolutionary time in O. nova and suggest that asexual oribatid mites can escape the dead-end fate usually associated with asexual lineages.
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Affiliation(s)
- Alexander Brandt
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Goettingen, 37073 Goettingen, Germany;
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Patrick Tran Van
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Christian Bluhm
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Goettingen, 37073 Goettingen, Germany
- Abteilung Boden und Umwelt, Forstliche Versuchs- und Forschungsanstalt Baden-Wuerttemberg, 79100 Freiburg, Germany
| | - Yoann Anselmetti
- Group Phylogeny and Molecular Evolution, Institut des Sciences de l'Evolution de Montpellier, 34090 Montpellier, France
- CoBIUS Lab, Department of Computer Science, University of Sherbrooke, Sherbrooke, QC J1K2R1, Canada
| | - Zoé Dumas
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Emeric Figuet
- Group Phylogeny and Molecular Evolution, Institut des Sciences de l'Evolution de Montpellier, 34090 Montpellier, France
| | - Clémentine M François
- Group Phylogeny and Molecular Evolution, Institut des Sciences de l'Evolution de Montpellier, 34090 Montpellier, France
- Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, École Nationale des Travaux Publics de l'État, Université Claude Bernard Lyon 1, 69622 Villeurbanne, France
| | - Nicolas Galtier
- Group Phylogeny and Molecular Evolution, Institut des Sciences de l'Evolution de Montpellier, 34090 Montpellier, France
| | - Bastian Heimburger
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Goettingen, 37073 Goettingen, Germany
| | - Kamil S Jaron
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Group Evolutionary Bioinformatics, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Marjorie Labédan
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Mark Maraun
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Goettingen, 37073 Goettingen, Germany
| | - Darren J Parker
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Group Evolutionary Bioinformatics, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Group Evolutionary Bioinformatics, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Ina Schaefer
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Goettingen, 37073 Goettingen, Germany
| | - Paul Simion
- Group Phylogeny and Molecular Evolution, Institut des Sciences de l'Evolution de Montpellier, 34090 Montpellier, France
- Laboratory of Evolutionary Genetics and Ecology, Unit in Environmental and Evolutionary Biology, Université de Namur, 5000 Namur, Belgium
| | - Stefan Scheu
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Goettingen, 37073 Goettingen, Germany
- Section Biodiversity and Ecology, Centre of Biodiversity and Sustainable Land Use, 37073 Goettingen, Germany
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Jens Bast
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Institute for Zoology, University of Cologne, 50674 Cologne, Germany
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6
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Tran Van P, Anselmetti Y, Bast J, Dumas Z, Galtier N, Jaron KS, Martens K, Parker DJ, Robinson-Rechavi M, Schwander T, Simion P, Schön I. First annotated draft genomes of nonmarine ostracods (Ostracoda, Crustacea) with different reproductive modes. G3 (Bethesda) 2021; 11:jkab043. [PMID: 33591306 PMCID: PMC8049415 DOI: 10.1093/g3journal/jkab043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/05/2021] [Indexed: 11/14/2022]
Abstract
Ostracods are one of the oldest crustacean groups with an excellent fossil record and high importance for phylogenetic analyses but genome resources for this class are still lacking. We have successfully assembled and annotated the first reference genomes for three species of nonmarine ostracods; two with obligate sexual reproduction (Cyprideis torosa and Notodromas monacha) and the putative ancient asexual Darwinula stevensoni. This kind of genomic research has so far been impeded by the small size of most ostracods and the absence of genetic resources such as linkage maps or BAC libraries that were available for other crustaceans. For genome assembly, we used an Illumina-based sequencing technology, resulting in assemblies of similar sizes for the three species (335-382 Mb) and with scaffold numbers and their N50 (19-56 kb) in the same orders of magnitude. Gene annotations were guided by transcriptome data from each species. The three assemblies are relatively complete with BUSCO scores of 92-96. The number of predicted genes (13,771-17,776) is in the same range as Branchiopoda genomes but lower than in most malacostracan genomes. These three reference genomes from nonmarine ostracods provide the urgently needed basis to further develop ostracods as models for evolutionary and ecological research.
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Affiliation(s)
- Patrick Tran Van
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Yoann Anselmetti
- ISEM—Institut des Sciences de l’Evolution, Montpellier 34090, France
| | - Jens Bast
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Zoé Dumas
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Nicolas Galtier
- ISEM—Institut des Sciences de l’Evolution, Montpellier 34090, France
| | - Kamil S Jaron
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Koen Martens
- Royal Belgian Institute of Natural Sciences, OD Nature, Freshwater Biology, Brussels 1000, Belgium
- Department of Biology, University of Ghent, Ghent 9000, Belgium
| | - Darren J Parker
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Paul Simion
- ISEM—Institut des Sciences de l’Evolution, Montpellier 34090, France
- Université de Namur, LEGE, URBE, Namur 5000, Belgium
| | - Isa Schön
- Royal Belgian Institute of Natural Sciences, OD Nature, Freshwater Biology, Brussels 1000, Belgium
- University of Hasselt, Research Group Zoology, Diepenbeek 3590, Belgium
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7
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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Parker DJ, Bast J, Jalvingh K, Dumas Z, Robinson-Rechavi M, Schwander T. Repeated Evolution of Asexuality Involves Convergent Gene Expression Changes. Mol Biol Evol 2019; 36:350-364. [PMID: 30445505 PMCID: PMC6404633 DOI: 10.1093/molbev/msy217] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Asexual reproduction has evolved repeatedly from sexual ancestors across a wide range of taxa. Whereas the costs and benefits associated with asexuality have received considerable attention, the molecular changes underpinning the evolution of asexual reproduction remain relatively unexplored. In particular, it is completely unknown whether the repeated evolution of asexual phenotypes involves similar molecular changes, as previous studies have focused on changes occurring in single lineages. Here, we investigate the extent of convergent gene expression changes across five independent transitions to asexuality in stick insects. We compared gene expression of asexual females to females of close sexual relatives in whole-bodies, reproductive tracts, and legs. We identified a striking amount of convergent gene expression change (up to 8% of genes), greatly exceeding that expected by chance. Convergent changes were also tissue-specific, and most likely driven by selection for functional changes. Genes showing convergent changes in the reproductive tract were associated with meiotic spindle formation and centrosome organization. These genes are particularly interesting as they can influence the production of unreduced eggs, a key barrier to asexual reproduction. Changes in legs and whole-bodies were likely involved in female sexual trait decay, with enrichment in terms such as sperm-storage and pigmentation. By identifying changes occurring across multiple independent transitions to asexuality, our results provide a rare insight into the molecular basis of asexual phenotypes and suggest that the evolutionary path to asexuality is highly constrained, requiring repeated changes to the same key genes.
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Affiliation(s)
- Darren J Parker
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jens Bast
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Kirsten Jalvingh
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Zoé Dumas
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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9
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Bast J, Parker DJ, Dumas Z, Jalvingh KM, Tran Van P, Jaron KS, Figuet E, Brandt A, Galtier N, Schwander T. Consequences of Asexuality in Natural Populations: Insights from Stick Insects. Mol Biol Evol 2019; 35:1668-1677. [PMID: 29659991 PMCID: PMC5995167 DOI: 10.1093/molbev/msy058] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Recombination is a fundamental process with significant impacts on genome evolution. Predicted consequences of the loss of recombination include a reduced effectiveness of selection, changes in the amount of neutral polymorphisms segregating in populations, and an arrest of GC-biased gene conversion. Although these consequences are empirically well documented for nonrecombining genome portions, it remains largely unknown if they extend to the whole genome scale in asexual organisms. We identify the consequences of asexuality using de novo transcriptomes of five independently derived, obligately asexual lineages of stick insects, and their sexual sister-species. We find strong evidence for higher rates of deleterious mutation accumulation, lower levels of segregating polymorphisms and arrested GC-biased gene conversion in asexuals as compared with sexuals. Taken together, our study conclusively shows that predicted consequences of genome evolution under asexuality can indeed be found in natural populations.
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Affiliation(s)
- Jens Bast
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Darren J Parker
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Zoé Dumas
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Kirsten M Jalvingh
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Patrick Tran Van
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Kamil S Jaron
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Emeric Figuet
- Institute of Evolutionary Sciences, University of Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Alexander Brandt
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Goettingen, Goettingen, Germany
| | - Nicolas Galtier
- Institute of Evolutionary Sciences, University of Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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10
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Lavanchy G, Strehler M, Llanos Roman MN, Lessard-Therrien M, Humbert JY, Dumas Z, Jalvingh K, Ghali K, Fontcuberta García-Cuenca A, Zijlstra B, Arlettaz R, Schwander T. Habitat heterogeneity favors asexual reproduction in natural populations of grassthrips. Evolution 2016; 70:1780-90. [PMID: 27346066 PMCID: PMC5129508 DOI: 10.1111/evo.12990] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 05/23/2016] [Accepted: 06/05/2016] [Indexed: 01/23/2023]
Abstract
Explaining the overwhelming success of sex among eukaryotes is difficult given the obvious costs of sex relative to asexuality. Different studies have shown that sex can provide benefits in spatially heterogeneous environments under specific conditions, but whether spatial heterogeneity commonly contributes to the maintenance of sex in natural populations remains unknown. We experimentally manipulated habitat heterogeneity for sexual and asexual thrips lineages in natural populations and under seminatural mesocosm conditions by varying the number of hostplants available to these herbivorous insects. Asexual lineages rapidly replaced the sexual ones, independently of the level of habitat heterogeneity in mesocosms. In natural populations, the success of sexual thrips decreased with increasing habitat heterogeneity, with sexual thrips apparently only persisting in certain types of hostplant communities. Our results illustrate how genetic diversity-based mechanisms can favor asexuality instead of sex when sexual lineages co-occur with genetically variable asexual lineages.
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Affiliation(s)
- Guillaume Lavanchy
- Department of Ecology and Evolution, University of Lausanne, Biophore, Lausanne, Switzerland.
| | - Marie Strehler
- Department of Ecology and Evolution, University of Lausanne, Biophore, Lausanne, Switzerland
| | - Maria Noemi Llanos Roman
- Graduate School-Doctoral program in Biomedical Sciences, National University of Trujillo, Trujillo, Peru
| | - Malie Lessard-Therrien
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse, Bern, Switzerland
| | - Jean-Yves Humbert
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse, Bern, Switzerland
| | - Zoé Dumas
- Department of Ecology and Evolution, University of Lausanne, Biophore, Lausanne, Switzerland
| | - Kirsten Jalvingh
- Department of Ecology and Evolution, University of Lausanne, Biophore, Lausanne, Switzerland
| | - Karim Ghali
- Department of Ecology and Evolution, University of Lausanne, Biophore, Lausanne, Switzerland
| | | | - Bart Zijlstra
- Department of Ecology and Evolution, University of Lausanne, Biophore, Lausanne, Switzerland
| | - Raphaël Arlettaz
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse, Bern, Switzerland
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, Biophore, Lausanne, Switzerland
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11
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Fontcuberta García-Cuenca A, Dumas Z, Schwander T. Extreme genetic diversity in asexual grass thrips populations. J Evol Biol 2016; 29:887-99. [PMID: 26864612 DOI: 10.1111/jeb.12843] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 02/03/2016] [Indexed: 12/01/2022]
Abstract
The continuous generation of genetic variation has been proposed as one of the main factors explaining the maintenance of sexual reproduction in nature. However, populations of asexual individuals may attain high levels of genetic diversity through within-lineage diversification, replicate transitions to asexuality from sexual ancestors and migration. How these mechanisms affect genetic variation in populations of closely related sexual and asexual taxa can therefore provide insights into the role of genetic diversity for the maintenance of sexual reproduction. Here, we evaluate patterns of intra- and interpopulation genetic diversity in sexual and asexual populations of Aptinothrips rufus grass thrips. Asexual A. rufus populations are found throughout the world, whereas sexual populations appear to be confined to few locations in the Mediterranean region. We found that asexual A. rufus populations are characterized by extremely high levels of genetic diversity, both in comparison with their sexual relatives and in comparison with other asexual species. Migration is extensive among asexual populations over large geographic distances, whereas close sexual populations are strongly isolated from each other. The combination of extensive migration with replicate evolution of asexual lineages, and a past demographic expansion in at least one of them, generated high local clone diversities in A. rufus. These high clone diversities in asexual populations may mimic certain benefits conferred by sex via genetic diversity and could help explain the extreme success of asexual A. rufus populations.
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Affiliation(s)
| | - Z Dumas
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - T Schwander
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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12
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Kümmerli R, Santorelli LA, Granato ET, Dumas Z, Dobay A, Griffin AS, West SA. Co-evolutionary dynamics between public good producers and cheats in the bacterium Pseudomonas aeruginosa. J Evol Biol 2015; 28:2264-74. [PMID: 26348785 DOI: 10.1111/jeb.12751] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 08/17/2015] [Indexed: 01/20/2023]
Abstract
The production of beneficial public goods is common in the microbial world, and so is cheating--the exploitation of public goods by nonproducing mutants. Here, we examine co-evolutionary dynamics between cooperators and cheats and ask whether cooperators can evolve strategies to reduce the burden of exploitation, and whether cheats in turn can improve their exploitation abilities. We evolved cooperators of the bacterium Pseudomonas aeruginosa, producing the shareable iron-scavenging siderophore pyoverdine, together with cheats, defective in pyoverdine production but proficient in uptake. We found that cooperators managed to co-exist with cheats in 56% of all replicates over approximately 150 generations of experimental evolution. Growth and competition assays revealed that co-existence was fostered by a combination of general adaptions to the media and specific adaptions to the co-evolving opponent. Phenotypic screening and whole-genome resequencing of evolved clones confirmed this pattern, and suggest that cooperators became less exploitable by cheats because they significantly reduced their pyoverdine investment. Cheats, meanwhile, improved exploitation efficiency through mutations blocking the costly pyoverdine-signalling pathway. Moreover, cooperators and cheats evolved reduced motility, a pattern that likely represents adaptation to laboratory conditions, but at the same time also affects social interactions by reducing strain mixing and pyoverdine sharing. Overall, we observed parallel evolution, where co-existence of cooperators and cheats was enabled by a combination of adaptations to the abiotic and social environment and their interactions.
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Affiliation(s)
- R Kümmerli
- Microbial Evolutionary Ecology, Institute of Plant Biology, University of Zürich, Zürich, Switzerland.,Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
| | | | - E T Granato
- Microbial Evolutionary Ecology, Institute of Plant Biology, University of Zürich, Zürich, Switzerland
| | - Z Dumas
- Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - A Dobay
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - A S Griffin
- Department of Zoology, University of Oxford, Oxford, UK
| | - S A West
- Department of Zoology, University of Oxford, Oxford, UK
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13
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Ross-Gillespie A, Dumas Z, Kümmerli R. Evolutionary dynamics of interlinked public goods traits: an experimental study of siderophore production in Pseudomonas aeruginosa. J Evol Biol 2015; 28:29-39. [DOI: 10.1111/jeb.12559] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 11/20/2014] [Accepted: 11/21/2014] [Indexed: 02/03/2023]
Affiliation(s)
- A. Ross-Gillespie
- Microbial Evolutionary Ecology; Institute of Plant Biology; University of Zürich; Zürich Switzerland
| | - Z. Dumas
- Environmental Microbiology; Swiss Federal Institute of Aquatic Science and Technology (EAWAG); Dübendorf Switzerland
- Department of Ecology and Evolution; University of Lausanne; Lausanne Switzerland
| | - R. Kümmerli
- Microbial Evolutionary Ecology; Institute of Plant Biology; University of Zürich; Zürich Switzerland
- Environmental Microbiology; Swiss Federal Institute of Aquatic Science and Technology (EAWAG); Dübendorf Switzerland
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14
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Dumas Z, Ross-Gillespie A, Kümmerli R. Switching between apparently redundant iron-uptake mechanisms benefits bacteria in changeable environments. Proc Biol Sci 2013; 280:20131055. [PMID: 23760867 DOI: 10.1098/rspb.2013.1055] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Bacteria often possess multiple siderophore-based iron uptake systems for scavenging this vital resource from their environment. However, some siderophores seem redundant, because they have limited iron-binding efficiency and are seldom expressed under iron limitation. Here, we investigate the conundrum of why selection does not eliminate this apparent redundancy. We focus on Pseudomonas aeruginosa, a bacterium that can produce two siderophores-the highly efficient but metabolically expensive pyoverdine, and the inefficient but metabolically cheap pyochelin. We found that the bacteria possess molecular mechanisms to phenotypically switch from mainly producing pyoverdine under severe iron limitation to mainly producing pyochelin when iron is only moderately limited. We further show that strains exclusively producing pyochelin grew significantly better than strains exclusively producing pyoverdine under moderate iron limitation, whereas the inverse was seen under severe iron limitation. This suggests that pyochelin is not redundant, but that switching between siderophore strategies might be beneficial to trade off efficiencies versus costs of siderophores. Indeed, simulations parameterized from our data confirmed that strains retaining the capacity to switch between siderophores significantly outcompeted strains defective for one or the other siderophore under fluctuating iron availabilities. Finally, we discuss how siderophore switching can be viewed as a form of collective decision-making, whereby a coordinated shift in behaviour at the group level emerges as a result of positive and negative feedback loops operating among individuals at the local scale.
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Affiliation(s)
- Zoé Dumas
- Department of Ecology and Evolution, University of Lausanne, , Biophore Building, 1015 Lausanne, Switzerland
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15
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Abstract
Bacteria secrete a large variety of beneficial metabolites into the environment, which can be shared as public goods among producing bacteria, but also be exploited by nonproducing cheats. Here, we focus on cooperative production of iron-chelating molecules (siderophores) in the bacterium Pseudomonas aeruginosa to study how relevant ecological factors influence selection for cheating. We designed patch-structured metapopulations that allowed us introducing among-patch ecological variation. We found that cheating readily evolved in uniform iron-limited environments. This finding is explained by severe iron limitation demanding high siderophore-production efforts, which results in high metabolic costs accruing to cooperators, and thereby facilitates the spread of cheats. In contrast, we observed a significant reduction or even negation of selection for cheating in metapopulations where we introduced patches with increased iron availability and/or opportunities to recycle siderophores. These findings are compatible with the view that cheats are less likely to invade in environments that allow bacteria to reduce siderophore-production efforts, as this lowers the overall metabolic costs accruing to cooperators. Because we increased iron availability and siderophore recycling opportunities moderately, and only in some patches, our findings demonstrate that already-small local variations in ecological conditions as occurring in nature can significantly affect selection for public-goods secretion in microbes. In addition, we found that most (84.6%) of the evolved cheats were partially deficient for siderophore production and not loss-of-function mutants. Genetic considerations indicate that mutations leading to partial deficiency occur more frequent than mutations leading to loss of function, but also suggest that partially deficient mutants might often be the more competitive cheats.
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Affiliation(s)
- Z Dumas
- Swiss Federal Institute of Aquatic Science and Technology (Eawag), Environmental Microbiology, Dübendorf, Switzerland
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16
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Stöck M, Horn A, Grossen C, Lindtke D, Sermier R, Betto-Colliard C, Dufresnes C, Bonjour E, Dumas Z, Luquet E, Maddalena T, Sousa HC, Martinez-Solano I, Perrin N. Ever-young sex chromosomes in European tree frogs. PLoS Biol 2011; 9:e1001062. [PMID: 21629756 PMCID: PMC3100596 DOI: 10.1371/journal.pbio.1001062] [Citation(s) in RCA: 139] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Accepted: 04/06/2011] [Indexed: 11/23/2022] Open
Abstract
Non-recombining sex chromosomes are expected to undergo evolutionary decay,
ending up genetically degenerated, as has happened in birds and mammals. Why are
then sex chromosomes so often homomorphic in cold-blooded vertebrates? One
possible explanation is a high rate of turnover events, replacing master
sex-determining genes by new ones on other chromosomes. An alternative is that
X-Y similarity is maintained by occasional recombination events, occurring in
sex-reversed XY females. Based on mitochondrial and nuclear gene sequences, we
estimated the divergence times between European tree frogs (Hyla
arborea, H. intermedia, and H.
molleri) to the upper Miocene, about 5.4–7.1 million years
ago. Sibship analyses of microsatellite polymorphisms revealed that all three
species have the same pair of sex chromosomes, with complete absence of X-Y
recombination in males. Despite this, sequences of sex-linked loci show no
divergence between the X and Y chromosomes. In the phylogeny, the X and Y
alleles cluster according to species, not in groups of gametologs. We conclude
that sex-chromosome homomorphy in these tree frogs does not result from a recent
turnover but is maintained over evolutionary timescales by occasional X-Y
recombination. Seemingly young sex chromosomes may thus carry old-established
sex-determining genes, a result at odds with the view that sex chromosomes
necessarily decay until they are replaced. This raises intriguing perspectives
regarding the evolutionary dynamics of sexually antagonistic genes and the
mechanisms that control X-Y recombination. Non-recombining sex chromosomes, such as the Y chromosome, are expected to
degenerate over evolutionary times because they accumulate deleterious mutations
that cannot be corrected by recombination with a pristine copy. In most
cold-blooded vertebrates, such as frogs, however, sex chromosomes are
undifferentiated. Why is that so? On the one hand, the
“high-turnover” hypothesis holds that these sex chromosomes are
regularly replaced before they had time to decay. On the other hand, the
“fountain-of-youth” hypothesis posits that they are regularly
rejuvenated by X-Y recombination in sex-reversed XY females. Here, we show that
three species of tree frogs that diverged more than 5.4 million years ago share
the same pair of undifferentiated sex chromosomes. Although male recombination
stopped before species divergence, X and Y alleles show no differentiation, and
cluster by species, not gametologs. We conclude that their sex chromosome
homomorphy is not due to a recent turnover but is maintained over long
evolutionary times by occasional recombination. Such rare episodes of X-Y
recombination are expected to have long-lasting consequences on the evolution of
sex chromosomes and sex antagonistic genes.
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Affiliation(s)
- Matthias Stöck
- Department of Ecology and Evolution, University of Lausanne, Lausanne,
Switzerland
| | - Agnès Horn
- Department of Ecology and Evolution, University of Lausanne, Lausanne,
Switzerland
| | - Christine Grossen
- Department of Ecology and Evolution, University of Lausanne, Lausanne,
Switzerland
| | - Dorothea Lindtke
- Department of Ecology and Evolution, University of Lausanne, Lausanne,
Switzerland
- Department of Biology, University of Fribourg, Fribourg,
Switzerland
| | - Roberto Sermier
- Department of Ecology and Evolution, University of Lausanne, Lausanne,
Switzerland
| | | | - Christophe Dufresnes
- Department of Ecology and Evolution, University of Lausanne, Lausanne,
Switzerland
| | - Emmanuel Bonjour
- Department of Ecology and Evolution, University of Lausanne, Lausanne,
Switzerland
| | - Zoé Dumas
- Department of Ecology and Evolution, University of Lausanne, Lausanne,
Switzerland
- Umweltmikrobiologie, EAWAG, Dübendorf, Switzerland
| | - Emilien Luquet
- UMR 5023 Ecology of Fluvial Hydrosystems, Bât. Darwin C,
Université Lyon, Villeurbanne, France
| | | | - Helena Clavero Sousa
- Department of Ecology and Evolution, University of Lausanne, Lausanne,
Switzerland
- Perpetuo Socorro, Puerto Santa María (Cádiz),
Spain
| | - Iñigo Martinez-Solano
- Instituto de Investigación en Recursos Cinegéticos
(UCLM-CSIC-JCCM), Ciudad Real, Spain
| | - Nicolas Perrin
- Department of Ecology and Evolution, University of Lausanne, Lausanne,
Switzerland
- * E-mail:
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