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Martinez-Sañudo I, Perotti MA, Carofano I, Santoiemma G, Marri L, Mazzon L. The biogeographic patterns of the olive fly and its primary symbiont Candidatus Erwinia dacicola across the distribution area of the olive tree. Sci Rep 2024; 14:22483. [PMID: 39341904 PMCID: PMC11438859 DOI: 10.1038/s41598-024-73055-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 09/12/2024] [Indexed: 10/01/2024] Open
Abstract
The olive fly, Bactrocera oleae (Rossi, 1790), is the major insect pest of olives attacking both cultivated and wild olive. Bactrocera oleae carries a primary and vertically transmitted symbiont, the bacterium Candidatus Erwinia dacicola. As any primary symbiont, it plays an important role in the reproduction and lifespan of the fly. The genetic 16S rRNA diversity of the primary symbiont and the mitochondrial haplotype variation of the insect host were simultaneously examined in 54 olive fly populations. The aim was to unravel the biogeographic patterns of this economically relevant host-bacteria interaction across a wide distribution area. Three symbiont haplotypes were identified. The primary symbiont showed a lower haplotype diversity than that of its host, a characteristic indicative of a long-term interaction. A significant genetic and geographic association between host and primary symbiont was observed, with an East-West genetic differentiation pattern in the Mediterranean basin, coinciding with the historical genetic distribution of the olive tree. The study shows promise, informing and aiding the development of future tools for the control of the olive fly.
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Affiliation(s)
- Isabel Martinez-Sañudo
- Department of Agronomy, Food, Natural Resources, Animals and the Environment (DAFNAE), University of Padova, Viale dell'Università, 16, 35020, Legnaro, PD, Italy.
| | - M Alejandra Perotti
- Ecology and Evolutionary Biology Section, School of Biological Sciences, University of Reading, Reading, GB, Great Britain
| | - Ivana Carofano
- Department of Agronomy, Food, Natural Resources, Animals and the Environment (DAFNAE), University of Padova, Viale dell'Università, 16, 35020, Legnaro, PD, Italy
| | - Giacomo Santoiemma
- Department of Agronomy, Food, Natural Resources, Animals and the Environment (DAFNAE), University of Padova, Viale dell'Università, 16, 35020, Legnaro, PD, Italy
| | - Laura Marri
- Department of Life Sciences, University of Siena, Siena, Italy
| | - Luca Mazzon
- Department of Agronomy, Food, Natural Resources, Animals and the Environment (DAFNAE), University of Padova, Viale dell'Università, 16, 35020, Legnaro, PD, Italy
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Půža V, Machado RAR. Systematics and phylogeny of the entomopathogenic nematobacterial complexes Steinernema-Xenorhabdus and Heterorhabditis-Photorhabdus. ZOOLOGICAL LETTERS 2024; 10:13. [PMID: 39020388 PMCID: PMC11256433 DOI: 10.1186/s40851-024-00235-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 06/08/2024] [Indexed: 07/19/2024]
Abstract
Entomopathogenic nematodes of the genera Steinernema and Heterorhabditis, along with their bacterial symbionts from the genera Xenorhabdus and Photorhabdus, respectively, are important biological control agents against agricultural pests. Rapid progress in the development of genomic tools has catalyzed a transformation of the systematics of these organisms, reshaping our understanding of their phylogenetic and cophlylogenetic relationships. In this review, we discuss the major historical events in the taxonomy and systematics of this group of organisms, highlighting the latest advancements in these fields. Additionally, we synthesize information on nematode-bacteria associations and assess the existing evidence regarding their cophylogenetic relationships.
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Affiliation(s)
- Vladimír Půža
- Institute of Entomology, Biology centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice, 37005, Czech Republic.
- Faculty of Agriculture and Technology, University of South Bohemia, Studentská 1668, České Budějovice, 37005, Czech Republic.
| | - Ricardo A R Machado
- Experimental Biology Research Group, Institute of Biology, Faculty of Sciences, University of Neuchâtel, Neuchâtel, 2000, Switzerland.
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3
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Liang Y, Dikow RB, Su X, Wen J, Ren Z. Comparative genomics of the primary endosymbiont Buchnera aphidicola in aphid hosts and their coevolutionary relationships. BMC Biol 2024; 22:137. [PMID: 38902723 PMCID: PMC11188193 DOI: 10.1186/s12915-024-01934-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 05/28/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND Coevolution between modern aphids and their primary obligate, bacterial endosymbiont, Buchnera aphidicola, has been previously reported at different classification levels based on molecular phylogenetic analyses. However, the Buchnera genome remains poorly understood within the Rhus gall aphids. RESULTS We assembled the complete genome of the endosymbiont Buchnera in 16 aphid samples, representing 13 species in all six genera of Rhus gall aphids by shotgun genome skimming method. We compared the newly assembled genomes with those from GenBank to comprehensively investigate patterns of coevolution between the bacteria Buchnera and their aphid hosts. Buchnera genomes were mostly collinear, and the pan-genome contained 684 genes, in which the core genome contained 256 genes with some lineages having large numbers of tandem gene duplications. There has been substantial gene-loss in each Buchnera lineage. We also reconstructed the phylogeny for Buchnera and their host aphids, respectively, using 72 complete genomes of Buchnera, along with the complete mitochondrial genomes and three nuclear genes of 31 corresponding host aphid accessions. The cophylogenetic test demonstrated significant coevolution between these two partner groups at individual, species, generic, and tribal levels. CONCLUSIONS Buchnera exhibits very high levels of genomic sequence divergence but relative stability in gene order. The relationship between the symbionts Buchnera and its aphid hosts shows a significant coevolutionary pattern and supports complexity of the obligate symbiotic relationship.
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Affiliation(s)
- Yukang Liang
- School of Life Science and Shanxi Key Laboratory of Nucleic Acid Biopesticides, Shanxi University, 92 Wucheng Rd, Taiyuan Shanxi, 030006, China
| | - Rebecca B Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, 600 Maryland Avenue SW, Washington, DC, 20024, USA
| | - Xu Su
- School of Geography and Life Science, Qinghai Normal University, 38 Wusixi Road, Xining, 810008, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, MRC-166, Washington, DC, 20013-7012, USA.
| | - Zhumei Ren
- School of Life Science and Shanxi Key Laboratory of Nucleic Acid Biopesticides, Shanxi University, 92 Wucheng Rd, Taiyuan Shanxi, 030006, China.
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Sato Y, Wippler J, Wentrup C, Ansorge R, Sadowski M, Gruber-Vodicka H, Dubilier N, Kleiner M. Fidelity varies in the symbiosis between a gutless marine worm and its microbial consortium. MICROBIOME 2022; 10:178. [PMID: 36273146 PMCID: PMC9587655 DOI: 10.1186/s40168-022-01372-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/15/2022] [Indexed: 05/30/2023]
Abstract
BACKGROUND Many animals live in intimate associations with a species-rich microbiome. A key factor in maintaining these beneficial associations is fidelity, defined as the stability of associations between hosts and their microbiota over multiple host generations. Fidelity has been well studied in terrestrial hosts, particularly insects, over longer macroevolutionary time. In contrast, little is known about fidelity in marine animals with species-rich microbiomes at short microevolutionary time scales, that is at the level of a single host population. Given that natural selection acts most directly on local populations, studies of microevolutionary partner fidelity are important for revealing the ecological and evolutionary processes that drive intimate beneficial associations within animal species. RESULTS In this study on the obligate symbiosis between the gutless marine annelid Olavius algarvensis and its consortium of seven co-occurring bacterial symbionts, we show that partner fidelity varies across symbiont species from strict to absent over short microevolutionary time. Using a low-coverage sequencing approach that has not yet been applied to microbial community analyses, we analysed the metagenomes of 80 O. algarvensis individuals from the Mediterranean and compared host mitochondrial and symbiont phylogenies based on single-nucleotide polymorphisms across genomes. Fidelity was highest for the two chemoautotrophic, sulphur-oxidizing symbionts that dominated the microbial consortium of all O. algarvensis individuals. In contrast, fidelity was only intermediate to absent in the sulphate-reducing and spirochaetal symbionts with lower abundance. These differences in fidelity are likely driven by both selective and stochastic forces acting on the consistency with which symbionts are vertically transmitted. CONCLUSIONS We hypothesize that variable degrees of fidelity are advantageous for O. algarvensis by allowing the faithful transmission of their nutritionally most important symbionts and flexibility in the acquisition of other symbionts that promote ecological plasticity in the acquisition of environmental resources. Video Abstract.
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Affiliation(s)
- Yui Sato
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany.
| | - Juliane Wippler
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany
| | - Cecilia Wentrup
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany
| | - Rebecca Ansorge
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich, NR4 7UQ, UK
| | - Miriam Sadowski
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany
| | - Harald Gruber-Vodicka
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany
| | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany.
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA.
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Qin M, Jiang L, Kholmatov BR, Qiao G, Chen J. Phylosymbiotic Structures of the Microbiota in Mollitrichosiphum tenuicorpus (Hemiptera: Aphididae: Greenideinae). MICROBIAL ECOLOGY 2022; 84:227-239. [PMID: 34387702 PMCID: PMC9250915 DOI: 10.1007/s00248-021-01830-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
Aphids harbor an array of symbionts that provide hosts with ecological benefits. Microbial community assembly generally varies with respect to aphid species, geography, and host plants. However, the influence of host genetics and ecological factors on shaping intraspecific microbial community structures has not been fully understood. In the present study, using Illumina sequencing of the V3 - V4 hypervariable region of the 16S rRNA gene, we characterized the microbial compositions associated with Mollitrichosiphum tenuicorpus from different regions and plants in China. The primary symbiont Buchnera aphidicola and the secondary symbiont Arsenophonus dominated the microbial flora in M. tenuicorpus. Ordination analyses and statistical tests suggested that geography and aphid genetics primarily contributed to the variation in the microbiota of M. tenuicorpus. We further confirmed the combined effect of aphid genetics and geography on shaping the structures of symbiont and secondary symbiont communities. Moreover, the significant correlation between aphid genetic divergence and symbiont community dissimilarity provides evidence for intraspecific phylosymbiosis in natural systems. Our study helped to elucidate the eco-evolutionary relationship between symbiont communities and aphids within one given species.
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Affiliation(s)
- Man Qin
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liyun Jiang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bakhtiyor R Kholmatov
- Institute of Zoology, Academy of Sciences Republic of Uzbekistan, Bagishamol Str., 232b, Tashkent, 100053, Uzbekistan
| | - Gexia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jing Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
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6
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Li Y, Leonard SP, Powell JE, Moran NA. Species divergence in gut-restricted bacteria of social bees. Proc Natl Acad Sci U S A 2022; 119:e2115013119. [PMID: 35467987 PMCID: PMC9170019 DOI: 10.1073/pnas.2115013119] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 03/16/2022] [Indexed: 01/07/2023] Open
Abstract
Host-associated microbiomes, particularly gut microbiomes, often harbor related but distinct microbial lineages, but how this diversity arises and is maintained is not well understood. A prerequisite for lineage diversification is reproductive isolation imposed by barriers to gene flow. In host-associated microbes, genetic recombination can be disrupted by confinement to different hosts, for example following host speciation, or by niche partitioning within the same host. Taking advantage of the simple gut microbiome of social bees, we explore the diversification of two groups of gut-associated bacteria, Gilliamella and Snodgrassella, which have evolved for 80 million y with honey bees and bumble bees. Our analyses of sequenced genomes show that these lineages have diversified into discrete populations with limited gene flow. Divergence has occurred between symbionts of different host species and, in some cases, between symbiont lineages within a single host individual. Populations have acquired genes to adapt to specific hosts and ecological niches; for example, Gilliamella lineages differ markedly in abilities to degrade dietary polysaccharides and to use the resulting sugar components. Using engineered fluorescent bacteria in vivo, we show that Gilliamella lineages localize to different hindgut regions, corresponding to differences in their abilities to use spatially concentrated nitrogenous wastes of hosts. Our findings show that bee gut bacteria can diversify due to isolation in different host species and also due to spatial niche partitioning within individual hosts, leading to barriers to gene flow.
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Affiliation(s)
- Yiyuan Li
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
| | - Sean P. Leonard
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
| | - J. Elijah Powell
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
| | - Nancy A. Moran
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
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7
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Co-haplotyping symbiont and host to unravel invasion pathways of the exotic pest Halyomorpha halys in Italy. Sci Rep 2020; 10:18441. [PMID: 33116256 PMCID: PMC7595193 DOI: 10.1038/s41598-020-75519-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 10/06/2020] [Indexed: 01/28/2023] Open
Abstract
The brown marmorated stink bug Halyomorpha halys (Stål) is a globally invasive species that harbours the primary bacterial symbiont ‘Candidatus Pantoea carbekii’. In this work, P. carbekii was used as another genetic marker to investigate the biodiversity and biogeographical patterns of this important pest, in native and newly invaded areas, especially in Italy. The correlation between the genetic structure of the symbiont and that of its host was studied through the analyses of one bacterial and one host marker, the putative pseudogene ΔybgF and the mitochondrial gene COI, respectively. As a result, five new P. carbekii haplotypes were identified, and an association pattern between host-symbiont haplotypes was observed. Host species showed higher haplotype diversity than symbiont, which can be expected in a long term host-symbiont association. Populations from the north-eastern Italy showed the highest values of genetic diversity for both markers, highlighting that this particular Italian area could be the result of multiple ongoing introductions. Moreover, some of the symbiont-host haplotypes observed were shared only by populations from north-eastern Italy and native areas, especially Japan, suggesting further introductions from this native country to Italy. Overall, our findings improve the understanding of the potential origin of multiple accidental introductions of H. halys in Italy.
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8
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Lindgren H, Moncada B, Lücking R, Magain N, Simon A, Goffinet B, Sérusiaux E, Nelsen MP, Mercado-Díaz JA, Widhelm TJ, Lumbsch HT. Cophylogenetic patterns in algal symbionts correlate with repeated symbiont switches during diversification and geographic expansion of lichen-forming fungi in the genus Sticta (Ascomycota, Peltigeraceae). Mol Phylogenet Evol 2020; 150:106860. [PMID: 32473336 DOI: 10.1016/j.ympev.2020.106860] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/10/2020] [Accepted: 05/21/2020] [Indexed: 12/19/2022]
Abstract
Species in the fungal genus Sticta form symbiotic associations primarily with either green algae or cyanobacteria, but tripartite associations or photosymbiodemes involving both types of photobionts occur in some species. Sticta is known to associate with green algae in the genus Symbiochloris. However, previous studies have shown that algae from other genera, such as Heveochlorella, may also be suitable partners for Sticta. We examined the diversity of green algal partners in the genus Sticta and assessed the patterns of association between the host fungus and its algal symbiont. We used multi-locus sequence data from multiple individuals collected in Australia, Cuba, Madagascar, Mauritius, New Zealand, Reunion and South America to infer phylogenies for fungal and algal partners and performed tests of congruence to assess coevolution between the partners. In addition, event-based methods were implemented to examine which cophylogenetic processes have led to the observed association patterns in Sticta and its green algal symbionts. Our results show that in addition to Symbiochloris, Sticta associates with green algae from the genera Chloroidium, Coccomyxa, Elliptochloris and Heveochlorella, the latter being the most common algal symbiont associated with Sticta in this study. Geography plays a strong role in shaping fungal-algal association patterns in Sticta as mycobionts associate with different algal lineages in different geographic locations. While fungal and algal phylogenies were mostly congruent, event-based methods did not find any evidence for cospeciation between the partners. Instead, the association patterns observed in Sticta and associated algae, were largely explained by other cophylogenetic events such as host-switches, losses of symbiont and failure of the symbiont to diverge with its host. Our results also show that tripartite associations with green algae evolved multiple times in Sticta.
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Affiliation(s)
- Hanna Lindgren
- Science and Education, The Field Museum, 1400 South Lake Shore Drive, Chicago, IL 60605, United States.
| | - Bibiana Moncada
- Licenciatura en Biología, Universidad Distrital Francisco José de Caldas, Cra. 4 No. 26D-54, Torre de Laboratorios, Herbario, Bogotá, Colombia
| | - Robert Lücking
- Botanical Garden and Botanical Museum, Koenigin-Luise-Strasse 6-8, 14195 Berlin, Germany
| | - Nicolas Magain
- Evolution and Conservation Biology, University of Liège, Sart Tilman B22, B-4000 Liège, Belgium; Department of Biology, Duke University, Durham, NC 27708-0338, USA
| | - Antoine Simon
- Evolution and Conservation Biology, University of Liège, Sart Tilman B22, B-4000 Liège, Belgium
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269-3043, USA
| | - Emmanuël Sérusiaux
- Evolution and Conservation Biology, University of Liège, Sart Tilman B22, B-4000 Liège, Belgium
| | - Matthew P Nelsen
- Science and Education, The Field Museum, 1400 South Lake Shore Drive, Chicago, IL 60605, United States
| | - Joel A Mercado-Díaz
- Science and Education, The Field Museum, 1400 South Lake Shore Drive, Chicago, IL 60605, United States; Committee on Evolutionary Biology, University of Chicago, 1025 E. 57(th) street, Chicago, IL 60637, USA
| | - Todd J Widhelm
- Science and Education, The Field Museum, 1400 South Lake Shore Drive, Chicago, IL 60605, United States
| | - H Thorsten Lumbsch
- Science and Education, The Field Museum, 1400 South Lake Shore Drive, Chicago, IL 60605, United States
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9
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Wang HL, Lei T, Xia WQ, Cameron SL, Liu YQ, Zhang Z, Gowda MMN, De Barro P, Navas-Castillo J, Omongo CA, Delatte H, Lee KY, Patel MV, Krause-Sakate R, Ng J, Wu SL, Fiallo-Olivé E, Liu SS, Colvin J, Wang XW. Insight into the microbial world of Bemisia tabaci cryptic species complex and its relationships with its host. Sci Rep 2019; 9:6568. [PMID: 31024030 PMCID: PMC6484021 DOI: 10.1038/s41598-019-42793-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 03/26/2019] [Indexed: 11/09/2022] Open
Abstract
The 37 currently recognized Bemisia tabaci cryptic species are economically important species and contain both primary and secondary endosymbionts, but their diversity has never been mapped systematically across the group. To achieve this, PacBio sequencing of full-length bacterial 16S rRNA gene amplicons was carried out on 21 globally collected species in the B. tabaci complex, and two samples from B. afer were used here as outgroups. The microbial diversity was first explored across the major lineages of the whole group and 15 new putative bacterial sequences were observed. Extensive comparison of our results with previous endosymbiont diversity surveys which used PCR or multiplex 454 pyrosequencing platforms showed that the bacterial diversity was underestimated. To validate these new putative bacteria, one of them (Halomonas) was first confirmed to be present in MED B. tabaci using Hiseq2500 and FISH technologies. These results confirmed PacBio is a reliable and informative venue to reveal the bacterial diversity of insects. In addition, many new secondary endosymbiotic strains of Rickettsia and Arsenophonus were found, increasing the known diversity in these groups. For the previously described primary endosymbionts, one Portiera Operational Taxonomic Units (OTU) was shared by all B. tabaci species. The congruence of the B. tabaci-host and Portiera phylogenetic trees provides strong support for the hypothesis that primary endosymbionts co-speciated with their hosts. Likewise, a comparison of bacterial alpha diversities, Principal Coordinate Analysis, indistinct endosymbiotic communities harbored by different species and the co-divergence analyses suggest a lack of association between overall microbial diversity with cryptic species, further indicate that the secondary endosymbiont-mediated speciation is unlikely to have occurred in the B. tabaci species group.
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Affiliation(s)
- Hua-Ling Wang
- Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.,Natural Resources Institute, University of Greenwich, Kent, ME4 4TB, United Kingdom
| | - Teng Lei
- Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Wen-Qiang Xia
- Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Stephen L Cameron
- Department of Entomology, Purdue University, 901West State Street, West Lafayette, IN, 479074, USA
| | - Yin-Quan Liu
- Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Zhen Zhang
- Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Maruthi M N Gowda
- Natural Resources Institute, University of Greenwich, Kent, ME4 4TB, United Kingdom
| | - Paul De Barro
- CSIRO Ecosystem Sciences, Brisbane, QLD, 4001, Australia
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29750, Algarrobo-Costa, Málaga, Spain
| | - Christopher A Omongo
- National Crops Resources Research Institute, Namulonge, P.O. Box, 7084, Kampala, Uganda
| | - Hélène Delatte
- CIRAD, UMR PVBMT CIRAD-Universitéde La Réunion, Pôle de Protection des Plantes, 7 chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France
| | - Kyeong-Yeoll Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, Republic of Korea
| | - Mitulkumar V Patel
- Natural Resources Institute, University of Greenwich, Kent, ME4 4TB, United Kingdom
| | | | - James Ng
- Department of Plant Pathology and Microbiology, University of California, Riverside, California, 92521, USA
| | - San-Ling Wu
- Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Elvira Fiallo-Olivé
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29750, Algarrobo-Costa, Málaga, Spain
| | - Shu-Sheng Liu
- Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - John Colvin
- Natural Resources Institute, University of Greenwich, Kent, ME4 4TB, United Kingdom.
| | - Xiao-Wei Wang
- Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.
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10
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Chattopadhyay S, Chi PB, Minin VN, Berg DE, Sokurenko EV. Recombination-independent rapid convergent evolution of the gastric pathogen Helicobacter pylori. BMC Genomics 2018; 19:835. [PMID: 30463511 PMCID: PMC6249973 DOI: 10.1186/s12864-018-5231-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 11/07/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Helicobacter pylori is a human stomach pathogen, naturally-competent for DNA uptake, and prone to homologous recombination. Extensive homoplasy (i.e., phylogenetically-unlinked identical variations) observed in H. pylori genes is considered a hallmark of such recombination. However, H. pylori also exhibits a high mutation rate. The relative adaptive role of homologous recombination and mutation in species diversity is a highly-debated issue in biology. Recombination results in homoplasy. While convergent mutation can also account for homoplasy, its contribution is thought to be minor. We demonstrate here that, contrary to dogma, convergent mutation is a key contributor to Helicobacter pylori homoplasy, potentially driven by adaptive evolution of proteins. RESULTS Our present genome-wide analysis shows that homoplastic nonsynonymous (amino acid replacement) changes are not typically accompanied by homoplastic synonymous (silent) variations. Moreover, the majority of the codon positions with homoplastic nonsynonymous changes also contain different (i.e. non-homoplastic) nonsynonymous changes arising from mutation only. This indicates that, to a considerable extent, nonsynonymous homoplasy is due to convergent mutations. High mutation rate or limited availability of evolvable sites cannot explain this excessive convergence, as suggested by our simulation studies. Rather, the genes with convergent mutations are overrepresented in distinct functional categories, suggesting possible selective responses to conditions such as distinct micro-niches in single hosts, and to differences in host genotype, physiology, habitat and diet. CONCLUSIONS We propose that mutational convergence is a key player in H. pylori's adaptation and extraordinary persistence in human hosts. High frequency of mutational convergence could be due to saturation of evolvable sites capable of responding to selection pressures, while the number of mutable residues is far from saturation. We anticipate a similar scenario of mutational vs. recombinational genome dynamics or plasticity for other naturally competent microbes where strong positive selection could favor frequent convergent mutations in adaptive protein evolution.
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Affiliation(s)
| | - Peter B Chi
- Department of Mathematics and Statistics, Villanova University, Villanova, PA, USA
| | - Vladimir N Minin
- Department of Statistics, University of California, Irvine, California, USA
| | - Douglas E Berg
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Evgeni V Sokurenko
- Department of Microbiology, University of Washington, Seattle, Washington, USA
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11
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Alleman A, Hertweck KL, Kambhampati S. Random Genetic Drift and Selective Pressures Shaping the Blattabacterium Genome. Sci Rep 2018; 8:13427. [PMID: 30194350 PMCID: PMC6128925 DOI: 10.1038/s41598-018-31796-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 08/21/2018] [Indexed: 01/30/2023] Open
Abstract
Estimates suggest that at least half of all extant insect genera harbor obligate bacterial mutualists. Whereas an endosymbiotic relationship imparts many benefits upon host and symbiont alike, the intracellular lifestyle has profound effects on the bacterial genome. The obligate endosymbiont genome is a product of opposing forces: genes important to host survival are maintained through physiological constraint, contrasted by the fixation of deleterious mutations and genome erosion through random genetic drift. The obligate cockroach endosymbiont, Blattabacterium - providing nutritional augmentation to its host in the form of amino acid synthesis - displays radical genome alterations when compared to its most recent free-living relative Flavobacterium. To date, eight Blattabacterium genomes have been published, affording an unparalleled opportunity to examine the direction and magnitude of selective forces acting upon this group of symbionts. Here, we find that the Blattabacterium genome is experiencing a 10-fold increase in selection rate compared to Flavobacteria. Additionally, the proportion of selection events is largely negative in direction, with only a handful of loci exhibiting signatures of positive selection. These findings suggest that the Blattabacterium genome will continue to erode, potentially resulting in an endosymbiont with an even further reduced genome, as seen in other insect groups such as Hemiptera.
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Affiliation(s)
- Austin Alleman
- Department of Biology, University of Texas at Tyler, 3900 University Blvd., Tyler, Texas, 75799, United States.
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Johannes von Müller Weg 6, Mainz, 55128, Germany.
| | - Kate L Hertweck
- Department of Biology, University of Texas at Tyler, 3900 University Blvd., Tyler, Texas, 75799, United States
| | - Srini Kambhampati
- Department of Biology, University of Texas at Tyler, 3900 University Blvd., Tyler, Texas, 75799, United States
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12
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Al-Khafaji AM, Clegg SR, Pinder AC, Luu L, Hansford KM, Seelig F, Dinnis RE, Margos G, Medlock JM, Feil EJ, Darby AC, McGarry JW, Gilbert L, Plantard O, Sassera D, Makepeace BL. Multi-locus sequence typing of Ixodes ricinus and its symbiont Candidatus Midichloria mitochondrii across Europe reveals evidence of local co-cladogenesis in Scotland. Ticks Tick Borne Dis 2018; 10:52-62. [PMID: 30197267 DOI: 10.1016/j.ttbdis.2018.08.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 07/17/2018] [Accepted: 08/29/2018] [Indexed: 01/09/2023]
Abstract
Ticks have relatively complex microbiomes, but only a small proportion of the bacterial symbionts recorded from ticks are vertically transmitted. Moreover, co-cladogenesis between ticks and their symbionts, indicating an intimate relationship over evolutionary history driven by a mutualistic association, is the exception rather than the rule. One of the most widespread tick symbionts is Candidatus Midichloria, which has been detected in all of the major tick genera of medical and veterinary importance. In some species of Ixodes, such as the sheep tick Ixodes ricinus (infected with Candidatus Midichloria mitochondrii), the symbiont is fixed in wild adult female ticks, suggesting an obligate mutualism. However, almost no information is available on genetic variation in Candidatus M. mitochondrii or possible co-cladogenesis with its host across its geographic range. Here, we report the first survey of Candidatus M. mitochondrii in I. ricinus in Great Britain and a multi-locus sequence typing (MLST) analysis of tick and symbiont between British ticks and those collected in continental Europe. We show that while the prevalence of the symbiont in nymphs collected in England is similar to that reported from the continent, a higher prevalence in nymphs and adult males is apparent in Wales. In general, Candidatus M. mitochondrii exhibits very low levels of sequence diversity, although a consistent signal of host-symbiont coevolution was apparent in Scotland. Moreover, the tick MLST scheme revealed that Scottish specimens form a clade that is partially separated from other British ticks, with almost no contribution of continental sequence types in this north-westerly border of the tick's natural range. The low diversity of Candidatus M. mitochondrii, in contrast with previously reported high rates of polymorphism in I. ricinus mitogenomes, suggests that the symbiont may have swept across Europe recently via a horizontal, rather than vertical, transmission route.
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Affiliation(s)
- Alaa M Al-Khafaji
- Institute of Infection & Global Health, University of Liverpool, 146 Brownlow Hill, Liverpool L3 5RF, UK; College of Veterinary Medicine, University of Al-Qadisiyah, Diwaniyah 58001, Qadisiyyah Province, Iraq
| | - Simon R Clegg
- Institute of Infection & Global Health, University of Liverpool, 146 Brownlow Hill, Liverpool L3 5RF, UK; School of Life Sciences, University of Lincoln, Brayford Pool, Lincoln LN6 7TS, UK
| | - Alice C Pinder
- Institute of Veterinary Science, University of Liverpool, 401 Great Newton Street, Liverpool L3 5RP, UK
| | - Lisa Luu
- Institute of Infection & Global Health, University of Liverpool, 146 Brownlow Hill, Liverpool L3 5RF, UK
| | - Kayleigh M Hansford
- Medical Entomology and Zoonoses Ecology, Public Health England, Manor Farm Road, Porton Down, Salisbury SP4 0JG, UK
| | - Frederik Seelig
- The Milner Centre for Evolution, Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Ruth E Dinnis
- The Milner Centre for Evolution, Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Gabriele Margos
- The Milner Centre for Evolution, Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Jolyon M Medlock
- Medical Entomology and Zoonoses Ecology, Public Health England, Manor Farm Road, Porton Down, Salisbury SP4 0JG, UK
| | - Edward J Feil
- The Milner Centre for Evolution, Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Alistair C Darby
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Liverpool L69 7ZB, UK
| | - John W McGarry
- Institute of Veterinary Science, University of Liverpool, 401 Great Newton Street, Liverpool L3 5RP, UK
| | - Lucy Gilbert
- Ecological Sciences Group, The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH, UK
| | - Olivier Plantard
- BIOEPAR, INRA, Oniris, Université Bretagne Loire, 44307, Nantes, France
| | - Davide Sassera
- Department of Biology & Biotechnology, University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Benjamin L Makepeace
- Institute of Infection & Global Health, University of Liverpool, 146 Brownlow Hill, Liverpool L3 5RF, UK.
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13
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Zhang Y, Su X, Harris AJ, Caraballo-Ortiz MA, Ren Z, Zhong Y. Genetic Structure of the Bacterial Endosymbiont Buchnera aphidicola from Its Host Aphid Schlechtendalia chinensis and Evolutionary Implications. Curr Microbiol 2017; 75:309-315. [PMID: 29085996 DOI: 10.1007/s00284-017-1381-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 10/23/2017] [Indexed: 11/25/2022]
Abstract
Buchnera aphidicola is a primary symbiotic bacterium which provides essential amino acids to aphids. In this study, we sequenced nuclear 16s rDNA and atpAGD genes for 156 individuals of B. aphidicola from eight geographically distant populations to investigate the genetic diversity and structure of B. aphidicola associated to the sumac gall aphid Schlechtendalia chinensis in central and southern China. Our analyses of the combined sequences showed that B. aphidicola from S. chinensis had high haplotype and nucleotide diversity (h = 0.893; π = 0.00164). One of the 16 haplotypes detected had a wide geographic distribution across the central and southern China and was probably the ancestral haplotype of B. aphidicola from S. chinensis. A network and phylogenetic analysis revealed a geographic structure in which the 16 haplotypes of B. aphidicola were divided into the northern and southern clades separated by the Yangtze River. The two clades diverged from each other at 22.1 ± 3.7 Mya according to our divergence time estimations. Therefore, the modern genetic structure in B. aphidicola from S. chinensis has been probably impacted by historical geological events. Combined with the data from GenBank, we also reconstructed the phylogenetic relationships of three aphid subfamilies and their symbiont bacteria. The results indicated significant topological correlations between the aphid and bacterial phylogenies at interspecific levels.
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Affiliation(s)
- Yang Zhang
- School of Life Sciences, Fudan University, Shanghai, 200438, China.,Natural History Research Center, Shanghai Natural History Museum, Shanghai, 200041, China
| | - Xu Su
- School of Life Science, Qinghai Normal University, Xining, 810008, China
| | - A J Harris
- Department of Botany MRC-166, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington, DC, 20013, USA
| | | | - Zhumei Ren
- School of Life Science, Shanxi University, Taiyuan, 030006, China.
| | - Yang Zhong
- School of Life Sciences, Fudan University, Shanghai, 200438, China.
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14
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Morella NM, Koskella B. The Value of a Comparative Approach to Understand the Complex Interplay between Microbiota and Host Immunity. Front Immunol 2017; 8:1114. [PMID: 28959258 PMCID: PMC5603614 DOI: 10.3389/fimmu.2017.01114] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 08/24/2017] [Indexed: 01/17/2023] Open
Abstract
The eukaryote immune system evolved and continues to evolve within a microbial world, and as such is critically shaped by-and in some cases even reliant upon-the presence of host-associated microbial species. There are clear examples of adaptations that allow the host to simultaneously tolerate and/or promote growth of symbiotic microbiota while protecting itself against pathogens, but the relationship between immunity and the microbiome reaches far beyond simple recognition and includes complex cross talk between host and microbe as well as direct microbiome-mediated protection against pathogens. Here, we present a broad but brief overview of how the microbiome is controlled by and interacts with diverse immune systems, with the goal of identifying questions that can be better addressed by taking a comparative approach across plants and animals and different types of immunity. As two key examples of such an approach, we focus on data examining the importance of early exposure on microbiome tolerance and immune system development and function, and the importance of transmission among hosts in shaping the potential coevolution between, and long-term stability of, host-microbiome associations. Then, by comparing existing evidence across short-lived plants, mouse model systems and humans, and insects, we highlight areas of microbiome research that are strong in some systems and absent in others with the hope of guiding future research that will allow for broad-scale comparisons moving forward. We argue that such an approach will not only help with identification of generalities in host-microbiome-immune interactions but also improve our understanding of the role of the microbiome in host health.
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Affiliation(s)
- Norma M. Morella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States
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15
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Chen R, Wang Z, Chen J, Jiang LY, Qiao GX. Insect-bacteria parallel evolution in multiple-co-obligate-aphid association: a case in Lachninae (Hemiptera: Aphididae). Sci Rep 2017; 7:10204. [PMID: 28860659 PMCID: PMC5579299 DOI: 10.1038/s41598-017-10761-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 08/14/2017] [Indexed: 11/21/2022] Open
Abstract
Parallel phylogenies between aphid and its obligate symbiont Buchnera are hot topics which always focused on aphid lower taxonomic levels. Symbionts in the subfamily Lachninae are special. Buchnera in many lachnine species has undergone functional and genome size reduction that was replaced by other co-obligate symbionts. In this study, we constructed the phylogenetic relationships of Lachninae with a combined dataset of five genes sequenced from Buchnera to estimate the effects of a dual symbiotic system in the aphid-Buchnera cospeciation association. The phylogeny of Buchnera in Lachninae was well-resolved in the combined dataset. Each of the genera formed strongly supported monophyletic groups, with the exception of the genus Cinara. The phylogeny based on sequences from Buchnera was divided into five tribes according to the clades of the Lachninae hosts tree, with the phylogenies of Buchnera and Lachninae being generally congruent. These results first provided evidence of parallel evolution at the aphid subfamily level comprehensively and supported the view that topological congruence between the phylogenies of Buchnera and Lachninae would not be interfered with the other co-obligate symbionts, such as Sarretia, in aphid-entosymbiont association. These results also provided new insight in understanding host-plant coevolution in lachnine lineages.
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Affiliation(s)
- Rui Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhe Wang
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang, 110161, China
| | - Jing Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Li-Yun Jiang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ge-Xia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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16
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Xu TT, Chen J, Jiang LY, Qiao GX. Historical and cospeciating associations between Cerataphidini aphids (Hemiptera: Aphididae: Hormaphidinae) and their primary endosymbiont Buchnera aphidicola. Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx048] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Ting-Ting Xu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, P.R. China
- College of Life Sciences, University of Chinese Academy of Sciences, Shijingshan District, Beijing, P.R. China
| | - Jing Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, P.R. China
| | - Li-Yun Jiang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, P.R. China
| | - Ge-Xia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, P.R. China
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17
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Fromont C, Riegler M, Cook JM. Phylogeographic analyses of bacterial endosymbionts in fig homotomids (Hemiptera: Psylloidea) reveal codiversification of both primary and secondary endosymbionts. FEMS Microbiol Ecol 2016; 92:fiw205. [PMID: 27702765 DOI: 10.1093/femsec/fiw205] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/02/2016] [Indexed: 11/12/2022] Open
Abstract
While obligate primary (P-) endosymbionts usually cospeciate with their insect hosts, less is known about codiversification of secondary (S-) endosymbionts that are generally considered facultative. Typically, insects of the superfamily Psylloidea harbour one P- (Carsonella) and at least one S-endosymbiont, thought to compensate for Carsonella genome reduction. Most codiversification studies have used phylogenies of psyllids and their endosymbionts across and within host families or genera, but few have explored patterns within species. We focussed on P- and S-endosymbionts of three Mycopsylla (Homotomidae) species to explore whether they have congruent phylogenies and within-species geographic structures. The P-endosymbiont Carsonella, a S-endosymbiont and Wolbachia all had 100% prevalence, while Arsenophonus was only found in one species at low prevalence. Congruent phylogenies of Mycopsylla and P-endosymbionts across populations and species support strict cospeciation. S-endosymbiont phylogenies were also congruent across host species but low genetic variation in the S-endosymbiont was not correlated with host phylogeography, possibly due to a shorter evolutionary association. Between species, Wolbachia and Mycopsylla phylogenies were incongruent, probably due to horizontal transmission events. Our study is the first to explore endosymbionts of Mycopsylla and further supports the codivergence of Psylloidea hosts and P-endosymbionts, with obligate host interactions for both P- and S-endosymbionts.
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Affiliation(s)
- Caroline Fromont
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
| | - Markus Riegler
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
| | - James M Cook
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
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18
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Salerno JL, Bowen BW, Rappé MS. Biogeography of planktonic and coral-associated microorganisms across the Hawaiian Archipelago. FEMS Microbiol Ecol 2016; 92:fiw109. [DOI: 10.1093/femsec/fiw109] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2016] [Indexed: 02/07/2023] Open
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19
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Manzano-Marín A, Simon JC, Latorre A. Reinventing the Wheel and Making It Round Again: Evolutionary Convergence in Buchnera-Serratia Symbiotic Consortia between the Distantly Related Lachninae Aphids Tuberolachnus salignus and Cinara cedri. Genome Biol Evol 2016; 8:1440-58. [PMID: 27190007 PMCID: PMC4898801 DOI: 10.1093/gbe/evw085] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2016] [Indexed: 12/23/2022] Open
Abstract
Virtually all aphids (Aphididae) harbor Buchnera aphidicola as an obligate endosymbiont to compensate nutritional deficiencies arising from their phloem diet. Many species within the Lachninae subfamily seem to be consistently associated also with Serratia symbiotica We have previously shown that both Cinara (Cinara) cedri and Cinara (Cupressobium) tujafilina (Lachninae: Eulachnini tribe) have indeed established co-obligate associations with both Buchnera and S. symbiotica However, while Buchnera genomes of both Cinara species are similar, genome degradation differs greatly between the two S. symbiotica strains. To gain insight into the essentiality and degree of integration of S. symbiotica within the Lachninae, we sequenced the genome of both Buchnera and S. symbiotica endosymbionts from the distantly related aphid Tuberolachnus salignus (Lachninae: Tuberolachnini tribe). We found a striking level of similarity between the endosymbiotic system of this aphid and that of C. cedri In both aphid hosts, S. symbiotica possesses a highly reduced genome and is found exclusively intracellularly inside bacteriocytes. Interestingly, T. salignus' endosymbionts present the same tryptophan biosynthetic metabolic complementation as C. cedri's, which is not present in C. tujafilina's. Moreover, we corroborate the riboflavin-biosynthetic-role take-over/rescue by S. symbiotica in T. salignus, and therefore, provide further evidence for the previously proposed establishment of a secondary co-obligate endosymbiont in the common ancestor of the Lachninae aphids. Finally, we propose that the putative convergent split of the tryptophan biosynthetic role between Buchnera and S. symbiotica could be behind the establishment of S. symbiotica as an obligate intracellular symbiont and the triggering of further genome degradation.
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Affiliation(s)
| | - Jean-Christophe Simon
- UMR1349 Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA), Rennes, France
| | - Amparo Latorre
- Institut Cavanilles de Biodiversitat I Biologia Evolutiva, Universitat de Valencia Área de Genómica y Salud de la Fundación para el fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)-Salud Pública, València, Spain
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20
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Parkinson JF, Gobin B, Hughes WOH. Heritability of symbiont density reveals distinct regulatory mechanisms in a tripartite symbiosis. Ecol Evol 2016; 6:2053-60. [PMID: 27099709 PMCID: PMC4831439 DOI: 10.1002/ece3.2005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 01/10/2016] [Accepted: 01/18/2016] [Indexed: 01/08/2023] Open
Abstract
Beneficial eukaryotic–bacterial partnerships are integral to animal and plant evolution. Understanding the density regulation mechanisms behind bacterial symbiosis is essential to elucidating the functional balance between hosts and symbionts. Citrus mealybugs, Planococcus citri (Risso), present an excellent model system for investigating the mechanisms of symbiont density regulation. They contain two obligate nutritional symbionts, Moranella endobia, which resides inside Tremblaya princeps, which has been maternally transmitted for 100–200 million years. We investigate whether host genotype may influence symbiont density by crossing mealybugs from two inbred laboratory‐reared populations that differ substantially in their symbiont density to create hybrids. The density of the M. endobia symbiont in the hybrid hosts matched that of the maternal parent population, in keeping with density being determined either by the symbiont or the maternal genotype. However, the density of the T. princeps symbiont was influenced by the paternal host genotype. The greater dependency of T. princeps on its host may be due to its highly reduced genome. The decoupling of T. princeps and M. endobia densities, in spite of their intimate association, suggests that distinct regulatory mechanisms can be at work in symbiotic partnerships, even when they are obligate and mutualistic.
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Affiliation(s)
| | - Bruno Gobin
- PCS-Ornamental Plant Research Schaessestraat 18 Destelbergen 9070 Belgium
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21
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Bittleston LS, Pierce NE, Ellison AM, Pringle A. Convergence in Multispecies Interactions. Trends Ecol Evol 2016; 31:269-280. [PMID: 26858111 DOI: 10.1016/j.tree.2016.01.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 01/05/2016] [Accepted: 01/12/2016] [Indexed: 12/29/2022]
Abstract
The concepts of convergent evolution and community convergence highlight how selective pressures can shape unrelated organisms or communities in similar ways. We propose a related concept, convergent interactions, to describe the independent evolution of multispecies interactions with similar physiological or ecological functions. A focus on convergent interactions clarifies how natural selection repeatedly favors particular kinds of associations among species. Characterizing convergent interactions in a comparative context is likely to facilitate prediction of the ecological roles of organisms (including microbes) in multispecies interactions and selective pressures acting in poorly understood or newly discovered multispecies systems. We illustrate the concept of convergent interactions with examples: vertebrates and their gut bacteria; ectomycorrhizae; insect-fungal-bacterial interactions; pitcher-plant food webs; and ants and ant-plants.
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Affiliation(s)
- Leonora S Bittleston
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA; Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
| | - Naomi E Pierce
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA; Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Aaron M Ellison
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA; Harvard Forest, Harvard University, 324 North Main Street, Petersham, MA 01366, USA
| | - Anne Pringle
- Departments of Bacteriology and Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA
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22
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Wernegreen JJ. Endosymbiont evolution: predictions from theory and surprises from genomes. Ann N Y Acad Sci 2015; 1360:16-35. [PMID: 25866055 DOI: 10.1111/nyas.12740] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 01/27/2015] [Accepted: 02/11/2015] [Indexed: 10/23/2022]
Abstract
Genome data have created new opportunities to untangle evolutionary processes shaping microbial variation. Among bacteria, long-term mutualists of insects represent the smallest and (typically) most AT-rich genomes. Evolutionary theory provides a context to predict how an endosymbiotic lifestyle may alter fundamental evolutionary processes--mutation, selection, genetic drift, and recombination--and thus contribute to extreme genomic outcomes. These predictions can then be explored by comparing evolutionary rates, genome size and stability, and base compositional biases across endosymbiotic and free-living bacteria. Recent surprises from such comparisons include genome reduction among uncultured, free-living species. Some studies suggest that selection generally drives this streamlining, while drift drives genome reduction in endosymbionts; however, this remains an hypothesis requiring additional data. Unexpected evidence of selection acting on endosymbiont GC content hints that even weak selection may be effective in some long-term mutualists. Moving forward, intraspecific analysis offers a promising approach to distinguish underlying mechanisms, by testing the null hypothesis of neutrality and by quantifying mutational spectra. Such analyses may clarify whether endosymbionts and free-living bacteria occupy distinct evolutionary trajectories or, alternatively, represent varied outcomes of similar underlying forces.
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Affiliation(s)
- Jennifer J Wernegreen
- Nicholas School of the Environment and Center for Genomic and Computational Biology, Duke University, Durham, North Carolina
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23
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Wade MJ. Paradox of mother's curse and the maternally provisioned offspring microbiome. Cold Spring Harb Perspect Biol 2014; 6:a017541. [PMID: 25274703 DOI: 10.1101/cshperspect.a017541] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Strict maternal transmission creates an "asymmetric sieve" favoring the spread of mutations in organelle genomes that increase female fitness, but diminish male fitness. This phenomenon, called "Mother's Curse," can be viewed as an asymmetrical case of intralocus sexual conflict. The evolutionary logic of Mother's Curse applies to each member of the offspring microbiome, the community of maternally provisioned microbes, believed to number in the hundreds, if not thousands, of species for host vertebrates, including humans. Taken together, these observations pose a compelling evolutionary paradox: How has maternal transmission of an offspring microbiome become a near universal characteristic of the animal kingdom when the genome of each member of that community poses a potential evolutionary threat to the fitness of host males? I review features that limit or reverse Mother's Curse and contribute to resolving this paradox. I suggest that the evolution of vertical symbiont transmission requires conditions that mitigate the evolutionary threat to host males.
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Affiliation(s)
- Michael J Wade
- Department of Biology, Indiana University, Bloomington, Indiana 47405-7005
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24
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Banks JC, Cary SC, Hogg ID. Isolated faecal bacterial communities found for Weddell seals, Leptonychotes weddellii, at White Island, McMurdo Sound, Antarctica. Polar Biol 2014. [DOI: 10.1007/s00300-014-1567-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Kodaman N, Sobota RS, Mera R, Schneider BG, Williams SM. Disrupted human-pathogen co-evolution: a model for disease. Front Genet 2014; 5:290. [PMID: 25202324 PMCID: PMC4142859 DOI: 10.3389/fgene.2014.00290] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 08/05/2014] [Indexed: 02/06/2023] Open
Abstract
A major goal in infectious disease research is to identify the human and pathogenic genetic variants that explain differences in microbial pathogenesis. However, neither pathogenic strain nor human genetic variation in isolation has proven adequate to explain the heterogeneity of disease pathology. We suggest that disrupted co-evolution between a pathogen and its human host can explain variation in disease outcomes, and that genome-by-genome interactions should therefore be incorporated into genetic models of disease caused by infectious agents. Genetic epidemiological studies that fail to take both the pathogen and host into account can lead to false and misleading conclusions about disease etiology. We discuss our model in the context of three pathogens, Helicobacter pylori, Mycobacterium tuberculosis and human papillomavirus, and generalize the conditions under which it may be applicable.
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Affiliation(s)
- Nuri Kodaman
- Department of Genetics, Geisel School of Medicine, Dartmouth College Hanover, NH, USA ; Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University Medical Center Nashville, TN, USA
| | - Rafal S Sobota
- Department of Genetics, Geisel School of Medicine, Dartmouth College Hanover, NH, USA ; Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University Medical Center Nashville, TN, USA
| | - Robertino Mera
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center Nashville, TN, USA
| | - Barbara G Schneider
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center Nashville, TN, USA
| | - Scott M Williams
- Department of Genetics, Geisel School of Medicine, Dartmouth College Hanover, NH, USA
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Peccoud J, Bonhomme J, Mahéo F, de la Huerta M, Cosson O, Simon JC. Inheritance patterns of secondary symbionts during sexual reproduction of pea aphid biotypes. INSECT SCIENCE 2014; 21:291-300. [PMID: 24382700 DOI: 10.1111/1744-7917.12083] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/08/2013] [Indexed: 06/03/2023]
Abstract
Herbivorous insects frequently harbor bacterial symbionts that affect their ecology and evolution. Aphids host the obligatory endosymbiont Buchnera, which is required for reproduction, together with facultative symbionts whose frequencies vary across aphid populations. These maternally transmitted secondary symbionts have been particularly studied in the pea aphid, Acyrthosiphon pisum, which harbors at least 8 distinct bacterial species (not counting Buchnera) having environmentally dependent effects on host fitness. In particular, these symbiont species are associated with pea aphid populations feeding on specific plants. Although they are maternally inherited, these bacteria are occasionally transferred across insect lineages. One mechanism of such nonmaternal transfer is paternal transmission to the progeny during sexual reproduction. To date, transmission of secondary symbionts during sexual reproduction of aphids has been investigated in only a handful of aphid lineages and 3 symbiont species. To better characterize this process, we investigated inheritance patterns of 7 symbiont species during sexual reproduction of pea aphids through a crossing experiment involving 49 clones belonging to 9 host-specialized biotypes, and 117 crosses. Symbiont species in the progeny were detected with diagnostic qualitative PCR at the fundatrix stage hatching from eggs and in later parthenogenetic generations. We found no confirmed case of paternal transmission of symbionts to the progeny, and we observed that maternal transmission of a particular symbiont species (Serratia symbiotica) was quite inefficient. We discuss these observations in respect to the ecology of the pea aphid.
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Affiliation(s)
- Jean Peccoud
- INRA, Institut de Génétique, Environnement et Protection des Plantes (UMR IGEPP), Domaine de La Motte, 35653 le Rheu cedex, France
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Liu L, Li XY, Huang XL, Qiao GX. Evolutionary relationships of Pemphigus and allied genera (Hemiptera: Aphididae: Eriosomatinae) and their primary endosymbiont, Buchnera aphidicola. INSECT SCIENCE 2014; 21:301-312. [PMID: 24482319 DOI: 10.1111/1744-7917.12113] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/26/2014] [Indexed: 06/03/2023]
Abstract
Aphids harbor primary endosymbionts, Buchnera aphidicola, in specialized cells within their body cavities. Aphids and Buchnera have strict mutualistic relationships in nutrition exchange. This ancient association has received much attention from researchers who are interested in endosymbiotic evolution. Previous studies have found parallel phylogenetic relationships between non-galling aphids and Buchnera at lower taxonomic levels (genus, species). To understand whether relatively isolated habitats such as galls have effect on the parallel relationships between aphids and Buchnera, the present paper investigated the phylogenetic relationships of gall aphids from Pemphigus and allied genera, which induce pseudo-galls or galls on Populus spp. (poplar) and Buchnera. The molecular phylogenies inferred from three aphid genes (COI, COII and EF-1α) and two Buchnera genes (gnd, 16S rRNA gene) indicated significant congruence between aphids and Buchnera at generic as well as interspecific levels. Interestingly, both aphid and Buchnera phylogenies supported three main clades corresponding to the galling locations of aphids, namely leaf, the joint of leaf blade and petiole, and branch of the host plant. The results suggest phylogenetic conservatism of gall characters, which indicates gall characters are more strongly affected by aphid phylogeny, rather than host plants.
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Affiliation(s)
- Lin Liu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Beijing, China
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Ebert D. The Epidemiology and Evolution of Symbionts with Mixed-Mode Transmission. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2013. [DOI: 10.1146/annurev-ecolsys-032513-100555] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Dieter Ebert
- Universität Basel, Zoologisches Institut, 4051 Basel, Switzerland; Wissenschaftskolleg zu Berlin, 14193 Berlin, Germany;
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29
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Nováková E, Hypša V, Klein J, Foottit RG, von Dohlen CD, Moran NA. Reconstructing the phylogeny of aphids (Hemiptera: Aphididae) using DNA of the obligate symbiont Buchnera aphidicola. Mol Phylogenet Evol 2013; 68:42-54. [DOI: 10.1016/j.ympev.2013.03.016] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 03/07/2013] [Accepted: 03/13/2013] [Indexed: 01/16/2023]
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Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster. PLoS Genet 2012; 8:e1003129. [PMID: 23284297 PMCID: PMC3527207 DOI: 10.1371/journal.pgen.1003129] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 10/02/2012] [Indexed: 11/23/2022] Open
Abstract
Wolbachia are maternally inherited symbiotic bacteria, commonly found in arthropods, which are able to manipulate the reproduction of their host in order to maximise their transmission. The evolutionary history of endosymbionts like Wolbachia can be revealed by integrating information on infection status in natural populations with patterns of sequence variation in Wolbachia and host mitochondrial genomes. Here we use whole-genome resequencing data from 290 lines of Drosophila melanogaster from North America, Europe, and Africa to predict Wolbachia infection status, estimate relative cytoplasmic genome copy number, and reconstruct Wolbachia and mitochondrial genome sequences. Overall, 63% of Drosophila strains were predicted to be infected with Wolbachia by our in silico analysis pipeline, which shows 99% concordance with infection status determined by diagnostic PCR. Complete Wolbachia and mitochondrial genomes show congruent phylogenies, consistent with strict vertical transmission through the maternal cytoplasm and imperfect transmission of Wolbachia. Bayesian phylogenetic analysis reveals that the most recent common ancestor of all Wolbachia and mitochondrial genomes in D. melanogaster dates to around 8,000 years ago. We find evidence for a recent global replacement of ancestral Wolbachia and mtDNA lineages, but our data suggest that the derived wMel lineage arose several thousand years ago, not in the 20th century as previously proposed. Our data also provide evidence that this global replacement event is incomplete and is likely to be one of several similar incomplete replacement events that have occurred since the out-of-Africa migration that allowed D. melanogaster to colonize worldwide habitats. This study provides a complete genomic analysis of the evolutionary mode and temporal dynamics of the D. melanogaster–Wolbachia symbiosis, as well as important resources for further analyses of the impact of Wolbachia on host biology. Host–microbe interactions play important roles in the physiology, development, and ecology of many organisms. Studying how hosts and their microbial symbionts evolve together over time is crucial for understanding the impact that microbes have on host biology. With the advent of high-throughput sequencing technologies, it is now possible to obtain complete genomic information for hosts and their associated microbes. Here we use whole-genome sequences from ∼300 strains of the fruitfly Drosophila melanogaster to reveal the evolutionary history of this model species and its intracellular bacterial symbiont Wolbachia. The major findings of this study are that Wolbachia in D. melanogaster is inherited strictly through the egg with no evidence of horizontal transfer from other species, that the genealogies of Wolbachia and mitochondrial genomes are virtually the same, and that both Wolbachia and mitochondrial genomes show evidence for a recent incomplete global replacement event, which has left remnant lineages in North America, Europe, and Africa. We also use the fact that Wolbachia and mitochondrial genomes have the same genealogy to estimate the rate of molecular evolution for Wolbachia, which allows us to put dates on key events in the history of this important host–microbe model system.
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Giraldo CE, Uribe SI. Taxonomy of Mechanitis (f.) (Lepidoptera: Nymphalidae) from the west Colombian Andes: an integrative approach. NEOTROPICAL ENTOMOLOGY 2012; 41:472-484. [PMID: 23949672 DOI: 10.1007/s13744-012-0071-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 07/03/2012] [Indexed: 06/02/2023]
Abstract
Species identification in the butterfly genus Mechanitis (F.) (Lepidoptera: Nymphalidae) becomes difficult when it is based only on wing color patterns, a common practice in butterfly taxonomy. Difficulties in Mechanitis taxonomy are related to the widespread mimicry and polymorphism among species belonging to this genus. Species recognition and inventories of Mechanitis genus in geographic areas as the Andean region of Colombia are of particular interest and the use of more than one character for taxonomic identification is desirable. In this study, we included morphological, ecological, and mitochondrial DNA data to identify the occurring species in this region. Species of Mechanitis were studied from ecological, morphological, and molecular perspectives considering host plant identification, oviposition behavior, and life cycles under laboratory conditions. Immature morphology, patterns of wing color, and genital structures of adults were also studied. The genetic barcoding region of the cytochrome oxidase I mitochondrial gene was sequenced and used to verify the limits between species previously defined by the other characters and to validate its usefulness for species delimitation in this particular genus. The integrative approach combining independent datasets successfully allowed species identification as compared to the approach based on a single dataset. Three well-differentiated species were found in the studied region, Mechanitis menapis (Hewitson), Mechanitis polymnia (Linnaeus), and Mechanitis lysimnia (Fabricius). New valuable characters that could improve taxonomic identification in this genus are considered.
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Affiliation(s)
- C E Giraldo
- Grupo de Investigación en Sistemática Molecular, Lab de Biología y Sistemática de Insectos, Univ Nacional de Colombia, Sede Medellín, Medellín, Colombia.
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Widmer I, Dal Grande F, Excoffier L, Holderegger R, Keller C, Mikryukov VS, Scheidegger C. European phylogeography of the epiphytic lichen fungusLobaria pulmonariaand its green algal symbiont. Mol Ecol 2012; 21:5827-44. [DOI: 10.1111/mec.12051] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2011] [Revised: 07/18/2012] [Accepted: 08/19/2012] [Indexed: 11/28/2022]
Affiliation(s)
- Ivo Widmer
- WSL Swiss Federal Research Institute; Zürcherstrasse 111; Birmensdorf; CH-8903; Switzerland
| | - Francesco Dal Grande
- WSL Swiss Federal Research Institute; Zürcherstrasse 111; Birmensdorf; CH-8903; Switzerland
| | | | - Rolf Holderegger
- WSL Swiss Federal Research Institute; Zürcherstrasse 111; Birmensdorf; CH-8903; Switzerland
| | - Christine Keller
- WSL Swiss Federal Research Institute; Zürcherstrasse 111; Birmensdorf; CH-8903; Switzerland
| | - Vladimir S. Mikryukov
- Laboratory of Population and Community Ecotoxicology; Institute of Plant and Animal Ecology, Ural Branch; Russian Academy of Sciences; ul. Vos'mogo Marta 202; Ekaterinburg; 620144; Russia
| | - Christoph Scheidegger
- WSL Swiss Federal Research Institute; Zürcherstrasse 111; Birmensdorf; CH-8903; Switzerland
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Kohnen A, Richter I, Brandl R. No concordant phylogeographies of the rose gall wasp Diplolepis rosae (Hymenoptera, Cynipidae) and two associated parasitoids across Europe. PLoS One 2012; 7:e47156. [PMID: 23071742 PMCID: PMC3469489 DOI: 10.1371/journal.pone.0047156] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 09/12/2012] [Indexed: 11/18/2022] Open
Abstract
According to the Host-tracking Hypothesis, species of higher trophic levels with a close relationship to their hosts, such as parasites or parasitoids, are expected to show spatio-temporal phylogeographic patterns similar to those of their host. Alternatively, with ecological sorting, a subset of the local species pools might shift to a related host species, thereby disengaging common phylogeographic patterns. Here, we compare the phylogeographic structures of the cynipid rose gall wasp Diplolepis rosae across Europe and of two of its most common parasitoids, the wasps Orthopelma mediator and Glyphomerus stigma, by analysing the sequences of two gene fragments (COI and ITS 2). The phylogeographic structures of the three species associated with roses were incongruent. D. rosae had the lowest genetic diversity with one major clade, O. mediator showed the classical phylogeographic structure for Europe with one eastern and one western clade, and G. stigma had the highest diversity but no geographical structuring. This discordance of geographical patterns may be explained by 1) the dispersal propensity of adult parasitoids or 2) the parasitoids having the ability to switch to another host, while the primary host becomes rare or is even not available. Furthermore there was no indication that phylogenetic patterns were affected by Wolbachia infections. Our results document that communities of closely interacting species may be the result of idiosyncratic biogeographic histories.
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Affiliation(s)
- Annette Kohnen
- Department of Animal Ecology, Philipps-Universität Marburg, Marburg, Germany.
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34
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Piffaretti J, Vanlerberghe-Masutti F, Tayeh A, Clamens AL, D’Acier AC, Jousselin E. Molecular phylogeny reveals the existence of two sibling species in the aphid pest Brachycaudus helichrysi (Hemiptera: Aphididae). ZOOL SCR 2012. [DOI: 10.1111/j.1463-6409.2012.00531.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Belda E, Moya A, Bentley S, Silva FJ. Mobile genetic element proliferation and gene inactivation impact over the genome structure and metabolic capabilities of Sodalis glossinidius, the secondary endosymbiont of tsetse flies. BMC Genomics 2010; 11:449. [PMID: 20649993 PMCID: PMC3091646 DOI: 10.1186/1471-2164-11-449] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Accepted: 07/22/2010] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Genome reduction is a common evolutionary process in symbiotic and pathogenic bacteria. This process has been extensively characterized in bacterial endosymbionts of insects, where primary mutualistic bacteria represent the most extreme cases of genome reduction consequence of a massive process of gene inactivation and loss during their evolution from free-living ancestors. Sodalis glossinidius, the secondary endosymbiont of tsetse flies, contains one of the few complete genomes of bacteria at the very beginning of the symbiotic association, allowing to evaluate the relative impact of mobile genetic element proliferation and gene inactivation over the structure and functional capabilities of this bacterial endosymbiont during the transition to a host dependent lifestyle. RESULTS A detailed characterization of mobile genetic elements and pseudogenes reveals a massive presence of different types of prophage elements together with five different families of IS elements that have proliferated across the genome of Sodalis glossinidius at different levels. In addition, a detailed survey of intergenic regions allowed the characterization of 1501 pseudogenes, a much higher number than the 972 pseudogenes described in the original annotation. Pseudogene structure reveals a minor impact of mobile genetic element proliferation in the process of gene inactivation, with most of pseudogenes originated by multiple frameshift mutations and premature stop codons. The comparison of metabolic profiles of Sodalis glossinidius and tsetse fly primary endosymbiont Wiglesworthia glossinidia based on their whole gene and pseudogene repertoires revealed a novel case of pathway inactivation, the arginine biosynthesis, in Sodalis glossinidius together with a possible case of metabolic complementation with Wigglesworthia glossinidia for thiamine biosynthesis. CONCLUSIONS The complete re-analysis of the genome sequence of Sodalis glossinidius reveals novel insights in the evolutionary transition from a free-living ancestor to a host-dependent lifestyle, with a massive proliferation of mobile genetic elements mainly of phage origin although with minor impact in the process of gene inactivation that is taking place in this bacterial genome. The metabolic analysis of the whole endosymbiotic consortia of tsetse flies have revealed a possible phenomenon of metabolic complementation between primary and secondary endosymbionts that can contribute to explain the co-existence of both bacterial endosymbionts in the context of the tsetse host.
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Affiliation(s)
- Eugeni Belda
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València. Apartat 22085, València E-46071, Spain
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València. Apartat 22085, València E-46071, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Barcelona, Spain
- Unidad Mixta de Investigación de Genómica y Salud (Centro Superior de Investigación en Salud Pública, CSISP/Institut Cavanilles, Universitat de València, Spain
| | | | - Francisco J Silva
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València. Apartat 22085, València E-46071, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Barcelona, Spain
- Unidad Mixta de Investigación de Genómica y Salud (Centro Superior de Investigación en Salud Pública, CSISP/Institut Cavanilles, Universitat de València, Spain
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36
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Harris HL, Brennan LJ, Keddie BA, Braig HR. Bacterial symbionts in insects: balancing life and death. Symbiosis 2010. [DOI: 10.1007/s13199-010-0065-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Combination of molecular data support the existence of three main lineages in the phylogeny of aphids (Hemiptera: Aphididae) and the basal position of the subfamily Lachninae. Mol Phylogenet Evol 2010; 55:305-317. [DOI: 10.1016/j.ympev.2009.12.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Revised: 11/16/2009] [Accepted: 12/03/2009] [Indexed: 12/31/2022]
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38
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Symbiont genomics, our new tangled bank. Genomics 2010; 95:129-37. [PMID: 20053372 DOI: 10.1016/j.ygeno.2009.12.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Revised: 12/24/2009] [Accepted: 12/25/2009] [Indexed: 12/24/2022]
Abstract
Microbial symbionts inhabit the soma and surfaces of most multicellular species and instigate both beneficial and harmful infections. Despite their ubiquity, we are only beginning to resolve major patterns of symbiont ecology and evolution. Here, we summarize the history, current progress, and projected future of the study of microbial symbiont evolution throughout the tree of life. We focus on the recent surge of data that whole-genome sequencing has introduced into the field, in particular the links that are now being made between symbiotic lifestyle and molecular evolution. Post-genomic and systems biology approaches are also emerging as powerful techniques to investigate host-microbe interactions, both at the molecular level of the species interface and at the global scale. In parallel, next-generation sequencing technologies are allowing new questions to be addressed by providing access to population genomic data, as well as the much larger genomes of microbial eukaryotic symbionts and hosts. Throughout we describe the questions that these techniques are tackling and we conclude by listing a series of unanswered questions in microbial symbiosis that can potentially be addressed with the new technologies.
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Genetics and Evolution of Deep-Sea Chemosynthetic Bacteria and Their Invertebrate Hosts. TOPICS IN GEOBIOLOGY 2010. [DOI: 10.1007/978-90-481-9572-5_2] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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40
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Kölsch G, Matz-Grund C, Pedersen BV. Ultrastructural and molecular characterization of endosymbionts of the reed beetle genusMacroplea(Chrysomelidae, Donaciinae), and proposal of “CandidatusMacropleicola appendiculatae” and “CandidatusMacropleicola muticae”. Can J Microbiol 2009; 55:1250-60. [DOI: 10.1139/w09-085] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Intracellular bacterial symbionts are known from various insect groups, particularly from those feeding on unbalanced diets, where the bacteria provide essential nutrients to the host. In the case of reed beetles (Coleoptera: Chrysomelidae, Donaciinae), however, the endosymbionts appear to be associated with specialized “glands” that secrete a material used for the beetles’ unusual water-tight cocoon. These glands were discovered over a century ago, but the bacteria they contain have yet to be characterized and placed in a phylogenetic context. Here, we describe the ultrastructure of two endosymbiotic species (“ Candidatus Macropleicola appendiculatae” and “ Candidatus Macropleicola muticae”) that reside in cells of the Malpighian tubules of the reed beetle species Macroplea appendiculata and Macroplea mutica , respectively. Fluorescent in situ hybridization using oligonucleotides targeting the 16S rRNA gene specific to Macroplea symbionts verified the localization of the symbionts in these organs. Phylogenetic analysis of 16S rRNA placed “Candidatus Macropleicola” in a clade of typically endosymbiotic Enterobacteriaceae (γ-proteobacteria). Finally, we discuss the evidence available for the hypothesis that the beetle larvae use a secretion produced by the bacteria for the formation of an underwater cocoon.
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Affiliation(s)
- Gregor Kölsch
- Zoological Institute, Department of Molecular Evolutionary Biology, University of Hamburg, Martin-Luther-King-Platz 3, D-20146 Hamburg, Germany
- Zoological Institute, Animal Ecology, University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
- University of Copenhagen, Department of Biology, Universitetsparken 15, DK 2100 Copenhagen Ø, Denmark
| | - Corinna Matz-Grund
- Zoological Institute, Department of Molecular Evolutionary Biology, University of Hamburg, Martin-Luther-King-Platz 3, D-20146 Hamburg, Germany
- Zoological Institute, Animal Ecology, University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
- University of Copenhagen, Department of Biology, Universitetsparken 15, DK 2100 Copenhagen Ø, Denmark
| | - Bo V. Pedersen
- Zoological Institute, Department of Molecular Evolutionary Biology, University of Hamburg, Martin-Luther-King-Platz 3, D-20146 Hamburg, Germany
- Zoological Institute, Animal Ecology, University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
- University of Copenhagen, Department of Biology, Universitetsparken 15, DK 2100 Copenhagen Ø, Denmark
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Peccoud J, Simon JC, McLaughlin HJ, Moran NA. Post-Pleistocene radiation of the pea aphid complex revealed by rapidly evolving endosymbionts. Proc Natl Acad Sci U S A 2009; 106:16315-20. [PMID: 19805299 PMCID: PMC2752580 DOI: 10.1073/pnas.0905129106] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2009] [Indexed: 11/18/2022] Open
Abstract
Adaptation to different resources has the potential to cause rapid species diversification, but few studies have been able to quantify the time scale of recent adaptive radiations. The pea aphid, Acyrthosiphon pisum, a model of speciation for host-specialized parasites, consists of several biotypes (races or species) living on distinct legume hosts. To document this radiation, we used rapidly evolving sequences from Buchnera, the maternally transmitted bacterial endosymbiont of aphids. Analyses of Buchnera pseudogene sequences revealed that 11 host-associated biotypes sort mostly into distinct matrilines despite low sequence divergence. A calibration based on divergence times of 7 sequenced genomes of Buchnera allowed us to date the last maternal ancestor of these biotypes between 8,000 and 16,000 years, with a burst of diversification at an estimated 3,600-9,500 years. The recency of this diversification, which is supported by microsatellite data, implies that the pea aphid complex ranks among the most rapid adaptive radiations yet documented. This diversification coincides with post-Pleistocene warming and with the domestication and anthropogenic range expansion of several of the legume hosts of pea aphids. Thus, we hypothesize that the new availability or abundance of resources triggered a cascade of divergence events in this newly formed complex.
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Affiliation(s)
- Jean Peccoud
- Unité Mixte de Recherche 1099 Biologie des Organismes et des Populations appliquée à la Protection des Plantes, Institut National de la Recherche Agronomique, Domaine de la Motte BP 35327, 35653 Le Rheu cedex, France; and
| | - Jean-Christophe Simon
- Unité Mixte de Recherche 1099 Biologie des Organismes et des Populations appliquée à la Protection des Plantes, Institut National de la Recherche Agronomique, Domaine de la Motte BP 35327, 35653 Le Rheu cedex, France; and
| | - Heather J. McLaughlin
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85718
| | - Nancy A. Moran
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85718
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Abstract
Insect heritable symbionts have proven to be ubiquitous, based on molecular screening of various insect lineages. Recently, molecular and experimental approaches have yielded an immensely richer understanding of their diverse biological roles, resulting in a burgeoning research literature. Increasingly, commonalities and intermediates are being discovered between categories of symbionts once considered distinct: obligate mutualists that provision nutrients, facultative mutualists that provide protection against enemies or stress, and symbionts such as Wolbachia that manipulate reproductive systems. Among the most far-reaching impacts of widespread heritable symbiosis is that it may promote speciation by increasing reproductive and ecological isolation of host populations, and it effectively provides a means for transfer of genetic information among host lineages. In addition, insect symbionts provide some of the extremes of cellular genomes, including the smallest and the fastest evolving, raising new questions about the limits of evolution of life.
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Affiliation(s)
- Nancy A Moran
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA.
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Crandall ED, Jones ME, Muñoz MM, Akinronbi B, Erdmann MV, Barber PH. Comparative phylogeography of two seastars and their ectosymbionts within the Coral Triangle. Mol Ecol 2008; 17:5276-90. [PMID: 19067797 DOI: 10.1111/j.1365-294x.2008.03995.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eric D Crandall
- Department of Biological Sciences, Old Dominion University, Norfolk, VA 23529, USA.
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PECCOUD J, FIGUEROA CC, SILVA AX, RAMIREZ CC, MIEUZET L, BONHOMME J, STOECKEL S, PLANTEGENEST M, SIMON JC. Host range expansion of an introduced insect pest through multiple colonizations of specialized clones. Mol Ecol 2008; 17:4608-18. [DOI: 10.1111/j.1365-294x.2008.03949.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Werren JH, Baldo L, Clark ME. Wolbachia: master manipulators of invertebrate biology. Nat Rev Microbiol 2008; 6:741-51. [PMID: 18794912 DOI: 10.1038/nrmicro1969] [Citation(s) in RCA: 1718] [Impact Index Per Article: 107.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Four years of DNA barcoding: Current advances and prospects. INFECTION GENETICS AND EVOLUTION 2008; 8:727-36. [DOI: 10.1016/j.meegid.2008.05.005] [Citation(s) in RCA: 240] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2008] [Revised: 05/23/2008] [Accepted: 05/27/2008] [Indexed: 11/21/2022]
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Toft C, Fares MA. The evolution of the flagellar assembly pathway in endosymbiotic bacterial genomes. Mol Biol Evol 2008; 25:2069-76. [PMID: 18635679 DOI: 10.1093/molbev/msn153] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genome shrinkage is a common feature of most intracellular pathogens and symbionts. Reduction of genome sizes is among the best-characterized evolutionary ways of intracellular organisms to save and avoid maintaining expensive redundant biological processes. Endosymbiotic bacteria of insects are examples of biological economy taken to completion because their genomes are dramatically reduced. These bacteria are nonmotile, and their biochemical processes are intimately related to those of their host. Because of this relationship, many of the processes in these bacteria have been either lost or have suffered massive remodeling to adapt to the intracellular symbiotic lifestyle. An example of such changes is the flagellum structure that is essential for bacterial motility and infectivity. Our analysis indicates that genes responsible for flagellar assembly have been partially or totally lost in most intracellular symbionts of gamma-Proteobacteria. Comparative genomic analyses show that flagellar genes have been differentially lost in endosymbiotic bacteria of insects. Only proteins involved in protein export within the flagella assembly pathway (type III secretion system and the basal body) have been kept in most of the endosymbionts, whereas those involved in building the filament and hook of flagella have only in few instances been kept, indicating a change in the functional purpose of this pathway. In some endosymbionts, genes controlling protein-export switch and hook length have undergone functional divergence as shown through an analysis of their evolutionary dynamics. Based on our results, we suggest that genes of flagellum have diverged functionally as to specialize in the export of proteins from the bacterium to the host.
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Affiliation(s)
- Christina Toft
- Department of Genetics, Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin, Ireland
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Whiteman NK, Kimball RT, Parker PG. Co-phylogeography and comparative population genetics of the threatened Galápagos hawk and three ectoparasite species: ecology shapes population histories within parasite communities. Mol Ecol 2007; 16:4759-73. [PMID: 18028178 DOI: 10.1111/j.1365-294x.2007.03512.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Noah K Whiteman
- Department of Biology and Harris World Ecology Center, University of Missouri-St. Louis, St Louis, MO 63121, USA.
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Nelsen MP, Gargas A. Dissociation and horizontal transmission of codispersing lichen symbionts in the genus Lepraria (Lecanorales: Stereocaulaceae). THE NEW PHYTOLOGIST 2007; 177:264-275. [PMID: 17944828 DOI: 10.1111/j.1469-8137.2007.02241.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Lichenized fungi of the genus Lepraria lack ascomata and conidiomata, and symbionts codisperse by soredia. Here, it is determined whether algal symbionts associated with Lepraria are monophyletic, and whether fungal and algal phylogenies are congruent, both of which are indicative of a long-term, continuous association between symbionts. The internal transcribed spacer (ITS) and part of the actin type I locus were sequenced from algae associated with Lepraria, and the fungal ITS and mitochondrial small subunit (mtSSU) were sequenced from fungal symbionts. Phylogenetic analyses tested for monophyly of algal symbionts and congruence between algal and fungal phylogenies. Algae associated with Lepraria were not monophyletic, and identical algae associated with different Lepraria individuals and species. Algal and fungal phylogenies were not congruent, suggesting a lack of strict codiversification. This study suggests that associations between symbionts are not strictly maintained over evolutionary time. The ability to switch partners may provide benefits similar to genetic recombination, which may have helped this lineage persist.
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Affiliation(s)
- Matthew P Nelsen
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706-1381, USA
- Present address: Biotechnology Research Center, School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931-1295, USA
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