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Riccieri A, Spagoni L, Li M, Franchini P, Rossi MN, Fratini E, Cervelli M, Bologna MA, Mancini E. Comparative genomics provides insights into molecular adaptation to hypermetamorphosis and cantharidin metabolism in blister beetles (Coleoptera: Meloidae). Integr Zool 2024. [PMID: 38488179 DOI: 10.1111/1749-4877.12819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Blister beetles (Coleoptera: Meloidae) are currently subdivided into three subfamilies: Eleticinae (a basal group), Nemognathinae, and Meloinae. These are all characterized by the endogenous production of the defensive terpene cantharidin (CA), whereas the two most derived subfamilies show a hypermetamorphic larval development. Here, we provide novel draft genome assemblies of five species sampled across the three blister beetle subfamilies (Iselma pallidipennis, Stenodera caucasica, Zonitis immaculata, Lydus trimaculatus, and Mylabris variabilis) and performed a comparative analysis with other available Meloidae genomes and the closely-related canthariphilous species (Pyrochroa serraticornis) to disclose adaptations at a molecular level. Our results highlighted the expansion and selection of genes potentially responsible for CA production and metabolism, as well as its mobilization and vesicular compartmentalization. Furthermore, we observed adaptive selection patterns and gain of genes devoted to epigenetic regulation, development, and morphogenesis, possibly related to hypermetamorphosis. We hypothesize that most genetic adaptations occurred to support both CA biosynthesis and hypermetamorphosis, two crucial aspects of Meloidae biology that likely contributed to their evolutionary success.
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Affiliation(s)
| | | | - Ming Li
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Paolo Franchini
- Department of Ecological and Biological Sciences, Tuscia University, Viterbo, Italy
| | | | - Emiliano Fratini
- Division of Health Protection Technologies, Italian National Agency for Energy New Technologies and Sustainable Economic Development (ENEA), Roma, Italy
| | - Manuela Cervelli
- Department of Sciences, University of Roma Tre, Roma, Italy
- Neurodevelopment, Neurogenetics and Molecular Neurobiology Unit, IRCCS Fondazione Santa Lucia, Roma, Italy
| | - Marco A Bologna
- Department of Sciences, University of Roma Tre, Roma, Italy
- National Biodiversity Future Center (NBFC), Università di Palermo, Palermo, Italy
| | - Emiliano Mancini
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University, Roma, Italy
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2
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Colangelo P, Di Civita M, Bento CM, Franchini P, Meyer A, Orel N, das Neves LCBG, Mulandane FC, Almeida JS, Senczuk G, Pilla F, Sabatelli S. Genome-wide diversity, population structure and signatures of inbreeding in the African buffalo in Mozambique. BMC Ecol Evol 2024; 24:29. [PMID: 38433185 PMCID: PMC10910738 DOI: 10.1186/s12862-024-02209-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/01/2024] [Indexed: 03/05/2024] Open
Abstract
The African buffalo, Syncerus caffer, is a key species in African ecosystems. Like other large herbivores, it plays a fundamental role in its habitat acting as an ecosystem engineer. Over the last few centuries, African buffalo populations have declined because of range contraction and demographic decline caused by direct or indirect human activities. In Mozambique, historically home to large buffalo herds, the combined effect of colonialism and subsequent civil wars has created a critical situation that urgently needs to be addressed. In this study, we focused on the analysis of genetic diversity of Syncerus caffer caffer populations from six areas of Mozambique. Using genome-wide SNPs obtained from ddRAD sequencing, we examined the population structure across the country, estimated gene flow between areas under conservation management, including national reserves, and assessed the inbreeding coefficients. Our results indicate that all studied populations of Syncerus caffer caffer are genetically depauperate, with a high level of inbreeding. Moreover, buffaloes in Mozambique present a significant population differentiation between southern and central areas. We found an unexpected genotype in the Gorongosa National Park, where buffaloes experienced a dramatic population size reduction, that shares a common ancestry with southern populations of Catuane and Namaacha. This could suggest the past occurrence of a connection between southern and central Mozambique and that the observed population structuring could reflect recent events of anthropogenic origin. All the populations analysed showed high levels of homozygosity, likely due to extensive inbreeding over the last few decades, which could have increased the frequency of recessive deleterious alleles. Improving the resilience of Syncerus caffer caffer in Mozambique is essential for preserving the ecosystem integrity. The most viable approach appears to be facilitating translocations and re-establishing connectivity between isolated herds. However, our results also highlight the importance of assessing intraspecific genetic diversity when considering interventions aimed at enhancing population viability such as selecting suitable source populations.
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Affiliation(s)
- Paolo Colangelo
- National Research Council, Research Institute on Terrestrial Ecosystems, Via Salaria km 29.300, 00015, Montelibretti (Roma), Italy
| | - Marika Di Civita
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University, Viale dell'Università 32, 00185, Roma, Italy
| | - Carlos M Bento
- Natural History Museum, Eduardo Mondlane University, Travessia do Zambeze 104, 1100, Maputo, Mozambique
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany.
- Department of Ecological and Biological Sciences, University of Tuscia, Viale dell'Università s.n.c, 01100, Viterbo, Italy.
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Nadiya Orel
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Luis C B G das Neves
- Biotechnology Centre of Eduardo Mondlane University, Maputo, Mozambique
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Sciences, University of Pretoria, Pretoria, South Africa
| | | | | | - Gabriele Senczuk
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy
| | - Fabio Pilla
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy
| | - Simone Sabatelli
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University, Viale dell'Università 32, 00185, Roma, Italy
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3
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Franchini P, Fruciano C, Wood TJ, Shastry V, Goulson D, Hughes WOH, Jones JC. Limited introgression from non-native commercial strains and signatures of adaptation in the key pollinator Bombus terrestris. Mol Ecol 2023; 32:5709-5723. [PMID: 37789741 DOI: 10.1111/mec.17151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 09/16/2023] [Accepted: 09/20/2023] [Indexed: 10/05/2023]
Abstract
Insect pollination is fundamental for natural ecosystems and agricultural crops. The bumblebee species Bombus terrestris has become a popular choice for commercial crop pollination worldwide due to its effectiveness and ease of mass rearing. Bumblebee colonies are mass produced for the pollination of more than 20 crops and imported into over 50 countries including countries outside their native ranges, and the risk of invasion by commercial non-native bumblebees is considered an emerging issue for global conservation and biological diversity. Here, we use genome-wide data from seven wild populations close to and far from farms using commercial colonies, as well as commercial populations, to investigate the implications of utilizing commercial bumblebee subspecies in the UK. We find evidence for generally low levels of introgression between commercial and wild bees, with higher admixture proportions in the bees occurring close to farms. We identify genomic regions putatively involved in local and global adaptation, and genes in locally adaptive regions were found to be enriched for functions related to taste receptor activity, oxidoreductase activity, fatty acid and lipid biosynthetic processes. Despite more than 30 years of bumblebee colony importation into the UK, we observe low impact on the genetic integrity of local B. terrestris populations, but we highlight that even limited introgression might negatively affect locally adapted populations.
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Affiliation(s)
- Paolo Franchini
- Department of Ecological and Biological Sciences, University of Tuscia, Viale dell'Università s.n.c, Viterbo, Italy
| | - Carmelo Fruciano
- Institute for Marine Biological Resources and Biotechnology, National Research Council (IRBIM-CNR), Messina, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Thomas J Wood
- School of Life Sciences, University of Sussex, Brighton, UK
- Laboratory of Zoology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Vivaswat Shastry
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, Illinois, USA
| | - Dave Goulson
- School of Life Sciences, University of Sussex, Brighton, UK
| | | | - Julia C Jones
- School of Life Sciences, University of Sussex, Brighton, UK
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
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4
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Kratochwil CF, Liang Y, Gerwin J, Franchini P, Meyer A. Comparative ontogenetic and transcriptomic analyses shed light on color pattern divergence in cichlid fishes. Evol Dev 2022; 24:158-170. [PMID: 35971657 DOI: 10.1111/ede.12416] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/01/2022] [Accepted: 08/02/2022] [Indexed: 11/27/2022]
Abstract
Stripe patterns are a striking example for a repeatedly evolved color pattern. In the African adaptive radiations of cichlid fishes, stripes evolved several times independently. Previously, it has been suggested that regulatory evolution of a single gene, agouti-related-peptide 2 (agrp2), explains the evolutionary lability of this trait. Here, using a comparative transcriptomic approach, we performed comparisons between (adult) striped and nonstriped cichlid fishes of representatives of Lake Victoria and the two major clades of Lake Malawi (mbuna and non-mbuna lineage). We identify agrp2 to be differentially expressed across all pairwise comparisons, reaffirming its association with stripe pattern divergence. We therefore also provide evidence that agrp2 is associated with the loss of the nonstereotypic oblique stripe of Mylochromis mola. Complementary ontogenetic data give insights into the development of stripe patterns as well as vertical bar patterns that both develop postembryonically. Lastly, using the Lake Victoria species pair Haplochromis sauvagei and Pundamilia nyererei, we investigated the differences between melanic and non-melanic regions to identify additional genes that contribute to the formation of stripes. Expression differences-that most importantly also do not include agrp2-are surprisingly small. This suggests, at least in this species pair, that the stripe phenotype might be caused by a combination of more subtle transcriptomic differences or cellular changes without transcriptional correlates. In summary, our comprehensive analysis highlights the ontogenetic and adult transcriptomic differences between cichlids with different color patterns and serves as a basis for further investigation of the mechanistic underpinnings of their diversification.
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Affiliation(s)
- Claudius F Kratochwil
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Yipeng Liang
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Jan Gerwin
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Paolo Franchini
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Axel Meyer
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
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5
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Jax E, Franchini P, Sekar V, Ottenburghs J, Monné Parera D, Kellenberger RT, Magor KE, Müller I, Wikelski M, Kraus RHS. Comparative genomics of the waterfowl innate immune system. Mol Biol Evol 2022; 39:6649919. [PMID: 35880574 PMCID: PMC9356732 DOI: 10.1093/molbev/msac160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Animal species differ considerably in their ability to fight off infections. Finding the genetic basis of these differences is not easy, as the immune response is comprised of a complex network of proteins that interact with one another to defend the body against infection. Here, we used population- and comparative genomics to study the evolutionary forces acting on the innate immune system in natural hosts of the avian influenza virus (AIV). For this purpose, we used a combination of hybrid capture, next- generation sequencing and published genomes to examine genetic diversity, divergence, and signatures of selection in 127 innate immune genes at a micro- and macroevolutionary time scale in 26 species of waterfowl. We show across multiple immune pathways (AIV-, toll-like-, and RIG-I -like receptors signalling pathways) that genes involved genes in pathogen detection (i.e., toll-like receptors) and direct pathogen inhibition (i.e., antimicrobial peptides and interferon-stimulated genes), as well as host proteins targeted by viral antagonist proteins (i.e., mitochondrial antiviral-signaling protein, [MAVS]) are more likely to be polymorphic, genetically divergent, and under positive selection than other innate immune genes. Our results demonstrate that selective forces vary across innate immune signaling signalling pathways in waterfowl, and we present candidate genes that may contribute to differences in susceptibility and resistance to infectious diseases in wild birds, and that may be manipulated by viruses. Our findings improve our understanding of the interplay between host genetics and pathogens, and offer the opportunity for new insights into pathogenesis and potential drug targets.
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Affiliation(s)
- Elinor Jax
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany.,Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany.,Department of Biology and Biotechnologies "Charles Darwin", Sapienza University, Rome, Italy
| | - Vaishnovi Sekar
- Department of Biology, Lund University, Lund, Sweden.,Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Jente Ottenburghs
- Wildlife Ecology and Conservation Group, Wageningen University, Wageningen, The Netherlands.,Forest Ecology and Forest Management Group, Wageningen University, Wageningen, The Netherlands
| | | | - Roman T Kellenberger
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Katharine E Magor
- Department of Biological Sciences and Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada
| | - Inge Müller
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Martin Wikelski
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany
| | - Robert H S Kraus
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
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6
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Burrichter AG, Dörr S, Bergmann P, Haiß S, Keller A, Fournier C, Franchini P, Isono E, Schleheck D. Bacterial microcompartments for isethionate desulfonation in the taurine-degrading human-gut bacterium Bilophila wadsworthia. BMC Microbiol 2021; 21:340. [PMID: 34903181 PMCID: PMC8667426 DOI: 10.1186/s12866-021-02386-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/08/2021] [Indexed: 11/15/2022] Open
Abstract
Background Bilophila wadsworthia, a strictly anaerobic, sulfite-reducing bacterium and common member of the human gut microbiota, has been associated with diseases such as appendicitis and colitis. It is specialized on organosulfonate respiration for energy conservation, i.e., utilization of dietary and host-derived organosulfonates, such as taurine (2-aminoethansulfonate), as sulfite donors for sulfite respiration, producing hydrogen sulfide (H2S), an important intestinal metabolite that may have beneficial as well as detrimental effects on the colonic environment. Its taurine desulfonation pathway involves the glycyl radical enzyme (GRE) isethionate sulfite-lyase (IslAB), which cleaves isethionate (2-hydroxyethanesulfonate) into acetaldehyde and sulfite. Results We demonstrate that taurine metabolism in B. wadsworthia 3.1.6 involves bacterial microcompartments (BMCs). First, we confirmed taurine-inducible production of BMCs by proteomic, transcriptomic and ultra-thin sectioning and electron-microscopical analyses. Then, we isolated BMCs from taurine-grown cells by density-gradient ultracentrifugation and analyzed their composition by proteomics as well as by enzyme assays, which suggested that the GRE IslAB and acetaldehyde dehydrogenase are located inside of the BMCs. Finally, we are discussing the recycling of cofactors in the IslAB-BMCs and a potential shuttling of electrons across the BMC shell by a potential iron-sulfur (FeS) cluster-containing shell protein identified by sequence analysis. Conclusions We characterized a novel subclass of BMCs and broadened the spectrum of reactions known to take place enclosed in BMCs, which is of biotechnological interest. We also provided more details on the energy metabolism of the opportunistic pathobiont B. wadsworthia and on microbial H2S production in the human gut. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02386-w.
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Affiliation(s)
- Anna G Burrichter
- Department of Biology, University of Konstanz, Konstanz, Germany. .,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany. .,Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany.
| | - Stefanie Dörr
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Paavo Bergmann
- Electron Microscopy Centre, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Sebastian Haiß
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Anja Keller
- Department of Biology, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | | | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Erika Isono
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - David Schleheck
- Department of Biology, University of Konstanz, Konstanz, Germany. .,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany.
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7
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Mao Z, Gräßle F, Frey J, Franchini P, Schleheck D, Müller N, Schink B. Phosphitispora fastidiosa gen. nov. sp. nov., a new dissimilatory phosphite-oxidizing anaerobic bacterium isolated from anaerobic sewage sludge. Int J Syst Evol Microbiol 2021; 71. [PMID: 34878375 DOI: 10.1099/ijsem.0.005142] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A new strictly anaerobic bacterium, strain DYL19T, was enriched and isolated with phosphite as the sole electron donor and CO2 as a single carbon source and electron acceptor from anaerobic sewage sludge sampled at a sewage treatment plant in Constance, Germany. It is a Gram-positive, spore-forming, slightly curved, rod-shaped bacterium which oxidizes phosphite to phosphate while reducing CO2 to biomass and small amounts of acetate. Optimal growth is observed at 30 °C, pH 7.2, with a doubling time of 3 days. Beyond phosphite, no further inorganic or organic electron donor can be used, and no other electron acceptor than CO2 is reduced. Sulphate inhibits growth with phosphite and CO2. The G+C content is 45.95 mol%, and dimethylmenaquinone-7 is the only quinone detectable in the cells. On the basis of 16S rRNA gene sequence analysis and other chemotaxonomic properties, strain DYL19T is described as the type strain of a new genus and species, Phosphitispora fastidiosa gen. nov., sp. nov.
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Affiliation(s)
- Zhuqing Mao
- Department of Biology, University of Konstanz, Constance, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Constance, Germany
| | - Fabian Gräßle
- Department of Biology, University of Konstanz, Constance, Germany
| | - Jasmin Frey
- Department of Biology, University of Konstanz, Constance, Germany
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Constance, Germany
| | - David Schleheck
- Department of Biology, University of Konstanz, Constance, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Constance, Germany
| | - Nicolai Müller
- Department of Biology, University of Konstanz, Constance, Germany
| | - Bernhard Schink
- Department of Biology, University of Konstanz, Constance, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Constance, Germany
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8
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Levin B, Simonov E, Franchini P, Mugue N, Golubtsov A, Meyer A. Rapid adaptive radiation in a hillstream cyprinid fish in the East African White Nile River basin. Mol Ecol 2021; 30:5530-5550. [PMID: 34409661 DOI: 10.1111/mec.16130] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/02/2021] [Accepted: 08/11/2021] [Indexed: 12/14/2022]
Abstract
Adaptive radiation of freshwater fishes was long thought to be possible only in lacustrine environments. Recently, several studies have shown that riverine and stream environments also provide the ecological opportunity for adaptive radiation. In this study, we report on a riverine adaptive radiation of six ecomorphs of cyprinid hillstream fishes of the genus Garra in a river located in the Ethiopian Highlands in East Africa. Garra are predominantly highly specialized algae-scrapers with a wide distribution ranging from Southeast Asia to West Africa. However, adaptive phenotypic diversification in mouth type, sucking disc morphology, gut length and body shape have probably been found among these ecomorphs in a single Ethiopian river. Moreover, we found two novel phenotypes of Garra ("thick-lipped" and "predatory") that had not been discovered before in this species-rich genus (>160 species). Mitochondrial and genome-wide data suggest monophyletic, intrabasin evolution of Garra phenotypic diversity with signatures of gene flow from other local populations. Although sympatric ecomorphs are genetically distinct and can be considered to being young species as suggested by genome-wide single nucleotide polymorphism data, mitochondrial DNA was unable to identify any genetic structure suggesting recent and rapid speciation events. Some data suggest a hybrid origin of the novel "thick-lipped" ecomorph. Here we highlight how, driven by ecological opportunity, an ancestral trophically highly specialized lineage is likely to have rapidly radiated in a riverine environment promoted by the evolution of novel feeding strategies.
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Affiliation(s)
- Boris Levin
- Papanin Institute of Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia.,Zoological Institute of Russian Academy of Sciences, Cherepovets State University, St. Petersburg, Russia
| | - Evgeniy Simonov
- Institute of Environmental and Agricultural Biology (X-BIO), University of Tyumen, Tyumen, Russia
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Nikolai Mugue
- Koltzov Institute for Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander Golubtsov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
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9
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Fruciano C, Franchini P, Jones JC. Capturing the rapidly evolving study of adaptation. J Evol Biol 2021; 34:856-865. [PMID: 34145685 DOI: 10.1111/jeb.13871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/12/2021] [Accepted: 05/12/2021] [Indexed: 11/30/2022]
Abstract
Research on the genomics of adaptation is rapidly changing. In the last few decades, progress in this area has been driven by methodological advances, not only in the way increasingly large amounts of molecular data are generated (e.g. with high-throughput sequencing), but also in the way these data are analysed. This includes a growing appreciation and quantitative treatment of covariation among units within the same data type (e.g. genes) or across data types (e.g. genes and phenotypes). The development and adoption of more and more integrative tools have resulted in richer and more interesting empirical work. This special issue - comprising methodological, empirical, and review papers - aims to capture a 'snapshot' of this rapidly evolving field. We discuss in particular three important themes in the study of adaptation: the genetic architecture of adaptive variation, protein-coding and regulatory changes, and parallel evolution. We highlight how more traditional key themes in the study of genetic architecture (e.g. the number of loci underlying adaptive traits and the distribution of their effects) are now being complemented by other factors (e.g. how patterns of linkage and number of loci interact to affect the ability to adapt). Similarly, apart from addressing the relative importance of protein-coding and regulatory changes, we now have the tools to look in-depth at specific types of regulatory variation to gain a clearer picture of regulatory networks. Finally, parallel evolution has always been central to the study of adaptation, but now we are often able to address the question of whether - and to what extent - parallelism at the organismal or phenotypic level is matched by parallelism at the genetic level. Perhaps most importantly, we can now determine what mechanisms are driving parallelism (or lack thereof) across levels of biological organization. All these recent methodological developments open up new directions for future studies of adaptive changes across traits, levels of biological organization, demographic contexts and time scales.
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Affiliation(s)
- Carmelo Fruciano
- National Research Council - Institute of Marine Biological Resources and Biotechnologies, Messina, Italy.,Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, PSL Université Paris, Paris, France.,School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Julia C Jones
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
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10
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Gräßle F, Plugge C, Franchini P, Schink B, Schleheck D, Müller N. Pelorhabdus rhamnosifermentans gen. nov., sp. nov., a strictly anaerobic rhamnose degrader from freshwater lake sediment. Syst Appl Microbiol 2021; 44:126225. [PMID: 34198168 DOI: 10.1016/j.syapm.2021.126225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 05/14/2021] [Accepted: 06/08/2021] [Indexed: 10/21/2022]
Abstract
A rhamnose-degrading bacterium, strain BoRhaAT, was isolated from profundal sediment of Lake Constance in agar dilution series with l-rhamnose as substrate and with a background lawn of Methanospirillum hungatei. The isolated strain was a motile rod that stained Gram positive. Growth was observed within a pH range of 4.0-7.5 and a temperature range of 15-30°C. Fermentation products of rhamnose or glucose were acetate, propionate, ethanol, butyrate, and 1-propanol. The G+C content was 40.6% G+C. The dominant fatty acids are C16:1ω9c, i-C13:03OH, C16:0 and C17:1ω8c with 8-21% relative abundance. Polar lipids were glycolipids, phosphatidylethanolamine, phosphoaminolipid and other lipids, of which phosphatidylethanolamine was most abundant. The sequence of the 16S rRNA gene of the new isolate matches the sequence of its closest relative Anaerosporomusa subterranea to 92.4%. A comparison of the genome with this strain showed 60.2% genome-wide average amino acid identity (AAI), comparisons with other type strains showed a maximum of 62.7% AAI. Thus, the definition of a new genus is justified for which we propose the name Pelorhabdus. For strain BoRhaAT, we propose the name Pelorhabdus rhamnosifermentans gen. nov., sp. nov., with strain BoRhaAT (DSM 111565T = JCM 39158T) as the type strain.
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Affiliation(s)
- Fabian Gräßle
- Department of Biology, University of Konstanz, Konstanz, Germany; Research Training Group R3 - Resilience of Lake Ecosystems, University of Konstanz, Konstanz, Germany
| | - Caroline Plugge
- Research Training Group R3 - Resilience of Lake Ecosystems, University of Konstanz, Konstanz, Germany; Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Bernhard Schink
- Department of Biology, University of Konstanz, Konstanz, Germany; Research Training Group R3 - Resilience of Lake Ecosystems, University of Konstanz, Konstanz, Germany
| | - David Schleheck
- Department of Biology, University of Konstanz, Konstanz, Germany; Research Training Group R3 - Resilience of Lake Ecosystems, University of Konstanz, Konstanz, Germany
| | - Nicolai Müller
- Department of Biology, University of Konstanz, Konstanz, Germany; Research Training Group R3 - Resilience of Lake Ecosystems, University of Konstanz, Konstanz, Germany.
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11
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Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Kim J, Lee C, Ko BJ, Chaisson M, Gedman GL, Cantin LJ, Thibaud-Nissen F, Haggerty L, Bista I, Smith M, Haase B, Mountcastle J, Winkler S, Paez S, Howard J, Vernes SC, Lama TM, Grutzner F, Warren WC, Balakrishnan CN, Burt D, George JM, Biegler MT, Iorns D, Digby A, Eason D, Robertson B, Edwards T, Wilkinson M, Turner G, Meyer A, Kautt AF, Franchini P, Detrich HW, Svardal H, Wagner M, Naylor GJP, Pippel M, Malinsky M, Mooney M, Simbirsky M, Hannigan BT, Pesout T, Houck M, Misuraca A, Kingan SB, Hall R, Kronenberg Z, Sović I, Dunn C, Ning Z, Hastie A, Lee J, Selvaraj S, Green RE, Putnam NH, Gut I, Ghurye J, Garrison E, Sims Y, Collins J, Pelan S, Torrance J, Tracey A, Wood J, Dagnew RE, Guan D, London SE, Clayton DF, Mello CV, Friedrich SR, Lovell PV, Osipova E, Al-Ajli FO, Secomandi S, Kim H, Theofanopoulou C, Hiller M, Zhou Y, Harris RS, Makova KD, Medvedev P, Hoffman J, Masterson P, Clark K, Martin F, Howe K, Flicek P, Walenz BP, Kwak W, Clawson H, Diekhans M, Nassar L, Paten B, Kraus RHS, Crawford AJ, Gilbert MTP, Zhang G, Venkatesh B, Murphy RW, Koepfli KP, Shapiro B, Johnson WE, Di Palma F, Marques-Bonet T, Teeling EC, Warnow T, Graves JM, Ryder OA, Haussler D, O'Brien SJ, Korlach J, Lewin HA, Howe K, Myers EW, Durbin R, Phillippy AM, Jarvis ED. Towards complete and error-free genome assemblies of all vertebrate species. Nature 2021; 592:737-746. [PMID: 33911273 PMCID: PMC8081667 DOI: 10.1038/s41586-021-03451-0] [Citation(s) in RCA: 591] [Impact Index Per Article: 197.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 03/12/2021] [Indexed: 02/02/2023]
Abstract
High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.
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Affiliation(s)
- Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shane A McCarthy
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - Olivier Fedrigo
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
| | - Joana Damas
- The Genome Center, University of California Davis, Davis, CA, USA
| | - Giulio Formenti
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marcela Uliano-Silva
- Leibniz Institute for Zoo and Wildlife Research, Department of Evolutionary Genetics, Berlin, Germany
- Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
| | | | | | - Juwan Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Chul Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Byung June Ko
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Mark Chaisson
- University of Southern California, Los Angeles, CA, USA
| | - Gregory L Gedman
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Lindsey J Cantin
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Francoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Iliana Bista
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | | | - Bettina Haase
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
| | | | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- DRESDEN-concept Genome Center, Dresden, Germany
| | - Sadye Paez
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | | | - Sonja C Vernes
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
- School of Biology, University of St Andrews, St Andrews, UK
| | - Tanya M Lama
- University of Massachusetts Cooperative Fish and Wildlife Research Unit, Amherst, MA, USA
| | - Frank Grutzner
- School of Biological Science, The Environment Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Wesley C Warren
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | | | - Dave Burt
- UQ Genomics, University of Queensland, Brisbane, Queensland, Australia
| | - Julia M George
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Matthew T Biegler
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - David Iorns
- The Genetic Rescue Foundation, Wellington, New Zealand
| | - Andrew Digby
- Kākāpō Recovery, Department of Conservation, Invercargill, New Zealand
| | - Daryl Eason
- Kākāpō Recovery, Department of Conservation, Invercargill, New Zealand
| | - Bruce Robertson
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | | | - Mark Wilkinson
- Department of Life Sciences, Natural History Museum, London, UK
| | - George Turner
- School of Natural Sciences, Bangor University, Gwynedd, UK
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Andreas F Kautt
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - H William Detrich
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA, USA
| | - Hannes Svardal
- Department of Biology, University of Antwerp, Antwerp, Belgium
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Maximilian Wagner
- Institute of Biology, Karl-Franzens University of Graz, Graz, Austria
| | - Gavin J P Naylor
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology, Dresden, Germany
| | - Milan Malinsky
- Wellcome Sanger Institute, Cambridge, UK
- Zoological Institute, University of Basel, Basel, Switzerland
| | | | | | | | - Trevor Pesout
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | | | | | | | | | | | - Ivan Sović
- Pacific Biosciences, Menlo Park, CA, USA
- Digital BioLogic, Ivanić-Grad, Croatia
| | | | - Zemin Ning
- Wellcome Sanger Institute, Cambridge, UK
| | | | - Joyce Lee
- Bionano Genomics, San Diego, CA, USA
| | | | - Richard E Green
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
- Dovetail Genomics, Santa Cruz, CA, USA
| | | | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Jay Ghurye
- Dovetail Genomics, Santa Cruz, CA, USA
- Department of Computer Science, University of Maryland College Park, College Park, MD, USA
| | - Erik Garrison
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Ying Sims
- Wellcome Sanger Institute, Cambridge, UK
| | | | | | | | | | | | | | - Dengfeng Guan
- Department of Genetics, University of Cambridge, Cambridge, UK
- School of Computer Science and Technology, Center for Bioinformatics, Harbin Institute of Technology, Harbin, China
| | - Sarah E London
- Department of Psychology, Institute for Mind and Biology, University of Chicago, Chicago, IL, USA
| | - David F Clayton
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Samantha R Friedrich
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Peter V Lovell
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Ekaterina Osipova
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Farooq O Al-Ajli
- Monash University Malaysia Genomics Facility, School of Science, Selangor Darul Ehsan, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Selangor Darul Ehsan, Malaysia
- Qatar Falcon Genome Project, Doha, Qatar
| | | | - Heebal Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- eGnome, Inc., Seoul, Republic of Korea
| | | | - Michael Hiller
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt, Germany
- Senckenberg Research Institute, Frankfurt, Germany
- Goethe-University, Faculty of Biosciences, Frankfurt, Germany
| | | | - Robert S Harris
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Kateryna D Makova
- Department of Biology, Pennsylvania State University, University Park, PA, USA
- Center for Medical Genomics, Pennsylvania State University, University Park, PA, USA
- Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, PA, USA
| | - Paul Medvedev
- Center for Medical Genomics, Pennsylvania State University, University Park, PA, USA
- Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, PA, USA
- Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Jinna Hoffman
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Patrick Masterson
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Karen Clark
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Fergal Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Kevin Howe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Brian P Walenz
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Woori Kwak
- eGnome, Inc., Seoul, Republic of Korea
- Hoonygen, Seoul, Korea
| | - Hiram Clawson
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Luis Nassar
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Robert H S Kraus
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
| | - Andrew J Crawford
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Guojie Zhang
- China National Genebank, BGI-Shenzhen, Shenzhen, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, Singapore
| | - Robert W Murphy
- Centre for Biodiversity, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Klaus-Peter Koepfli
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC, USA
- The Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Suitland, MD, USA
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Federica Di Palma
- Department of Biological Sciences, Earlham Institute, University of East Anglia, Norwich, UK
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Tandy Warnow
- Department of Computer Science, The University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Oliver A Ryder
- San Diego Zoo Global, Escondido, CA, USA
- Department of Evolution, Behavior, and Ecology, University of California San Diego, La Jolla, CA, USA
| | - David Haussler
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Stephen J O'Brien
- Laboratory of Genomics Diversity-Center for Computer Technologies, ITMO University, St. Petersburg, Russian Federation
- Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, FL, USA
| | | | - Harris A Lewin
- The Genome Center, University of California Davis, Davis, CA, USA
- Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
- John Muir Institute for the Environment, University of California Davis, Davis, CA, USA
| | | | - Eugene W Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
- Center for Systems Biology, Dresden, Germany.
- Faculty of Computer Science, Technical University Dresden, Dresden, Germany.
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Cambridge, UK.
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Erich D Jarvis
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA.
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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12
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Xiong P, Hulsey CD, Fruciano C, Wong WY, Nater A, Kautt AF, Simakov O, Pippel M, Kuraku S, Meyer A, Franchini P. The comparative genomic landscape of adaptive radiation in crater lake cichlid fishes. Mol Ecol 2021; 30:955-972. [PMID: 33305470 PMCID: PMC8607476 DOI: 10.1111/mec.15774] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 11/21/2020] [Accepted: 11/30/2020] [Indexed: 12/13/2022]
Abstract
Factors ranging from ecological opportunity to genome composition might explain why only some lineages form adaptive radiations. While being rare, particular systems can provide natural experiments within an identical ecological setting where species numbers and phenotypic divergence in two closely related lineages are notably different. We investigated one such natural experiment using two de novo assembled and 40 resequenced genomes and asked why two closely related Neotropical cichlid fish lineages, the Amphilophus citrinellus species complex (Midas cichlids; radiating) and Archocentrus centrarchus (Flyer cichlid; nonradiating), have resulted in such disparate evolutionary outcomes. Although both lineages inhabit many of the same Nicaraguan lakes, whole-genome inferred demography suggests that priority effects are not likely to be the cause of the dissimilarities. Also, genome-wide levels of selection, transposable element dynamics, gene family expansion, major chromosomal rearrangements and the number of genes under positive selection were not markedly different between the two lineages. To more finely investigate particular subsets of the genome that have undergone adaptive divergence in Midas cichlids, we also examined if there was evidence for 'molecular pre-adaptation' in regions identified by QTL mapping of repeatedly diverging adaptive traits. Although most of our analyses failed to pinpoint substantial genomic differences, we did identify functional categories containing many genes under positive selection that provide candidates for future studies on the propensity of Midas cichlids to radiate. Our results point to a disproportionate role of local, rather than genome-wide factors underlying the propensity for these cichlid fishes to adaptively radiate.
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Affiliation(s)
- Peiwen Xiong
- Department of BiologyUniversity of KonstanzKonstanzGermany
| | - C. Darrin Hulsey
- Department of BiologyUniversity of KonstanzKonstanzGermany
- School of Biology and Environmental ScienceUniversity College DublinDublinIreland
| | - Carmelo Fruciano
- Department of BiologyUniversity of KonstanzKonstanzGermany
- National Research Council (CNR) – IRBIMMessinaItaly
| | - Wai Y. Wong
- Department of Molecular Evolution and DevelopmentUniversity of ViennaViennaAustria
| | | | - Andreas F. Kautt
- Department of BiologyUniversity of KonstanzKonstanzGermany
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMAUSA
| | - Oleg Simakov
- Department of Molecular Evolution and DevelopmentUniversity of ViennaViennaAustria
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Shigehiro Kuraku
- Laboratory for PhyloinformaticsRIKEN Center for Biosystems Dynamics Research (BDR)KobeJapan
| | - Axel Meyer
- Department of BiologyUniversity of KonstanzKonstanzGermany
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13
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Meyer A, Schloissnig S, Franchini P, Du K, Woltering JM, Irisarri I, Wong WY, Nowoshilow S, Kneitz S, Kawaguchi A, Fabrizius A, Xiong P, Dechaud C, Spaink HP, Volff JN, Simakov O, Burmester T, Tanaka EM, Schartl M. Giant lungfish genome elucidates the conquest of land by vertebrates. Nature 2021; 590:284-289. [PMID: 33461212 PMCID: PMC7875771 DOI: 10.1038/s41586-021-03198-8] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 01/06/2021] [Indexed: 01/29/2023]
Abstract
Lungfishes belong to lobe-fined fish (Sarcopterygii) that, in the Devonian period, 'conquered' the land and ultimately gave rise to all land vertebrates, including humans1-3. Here we determine the chromosome-quality genome of the Australian lungfish (Neoceratodus forsteri), which is known to have the largest genome of any animal. The vast size of this genome, which is about 14× larger than that of humans, is attributable mostly to huge intergenic regions and introns with high repeat content (around 90%), the components of which resemble those of tetrapods (comprising mainly long interspersed nuclear elements) more than they do those of ray-finned fish. The lungfish genome continues to expand independently (its transposable elements are still active), through mechanisms different to those of the enormous genomes of salamanders. The 17 fully assembled lungfish macrochromosomes maintain synteny to other vertebrate chromosomes, and all microchromosomes maintain conserved ancient homology with the ancestral vertebrate karyotype. Our phylogenomic analyses confirm previous reports that lungfish occupy a key evolutionary position as the closest living relatives to tetrapods4,5, underscoring the importance of lungfish for understanding innovations associated with terrestrialization. Lungfish preadaptations to living on land include the gain of limb-like expression in developmental genes such as hoxc13 and sall1 in their lobed fins. Increased rates of evolution and the duplication of genes associated with obligate air-breathing, such as lung surfactants and the expansion of odorant receptor gene families (which encode proteins involved in detecting airborne odours), contribute to the tetrapod-like biology of lungfishes. These findings advance our understanding of this major transition during vertebrate evolution.
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Affiliation(s)
- Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany.
| | | | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Kang Du
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA
| | | | - Iker Irisarri
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Wai Yee Wong
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | | | - Susanne Kneitz
- Biochemistry and Cell Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Akane Kawaguchi
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | | | - Peiwen Xiong
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Corentin Dechaud
- Institut de Génomique Fonctionnelle, École Normale Superieure, Université Claude Bernard, Lyon, France
| | - Herman P Spaink
- Faculty of Science, Universiteit Leiden, Leiden, The Netherlands
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle, École Normale Superieure, Université Claude Bernard, Lyon, France
| | - Oleg Simakov
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria.
| | | | - Elly M Tanaka
- Research Institute of Molecular Pathology (IMP), Vienna, Austria.
| | - Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany.
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA.
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14
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Fruciano C, Colangelo P, Castiglia R, Franchini P. Does divergence from normal patterns of integration increase as chromosomal fusions increase in number? A test on a house mouse hybrid zone. Curr Zool 2020; 66:527-538. [PMID: 33293931 PMCID: PMC7705516 DOI: 10.1093/cz/zoaa035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/03/2020] [Indexed: 11/14/2022] Open
Abstract
Chromosomal evolution is widely considered an important driver of speciation because it can promote the establishment of reproductive barriers. Karyotypic reorganization is also expected to affect the mean phenotype, as well as its development and patterns of phenotypic integration, through processes such as variation in genetic linkage between quantitative trait loci or between regulatory regions and their targets. Here we explore the relationship between chromosomal evolution and phenotypic integration by analyzing a well-known house mouse parapatric contact zone between a highly derived Robertsonian (Rb) race (2n = 22) and populations with standard karyotype (2n = 40). Populations with hybrid karyotypes are scattered throughout the hybrid zone connecting the two parental races. Using mandible shape data and geometric morphometrics, we test the hypothesis that patterns of integration progressively diverge from the “normal” integration pattern observed in the standard race as they accumulate Rb fusions. We find that the main pattern of integration observed between the posterior and anterior part of the mandible can be largely attributed to allometry. We find no support for a gradual increase in divergence from normal patterns of integration as fusions accumulate. Surprisingly, however, we find that the derived Rb race (2n = 22) has a distinct allometric trajectory compared with the standard race. Our results suggest that either individual fusions disproportionately affect patterns of integration or that there are mechanisms which “purge” extreme variants in hybrids (e.g. reduced fitness of hybrid shape).
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Affiliation(s)
- Carmelo Fruciano
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, PSL Université Paris, Paris, 75005, France.,School of Biological Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - Paolo Colangelo
- National Research Council, Research Institute on Terrestrial Ecosystems, Montelibretti (RM), 00010, Italy
| | - Riccardo Castiglia
- Department of Biology and Biotechnology "Charles Darwin", "La Sapienza" University of Rome, Rome, 00161, Italy
| | - Paolo Franchini
- Department of Biology, Lehrstuhl für Zoologie und Evolutionsbiologie, University of Konstanz, Konstanz, 78457, Germany
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15
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Kautt AF, Kratochwil CF, Nater A, Machado-Schiaffino G, Olave M, Henning F, Torres-Dowdall J, Härer A, Hulsey CD, Franchini P, Pippel M, Myers EW, Meyer A. Contrasting signatures of genomic divergence during sympatric speciation. Nature 2020; 588:106-111. [PMID: 33116308 PMCID: PMC7759464 DOI: 10.1038/s41586-020-2845-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/23/2020] [Indexed: 01/25/2023]
Abstract
The transition from 'well-marked varieties' of a single species into 'well-defined species'-especially in the absence of geographic barriers to gene flow (sympatric speciation)-has puzzled evolutionary biologists ever since Darwin1,2. Gene flow counteracts the buildup of genome-wide differentiation, which is a hallmark of speciation and increases the likelihood of the evolution of irreversible reproductive barriers (incompatibilities) that complete the speciation process3. Theory predicts that the genetic architecture of divergently selected traits can influence whether sympatric speciation occurs4, but empirical tests of this theory are scant because comprehensive data are difficult to collect and synthesize across species, owing to their unique biologies and evolutionary histories5. Here, within a young species complex of neotropical cichlid fishes (Amphilophus spp.), we analysed genomic divergence among populations and species. By generating a new genome assembly and re-sequencing 453 genomes, we uncovered the genetic architecture of traits that have been suggested to be important for divergence. Species that differ in monogenic or oligogenic traits that affect ecological performance and/or mate choice show remarkably localized genomic differentiation. By contrast, differentiation among species that have diverged in polygenic traits is genomically widespread and much higher overall, consistent with the evolution of effective and stable genome-wide barriers to gene flow. Thus, we conclude that simple trait architectures are not always as conducive to speciation with gene flow as previously suggested, whereas polygenic architectures can promote rapid and stable speciation in sympatry.
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Affiliation(s)
- Andreas F Kautt
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | | | - Alexander Nater
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Gonzalo Machado-Schiaffino
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Functional Biology, Area of Genetics, University of Oviedo, Oviedo, Spain
| | - Melisa Olave
- Department of Biology, University of Konstanz, Konstanz, Germany
- Argentine Dryland Research Institute of the National Council for Scientific Research (IADIZA-CONICET), Mendoza, Argentina
| | - Frederico Henning
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | | | - Andreas Härer
- Department of Biology, University of Konstanz, Konstanz, Germany
- Division of Biological Sciences, Section of Ecology, Behavior & Evolution, University of California San Diego, La Jolla, CA, USA
| | - C Darrin Hulsey
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | - Eugene W Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany.
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16
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M Real F, Haas SA, Franchini P, Xiong P, Simakov O, Kuhl H, Schöpflin R, Heller D, Moeinzadeh MH, Heinrich V, Krannich T, Bressin A, Hartmann MF, Wudy SA, Dechmann DKN, Hurtado A, Barrionuevo FJ, Schindler M, Harabula I, Osterwalder M, Hiller M, Wittler L, Visel A, Timmermann B, Meyer A, Vingron M, Jiménez R, Mundlos S, Lupiáñez DG. The mole genome reveals regulatory rearrangements associated with adaptive intersexuality. Science 2020; 370:208-214. [PMID: 33033216 DOI: 10.1126/science.aaz2582] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 04/19/2020] [Accepted: 08/17/2020] [Indexed: 01/01/2023]
Abstract
Linking genomic variation to phenotypical traits remains a major challenge in evolutionary genetics. In this study, we use phylogenomic strategies to investigate a distinctive trait among mammals: the development of masculinizing ovotestes in female moles. By combining a chromosome-scale genome assembly of the Iberian mole, Talpa occidentalis, with transcriptomic, epigenetic, and chromatin interaction datasets, we identify rearrangements altering the regulatory landscape of genes with distinct gonadal expression patterns. These include a tandem triplication involving CYP17A1, a gene controlling androgen synthesis, and an intrachromosomal inversion involving the pro-testicular growth factor gene FGF9, which is heterochronically expressed in mole ovotestes. Transgenic mice with a knock-in mole CYP17A1 enhancer or overexpressing FGF9 showed phenotypes recapitulating mole sexual features. Our results highlight how integrative genomic approaches can reveal the phenotypic impact of noncoding sequence changes.
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Affiliation(s)
- Francisca M Real
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute for Medical and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Stefan A Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Paolo Franchini
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Peiwen Xiong
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Oleg Simakov
- Department of Molecular Evolution and Development, University of Vienna, 1090 Vienna, Austria
| | - Heiner Kuhl
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Robert Schöpflin
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute for Medical and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - David Heller
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - M-Hossein Moeinzadeh
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Verena Heinrich
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Thomas Krannich
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Annkatrin Bressin
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Michaela F Hartmann
- Steroid Research & Mass Spectrometry Unit, Laboratory for Translational Hormone Analytics in Paediatric Endocrinology, Division of Paediatric Endocrinology & Diabetology, Center of Child and Adolescent Medicine, Justus Liebig University, Giessen, Germany
| | - Stefan A Wudy
- Steroid Research & Mass Spectrometry Unit, Laboratory for Translational Hormone Analytics in Paediatric Endocrinology, Division of Paediatric Endocrinology & Diabetology, Center of Child and Adolescent Medicine, Justus Liebig University, Giessen, Germany
| | - Dina K N Dechmann
- Department of Migration and Immuno-Ecology, Max Planck Institute for Animal Behavior, Radolfzell, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Alicia Hurtado
- Departamento de Genética, Universidad de Granada, Granada, Spain.,Instituto de Biotecnología, Centro de Investigación Biomédica, Universidad de Granada, Armilla, Granada, Spain
| | - Francisco J Barrionuevo
- Departamento de Genética, Universidad de Granada, Granada, Spain.,Instituto de Biotecnología, Centro de Investigación Biomédica, Universidad de Granada, Armilla, Granada, Spain
| | - Magdalena Schindler
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute for Medical and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Izabela Harabula
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Marco Osterwalder
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany.,Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Lars Wittler
- Department of Developmental Genetics, Transgenic Unit, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,U.S. Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA.,School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Bernd Timmermann
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Axel Meyer
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Rafael Jiménez
- Departamento de Genética, Universidad de Granada, Granada, Spain.,Instituto de Biotecnología, Centro de Investigación Biomédica, Universidad de Granada, Armilla, Granada, Spain
| | - Stefan Mundlos
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany. .,Institute for Medical and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Darío G Lupiáñez
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany. .,Institute for Medical and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Berlin, Germany.,Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
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17
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Frommeyer B, Fiedler AW, Oehler SR, Hanson BT, Loy A, Franchini P, Spiteller D, Schleheck D. Environmental and Intestinal Phylum Firmicutes Bacteria Metabolize the Plant Sugar Sulfoquinovose via a 6-Deoxy-6-sulfofructose Transaldolase Pathway. iScience 2020; 23:101510. [PMID: 32919372 PMCID: PMC7491151 DOI: 10.1016/j.isci.2020.101510] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 07/04/2020] [Accepted: 08/25/2020] [Indexed: 01/22/2023] Open
Abstract
Bacterial degradation of the sugar sulfoquinovose (SQ, 6-deoxy-6-sulfoglucose) produced by plants, algae, and cyanobacteria, is an important component of the biogeochemical carbon and sulfur cycles. Here, we reveal a third biochemical pathway for primary SQ degradation in an aerobic Bacillus aryabhattai strain. An isomerase converts SQ to 6-deoxy-6-sulfofructose (SF). A novel transaldolase enzyme cleaves the SF to 3-sulfolactaldehyde (SLA), while the non-sulfonated C3-(glycerone)-moiety is transferred to an acceptor molecule, glyceraldehyde phosphate (GAP), yielding fructose-6-phosphate (F6P). Intestinal anaerobic bacteria such as Enterococcus gilvus, Clostridium symbiosum, and Eubacterium rectale strains also express transaldolase pathway gene clusters during fermentative growth with SQ. The now three known biochemical strategies for SQ catabolism reflect adaptations to the aerobic or anaerobic lifestyle of the different bacteria. The occurrence of these pathways in intestinal (family) Enterobacteriaceae and (phylum) Firmicutes strains further highlights a potential importance of metabolism of green-diet SQ by gut microbial communities to, ultimately, hydrogen sulfide.
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Affiliation(s)
- Benjamin Frommeyer
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, 78457 Konstanz, Germany
| | | | | | - Buck T. Hanson
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090 Wien, Austria
| | - Alexander Loy
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090 Wien, Austria
| | - Paolo Franchini
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Dieter Spiteller
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, 78457 Konstanz, Germany
| | - David Schleheck
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, 78457 Konstanz, Germany
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18
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Franchini P, Kautt AF, Nater A, Antonini G, Castiglia R, Meyer A, Solano E. Reconstructing the Evolutionary History of Chromosomal Races on Islands: A Genome-Wide Analysis of Natural House Mouse Populations. Mol Biol Evol 2020; 37:2825-2837. [DOI: 10.1093/molbev/msaa118] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
AbstractChromosomal evolution is widely considered to be an important driver of speciation, as karyotypic reorganization can bring about the establishment of reproductive barriers between incipient species. One textbook example for genetic mechanisms of speciation are large-scale chromosomal rearrangements such as Robertsonian (Rb) fusions, a common class of structural variants that can drastically change the recombination landscape by suppressing crossing-over and influence gene expression by altering regulatory networks. Here, we explore the population structure and demographic patterns of a well-known house mouse Rb system in the Aeolian archipelago in Southern Italy using genome-wide data. By analyzing chromosomal regions characterized by different levels of recombination, we trace the evolutionary history of a set of Rb chromosomes occurring in different geographical locations and test whether chromosomal fusions have a single shared origin or occurred multiple times. Using a combination of phylogenetic and population genetic approaches, we find support for multiple, independent origins of three focal Rb chromosomes. The elucidation of the demographic patterns of the mouse populations within the Aeolian archipelago shows that an interplay between fixation of newly formed Rb chromosomes and hybridization events has contributed to shaping their current karyotypic distribution. Overall, our results illustrate that chromosome structure is much more dynamic than anticipated and emphasize the importance of large-scale chromosomal translocations in speciation.
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Affiliation(s)
- Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Andreas F Kautt
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA
| | - Alexander Nater
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Gloria Antonini
- Department of Biology and Biotechnology “Charles Darwin,” “La Sapienza” University of Rome, Rome, Italy
| | - Riccardo Castiglia
- Department of Biology and Biotechnology “Charles Darwin,” “La Sapienza” University of Rome, Rome, Italy
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Emanuela Solano
- Department of Biology and Biotechnology “Charles Darwin,” “La Sapienza” University of Rome, Rome, Italy
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19
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Raffini F, Schneider RF, Franchini P, Kautt AF, Meyer A. Diving into divergence: Differentiation in swimming performances, physiology and gene expression between locally‐adapted sympatric cichlid fishes. Mol Ecol 2019; 29:1219-1234. [DOI: 10.1111/mec.15304] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 10/24/2019] [Accepted: 11/08/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Francesca Raffini
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Konstanz Germany
- International Max Planck Research School (IMPRS) for Organismal Biology Max‐Planck‐Institut für Ornithologie Radolfzell Germany
- Max Planck Institute for Ornithology Radolfzell Germany
| | - Ralf F. Schneider
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Konstanz Germany
- International Max Planck Research School (IMPRS) for Organismal Biology Max‐Planck‐Institut für Ornithologie Radolfzell Germany
| | - Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Konstanz Germany
| | - Andreas F. Kautt
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Konstanz Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Konstanz Germany
- International Max Planck Research School (IMPRS) for Organismal Biology Max‐Planck‐Institut für Ornithologie Radolfzell Germany
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20
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Fruciano C, Meyer A, Franchini P. Divergent Allometric Trajectories in Gene Expression and Coexpression Produce Species Differences in Sympatrically Speciating Midas Cichlid Fish. Genome Biol Evol 2019; 11:1644-1657. [PMID: 31124568 PMCID: PMC6563553 DOI: 10.1093/gbe/evz108] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2019] [Indexed: 12/19/2022] Open
Abstract
The mechanisms of speciation without geographic isolation (i.e., sympatric speciation) remain debated. This is due in part to the fact that the genomic landscape that could promote or hinder species divergence in the presence of gene flow is still largely unknown. However, intensive research is now centered on understanding the genetic architecture of adaptive traits associated with this process as well as how gene expression might affect these traits. Here, using RNA-Seq data, we investigated gene expression of sympatrically speciating benthic and limnetic Neotropical cichlid fishes at two developmental stages. First, we identified groups of coexpressed genes (modules) at each stage. Although there are a few large and well-preserved modules, most of the other modules are not preserved across life stages. Second, we show that later in development more and larger coexpression modules are associated with divergence between benthic and limnetic fish compared with the earlier life stage. This divergence between benthic and limnetic fish in coexpression mirrors divergence in overall expression between benthic and limnetic fish, which is more pronounced later in life. Our results reveal that already at 1-day posthatch benthic and limnetic fish diverge in (co)expression, and that this divergence becomes more substantial when fish are free-swimming but still unlikely to have divergent swimming and feeding habits. More importantly, our study describes how the coexpression of several genes through development, as opposed to individual genes, is associated with benthic–limnetic species differences, and how two morphogenetic trajectories diverge as fish grow older.
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Affiliation(s)
- Carmelo Fruciano
- Department of Biology, University of Konstanz, Germany.,Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS UMR 8197, Paris, France
| | - Axel Meyer
- Department of Biology, University of Konstanz, Germany
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21
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Xiong P, Schneider RF, Hulsey CD, Meyer A, Franchini P. Conservation and novelty in the microRNA genomic landscape of hyperdiverse cichlid fishes. Sci Rep 2019; 9:13848. [PMID: 31554838 PMCID: PMC6761260 DOI: 10.1038/s41598-019-50124-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/05/2019] [Indexed: 12/23/2022] Open
Abstract
MicroRNAs (miRNAs) play crucial roles in the post-transcriptional control of messenger RNA (mRNA). These miRNA-mRNA regulatory networks are present in nearly all organisms and contribute to development, phenotypic divergence, and speciation. To examine the miRNA landscape of cichlid fishes, one of the most species-rich families of vertebrates, we profiled the expression of both miRNA and mRNA in a diverse set of cichlid lineages. Among these, we found that conserved miRNAs differ from recently arisen miRNAs (i.e. lineage specific) in average expression levels, number of target sites, sequence variability, and physical clustering patterns in the genome. Furthermore, conserved miRNA target sites tend to be enriched at the 5' end of protein-coding gene 3' UTRs. Consistent with the presumed regulatory role of miRNAs, we detected more negative correlations between the expression of miRNA-mRNA functional pairs than in random pairings. Finally, we provide evidence that novel miRNA targets sites are enriched in genes involved in protein synthesis pathways. Our results show how conserved and evolutionarily novel miRNAs differ in their contribution to the genomic landscape and highlight their particular evolutionary roles in the adaptive diversification of cichlids.
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Affiliation(s)
- Peiwen Xiong
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Ralf F Schneider
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
- Marine Ecology, Helmholtz-Zentrum für Ozeanforschung Kiel (GEOMAR), 24105 Kiel, Germany
| | - C Darrin Hulsey
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Axel Meyer
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Paolo Franchini
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany.
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22
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Franchini P, Xiong P, Fruciano C, Schneider RF, Woltering JM, Hulsey CD, Meyer A. MicroRNA Gene Regulation in Extremely Young and Parallel Adaptive Radiations of Crater Lake Cichlid Fish. Mol Biol Evol 2019; 36:2498-2511. [PMID: 31397871 DOI: 10.1093/molbev/msz168] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/03/2019] [Accepted: 07/17/2019] [Indexed: 12/20/2022] Open
Abstract
AbstractCichlid fishes provide textbook examples of explosive phenotypic diversification and sympatric speciation, thereby making them ideal systems for studying the molecular mechanisms underlying rapid lineage divergence. Despite the fact that gene regulation provides a critical link between diversification in gene function and speciation, many genomic regulatory mechanisms such as microRNAs (miRNAs) have received little attention in these rapidly diversifying groups. Therefore, we investigated the posttranscriptional regulatory role of miRNAs in the repeated sympatric divergence of Midas cichlids (Amphilophus spp.) from Nicaraguan crater lakes. Using miRNA and mRNA sequencing of embryos from five Midas species, we first identified miRNA binding sites in mRNAs and highlighted the presences of a surprising number of novel miRNAs in these adaptively radiating species. Then, through analyses of expression levels, we identified putative miRNA/gene target pairs with negatively correlated expression level that were consistent with the role of miRNA in downregulating mRNA. Furthermore, we determined that several miRNA/gene pairs show convergent expression patterns associated with the repeated benthic/limnetic sympatric species divergence implicating these miRNAs as potential molecular mechanisms underlying replicated sympatric divergence. Finally, as these candidate miRNA/gene pairs may play a central role in phenotypic diversification in these cichlids, we characterized the expression domains of selected miRNAs and their target genes via in situ hybridization, providing further evidence that miRNA regulation likely plays a role in the Midas cichlid adaptive radiation. These results provide support for the hypothesis that extremely quickly evolving miRNA regulation can contribute to rapid evolutionary divergence even in the presence of gene flow.
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Affiliation(s)
- Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Peiwen Xiong
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Carmelo Fruciano
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
- Institut de biologie de l’Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, PSL Université Paris, Paris, France
| | - Ralf F Schneider
- Marine Ecology, Helmholtz-Zentrum für Ozeanforschung Kiel (GEOMAR), Düsternbrooker Weg 20, Kiel, Germany
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Joost M Woltering
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Christopher Darrin Hulsey
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
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23
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Franchini P, Jones JC, Xiong P, Kneitz S, Gompert Z, Warren WC, Walter RB, Meyer A, Schartl M. Long-term experimental hybridisation results in the evolution of a new sex chromosome in swordtail fish. Nat Commun 2018; 9:5136. [PMID: 30510159 PMCID: PMC6277394 DOI: 10.1038/s41467-018-07648-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 11/13/2018] [Indexed: 01/13/2023] Open
Abstract
The remarkable diversity of sex determination mechanisms known in fish may be fuelled by exceptionally high rates of sex chromosome turnovers or transitions. However, the evolutionary causes and genomic mechanisms underlying this variation and instability are yet to be understood. Here we report on an over 30-year evolutionary experiment in which we tested the genomic consequences of hybridisation and selection between two Xiphophorus fish species with different sex chromosome systems. We find that introgression and imposing selection for pigmentation phenotypes results in the retention of an unexpectedly large maternally derived genomic region. During the hybridisation process, the sex-determining region of the X chromosome from one parental species was translocated to an autosome in the hybrids leading to the evolution of a new sex chromosome. Our results highlight the complexity of factors contributing to patterns observed in hybrid genomes, and we experimentally demonstrate that hybridisation can catalyze rapid evolution of a new sex chromosome. Fish have a high diversity of sex-determining systems, but the mechanisms responsible for this are not well understood. Here, Franchini et al. show how hybridization and backcrossing have led to the evolution of a new sex chromosome in swordtail fish during 30 years of experimental evolution.
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Affiliation(s)
- Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Julia C Jones
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany.,Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, 75123, Sweden
| | - Peiwen Xiong
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Susanne Kneitz
- Physiological Chemistry, Biozentrum, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | | | - Wesley C Warren
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, 63108, MO, USA
| | - Ronald B Walter
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, 78666-4616, TX, USA
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany. .,Radcliffe Institute for Advanced Study, Harvard University, 9 Garden Street, Cambridge, MA, 02139, USA.
| | - Manfred Schartl
- Physiological Chemistry, Biozentrum, University of Würzburg, Am Hubland, 97074, Würzburg, Germany. .,Comprehensive Cancer Centre, University Clinic Würzburg, Josef Schneider Straße 6, 97074, Würzburg, Germany. .,Hagler Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, TX, 77843, USA.
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24
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Burrichter A, Denger K, Franchini P, Huhn T, Müller N, Spiteller D, Schleheck D. Anaerobic Degradation of the Plant Sugar Sulfoquinovose Concomitant With H 2S Production: Escherichia coli K-12 and Desulfovibrio sp. Strain DF1 as Co-culture Model. Front Microbiol 2018; 9:2792. [PMID: 30546350 PMCID: PMC6278857 DOI: 10.3389/fmicb.2018.02792] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/30/2018] [Indexed: 11/13/2022] Open
Abstract
Sulfoquinovose (SQ, 6-deoxy-6-sulfoglucose) is produced by plants and other phototrophs and its biodegradation is a relevant component of the biogeochemical carbon and sulfur cycles. SQ is known to be degraded by aerobic bacterial consortia in two tiers via C3-organosulfonates as transient intermediates to CO2, water and sulfate. In this study, we present a first laboratory model for anaerobic degradation of SQ by bacterial consortia in two tiers to acetate and hydrogen sulfide (H2S). For the first tier, SQ-degrading Escherichia coli K-12 was used. It catalyzes the fermentation of SQ to 2,3-dihydroxypropane-1-sulfonate (DHPS), succinate, acetate and formate, thus, a novel type of mixed-acid fermentation. It employs the characterized SQ Embden-Meyerhof-Parnas pathway, as confirmed by mutational and proteomic analyses. For the second tier, a DHPS-degrading Desulfovibrio sp. isolate from anaerobic sewage sludge was used, strain DF1. It catalyzes another novel fermentation, of the DHPS to acetate and H2S. Its DHPS desulfonation pathway was identified by differential proteomics and demonstrated by heterologously produced enzymes: DHPS is oxidized via 3-sulfolactaldehyde to 3-sulfolactate (SL) by two NAD+-dependent dehydrogenases (DhpA, SlaB); the SL is cleaved by an SL sulfite-lyase known from aerobic bacteria (SuyAB) to pyruvate and sulfite. The pyruvate is oxidized to acetate, while the sulfite is used as electron acceptor in respiration and reduced to H2S. In conclusion, anaerobic sulfidogenic SQ degradation was demonstrated as a novel link in the biogeochemical sulfur cycle. SQ is also a constituent of the green-vegetable diet of herbivores and omnivores and H2S production in the intestinal microbiome has many recognized and potential contributions to human health and disease. Hence, it is important to examine bacterial SQ degradation also in the human intestinal microbiome, in relation to H2S production, dietary conditions and human health.
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Affiliation(s)
- Anna Burrichter
- Department of Biology, University of Konstanz, Konstanz, Germany.,The Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Karin Denger
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Thomas Huhn
- The Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany.,Department of Chemistry, University of Konstanz, Konstanz, Germany
| | - Nicolai Müller
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Dieter Spiteller
- Department of Biology, University of Konstanz, Konstanz, Germany.,The Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - David Schleheck
- Department of Biology, University of Konstanz, Konstanz, Germany.,The Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
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25
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Irisarri I, Singh P, Koblmüller S, Torres-Dowdall J, Henning F, Franchini P, Fischer C, Lemmon AR, Lemmon EM, Thallinger GG, Sturmbauer C, Meyer A. Phylogenomics uncovers early hybridization and adaptive loci shaping the radiation of Lake Tanganyika cichlid fishes. Nat Commun 2018; 9:3159. [PMID: 30089797 PMCID: PMC6082878 DOI: 10.1038/s41467-018-05479-9] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 05/30/2018] [Indexed: 11/21/2022] Open
Abstract
Lake Tanganyika is the oldest and phenotypically most diverse of the three East African cichlid fish adaptive radiations. It is also the cradle for the younger parallel haplochromine cichlid radiations in Lakes Malawi and Victoria. Despite its evolutionary significance, the relationships among the main Lake Tanganyika lineages remained unresolved, as did the general timescale of cichlid evolution. Here, we disentangle the deep phylogenetic structure of the Lake Tanganyika radiation using anchored phylogenomics and uncover hybridization at its base, as well as early in the haplochromine radiation. This suggests that hybridization might have facilitated these speciation bursts. Time-calibrated trees support that the radiation of Tanganyika cichlids coincided with lake formation and that Gondwanan vicariance concurred with the earliest splits in the cichlid family tree. Genes linked to key innovations show signals of introgression or positive selection following colonization of lake habitats and species' dietary adaptations are revealed as major drivers of colour vision evolution. These findings shed light onto the processes shaping the evolution of adaptive radiations.
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Affiliation(s)
- Iker Irisarri
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78457, Germany
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, 2, Madrid, 28006, Spain
| | - Pooja Singh
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78457, Germany
- Institute of Biology, University of Graz, Universitätsplatz 2, Graz, 8010, Austria
| | - Stephan Koblmüller
- Institute of Biology, University of Graz, Universitätsplatz 2, Graz, 8010, Austria
| | - Julián Torres-Dowdall
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78457, Germany
| | - Frederico Henning
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78457, Germany
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Ilha do Fundão, Rio de Janeiro, 21944-970, Brazil
| | - Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78457, Germany
| | - Christoph Fischer
- Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14, Graz, 8010, Austria
- OMICS Center Graz, BioTechMed Graz, Stiftingtalstraße 24, Graz, 8010, Austria
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL, 32306, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Biomedical Research Facility, Tallahassee, FL, 32306, USA
| | - Gerhard G Thallinger
- Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14, Graz, 8010, Austria
- OMICS Center Graz, BioTechMed Graz, Stiftingtalstraße 24, Graz, 8010, Austria
| | - Christian Sturmbauer
- Institute of Biology, University of Graz, Universitätsplatz 2, Graz, 8010, Austria.
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78457, Germany.
- Radcliffe Institute for Advanced Study, Harvard University, Cambridge, 02138, MA, USA.
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26
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Abstract
Background Post-transcriptional regulation is crucial for the control of eukaryotic gene expression and might contribute to adaptive divergence. The three prime untranslated regions (3’ UTRs), that are located downstream of protein-coding sequences, play important roles in post-transcriptional regulation. These regions contain functional elements that influence the fate of mRNAs and could be exceptionally important in groups such as rapidly evolving cichlid fishes. Results To examine cichlid 3’ UTR evolution, we 1) identified gene features in nine teleost genomes and 2) performed comparative analyses to assess evolutionary variation in length, functional motifs, and evolutionary rates of 3’ UTRs. In all nine teleost genomes, we found a smaller proportion of repetitive elements in 3’ UTRs than in the whole genome. We found that the 3’ UTRs in cichlids tend to be longer than those in non-cichlids, and this was associated, on average, with one more miRNA target per gene in cichlids. Moreover, we provided evidence that 3’ UTRs on average have evolved faster in cichlids than in non-cichlids. Finally, analyses of gene function suggested that both the top 5% longest and 5% most rapidly evolving 3’ UTRs in cichlids tended to be involved in ribosome-associated pathways and translation. Conclusions Our results reveal novel patterns of evolution in the 3’ UTRs of teleosts in general and cichlids in particular. The data suggest that 3’ UTRs might serve as important meta-regulators, regulators of other mechanisms governing post-transcriptional regulation, especially in groups like cichlids that have undergone extremely fast rates of phenotypic diversification and speciation. Electronic supplementary material The online version of this article (10.1186/s12864-018-4821-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Peiwen Xiong
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - C Darrin Hulsey
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Axel Meyer
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany.,Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA, 02138, USA
| | - Paolo Franchini
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany.
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27
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Lee HJ, Schneider RF, Manousaki T, Kang JH, Lein E, Franchini P, Meyer A. Lateralized Feeding Behavior is Associated with Asymmetrical Neuroanatomy and Lateralized Gene Expressions in the Brain in Scale-Eating Cichlid Fish. Genome Biol Evol 2017; 9:3122-3136. [PMID: 29069363 PMCID: PMC5737854 DOI: 10.1093/gbe/evx218] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2017] [Indexed: 12/20/2022] Open
Abstract
Lateralized behavior ("handedness") is unusual, but consistently found across diverse animal lineages, including humans. It is thought to reflect brain anatomical and/or functional asymmetries, but its neuro-molecular mechanisms remain largely unknown. Lake Tanganyika scale-eating cichlid fish, Perissodus microlepis show pronounced asymmetry in their jaw morphology as well as handedness in feeding behavior-biting scales preferentially only from one or the other side of their victims. This makes them an ideal model in which to investigate potential laterality in neuroanatomy and transcription in the brain in relation to behavioral handedness. After determining behavioral handedness in P. microlepis (preferred attack side), we estimated the volume of the hemispheres of brain regions and captured their gene expression profiles. Our analyses revealed that the degree of behavioral handedness is mirrored at the level of neuroanatomical asymmetry, particularly in the tectum opticum. Transcriptome analyses showed that different brain regions (tectum opticum, telencephalon, hypothalamus, and cerebellum) display distinct expression patterns, potentially reflecting their developmental interrelationships. For numerous genes in each brain region, their extent of expression differences between hemispheres was found to be correlated with the degree of behavioral lateralization. Interestingly, the tectum opticum and telencephalon showed divergent biases on the direction of up- or down-regulation of the laterality candidate genes (e.g., grm2) in the hemispheres, highlighting the connection of handedness with gene expression profiles and the different roles of these brain regions. Hence, handedness in predation behavior may be caused by asymmetric size of brain hemispheres and also by lateralized gene expressions in the brain.
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Affiliation(s)
- Hyuk Je Lee
- Department of Biology, Lehrstuhl für Zoologie und Evolutionsbiologie, University of Konstanz, Konstanz, Germany
- Present address: Molecular Ecology and Evolution Laboratory, Department of Biological Science, Sangji University, Wonju, Korea
| | - Ralf F Schneider
- Department of Biology, Lehrstuhl für Zoologie und Evolutionsbiologie, University of Konstanz, Konstanz, Germany
| | - Tereza Manousaki
- Department of Biology, Lehrstuhl für Zoologie und Evolutionsbiologie, University of Konstanz, Konstanz, Germany
- Present address: Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology, Biotechnology, and Aquaculture (IMBBC), Heraklion, Greece
| | - Ji Hyoun Kang
- Department of Biology, Lehrstuhl für Zoologie und Evolutionsbiologie, University of Konstanz, Konstanz, Germany
- Present address: Korean Entomological Institute, Korea University, Seoul, Korea
| | - Etienne Lein
- Department of Biology, Lehrstuhl für Zoologie und Evolutionsbiologie, University of Konstanz, Konstanz, Germany
- Present address: Department of Collective Behaviour, Max Planck Institute for Ornithology and University of Konstanz, Konstanz, Germany
| | - Paolo Franchini
- Department of Biology, Lehrstuhl für Zoologie und Evolutionsbiologie, University of Konstanz, Konstanz, Germany
| | - Axel Meyer
- Department of Biology, Lehrstuhl für Zoologie und Evolutionsbiologie, University of Konstanz, Konstanz, Germany
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28
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Franchini P, Irisarri I, Fudickar A, Schmidt A, Meyer A, Wikelski M, Partecke J. Animal tracking meets migration genomics: transcriptomic analysis of a partially migratory bird species. Mol Ecol 2017; 26:3204-3216. [PMID: 28316119 DOI: 10.1111/mec.14108] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 03/10/2017] [Accepted: 03/10/2017] [Indexed: 12/23/2022]
Abstract
Seasonal migration is a widespread phenomenon, which is found in many different lineages of animals. This spectacular behaviour allows animals to avoid seasonally adverse environmental conditions to exploit more favourable habitats. Migration has been intensively studied in birds, which display astonishing variation in migration strategies, thus providing a powerful system for studying the ecological and evolutionary processes that shape migratory behaviour. Despite intensive research, the genetic basis of migration remains largely unknown. Here, we used state-of-the-art radio-tracking technology to characterize the migratory behaviour of a partially migratory population of European blackbirds (Turdus merula) in southern Germany. We compared gene expression of resident and migrant individuals using high-throughput transcriptomics in blood samples. Analyses of sequence variation revealed a nonsignificant genetic structure between blackbirds differing by their migratory phenotype. We detected only four differentially expressed genes between migrants and residents, which might be associated with hyperphagia, moulting and enhanced DNA replication and transcription. The most pronounced changes in gene expression occurred between migratory birds depending on when, in relation to their date of departure, blood was collected. Overall, the differentially expressed genes detected in this analysis may play crucial roles in determining the decision to migrate, or in controlling the physiological processes required for the onset of migration. These results provide new insights into, and testable hypotheses for, the molecular mechanisms controlling the migratory phenotype and its underlying physiological mechanisms in blackbirds and other migratory bird species.
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Affiliation(s)
- Paolo Franchini
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Iker Irisarri
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Adam Fudickar
- Department of Migration and Immuno-Ecology, Max Planck Institute for Ornithology, 78315, Radolfzell, Germany
| | - Andreas Schmidt
- Department of Migration and Immuno-Ecology, Max Planck Institute for Ornithology, 78315, Radolfzell, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Martin Wikelski
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany.,Department of Migration and Immuno-Ecology, Max Planck Institute for Ornithology, 78315, Radolfzell, Germany
| | - Jesko Partecke
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany.,Department of Migration and Immuno-Ecology, Max Planck Institute for Ornithology, 78315, Radolfzell, Germany
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29
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Franchini P, Monné Parera D, Kautt AF, Meyer A. quaddRAD: a new high-multiplexing and PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a nonradiating cichlid lineage. Mol Ecol 2017; 26:2783-2795. [PMID: 28247584 DOI: 10.1111/mec.14077] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 02/20/2017] [Accepted: 02/21/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Paolo Franchini
- Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstraße 10 78457 Konstanz Germany
| | - Daniel Monné Parera
- Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstraße 10 78457 Konstanz Germany
| | - Andreas F. Kautt
- Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstraße 10 78457 Konstanz Germany
| | - Axel Meyer
- Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstraße 10 78457 Konstanz Germany
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30
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Franchini P, Monné Parera D, Kautt AF, Meyer A. quaddRAD: a new high-multiplexing and PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a nonradiating cichlid lineage. Mol Ecol 2017. [PMID: 28247584 DOI: 10.1111/mec.14077.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The identification of thousands of variants across the genomes and their accurate genotyping are crucial for estimating the genetic parameters needed to address a host of molecular ecological and evolutionary questions. With rapid advances of massively parallel high-throughput sequencing technologies, several methods have recently been developed to access genomewide data on population variation. One of the most successful and widely used techniques relies on the combination of restriction enzymes and sequencing-by-synthesis: restriction-site-associated DNA sequencing (RADSeq). We developed a new, more time- and cost-efficient double-digest RAD paired-end protocol (quaddRAD) that simplifies and speeds up the identification of PCR duplicates and permits large-scale multiplexing. Assessing its performance on a technical data set, we also applied the quaddRAD method on population samples of a Neotropical cichlid fish lineage (Archocentrus centrarchus) to assess its genetic structure and demographic history. While we identified allopatric interlake genetic divergence, most likely driven by drift, no signature of sympatric divergence was detected. This differs from what has been observed in the clade of Midas cichlids (Amphilophus citrinellus spp.), another cichlid lineage that inhabits the same lakes and shares a similar demographic history, but has evolved into small-scale adaptive radiations via sympatric speciation. We demonstrate that quaddRAD is a robust and efficient method for genotyping a massive number and widely overlapping set of loci with high accuracy. Furthermore, the results on A. centrarchus open new research avenues providing an ideal system to investigate genome-level mechanisms that could alter the speciation potential of different but closely related cichlid lineages.
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Affiliation(s)
- Paolo Franchini
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Daniel Monné Parera
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Andreas F Kautt
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Axel Meyer
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
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31
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Fruciano C, Franchini P, Kovacova V, Elmer KR, Henning F, Meyer A. Genetic linkage of distinct adaptive traits in sympatrically speciating crater lake cichlid fish. Nat Commun 2016; 7:12736. [PMID: 27597183 PMCID: PMC5025864 DOI: 10.1038/ncomms12736] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 07/28/2016] [Indexed: 01/03/2023] Open
Abstract
Our understanding of how biological diversity arises is limited, especially in the case of speciation in the face of gene flow. Here we investigate the genomic basis of adaptive traits, focusing on a sympatrically diverging species pair of crater lake cichlid fishes. We identify the main quantitative trait loci (QTL) for two eco-morphological traits: body shape and pharyngeal jaw morphology. These traits diverge in parallel between benthic and limnetic species in the repeated adaptive radiations of this and other fish lineages. Remarkably, a single chromosomal region contains the highest effect size QTL for both traits. Transcriptomic data show that the QTL regions contain genes putatively under selection. Independent population genomic data corroborate QTL regions as areas of high differentiation between the sympatric sister species. Our results provide empirical support for current theoretical models that emphasize the importance of genetic linkage and pleiotropy in facilitating rapid divergence in sympatry.
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Affiliation(s)
- Carmelo Fruciano
- Lehrstuhl für Zoologie and Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.,School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland 4000, Australia
| | - Paolo Franchini
- Lehrstuhl für Zoologie and Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Viera Kovacova
- Lehrstuhl für Zoologie and Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.,Department for Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Kathryn R Elmer
- Lehrstuhl für Zoologie and Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.,Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences University of Glasgow, Glasgow G12 8QQ, UK
| | - Frederico Henning
- Lehrstuhl für Zoologie and Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie and Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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32
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Raffini F, Fruciano C, Franchini P, Meyer A. Towards understanding the genetic basis of mouth asymmetry in the scale-eating cichlidPerissodus microlepis. Mol Ecol 2016; 26:77-91. [DOI: 10.1111/mec.13699] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 04/29/2016] [Accepted: 05/09/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Francesca Raffini
- Lehrstuhl für Zoologie und Evolutionsbiologie; Department of Biology; University of Konstanz; Universitätsstrasse 10 78464 Konstanz Germany
- International Max Planck Research School (IMPRS) for Organismal Biology; Max-Planck-Institut für Ornithologie; Am Obstberg 1 78315 Radolfzell Germany
| | - Carmelo Fruciano
- Lehrstuhl für Zoologie und Evolutionsbiologie; Department of Biology; University of Konstanz; Universitätsstrasse 10 78464 Konstanz Germany
| | - Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie; Department of Biology; University of Konstanz; Universitätsstrasse 10 78464 Konstanz Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie; Department of Biology; University of Konstanz; Universitätsstrasse 10 78464 Konstanz Germany
- International Max Planck Research School (IMPRS) for Organismal Biology; Max-Planck-Institut für Ornithologie; Am Obstberg 1 78315 Radolfzell Germany
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33
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Franchini P, Xiong P, Fruciano C, Meyer A. The Role of microRNAs in the Repeated Parallel Diversification of Lineages of Midas Cichlid Fish from Nicaragua. Genome Biol Evol 2016; 8:1543-55. [PMID: 27189980 PMCID: PMC4898811 DOI: 10.1093/gbe/evw097] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Cichlid fishes are an ideal model system for studying biological diversification because they provide textbook examples of rapid speciation. To date, there has been little focus on the role of gene regulation during cichlid speciation. However, in recent years, gene regulation has been recognized as a powerful force linking diversification in gene function to speciation. Here, we investigated the potential role of miRNA regulation in the diversification of six cichlid species of the Midas cichlid lineage (Amphilophus spp.) inhabiting the Nicaraguan crater lakes. Using several genomic resources, we inferred 236 Midas miRNA genes that were used to predict the miRNA target sites on 8,232 Midas 3′-UTRs. Using population genomic calculations of SNP diversity, we found the miRNA genes to be more conserved than protein coding genes. In contrast to what has been observed in other cichlid fish, but similar to what has been typically found in other groups, we observed genomic signatures of purifying selection on the miRNA targets by comparing these sites with the less conserved nontarget portion of the 3′-UTRs. However, in one species pair that has putatively speciated sympatrically in crater Lake Apoyo, we recovered a different pattern of relaxed purifying selection and high genetic divergence at miRNA targets. Our results suggest that sequence evolution at miRNA binding sites could be a critical genomic mechanism contributing to the rapid phenotypic evolution of Midas cichlids.
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Affiliation(s)
- Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Peiwen Xiong
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Carmelo Fruciano
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany School of Earth Environmental & Biological Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
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Fruciano C, Franchini P, Raffini F, Fan S, Meyer A. Are sympatrically speciating Midas cichlid fish special? Patterns of morphological and genetic variation in the closely related species Archocentrus centrarchus. Ecol Evol 2016; 6:4102-14. [PMID: 27516867 PMCID: PMC4877357 DOI: 10.1002/ece3.2184] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 04/18/2016] [Accepted: 04/22/2016] [Indexed: 12/14/2022] Open
Abstract
Established empirical cases of sympatric speciation are scarce, although there is an increasing consensus that sympatric speciation might be more common than previously thought. Midas cichlid fish are one of the few substantiated cases of sympatric speciation, and they formed repeated radiations in crater lakes. In contrast, in the same environment, such radiation patterns have not been observed in other species of cichlids and other families of fish. We analyze morphological and genetic variation in a cichlid species (Archocentrus centrarchus) that co-inhabits several crater lakes with the Midas species complex. In particular, we analyze variation in body and pharyngeal jaw shape (two ecologically important traits in sympatrically divergent Midas cichlids) and relate that to genetic variation in mitochondrial control region and microsatellites. Using these four datasets, we analyze variation between and within two Nicaraguan lakes: a crater lake where multiple Midas cichlids have been described and a lake where the source population lives. We do not observe any within-lake clustering consistent across morphological traits and genetic markers, suggesting the absence of sympatric divergence in A. centrarchus. Genetic differentiation between lakes was low and morphological divergence absent. Such morphological similarity between lakes is found not only in average morphology, but also when analyzing covariation between traits and degree of morphospace occupation. A combined analysis of the mitochondrial control region in A. centrarchus and Midas cichlids suggests that a difference between lineages in the timing of crater lake colonization cannot be invoked as an explanation for the difference in their levels of diversification. In light of our results, A. centrarchus represents the ideal candidate to study the genomic differences between these two lineages that might explain why some lineages are more likely to speciate and diverge in sympatry than others.
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Affiliation(s)
- Carmelo Fruciano
- Department of Biology Chair of Zoology and Evolutionary Biology University of Konstanz Universitätsstrasse 1078457 Konstanz Germany; School of Earth, Environmental & Biological Sciences Queensland University of Technology Brisbane Qld 4000 Australia
| | - Paolo Franchini
- Department of Biology Chair of Zoology and Evolutionary Biology University of Konstanz Universitätsstrasse 10 78457 Konstanz Germany
| | - Francesca Raffini
- Department of Biology Chair of Zoology and Evolutionary Biology University of Konstanz Universitätsstrasse 1078457 Konstanz Germany; International Max Planck Research School (IMPRS) for Organismal Biology Max-Planck-Institut für Ornithologie Am Obstberg 178315 Radolfzell Germany
| | - Shaohua Fan
- Department of Biology Chair of Zoology and Evolutionary Biology University of Konstanz Universitätsstrasse 10 78457 Konstanz Germany
| | - Axel Meyer
- Department of Biology Chair of Zoology and Evolutionary Biology University of Konstanz Universitätsstrasse 10 78457 Konstanz Germany
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Franchini P, Colangelo P, Meyer A, Fruciano C. Chromosomal rearrangements, phenotypic variation and modularity: a case study from a contact zone between house mouse Robertsonian races in Central Italy. Ecol Evol 2016; 6:1353-62. [PMID: 26855768 PMCID: PMC4733104 DOI: 10.1002/ece3.1912] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 12/03/2015] [Indexed: 11/21/2022] Open
Abstract
The Western European house mouse, Mus musculus domesticus, is well‐known for the high frequency of Robertsonian fusions that have rapidly produced more than 50 karyotipic races, making it an ideal model for studying the mechanisms of chromosomal speciation. The mouse mandible is one of the traits studied most intensively to investigate the effect of Robertsonian fusions on phenotypic variation within and between populations. This complex bone structure has also been widely used to study the level of integration between different morphogenetic units. Here, with the aim of testing the effect of different karyotypic assets on the morphology of the mouse mandible and on its level of modularity, we performed morphometric analyses of mice from a contact area between two highly metacentric races in Central Italy. We found no difference in size, while the mandible shape was found to be different between the two Robertsonian races, even after accounting for the genetic relationships among individuals and geographic proximity. Our results support the existence of two modules that indicate a certain degree of evolutionary independence, but no difference in the strength of modularity between chromosomal races. Moreover, the ascending ramus showed more pronounced interpopulation/race phenotypic differences than the alveolar region, an effect that could be associated to their different polygenic architecture. This study suggests that chromosomal rearrangements play a role in the house mouse phenotypic divergence, and that the two modules of the mouse mandible are differentially affected by environmental factors and genetic makeup.
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Affiliation(s)
- Paolo Franchini
- Department of Biology Lehrstuhl für Zoologie und Evolutionsbiologie University of Konstanz Universitätsstraße 1078457 Konstanz Germany; Dipartimento di Biologia e Biotecnologie "Charles Darwin" Universitá di Roma "La Sapienza" via Borelli 5000161 Roma Italy
| | | | - Axel Meyer
- Department of Biology Lehrstuhl für Zoologie und Evolutionsbiologie University of Konstanz Universitätsstraße 10 78457 Konstanz Germany
| | - Carmelo Fruciano
- Department of Biology Lehrstuhl für Zoologie und Evolutionsbiologie University of Konstanz Universitätsstraße 1078457 Konstanz Germany; School of Earth Environmental and Biological Sciences Queensland University of Technology Gardens Point 4000 Brisbane Australia
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Kavembe GD, Franchini P, Irisarri I, Machado-Schiaffino G, Meyer A. Genomics of Adaptation to Multiple Concurrent Stresses: Insights from Comparative Transcriptomics of a Cichlid Fish from One of Earth’s Most Extreme Environments, the Hypersaline Soda Lake Magadi in Kenya, East Africa. J Mol Evol 2015; 81:90-109. [DOI: 10.1007/s00239-015-9696-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 08/29/2015] [Indexed: 11/29/2022]
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Felux AK, Franchini P, Schleheck D. Permanent draft genome sequence of sulfoquinovose-degrading Pseudomonas putida strain SQ1. Stand Genomic Sci 2015; 10:42. [PMID: 27408681 PMCID: PMC4940961 DOI: 10.1186/s40793-015-0033-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 07/01/2015] [Indexed: 11/10/2022] Open
Abstract
Pseudomonas putida SQ1 was isolated for its ability to utilize the plant sugar sulfoquinovose (6-deoxy-6-sulfoglucose) for growth, in order to define its SQ-degradation pathway and the enzymes and genes involved. Here we describe the features of the organism, together with its draft genome sequence and annotation. The draft genome comprises 5,328,888 bp and is predicted to encode 5,824 protein-coding genes; the overall G + C content is 61.58 %. The genome annotation is being used for identification of proteins that might be involved in SQ degradation by peptide fingerprinting-mass spectrometry.
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Affiliation(s)
- Ann-Katrin Felux
- />Department of Biology, University of Konstanz, Konstanz, Germany
- />Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Paolo Franchini
- />Department of Biology, University of Konstanz, Konstanz, Germany
- />Genomics Center Konstanz, University of Konstanz, Konstanz, Germany
| | - David Schleheck
- />Department of Biology, University of Konstanz, Konstanz, Germany
- />Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
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Modica MV, Lombardo F, Franchini P, Oliverio M. The venomous cocktail of the vampire snail Colubraria reticulata (Mollusca, Gastropoda). BMC Genomics 2015; 16:441. [PMID: 26054852 PMCID: PMC4460706 DOI: 10.1186/s12864-015-1648-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 05/20/2015] [Indexed: 01/13/2023] Open
Abstract
Background Hematophagy arose independently multiple times during metazoan evolution, with several lineages of vampire animals particularly diversified in invertebrates. However, the biochemistry of hematophagy has been studied in a few species of direct medical interest and is still underdeveloped in most invertebrates, as in general is the study of venom toxins. In cone snails, leeches, arthropods and snakes, the strong target specificity of venom toxins uniquely aligns them to industrial and academic pursuits (pharmacological applications, pest control etc.) and provides a biochemical tool for studying biological activities including cell signalling and immunological response. Neogastropod snails (cones, oyster drills etc.) are carnivorous and include active predators, scavengers, grazers on sessile invertebrates and hematophagous parasites; most of them use venoms to efficiently feed. It has been hypothesized that trophic innovations were the main drivers of rapid radiation of Neogastropoda in the late Cretaceous. We present here the first molecular characterization of the alimentary secretion of a non-conoidean neogastropod, Colubraria reticulata. Colubrariids successfully feed on the blood of fishes, throughout the secretion into the host of a complex mixture of anaesthetics and anticoagulants. We used a NGS RNA-Seq approach, integrated with differential expression analyses and custom searches for putative secreted feeding-related proteins, to describe in detail the salivary and mid-oesophageal transcriptomes of this Mediterranean vampire snail, with functional and evolutionary insights on major families of bioactive molecules. Results A remarkably low level of overlap was observed between the gene expression in the two target tissues, which also contained a high percentage of putatively secreted proteins when compared to the whole body. At least 12 families of feeding-related proteins were identified, including: 1) anaesthetics, such as ShK Toxin-containing proteins and turripeptides (ion-channel blockers), Cysteine-rich secretory proteins (CRISPs), Adenosine Deaminase (ADA); 2) inhibitors of primary haemostasis, such as novel vWFA domain-containing proteins, the Ectonucleotide pyrophosphatase/phosphodiesterase family member 5 (ENPP5) and the wasp Antigen-5; 3) anticoagulants, such as TFPI-like multiple Kunitz-type protease inhibitors, Peptidases S1 (PS1), CAP/ShKT domain-containing proteins, Astacin metalloproteases and Astacin/ShKT domain-containing proteins; 4) additional proteins, such the Angiotensin-Converting Enzyme (ACE: vasopressive) and the cytolytic Porins. Conclusions Colubraria feeding physiology seems to involve inhibitors of both primary and secondary haemostasis, anaesthetics, a vasoconstrictive enzyme to reduce feeding time and tissue-degrading proteins such as Porins and Astacins. The complexity of Colubraria venomous cocktail and the divergence from the arsenal of the few neogastropods studied to date (mostly conoideans) suggest that biochemical diversification of neogastropods might be largely underestimated and worth of extensive investigation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1648-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maria Vittoria Modica
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University, I-00185, Rome, Italy.
| | - Fabrizio Lombardo
- Department of Public Health and Infectious Diseases, Sapienza University, I-00185, Rome, Italy.
| | - Paolo Franchini
- Department of Biology, University of Konstanz, D-78745, Konstanz, Germany.
| | - Marco Oliverio
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University, I-00185, Rome, Italy.
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Kang JH, Manousaki T, Franchini P, Kneitz S, Schartl M, Meyer A. Transcriptomics of two evolutionary novelties: how to make a sperm-transfer organ out of an anal fin and a sexually selected "sword" out of a caudal fin. Ecol Evol 2015; 5:848-64. [PMID: 25750712 PMCID: PMC4338968 DOI: 10.1002/ece3.1390] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 12/10/2014] [Accepted: 12/12/2014] [Indexed: 01/09/2023] Open
Abstract
Swords are exaggerated male ornaments of swordtail fishes that have been of great interest to evolutionary biologists ever since Darwin described them in the Descent of Man (1871). They are a novel sexually selected trait derived from modified ventral caudal fin rays and are only found in the genus Xiphophorus. Another phylogenetically more widespread and older male trait is the gonopodium, an intromittent organ found in all poeciliid fishes, that is derived from a modified anal fin. Despite many evolutionary and behavioral studies on both traits, little is known so far about the molecular mechanisms underlying their development. By investigating transcriptomic changes (utilizing a RNA-Seq approach) in response to testosterone treatment in the swordtail fish, Xiphophorus hellerii, we aimed to better understand the architecture of the gene regulatory networks underpinning the development of these two evolutionary novelties. Large numbers of genes with tissue-specific expression patterns were identified. Among the "sword genes" those involved in embryonic organ development, sexual character development and coloration were highly expressed, while in the gonopodium rather more morphogenesis-related genes were found. Interestingly, many genes and genetic pathways are shared between both developing novel traits derived from median fins: the sword and the gonopodium. Our analyses show that a larger set of gene networks was co-opted during the development and evolution of the "older" gonopodium than in the "younger," and morphologically less complex trait, the sword. We provide a catalog of candidate genes for future efforts to dissect the development of those sexually selected exaggerated male traits in swordtails.
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Affiliation(s)
- Ji Hyoun Kang
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of KonstanzUniversitätsstraβe 10, 78457, Konstanz, Germany
- Konstanz Research School Chemical Biology, University of KonstanzKonstanz, Germany
| | - Tereza Manousaki
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of KonstanzUniversitätsstraβe 10, 78457, Konstanz, Germany
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine ResearchHeraklion, Greece
| | - Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of KonstanzUniversitätsstraβe 10, 78457, Konstanz, Germany
| | - Susanne Kneitz
- Physiological Chemistry, Biozentrum, University of WürzburgAm Hubland, Würzburg, Germany
| | - Manfred Schartl
- Physiological Chemistry, Biozentrum, University of WürzburgAm Hubland, Würzburg, Germany
- Comprehensive Cancer Center, University Clinic WürzburgJosef Schneider Straβe 6, 97074, Würzburg, Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of KonstanzUniversitätsstraβe 10, 78457, Konstanz, Germany
- Konstanz Research School Chemical Biology, University of KonstanzKonstanz, Germany
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Henning F, Lee HJ, Franchini P, Meyer A. Genetic mapping of horizontal stripes in Lake Victoria cichlid fishes: benefits and pitfalls of using RAD markers for dense linkage mapping. Mol Ecol 2014; 23:5224-40. [PMID: 25039588 DOI: 10.1111/mec.12860] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/02/2014] [Accepted: 07/12/2014] [Indexed: 01/25/2023]
Abstract
The genetic dissection of naturally occurring phenotypes sheds light on many fundamental and longstanding questions in speciation and adaptation and is a central research topic in evolutionary biology. Until recently, forward-genetic approaches were virtually impossible to apply to nonmodel organisms, but the development of next-generation sequencing techniques eases this difficulty. Here, we use the ddRAD-seq method to map a colour trait with a known adaptive function in cichlid fishes, well-known textbook examples for rapid rates of speciation and astonishing phenotypic diversification. A suite of phenotypic key innovations is related to speciation and adaptation in cichlids, among which body coloration features prominently. The focal trait of this study, horizontal stripes, evolved in parallel in several cichlid radiations and is associated with piscivorous foraging behaviour. We conducted interspecific crosses between Haplochromis sauvagei and H. nyererei and constructed a linkage map with 867 SNP markers distributed on 22 linkage groups and total size of 1130.63 cM. Lateral stripes are inherited as a Mendelian trait and map to a single genomic interval that harbours a paralog of a gene with known function in stripe patterning. Dorsolateral and mid-lateral stripes were always coinherited and are thus under the same genetic control. Additionally, we directly quantify the genotyping error rates in RAD markers and offer guidelines for identifying and dealing with errors. Uncritical marker selection was found to severely impact linkage map construction. Fortunately, by applying appropriate quality control steps, a genotyping accuracy of >99.9% can be reached, thus allowing for efficient linkage mapping of evolutionarily relevant traits.
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Affiliation(s)
- Frederico Henning
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, Konstanz, 78457, Germany
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Seehausen O, Butlin RK, Keller I, Wagner CE, Boughman JW, Hohenlohe PA, Peichel CL, Saetre GP, Bank C, Brännström A, Brelsford A, Clarkson CS, Eroukhmanoff F, Feder JL, Fischer MC, Foote AD, Franchini P, Jiggins CD, Jones FC, Lindholm AK, Lucek K, Maan ME, Marques DA, Martin SH, Matthews B, Meier JI, Möst M, Nachman MW, Nonaka E, Rennison DJ, Schwarzer J, Watson ET, Westram AM, Widmer A. Genomics and the origin of species. Nat Rev Genet 2014; 15:176-92. [PMID: 24535286 DOI: 10.1038/nrg3644] [Citation(s) in RCA: 583] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Speciation is a fundamental evolutionary process, the knowledge of which is crucial for understanding the origins of biodiversity. Genomic approaches are an increasingly important aspect of this research field. We review current understanding of genome-wide effects of accumulating reproductive isolation and of genomic properties that influence the process of speciation. Building on this work, we identify emergent trends and gaps in our understanding, propose new approaches to more fully integrate genomics into speciation research, translate speciation theory into hypotheses that are testable using genomic tools and provide an integrative definition of the field of speciation genomics.
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Affiliation(s)
- Ole Seehausen
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; and Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Roger K Butlin
- Department of Animal and Plant Sciences, the University of Sheffield, Sheffield S10 2TN, UK; and the Sven Lovén Centre - Tjärnö, University of Gothenburg, S-452 96 Strömstad, Sweden
| | - Irene Keller
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; the Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland; and the Institute of Integrative Biology, ETH Zürich, ETH Zentrum CHN, 8092 Zürich, Switzerland
| | - Catherine E Wagner
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; and the Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Janette W Boughman
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; and the Department of Zoology; Ecology, Evolutionary Biology and Behavior Program; BEACON Center, Michigan State University, 203 Natural Sciences, East Lansing, Michigan 48824, USA
| | - Paul A Hohenlohe
- Department of Biological Sciences, Institute of Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho 83844-3051, USA
| | - Catherine L Peichel
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Glenn-Peter Saetre
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, PO BOX 1066, Blindern, N-0316 Oslo, Norway
| | - Claudia Bank
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Ake Brännström
- Integrated Science Laboratory and the Department of Mathematics and Mathematical Statistics, Umeå University, 90187 Umeå, Sweden
| | - Alan Brelsford
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | | | - Fabrice Eroukhmanoff
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, PO BOX 1066, Blindern, N-0316 Oslo, Norway
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556-0369 USA
| | - Martin C Fischer
- Institute of Integrative Biology, ETH Zürich, ETH Zentrum CHN, 8092 Zürich, Switzerland
| | - Andrew D Foote
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark. Present address: the Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Felicity C Jones
- Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany
| | - Anna K Lindholm
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, CH-8057 Zurich, Switzerland
| | - Kay Lucek
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; and the Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Martine E Maan
- Behavioural Biology Group, Centre for Behaviour and Neurosciences, University of Groningen, PO BOX 11103, 9700 CC Groningen, The Netherlands
| | - David A Marques
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; the Division of Aquatic Ecology and Evolution, and the Computational and Molecular Population Genetics Laboratory, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Simon H Martin
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Blake Matthews
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland
| | - Joana I Meier
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; the Division of Aquatic Ecology and Evolution, and the Computational and Molecular Population Genetics Laboratory, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Markus Möst
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK; and the Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Michael W Nachman
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, California 94720-3160, USA
| | - Etsuko Nonaka
- Integrated Science Laboratory and Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden
| | - Diana J Rennison
- Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Julia Schwarzer
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; the Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland; and Zoologisches Forschungsmuseum Alexander Koenig, 53113 Bonn, Germany
| | - Eric T Watson
- Department of Biology, The University of Texas at Arlington, 76010-0498 Texas, USA
| | - Anja M Westram
- Department of Animal and Plant Sciences, the University of Sheffield, Sheffield S10 2TN, UK
| | - Alex Widmer
- Institute of Integrative Biology, ETH Zürich, ETH Zentrum CHN, 8092 Zürich, Switzerland
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Franchini P, Fruciano C, Spreitzer ML, Jones JC, Elmer KR, Henning F, Meyer A. Genomic architecture of ecologically divergent body shape in a pair of sympatric crater lake cichlid fishes. Mol Ecol 2013; 23:1828-45. [PMID: 24237636 DOI: 10.1111/mec.12590] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 10/18/2013] [Accepted: 10/28/2013] [Indexed: 12/26/2022]
Abstract
Determining the genetic bases of adaptations and their roles in speciation is a prominent issue in evolutionary biology. Cichlid fish species flocks are a prime example of recent rapid radiations, often associated with adaptive phenotypic divergence from a common ancestor within a short period of time. In several radiations of freshwater fishes, divergence in ecomorphological traits - including body shape, colour, lips and jaws - is thought to underlie their ecological differentiation, specialization and, ultimately, speciation. The Midas cichlid species complex (Amphilophus spp.) of Nicaragua provides one of the few known examples of sympatric speciation where species have rapidly evolved different but parallel morphologies in young crater lakes. This study identified significant QTL for body shape using SNPs generated via ddRAD sequencing and geometric morphometric analyses of a cross between two ecologically and morphologically divergent, sympatric cichlid species endemic to crater Lake Apoyo: an elongated limnetic species (Amphilophus zaliosus) and a high-bodied benthic species (Amphilophus astorquii). A total of 453 genome-wide informative SNPs were identified in 240 F2 hybrids. These markers were used to construct a genetic map in which 25 linkage groups were resolved. Seventy-two segregating SNPs were linked to 11 QTL. By annotating the two most highly supported QTL-linked genomic regions, genes that might contribute to divergence in body shape along the benthic-limnetic axis in Midas cichlid sympatric adaptive radiations were identified. These results suggest that few genomic regions of large effect contribute to early stage divergence in Midas cichlids.
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Affiliation(s)
- Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstraße 10, 78457, Konstanz, Germany
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Gunter HM, Fan S, Xiong F, Franchini P, Fruciano C, Meyer A. Shaping development through mechanical strain: the transcriptional basis of diet-induced phenotypic plasticity in a cichlid fish. Mol Ecol 2013; 22:4516-31. [PMID: 23952004 DOI: 10.1111/mec.12417] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/25/2013] [Accepted: 05/28/2013] [Indexed: 11/29/2022]
Abstract
Adaptive phenotypic plasticity, the ability of an organism to change its phenotype to match local environments, is increasingly recognized for its contribution to evolution. However, few empirical studies have explored the molecular basis of plastic traits. The East African cichlid fish Astatoreochromis alluaudi displays adaptive phenotypic plasticity in its pharyngeal jaw apparatus, a structure that is widely seen as an evolutionary key innovation that has contributed to the remarkable diversity of cichlid fishes. It has previously been shown that in response to different diets, the pharyngeal jaws change their size, shape and dentition: hard diets induce an adaptive robust molariform tooth phenotype with short jaws and strong internal bone structures, while soft diets induce a gracile papilliform tooth phenotype with elongated jaws and slender internal bone structures. To gain insight into the molecular underpinnings of these adaptations and enable future investigations of the role that phenotypic plasticity plays during the formation of adaptive radiations, the transcriptomes of the two divergent jaw phenotypes were examined. Our study identified a total of 187 genes whose expression differs in response to hard and soft diets, including immediate early genes, extracellular matrix genes and inflammatory factors. Transcriptome results are interpreted in light of expression of candidate genes-markers for tooth size and shape, bone cells and mechanically sensitive pathways. This study opens up new avenues of research at new levels of biological organization into the roles of phenotypic plasticity during speciation and radiation of cichlid fishes.
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Affiliation(s)
- Helen M Gunter
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstrasse 10, 78457, Konstanz, Germany
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Jones JC, Fan S, Franchini P, Schartl M, Meyer A. The evolutionary history of Xiphophorus fish and their sexually selected sword: a genome-wide approach using restriction site-associated DNA sequencing. Mol Ecol 2013; 22:2986-3001. [PMID: 23551333 DOI: 10.1111/mec.12269] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Revised: 01/10/2013] [Accepted: 01/15/2013] [Indexed: 11/27/2022]
Abstract
Next-generation sequencing (NGS) techniques are now key tools in the detection of population genomic and gene expression differences in a large array of organisms. However, so far few studies have utilized such data for phylogenetic estimations. Here, we use NGS data obtained from genome-wide restriction site-associated DNA (RAD) (∼66000 SNPs) to estimate the phylogenetic relationships among all 26 species of swordtail and platyfish (genus Xiphophorus) from Central America. Past studies, both sequence and morphology-based, have differed in their inferences of the evolutionary relationships within this genus, particularly at the species-level and among monophyletic groupings. We show that using a large number of markers throughout the genome, we are able to infer the phylogenetic relationships with unparalleled resolution for this genus. The relationships among all three major clades and species within each of them are highly resolved and consistent under maximum likelihood, Bayesian inference and maximum parsimony. However, we also highlight the current cautions with this data type and analyses. This genus exhibits a particularly interesting evolutionary history where at least two species may have arisen through hybridization events. Here, we are able to infer the paternal lineages of these putative hybrid species. Using the RAD-marker-based tree we reconstruct the evolutionary history of the sexually selected sword trait and show that it may have been present in the common ancestor of the genus. Together our results highlight the outstanding capacity that RAD sequencing data has for resolving previously problematic phylogenetic relationships, particularly among relatively closely related species.
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Affiliation(s)
- Julia C Jones
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasße 10, 78457, Konstanz, Germany
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Henning F, Jones JC, Franchini P, Meyer A. Transcriptomics of morphological color change in polychromatic Midas cichlids. BMC Genomics 2013; 14:171. [PMID: 23497064 PMCID: PMC3623868 DOI: 10.1186/1471-2164-14-171] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Accepted: 03/06/2013] [Indexed: 12/30/2022] Open
Abstract
Background Animal pigmentation has received much attention in evolutionary biology research due to its strong implications for adaptation and speciation. However, apart from a few cases the genetic changes associated with these evolutionary processes remain largely unknown. The Midas cichlid fish from Central America are an ideal model system for investigating pigmentation traits that may also play a role in speciation. Most Midas cichlids maintain their melanophores and exhibit a grayish (normal) color pattern throughout their lives. A minority of individuals, however, undergo color change and exhibit a distinctive gold or even white coloration in adulthood. The ontogenetic color change in the Midas cichlids may also shed light on the molecular mechanisms underlying pigmentation disorders in humans. Results Here we use next-generation sequencing (Illumina) RNAseq analyses to compare skin transcriptome-wide expression levels in three distinct stages of color transformation in Midas cichlids. cDNA libraries of scale tissue, for six biological replicates of each group, were generated and sequenced using Illumina technology. Using a combination of three differential expression (DE) analyses we identified 46 candidate genes that showed DE between the color morphs. We find evidence for two key DE patterns: a) genes involved in melanosomal pathways are up-regulated in normally pigmented fish; and b) immediate early and inflammatory response genes were up-regulated in transitional fish, a response that parallels some human skin disorders such as melanoma formation and psoriasis. One of the DE genes segregates with the gold phenotype in a genetic cross and might be associated with incipient speciation in this highly “species-rich” lineage of cichlids. Conclusions Using transcriptomic analyses we successfully identified key expression differences between different color morphs of Midas cichlid fish. These differentially expressed genes have important implications for our understanding of the molecular mechanisms underlying speciation in this lineage of extremely young species since they mate strongly assortatively, and new species may arise by sexual selection due to this color polymorphism. Some of the human orthologues of the genes identified here may also be involved in pigmentation differences and diseases and therefore provide genetic markers for the detection of human pigmentation disorders.
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Affiliation(s)
- Frederico Henning
- Laboratory of Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz 78457, Germany
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Manousaki T, Hull PM, Kusche H, Machado-Schiaffino G, Franchini P, Harrod C, Elmer KR, Meyer A. Parsing parallel evolution: ecological divergence and differential gene expression in the adaptive radiations of thick-lipped Midas cichlid fishes from Nicaragua. Mol Ecol 2012; 22:650-69. [DOI: 10.1111/mec.12034] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 06/11/2012] [Accepted: 07/26/2012] [Indexed: 01/31/2023]
Affiliation(s)
| | | | | | - Gonzalo Machado-Schiaffino
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology; University of Konstanz, Universitätsstrasse 10; 78457; Konstanz; Germany
| | - Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology; University of Konstanz, Universitätsstrasse 10; 78457; Konstanz; Germany
| | | | - Kathryn R. Elmer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology; University of Konstanz, Universitätsstrasse 10; 78457; Konstanz; Germany
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Colangelo P, Aloise G, Franchini P, Annesi F, Amori G. Mitochondrial DNA reveals hidden diversity and an ancestral lineage of the bank vole in the Italian peninsula. J Zool (1987) 2011. [DOI: 10.1111/j.1469-7998.2011.00884.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
| | - G. Aloise
- Museo di Storia Naturale della Calabria e Orto Botanico; University of Calabria; Rende; Italy
| | | | - F. Annesi
- Department of Biology and Biotechnologies ‘Charles Darwin’; Sapienza University of Rome; Roma; Italy
| | - G. Amori
- Institute of Ecosystem Study; National Research Council; Roma; Italy
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van der Merwe M, Franchini P, Roodt-Wilding R. Differential growth-related gene expression in abalone (Haliotis midae). Mar Biotechnol (NY) 2011; 13:1125-1139. [PMID: 21533523 DOI: 10.1007/s10126-011-9376-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2010] [Accepted: 03/29/2011] [Indexed: 05/30/2023]
Abstract
The slow growth rate of Haliotis midae impedes the optimal commercial production of this most profitable South African aquaculture species. To date, no comprehensive effort has been made to identify genes associated with growth variation in farmed H. midae. The aim of this study was therefore to investigate growth variation in H. midae and to identify and quantify the expression of selected growth-related genes. Towards this aim, molecular methodologies and cell cultures were combined as a time-efficient and economical way of studying abalone transcriptomics and cell biology. Modern Illumina sequencing-by-synthesis technology and subsequent sequence annotation were used to elucidate differential gene expression between two sibling groups of abalone demonstrating significant growth variation. The expression of selected target genes involved in growth was subsequently analysed by quantitative real-time PCR (qPCR). Fast- and slow-growing abalone and in vitro primary haemocyte cultures treated with different growth-stimulating factors were used. The results obtained from transcriptome analysis and qPCR revealed significant differences in gene expression between large and small abalone, and between treated and untreated haemocyte cell cultures. Throughout in vivo and in vitro qPCR experiments, the up-regulation of genes involved in the insulin signalling pathway suggests that insulin may be involved in enhanced growth rate for various H. midae tissues.
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Affiliation(s)
- Mathilde van der Merwe
- Molecular Aquatic Research Group, Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
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Sanchez PDA, Lees JP, Poireau V, Prencipe E, Tisserand V, Garra Tico J, Grauges E, Martinelli M, Palano A, Pappagallo M, Eigen G, Stugu B, Sun L, Battaglia M, Brown DN, Hooberman B, Kerth LT, Kolomensky YG, Lynch G, Osipenkov IL, Tanabe T, Hawkes CM, Watson AT, Koch H, Schroeder T, Asgeirsson DJ, Hearty C, Mattison TS, McKenna JA, Khan A, Randle-Conde A, Blinov VE, Buzykaev AR, Druzhinin VP, Golubev VB, Onuchin AP, Serednyakov SI, Skovpen YI, Solodov EP, Todyshev KY, Yushkov AN, Bondioli M, Curry S, Kirkby D, Lankford AJ, Mandelkern M, Martin EC, Stoker DP, Atmacan H, Gary JW, Liu F, Long O, Vitug GM, Campagnari C, Hong TM, Kovalskyi D, Richman JD, Eisner AM, Heusch CA, Kroseberg J, Lockman WS, Martinez AJ, Schalk T, Schumm BA, Seiden A, Winstrom LO, Cheng CH, Doll DA, Echenard B, Hitlin DG, Ongmongkolkul P, Porter FC, Rakitin AY, Andreassen R, Dubrovin MS, Mancinelli G, Meadows BT, Sokoloff MD, Bloom PC, Ford WT, Gaz A, Nagel M, Nauenberg U, Smith JG, Wagner SR, Ayad R, Toki WH, Jasper H, Karbach TM, Merkel J, Petzold A, Spaan B, Wacker K, Kobel MJ, Schubert KR, Schwierz R, Bernard D, Verderi M, Clark PJ, Playfer S, Watson JE, Andreotti M, Bettoni D, Bozzi C, Calabrese R, Cecchi A, Cibinetto G, Fioravanti E, Franchini P, Luppi E, Munerato M, Negrini M, Petrella A, Piemontese L, Baldini-Ferroli R, Calcaterra A, de Sangro R, Finocchiaro G, Nicolaci M, Pacetti S, Patteri P, Peruzzi IM, Piccolo M, Rama M, Zallo A, Contri R, Guido E, Lo Vetere M, Monge MR, Passaggio S, Patrignani C, Robutti E, Tosi S, Bhuyan B, Prasad V, Lee CL, Morii M, Adametz A, Marks J, Schenk S, Uwer U, Bernlochner FU, Ebert M, Lacker HM, Lueck T, Volk A, Dauncey PD, Tibbetts M, Behera PK, Mallik U, Chen C, Cochran J, Crawley HB, Dong L, Meyer WT, Prell S, Rosenberg EI, Rubin AE, Gao YY, Gritsan AV, Guo ZJ, Arnaud N, Davier M, Derkach D, da Costa JF, Grosdidier G, Le Diberder F, Lutz AM, Malaescu B, Perez A, Roudeau P, Schune MH, Serrano J, Sordini V, Stocchi A, Wang L, Wormser G, Lange DJ, Wright DM, Bingham I, Chavez CA, Coleman JP, Fry JR, Gabathuler E, Gamet R, Hutchcroft DE, Payne DJ, Touramanis C, Bevan AJ, Di Lodovico F, Sacco R, Sigamani M, Cowan G, Paramesvaran S, Wren AC, Brown DN, Davis CL, Denig AG, Fritsch M, Gradl W, Hafner A, Alwyn KE, Bailey D, Barlow RJ, Jackson G, Lafferty GD, West TJ, Anderson J, Cenci R, Jawahery A, Roberts DA, Simi G, Tuggle JM, Dallapiccola C, Salvati E, Cowan R, Dujmic D, Fisher PH, Sciolla G, Zhao M, Lindemann D, Patel PM, Robertson SH, Schram M, Biassoni P, Lazzaro A, Lombardo V, Palombo F, Stracka S, Cremaldi L, Godang R, Kroeger R, Sonnek P, Summers DJ, Nguyen X, Simard M, Taras P, De Nardo G, Monorchio D, Onorato G, Sciacca C, Raven G, Snoek HL, Jessop CP, Knoepfel KJ, LoSecco JM, Wang WF, Corwin LA, Honscheid K, Kass R, Morris JP, Rahimi AM, Blount NL, Brau J, Frey R, Igonkina O, Kolb JA, Rahmat R, Sinev NB, Strom D, Strube J, Torrence E, Castelli G, Feltresi E, Gagliardi N, Margoni M, Morandin M, Posocco M, Rotondo M, Simonetto F, Stroili R, Ben-Haim E, Bonneaud GR, Briand H, Calderini G, Chauveau J, Hamon O, Leruste P, Marchiori G, Ocariz J, Prendki J, Sitt S, Biasini M, Manoni E, Rossi A, Angelini C, Batignani G, Bettarini S, Carpinelli M, Casarosa G, Cervelli A, Forti F, Giorgi MA, Lusiani A, Neri N, Paoloni E, Rizzo G, Walsh JJ, Pegna DL, Lu C, Olsen J, Smith AJS, Telnov AV, Anulli F, Baracchini E, Cavoto G, Faccini R, Ferrarotto F, Ferroni F, Gaspero M, Li Gioi L, Mazzoni MA, Piredda G, Renga F, Hartmann T, Leddig T, Schröder H, Waldi R, Adye T, Franek B, Olaiya EO, Wilson FF, Emery S, de Monchenault GH, Vasseur G, Yèche C, Zito M, Allen MT, Aston D, Bard DJ, Bartoldus R, Benitez JF, Cartaro C, Convery MR, Dorfan J, Dubois-Felsmann GP, Dunwoodie W, Field RC, Sevilla MF, Fulsom BG, Gabareen AM, Graham MT, Grenier P, Hast C, Innes WR, Kelsey MH, Kim H, Kim P, Kocian ML, Leith DWGS, Li S, Lindquist B, Luitz S, Luth V, Lynch HL, MacFarlane DB, Marsiske H, Muller DR, Neal H, Nelson S, O'Grady CP, Ofte I, Perl M, Pulliam T, Ratcliff BN, Roodman A, Salnikov AA, Santoro V, Schindler RH, Schwiening J, Snyder A, Su D, Sullivan MK, Sun S, Suzuki K, Thompson JM, Va'vra J, Wagner AP, Weaver M, West CA, Wisniewski WJ, Wittgen M, Wright DH, Wulsin HW, Yarritu AK, Young CC, Ziegler V, Chen XR, Park W, Purohit MV, White RM, Wilson JR, Sekula SJ, Bellis M, Burchat PR, Edwards AJ, Miyashita TS, Ahmed S, Alam MS, Ernst JA, Pan B, Saeed MA, Zain SB, Guttman N, Soffer A, Lund P, Spanier SM, Eckmann R, Ritchie JL, Ruland AM, Schilling CJ, Schwitters RF, Wray BC, Izen JM, Lou XC, Bianchi F, Gamba D, Pelliccioni M, Bomben M, Lanceri L, Vitale L, Lopez-March N, Martinez-Vidal F, Milanes DA, Oyanguren A, Albert J, Banerjee S, Choi HHF, Hamano K, King GJ, Kowalewski R, Lewczuk MJ, Nugent IM, Roney JM, Sobie RJ, Gershon TJ, Harrison PF, Latham TE, Puccio EMT, Band HR, Dasu S, Flood KT, Pan Y, Prepost R, Vuosalo CO, Wu SL. Observation of the decay B- → D(s)((*)+) K- ℓ- ν(ℓ). Phys Rev Lett 2011; 107:041804. [PMID: 21866995 DOI: 10.1103/physrevlett.107.041804] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Indexed: 05/31/2023]
Abstract
We report the observation of the decay B- → D(s)((*)+) K- ℓ- ν(ℓ) based on 342 fb(-1) of data collected at the Υ(4S) resonance with the BABAR detector at the PEP-II e+ e- storage rings at SLAC. A simultaneous fit to three D(s)(+) decay chains is performed to extract the signal yield from measurements of the squared missing mass in the B meson decay. We observe the decay B- → D(s)((*)+) K- ℓ- ν(ℓ) with a significance greater than 5 standard deviations (including systematic uncertainties) and measure its branching fraction to be B(B- → D(s)((*)+) K- ℓ- ν(ℓ)) = [6.13(-1.03)(+1.04)(stat)±0.43(syst)±0.51(B(D(s)))]×10(-4), where the last error reflects the limited knowledge of the D(s) branching fractions.
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Affiliation(s)
- P del Amo Sanchez
- Laboratoire d'Annecy-le-Vieux de Physique des Particules (LAPP), Université de Savoie, CNRS/IN2P3, F-74941 Annecy-Le-Vieux, France
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Search for production of invisible final states in single-photon decays of Υ(1S). Phys Rev Lett 2011; 107:021804. [PMID: 21797597 DOI: 10.1103/physrevlett.107.021804] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Indexed: 05/31/2023]
Abstract
We search for single-photon decays of the Υ(1S) resonance, Υ → γ + invisible, where the invisible state is either a particle of definite mass, such as a light Higgs boson A⁰, or a pair of dark matter particles, χχ. Both A⁰ and χ are assumed to have zero spin. We tag Υ(1S) decays with a dipion transition Υ(2S) → π⁺π⁻Υ(1S) and look for events with a single energetic photon and significant missing energy. We find no evidence for such processes in the mass range m(A⁰) ≤ 9.2 GeV and m(χ) ≤ 4.5 GeV in the sample of 98 × 10⁶ Υ(2S) decays collected with the BABAR detector and set stringent limits on new physics models that contain light dark matter states.
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Affiliation(s)
- P del Amo Sanchez
- Laboratoire d'Annecy-le-Vieux de Physique des Particules (LAPP), Université de Savoie, CNRS/IN2P3, F-74941 Annecy-Le-Vieux, France
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