[{"department":[{"_id":"JoBo"},{"_id":"LifeSc"}],"publisher":"American Society for Microbiology","publication_status":"published","year":"2013","volume":1,"date_created":"2018-12-11T11:57:30Z","date_updated":"2021-01-12T06:57:19Z","author":[{"full_name":"Fernandes Redondo, Rodrigo A","first_name":"Rodrigo A","last_name":"Fernandes Redondo","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5837-2793"},{"id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Kupczok","first_name":"Anne","full_name":"Kupczok, Anne"},{"last_name":"Stift","first_name":"Gertraud","id":"2DB195CA-F248-11E8-B48F-1D18A9856A87","full_name":"Stift, Gertraud"},{"full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P"}],"publist_id":"4516","file_date_updated":"2020-07-14T12:45:40Z","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1128/genomeA.00216-13","month":"06","intvolume":" 1","ddc":["576"],"status":"public","title":"Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2410","file":[{"checksum":"0751ec74b695567e0cdf02aaf9c26829","date_updated":"2020-07-14T12:45:40Z","date_created":"2018-12-12T10:17:36Z","file_id":"5291","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":130026,"access_level":"open_access","file_name":"IST-2015-398-v1+1_Genome_Announc.-2013-Redondo-.pdf"}],"oa_version":"Published Version","pubrep_id":"398","type":"journal_article","issue":"3","abstract":[{"text":"Here, we describe a novel virulent bacteriophage that infects Bacillus weihenstephanensis, isolated from soil in Austria. It is the first phage to be discovered that infects this species. Here, we present the complete genome sequence of this podovirus. ","lang":"eng"}],"citation":{"chicago":"Fernandes Redondo, Rodrigo A, Anne Kupczok, Gertraud Stift, and Jonathan P Bollback. “Complete Genome Sequence of the Novel Phage MG-B1 Infecting Bacillus Weihenstephanensis.” Genome Announcements. American Society for Microbiology, 2013. https://doi.org/10.1128/genomeA.00216-13.","short":"R.A. Fernandes Redondo, A. Kupczok, G. Stift, J.P. Bollback, Genome Announcements 1 (2013).","mla":"Fernandes Redondo, Rodrigo A., et al. “Complete Genome Sequence of the Novel Phage MG-B1 Infecting Bacillus Weihenstephanensis.” Genome Announcements, vol. 1, no. 3, American Society for Microbiology, 2013, doi:10.1128/genomeA.00216-13.","ieee":"R. A. Fernandes Redondo, A. Kupczok, G. Stift, and J. P. Bollback, “Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis,” Genome Announcements, vol. 1, no. 3. American Society for Microbiology, 2013.","apa":"Fernandes Redondo, R. A., Kupczok, A., Stift, G., & Bollback, J. P. (2013). Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome Announcements. American Society for Microbiology. https://doi.org/10.1128/genomeA.00216-13","ista":"Fernandes Redondo RA, Kupczok A, Stift G, Bollback JP. 2013. Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome Announcements. 1(3).","ama":"Fernandes Redondo RA, Kupczok A, Stift G, Bollback JP. Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome Announcements. 2013;1(3). doi:10.1128/genomeA.00216-13"},"publication":"Genome Announcements","date_published":"2013-06-13T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"13"},{"scopus_import":1,"day":"09","has_accepted_license":"1","publication":"BMC Evolutionary Biology","citation":{"ama":"Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. BMC Evolutionary Biology. 2013;13(1). doi:10.1186/1471-2148-13-222","ieee":"M. Ward, S. Lycett, D. Avila, J. P. Bollback, and A. Leigh Brown, “Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza,” BMC Evolutionary Biology, vol. 13, no. 1. BioMed Central, 2013.","apa":"Ward, M., Lycett, S., Avila, D., Bollback, J. P., & Leigh Brown, A. (2013). Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-13-222","ista":"Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. 2013. Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. BMC Evolutionary Biology. 13(1), 222.","short":"M. Ward, S. Lycett, D. Avila, J.P. Bollback, A. Leigh Brown, BMC Evolutionary Biology 13 (2013).","mla":"Ward, Melissa, et al. “Evolutionary Interactions between Haemagglutinin and Neuraminidase in Avian Influenza.” BMC Evolutionary Biology, vol. 13, no. 1, 222, BioMed Central, 2013, doi:10.1186/1471-2148-13-222.","chicago":"Ward, Melissa, Samantha Lycett, Dorita Avila, Jonathan P Bollback, and Andrew Leigh Brown. “Evolutionary Interactions between Haemagglutinin and Neuraminidase in Avian Influenza.” BMC Evolutionary Biology. BioMed Central, 2013. https://doi.org/10.1186/1471-2148-13-222."},"date_published":"2013-10-09T00:00:00Z","type":"journal_article","abstract":[{"text":"Background: Reassortment between the RNA segments encoding haemagglutinin (HA) and neuraminidase (NA), the major antigenic influenza proteins, produces viruses with novel HA and NA subtype combinations and has preceded the emergence of pandemic strains. It has been suggested that productive viral infection requires a balance in the level of functional activity of HA and NA, arising from their closely interacting roles in the viral life cycle, and that this functional balance could be mediated by genetic changes in the HA and NA. Here, we investigate how the selective pressure varies for H7 avian influenza HA on different NA subtype backgrounds. Results: By extending Bayesian stochastic mutational mapping methods to calculate the ratio of the rate of non-synonymous change to the rate of synonymous change (d N/d S), we found the average d N/d S across the avian influenza H7 HA1 region to be significantly greater on an N2 NA subtype background than on an N1, N3 or N7 background. Observed differences in evolutionary rates of H7 HA on different NA subtype backgrounds could not be attributed to underlying differences between avian host species or virus pathogenicity. Examination of d N/d S values for each subtype on a site-by-site basis indicated that the elevated d N/d S on the N2 NA background was a result of increased selection, rather than a relaxation of selective constraint. Conclusions: Our results are consistent with the hypothesis that reassortment exposes influenza HA to significant changes in selective pressure through genetic interactions with NA. Such epistatic effects might be explicitly accounted for in future models of influenza evolution.","lang":"eng"}],"issue":"1","_id":"500","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"status":"public","title":"Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza","intvolume":" 13","pubrep_id":"941","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":1150052,"creator":"system","file_name":"IST-2018-941-v1+1_2013_Bollback_Evolutionary_interactionspdf.pdf","access_level":"open_access","date_created":"2018-12-12T10:08:59Z","date_updated":"2020-07-14T12:46:36Z","checksum":"52cf48a7c1794676ae8b0029573a84a9","relation":"main_file","file_id":"4722"}],"month":"10","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1186/1471-2148-13-222","language":[{"iso":"eng"}],"article_number":"222","file_date_updated":"2020-07-14T12:46:36Z","publist_id":"7320","year":"2013","acknowledgement":"This work was supported by the Biotechnology and Biological Sciences Research Council, the Government of the Republic of Panama, the Interdisciplinary Centre for Human and Avian Influenza Research (www.ichair-flu.org) funded by the Scottish Funding Council, and the Institute for Science and Technology Austria.\r\nCC BY 2.0\r\n","publication_status":"published","publisher":"BioMed Central","department":[{"_id":"JoBo"}],"author":[{"last_name":"Ward","first_name":"Melissa","full_name":"Ward, Melissa"},{"full_name":"Lycett, Samantha","last_name":"Lycett","first_name":"Samantha"},{"full_name":"Avila, Dorita","first_name":"Dorita","last_name":"Avila"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","last_name":"Bollback","full_name":"Bollback, Jonathan P"},{"first_name":"Andrew","last_name":"Leigh Brown","full_name":"Leigh Brown, Andrew"}],"date_created":"2018-12-11T11:46:49Z","date_updated":"2021-01-12T08:01:08Z","volume":13},{"scopus_import":1,"has_accepted_license":"1","day":"01","page":"1331 - 1345","citation":{"chicago":"Cozzuol, Mario, Camila Clozato, Elizete Holanda, Flávio Rodrigues, Samuel Nienow, Benoit De Thoisy, Rodrigo A Fernandes Redondo, and Fabrício Santos. “A New Species of Tapir from the Amazon.” Journal of Mammalogy. Oxford University Press, 2013. https://doi.org/10.1644/12-MAMM-A-169.1.","mla":"Cozzuol, Mario, et al. “A New Species of Tapir from the Amazon.” Journal of Mammalogy, vol. 94, no. 6, Oxford University Press, 2013, pp. 1331–45, doi:10.1644/12-MAMM-A-169.1.","short":"M. Cozzuol, C. Clozato, E. Holanda, F. Rodrigues, S. Nienow, B. De Thoisy, R.A. Fernandes Redondo, F. Santos, Journal of Mammalogy 94 (2013) 1331–1345.","ista":"Cozzuol M, Clozato C, Holanda E, Rodrigues F, Nienow S, De Thoisy B, Fernandes Redondo RA, Santos F. 2013. A new species of tapir from the Amazon. Journal of Mammalogy. 94(6), 1331–1345.","apa":"Cozzuol, M., Clozato, C., Holanda, E., Rodrigues, F., Nienow, S., De Thoisy, B., … Santos, F. (2013). A new species of tapir from the Amazon. Journal of Mammalogy. Oxford University Press. https://doi.org/10.1644/12-MAMM-A-169.1","ieee":"M. Cozzuol et al., “A new species of tapir from the Amazon,” Journal of Mammalogy, vol. 94, no. 6. Oxford University Press, pp. 1331–1345, 2013.","ama":"Cozzuol M, Clozato C, Holanda E, et al. A new species of tapir from the Amazon. Journal of Mammalogy. 2013;94(6):1331-1345. doi:10.1644/12-MAMM-A-169.1"},"publication":"Journal of Mammalogy","date_published":"2013-12-01T00:00:00Z","type":"journal_article","issue":"6","abstract":[{"text":"All known species of extant tapirs are allopatric: 1 in southeastern Asia and 3 in Central and South America. The fossil record for tapirs, however, is much wider in geographical range, including Europe, Asia, and North and South America, going back to the late Oligocene, making the present distribution a relict of the original one. We here describe a new species of living Tapirus from the Amazon rain forest, the 1st since T. bairdii Gill, 1865, and the 1st new Perissodactyla in more than 100 years, from both morphological and molecular characters. It is shorter in stature than T. terrestris (Linnaeus, 1758) and has distinctive skull morphology, and it is basal to the clade formed by T. terrestris and T. pinchaque (Roulin, 1829). This highlights the unrecognized biodiversity in western Amazonia, where the biota faces increasing threats. Local peoples have long recognized our new species, suggesting a key role for traditional knowledge in understanding the biodiversity of the region.","lang":"eng"}],"intvolume":" 94","status":"public","title":"A new species of tapir from the Amazon","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"501","oa_version":"Published Version","file":[{"checksum":"8007815078dccac21ecd1cf73a269dc6","date_updated":"2020-07-14T12:46:36Z","date_created":"2018-12-12T10:12:59Z","relation":"main_file","file_id":"4980","file_size":1040765,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2018-940-v1+1_2013_Redondo_A_new.pdf"}],"pubrep_id":"940","month":"12","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1644/12-MAMM-A-169.1","publist_id":"7319","file_date_updated":"2020-07-14T12:46:36Z","department":[{"_id":"JoBo"}],"publisher":"Oxford University Press","publication_status":"published","year":"2013","volume":94,"date_updated":"2021-01-12T08:01:09Z","date_created":"2018-12-11T11:46:49Z","author":[{"full_name":"Cozzuol, Mario","first_name":"Mario","last_name":"Cozzuol"},{"full_name":"Clozato, Camila","first_name":"Camila","last_name":"Clozato"},{"full_name":"Holanda, Elizete","last_name":"Holanda","first_name":"Elizete"},{"full_name":"Rodrigues, Flávio","last_name":"Rodrigues","first_name":"Flávio"},{"first_name":"Samuel","last_name":"Nienow","full_name":"Nienow, Samuel"},{"first_name":"Benoit","last_name":"De Thoisy","full_name":"De Thoisy, Benoit"},{"full_name":"Fernandes Redondo, Rodrigo A","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5837-2793","first_name":"Rodrigo A","last_name":"Fernandes Redondo"},{"full_name":"Santos, Fabrício","first_name":"Fabrício","last_name":"Santos"}]},{"scopus_import":1,"day":"01","publication":"Molecular Biology and Evolution","citation":{"ista":"Tarazona Santos E, Machado M, Magalhães W, Chen R, Lyon F, Burdett L, Crenshaw A, Fabbri C, Pereira L, Pinto L, Fernandes Redondo RA, Sestanovich B, Yeager M, Chanock S. 2013. Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications. Molecular Biology and Evolution. 30(9), 2157–2167.","ieee":"E. Tarazona Santos et al., “Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications,” Molecular Biology and Evolution, vol. 30, no. 9. Oxford University Press, pp. 2157–2167, 2013.","apa":"Tarazona Santos, E., Machado, M., Magalhães, W., Chen, R., Lyon, F., Burdett, L., … Chanock, S. (2013). Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/mst119","ama":"Tarazona Santos E, Machado M, Magalhães W, et al. Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications. Molecular Biology and Evolution. 2013;30(9):2157-2167. doi:10.1093/molbev/mst119","chicago":"Tarazona Santos, Eduardo, Moara Machado, Wagner Magalhães, Renee Chen, Fernanda Lyon, Laurie Burdett, Andrew Crenshaw, et al. “Evolutionary Dynamics of the Human NADPH Oxidase Genes CYBB, CYBA, NCF2, and NCF4: Functional Implications.” Molecular Biology and Evolution. Oxford University Press, 2013. https://doi.org/10.1093/molbev/mst119.","mla":"Tarazona Santos, Eduardo, et al. “Evolutionary Dynamics of the Human NADPH Oxidase Genes CYBB, CYBA, NCF2, and NCF4: Functional Implications.” Molecular Biology and Evolution, vol. 30, no. 9, Oxford University Press, 2013, pp. 2157–67, doi:10.1093/molbev/mst119.","short":"E. Tarazona Santos, M. Machado, W. Magalhães, R. Chen, F. Lyon, L. Burdett, A. Crenshaw, C. Fabbri, L. Pereira, L. Pinto, R.A. Fernandes Redondo, B. Sestanovich, M. Yeager, S. Chanock, Molecular Biology and Evolution 30 (2013) 2157–2167."},"page":"2157 - 2167","date_published":"2013-09-01T00:00:00Z","type":"journal_article","abstract":[{"text":"The phagocyte NADPH oxidase catalyzes the reduction of O2 to reactive oxygen species with microbicidal activity. It is composed of two membrane-spanning subunits, gp91-phox and p22-phox (encoded by CYBB and CYBA, respectively), and three cytoplasmic subunits, p40-phox, p47-phox, and p67-phox (encoded by NCF4, NCF1, and NCF2, respectively). Mutations in any of these genes can result in chronic granulomatous disease, a primary immunodeficiency characterized by recurrent infections. Using evolutionary mapping, we determined that episodes of adaptive natural selection have shaped the extracellular portion of gp91-phox during the evolution of mammals, which suggests that this region may have a function in host-pathogen interactions. On the basis of a resequencing analysis of approximately 35 kb of CYBB, CYBA, NCF2, and NCF4 in 102 ethnically diverse individuals (24 of African ancestry, 31 of European ancestry, 24 of Asian/Oceanians, and 23 US Hispanics), we show that the pattern of CYBA diversity is compatible with balancing natural selection, perhaps mediated by catalase-positive pathogens. NCF2 in Asian populations shows a pattern of diversity characterized by a differentiated haplotype structure. Our study provides insight into the role of pathogen-driven natural selection in an innate immune pathway and sheds light on the role of CYBA in endothelial, nonphagocytic NADPH oxidases, which are relevant in the pathogenesis of cardiovascular and other complex diseases.","lang":"eng"}],"issue":"9","_id":"508","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications","status":"public","intvolume":" 30","oa_version":"Submitted Version","month":"09","external_id":{"pmid":["23821607"]},"oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3748357/","open_access":"1"}],"quality_controlled":"1","doi":"10.1093/molbev/mst119","language":[{"iso":"eng"}],"publist_id":"7310","year":"2013","pmid":1,"publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"JoBo"}],"author":[{"first_name":"Eduardo","last_name":"Tarazona Santos","full_name":"Tarazona Santos, Eduardo"},{"full_name":"Machado, Moara","first_name":"Moara","last_name":"Machado"},{"full_name":"Magalhães, Wagner","first_name":"Wagner","last_name":"Magalhães"},{"full_name":"Chen, Renee","last_name":"Chen","first_name":"Renee"},{"full_name":"Lyon, Fernanda","last_name":"Lyon","first_name":"Fernanda"},{"last_name":"Burdett","first_name":"Laurie","full_name":"Burdett, Laurie"},{"full_name":"Crenshaw, Andrew","first_name":"Andrew","last_name":"Crenshaw"},{"last_name":"Fabbri","first_name":"Cristina","full_name":"Fabbri, Cristina"},{"full_name":"Pereira, Latife","first_name":"Latife","last_name":"Pereira"},{"full_name":"Pinto, Laelia","first_name":"Laelia","last_name":"Pinto"},{"full_name":"Fernandes Redondo, Rodrigo A","last_name":"Fernandes Redondo","first_name":"Rodrigo A","orcid":"0000-0002-5837-2793","id":"409D5C96-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sestanovich, Ben","last_name":"Sestanovich","first_name":"Ben"},{"last_name":"Yeager","first_name":"Meredith","full_name":"Yeager, Meredith"},{"first_name":"Stephen","last_name":"Chanock","full_name":"Chanock, Stephen"}],"date_created":"2018-12-11T11:46:52Z","date_updated":"2021-01-12T08:01:12Z","volume":30},{"date_published":"2012-05-01T00:00:00Z","citation":{"ama":"Ebersberger I, De Matos Simoes R, Kupczok A, et al. A consistent phylogenetic backbone for the fungi. Molecular Biology and Evolution. 2012;29(5):1319-1334. doi:10.1093/molbev/msr285","apa":"Ebersberger, I., De Matos Simoes, R., Kupczok, A., Gube, M., Kothe, E., Voigt, K., & Von Haeseler, A. (2012). A consistent phylogenetic backbone for the fungi. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msr285","ieee":"I. Ebersberger et al., “A consistent phylogenetic backbone for the fungi,” Molecular Biology and Evolution, vol. 29, no. 5. Oxford University Press, pp. 1319–1334, 2012.","ista":"Ebersberger I, De Matos Simoes R, Kupczok A, Gube M, Kothe E, Voigt K, Von Haeseler A. 2012. A consistent phylogenetic backbone for the fungi. Molecular Biology and Evolution. 29(5), 1319–1334.","short":"I. Ebersberger, R. De Matos Simoes, A. Kupczok, M. Gube, E. Kothe, K. Voigt, A. Von Haeseler, Molecular Biology and Evolution 29 (2012) 1319–1334.","mla":"Ebersberger, Ingo, et al. “A Consistent Phylogenetic Backbone for the Fungi.” Molecular Biology and Evolution, vol. 29, no. 5, Oxford University Press, 2012, pp. 1319–34, doi:10.1093/molbev/msr285.","chicago":"Ebersberger, Ingo, Ricardo De Matos Simoes, Anne Kupczok, Matthias Gube, Erika Kothe, Kerstin Voigt, and Arndt Von Haeseler. “A Consistent Phylogenetic Backbone for the Fungi.” Molecular Biology and Evolution. Oxford University Press, 2012. https://doi.org/10.1093/molbev/msr285."},"publication":"Molecular Biology and Evolution","page":"1319 - 1334","has_accepted_license":"1","day":"01","scopus_import":1,"pubrep_id":"384","file":[{"file_name":"IST-2015-384-v1+1_Mol_Biol_Evol-2012-Ebersberger-1319-34.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":754922,"file_id":"5013","relation":"main_file","date_created":"2018-12-12T10:13:30Z","date_updated":"2020-07-14T12:45:40Z","checksum":"d565dcac27d1736c0c378ea6fcf22d69"}],"oa_version":"Published Version","_id":"2411","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 29","title":"A consistent phylogenetic backbone for the fungi","status":"public","ddc":["570","576"],"issue":"5","abstract":[{"text":"The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data-a common practice in phylogenomic analyses-introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses.","lang":"eng"}],"type":"journal_article","doi":"10.1093/molbev/msr285","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"quality_controlled":"1","month":"05","author":[{"first_name":"Ingo","last_name":"Ebersberger","full_name":"Ebersberger, Ingo"},{"last_name":"De Matos Simoes","first_name":"Ricardo","full_name":"De Matos Simoes, Ricardo"},{"full_name":"Kupczok, Anne","last_name":"Kupczok","first_name":"Anne","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gube","first_name":"Matthias","full_name":"Gube, Matthias"},{"last_name":"Kothe","first_name":"Erika","full_name":"Kothe, Erika"},{"full_name":"Voigt, Kerstin","first_name":"Kerstin","last_name":"Voigt"},{"full_name":"Von Haeseler, Arndt","first_name":"Arndt","last_name":"Von Haeseler"}],"volume":29,"date_created":"2018-12-11T11:57:30Z","date_updated":"2021-01-12T06:57:19Z","year":"2012","publisher":"Oxford University Press","department":[{"_id":"JoBo"}],"publication_status":"published","publist_id":"4515","file_date_updated":"2020-07-14T12:45:40Z"},{"quality_controlled":"1","page":"262 - 266","publication":"Behavioural Processes","citation":{"ista":"Jesse F, Riebel K. 2012. Social facilitation of male song by male and female conspecifics in the zebra finch, Taeniopygia guttata. Behavioural Processes. 91(3), 262–266.","apa":"Jesse, F., & Riebel, K. (2012). Social facilitation of male song by male and female conspecifics in the zebra finch, Taeniopygia guttata. Behavioural Processes. Elsevier. https://doi.org/10.1016/j.beproc.2012.09.006","ieee":"F. Jesse and K. Riebel, “Social facilitation of male song by male and female conspecifics in the zebra finch, Taeniopygia guttata,” Behavioural Processes, vol. 91, no. 3. Elsevier, pp. 262–266, 2012.","ama":"Jesse F, Riebel K. Social facilitation of male song by male and female conspecifics in the zebra finch, Taeniopygia guttata. Behavioural Processes. 2012;91(3):262-266. doi:10.1016/j.beproc.2012.09.006","chicago":"Jesse, Fabienne, and Katharina Riebel. “Social Facilitation of Male Song by Male and Female Conspecifics in the Zebra Finch, Taeniopygia Guttata.” Behavioural Processes. Elsevier, 2012. https://doi.org/10.1016/j.beproc.2012.09.006.","mla":"Jesse, Fabienne, and Katharina Riebel. “Social Facilitation of Male Song by Male and Female Conspecifics in the Zebra Finch, Taeniopygia Guttata.” Behavioural Processes, vol. 91, no. 3, Elsevier, 2012, pp. 262–66, doi:10.1016/j.beproc.2012.09.006.","short":"F. Jesse, K. Riebel, Behavioural Processes 91 (2012) 262–266."},"language":[{"iso":"eng"}],"doi":"10.1016/j.beproc.2012.09.006","date_published":"2012-11-01T00:00:00Z","day":"01","month":"11","title":"Social facilitation of male song by male and female conspecifics in the zebra finch, Taeniopygia guttata","status":"public","publication_status":"published","department":[{"_id":"JoBo"}],"intvolume":" 91","publisher":"Elsevier","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2963","year":"2012","date_updated":"2021-01-12T07:40:06Z","date_created":"2018-12-11T12:00:35Z","volume":91,"oa_version":"None","author":[{"full_name":"Jesse, Fabienne","first_name":"Fabienne","last_name":"Jesse","id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Riebel","first_name":"Katharina","full_name":"Riebel, Katharina"}],"type":"journal_article","abstract":[{"text":"Zebra finches are an ubiquitous model system for the study of vocal learning in animal communication. Their song has been well described, but its possible function(s) in social communication are only partly understood. The so-called ‘directed song’ is a high-intensity, high-performance song given during courtship in close proximity to the female, which is known to mediate mate choice and mating. However, this singing mode constitutes only a fraction of zebra finch males’ prolific song output. Potential communicative functions of their second, ‘undirected’ singing mode remain unresolved in the face of contradicting reports of both facilitating and inhibiting effects of social company on singing. We addressed this issue by experimentally manipulating social contexts in a within-subject design, comparing a solo versus male or female only company condition, each lasting for 24 hours. Males’ total song output was significantly higher when a conspecific was in audible and visible distance than when they were alone. Male and female company had an equally facilitating effect on song output. Our findings thus indicate that singing motivation is facilitated rather than inhibited by social company, suggesting that singing in zebra finches might function both in inter- and intrasexual communication. ","lang":"eng"}],"issue":"3","publist_id":"3756"},{"citation":{"ama":"Vilaça S, Fernandes Redondo RA, Lins L, Santos F. Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus). Conservation Genetics. 2012;13(1):293-298. doi:10.1007/s10592-011-0262-5","ista":"Vilaça S, Fernandes Redondo RA, Lins L, Santos F. 2012. Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus). Conservation Genetics. 13(1), 293–298.","apa":"Vilaça, S., Fernandes Redondo, R. A., Lins, L., & Santos, F. (2012). Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus). Conservation Genetics. Springer. https://doi.org/10.1007/s10592-011-0262-5","ieee":"S. Vilaça, R. A. Fernandes Redondo, L. Lins, and F. Santos, “Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus),” Conservation Genetics, vol. 13, no. 1. Springer, pp. 293–298, 2012.","mla":"Vilaça, Sibelle, et al. “Remaining Genetic Diversity in Brazilian Merganser (Mergus Octosetaceus).” Conservation Genetics, vol. 13, no. 1, Springer, 2012, pp. 293–98, doi:10.1007/s10592-011-0262-5.","short":"S. Vilaça, R.A. Fernandes Redondo, L. Lins, F. Santos, Conservation Genetics 13 (2012) 293–298.","chicago":"Vilaça, Sibelle, Rodrigo A Fernandes Redondo, Lívia Lins, and Fabrício Santos. “Remaining Genetic Diversity in Brazilian Merganser (Mergus Octosetaceus).” Conservation Genetics. Springer, 2012. https://doi.org/10.1007/s10592-011-0262-5."},"publication":"Conservation Genetics","page":"293 - 298","quality_controlled":"1","date_published":"2012-02-01T00:00:00Z","doi":"10.1007/s10592-011-0262-5","language":[{"iso":"eng"}],"scopus_import":1,"day":"01","month":"02","_id":"3247","acknowledgement":"The present study received grants from FAPEMIG, CNPq, Petrobras Ambiental and Fundação O Boticário de Conservação da Natureza, and followed all ethical guidelines and legal requirements of Brazil for sampling and studying an endangered species.\r\nWe thank the Specialist Work Group for the Conservation of Brazilian Merganser for valuable discussions and opinions on this manuscript. We also thank all the staff from Instituto Terra Brasilis and Funatura (Vivian S. Braz and Gislaine Disconzi) for collecting the samples at Serra da Canastra and Chapada dos Veadeiros, respectively; Dario A. Lijtmaerand and Pablo Tubaro for providing the samples from Argentina, Bradley C. Livezey for sending copies of his papers, and Geoff M. Hilton and Paulo de Tarso Z. Antas for useful suggestions that greatly improved this manuscript.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2012","department":[{"_id":"JoBo"}],"publisher":"Springer","intvolume":" 13","title":"Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus)","publication_status":"published","status":"public","author":[{"first_name":"Sibelle","last_name":"Vilaça","full_name":"Vilaça, Sibelle"},{"first_name":"Rodrigo A","last_name":"Fernandes Redondo","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5837-2793","full_name":"Fernandes Redondo, Rodrigo A"},{"last_name":"Lins","first_name":"Lívia","full_name":"Lins, Lívia"},{"first_name":"Fabrício","last_name":"Santos","full_name":"Santos, Fabrício"}],"volume":13,"oa_version":"None","date_created":"2018-12-11T12:02:15Z","date_updated":"2021-01-12T07:42:05Z","type":"journal_article","issue":"1","publist_id":"3420","abstract":[{"text":"The Brazilian Merganser is a very rare and threatened species that nowadays inhabits only a few protected areas and their surroundings in the Brazilian territory. In order to estimate the remaining genetic diversity and population structure in this species, two mitochondrial genes were sequenced in 39 individuals belonging to two populations and in one individual collected in Argentina in 1950. We found a highly significant divergence between two major remaining populations of Mergus octosetaceus, which suggests a historical population structure in this species. Furthermore, two deeply divergent lineages were found in a single location, which could due to current or historical secondary contact. Based on the available genetic data, we point out future directions which would contribute to design strategies for conservation and management of this threatened species.","lang":"eng"}]},{"scopus_import":1,"day":"01","page":"172 - 184","citation":{"ieee":"A. Pereira et al., “A vaccinia virus-driven interplay between the MKK4/7-JNK1/2 pathway and cytoskeleton reorganization,” Journal of Virology, vol. 86, no. 1. ASM, pp. 172–184, 2012.","apa":"Pereira, A., Leite, F., Brasil, B., Soares Martins, J., Torres, A., Pimenta, P., … Bonjardim, C. (2012). A vaccinia virus-driven interplay between the MKK4/7-JNK1/2 pathway and cytoskeleton reorganization. Journal of Virology. ASM. https://doi.org/10.1128/JVI.05638-11","ista":"Pereira A, Leite F, Brasil B, Soares Martins J, Torres A, Pimenta P, Souto Padrón T, Tranktman P, Ferreira P, Kroon E, Bonjardim C. 2012. A vaccinia virus-driven interplay between the MKK4/7-JNK1/2 pathway and cytoskeleton reorganization. Journal of Virology. 86(1), 172–184.","ama":"Pereira A, Leite F, Brasil B, et al. A vaccinia virus-driven interplay between the MKK4/7-JNK1/2 pathway and cytoskeleton reorganization. Journal of Virology. 2012;86(1):172-184. doi:10.1128/JVI.05638-11","chicago":"Pereira, Anna, Flávia Leite, Bruno Brasil, Jamaria Soares Martins, Alice Torres, Paulo Pimenta, Thais Souto Padrón, et al. “A Vaccinia Virus-Driven Interplay between the MKK4/7-JNK1/2 Pathway and Cytoskeleton Reorganization.” Journal of Virology. ASM, 2012. https://doi.org/10.1128/JVI.05638-11.","short":"A. Pereira, F. Leite, B. Brasil, J. Soares Martins, A. Torres, P. Pimenta, T. Souto Padrón, P. Tranktman, P. Ferreira, E. Kroon, C. Bonjardim, Journal of Virology 86 (2012) 172–184.","mla":"Pereira, Anna, et al. “A Vaccinia Virus-Driven Interplay between the MKK4/7-JNK1/2 Pathway and Cytoskeleton Reorganization.” Journal of Virology, vol. 86, no. 1, ASM, 2012, pp. 172–84, doi:10.1128/JVI.05638-11."},"publication":"Journal of Virology","date_published":"2012-01-01T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Viral manipulation of transduction pathways associated with key cellular functions such as survival, response to microbial infection, and cytoskeleton reorganization can provide the supportive milieu for a productive infection. Here, we demonstrate that vaccinia virus (VACV) infection leads to activation of the stress-activated protein kinase (SAPK)/extracellular signal-regulated kinase (ERK) 4/7 (MKK4/7)-c-Jun N-terminal protein kinase 1/2 (JNK1/2) pathway; further, the stimulation of this pathway requires postpenetration, prereplicative events in the viral replication cycle. Although the formation of intracellular mature virus (IMV) was not affected in MKK4/7- or JNK1/2-knockout (KO) cells, we did note an accentuated deregulation of microtubule and actin network organization in infected JNK1/2-KO cells. This was followed by deregulated viral trafficking to the periphery and enhanced enveloped particle release. Furthermore, VACV infection induced alterations in the cell contractility and morphology, and cell migration was reduced in the JNK-KO cells. In addition, phosphorylation of proteins implicated with early cell contractility and cell migration, such as microtubule-associated protein 1B and paxillin, respectively, was not detected in the VACV-infected KO cells. In sum, our findings uncover a regulatory role played by the MKK4/7-JNK1/2 pathway in cytoskeleton reorganization during VACV infection.\r\n"}],"intvolume":" 86","status":"public","title":"A vaccinia virus-driven interplay between the MKK4/7-JNK1/2 pathway and cytoskeleton reorganization","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3289","oa_version":"Submitted Version","month":"01","quality_controlled":"1","external_id":{"pmid":["22031940"]},"oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3255887/"}],"language":[{"iso":"eng"}],"doi":"10.1128/JVI.05638-11","publist_id":"3356","publisher":"ASM","department":[{"_id":"JoBo"}],"publication_status":"published","pmid":1,"year":"2012","acknowledgement":"This work was supported by grants from Fundação de Amparo a Pesquisa do Estado de Minas Gerais (FAPEMIG), the Brazilian Federal Agency for Support and Evaluation of Graduate Education (CAPES), and the National Council for Scientific and Technological Development (CNPq). A.C.T.C.P., B.S.A.F.B., F.G.G.L., and J.A.P.S.-M. were recipients of predoctoral fellowships from CNPq. C.A.B., E.G.K., T.S.-P., P.F.P.P., and P.C.P.F. are recipients of research fellowships from CNPq. \r\n\r\n\r\nWe are grateful to Angela S. Lopes, Ilda M. V. Gama, João R. dos Santos, and Andreza A. Carvalho for their secretarial/technical assistance and to Fernanda Gambogi for help with immunofluorescence microscopy. We also thank M. C. Sogayar (Department of Biochemistry, University of São Paulo, São Paulo, Brazil), who kindly provided us with the A31 cell line, and R. Davis (Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA) for the WT and JNK1/2-, MKK4-, MKK7-, and MKK4/7-KO cells. VACV WR was from C. Jungwirth (Universität Würzburg, Würzburg, Germany). The recombinant VACV vF13L-GFP and the rabbit polyclonal antibodies against viral proteins, B5R, D8L, L1R, and A36R, were from B. Moss (NIAID, Bethesda, MD). The pcDNA3-Myc-JNK2-MKK7 WT plasmid was from Eugen Kerkhoff (Universität Würzburg, Würzburg, Germany). We also thank Flávio G. da Fonseca (UFMG, Belo Horizonte, MG, Brazil) and Kathleen A. Boyle (Medical College of Wisconsin, Milwaukee, WI) for critically reading the manuscript.","volume":86,"date_updated":"2021-01-12T07:42:25Z","date_created":"2018-12-11T12:02:29Z","author":[{"full_name":"Pereira, Anna","last_name":"Pereira","first_name":"Anna"},{"full_name":"Leite, Flávia","id":"36705F98-F248-11E8-B48F-1D18A9856A87","first_name":"Flávia","last_name":"Leite"},{"full_name":"Brasil, Bruno","last_name":"Brasil","first_name":"Bruno"},{"full_name":"Soares Martins, Jamaria","first_name":"Jamaria","last_name":"Soares Martins"},{"full_name":"Torres, Alice","last_name":"Torres","first_name":"Alice"},{"first_name":"Paulo","last_name":"Pimenta","full_name":"Pimenta, Paulo"},{"full_name":"Souto Padrón, Thais","last_name":"Souto Padrón","first_name":"Thais"},{"last_name":"Tranktman","first_name":"Paula","full_name":"Tranktman, Paula"},{"first_name":"Paulo","last_name":"Ferreira","full_name":"Ferreira, Paulo"},{"first_name":"Erna","last_name":"Kroon","full_name":"Kroon, Erna"},{"full_name":"Bonjardim, Cláudio","last_name":"Bonjardim","first_name":"Cláudio"}]},{"date_created":"2018-12-11T12:02:57Z","date_updated":"2021-01-12T07:43:01Z","volume":60,"oa_version":"Submitted Version","author":[{"full_name":"Kupczok, Anne","first_name":"Anne","last_name":"Kupczok","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87"}],"status":"public","publication_status":"published","title":"Consequences of different null models on the tree shape bias of supertree methods","department":[{"_id":"JoBo"}],"intvolume":" 60","publisher":"Oxford University Press","_id":"3370","year":"2011","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Supertree methods are widely applied and give rise to new conclusions about phylogenies (e.g., Bininda-Emonds et al. 2007). Although several desiderata for supertree methods exist (Wilkinson, Thorley, et al. 2004), only few of them have been studied in greater detail, examples include shape bias (Wilkinson et al. 2005) or pareto properties (Wilkinson et al. 2007). Here I look more closely at two matrix representation methods, matrix representation with compatibility (MRC) and matrix representation with parsimony (MRP). Different null models of random data are studied and the resulting tree shapes are investigated. Thereby I consider unrooted trees and a bias in tree shape is determined by a tree balance measure. The measure for unrooted trees is a modification of a tree balance measure for rooted trees. I observe that depending on the underlying null model of random data, the methods may resolve conflict in favor of more balanced tree shapes. The analyses refer only to trees with the same taxon set, also known as the consensus setting (e.g., Wilkinson et al. 2007), but I will be able to draw conclusions on how to deal with missing data."}],"issue":"2","publist_id":"3241","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1093/sysbio/syq086","date_published":"2011-03-01T00:00:00Z","quality_controlled":"1","page":"218 - 225","publication":"Systematic Biology","main_file_link":[{"open_access":"1","url":"http://eprints.cs.univie.ac.at/3226/"}],"citation":{"chicago":"Kupczok, Anne. “Consequences of Different Null Models on the Tree Shape Bias of Supertree Methods.” Systematic Biology. Oxford University Press, 2011. https://doi.org/10.1093/sysbio/syq086.","short":"A. Kupczok, Systematic Biology 60 (2011) 218–225.","mla":"Kupczok, Anne. “Consequences of Different Null Models on the Tree Shape Bias of Supertree Methods.” Systematic Biology, vol. 60, no. 2, Oxford University Press, 2011, pp. 218–25, doi:10.1093/sysbio/syq086.","apa":"Kupczok, A. (2011). Consequences of different null models on the tree shape bias of supertree methods. Systematic Biology. Oxford University Press. https://doi.org/10.1093/sysbio/syq086","ieee":"A. Kupczok, “Consequences of different null models on the tree shape bias of supertree methods,” Systematic Biology, vol. 60, no. 2. Oxford University Press, pp. 218–225, 2011.","ista":"Kupczok A. 2011. Consequences of different null models on the tree shape bias of supertree methods. Systematic Biology. 60(2), 218–225.","ama":"Kupczok A. Consequences of different null models on the tree shape bias of supertree methods. Systematic Biology. 2011;60(2):218-225. doi:10.1093/sysbio/syq086"},"oa":1,"day":"01","month":"03"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Background: Supertree methods combine overlapping input trees into a larger supertree. Here, I consider split-based supertree methods that first extract the split information of the input trees and subsequently combine this split information into a phylogeny. Well known split-based supertree methods are matrix representation with parsimony and matrix representation with compatibility. Combining input trees on the same taxon set, as in the consensus setting, is a well-studied task and it is thus desirable to generalize consensus methods to supertree methods. Results: Here, three variants of majority-rule (MR) supertrees that generalize majority-rule consensus trees are investigated. I provide simple formulas for computing the respective score for bifurcating input- and supertrees. These score computations, together with a heuristic tree search minmizing the scores, were implemented in the python program PluMiST (Plus- and Minus SuperTrees) available from http://www.cibiv.at/software/ plumist. The different MR methods were tested by simulation and on real data sets. The search heuristic was successful in combining compatible input trees. When combining incompatible input trees, especially one variant, MR(-) supertrees, performed well. Conclusions: The presented framework allows for an efficient score computation of three majority-rule supertree variants and input trees. I combined the score computation with a heuristic search over the supertree space. The implementation was tested by simulation and on real data sets and showed promising results. Especially the MR(-) variant seems to be a reasonable score for supertree reconstruction. Generalizing these computations to multifurcating trees is an open problem, which may be tackled using this framework."}],"issue":"205","status":"public","ddc":["576"],"title":"Split based computation of majority rule supertrees","intvolume":" 11","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"3387","file":[{"creator":"system","file_size":465042,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2015-372-v1+1_1471-2148-11-205.pdf","checksum":"68da8d04af1b97b4cbe8606e2f92ddd8","date_updated":"2020-07-14T12:46:11Z","date_created":"2018-12-12T10:14:09Z","file_id":"5058","relation":"main_file"}],"oa_version":"Published Version","pubrep_id":"372","scopus_import":1,"day":"13","has_accepted_license":"1","publication":"BMC Evolutionary Biology","citation":{"chicago":"Kupczok, Anne. “Split Based Computation of Majority Rule Supertrees.” BMC Evolutionary Biology. BioMed Central, 2011. https://doi.org/10.1186/1471-2148-11-205.","short":"A. Kupczok, BMC Evolutionary Biology 11 (2011).","mla":"Kupczok, Anne. “Split Based Computation of Majority Rule Supertrees.” BMC Evolutionary Biology, vol. 11, no. 205, 205, BioMed Central, 2011, doi:10.1186/1471-2148-11-205.","ieee":"A. Kupczok, “Split based computation of majority rule supertrees,” BMC Evolutionary Biology, vol. 11, no. 205. BioMed Central, 2011.","apa":"Kupczok, A. (2011). Split based computation of majority rule supertrees. BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-11-205","ista":"Kupczok A. 2011. Split based computation of majority rule supertrees. BMC Evolutionary Biology. 11(205), 205.","ama":"Kupczok A. Split based computation of majority rule supertrees. BMC Evolutionary Biology. 2011;11(205). doi:10.1186/1471-2148-11-205"},"date_published":"2011-07-13T00:00:00Z","article_number":"205","file_date_updated":"2020-07-14T12:46:11Z","publist_id":"3219","publication_status":"published","publisher":"BioMed Central","department":[{"_id":"JoBo"}],"year":"2011","date_created":"2018-12-11T12:03:03Z","date_updated":"2021-01-12T07:43:08Z","volume":11,"author":[{"last_name":"Kupczok","first_name":"Anne","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Kupczok, Anne"}],"month":"07","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1186/1471-2148-11-205"},{"article_number":"37","file_date_updated":"2020-07-14T12:45:40Z","publist_id":"4517","publication_status":"published","department":[{"_id":"JoBo"}],"publisher":"BioMed Central","acknowledgement":"Financial support from the Wiener Wissenschafts-, Forschungs- and Technologiefonds (WWTF) is greatly appreciated. A.v.H. acknowledges support from the German Research Foundation (DFG, SPP-1174).","year":"2010","date_created":"2018-12-11T11:57:30Z","date_updated":"2021-01-12T06:57:18Z","volume":5,"author":[{"full_name":"Kupczok, Anne","first_name":"Anne","last_name":"Kupczok","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schmidt","first_name":"Heiko","full_name":"Schmidt, Heiko"},{"first_name":"Arndt","last_name":"Von Haeseler","full_name":"Von Haeseler, Arndt"}],"month":"12","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1186/1748-7188-5-37","type":"journal_article","abstract":[{"lang":"eng","text":"Background: The availability of many gene alignments with overlapping taxon sets raises the question of which strategy is the best to infer species phylogenies from multiple gene information. Methods and programs abound that use the gene alignment in different ways to reconstruct the species tree. In particular, different methods combine the original data at different points along the way from the underlying sequences to the final tree. Accordingly, they are classified into superalignment, supertree and medium-level approaches. Here, we present a simulation study to compare different methods from each of these three approaches.\r\n\r\nResults: We observe that superalignment methods usually outperform the other approaches over a wide range of parameters including sparse data and gene-specific evolutionary parameters. In the presence of high incongruency among gene trees, however, other combination methods show better performance than the superalignment approach. Surprisingly, some supertree and medium-level methods exhibit, on average, worse results than a single gene phylogeny with complete taxon information.\r\n\r\nConclusions: For some methods, using the reconstructed gene tree as an estimation of the species tree is superior to the combination of incomplete information. Superalignment usually performs best since it is less susceptible to stochastic error. Supertree methods can outperform superalignment in the presence of gene-tree conflict."}],"issue":"1","ddc":["576"],"title":"Accuracy of phylogeny reconstruction methods combining overlapping gene data sets ","status":"public","intvolume":" 5","_id":"2409","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"content_type":"application/pdf","file_size":723929,"creator":"system","access_level":"open_access","file_name":"IST-2018-939-v1+1_2010_Kupczok_Accuracy_of.pdf","checksum":"e2497285388bc4da629bafb46662eb43","date_updated":"2020-07-14T12:45:40Z","date_created":"2018-12-12T10:09:16Z","relation":"main_file","file_id":"4739"}],"oa_version":"Published Version","pubrep_id":"939","scopus_import":1,"day":"06","has_accepted_license":"1","publication":"Algorithms for Molecular Biology","citation":{"apa":"Kupczok, A., Schmidt, H., & Von Haeseler, A. (2010). Accuracy of phylogeny reconstruction methods combining overlapping gene data sets . Algorithms for Molecular Biology. BioMed Central. https://doi.org/10.1186/1748-7188-5-37","ieee":"A. Kupczok, H. Schmidt, and A. Von Haeseler, “Accuracy of phylogeny reconstruction methods combining overlapping gene data sets ,” Algorithms for Molecular Biology, vol. 5, no. 1. BioMed Central, 2010.","ista":"Kupczok A, Schmidt H, Von Haeseler A. 2010. Accuracy of phylogeny reconstruction methods combining overlapping gene data sets . Algorithms for Molecular Biology. 5(1), 37.","ama":"Kupczok A, Schmidt H, Von Haeseler A. Accuracy of phylogeny reconstruction methods combining overlapping gene data sets . Algorithms for Molecular Biology. 2010;5(1). doi:10.1186/1748-7188-5-37","chicago":"Kupczok, Anne, Heiko Schmidt, and Arndt Von Haeseler. “Accuracy of Phylogeny Reconstruction Methods Combining Overlapping Gene Data Sets .” Algorithms for Molecular Biology. BioMed Central, 2010. https://doi.org/10.1186/1748-7188-5-37.","short":"A. Kupczok, H. Schmidt, A. Von Haeseler, Algorithms for Molecular Biology 5 (2010).","mla":"Kupczok, Anne, et al. “Accuracy of Phylogeny Reconstruction Methods Combining Overlapping Gene Data Sets .” Algorithms for Molecular Biology, vol. 5, no. 1, 37, BioMed Central, 2010, doi:10.1186/1748-7188-5-37."},"date_published":"2010-12-06T00:00:00Z"}]