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  • 1.
    Baiao, Guilherme Costa
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Swedish Museum Nat Hist, Dept Zool, Stockholm, Sweden.
    Forshage, Mattias
    Swedish Museum Nat Hist, Dept Zool, Stockholm, Sweden.
    Revision of the West Palaearctic species of Rhoptromeris Forster, 1869 (Hymenoptera: Figitidae: Eucoilinae)2018In: Journal of Natural History, ISSN 0022-2933, E-ISSN 1464-5262, Vol. 52, no 17-18, p. 1201-1224Article in journal (Refereed)
    Abstract [en]

    The West Palearctic species of Rhoptromeris are revised. A total of 11 species are recognised as valid in this region, including four newly described species: Rhoptromeris dichromata sp. nov., Rhoptromeris koponeni sp. nov., Rhoptromeris leptocornis sp. nov. and Rhoptromeris macaronesiensis sp. nov. Eucoila luteicornis Ionescu, 1959 is synonymised with Rhoptromeris heptoma (Hartig, 1840) syn. nov. A checklist of the Holarctic Rhoptromeris is presented and an identification key to the West Palearctic species is provided.

    www.zoobank.org/urn:lsid:zoobank.org:pub:8164332C-93E2-4E3F-A408-F5FF5DFB366E

    Download full text (pdf)
    fulltext
  • 2.
    Baiao, Guilherme Costa
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Schneider, Daniela I.
    Med Univ Vienna, Ctr Anat & Cell Biol, Lab Genome Dynam, Deparment Cell & Dev Biol, Schwarzspanierstr 17, A-1090 Vienna, Austria;Yale Univ, Dept Epidemiol Microbial Dis, 60 Coll St, New Haven, CT 06510 USA.
    Miller, Wolfgang J.
    Med Univ Vienna, Ctr Anat & Cell Biol, Lab Genome Dynam, Deparment Cell & Dev Biol, Schwarzspanierstr 17, A-1090 Vienna, Austria.
    Klasson, Lisa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    The effect of Wolbachia on gene expression in Drosophila paulistorum and its implications for symbiont-induced host speciation2019In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 20, article id 465Article in journal (Refereed)
    Abstract [en]

    Background: The Neotropical fruit fly Drosophila paulistorum (Diptera: Drosophilidae) is a species complex in statu nascendi comprising six reproductively isolated semispecies, each harboring mutualistic Wolbachia strains. Although wild type flies of each semispecies are isolated from the others by both pre- and postmating incompatibilities, mating between semispecies and successful offspring development can be achieved once flies are treated with antibiotics to reduce Wolbachia titer. Here we use RNA-seq to study the impact of Wolbachia on D. paulistorum and investigate the hypothesis that the symbiont may play a role in host speciation. For that goal, we analyze samples of heads and abdomens of both sexes of the Amazonian, Centro American and Orinocan semispecies of D. paulistorum.

    Results: We identify between 175 and 1192 differentially expressed genes associated with a variety of biological processes that respond either globally or according to tissue, sex or condition in the three semispecies. Some of the functions associated with differentially expressed genes are known to be affected by Wolbachia in other species, such as metabolism and immunity, whereas others represent putative novel phenotypes involving muscular functions, pheromone signaling, and visual perception.

    Conclusions: Our results show that Wolbachia affect a large number of biological functions in D. paulistorum, particularly when present in high titer. We suggest that the significant metabolic impact of the infection on the host may cause several of the other putative and observed phenotypes. We also speculate that the observed differential expression of genes associated with chemical communication and reproduction may be associated with the emergence of pre- and postmating barriers between semispecies, which supports a role for Wolbachia in the speciation of D. paulistorum.

    Download full text (pdf)
    FULLTEXT01
  • 3.
    Baiao, Guilherme Costa
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Schneider, Daniela
    Department of epidemiology of microbial diseases, Yale University.
    Miller, Wolfgang
    Department of cell and developmental biology, Medical university of Vienna.
    Klasson, Lisa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Differential gene expression in semispecies and hybrids of Drosophila paulistorumManuscript (preprint) (Other academic)
    Abstract [en]

    Gene expression divergence is correlated with and can be either a cause or a consequence of species divergence. Studying gene expression differences between closely related species, and their hybrid offspring, can thus give us clues about genes and mechanisms associated with reproductive isolation (RI) between them and allow us to better understand early stages of speciation. In this study, we use RNA-Seq to investigate gene expression divergence between the Amazonian, Centro-American and Orinocan semispecies of Drosophila paulistorum, a species cluster in statu nascendi, and between inter-semispecies hybrids and their parents. We uncover a large number of genes with varying expression between semispecies, with the highest numbers in male abdomens. The differentially expressed genes are associated with a range of biological functions, but especially with broad, regulatory functions, that are governed by transcription, translation, post-translational modifications and induced by signal transduction. We found that the expression pattern of hybrids was much more similar to the maternal line and that very few genes have a different expression than both of their parents. When comparing the differentially expressed genes in semispecies and hybrids to gene affected by Wolbachia in D. paulistorum, we see a small overlap. However, especially in hybrids, some of the overlapping genes appear to be highly relevant. Our study provides insights about expression differences associated with RI in D. paulistorum, and the impact of Wolbachia on the divergence of semispecies and hybrid sterility.

  • 4.
    Baiao, Guilherme Costa
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Strunov, Anton
    Department of Cell and Developmental Biology, Medical University of Vienna.
    Heyworth, Eleanor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Schneider, Daniela
    Department of Epidemiology of Microbial Diseases, Yale University.
    Thoma, Julia
    Department of Cell and Developmental Biology, Medical University of Vienna.
    Klasson, Lisa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Miller, Wolfgang
    Department of Cell and Developmental Biology, Medical University of Vienna.
    Persistence of high-level heteroplasmy through biparental transmission of a selfish mitochondrion in Drosophila paulistorumManuscript (preprint) (Other academic)
    Abstract [en]

    Heteroplasmy, or the coexistence of multiple mitotypes in an individual, has during recent years been shown to be more common in animals than previously anticipated. However, cases of stable, high-titer heteroplasmy are still relatively rare, as are systems with consistent paternal mitochondrial inheritance. In this study, we sequenced and assembled the full mitochondrial genomes of 23 Neotropical Drosophila lines belonging to six species of the willistoni group and three of the saltans group and discovered that 40% the 13 sequenced Drosophila paulistorum lines, are persistently heteroplasmic. We further showed that the mitochondria of D. paulistorum are polyphyletic, forming two clades, a and b, and that mitochondria of the a2 clade are exclusively found in heteroplasmic flies. Genomic analysis indicates that a2 is a functional mitochondrion, with no signs of loss of function mutations. Even so, our results demonstrate that a2 displays unusual features, including lack of titer response to energetic demands, higher titer in males than females, and consistent biparental transmission due to rapid replication during early embryo development. Together these features indicate that a2 might be a selfish mitochondrion that persists due to efficient biparental transmission.

    Using the assembled genomes, we reconstructed the evolutionary history of mitochondria in the willistoni subgroup and identified signs of multiple mitochondrial losses, gains and introgressions. The data indicated an a-like mitochondrial ancestor in the willistoni subgroup, with the b mitochondrion likely being acquired through introgression from an unidentified donor. We hypothesize that the selfish characteristics of a2 might have emerged as a response to competition for inheritance with the introgressed b

  • 5.
    Baião, Guilherme Costa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Genomic and transcriptomic investigation of reproductive incompatibility in Drosophila2020Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Both nuclear and cytoplasmic elements can contribute to the emergence of reproductive incompatibilities that influence evolution and speciation. In the projects that compose this thesis, we use genomics and transcriptomics to study some of those elements in Drosophila.

    In the first study, we show that Wolbachia, an endosymbiotic bacterium known to cause reproductive alterations in its hosts, influences gene expression in D. paulistorum. Affected genes were associated with biological functions such as metabolism, immunity, reproduction, and chemical communication. Our results indicate that Wolbachia accentuates the differences in expression profiles between semispecies and suggest that the symbiont influences host pre-and postmating isolation.

    In the second paper, we uncover widespread persistent heteroplasmy in D. paulistorum. We reveal that D. paulistorum mitochondria are polyphyletic, with two divergent mitotypes, and that the heteroplasmy likely originated through introgression. One of the mitotypes shows biparental inheritance, non-responsiveness to host energy demands and rapid titer increase in the early embryo. We hypothesize that such selfish traits evolved in response to competition between mitotypes.

    In the third project, we show that differentially expressed genes between D. paulistorum semispecies are associated with a variety of biological processes, especially broad regulatory functions that occur via variability in transcription, translation and ubiquitination of post-translational modification. We reveal that the expression profile of F1 inter-semispecies hybrids is markedly similar to that of the maternal line, and that Wolbachia has a small but potentially significant interaction with genes that are differentially expressed in semispecies and F1 hybrids.

    Finally, we use comparative genomics to study the evolution of closely related Wolbachia strains with known reproductive phenotypes. We confirm previous observations that Wolbachia genomes are very dynamic and that phage-associated regions are particularly variable and likely involved in horizontal transfer of genes linked to reproductive phenotypes. An in-depth screen for genetic elements potentially involved in Wolbachia-induced cytoplasmic incompatibility recovers genes previously known to be involved in the phenotype and novel candidates.

    In conclusion, this thesis contributes to our understanding of genetic factors that affect Drosophila evolution, particularly those leading to reproductive incompatibility in D. paulistorum and associated with Wolbachia.

    List of papers
    1. The effect of Wolbachia on gene expression in Drosophila paulistorum and its implications for symbiont-induced host speciation
    Open this publication in new window or tab >>The effect of Wolbachia on gene expression in Drosophila paulistorum and its implications for symbiont-induced host speciation
    2019 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 20, article id 465Article in journal (Refereed) Published
    Abstract [en]

    Background: The Neotropical fruit fly Drosophila paulistorum (Diptera: Drosophilidae) is a species complex in statu nascendi comprising six reproductively isolated semispecies, each harboring mutualistic Wolbachia strains. Although wild type flies of each semispecies are isolated from the others by both pre- and postmating incompatibilities, mating between semispecies and successful offspring development can be achieved once flies are treated with antibiotics to reduce Wolbachia titer. Here we use RNA-seq to study the impact of Wolbachia on D. paulistorum and investigate the hypothesis that the symbiont may play a role in host speciation. For that goal, we analyze samples of heads and abdomens of both sexes of the Amazonian, Centro American and Orinocan semispecies of D. paulistorum.

    Results: We identify between 175 and 1192 differentially expressed genes associated with a variety of biological processes that respond either globally or according to tissue, sex or condition in the three semispecies. Some of the functions associated with differentially expressed genes are known to be affected by Wolbachia in other species, such as metabolism and immunity, whereas others represent putative novel phenotypes involving muscular functions, pheromone signaling, and visual perception.

    Conclusions: Our results show that Wolbachia affect a large number of biological functions in D. paulistorum, particularly when present in high titer. We suggest that the significant metabolic impact of the infection on the host may cause several of the other putative and observed phenotypes. We also speculate that the observed differential expression of genes associated with chemical communication and reproduction may be associated with the emergence of pre- and postmating barriers between semispecies, which supports a role for Wolbachia in the speciation of D. paulistorum.

    Keywords
    Speciation, symbiosis, Wolbachia, transcriptome, Drosophila paulistorum, host-symbiont interactions
    National Category
    Genetics Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-389597 (URN)10.1186/s12864-019-5816-9 (DOI)000470715200001 ()31174466 (PubMedID)
    Funder
    Swedish Research Council, 2014-4353
    Available from: 2019-07-24 Created: 2019-07-24 Last updated: 2020-03-12Bibliographically approved
    2. Persistence of high-level heteroplasmy through biparental transmission of a selfish mitochondrion in Drosophila paulistorum
    Open this publication in new window or tab >>Persistence of high-level heteroplasmy through biparental transmission of a selfish mitochondrion in Drosophila paulistorum
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Heteroplasmy, or the coexistence of multiple mitotypes in an individual, has during recent years been shown to be more common in animals than previously anticipated. However, cases of stable, high-titer heteroplasmy are still relatively rare, as are systems with consistent paternal mitochondrial inheritance. In this study, we sequenced and assembled the full mitochondrial genomes of 23 Neotropical Drosophila lines belonging to six species of the willistoni group and three of the saltans group and discovered that 40% the 13 sequenced Drosophila paulistorum lines, are persistently heteroplasmic. We further showed that the mitochondria of D. paulistorum are polyphyletic, forming two clades, a and b, and that mitochondria of the a2 clade are exclusively found in heteroplasmic flies. Genomic analysis indicates that a2 is a functional mitochondrion, with no signs of loss of function mutations. Even so, our results demonstrate that a2 displays unusual features, including lack of titer response to energetic demands, higher titer in males than females, and consistent biparental transmission due to rapid replication during early embryo development. Together these features indicate that a2 might be a selfish mitochondrion that persists due to efficient biparental transmission.

    Using the assembled genomes, we reconstructed the evolutionary history of mitochondria in the willistoni subgroup and identified signs of multiple mitochondrial losses, gains and introgressions. The data indicated an a-like mitochondrial ancestor in the willistoni subgroup, with the b mitochondrion likely being acquired through introgression from an unidentified donor. We hypothesize that the selfish characteristics of a2 might have emerged as a response to competition for inheritance with the introgressed b

    National Category
    Evolutionary Biology
    Research subject
    Biology with specialization in Molecular Evolution
    Identifiers
    urn:nbn:se:uu:diva-406755 (URN)
    Available from: 2020-03-11 Created: 2020-03-11 Last updated: 2020-03-12
    3. Differential gene expression in semispecies and hybrids of Drosophila paulistorum
    Open this publication in new window or tab >>Differential gene expression in semispecies and hybrids of Drosophila paulistorum
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Gene expression divergence is correlated with and can be either a cause or a consequence of species divergence. Studying gene expression differences between closely related species, and their hybrid offspring, can thus give us clues about genes and mechanisms associated with reproductive isolation (RI) between them and allow us to better understand early stages of speciation. In this study, we use RNA-Seq to investigate gene expression divergence between the Amazonian, Centro-American and Orinocan semispecies of Drosophila paulistorum, a species cluster in statu nascendi, and between inter-semispecies hybrids and their parents. We uncover a large number of genes with varying expression between semispecies, with the highest numbers in male abdomens. The differentially expressed genes are associated with a range of biological functions, but especially with broad, regulatory functions, that are governed by transcription, translation, post-translational modifications and induced by signal transduction. We found that the expression pattern of hybrids was much more similar to the maternal line and that very few genes have a different expression than both of their parents. When comparing the differentially expressed genes in semispecies and hybrids to gene affected by Wolbachia in D. paulistorum, we see a small overlap. However, especially in hybrids, some of the overlapping genes appear to be highly relevant. Our study provides insights about expression differences associated with RI in D. paulistorum, and the impact of Wolbachia on the divergence of semispecies and hybrid sterility.

    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-406757 (URN)
    Available from: 2020-03-11 Created: 2020-03-11 Last updated: 2020-03-12
    4. Comparative genomics of closely related Wolbachia strains infecting Drosophila
    Open this publication in new window or tab >>Comparative genomics of closely related Wolbachia strains infecting Drosophila
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Cytoplasmic incompatibility (CI) is the most common form of reproductive manipulation induced by the vertically inherited endosymbiont Wolbachia. The phenotype causes partial or complete sterility in crosses between infected males and non-infected females, thus benefiting infected females in the population and the spread of the bacteria. Because of these properties, CI-inducing Wolbachia has been implicated as a mean for biological pest control. Although CI has been known for several decades, the first CI-associated genes, cifA and cifB, were only recently discovered. In this study, we sequenced five complete Wolbachia genomes (wSan, wYak, wTei, wAu, wMa,) and performed comparative genomic analyses between these and four previously published complete Wolbachia genomes (wRi, wNo, wHa, wMel), that have all had their CI properties tested in the same genetic host background, Drosophila simulans STC. Using these genomes, we investigate what types of genes differ between closely related Wolbachia strains and compare the sequences from some of the strains in their natural host vs. after transfer to D. simulans STC. We find that phage-associated and hypothetical genes are likely to vary more between genomes and that very few mutations have occurred when strains were transferred to D. simulans. Furthermore, we investigate the evolution of the known CI genes and take advantage of the highly similar genomes of some strains as well as their complex CI properties to identify further genes associated with both mod and resc functions of CI.

    National Category
    Evolutionary Biology
    Research subject
    Biology with specialization in Molecular Evolution
    Identifiers
    urn:nbn:se:uu:diva-406756 (URN)
    Available from: 2020-03-11 Created: 2020-03-11 Last updated: 2020-03-12
    Download full text (pdf)
    fulltext
    Download (jpg)
    presentationsbild
  • 6.
    Janice, Jessin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Baiao, Guilherme Costa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Galinou, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Bourtzis, Kostas
    IAEA Division of Nuclear Techniques in Food and Agriculture.
    Klasson, Lisa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Comparative genomics of closely related Wolbachia strains infecting DrosophilaManuscript (preprint) (Other academic)
    Abstract [en]

    Cytoplasmic incompatibility (CI) is the most common form of reproductive manipulation induced by the vertically inherited endosymbiont Wolbachia. The phenotype causes partial or complete sterility in crosses between infected males and non-infected females, thus benefiting infected females in the population and the spread of the bacteria. Because of these properties, CI-inducing Wolbachia has been implicated as a mean for biological pest control. Although CI has been known for several decades, the first CI-associated genes, cifA and cifB, were only recently discovered. In this study, we sequenced five complete Wolbachia genomes (wSan, wYak, wTei, wAu, wMa,) and performed comparative genomic analyses between these and four previously published complete Wolbachia genomes (wRi, wNo, wHa, wMel), that have all had their CI properties tested in the same genetic host background, Drosophila simulans STC. Using these genomes, we investigate what types of genes differ between closely related Wolbachia strains and compare the sequences from some of the strains in their natural host vs. after transfer to D. simulans STC. We find that phage-associated and hypothetical genes are likely to vary more between genomes and that very few mutations have occurred when strains were transferred to D. simulans. Furthermore, we investigate the evolution of the known CI genes and take advantage of the highly similar genomes of some strains as well as their complex CI properties to identify further genes associated with both mod and resc functions of CI.

1 - 6 of 6
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