[{"citation":{"mla":"Vilaça, Sibelle, et al. “Remaining Genetic Diversity in Brazilian Merganser (Mergus Octosetaceus).” <i>Conservation Genetics</i>, vol. 13, no. 1, Springer, 2012, pp. 293–98, doi:<a href=\"https://doi.org/10.1007/s10592-011-0262-5\">10.1007/s10592-011-0262-5</a>.","short":"S. Vilaça, R.A. Fernandes Redondo, L. Lins, F. Santos, Conservation Genetics 13 (2012) 293–298.","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.","ama":"Vilaça S, Fernandes Redondo RA, Lins L, Santos F. Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus). <i>Conservation Genetics</i>. 2012;13(1):293-298. doi:<a href=\"https://doi.org/10.1007/s10592-011-0262-5\">10.1007/s10592-011-0262-5</a>","apa":"Vilaça, S., Fernandes Redondo, R. A., Lins, L., &#38; Santos, F. (2012). Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus). <i>Conservation Genetics</i>. Springer. <a href=\"https://doi.org/10.1007/s10592-011-0262-5\">https://doi.org/10.1007/s10592-011-0262-5</a>","chicago":"Vilaça, Sibelle, Rodrigo A Fernandes Redondo, Lívia Lins, and Fabrício Santos. “Remaining Genetic Diversity in Brazilian Merganser (Mergus Octosetaceus).” <i>Conservation Genetics</i>. Springer, 2012. <a href=\"https://doi.org/10.1007/s10592-011-0262-5\">https://doi.org/10.1007/s10592-011-0262-5</a>.","ieee":"S. Vilaça, R. A. Fernandes Redondo, L. Lins, and F. Santos, “Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus),” <i>Conservation Genetics</i>, vol. 13, no. 1. Springer, pp. 293–298, 2012."},"year":"2012","date_updated":"2021-01-12T07:42:05Z","type":"journal_article","date_published":"2012-02-01T00:00:00Z","day":"01","doi":"10.1007/s10592-011-0262-5","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"}],"volume":13,"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","status":"public","scopus_import":1,"_id":"3247","publication":"Conservation Genetics","issue":"1","author":[{"last_name":"Vilaça","first_name":"Sibelle","full_name":"Vilaça, Sibelle"},{"last_name":"Fernandes Redondo","first_name":"Rodrigo A","full_name":"Fernandes Redondo, Rodrigo A","orcid":"0000-0002-5837-2793","id":"409D5C96-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lins, Lívia","last_name":"Lins","first_name":"Lívia"},{"first_name":"Fabrício","last_name":"Santos","full_name":"Santos, Fabrício"}],"date_created":"2018-12-11T12:02:15Z","department":[{"_id":"JoBo"}],"publication_status":"published","oa_version":"None","intvolume":"        13","month":"02","title":"Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus)","quality_controlled":"1","page":"293 - 298","language":[{"iso":"eng"}],"publisher":"Springer"},{"publisher":"ASM","page":"172 - 184","quality_controlled":"1","publication_status":"published","date_created":"2018-12-11T12:02:29Z","department":[{"_id":"JoBo"}],"title":"A vaccinia virus-driven interplay between the MKK4/7-JNK1/2 pathway and cytoskeleton reorganization","intvolume":"        86","_id":"3289","pmid":1,"scopus_import":1,"author":[{"first_name":"Anna","last_name":"Pereira","full_name":"Pereira, Anna"},{"id":"36705F98-F248-11E8-B48F-1D18A9856A87","first_name":"Flávia","last_name":"Leite","full_name":"Leite, Flávia"},{"full_name":"Brasil, Bruno","first_name":"Bruno","last_name":"Brasil"},{"full_name":"Soares Martins, Jamaria","first_name":"Jamaria","last_name":"Soares Martins"},{"last_name":"Torres","first_name":"Alice","full_name":"Torres, Alice"},{"first_name":"Paulo","last_name":"Pimenta","full_name":"Pimenta, Paulo"},{"full_name":"Souto Padrón, Thais","last_name":"Souto Padrón","first_name":"Thais"},{"full_name":"Tranktman, Paula","first_name":"Paula","last_name":"Tranktman"},{"full_name":"Ferreira, Paulo","first_name":"Paulo","last_name":"Ferreira"},{"first_name":"Erna","last_name":"Kroon","full_name":"Kroon, Erna"},{"full_name":"Bonjardim, Cláudio","last_name":"Bonjardim","first_name":"Cláudio"}],"issue":"1","volume":86,"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.","doi":"10.1128/JVI.05638-11","day":"01","abstract":[{"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","lang":"eng"}],"date_updated":"2021-01-12T07:42:25Z","citation":{"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. <i>Journal of Virology</i>. ASM. <a href=\"https://doi.org/10.1128/JVI.05638-11\">https://doi.org/10.1128/JVI.05638-11</a>","ama":"Pereira A, Leite F, Brasil B, et al. A vaccinia virus-driven interplay between the MKK4/7-JNK1/2 pathway and cytoskeleton reorganization. <i>Journal of Virology</i>. 2012;86(1):172-184. doi:<a href=\"https://doi.org/10.1128/JVI.05638-11\">10.1128/JVI.05638-11</a>","ieee":"A. Pereira <i>et al.</i>, “A vaccinia virus-driven interplay between the MKK4/7-JNK1/2 pathway and cytoskeleton reorganization,” <i>Journal of Virology</i>, vol. 86, no. 1. ASM, pp. 172–184, 2012.","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.” <i>Journal of Virology</i>. ASM, 2012. <a href=\"https://doi.org/10.1128/JVI.05638-11\">https://doi.org/10.1128/JVI.05638-11</a>.","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.” <i>Journal of Virology</i>, vol. 86, no. 1, ASM, 2012, pp. 172–84, doi:<a href=\"https://doi.org/10.1128/JVI.05638-11\">10.1128/JVI.05638-11</a>.","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."},"year":"2012","external_id":{"pmid":["22031940"]},"language":[{"iso":"eng"}],"oa_version":"Submitted Version","month":"01","publication":"Journal of Virology","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3255887/"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","oa":1,"publist_id":"3356","date_published":"2012-01-01T00:00:00Z","type":"journal_article"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","file":[{"file_size":754922,"checksum":"d565dcac27d1736c0c378ea6fcf22d69","date_created":"2018-12-12T10:13:30Z","content_type":"application/pdf","file_name":"IST-2015-384-v1+1_Mol_Biol_Evol-2012-Ebersberger-1319-34.pdf","date_updated":"2020-07-14T12:45:40Z","access_level":"open_access","relation":"main_file","creator":"system","file_id":"5013"}],"date_published":"2012-05-01T00:00:00Z","type":"journal_article","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"publist_id":"4515","oa":1,"language":[{"iso":"eng"}],"publication":"Molecular Biology and Evolution","has_accepted_license":"1","month":"05","oa_version":"Published Version","ddc":["570","576"],"volume":29,"date_updated":"2021-01-12T06:57:19Z","year":"2012","citation":{"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.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2012. <a href=\"https://doi.org/10.1093/molbev/msr285\">https://doi.org/10.1093/molbev/msr285</a>.","ieee":"I. Ebersberger <i>et al.</i>, “A consistent phylogenetic backbone for the fungi,” <i>Molecular Biology and Evolution</i>, vol. 29, no. 5. Oxford University Press, pp. 1319–1334, 2012.","apa":"Ebersberger, I., De Matos Simoes, R., Kupczok, A., Gube, M., Kothe, E., Voigt, K., &#38; Von Haeseler, A. (2012). A consistent phylogenetic backbone for the fungi. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msr285\">https://doi.org/10.1093/molbev/msr285</a>","ama":"Ebersberger I, De Matos Simoes R, Kupczok A, et al. A consistent phylogenetic backbone for the fungi. <i>Molecular Biology and Evolution</i>. 2012;29(5):1319-1334. doi:<a href=\"https://doi.org/10.1093/molbev/msr285\">10.1093/molbev/msr285</a>","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.” <i>Molecular Biology and Evolution</i>, vol. 29, no. 5, Oxford University Press, 2012, pp. 1319–34, doi:<a href=\"https://doi.org/10.1093/molbev/msr285\">10.1093/molbev/msr285</a>."},"abstract":[{"lang":"eng","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."}],"doi":"10.1093/molbev/msr285","day":"01","file_date_updated":"2020-07-14T12:45:40Z","page":"1319 - 1334","quality_controlled":"1","publisher":"Oxford University Press","author":[{"full_name":"Ebersberger, Ingo","last_name":"Ebersberger","first_name":"Ingo"},{"full_name":"De Matos Simoes, Ricardo","first_name":"Ricardo","last_name":"De Matos Simoes"},{"full_name":"Kupczok, Anne","last_name":"Kupczok","first_name":"Anne","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matthias","last_name":"Gube","full_name":"Gube, Matthias"},{"last_name":"Kothe","first_name":"Erika","full_name":"Kothe, Erika"},{"full_name":"Voigt, Kerstin","last_name":"Voigt","first_name":"Kerstin"},{"first_name":"Arndt","last_name":"Von Haeseler","full_name":"Von Haeseler, Arndt"}],"issue":"5","_id":"2411","scopus_import":1,"license":"https://creativecommons.org/licenses/by-nc/4.0/","title":"A consistent phylogenetic backbone for the fungi","pubrep_id":"384","intvolume":"        29","publication_status":"published","department":[{"_id":"JoBo"}],"date_created":"2018-12-11T11:57:30Z"},{"oa_version":"Submitted Version","publication_status":"published","department":[{"_id":"JoBo"}],"date_created":"2018-12-11T12:02:57Z","title":"Consequences of different null models on the tree shape bias of supertree methods","month":"03","intvolume":"        60","publication":"Systematic Biology","_id":"3370","author":[{"id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Kupczok","first_name":"Anne","full_name":"Kupczok, Anne"}],"issue":"2","publisher":"Oxford University Press","page":"218 - 225","quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1093/sysbio/syq086","day":"01","abstract":[{"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.","lang":"eng"}],"oa":1,"publist_id":"3241","date_updated":"2021-01-12T07:43:01Z","year":"2011","citation":{"chicago":"Kupczok, Anne. “Consequences of Different Null Models on the Tree Shape Bias of Supertree Methods.” <i>Systematic Biology</i>. Oxford University Press, 2011. <a href=\"https://doi.org/10.1093/sysbio/syq086\">https://doi.org/10.1093/sysbio/syq086</a>.","ieee":"A. Kupczok, “Consequences of different null models on the tree shape bias of supertree methods,” <i>Systematic Biology</i>, vol. 60, no. 2. Oxford University Press, pp. 218–225, 2011.","apa":"Kupczok, A. (2011). Consequences of different null models on the tree shape bias of supertree methods. <i>Systematic Biology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/sysbio/syq086\">https://doi.org/10.1093/sysbio/syq086</a>","ama":"Kupczok A. Consequences of different null models on the tree shape bias of supertree methods. <i>Systematic Biology</i>. 2011;60(2):218-225. doi:<a href=\"https://doi.org/10.1093/sysbio/syq086\">10.1093/sysbio/syq086</a>","ista":"Kupczok A. 2011. Consequences of different null models on the tree shape bias of supertree methods. Systematic Biology. 60(2), 218–225.","mla":"Kupczok, Anne. “Consequences of Different Null Models on the Tree Shape Bias of Supertree Methods.” <i>Systematic Biology</i>, vol. 60, no. 2, Oxford University Press, 2011, pp. 218–25, doi:<a href=\"https://doi.org/10.1093/sysbio/syq086\">10.1093/sysbio/syq086</a>.","short":"A. Kupczok, Systematic Biology 60 (2011) 218–225."},"date_published":"2011-03-01T00:00:00Z","type":"journal_article","volume":60,"main_file_link":[{"open_access":"1","url":"http://eprints.cs.univie.ac.at/3226/"}],"status":"public","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"ddc":["576"],"volume":11,"citation":{"ieee":"A. Kupczok, “Split based computation of majority rule supertrees,” <i>BMC Evolutionary Biology</i>, vol. 11, no. 205. BioMed Central, 2011.","chicago":"Kupczok, Anne. “Split Based Computation of Majority Rule Supertrees.” <i>BMC Evolutionary Biology</i>. BioMed Central, 2011. <a href=\"https://doi.org/10.1186/1471-2148-11-205\">https://doi.org/10.1186/1471-2148-11-205</a>.","ama":"Kupczok A. Split based computation of majority rule supertrees. <i>BMC Evolutionary Biology</i>. 2011;11(205). doi:<a href=\"https://doi.org/10.1186/1471-2148-11-205\">10.1186/1471-2148-11-205</a>","apa":"Kupczok, A. (2011). Split based computation of majority rule supertrees. <i>BMC Evolutionary Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2148-11-205\">https://doi.org/10.1186/1471-2148-11-205</a>","ista":"Kupczok A. 2011. Split based computation of majority rule supertrees. BMC Evolutionary Biology. 11(205), 205.","mla":"Kupczok, Anne. “Split Based Computation of Majority Rule Supertrees.” <i>BMC Evolutionary Biology</i>, vol. 11, no. 205, 205, BioMed Central, 2011, doi:<a href=\"https://doi.org/10.1186/1471-2148-11-205\">10.1186/1471-2148-11-205</a>.","short":"A. Kupczok, BMC Evolutionary Biology 11 (2011)."},"year":"2011","date_updated":"2021-01-12T07:43:08Z","abstract":[{"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.","lang":"eng"}],"day":"13","doi":"10.1186/1471-2148-11-205","file_date_updated":"2020-07-14T12:46:11Z","quality_controlled":"1","publisher":"BioMed Central","issue":"205","author":[{"id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Kupczok","first_name":"Anne","full_name":"Kupczok, Anne"}],"license":"https://creativecommons.org/licenses/by/4.0/","scopus_import":1,"_id":"3387","intvolume":"        11","pubrep_id":"372","title":"Split based computation of majority rule supertrees","department":[{"_id":"JoBo"}],"date_created":"2018-12-11T12:03:03Z","publication_status":"published","status":"public","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"system","file_id":"5058","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_name":"IST-2015-372-v1+1_1471-2148-11-205.pdf","date_updated":"2020-07-14T12:46:11Z","checksum":"68da8d04af1b97b4cbe8606e2f92ddd8","file_size":465042,"date_created":"2018-12-12T10:14:09Z"}],"type":"journal_article","date_published":"2011-07-13T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publist_id":"3219","oa":1,"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"BMC Evolutionary Biology","article_number":"205","month":"07","oa_version":"Published Version"},{"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"Algorithms for Molecular Biology","article_number":"37","month":"12","oa_version":"Published Version","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","relation":"main_file","creator":"system","file_id":"4739","file_size":723929,"checksum":"e2497285388bc4da629bafb46662eb43","date_created":"2018-12-12T10:09:16Z","file_name":"IST-2018-939-v1+1_2010_Kupczok_Accuracy_of.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:45:40Z"}],"type":"journal_article","date_published":"2010-12-06T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publist_id":"4517","oa":1,"file_date_updated":"2020-07-14T12:45:40Z","quality_controlled":"1","publisher":"BioMed Central","issue":"1","author":[{"first_name":"Anne","last_name":"Kupczok","full_name":"Kupczok, Anne","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schmidt, Heiko","last_name":"Schmidt","first_name":"Heiko"},{"full_name":"Von Haeseler, Arndt","last_name":"Von Haeseler","first_name":"Arndt"}],"scopus_import":1,"_id":"2409","intvolume":"         5","title":"Accuracy of phylogeny reconstruction methods combining overlapping gene data sets ","pubrep_id":"939","date_created":"2018-12-11T11:57:30Z","department":[{"_id":"JoBo"}],"publication_status":"published","ddc":["576"],"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).","volume":5,"citation":{"apa":"Kupczok, A., Schmidt, H., &#38; Von Haeseler, A. (2010). Accuracy of phylogeny reconstruction methods combining overlapping gene data sets . <i>Algorithms for Molecular Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1748-7188-5-37\">https://doi.org/10.1186/1748-7188-5-37</a>","ama":"Kupczok A, Schmidt H, Von Haeseler A. Accuracy of phylogeny reconstruction methods combining overlapping gene data sets . <i>Algorithms for Molecular Biology</i>. 2010;5(1). doi:<a href=\"https://doi.org/10.1186/1748-7188-5-37\">10.1186/1748-7188-5-37</a>","ieee":"A. Kupczok, H. Schmidt, and A. Von Haeseler, “Accuracy of phylogeny reconstruction methods combining overlapping gene data sets ,” <i>Algorithms for Molecular Biology</i>, vol. 5, no. 1. BioMed Central, 2010.","chicago":"Kupczok, Anne, Heiko Schmidt, and Arndt Von Haeseler. “Accuracy of Phylogeny Reconstruction Methods Combining Overlapping Gene Data Sets .” <i>Algorithms for Molecular Biology</i>. BioMed Central, 2010. <a href=\"https://doi.org/10.1186/1748-7188-5-37\">https://doi.org/10.1186/1748-7188-5-37</a>.","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 .” <i>Algorithms for Molecular Biology</i>, vol. 5, no. 1, 37, BioMed Central, 2010, doi:<a href=\"https://doi.org/10.1186/1748-7188-5-37\">10.1186/1748-7188-5-37</a>.","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."},"year":"2010","date_updated":"2021-01-12T06:57:18Z","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."}],"day":"06","doi":"10.1186/1748-7188-5-37"}]