1
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Santhosh S, Ebert D, Janicke T. Sperm competition favours intermediate sperm size in a hermaphrodite. J Evol Biol 2024:voae058. [PMID: 38738700 DOI: 10.1093/jeb/voae058] [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: 12/06/2023] [Indexed: 05/14/2024]
Abstract
Sperm competition is a potent mechanism of post-copulatory sexual selection that has been found to shape reproductive morphologies and behaviours in promiscuous animals. Especially sperm size has been argued to evolve in response to sperm competition through its effect on sperm longevity, sperm motility, the ability to displace competing sperm and ultimately fertilization success. Additionally, sperm size has been observed to co-evolve with female reproductive morphology. Theoretical work predicts that sperm competition may select for longer sperm but may also favour shorter sperm if sperm size trades off with number. In this study, we studied the relationship between sperm size and post-mating success in the free-living flatworm, Macrostomum lignano. Specifically, we used inbred isolines of M. lignano that varied in sperm size to investigate how sperm size translated into the ability of worms to transfer and deposit sperm in a mating partner. Our results revealed a hump-shaped relationship with individuals producing sperm of intermediate size having highest sperm competitiveness. This finding broadens our understanding of the evolution of sperm morphology by providing empirical support for stabilizing selection on sperm size under sperm competition.
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Affiliation(s)
- Santhosh Santhosh
- Department of Environmental Sciences, Zoology, University of Basel, CH-4 4051 Basel, Switzerland
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, CH-4 4051 Basel, Switzerland
| | - Tim Janicke
- CEFE, Univ. Montpellier, CNRS, EPHE, IRD, 34293 Montpellier Cedex 05, France
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2
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Otte KA, Fredericksen M, Fields P, Fröhlich T, Laforsch C, Ebert D. The cuticle proteome of a planktonic crustacean. Proteomics 2024:e2300292. [PMID: 38676470 DOI: 10.1002/pmic.202300292] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 04/29/2024]
Abstract
The cuticles of arthropods provide an interface between the organism and its environment. Thus, the cuticle's structure influences how the organism responds to and interacts with its surroundings. Here, we used label-free quantification proteomics to provide a proteome of the moulted cuticle of the aquatic crustacean Daphnia magna, which has long been a prominent subject of studies on ecology, evolution, and developmental biology. We detected a total of 278 high-confidence proteins. Using protein sequence domain and functional enrichment analyses, we identified chitin-binding structural proteins and chitin-modifying enzymes as the most abundant protein groups in the cuticle proteome. Structural cuticular protein families showed a similar distribution to those found in other arthropods and indicated proteins responsible for the soft and flexible structure of the Daphnia cuticle. Finally, cuticle protein genes were also clustered as tandem gene arrays in the D. magna genome. The cuticle proteome presented here will be a valuable resource to the Daphnia research community, informing genome annotations and investigations on diverse topics such as the genetic basis of interactions with predators and parasites.
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Affiliation(s)
- Kathrin A Otte
- Institute of Cell and Systems Biology of Animals, University of Hamburg, Hamburg, Germany
| | - Maridel Fredericksen
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Peter Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Thomas Fröhlich
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | | | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
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3
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Huessy B, Bumann D, Ebert D. Ectopical expression of bacterial collagen-like protein supports its role as adhesin in host-parasite coevolution. R Soc Open Sci 2024; 11:231441. [PMID: 38577215 PMCID: PMC10987987 DOI: 10.1098/rsos.231441] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 01/10/2024] [Accepted: 02/13/2024] [Indexed: 04/06/2024]
Abstract
For a profound understanding of antagonistic coevolution, it is necessary to identify the coevolving genes. The bacterium Pasteuria and its host, the microcrustacean Daphnia, are a well-characterized paradigm for co-evolution, but the underlying genes remain largely unknown. A genome-wide association study suggested a Pasteuria collagen-like protein 7 (Pcl7) as a candidate mediating parasite attachment and driving its coevolution with the host. Since Pasteuria ramosa cannot currently be genetically manipulated, we used Bacillus thuringiensis to express a fusion protein of a Pcl7 carboxy-terminus from P. ramosa and the amino-terminal domain of a B. thuringiensis collagen-like protein (CLP). Mutant B. thuringiensis (Pcl7-Bt) spores but not wild-type B. thuringiensis (WT-Bt) spores attached to the same site of susceptible hosts as P. ramosa. Furthermore, Pcl7-Bt spores attached readily to susceptible host genotypes, but only slightly to resistant host genotypes. These findings indicated that the fusion protein was properly expressed and folded and demonstrated that indeed the C-terminus of Pcl7 mediates attachment in a host genotype-specific manner. These results provide strong evidence for the involvement of a CLP in the coevolution of Daphnia and P. ramosa and open new avenues for genetic epidemiological studies of host-parasite interactions.
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Affiliation(s)
- Benjamin Huessy
- Department of Environmental Sciences, Zoology, University of Basel, Basel4051, Switzerland
- University of Basel, Basel4056, Switzerland
| | | | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel4051, Switzerland
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4
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Van de Schoot E, Merckx T, Ebert D, Wesselingh RA, Altermatt F, Van Dyck H. Evolutionary change in flight-to-light response in urban moths comes with changes in wing morphology. Biol Lett 2024; 20:20230486. [PMID: 38471566 PMCID: PMC10932693 DOI: 10.1098/rsbl.2023.0486] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/12/2024] [Indexed: 03/14/2024] Open
Abstract
Moths and other insects are attracted by artificial light sources. This flight-to-light behaviour disrupts their general activity focused on finding resources, such as mating partners, and increases predation risk. It thus has substantial fitness costs. In illuminated urban areas, spindle ermine moths Yponomeuta cagnagella were reported to have evolved a reduced flight-to-light response. Yet, the specific mechanism remained unknown, and was hypothesized to involve either changes in visual perception or general flight ability or overall mobility traits. Here, we test whether spindle ermine moths from urban and rural populations-with known differences in flight-to-light responses-differ in flight-related morphological traits. Urban individuals were found to have on average smaller wings than rural moths, which in turn correlated with a lower probability of being attracted to an artificial light source. Our finding supports the reduced mobility hypothesis, which states that reduced mobility in urban areas is associated with specific morphological changes in the flight apparatus.
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Affiliation(s)
| | - Thomas Merckx
- WILD, Biology Department, Vrije Universiteit Brussel, Brussels 1050, Belgium
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | | | - Florian Altermatt
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Hans Van Dyck
- Earth & Life Institute, UCLouvain, Louvain-la-Neuve 1348, Belgium
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5
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Friedel EBN, Tebartz van Elst L, Schäfer M, Maier S, Runge K, Küchlin S, Reich M, Lagrèze WA, Kornmeier J, Ebert D, Endres D, Domschke K, Nickel K. Retinal Thinning in Adults with Autism Spectrum Disorder. J Autism Dev Disord 2024; 54:1143-1156. [PMID: 36550331 PMCID: PMC10907434 DOI: 10.1007/s10803-022-05882-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Since the retina shares its embryological origin with the central nervous system, optical coherence tomography (OCT), an imaging technique frequently employed in ophthalmology to analyze the macula and intraretinal layer thicknesses and volumes, has recently become increasingly important in psychiatric research. We examined 34 autistic and 31 neurotypical adults (NT) using OCT. Autistic adults had reduced overall macular and outer nuclear layer (ONL) thickness and volume compared to NT. Both macular and ONL thickness showed significant inverse associations with the severity of autistic symptoms measured with the Social Responsiveness Scale 2 (SRS-2). Longitudinal studies across different age groups are required to clarify whether retinal changes may represent a possible trait marker.
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Affiliation(s)
- Evelyn B N Friedel
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Eye Center, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Ludger Tebartz van Elst
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Mirjam Schäfer
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Simon Maier
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Kimon Runge
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sebastian Küchlin
- Eye Center, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michael Reich
- Eye Center, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Wolf A Lagrèze
- Eye Center, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jürgen Kornmeier
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Institute for Frontier Areas of Psychology and Mental Health, Freiburg, Germany
| | - Dieter Ebert
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dominique Endres
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Katharina Domschke
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Basics in Neuromodulation, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Kathrin Nickel
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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6
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Domschke K, Ebert D. [Jon Fosse: "Melancholy"-A reading from a psychiatric perspective]. Nervenarzt 2024; 95:279-282. [PMID: 38366122 PMCID: PMC10914914 DOI: 10.1007/s00115-024-01623-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/20/2024] [Indexed: 02/18/2024]
Affiliation(s)
- Katharina Domschke
- Klinik für Psychiatrie und Psychotherapie, Medizinische Fakultät, Universitätsklinikum Freiburg, Albert-Ludwigs-Universität Freiburg, Hauptstr. 5, 79104, Freiburg, Deutschland.
| | - Dieter Ebert
- Klinik für Psychiatrie und Psychotherapie, Medizinische Fakultät, Universitätsklinikum Freiburg, Albert-Ludwigs-Universität Freiburg, Hauptstr. 5, 79104, Freiburg, Deutschland
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7
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Santos JL, Ebert D. The limits of stress-tolerance for zooplankton resting stages in freshwater ponds. Oecologia 2023; 203:453-465. [PMID: 37971560 PMCID: PMC10684647 DOI: 10.1007/s00442-023-05478-8] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023]
Abstract
In seasonal environments, many organisms evolve strategies such as diapause to survive stressful periods. Understanding the link between habitat stability and diapause strategy can help predict a population's survival in a changing world. Indeed, resting stages may be an important way freshwater organisms can survive periods of drought or freezing, and as the frequency and extent of drought or freezing vary strongly among habitats and are predicted to change with climate change, it raises questions about how organisms cope with, and survive, environmental stress. Using Daphnia magna as a model system, we tested the ability of resting stages from different populations to cope with stress during diapause. The combination of elevated temperatures and wet conditions during diapause shows to prevent hatching altogether. In contrast, hatching is relatively higher after a dry and warm diapause, but declines with rising temperatures, while time to hatch increases. Resting stages produced by populations from summer-dry habitats perform slightly, but consistently, better at higher temperatures and dryness, supporting the local adaptation hypothesis. A higher trehalose content in resting eggs from summer-dry habitat might explain such pattern. Considering that temperatures and summer droughts are projected to increase in upcoming years, it is fundamental to know how resting stages resist stressful conditions so as to predict and protect the ecological functioning of freshwater ecosystems.
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Affiliation(s)
- Joana L Santos
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland.
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
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8
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Angst P, Pombert JF, Ebert D, Fields PD. Near chromosome-level genome assembly of the microsporidium Hamiltosporidium tvaerminnensis. G3 (Bethesda) 2023; 13:jkad185. [PMID: 37565496 PMCID: PMC10542269 DOI: 10.1093/g3journal/jkad185] [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] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/05/2023] [Indexed: 08/12/2023]
Abstract
Microsporidia are intracellular parasitic fungi whose genomes rank among the smallest of all known eukaryotes. A number of outstanding questions remain concerning the evolution of their large-scale variation in genome architecture, responsible for genome size variation of more than an order of magnitude. This genome report presents the first near-chromosomal assembly of a large-genome microsporidium, Hamiltosporidium tvaerminnensis. Combined Oxford Nanopore, Pacific Biosciences (PacBio), and Illumina sequencing led to a genome assembly of 17 contigs, 11 of which represent complete chromosomes. Our assembly is 21.64 Mb in length, has an N50 of 1.44 Mb, and consists of 39.56% interspersed repeats. We introduce a novel approach in microsporidia, PacBio Iso-Seq, as part of a larger annotation pipeline for obtaining high-quality annotations of 3,573 protein-coding genes. Based on direct evidence from the full-length Iso-Seq transcripts, we present evidence for alternative polyadenylation and variation in splicing efficiency, which are potential regulation mechanisms for gene expression in microsporidia. The generated high-quality genome assembly is a necessary resource for comparative genomics that will help elucidate the evolution of genome architecture in response to intracellular parasitism.
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Affiliation(s)
- Pascal Angst
- Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland
| | | | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland
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9
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Dexter E, Fields PD, Ebert D. Uncovering the genomic basis of infection through co-genomic sequencing of hosts and parasites. Mol Biol Evol 2023:msad145. [PMID: 37326294 DOI: 10.1093/molbev/msad145] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 05/21/2023] [Accepted: 06/01/2023] [Indexed: 06/17/2023] Open
Abstract
Understanding the genomic basis of infectious disease is fundamental objective in coevolutionary theory with relevance to healthcare, agriculture, and epidemiology. Models of host-parasite coevolution often assume that infection requires specific combinations of host and parasite genotypes. Coevolving host and parasite loci are therefor expected to show associations that reflects an underlying infection/resistance allele matrix, yet little evidence for such genome-to-genome interactions has been observed among natural populations. We conducted a study to search for this genomic signature across 258 linked host (Daphnia magna) and parasite (Pasteuria ramosa) genomes. Our results show a clear signal of genomic association between multiple epistatically-interacting loci in the host genome, and a family of genes encoding for collagen-like protein in the parasite genome. These findings are supported by laboratory-based infection trials, which show strong correspondence between phenotype and genotype at the identified loci. Our study provides clear genomic evidence of antagonistic coevolution among wild populations.
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Affiliation(s)
- Eric Dexter
- Department of Environmental Sciences, The University of Basel; Basel, 4051, Switzerland
| | - Peter D Fields
- Department of Environmental Sciences, The University of Basel; Basel, 4051, Switzerland
| | - Dieter Ebert
- Department of Environmental Sciences, The University of Basel; Basel, 4051, Switzerland
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10
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Angst P, Ebert D, Fields PD. Population genetic analysis of the microsporidium Ordospora colligata reveals the role of natural selection and phylogeography on its extremely compact and reduced genome. G3 (Bethesda) 2023; 13:jkad017. [PMID: 36655395 PMCID: PMC9997559 DOI: 10.1093/g3journal/jkad017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 01/02/2023] [Accepted: 01/11/2023] [Indexed: 01/20/2023]
Abstract
The determinants of variation in a species' genome-wide nucleotide diversity include historical, environmental, and stochastic aspects. This diversity can inform us about the species' past and present evolutionary dynamics. In parasites, the mode of transmission and the interactions with the host might supersede the effects of these aspects in shaping parasite genomic diversity. We used genomic samples from 10 populations of the microsporidian parasite Ordospora colligata to investigate present genomic diversity and how it was shaped by evolutionary processes, specifically, the role of phylogeography, co-phylogeography (with the host), natural selection, and transmission mode. Although very closely related microsporidia cause diseases in humans, O. colligata is specific to the freshwater crustacean Daphnia magna and has one of the smallest known eukaryotic genomes. We found an overlapping phylogeography between O. colligata and its host highlighting the long-term, intimate relationship between them. The observed geographic distribution reflects previous findings that O. colligata exhibits adaptations to colder habitats, which differentiates it from other microsporidian gut parasites of D. magna predominantly found in warmer areas. The co-phylogeography allowed us to calibrate the O. colligata phylogeny and thus estimate its mutation rate. We identified several genetic regions under potential selection. Our whole-genome study provides insights into the evolution of one of the most reduced eukaryotic genomes and shows how different processes shape genomic diversity of an obligate parasite.
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Affiliation(s)
- Pascal Angst
- Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland
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11
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Maier S, Philipsen A, Perlov E, Runge K, Matthies S, Ebert D, Endres D, Domschke K, Tebartz van Elst L, Nickel K. Left insular cortical thinning differentiates the inattentive and combined subtype of adult attention-deficit/hyperactivity disorder. J Psychiatr Res 2023; 159:196-204. [PMID: 36739847 DOI: 10.1016/j.jpsychires.2023.01.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 10/27/2022] [Accepted: 01/26/2023] [Indexed: 01/30/2023]
Abstract
BACKGROUND Neuroimaging studies in attention-deficit/hyperactivity disorder (ADHD) demonstrated decreased global gray matter volume. In terms of surface parameters, most investigations focused on cortical thickness with a multi-center MEGA-analysis indicating cortical thinning in children, but not in adults with ADHD. In this single-scanner study, for the first time in adult ADHD, we additionally examined metrics beyond cortical thickness and surface area, namely sulcal depth and fractal dimension as measures of cortical alteration and complexity. Unlike most previous studies, ADHD subtypes were considered. METHODS As part of the Comparison of Methylphenidate and Psychotherapy in Adult ADHD Study (COMPAS), surface parameters were analyzed in 131 adults with ADHD (66 combined, 60 inattentive and 5 hyperactive/impulsive subtype) and 95 healthy controls with the Computational Anatomy Toolbox (CAT12) using Statistical Parametric Mapping Software (SPM). RESULTS Neither at the vertex- nor at the region of interest-level, the ADHD and control group differed significantly with regard to cortical thickness, gyrification index, sulcal depth or fractal dimension. Contrasting the combined and the inattentive subtype, patients of the combined subtype showed a significant thinning of the left anterior insular cortex. Thinner left pars opercularis cortical thickness was associated with symptoms of hyperactivity/restlessness. CONCLUSIONS Resembling previous findings of a correlation of the left anterior insular gray matter volume with oppositional symptoms in adolescents with ADHD, we detected left anterior insular cortical thinning in the ADHD combined subtype. Left insular cortical thickness could represent a potential marker to distinguish the predominantly inattentive and the combined ADHD subtype in adulthood.
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Affiliation(s)
- Simon Maier
- Section for Experimental Neuropsychiatry, Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Alexandra Philipsen
- Department of Psychiatry and Psychotherapy, University Hospital Bonn, Bonn, Germany.
| | - Evgeniy Perlov
- Section for Experimental Neuropsychiatry, Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Clinic for Psychiatry Luzern, St. Urban, St. Urban, Switzerland.
| | - Kimon Runge
- Section for Experimental Neuropsychiatry, Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Swantje Matthies
- Section for Experimental Neuropsychiatry, Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Dieter Ebert
- Section for Experimental Neuropsychiatry, Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Dominique Endres
- Section for Experimental Neuropsychiatry, Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Katharina Domschke
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Basics in Neuromodulation, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Ludger Tebartz van Elst
- Section for Experimental Neuropsychiatry, Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Kathrin Nickel
- Section for Experimental Neuropsychiatry, Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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12
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Fredericksen M, Fields PD, Du Pasquier L, Ricci V, Ebert D. QTL study reveals candidate genes underlying host resistance in a Red Queen model system. PLoS Genet 2023; 19:e1010570. [PMID: 36730161 PMCID: PMC9894429 DOI: 10.1371/journal.pgen.1010570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 12/14/2022] [Indexed: 02/03/2023] Open
Abstract
Specific interactions of host and parasite genotypes can lead to balancing selection, maintaining genetic diversity within populations. In order to understand the drivers of such specific coevolution, it is necessary to identify the molecular underpinnings of these genotypic interactions. Here, we investigate the genetic basis of resistance in the crustacean host, Daphnia magna, to attachment and subsequent infection by the bacterial parasite, Pasteuria ramosa. We discover a single locus with Mendelian segregation (3:1 ratio) with resistance being dominant, which we call the F locus. We use QTL analysis and fine mapping to localize the F locus to a 28.8-kb region in the host genome, adjacent to a known resistance supergene. We compare the 28.8-kb region in the two QTL parents to identify differences between host genotypes that are resistant versus susceptible to attachment and infection by the parasite. We identify 13 genes in the region, from which we highlight eight biological candidates for the F locus, based on presence/absence polymorphisms and differential gene expression. The top candidates include a fucosyltransferase gene that is only present in one of the two QTL parents, as well as several Cladoceran-specific genes belonging to a large family that is represented in multiple locations of the host genome. Fucosyltransferases have been linked to resistance in previous studies of Daphnia-Pasteuria and other host-parasite systems, suggesting that P. ramosa spore attachment could be mediated by changes in glycan structures on D. magna cuticle proteins. The Cladoceran-specific candidate genes suggest a resistance strategy that relies on gene duplication. Our results add a new locus to a growing genetic model of resistance in the D. magna-P. ramosa system. The identified candidate genes will be used in future functional genetic studies, with the ultimate aim to test for cycles of allele frequencies in natural populations.
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Affiliation(s)
- Maridel Fredericksen
- University of Basel, Department of Environmental Sciences, Zoology, Basel, Switzerland
- * E-mail:
| | - Peter D. Fields
- University of Basel, Department of Environmental Sciences, Zoology, Basel, Switzerland
| | - Louis Du Pasquier
- University of Basel, Department of Environmental Sciences, Zoology, Basel, Switzerland
| | - Virginie Ricci
- University of Basel, Department of Environmental Sciences, Zoology, Basel, Switzerland
| | - Dieter Ebert
- University of Basel, Department of Environmental Sciences, Zoology, Basel, Switzerland
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13
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Angst P, Ameline C, Haag CR, Ben-Ami F, Ebert D, Fields PD. Genetic Drift Shapes the Evolution of a Highly Dynamic Metapopulation. Mol Biol Evol 2022; 39:6874788. [PMID: 36472514 PMCID: PMC9778854 DOI: 10.1093/molbev/msac264] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
The dynamics of extinction and (re)colonization in habitat patches are characterizing features of dynamic metapopulations, causing them to evolve differently than large, stable populations. The propagule model, which assumes genetic bottlenecks during colonization, posits that newly founded subpopulations have low genetic diversity and are genetically highly differentiated from each other. Immigration may then increase diversity and decrease differentiation between subpopulations. Thus, older and/or less isolated subpopulations are expected to have higher genetic diversity and less genetic differentiation. We tested this theory using whole-genome pool-sequencing to characterize nucleotide diversity and differentiation in 60 subpopulations of a natural metapopulation of the cyclical parthenogen Daphnia magna. For comparison, we characterized diversity in a single, large, and stable D. magna population. We found reduced (synonymous) genomic diversity, a proxy for effective population size, weak purifying selection, and low rates of adaptive evolution in the metapopulation compared with the large, stable population. These differences suggest that genetic bottlenecks during colonization reduce effective population sizes, which leads to strong genetic drift and reduced selection efficacy in the metapopulation. Consistent with the propagule model, we found lower diversity and increased differentiation in younger and also in more isolated subpopulations. Our study sheds light on the genomic consequences of extinction-(re)colonization dynamics to an unprecedented degree, giving strong support for the propagule model. We demonstrate that the metapopulation evolves differently from a large, stable population and that evolution is largely driven by genetic drift.
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Affiliation(s)
| | - Camille Ameline
- Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland,Evolutionary Biology, Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal
| | - Christoph R Haag
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, Montpellier 34293, France,Tvärminne Zoological Station, University of Helsinki, Hanko 10900, Finland
| | - Frida Ben-Ami
- Tvärminne Zoological Station, University of Helsinki, Hanko 10900, Finland,George S. Wise Faculty of Life Sciences, School of Zoology, Tel Aviv University, Tel Aviv 69978, Israel
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland,Tvärminne Zoological Station, University of Helsinki, Hanko 10900, Finland
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland,Tvärminne Zoological Station, University of Helsinki, Hanko 10900, Finland
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14
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Ameline C, Voegtli F, Andras J, Dexter E, Engelstädter J, Ebert D. Genetic slippage after sex maintains diversity for parasite resistance in a natural host population. Sci Adv 2022; 8:eabn0051. [PMID: 36399570 PMCID: PMC9674289 DOI: 10.1126/sciadv.abn0051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Although parasite-mediated selection is a major driver of host evolution, its influence on genetic variation for parasite resistance is not yet well understood. We monitored resistance in a large population of the planktonic crustacean Daphnia magna over 8 years, as it underwent yearly epidemics of the bacterial pathogen Pasteuria ramosa. We observed cyclic dynamics of resistance: Resistance increased throughout the epidemics, but susceptibility was restored each spring when hosts hatched from sexual resting stages. Host resting stages collected across the year showed that largely resistant host populations can produce susceptible sexual offspring. A genetic model of resistance developed for this host-parasite system, based on multiple loci and strong epistasis, is in partial agreement with our findings. Our results reveal that, despite strong selection for resistance in a natural host population, genetic slippage after sexual reproduction can be a strong factor for the maintenance of genetic diversity of host resistance.
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Affiliation(s)
- Camille Ameline
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Felix Voegtli
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Jason Andras
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Eric Dexter
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Jan Engelstädter
- School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
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15
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Friedel EBN, Schäfer M, Endres D, Maier S, Runge K, Bach M, Heinrich SP, Ebert D, Domschke K, Tebartz van Elst L, Nickel K. Electroretinography in adults with high-functioning autism spectrum disorder. Autism Res 2022; 15:2026-2037. [PMID: 36217563 DOI: 10.1002/aur.2823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 07/25/2022] [Accepted: 09/19/2022] [Indexed: 12/15/2022]
Abstract
The electroretinogram (ERG) allows the investigation of retinal signaling pathways and has increasingly been applied in individuals with mental disorders in search for potential biomarkers of neurodevelopmental disorders. Preceding ERG examinations in individuals with autism spectrum disorders (ASD) showed inconsistent results, which might be due to the small number of participants, heterogeneity of the ASD population, differences in age ranges, and stimulation methods. The aim of this study was to investigate functional retinal responses in adults with ASD by means of the light-adapted (photopic) ERG. Light-adapted ERG measurements were obtained with the RETeval® system applying three different stimulation protocols. In the final analysis, the ERG parameters a-wave, b-wave, the photopic negative response (PhNR), the photopic hill parameters as well as additional amplitude ratios were compared between 32 adults with high-functioning ASD and 31 non-autistic controls. Both groups were matched with regard to sex and age. No significant functional retinal differences in amplitude or peak time of the a- or b-wave, PhNR, the photopic hill parameters or the ERG-amplitude ratios could be detected in individuals with ASD compared to non-autistic participants. The absence of electrophysiological functional retinal alterations in ASD, suggests that changes in visual perception, such as increased attention to detail or visual hypersensitivity in ASD, are not due to impairments at early levels of retinal signal processing.
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Affiliation(s)
- Evelyn B N Friedel
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Eye Center, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Mirjam Schäfer
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dominique Endres
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Simon Maier
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Kimon Runge
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michael Bach
- Eye Center, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sven P Heinrich
- Eye Center, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dieter Ebert
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Katharina Domschke
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Center for Basics in Neuromodulation, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ludger Tebartz van Elst
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Kathrin Nickel
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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16
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Abstract
Water fleas of the genus Daphnia have been a model system for hundreds of years and is among the best studied ecological model organisms to date. Daphnia are planktonic crustaceans with a cyclic parthenogenetic life-cycle. They have a nearly worldwide distribution, inhabiting standing fresh- and brackish water bodies, from small temporary pools to large lakes. Their predominantly asexual reproduction allows for the study of phenotypes excluding genetic variation, enabling us to separate genetic from non-genetic effects. Daphnia are often used in studies related to ecotoxicology, predator-induced defence, host–parasite interactions, phenotypic plasticity and, increasingly, in evolutionary genomics. The most commonly studied species are Daphnia magna and D. pulex, for which a rapidly increasing number of genetic and genomic tools are available. Here, I review current research topics, where the Daphnia model system plays a critical role.
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Affiliation(s)
- Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland.
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17
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Amandine C, Ebert D, Stukenbrock E, Rodríguez de la Vega RC, Tiffin P, Croll D, Tellier A. Unraveling coevolutionary dynamics using ecological genomics. Trends Genet 2022; 38:1003-1012. [PMID: 35715278 DOI: 10.1016/j.tig.2022.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 10/31/2021] [Revised: 05/08/2022] [Accepted: 05/10/2022] [Indexed: 11/27/2022]
Abstract
Coevolutionary interactions, from the delicate co-dependency in mutualistic interactions to the antagonistic relationship of hosts and parasites, are a ubiquitous driver of adaptation. Surprisingly, little is known about the genomic processes underlying coevolution in an ecological context. However, species comprise genetically differentiated populations that interact with temporally variable abiotic and biotic environments. We discuss the recent advances in coevolutionary theory and genomics as well as shortcomings, to identify coevolving genes that take into account this spatial and temporal variability of coevolution, and propose a practical guide to understand the dynamic of coevolution using an ecological genomics lens.
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Affiliation(s)
- Cornille Amandine
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France.
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Eva Stukenbrock
- Max Planck Institute for Terrestrial Microbiology, Max Planck Research Group, Fungal Biodiversity, Marburg, Germany
| | | | - Peter Tiffin
- Department of Plant and Microbial Biology, 250 Biological Sciences, 1445 Gortner Ave., University of Minnesota, Saint Paul, MN 55108, USA
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland.
| | - Aurélien Tellier
- Population Genetics, Department of Life Science Systems, Technical University of Munich, Liesel-Beckman-Str. 2, 85354 Freising, Germany.
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18
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Nickel K, Perlov E, Reisert M, Runge K, Friedel E, Denzel D, Ebert D, Endres D, Domschke K, Tebartz van Elst L, Maier S. Altered transcallosal fiber count and volume in high-functioning adults with autism spectrum disorder. Psychiatry Res Neuroimaging 2022; 322:111464. [PMID: 35220205 DOI: 10.1016/j.pscychresns.2022.111464] [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] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/25/2022] [Accepted: 02/21/2022] [Indexed: 11/20/2022]
Abstract
An altered pattern of information processing has been hypothesized in autism spectrum disorder (ASD), characterized by enhanced local network connectivity and reduced long-distance communication. Previous findings of impaired white matter integrity in the genu and the body of the corpus callosum already indicated reduced long-distance connectivity in patients with ASD. However, it remained unclear how this reduced white matter integrity affects the structural connectivity of the corresponding brain areas. To this end, we analyzed magnetic resonance images (MRI) from 30 participants with high-functioning ASD and 30 typically developed individuals using a global tracking approach to estimate the fiber count and volume of the transcallosal fiber tracts of the five corpus callosum subsections. A reduced fiber count and fiber volume in the anterior subsection of the corpus callosum was detected, supporting the hypothesis of reduced long-distance connectivity in ASD.
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Affiliation(s)
- Kathrin Nickel
- Section for Experimental Neuropsychiatry, Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Evgeniy Perlov
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Luzerner Psychiatrie, Hospital St. Urban, St. Urban, Switzerland
| | - Marco Reisert
- Department of Radiology, Medical Physics, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Kimon Runge
- Section for Experimental Neuropsychiatry, Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Evelyn Friedel
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dominik Denzel
- Section for Experimental Neuropsychiatry, Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dieter Ebert
- Section for Experimental Neuropsychiatry, Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dominique Endres
- Section for Experimental Neuropsychiatry, Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Katharina Domschke
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Basics in Neuromodulation, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ludger Tebartz van Elst
- Section for Experimental Neuropsychiatry, Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Simon Maier
- Section for Experimental Neuropsychiatry, Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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19
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Maier S, Düppers AL, Runge K, Dacko M, Lange T, Fangmeier T, Riedel A, Ebert D, Endres D, Domschke K, Perlov E, Nickel K, Tebartz van Elst L. Increased prefrontal GABA concentrations in adults with autism spectrum disorders. Autism Res 2022; 15:1222-1236. [PMID: 35587691 DOI: 10.1002/aur.2740] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [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: 11/16/2021] [Accepted: 04/28/2022] [Indexed: 11/10/2022]
Abstract
The excitatory-inhibitory imbalance hypothesis postulates dysregulation of the gamma-aminobutyric acid (GABA) and glutamate (Glu) neurotransmitter systems as a common underlying deficit in individuals with autism spectrum disorders (ASD). Previous studies suggest an important role of these systems in the pathophysiology of ASD, including a study of our group reporting decreased glutamate concentrations in the pregenual anterior cingulate cortex (ACC) of adults with ASD. The aim of this study was to replicate our previous findings of impaired glutamate metabolism in ASD in a new sample and to additionally quantify GABA in the ACC and dorsolateral prefrontal cortex (dlPFC). Concentrations of GABA and glutamate-glutamine (Glx; combined glutamate and glutamine signal) were quantified in the ACC and dlPFC of 43 adults with ASD and 43 neurotypical controls (NTC) by magnetic resonance spectroscopy (MRS). The ASD group showed increased absolute GABA concentrations and elevated GABA/creatine ratios in the left dlPFC compared to NTC, while no group differences were detected in the pregenual and dorsal ACC. Previous findings of altered Glx concentration in the pregenual ACC of the ASD group could not be replicated. Regarding Glx concentrations and Glx/creatine ratios, there were no significant differences in the dlPFC and ACC either. The study supports the hypothesis of an altered GABA and glutamate equilibrium, indicating an imbalance between excitatory and inhibitory metabolism in ASD patients. However, inconsistent results across studies and brain regions suggest a complex underlying phenomenon. LAY SUMMARY: Adults of the autism spectrum exhibit elevated levels of the inhibitory neurotransmitter GABA in the left dorsolateral prefrontal cortex. This finding supports the hypothesis of an imbalance between excitatory and inhibitory equilibrium in patients with autism spectrum disorders.
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Affiliation(s)
- Simon Maier
- Section for Experimental Neuropsychiatry, Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | - Kimon Runge
- Section for Experimental Neuropsychiatry, Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michael Dacko
- Department of Radiology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Thomas Lange
- Department of Radiology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Thomas Fangmeier
- Section for Experimental Neuropsychiatry, Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Andreas Riedel
- Section for Experimental Neuropsychiatry, Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Luzerner Psychiatrie, Ambulante Dienste, Luzern, Switzerland
| | - Dieter Ebert
- Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dominique Endres
- Section for Experimental Neuropsychiatry, Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Katharina Domschke
- Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Center for Basics in Neuromodulation, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Evgeniy Perlov
- Section for Experimental Neuropsychiatry, Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Clinic for Psychiatry Luzern, Hospital St. Urban, St. Urban, Switzerland
| | - Kathrin Nickel
- Section for Experimental Neuropsychiatry, Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ludger Tebartz van Elst
- Section for Experimental Neuropsychiatry, Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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20
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Maier S, Joos A, Tebartz van Elst L, Ebert D, Endres D, Domschke K, Lahmann C, Zeeck A, Runge K, Denzel D, Reisert M, Nickel K. Reduced structural connectivity in the corpus callosum in patients with anorexia nervosa. Euro Eating Disorders Rev 2022; 30:341-352. [DOI: 10.1002/erv.2894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 02/19/2022] [Accepted: 02/21/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Simon Maier
- Department of Psychiatry and Psychotherapy, Medical Center – University of Freiburg, Faculty of Medicine University of Freiburg Freiburg Germany
| | - Andreas Joos
- Department of Psychosomatic Medicine and Psychotherapy, Medical Center – University of Freiburg, Faculty of Medicine University of Freiburg Freiburg Germany
| | - Ludger Tebartz van Elst
- Department of Psychiatry and Psychotherapy, Medical Center – University of Freiburg, Faculty of Medicine University of Freiburg Freiburg Germany
| | - Dieter Ebert
- Department of Psychiatry and Psychotherapy, Medical Center – University of Freiburg, Faculty of Medicine University of Freiburg Freiburg Germany
| | - Dominique Endres
- Department of Psychiatry and Psychotherapy, Medical Center – University of Freiburg, Faculty of Medicine University of Freiburg Freiburg Germany
| | - Katharina Domschke
- Department of Psychiatry and Psychotherapy, Medical Center – University of Freiburg, Faculty of Medicine University of Freiburg Freiburg Germany
- Center for Basics in Neuromodulation, Faculty of Medicine University of Freiburg Freiburg Germany
| | - Claas Lahmann
- Department of Psychosomatic Medicine and Psychotherapy, Medical Center – University of Freiburg, Faculty of Medicine University of Freiburg Freiburg Germany
| | - Almut Zeeck
- Department of Psychosomatic Medicine and Psychotherapy, Medical Center – University of Freiburg, Faculty of Medicine University of Freiburg Freiburg Germany
| | - Kimon Runge
- Department of Psychiatry and Psychotherapy, Medical Center – University of Freiburg, Faculty of Medicine University of Freiburg Freiburg Germany
| | - Dominik Denzel
- Department of Psychiatry and Psychotherapy, Medical Center – University of Freiburg, Faculty of Medicine University of Freiburg Freiburg Germany
| | - Marco Reisert
- Department of Radiology, Medical Physics, Medical Center – University of Freiburg, Faculty of Medicine University of Freiburg Freiburg Germany
| | - Kathrin Nickel
- Department of Psychiatry and Psychotherapy, Medical Center – University of Freiburg, Faculty of Medicine University of Freiburg Freiburg Germany
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21
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de Albuquerque NRM, Haag KL, Fields PD, Cabalzar A, Ben-Ami F, Pombert JF, Ebert D. A new microsporidian parasite, Ordospora pajunii sp. nov (Ordosporidae), of Daphnia longispina highlights the value of genomic data for delineating species boundaries. J Eukaryot Microbiol 2022; 69:e12902. [PMID: 35279911 DOI: 10.1111/jeu.12902] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 12/13/2021] [Revised: 03/03/2022] [Accepted: 03/03/2022] [Indexed: 11/27/2022]
Abstract
Speciation is a complex and continuous process that makes the delineation of species boundaries a challenging task in particular in species with little morphological differentiation, such as parasites. In this case, the use of genomic data is often necessary, such as for the intracellular Microsporidian parasites. Here we characterize the genome of a gut parasite of the cladoceran Daphnia longispina (isolate FI-F-10), which we propose as a new species within the genus Ordospora: O. pajunii sp. nov (Ordosporidae). FI-F-10 closest relative, O. colligata is only found in D. magna. Both microsporidian species share several morphological features. Although it is not possible to estimate divergence times for Microsporidia due to the lack of fossil records and accelerated evolutionary rates, we base our proposal on the phylogenomic and genomic distances between both microsporidian lineages. Phylogenomic reconstruction shows that FI-F-10 forms an early diverging branch basal to the cluster that contains all known O. colligata strains. Whole-genome comparisons show that FI-F-10 presents a greater divergence at the sequence level than observed among O. colligata strains, and its genomic Average Nucleotide Identity (ANI) values against O. colligata are beyond the intra-specific range previously established for yeast and prokaryotes. Our data confirm that the ANI metrics are useful for fine genetic divergence calibration across Microsporidia taxa. In combination with phylogenetic and ecological data, genome-based metrics provide a powerful approach to delimitate species boundaries.
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Affiliation(s)
- Nathalia R M de Albuquerque
- Department of Genetics and Post-Graduation Program of Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Av. Bento Gonçalves 9500, Porto Alegre, RS, 91501-970, Brazil
| | - Karen L Haag
- Department of Genetics and Post-Graduation Program of Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Av. Bento Gonçalves 9500, Porto Alegre, RS, 91501-970, Brazil
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, Basel University, Vesalgasse 1, 4051, Basel, Switzerland
| | - Andrea Cabalzar
- Department of Environmental Sciences, Zoology, Basel University, Vesalgasse 1, 4051, Basel, Switzerland
| | - Frida Ben-Ami
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Jean-François Pombert
- Department of Biology, Illinois Institute of Technology, 3105 S Dearborn St, Chicago, IL, 60616, USA
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, Basel University, Vesalgasse 1, 4051, Basel, Switzerland
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22
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Angst P, Ebert D, Fields PD. Demographic history shapes genomic variation in an intracellular parasite with a wide geographic distribution. Mol Ecol 2022; 31:2528-2544. [DOI: 10.1111/mec.16419] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/14/2022] [Accepted: 02/28/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Pascal Angst
- Department of Environmental Sciences, Zoology University of Basel Vesalgasse 1 4051 Basel Switzerland
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology University of Basel Vesalgasse 1 4051 Basel Switzerland
| | - Peter D. Fields
- Department of Environmental Sciences, Zoology University of Basel Vesalgasse 1 4051 Basel Switzerland
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23
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Fields PD, McTaggart S, Reisser CMO, Haag C, Palmer WH, Little TJ, Ebert D, Obbard DJ. Population-genomic analysis identifies a low rate of global adaptive fixation in the proteins of the cyclical parthenogen Daphnia magna. Mol Biol Evol 2022; 39:6542319. [PMID: 35244177 PMCID: PMC8963301 DOI: 10.1093/molbev/msac048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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] [Indexed: 11/26/2022] Open
Abstract
Daphnia are well-established ecological and evolutionary models, and the interaction between D. magna and its microparasites is widely considered a paragon of the host-parasite coevolutionary process. Like other well-studied arthropods such as Drosophila melanogaster and Anopheles gambiae, D. magna is a small, widespread, and abundant species that is therefore expected to display a large long-term population size and high rates of adaptive protein evolution. However, unlike these other species, D. magna is cyclically asexual and lives in a highly structured environment (ponds and lakes) with moderate levels of dispersal, both of which are predicted to impact upon long-term effective population size and adaptive protein evolution. To investigate patterns of adaptive protein fixation, we produced the complete coding genomes of 36 D. magna clones sampled from across the European range (Western Palaearctic), along with draft sequences for the close relatives D. similis and D. lumholtzi, used as outgroups. We analyzed genome-wide patterns of adaptive fixation, with a particular focus on genes that have an a priori expectation of high rates, such as those likely to mediate immune responses, RNA interference against viruses and transposable elements, and those with a strongly male-biased expression pattern. We find that, as expected, D. magna displays high levels of diversity and that this is highly structured among populations. However, compared with Drosophila, we find that D. magna proteins appear to have a high proportion of weakly deleterious variants and do not show evidence of pervasive adaptive fixation across its entire range. This is true of the genome as a whole, and also of putative ‘arms race’ genes that often show elevated levels of adaptive substitution in other species. In addition to the likely impact of extensive, and previously documented, local adaptation, we speculate that these findings may reflect reduced efficacy of selection associated with cyclical asexual reproduction.
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Affiliation(s)
- Peter D Fields
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, Basel, CH-4051, Switzerland
| | - Seanna McTaggart
- Institute of Evolutionary Biology; School of Biological Sciences University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom
| | - Céline M O Reisser
- Centre d'Ecologie Fonctionnelle et Evolutive CEFE UMR 5175, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, campus CNRS, 1919, route de Mende, 34293 Montpellier Cedex 5, France.,MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France
| | - Christoph Haag
- Centre d'Ecologie Fonctionnelle et Evolutive CEFE UMR 5175, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, campus CNRS, 1919, route de Mende, 34293 Montpellier Cedex 5, France
| | - William H Palmer
- Institute of Evolutionary Biology; School of Biological Sciences University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom
| | - Tom J Little
- Institute of Evolutionary Biology; School of Biological Sciences University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom
| | - Dieter Ebert
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, Basel, CH-4051, Switzerland
| | - Darren J Obbard
- Institute of Evolutionary Biology; School of Biological Sciences University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom
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24
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Abstract
Environmental fluctuations often select for adaptations such as diapause states, allowing species to outlive harsh conditions. The natural sugar trehalose which provides both cryo- and desiccation-protection, has been found in diapause stages of diverse taxa. Here, we hypothesize that trehalose deposition in resting stages is a locally adapted trait, with higher concentrations produced in harsher habitats. We used resting stages, produced under standardized conditions, by 37 genotypes of Daphnia magna collected from Western Palaearctic habitats varying in their propensity to dry in summer and freeze in winter. Resting eggs produced by D. magna from populations from summer-dry habitats showed significantly higher trehalose than those from summer-wet habitats, suggesting that trehalose has a protective function during desiccation. By contrast, winter-freezing did not explain variation in trehalose content. Adaptations to droughts are important, as summer dryness of water bodies is foreseen to increase with ongoing climate change.
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Affiliation(s)
- Joana L. Santos
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
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25
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Van Damme K, Cornetti L, Fields PD, Ebert D. Whole-Genome Phylogenetic Reconstruction as a Powerful Tool to Reveal Homoplasy and Ancient Rapid Radiation in Waterflea Evolution. Syst Biol 2021; 71:777-787. [PMID: 34850935 PMCID: PMC9203061 DOI: 10.1093/sysbio/syab094] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 08/15/2020] [Revised: 10/04/2021] [Accepted: 11/15/2021] [Indexed: 11/28/2022] Open
Abstract
Although phylogeny estimation is notoriously difficult in radiations that occurred several hundred million years ago, phylogenomic approaches offer new ways to examine relationships among ancient lineages and evaluate hypotheses that are key to evolutionary biology. Here, we reconstruct the deep-rooted relationships of one of the oldest living arthropod clades, the branchiopod crustaceans, using a kaleidoscopic approach. We use concatenation and coalescent tree-building methods to analyze a large multigene data set at the nucleotide and amino acid level and examine gene tree versus species tree discordance. We unequivocally resolve long-debated relationships among extant orders of the Cladocera, the waterfleas, an ecologically relevant zooplankton group in global aquatic and marine ecosystems that is famous for its model systems in ecology and evolution. To build the data set, we assembled eight de novo genomes of key taxa including representatives of all extant cladoceran orders and suborders. Our phylogenetic analysis focused on a BUSCO-based set of 823 conserved single-copy orthologs shared among 23 representative taxa spanning all living branchiopod orders, including 11 cladoceran families. Our analysis supports the monophyly of the Cladocera and reveals remarkable homoplasy in their body plans. We found large phylogenetic distances between lineages with similar ecological specializations, indicating independent evolution in major body plans, such as in the pelagic predatory orders Haplopoda and Onychopoda (the “Gymnomera”). In addition, we assessed rapid cladogenesis by estimating relative timings of divergence in major lineages using reliable fossil-calibrated priors on eight nodes in the branchiopod tree, suggesting a Paleozoic origin around 325 Ma for the cladoceran ancestor and an ancient rapid radiation around 252 Ma at the Perm/Triassic boundary. These findings raise new questions about the roles of homoplasy and rapid radiation in the diversification of the cladocerans and help examine trait evolution from a genomic perspective in a functionally well understood, ancient arthropod group. [Cladocera; Daphnia; evolution; homoplasy; molecular clock; phylogenomics; systematics; waterfleas.]
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Affiliation(s)
- Kay Van Damme
- Centre for Academic Heritage and Archives & Ghent University Botanical Garden, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium.,Tvärminne Zoological Station (TZS), University of Helsinki, J.A. Palménin tie 260, Hanko, Finland
| | - Luca Cornetti
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, 4051 Basel, Switzerland
| | - Peter D Fields
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, 4051 Basel, Switzerland
| | - Dieter Ebert
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, 4051 Basel, Switzerland
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26
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Friedel EBN, Tebartz van Elst L, Schmelz C, Ebert D, Maier S, Endres D, Runge K, Domschke K, Bubl E, Kornmeier J, Bach M, Heinrich SP, Nickel K. Replication of Reduced Pattern Electroretinogram Amplitudes in Depression With Improved Recording Parameters. Front Med (Lausanne) 2021; 8:732222. [PMID: 34778295 PMCID: PMC8585854 DOI: 10.3389/fmed.2021.732222] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 10/06/2021] [Indexed: 12/02/2022] Open
Abstract
Background: The retina has gained increasing attention in non-ophthalmological research in recent years. The pattern electroretinogram (PERG), a method to evaluate retinal ganglion cell function, has been used to identify objective correlates of the essentially subjective state of depression. A reduction in the PERG contrast gain was demonstrated in patients with depression compared to healthy controls with normalization after remission. PERG responses are not only modulated by stimulus contrast, but also by check size and stimulation frequency. Therefore, the rationale was to evaluate potentially more feasible procedures for PERG recordings in daily diagnostics in psychiatry. Methods: Twenty-four participants (12 patients with major depression (MDD) and 12 age- and sex-matched healthy controls) were examined in this pilot study. We investigated PERG amplitudes for two steady-state pattern reversal frequencies (12.5/18.75 rps) and four sizes of a checkerboard stimulus (0.8°, 1.6°, 3.2°, and 16°) to optimize the PERG recordings in MDD patients. Results: Smaller PERG amplitudes in MDD patients were observed for all parameters, whereby the extent of the reduction appeared to be stimulus-specific. The most pronounced decline in the PERG of MDD patients was observed at the higher stimulation frequency and the finest pattern, whilst responses for the largest check size were less affected. Following the PERG ratio protocol for early glaucoma, where similar stimulus dependent modulations have been reported, we calculated PERG ratios (0.8°/16°) for all participants. At the higher frequency (18.75 rps), significantly reduced ratios were observed in MDD patients. Conclusion: The “normalization” of the PERG responses—via building a ratio—appears to be a very promising approach with regard to the development of an objective biomarker of the depressive state, facilitating inter-individual assessments of PERG recordings in patients with psychiatric disorders.
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Affiliation(s)
- Evelyn B N Friedel
- Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Eye Center, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Ludger Tebartz van Elst
- Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Céline Schmelz
- Pfalzklinikum-Clinic for Psychiatry and Neurology, Klingenmünster, Germany
| | - Dieter Ebert
- Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Simon Maier
- Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dominique Endres
- Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Kimon Runge
- Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Katharina Domschke
- Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Center for Basics in Neuromodulation, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Emanuel Bubl
- Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jürgen Kornmeier
- Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Institute for Frontier Areas of Psychology and Mental Health, Freiburg, Germany
| | - Michael Bach
- Eye Center, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sven P Heinrich
- Eye Center, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Kathrin Nickel
- Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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27
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Fredericksen M, Ameline C, Krebs M, Hüssy B, Fields PD, Andras JP, Ebert D. Infection phenotypes of a coevolving parasite are highly diverse, structured, and specific. Evolution 2021; 75:2540-2554. [PMID: 34431523 PMCID: PMC9290032 DOI: 10.1111/evo.14323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 03/13/2021] [Revised: 06/30/2021] [Accepted: 07/26/2021] [Indexed: 12/27/2022]
Abstract
Understanding how diversity is maintained in natural populations is a major goal of evolutionary biology. In coevolving hosts and parasites, negative frequency-dependent selection is one mechanism predicted to maintain genetic variation. While much is known about host diversity, parasite diversity remains understudied in coevolutionary research. Here, we survey natural diversity in a bacterial parasite by characterizing infection phenotypes for over 50 isolates in relation to 12 genotypes of their host, Daphnia magna. We find striking phenotypic variation among parasite isolates, and we discover the parasite can infect its host through at least five different attachment sites. Variation in attachment success at each site is explained to varying degrees by host and parasite genotypes. A spatial correlation analysis showed that infectivity of different isolates does not correlate with geographic distance, meaning isolates from widespread populations are equally able to infect the host. Overall, our results reveal that infection phenotypes of this parasite are highly diverse. Our results are consistent with the prediction that under Red Queen coevolutionary dynamics both the host and the parasite should show high genetic diversity for traits of functional importance in their interactions.
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Affiliation(s)
- Maridel Fredericksen
- Department of Environmental Sciences, Zoology, University of Basel, CH-4051, Switzerland
| | - Camille Ameline
- Department of Environmental Sciences, Zoology, University of Basel, CH-4051, Switzerland
| | - Michelle Krebs
- Department of Environmental Sciences, Zoology, University of Basel, CH-4051, Switzerland
| | - Benjamin Hüssy
- Department of Environmental Sciences, Zoology, University of Basel, CH-4051, Switzerland
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, CH-4051, Switzerland
| | - Jason P Andras
- Department of Environmental Sciences, Zoology, University of Basel, CH-4051, Switzerland.,Department of Biological Sciences, Clapp Laboratory, Mount Holyoke College, South Hadley, Massachusetts
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, CH-4051, Switzerland
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28
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Bourgeois Y, Fields P, Bento G, Ebert D. Balancing selection for pathogen resistance reveals an intercontinental signature of Red Queen coevolution. Mol Biol Evol 2021; 38:4918-4933. [PMID: 34289047 PMCID: PMC8557431 DOI: 10.1093/molbev/msab217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The link between long-term host–parasite coevolution and genetic diversity is key to understanding genetic epidemiology and the evolution of resistance. The model of Red Queen host–parasite coevolution posits that high genetic diversity is maintained when rare host resistance variants have a selective advantage, which is believed to be the mechanistic basis for the extraordinarily high levels of diversity at disease-related genes such as the major histocompatibility complex in jawed vertebrates and R-genes in plants. The parasites that drive long-term coevolution are, however, often elusive. Here we present evidence for long-term balancing selection at the phenotypic (variation in resistance) and genomic (resistance locus) level in a particular host–parasite system: the planktonic crustacean Daphnia magna and the bacterium Pasteuria ramosa. The host shows widespread polymorphisms for pathogen resistance regardless of geographic distance, even though there is a clear genome-wide pattern of isolation by distance at other sites. In the genomic region of a previously identified resistance supergene, we observed consistent molecular signals of balancing selection, including higher genetic diversity, older coalescence times, and lower differentiation between populations, which set this region apart from the rest of the genome. We propose that specific long-term coevolution by negative-frequency-dependent selection drives this elevated diversity at the host's resistance loci on an intercontinental scale and provide an example of a direct link between the host’s resistance to a virulent pathogen and the large-scale diversity of its underlying genes.
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Affiliation(s)
- Yann Bourgeois
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, 4051 Basel, Switzerland
| | - Peter Fields
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, 4051 Basel, Switzerland
| | - Gilberto Bento
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, 4051 Basel, Switzerland
| | - Dieter Ebert
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, 4051 Basel, Switzerland
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29
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Ameline C, Bourgeois Y, Vögtli F, Savola E, Andras J, Engelstädter J, Ebert D. A Two-Locus System with Strong Epistasis Underlies Rapid Parasite-Mediated Evolution of Host Resistance. Mol Biol Evol 2021; 38:1512-1528. [PMID: 33258959 PMCID: PMC8042741 DOI: 10.1093/molbev/msaa311] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Parasites are a major evolutionary force, driving adaptive responses in host populations. Although the link between phenotypic response to parasite-mediated natural selection and the underlying genetic architecture often remains obscure, this link is crucial for understanding the evolution of resistance and predicting associated allele frequency changes in the population. To close this gap, we monitored the response to selection during epidemics of a virulent bacterial pathogen, Pasteuria ramosa, in a natural host population of Daphnia magna. Across two epidemics, we observed a strong increase in the proportion of resistant phenotypes as the epidemics progressed. Field and laboratory experiments confirmed that this increase in resistance was caused by selection from the local parasite. Using a genome-wide association study, we built a genetic model in which two genomic regions with dominance and epistasis control resistance polymorphism in the host. We verified this model by selfing host genotypes with different resistance phenotypes and scoring their F1 for segregation of resistance and associated genetic markers. Such epistatic effects with strong fitness consequences in host–parasite coevolution are believed to be crucial in the Red Queen model for the evolution of genetic recombination.
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Affiliation(s)
- Camille Ameline
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Yann Bourgeois
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland.,School of Biological Sciences, University of Portsmouth, Portsmouth, United Kingdom
| | - Felix Vögtli
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Eevi Savola
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland.,Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh, United Kingdom
| | - Jason Andras
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland.,Department of Biological Sciences, Clapp Laboratory, Mount Holyoke College, South Hadley, MA, USA
| | - Jan Engelstädter
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
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30
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Cornetti L, Ebert D. No evidence for genetic sex determination in Daphnia magna. R Soc Open Sci 2021; 8:202292. [PMID: 34150315 PMCID: PMC8206689 DOI: 10.1098/rsos.202292] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/18/2021] [Indexed: 06/12/2023]
Abstract
Mechanisms of sex determination (SD) differ widely across the tree of life. In genotypic sex determination (GSD), genetic elements determine whether individuals are male or female, while in environmental sex determination (ESD), external cues control the sex of the offspring. In cyclical parthenogens, females produce mostly asexual daughters, but environmental stimuli such as crowding, temperature or photoperiod may cause them to produce sons. In aphids, sons are induced by ESD, even though GSD is present, with females carrying two X chromosomes and males only one (X0 SD system). By contrast, although ESD exists in Daphnia, the two sexes were suggested to be genetically identical, based on a 1972 study on Daphnia magna (2n=20) that used three allozyme markers. This study cannot, however, rule out an X0 system, as all three markers may be located on autosomes. Motivated by the life cycle similarities of Daphnia and aphids, and the absence of karyotype information for Daphnia males, we tested for GSD (homomorphic sex chromosomes and X0) systems in D. magna using a whole-genome approach by comparing males and females of three genotypes. Our results confirm the absence of haploid chromosomes or haploid genomic regions in D. magna males as well as the absence of sex-linked genomic regions and sex-specific single-nucleotide polymorphisms. Within the limitations of the three studied populations here and the methods used, we suggest that our results make the possibility of genetic differences among sexes in the widely used Daphnia model system very unlikely.
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Affiliation(s)
- Luca Cornetti
- Department of Environmental Sciences, Zoology, University of Basel, 4051, Basel, Switzerland
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, 4051, Basel, Switzerland
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31
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Andras JP, Fields PD, Du Pasquier L, Fredericksen M, Ebert D. Genome-Wide Association Analysis Identifies a Genetic Basis of Infectivity in a Model Bacterial Pathogen. Mol Biol Evol 2021; 37:3439-3452. [PMID: 32658956 PMCID: PMC7743900 DOI: 10.1093/molbev/msaa173] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 06/22/2020] [Accepted: 07/08/2020] [Indexed: 12/22/2022] Open
Abstract
Knowledge of the genetic architecture of pathogen infectivity and host resistance is essential for a mechanistic understanding of coevolutionary processes, yet the genetic basis of these interacting traits remains unknown for most host-pathogen systems. We used a comparative genomic approach to explore the genetic basis of infectivity in Pasteuria ramosa, a Gram-positive bacterial pathogen of planktonic crustaceans that has been established as a model for studies of Red Queen host-pathogen coevolution. We sequenced the genomes of a geographically, phenotypically, and genetically diverse collection of P. ramosa strains and performed a genome-wide association study to identify genetic correlates of infection phenotype. We found multiple polymorphisms within a single gene, Pcl7, that correlate perfectly with one common and widespread infection phenotype. We then confirmed this perfect association via Sanger sequencing in a large and diverse sample set of P. ramosa clones. Pcl7 codes for a collagen-like protein, a class of adhesion proteins known or suspected to be involved in the infection mechanisms of a number of important bacterial pathogens. Consistent with expectations under Red Queen coevolution, sequence variation of Pcl7 shows evidence of balancing selection, including extraordinarily high diversity and absence of geographic structure. Based on structural homology with a collagen-like protein of Bacillus anthracis, we propose a hypothesis for the structure of Pcl7 and the physical location of the phenotype-associated polymorphisms. Our results offer strong evidence for a gene governing infectivity and provide a molecular basis for further study of Red Queen dynamics in this model host-pathogen system.
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Affiliation(s)
- Jason P Andras
- Department of Biological Sciences, Mount Holyoke College, South Hadley, MA
| | - Peter D Fields
- Division of Zoology, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Louis Du Pasquier
- Division of Zoology, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Maridel Fredericksen
- Division of Zoology, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Dieter Ebert
- Division of Zoology, Department of Environmental Sciences, University of Basel, Basel, Switzerland
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32
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Abstract
The rate and spectrum of spontaneous mutations are critical parameters in basic and applied biology because they dictate the pace and character of genetic variation introduced into populations, which is a prerequisite for evolution. We use a mutation–accumulation approach to estimate mutation parameters from whole-genome sequence data from multiple genotypes from multiple populations of Daphnia magna, an ecological and evolutionary model system. We report extremely high base substitution mutation rates (µ-n,bs = 8.96 × 10−9/bp/generation [95% CI: 6.66–11.97 × 10−9/bp/generation] in the nuclear genome and µ-m,bs = 8.7 × 10−7/bp/generation [95% CI: 4.40–15.12 × 10−7/bp/generation] in the mtDNA), the highest of any eukaryote examined using this approach. Levels of intraspecific variation based on the range of estimates from the nine genotypes collected from three populations (Finland, Germany, and Israel) span 1 and 3 orders of magnitude, respectively, resulting in up to a ∼300-fold difference in rates among genomic partitions within the same lineage. In contrast, mutation spectra exhibit very consistent patterns across genotypes and populations, suggesting the mechanisms underlying the mutational process may be similar, even when the rates at which they occur differ. We discuss the implications of high levels of intraspecific variation in rates, the importance of estimating gene conversion rates using a mutation–accumulation approach, and the interacting factors influencing the evolution of mutation parameters. Our findings deepen our knowledge about mutation and provide both challenges to and support for current theories aimed at explaining the evolution of the mutation rate, as a trait, across taxa.
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Affiliation(s)
- Eddie K H Ho
- Department of Biology, Reed College, Portland, OR
| | | | - Leigh C Latta
- Department of Biology, Reed College, Portland, OR.,Division of Natural Sciences and Mathematics, Lewis-Clark State College, Lewiston, ID
| | | | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
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33
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Ameline C, Bourgeois Y, Vögtli F, Savola E, Andras J, Engelstädter J, Ebert D. Erratum to: A Two-Locus System with Strong Epistasis Underlies Rapid Parasite-Mediated Evolution of Host Resistance. Mol Biol Evol 2021; 38:2674. [PMID: 33846744 PMCID: PMC8136482 DOI: 10.1093/molbev/msab076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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34
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Vega FE, Emche S, Shao J, Simpkins A, Summers RM, Mock MB, Ebert D, Infante F, Aoki S, Maul JE. Cultivation and Genome Sequencing of Bacteria Isolated From the Coffee Berry Borer ( Hypothenemus hampei), With Emphasis on the Role of Caffeine Degradation. Front Microbiol 2021; 12:644768. [PMID: 33889142 PMCID: PMC8055839 DOI: 10.3389/fmicb.2021.644768] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 12/21/2020] [Accepted: 03/08/2021] [Indexed: 12/15/2022] Open
Abstract
The coffee berry borer, the most economically important insect pest of coffee worldwide, is the only insect capable of feeding and reproducing solely on the coffee seed, a food source containing the purine alkaloid caffeine. Twenty-one bacterial species associated with coffee berry borers from Hawai’i, Mexico, or a laboratory colony in Maryland (Acinetobacter sp. S40, S54, S55, Bacillus aryabhattai, Delftia lacustris, Erwinia sp. S38, S43, S63, Klebsiella oxytoca, Ochrobactrum sp. S45, S46, Pantoea sp. S61, Pseudomonas aeruginosa, P. parafulva, and Pseudomonas sp. S30, S31, S32, S37, S44, S60, S75) were found to have at least one of five caffeine N-demethylation genes (ndmA, ndmB, ndmC, ndmD, ndmE), with Pseudomonas spp. S31, S32, S37, S60 and P. parafulva having the full complement of these genes. Some of the bacteria carrying the ndm genes were detected in eggs, suggesting possible vertical transmission, while presence of caffeine-degrading bacteria in frass, e.g., P. parafulva (ndmABCDE) and Bacillus aryabhattai (ndmA) could result in horizontal transmission to all insect life stages. Thirty-five bacterial species associated with the insect (Acinetobacter sp. S40, S54, S55, B. aryabhattai, B. cereus group, Bacillus sp. S29, S70, S71, S72, S73, D. lacustris, Erwinia sp. S38, S43, S59, S63, K. oxytoca, Kosakonia cowanii, Ochrobactrum sp. S45, S46, Paenibacillus sp. S28, Pantoea sp. S61, S62, P. aeruginosa, P. parafulva, Pseudomonas sp. S30, S31, S32, S37, S44, S60, S75, Stenotrophomonas sp. S39, S41, S48, S49) might contribute to caffeine breakdown using the C-8 oxidation pathway, based on presence of genes required for this pathway. It is possible that caffeine-degrading bacteria associated with the coffee berry borer originated as epiphytes and endophytes in the coffee plant microbiota.
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Affiliation(s)
- Fernando E Vega
- Sustainable Perennial Crops Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Sarah Emche
- Sustainable Agricultural Systems Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Jonathan Shao
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Ann Simpkins
- Sustainable Perennial Crops Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Ryan M Summers
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, AL, United States
| | - Meredith B Mock
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, AL, United States
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | | | - Sayaka Aoki
- Department of Plant and Environmental Protection Sciences, University of Hawai'i at Mānoa, Honolulu, HI, United States
| | - Jude E Maul
- Sustainable Agricultural Systems Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
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35
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Cornetti L, Fields PD, Ebert D. Genomic characterization of selfing in the cyclic parthenogen Daphnia magna. J Evol Biol 2021; 34:792-802. [PMID: 33704857 DOI: 10.1111/jeb.13780] [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: 12/06/2020] [Revised: 02/23/2021] [Accepted: 03/06/2021] [Indexed: 11/29/2022]
Abstract
Inbreeding refers to the fusion of related individuals' gametes, with self-fertilization (selfing) being an extreme form of inbreeding-involving gametes produced by the same individual. Selfing is expected to reduce heterozygosity by an average of 50% in one generation; however, little is known about the empirical variation on a genome level surrounding this figure and the factors that affect variation. We selfed genotypes of the cyclic parthenogen Daphnia magna and analysed whole genomes of mothers and selfed offspring, observing the predicted 50% heterozygosity reduction on average. We also saw substantial variation around this value and significant differences among mother-offspring pairs. Crossover analysis confirmed the known trend of recombination occurring more often towards the telomeres. This effect was shown, through simulations, to increase the variance of heterozygosity reduction compared to when a uniform distribution of crossovers was used. Similarly, we simulated inbred line production after several generations of selfing and we observed higher variance in achieved homozygosity when we consider a higher recombination rate towards the telomeres. Our empirical and simulation study highlights that the expected mean values of heterozygosity reduction show remarkable variation, which can help understand, for example, differences among inbred individuals.
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Affiliation(s)
- Luca Cornetti
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
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36
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Haag KL, Pombert JF, Sun Y, de Albuquerque NRM, Batliner B, Fields P, Lopes TF, Ebert D. Microsporidia with Vertical Transmission Were Likely Shaped by Nonadaptive Processes. Genome Biol Evol 2020; 12:3599-3614. [PMID: 31825473 PMCID: PMC6944219 DOI: 10.1093/gbe/evz270] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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] [Accepted: 12/05/2019] [Indexed: 12/14/2022] Open
Abstract
Microsporidia have the leanest genomes among eukaryotes, and their physiological and genomic simplicity has been attributed to their intracellular, obligate parasitic life-style. However, not all microsporidia genomes are small or lean, with the largest dwarfing the smallest ones by at least an order of magnitude. To better understand the evolutionary mechanisms behind this genomic diversification, we explore here two clades of microsporidia with distinct life histories, Ordospora and Hamiltosporidium, parasitizing the same host species, Daphnia magna. Based on seven newly assembled genomes, we show that mixed-mode transmission (the combination of horizontal and vertical transmission), which occurs in Hamiltosporidium, is found to be associated with larger and AT-biased genomes, more genes, and longer intergenic regions, as compared with the exclusively horizontally transmitted Ordospora. Furthermore, the Hamiltosporidium genome assemblies contain a variety of repetitive elements and long segmental duplications. We show that there is an excess of nonsynonymous substitutions in the microsporidia with mixed-mode transmission, which cannot be solely attributed to the lack of recombination, suggesting that bursts of genome size in these microsporidia result primarily from genetic drift. Overall, these findings suggest that the switch from a horizontal-only to a mixed mode of transmission likely produces population bottlenecks in Hamiltosporidium species, therefore reducing the effectiveness of natural selection, and allowing their genomic features to be largely shaped by nonadaptive processes.
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Affiliation(s)
- Karen L Haag
- Department of Genetics and Post-Graduation Program of Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Yukun Sun
- Department of Biology, Illinois Institute of Technology
| | - Nathalia Rammé M de Albuquerque
- Department of Genetics and Post-Graduation Program of Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Peter Fields
- Department of Environmental Sciences, Zoology, Basel University, Switzerland
| | - Tiago Falcon Lopes
- Department of Genetics and Post-Graduation Program of Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, Basel University, Switzerland
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37
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Abstract
Studies in diverse biological systems have indicated that host-parasite co-evolution is responsible for the extraordinary genetic diversity seen in some genomic regions, such as major histocompatibility (MHC) genes in jawed vertebrates and resistance genes in plants. This diversity is believed to evolve under balancing selection on hosts by parasites. However, the mechanisms that link the genomic signatures in these regions to the underlying co-evolutionary process are only slowly emerging. We still lack a clear picture of the co-evolutionary concepts and of the genetic basis of the co-evolving phenotypic traits in the interacting antagonists. Emerging genomic tools that provide new options for identifying underlying genes will contribute to a fuller understanding of the co-evolutionary process.
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Affiliation(s)
- Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland. .,Wissenschaftskolleg zu Berlin, Berlin, Germany.
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
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38
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de Albuquerque NRM, Ebert D, Haag KL. Transposable element abundance correlates with mode of transmission in microsporidian parasites. Mob DNA 2020; 11:19. [PMID: 32587636 PMCID: PMC7313128 DOI: 10.1186/s13100-020-00218-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/18/2020] [Indexed: 01/16/2023] Open
Abstract
The extreme genome reduction and physiological simplicity of some microsporidia has been attributed to their intracellular, obligate parasitic lifestyle. Although not all microsporidian genomes are small (size range from about 2 to 50 MB), it is suggested that the size of their genomes has been streamlined by natural selection. We explore the hypothesis that vertical transmission in microsporidia produces population bottlenecks, and thus reduces the effectiveness of natural selection. Here we compare the transposable element (TE) content of 47 microsporidian genomes, and show that genome size is positively correlated with the amount of TEs, and that species that experience vertical transmission have larger genomes with higher proportion of TEs. Our findings are consistent with earlier studies inferring that nonadaptive processes play an important role in microsporidian evolution.
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Affiliation(s)
- Nathalia Rammé Medeiros de Albuquerque
- Department of Genetics and Post-Graduation Program of Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Av. Bento Gonçalves 9500, Porto Alegre, RS 91501-970 Brazil
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, Basel University, Vesalgasse 1, 4051 Basel, Switzerland
| | - Karen Luisa Haag
- Department of Genetics and Post-Graduation Program of Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Av. Bento Gonçalves 9500, Porto Alegre, RS 91501-970 Brazil
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39
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Werner AL, Tebartz van Elst L, Ebert D, Friedel E, Bubl A, Clement HW, Lukačin R, Bach M, Bubl E. Normalization of increased retinal background noise after ADHD treatment: A neuronal correlate. Schizophr Res 2020; 219:77-83. [PMID: 31053491 DOI: 10.1016/j.schres.2019.04.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/14/2019] [Accepted: 04/17/2019] [Indexed: 02/06/2023]
Abstract
Inattention, distractibility, and problems inhibiting irrelevant information impose a large disease burden in attention deficit hyperactivity disorder (ADHD). Problems with cognitive function are found in many major psychiatric disorders, and our understanding of ADHD might add to our knowledge of other neuropsychiatric disorders. Despite the high impact of ADHD, the pathophysiology and the mechanism of treatment action remains poorly understood. Increasing evidence suggests that elevated neuronal and retinal background noise plays a prominent role in ADHD. However, the effect of treatment (e.g., methylphenidate) on noise remains unclear. For this study, retinal background noise was assessed with the pattern-electroretinogram (PERG) in 20 drug-naïve adults with ADHD before and after treatment with methylphenidate and in 21 control subjects. Background noise was identified using the Fourier magnitude at frequencies adjacent to the stimulus-response frequency of 12.5 Hz. At baseline, we found an elevated retinal background noise in ADHD patients (Mdn = 0.079 μV) compared to controls (Mdn = 0.062 μV; z = -2.79, p = 0.016, r = -0.44). The noise in the ADHD group decreased significantly at follow-up after treatment with methylphenidate (Mdn = 0.069 μV, z = -2.39, p = 0.035, r = -0.39) while there was no change in the control group. PERG-based retinal noise is increased in adult ADHD and normalizes along with clinical symptoms following treatment with methylphenidate. The retinal noise level might be a promising marker of ADHD in clinical and basic research and illustrates the biological match with nonhuman ADHD models.
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Affiliation(s)
- Anna Lisa Werner
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Germany
| | - Ludger Tebartz van Elst
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Germany
| | - Dieter Ebert
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Germany
| | - Evelyn Friedel
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Germany
| | - Anna Bubl
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Germany; Department of Psychiatry and Psychotherapy, University of Saarland, Germany
| | - Hans-Willi Clement
- Department of Child and Adolescent Psychiatry, Medical Center - University of Freiburg, Germany
| | - Richard Lukačin
- Chromsystems Instruments & Chemicals GmbH, Gräfelfing, Munich, Germany
| | - Michael Bach
- Eye Center, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
| | - Emanuel Bubl
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Germany; Department of Psychiatry and Psychotherapy, University of Saarland, Germany.
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40
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Abstract
Microsatellite loci (tandem repeats of short nucleotide motifs) are highly abundant in eukaryotic genomes and often used as genetic markers because they can exhibit variation both within and between populations. Although widely recognized for their mutability and utility, the mutation rates of microsatellites have only been empirically estimated in a few species, and have rarely been compared across genotypes and populations within a species. Here, we investigate the dynamics of microsatellite mutation over long- and short-time periods by quantifying the starting abundance and mutation rates for microsatellites for six different genotypes of Daphnia magna, an aquatic microcrustacean, collected from three populations (Finland, Germany, and Israel). Using whole-genome sequences of these six starting genotypes, descendent mutation accumulation (MA) lines, and large population controls (non-MA lines), we find each genotype exhibits a distinctive initial microsatellite profile which clusters according to the population-of-origin. During the period of MA, we observe motif-specific, highly variable, and rapid microsatellite mutation rates across genotypes of D. magna, the average of which is order of magnitude greater than the recently reported rate observed in a single genotype of the congener, Daphnia pulex. In our experiment, genotypes with more microsatellites starting out exhibit greater losses and those with fewer microsatellites starting out exhibit greater gains—a context-dependent mutation bias that has not been reported previously. We discuss how genotype-specific mutation rates and spectra, in conjunction with evolutionary forces, can shape both the differential accumulation of repeat content in the genome and the evolution of mutation rates.
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Affiliation(s)
- Eddie K H Ho
- Department of Biology, Reed College, Portland, OR
| | | | - Leigh C Latta
- Department of Biology, Reed College, Portland, OR
- Division of Natural Sciences and Mathematics, Lewis-Clark State College, Lewiston, ID
| | | | - Cheng Sun
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Sarah Schaack
- Department of Biology, Reed College, Portland, OR
- Corresponding author: E-mail:
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41
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Czypionka T, Fields PD, Routtu J, van den Berg E, Ebert D, De Meester L. The genetic architecture underlying diapause termination in a planktonic crustacean. Mol Ecol 2019; 28:998-1008. [PMID: 30592346 DOI: 10.1111/mec.15001] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 07/05/2018] [Revised: 11/15/2018] [Accepted: 11/27/2018] [Indexed: 01/17/2023]
Abstract
Diapause is a feature of the life cycle of many invertebrates by which unfavourable environmental conditions can be outlived. The seasonal timing of diapause allows organisms to adapt to seasonal changes in habitat suitability and thus is key to their fitness. In the planktonic crustacean Daphnia, various cues can induce the production of diapause stages that are resistant to heat, drought or freezing and contain one to two embryos in developmental arrest. Daphnia is a keystone species of many freshwater ecosystems, where it acts as the main link between phytoplankton and higher trophic levels. The correct seasonal timing of diapause termination is essential to maintain trophic interactions and is achieved via a genetically based interpretation of environmental cues like photoperiod and temperature. Field monitoring and modelling studies raised concerns on whether populations can advance their seasonal release from diapause to advances in spring phenology under global change, or if a failure to adapt will cause trophic mismatches negatively affecting ecosystem functioning. Our capacity to understand and predict the evolution of diapause timing requires information about the genetic architecture underlying this trait. In this study, we identified eight quantitative trait loci (QTLs) and four epistatic interactions that together explained 66.5% of the variation in diapause termination in Daphnia magna using QTL mapping. Our results suggest that the most significant QTL is modulating diapause termination dependent on photoperiod and is involved in three of the four detected epistatic interactions. Candidate genes at this QTL could be identified through the integration with genome data and included the presynaptic active zone protein bruchpilot. Our findings contribute to understanding the genomic control of seasonal diapause timing in an ecological relevant species.
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Affiliation(s)
- Till Czypionka
- Laboratory of Aquatic Ecology and Evolutionary Biology, KU Leuven, Leuven, Belgium
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Jarkko Routtu
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland.,Molecular Ecology, Martin-Luther-Universität, Halle-Wittenberg, Germany
| | - Edwin van den Berg
- Laboratory of Aquatic Ecology and Evolutionary Biology, KU Leuven, Leuven, Belgium
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Luc De Meester
- Laboratory of Aquatic Ecology and Evolutionary Biology, KU Leuven, Leuven, Belgium
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42
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Cabalzar AP, Fields PD, Kato Y, Watanabe H, Ebert D. Parasite-mediated selection in a natural metapopulation of Daphnia magna. Mol Ecol 2019; 28:4770-4785. [PMID: 31591747 DOI: 10.1111/mec.15260] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 05/23/2019] [Revised: 09/17/2019] [Accepted: 09/27/2019] [Indexed: 01/03/2023]
Abstract
Parasite-mediated selection varying across time and space in metapopulations is expected to result in host local adaptation and the maintenance of genetic diversity in disease-related traits. However, nonadaptive processes like migration and extinction-(re)colonization dynamics might interfere with adaptive evolution. Understanding how adaptive and nonadaptive processes interact to shape genetic variability in life-history and disease-related traits can provide important insights into their evolution in subdivided populations. Here we investigate signatures of spatially fluctuating, parasite-mediated selection in a natural metapopulation of Daphnia magna. Host genotypes from infected and uninfected populations were genotyped at microsatellite markers, and phenotyped for life-history and disease traits in common garden experiments. Combining phenotypic and genotypic data a QST -FST -like analysis was conducted to test for signatures of parasite mediated selection. We observed high variation within and among populations for phenotypic traits, but neither an indication of host local adaptation nor a cost of resistance. Infected populations have a higher gene diversity (Hs) than uninfected populations and Hs is strongly positively correlated with fitness. These results suggest a strong parasite effect on reducing population level inbreeding. We discuss how stochastic processes related to frequent extinction-(re)colonization dynamics as well as host and parasite migration impede the evolution of resistance in the infected populations. We suggest that the genetic and phenotypic patterns of variation are a product of dynamic changes in the host gene pool caused by the interaction of colonization bottlenecks, inbreeding, immigration, hybrid vigor, rare host genotype advantage and parasitism. Our study highlights the effect of the parasite in ameliorating the negative fitness consequences caused by the high drift load in this metapopulation.
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Affiliation(s)
- Andrea P Cabalzar
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Yasuhiko Kato
- Department of Biotechnology, Division of Advance Science and Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
| | - Hajime Watanabe
- Department of Biotechnology, Division of Advance Science and Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland.,Tvärminne Zoological Station, Tvärminne, Finland
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43
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Cornetti L, Fields PD, Van Damme K, Ebert D. A fossil-calibrated phylogenomic analysis of Daphnia and the Daphniidae. Mol Phylogenet Evol 2019; 137:250-262. [DOI: 10.1016/j.ympev.2019.05.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 05/03/2019] [Accepted: 05/20/2019] [Indexed: 11/16/2022]
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44
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Hall MD, Routtu J, Ebert D. Dissecting the genetic architecture of a stepwise infection process. Mol Ecol 2019; 28:3942-3957. [PMID: 31283079 DOI: 10.1111/mec.15166] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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: 03/18/2019] [Revised: 06/27/2019] [Accepted: 06/28/2019] [Indexed: 02/06/2023]
Abstract
How a host fights infection depends on an ordered sequence of steps, beginning with attempts to prevent a pathogen from establishing an infection, through to steps that mitigate a pathogen's control of host resources or minimize the damage caused during infection. Yet empirically characterizing the genetic basis of these steps remains challenging. Although each step is likely to have a unique genetic and environmental signature, and may therefore respond to selection in different ways, events that occur earlier in the infection process can mask or overwhelm the contributions of subsequent steps. In this study, we dissect the genetic architecture of a stepwise infection process using a quantitative trait locus (QTL) mapping approach. We control for variation at the first line of defence against a bacterial pathogen and expose downstream genetic variability related to the host's ability to mitigate the damage pathogens cause. In our model, the water-flea Daphnia magna, we found a single major effect QTL, explaining 64% of the variance, that is linked to the host's ability to completely block pathogen entry by preventing their attachment to the host oesophagus; this is consistent with the detection of this locus in previous studies. In susceptible hosts allowing attachment, however, a further 23 QTLs, explaining between 5% and 16% of the variance, were mapped to traits related to the expression of disease. The general lack of pleiotropy and epistasis for traits related to the different stages of the infection process, together with the wide distribution of QTLs across the genome, highlights the modular nature of a host's defence portfolio, and the potential for each different step to evolve independently. We discuss how isolating the genetic basis of individual steps can help to resolve discussion over the genetic architecture of host resistance.
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Affiliation(s)
- Matthew D Hall
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland.,School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Jarkko Routtu
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland.,Molecular Ecology, Martin-Luther-Universität, Halle-Wittenberg, Germany
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
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45
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Abstract
Species with wide geographical distributions are often adapted locally to the prevailing temperatures. To understand how they respond to ongoing climatic change, we must appreciate the interplay between temperature, seasonality and the organism's life cycle. The temperature experienced by many organisms results from an often-overlooked combination of climate and phenology. Summer-active (high latitude) populations are expected to adapt to local summer temperatures, but this is not expected for populations that outlive the summer in their dormant stage (low latitude, precipitation-limited). We recorded reproduction and survival in genotypes from 123 Holarctic populations of Daphnia magna during a multi-generation thermal ramp experiment. Genotypes from summer-active populations showed a positive relationship between heat tolerance and local summer temperature, whereas winter-active populations did not. These findings are consistent with the hypothesis that D. magna adapts to the local temperatures the animals experience during their planktonic phase. We conclude that predicting local temperature adaptation, in particular in the light of climate change, needs to consider the phenology of geographically wide-ranging species.
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Affiliation(s)
- Leonie Seefeldt
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
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46
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Martin-Creuzburg D, Coggins BL, Ebert D, Yampolsky LY. Rearing Temperature and Fatty Acid Supplementation Jointly Affect Lipid Fluorescence Polarization and Heat Tolerance in Daphnia. Physiol Biochem Zool 2019; 92:408-418. [DOI: 10.1086/704365] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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47
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Dukić M, Berner D, Haag CR, Ebert D. How clonal are clones? A quest for loss of heterozygosity during asexual reproduction in Daphnia magna. J Evol Biol 2019; 32:619-628. [PMID: 30888725 PMCID: PMC6850383 DOI: 10.1111/jeb.13443] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 06/07/2018] [Accepted: 03/04/2019] [Indexed: 12/25/2022]
Abstract
Due to the lack of recombination, asexual organisms are predicted to accumulate mutations and show high levels of within‐individual allelic divergence (heterozygosity); however, empirical evidence for this prediction is largely missing. Instead, evidence of genome homogenization during asexual reproduction is accumulating. Ameiotic crossover recombination is a mechanism that could lead to long genomic stretches of loss of heterozygosity (LOH) and unmasking of mutations that have little or no effect in heterozygous state. Therefore, LOH might be an important force for inducing variation among asexual offspring and may contribute to the limited longevity of asexual lineages. To investigate the genetic consequences of asexuality, here we used high‐throughput sequencing of Daphnia magna for assessing the rate of LOH over a single generation of asexual reproduction. Comparing parthenogenetic daughters with their mothers at several thousand genetic markers generated by restriction site‐associated DNA (RAD) sequencing resulted in high LOH rate estimation that largely overlapped with our estimates for the error rate. To distinguish these two, we Sanger re‐sequenced the top 17 candidate RAD‐loci for LOH, and all of them proved to be false positives. Hence, even though we cannot exclude the possibility that short stretches of LOH occur in genomic regions not covered by our markers, we conclude that LOH does not occur frequently during asexual reproduction in D. magna and ameiotic crossovers are very rare or absent. This finding suggests that clonal lineages of D. magna will remain genetically homogeneous at least over time periods typically relevant for experimental work.
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Affiliation(s)
- Marinela Dukić
- Zoological Institute, University of Basel, Basel, Switzerland.,Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Daniel Berner
- Zoological Institute, University of Basel, Basel, Switzerland
| | - Christoph R Haag
- Centre d'Ecologie Fonctionnelle et Evolutive-CEFE UMR 5175, CNRS-Université de Montpellier-Université Paul-Valéry Montpellier-EPHE, campus CNRS, Montpellier, France.,Department of Biology, Ecology and Evolution, University of Fribourg, Fribourg, Switzerland
| | - Dieter Ebert
- Zoological Institute, University of Basel, Basel, Switzerland
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Abstract
Background Understanding the impact of disease in natural populations requires an understanding of infection risk and the damage that parasites cause to their hosts (= virulence). However, because these disease traits are often studied and quantified under controlled laboratory conditions and with reference to healthy control hosts, we have little knowledge about how they play out in natural conditions. In the Daphnia–Pasteuria host–parasite system, field assessments often show very low estimates of virulence, while controlled laboratory experiments indicate extremely high virulence. Results To examine this discrepancy, we sampled Daphnia magna hosts from the field during a parasite epidemic and recorded disease traits over a subsequent 3-week period in the laboratory. As predicted for chronic disease where infections in older (larger) hosts are also, on average, older, we found that larger D. magna females were infected more often, had fewer offspring prior to the onset of castration and showed signs of infection sooner than smaller hosts. Also consistent with laboratory experiments, infected animals were found in both sexes and in all sizes of hosts. Infected females were castrated at capture or became castrated soon after. As most females in the field carried no eggs in their brood pouch at the time of sampling, virulence estimates of infected females relative to uninfected females were low. However, with improved feeding conditions in the laboratory, only uninfected females resumed reproduction, resulting in very high relative virulence estimates. Conclusions Overall, our study shows that the disease manifestation of P. ramosa, as expressed under natural conditions, is consistent with what we know from laboratory experiments. However, parasite induced fecundity reduction of infected, relative to uninfected hosts depended strongly on the environmental conditions. We argue that this effect is particularly strong for castrating parasites, because infected hosts have low fecundity under all conditions.
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Affiliation(s)
- Eevi Savola
- Department of Environmental Sciences, Zoology, Basel University, Vesalgasse 1, 4051, Basel, Switzerland.,Institute of Evolutionary Biology, School of Biological Sciences, The University of Edinburgh, Ashworth Laboratories, Edinburgh, EH9 3FL, UK
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, Basel University, Vesalgasse 1, 4051, Basel, Switzerland.
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Brun NR, Fields PD, Horsfield S, Mirbahai L, Ebert D, Colbourne JK, Fent K. Mixtures of Aluminum and Indium Induce More than Additive Phenotypic and Toxicogenomic Responses in Daphnia magna. Environ Sci Technol 2019; 53:1639-1649. [PMID: 30608651 DOI: 10.1021/acs.est.8b05457] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Aquatic systems are contaminated by many metals but their effects as mixtures on organisms are not well understood. Here, we assessed effects of aluminum with fairly well-known modes of actions and indium, an understudied emerging contaminant from electronics, followed by studying equi-effective mixtures thereof. We report acute and adverse phenotypic effects in Daphnia magna adults and global transcriptomic effects employing RNA sequencing in neonates. The mixture induced more than additive activity in mortality and in physiological effects, including growth and reproduction. Similarly, transcriptomic effects were more than additive, as indicated by a markedly higher number of 463 differentially expressed transcripts in the mixture and by distinct classes of genes assigned to several biological functions, including metabolic processes, suggesting depleted energy reserves, which may be responsible for the observed impaired reproduction and growth. A gene set enrichment analysis (GSEA) of a priori known response pathways for aluminum confirmed activation of distinct molecular pathways by indium. Our study is highlighting more than additive effects at the transcriptional and physiological level and is providing a state-of-the art approach to mixture analysis, which is important for risk assessment of these metals and metal mixtures.
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Affiliation(s)
- Nadja R Brun
- School of Life Sciences , University of Applied Sciences and Arts Northwestern Switzerland , Langackerstrasse 30 , 4132 Muttenz , Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics , ETH Zürich , Universitätsstrasse 16 , 8092 Zürich , Switzerland
| | - Peter D Fields
- Zoological Institute , University of Basel , Vesalgasse 1 , 4051 Basel , Switzerland
| | - Samuel Horsfield
- School of Biosciences , University of Birmingham , Edgbaston, Birmingham B15 2TT , United Kingdom
| | - Leda Mirbahai
- School of Biosciences , University of Birmingham , Edgbaston, Birmingham B15 2TT , United Kingdom
| | - Dieter Ebert
- Zoological Institute , University of Basel , Vesalgasse 1 , 4051 Basel , Switzerland
| | - John K Colbourne
- School of Biosciences , University of Birmingham , Edgbaston, Birmingham B15 2TT , United Kingdom
| | - Karl Fent
- School of Life Sciences , University of Applied Sciences and Arts Northwestern Switzerland , Langackerstrasse 30 , 4132 Muttenz , Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics , ETH Zürich , Universitätsstrasse 16 , 8092 Zürich , Switzerland
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50
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Bond JJ, Donaldson AJ, Coumans JVF, Austin K, Ebert D, Wheeler D, Oddy VH. Protein profiles of enzymatically isolated rumen epithelium in sheep fed a fibrous diet. J Anim Sci Biotechnol 2019; 10:5. [PMID: 30697422 PMCID: PMC6346531 DOI: 10.1186/s40104-019-0314-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 01/04/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The rumen wall plays a major role in efficient transfer of digested nutrients in the rumen to peripheral tissues through the portal venous system. Some of these substrates are metabolised in the epithelium during this process. To identify the specific proteins involved in these processes, we used proteomic technologies. Protein extracts were prepared from ventral rumen tissue of six sheep fed a fibrous diet at 1.5× maintenance energy requirements. Using a newly developed method, we were able to enzymatically isolate the epithelial cells from underlying tissue layers, thus allowing cytosol and membrane fractions to be independently analysed using liquid chromatography tandem mass spectrometry (LC MS/MS). RESULTS Using our procedure we identified 570 epithelial proteins in the Ovis aries sequence database. Subcellular locations were largely cytosolic (n = 221) and extracellular (n = 85). However, a quarter of the proteins identified were assigned to the plasma membrane or organelle membranes, some of which transport nutrients and metabolites. Of these 91 were transmembrane proteins (TMHMM), 27 had an N-terminal signal peptide (signalP) and TMHMM motif, 13 had a glycosylphosphatidylinositol (GPI) anchor and signalP sequence, 67 had beta (β) strands or 17 β strands and a transit peptide sequence, indicating the identified proteins were integral or peripheral membrane proteins. Subunits of the 5 protein complexes involved in mitochondrial cellular energy production were well represented. Structural proteins (15%), proteins involved in the metabolism of lipids and proteins (26%) and those with steroid or cytokine action were a feature of the proteome. CONCLUSION Our research has developed a procedure to isolate rumen epithelium proteins from the underlying tissue layers so that they may be profiled using proteomic technologies. The approach improves the number of proteins that can be profiled that are specific to the epithelium of the rumen wall. It provides new insights into the proteins of structural and nutritional importance in the rumen epithelium, that carry out nutrient transport and metabolism, cell growth and signalling.
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Affiliation(s)
- J. J. Bond
- NSW Department of Primary Industries, Extensive Livestock Industry Centre, University of New England, Trevenna Rd, Armidale, NSW 2351 Australia
| | - A. J. Donaldson
- NSW Department of Primary Industries, Extensive Livestock Industry Centre, University of New England, Trevenna Rd, Armidale, NSW 2351 Australia
| | - J. V. F. Coumans
- School of Rural Medicine, University of New England, Armidale, NSW 2351 Australia
| | - K. Austin
- NSW Department of Primary Industries, Extensive Livestock Industry Centre, University of New England, Trevenna Rd, Armidale, NSW 2351 Australia
| | - D. Ebert
- School of Rural Medicine, University of New England, Armidale, NSW 2351 Australia
| | - D. Wheeler
- NSW Department of Primary Industries, Orange Agricultural Institute, Orange, NSW 2800 Australia
| | - V. H. Oddy
- NSW Department of Primary Industries, Extensive Livestock Industry Centre, University of New England, Trevenna Rd, Armidale, NSW 2351 Australia
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