--- _id: '820' abstract: - lang: eng text: "The lac operon is a classic model system for bacterial gene regulation, and has been studied extensively in E. coli, a classic model organism. However, not much is known about E. coli’s ecology and life outside the laboratory, in particular in soil and water environments. The natural diversity of the lac operon outside the laboratory, its role in the ecology of E. coli and the selection pressures it is exposed to, are similarly unknown.\r\nIn Chapter Two of this thesis, I explore the genetic diversity, phylogenetic history and signatures of selection of the lac operon across 20 natural isolates of E. coli and divergent clades of Escherichia. I found that complete lac operons were present in all isolates examined, which in all but one case were functional. The lac operon phylogeny conformed to the whole-genome phylogeny of the divergent Escherichia clades, which excludes horizontal gene transfer as an explanation for the presence of functional lac operons in these clades. All lac operon genes showed a signature of purifying selection; this signature was strongest for the lacY gene. Lac operon genes of human and environmental isolates showed similar signatures of selection, except the lacZ gene, which showed a stronger signature of selection in environmental isolates.\r\nIn Chapter Three, I try to identify the natural genetic variation relevant for phenotype and fitness in the lac operon, comparing growth rate on lactose and LacZ activity of the lac operons of these wild isolates in a common genetic background. Sequence variation in the lac promoter region, upstream of the -10 and -35 RNA polymerase binding motif, predicted variation in LacZ activity at full induction, using a thermodynamic model of polymerase binding (Tugrul, 2016). However, neither variation in LacZ activity, nor RNA polymerase binding predicted by the model correlated with variation in growth rate. Lac operons of human and environmental isolates did not differ systematically in either growth rate on lactose or LacZ protein activity, suggesting that these lac operons have been exposed to similar selection pressures. We thus have no evidence that the phenotypic variation we measured is relevant for fitness.\r\nTo start assessing the effect of genomic background on the growth phenotype conferred by the lac operon, I compared growth on minimal medium with lactose between lac operon constructs and the corresponding original isolates, I found that maximal growth rate was determined by genomic background, with almost all backgrounds conferring higher growth rates than lab strain K12 MG1655. However, I found no evidence that the lactose concentration at which growth was half maximal depended on genomic background." acknowledgement: "ERC H2020 programme (grant agreement no. 648440)\r\nThanks to Jon Bollback for giving me the chance to do this work, for sharing the ideas that lay at the basis of this work, for his honesty and openness, showing himself to me as a person and not just as a boss. Thanks to Nick Barton for his guidance at the last stage, reading and commenting extensively on several versions of this manuscript, and for his encouragement; thanks to both Jon and Nick for their kindness and patience. Thanks to Erik van Nimwegen and Calin Guet for their time and willingness to be in my thesis committee, and to Erik van Nimwegen especially for agreeing to enter my thesis committee at the last moment, and for his very sharp, helpful and relevant comments during and after the defense. Thanks to my collaborators and discussion partners: Anne Kupczok, for her guidance, ideas and discussions during the construction of the manuscript of Chapter Two, and her comments on the manuscript; Georg Rieckh for making me aware of the issue of parameter identifiability, suggesting how to solve it, and for his unfortunate idea to start the plasmid enterprise in the first place; Murat Tugrul for sharing his model, for his enthusiasm, and his comments on Chapter Three; Srdjan Sarikas for his collaboration on the Monod model fitting, fast forwarding the analysis to turbo speed and making beautiful figures, and making the discussion fun on top of it all; Vanessa Barone for her last minute comments, especially on Chapter Three, providing a sharp and very helpful experimentalist perspective at the last moment; Maros Pleska and Marjon de Vos for their comments on the manuscript of Chapter Two; Gasper Tkacik for his crucial input on the relation between growth rate and lactose concentration; Bor Kavcic for his input on growth rate modeling and error propagation. Thanks to the Bollback, Bollenbach, Barton, Guet and Tkacik group members for both pro- viding an inspiring and supportive scientific environment to work in, as well as a lot of warmth and colour to everyday life. And thanks to the friends I found here, to the people who were there for me and to the people who changed my life, making it stranger and more beautiful than I could have imagined, Maros, Vanessa, Tade, Suzi, Andrej, Peter, Tiago, Kristof, Karin, Irene, Misha, Mato, Guillaume and Zanin. " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Fabienne full_name: Jesse, Fabienne id: 4C8C26A4-F248-11E8-B48F-1D18A9856A87 last_name: Jesse citation: ama: Jesse F. The lac operon in the wild. 2017. doi:10.15479/AT:ISTA:th_857 apa: Jesse, F. (2017). The lac operon in the wild. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_857 chicago: Jesse, Fabienne. “The Lac Operon in the Wild.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_857. ieee: F. Jesse, “The lac operon in the wild,” Institute of Science and Technology Austria, 2017. ista: Jesse F. 2017. The lac operon in the wild. Institute of Science and Technology Austria. mla: Jesse, Fabienne. The Lac Operon in the Wild. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_857. short: F. Jesse, The Lac Operon in the Wild, Institute of Science and Technology Austria, 2017. date_created: 2018-12-11T11:48:41Z date_published: 2017-08-25T00:00:00Z date_updated: 2023-09-07T12:01:21Z day: '25' ddc: - '576' - '577' - '579' degree_awarded: PhD department: - _id: JoBo doi: 10.15479/AT:ISTA:th_857 ec_funded: 1 file: - access_level: open_access checksum: c62257a7bff0c5f39e1abffc6bfcca5c content_type: application/pdf creator: system date_created: 2018-12-12T10:17:00Z date_updated: 2020-07-14T12:48:10Z file_id: '5252' file_name: IST-2017-857-v1+1_thesis_fabienne.pdf file_size: 3417773 relation: main_file - access_level: closed checksum: fc87d7d72fce52824a3ae7dcad0413a8 content_type: application/x-tex creator: dernst date_created: 2019-04-05T08:51:59Z date_updated: 2020-07-14T12:48:10Z file_id: '6212' file_name: 2017_thesis_Jesse_source.tex file_size: 215899 relation: source_file file_date_updated: 2020-07-14T12:48:10Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '87' project: - _id: 2578D616-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '648440' name: Selective Barriers to Horizontal Gene Transfer publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6829' pubrep_id: '857' status: public supervisor: - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 title: The lac operon in the wild tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '1077' abstract: - lang: eng text: Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the fX174 phage family by first reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima. article_number: '20160139' article_processing_charge: Yes (in subscription journal) author: - first_name: Rodrigo A full_name: Fernandes Redondo, Rodrigo A id: 409D5C96-F248-11E8-B48F-1D18A9856A87 last_name: Fernandes Redondo orcid: 0000-0002-5837-2793 - first_name: Harold full_name: Vladar, Harold id: 2A181218-F248-11E8-B48F-1D18A9856A87 last_name: Vladar orcid: 0000-0002-5985-7653 - first_name: Tomasz full_name: Włodarski, Tomasz last_name: Włodarski - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: ama: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. 2017;14(126). doi:10.1098/rsif.2016.0139 apa: Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., & Bollback, J. P. (2017). Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. Royal Society of London. https://doi.org/10.1098/rsif.2016.0139 chicago: Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” Journal of the Royal Society Interface. Royal Society of London, 2017. https://doi.org/10.1098/rsif.2016.0139. ieee: R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family,” Journal of the Royal Society Interface, vol. 14, no. 126. Royal Society of London, 2017. ista: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2017. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. 14(126), 20160139. mla: Fernandes Redondo, Rodrigo A., et al. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” Journal of the Royal Society Interface, vol. 14, no. 126, 20160139, Royal Society of London, 2017, doi:10.1098/rsif.2016.0139. short: R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, Journal of the Royal Society Interface 14 (2017). date_created: 2018-12-11T11:50:01Z date_published: 2017-01-04T00:00:00Z date_updated: 2023-09-20T11:56:34Z day: '04' ddc: - '570' department: - _id: NiBa - _id: JoBo doi: 10.1098/rsif.2016.0139 ec_funded: 1 external_id: isi: - '000393380400001' file: - access_level: open_access content_type: application/pdf creator: dernst date_created: 2019-01-18T09:14:02Z date_updated: 2019-01-18T09:14:02Z file_id: '5843' file_name: 2017_JRSI_Redondo.pdf file_size: 1092015 relation: main_file success: 1 file_date_updated: 2019-01-18T09:14:02Z has_accepted_license: '1' intvolume: ' 14' isi: 1 issue: '126' language: - iso: eng month: '01' oa: 1 oa_version: Published Version project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation - _id: 2578D616-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '648440' name: Selective Barriers to Horizontal Gene Transfer publication: Journal of the Royal Society Interface publication_identifier: issn: - '17425689' publication_status: published publisher: Royal Society of London publist_id: '6303' quality_controlled: '1' related_material: record: - id: '9864' relation: research_data status: public scopus_import: '1' status: public title: Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 14 year: '2017' ... --- _id: '954' abstract: - lang: eng text: Understanding the relation between genotype and phenotype remains a major challenge. The difficulty of predicting individual mutation effects, and particularly the interactions between them, has prevented the development of a comprehensive theory that links genotypic changes to their phenotypic effects. We show that a general thermodynamic framework for gene regulation, based on a biophysical understanding of protein-DNA binding, accurately predicts the sign of epistasis in a canonical cis-regulatory element consisting of overlapping RNA polymerase and repressor binding sites. Sign and magnitude of individual mutation effects are sufficient to predict the sign of epistasis and its environmental dependence. Thus, the thermodynamic model offers the correct null prediction for epistasis between mutations across DNA-binding sites. Our results indicate that a predictive theory for the effects of cis-regulatory mutations is possible from first principles, as long as the essential molecular mechanisms and the constraints these impose on a biological system are accounted for. article_number: e25192 article_processing_charge: Yes author: - first_name: Mato full_name: Lagator, Mato id: 345D25EC-F248-11E8-B48F-1D18A9856A87 last_name: Lagator - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 citation: ama: Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. On the mechanistic nature of epistasis in a canonical cis-regulatory element. eLife. 2017;6. doi:10.7554/eLife.25192 apa: Lagator, M., Paixao, T., Barton, N. H., Bollback, J. P., & Guet, C. C. (2017). On the mechanistic nature of epistasis in a canonical cis-regulatory element. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.25192 chicago: Lagator, Mato, Tiago Paixao, Nicholas H Barton, Jonathan P Bollback, and Calin C Guet. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory Element.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.25192. ieee: M. Lagator, T. Paixao, N. H. Barton, J. P. Bollback, and C. C. Guet, “On the mechanistic nature of epistasis in a canonical cis-regulatory element,” eLife, vol. 6. eLife Sciences Publications, 2017. ista: Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. 2017. On the mechanistic nature of epistasis in a canonical cis-regulatory element. eLife. 6, e25192. mla: Lagator, Mato, et al. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory Element.” ELife, vol. 6, e25192, eLife Sciences Publications, 2017, doi:10.7554/eLife.25192. short: M. Lagator, T. Paixao, N.H. Barton, J.P. Bollback, C.C. Guet, ELife 6 (2017). date_created: 2018-12-11T11:49:23Z date_published: 2017-05-18T00:00:00Z date_updated: 2023-09-22T10:01:17Z day: '18' ddc: - '576' department: - _id: CaGu - _id: NiBa - _id: JoBo doi: 10.7554/eLife.25192 ec_funded: 1 external_id: isi: - '000404024800001' file: - access_level: open_access checksum: 59cdd4400fb41280122d414fea971546 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:49Z date_updated: 2020-07-14T12:48:16Z file_id: '5306' file_name: IST-2017-841-v1+1_elife-25192-v2.pdf file_size: 2441529 relation: main_file - access_level: open_access checksum: b69024880558b858eb8c5d47a92b6377 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:50Z date_updated: 2020-07-14T12:48:16Z file_id: '5307' file_name: IST-2017-841-v1+2_elife-25192-figures-v2.pdf file_size: 3752660 relation: main_file file_date_updated: 2020-07-14T12:48:16Z has_accepted_license: '1' intvolume: ' 6' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Published Version project: - _id: 25B1EC9E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618091' name: Speed of Adaptation in Population Genetics and Evolutionary Computation - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 2578D616-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '648440' name: Selective Barriers to Horizontal Gene Transfer publication: eLife publication_identifier: issn: - 2050084X publication_status: published publisher: eLife Sciences Publications publist_id: '6460' pubrep_id: '841' quality_controlled: '1' scopus_import: '1' status: public title: On the mechanistic nature of epistasis in a canonical cis-regulatory element tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 6 year: '2017' ... --- _id: '1427' abstract: - lang: eng text: Changes in gene expression are an important mode of evolution; however, the proximate mechanism of these changes is poorly understood. In particular, little is known about the effects of mutations within cis binding sites for transcription factors, or the nature of epistatic interactions between these mutations. Here, we tested the effects of single and double mutants in two cis binding sites involved in the transcriptional regulation of the Escherichia coli araBAD operon, a component of arabinose metabolism, using a synthetic system. This system decouples transcriptional control from any posttranslational effects on fitness, allowing a precise estimate of the effect of single and double mutations, and hence epistasis, on gene expression. We found that epistatic interactions between mutations in the araBAD cis-regulatory element are common, and that the predominant form of epistasis is negative. The magnitude of the interactions depended on whether the mutations are located in the same or in different operator sites. Importantly, these epistatic interactions were dependent on the presence of arabinose, a native inducer of the araBAD operon in vivo, with some interactions changing in sign (e.g., from negative to positive) in its presence. This study thus reveals that mutations in even relatively simple cis-regulatory elements interact in complex ways such that selection on the level of gene expression in one environment might perturb regulation in the other environment in an unpredictable and uncorrelated manner. author: - first_name: Mato full_name: Lagator, Mato id: 345D25EC-F248-11E8-B48F-1D18A9856A87 last_name: Lagator - first_name: Claudia full_name: Igler, Claudia id: 46613666-F248-11E8-B48F-1D18A9856A87 last_name: Igler - first_name: Anaisa full_name: Moreno, Anaisa last_name: Moreno - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: ama: Lagator M, Igler C, Moreno A, Guet CC, Bollback JP. Epistatic interactions in the arabinose cis-regulatory element. Molecular Biology and Evolution. 2016;33(3):761-769. doi:10.1093/molbev/msv269 apa: Lagator, M., Igler, C., Moreno, A., Guet, C. C., & Bollback, J. P. (2016). Epistatic interactions in the arabinose cis-regulatory element. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msv269 chicago: Lagator, Mato, Claudia Igler, Anaisa Moreno, Calin C Guet, and Jonathan P Bollback. “Epistatic Interactions in the Arabinose Cis-Regulatory Element.” Molecular Biology and Evolution. Oxford University Press, 2016. https://doi.org/10.1093/molbev/msv269. ieee: M. Lagator, C. Igler, A. Moreno, C. C. Guet, and J. P. Bollback, “Epistatic interactions in the arabinose cis-regulatory element,” Molecular Biology and Evolution, vol. 33, no. 3. Oxford University Press, pp. 761–769, 2016. ista: Lagator M, Igler C, Moreno A, Guet CC, Bollback JP. 2016. Epistatic interactions in the arabinose cis-regulatory element. Molecular Biology and Evolution. 33(3), 761–769. mla: Lagator, Mato, et al. “Epistatic Interactions in the Arabinose Cis-Regulatory Element.” Molecular Biology and Evolution, vol. 33, no. 3, Oxford University Press, 2016, pp. 761–69, doi:10.1093/molbev/msv269. short: M. Lagator, C. Igler, A. Moreno, C.C. Guet, J.P. Bollback, Molecular Biology and Evolution 33 (2016) 761–769. date_created: 2018-12-11T11:51:57Z date_published: 2016-03-01T00:00:00Z date_updated: 2021-01-12T06:50:39Z day: '01' ddc: - '570' - '576' department: - _id: CaGu - _id: JoBo doi: 10.1093/molbev/msv269 ec_funded: 1 file: - access_level: open_access checksum: 1f456ce1d2aa2f67176a1709f9702ecf content_type: application/pdf creator: system date_created: 2018-12-12T10:09:27Z date_updated: 2020-07-14T12:44:53Z file_id: '4751' file_name: IST-2016-588-v1+1_Mol_Biol_Evol-2016-Lagator-761-9.pdf file_size: 648115 relation: main_file file_date_updated: 2020-07-14T12:44:53Z has_accepted_license: '1' intvolume: ' 33' issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 761 - 769 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Molecular Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '5772' pubrep_id: '588' quality_controlled: '1' scopus_import: 1 status: public title: Epistatic interactions in the arabinose cis-regulatory element tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 33 year: '2016' ... --- _id: '1121' abstract: - lang: eng text: "Horizontal gene transfer (HGT), the lateral acquisition of genes across existing species\r\nboundaries, is a major evolutionary force shaping microbial genomes that facilitates\r\nadaptation to new environments as well as resistance to antimicrobial drugs. As such,\r\nunderstanding the mechanisms and constraints that determine the outcomes of HGT\r\nevents is crucial to understand the dynamics of HGT and to design better strategies to\r\novercome the challenges that originate from it.\r\nFollowing the insertion and expression of a newly transferred gene, the success of an\r\nHGT event will depend on the fitness effect it has on the recipient (host) cell. Therefore,\r\npredicting the impact of HGT on the genetic composition of a population critically\r\ndepends on the distribution of fitness effects (DFE) of horizontally transferred genes.\r\nHowever, to date, we have little knowledge of the DFE of newly transferred genes, and\r\nhence little is known about the shape and scale of this distribution.\r\nIt is particularly important to better understand the selective barriers that determine\r\nthe fitness effects of newly transferred genes. In spite of substantial bioinformatics\r\nefforts to identify horizontally transferred genes and selective barriers, a systematic\r\nexperimental approach to elucidate the roles of different selective barriers in defining\r\nthe fate of a transfer event has largely been absent. Similarly, although the fact that\r\nenvironment might alter the fitness effect of a horizontally transferred gene may seem\r\nobvious, little attention has been given to it in a systematic experimental manner.\r\nIn this study, we developed a systematic experimental approach that consists of\r\ntransferring 44 arbitrarily selected Salmonella typhimurium orthologous genes into an\r\nEscherichia coli host, and estimating the fitness effects of these transferred genes at a\r\nconstant expression level by performing competition assays against the wild type.\r\nIn chapter 2, we performed one-to-one competition assays between a mutant strain\r\ncarrying a transferred gene and the wild type strain. By using flow cytometry we\r\nestimated selection coefficients for the transferred genes with a precision level of 10-3,and obtained the DFE of horizontally transferred genes. We then investigated if these\r\nfitness effects could be predicted by any of the intrinsic properties of the genes, namely,\r\nfunctional category, degree of complexity (protein-protein interactions), GC content,\r\ncodon usage and length. Our analyses revealed that the functional category and length\r\nof the genes act as potential selective barriers. Finally, using the same procedure with\r\nthe endogenous E. coli orthologs of these 44 genes, we demonstrated that gene dosage is\r\nthe most prominent selective barrier to HGT.\r\nIn chapter 3, using the same set of genes we investigated the role of environment on the\r\nsuccess of HGT events. Under six different environments with different levels of stress\r\nwe performed more complex competition assays, where we mixed all 44 mutant strains\r\ncarrying transferred genes with the wild type strain. To estimate the fitness effects of\r\ngenes relative to wild type we used next generation sequencing. We found that the DFEs\r\nof horizontally transferred genes are highly dependent on the environment, with\r\nabundant gene–by-environment interactions. Furthermore, we demonstrated a\r\nrelationship between average fitness effect of a gene across all environments and its\r\nenvironmental variance, and thus its predictability. Finally, in spite of the fitness effects\r\nof genes being highly environment-dependent, we still observed a common shape of\r\nDFEs across all tested environments." acknowledgement: "This study was supported by European Research Council ERC CoG 2014 – EVOLHGT,\r\nunder the grant number 648440.\r\n\r\nIt is a pleasure to thank the many people who made this thesis possible.\r\nI would like to first thank my advisor, Jonathan Paul Bollback for providing guidance in\r\nall aspects of my life, encouragement, sound advice, and good teaching over the last six\r\nyears.\r\nI would also like to thank the members of my dissertation committee – Călin C. Guet\r\nand John F. Baines – not only for their time and guidance, but for their intellectual\r\ncontributions to my development as a scientist.\r\nI would like to thank Flavia Gama and Rodrigo Redondo who have taught me all the\r\nskills in the laboratory with their graciousness and friendship. Also special thanks to\r\nBollback group for their support and for providing a stimulating and fun environment:\r\nIsabella Tomanek, Fabienne Jesse, Claudia Igler, and Pavel Payne.\r\nJerneja Beslagic is not only an amazing assistant, she also has a smile brighter and\r\nwarmer than the sunshine, bringing happiness to every moment. Always keep your light\r\nNeja, I will miss our invaluable chatters a lot." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Hande full_name: Acar, Hande id: 2DDF136A-F248-11E8-B48F-1D18A9856A87 last_name: Acar orcid: 0000-0003-1986-9753 citation: ama: Acar H. Selective barriers to horizontal gene transfer. 2016. apa: Acar, H. (2016). Selective barriers to horizontal gene transfer. Institute of Science and Technology Austria. chicago: Acar, Hande. “Selective Barriers to Horizontal Gene Transfer.” Institute of Science and Technology Austria, 2016. ieee: H. Acar, “Selective barriers to horizontal gene transfer,” Institute of Science and Technology Austria, 2016. ista: Acar H. 2016. Selective barriers to horizontal gene transfer. Institute of Science and Technology Austria. mla: Acar, Hande. Selective Barriers to Horizontal Gene Transfer. Institute of Science and Technology Austria, 2016. short: H. Acar, Selective Barriers to Horizontal Gene Transfer, Institute of Science and Technology Austria, 2016. date_created: 2018-12-11T11:50:16Z date_published: 2016-12-01T00:00:00Z date_updated: 2023-09-07T11:42:26Z day: '01' ddc: - '570' degree_awarded: PhD department: - _id: JoBo ec_funded: 1 file: - access_level: closed checksum: 94bbbc754c36115bf37f8fc11fad43c4 content_type: application/pdf creator: dernst date_created: 2019-08-13T11:17:50Z date_updated: 2019-08-13T11:17:50Z file_id: '6814' file_name: PhDThesis_HandeAcar_1230.pdf file_size: 3682711 relation: main_file - access_level: open_access checksum: 94bbbc754c36115bf37f8fc11fad43c4 content_type: application/pdf creator: dernst date_created: 2021-02-22T11:51:13Z date_updated: 2021-02-22T11:51:13Z file_id: '9184' file_name: 2016_Thesis_HandeAcar.pdf file_size: 3682711 relation: main_file success: 1 file_date_updated: 2021-02-22T11:51:13Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '75' project: - _id: 2578D616-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '648440' name: Selective Barriers to Horizontal Gene Transfer publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6239' status: public supervisor: - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 title: Selective barriers to horizontal gene transfer type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2016' ... --- _id: '9864' abstract: - lang: eng text: Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the ϕX174 phage family by, first, reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima. article_processing_charge: No author: - first_name: Rodrigo A full_name: Fernandes Redondo, Rodrigo A id: 409D5C96-F248-11E8-B48F-1D18A9856A87 last_name: Fernandes Redondo orcid: 0000-0002-5837-2793 - first_name: Harold full_name: de Vladar, Harold id: 2A181218-F248-11E8-B48F-1D18A9856A87 last_name: de Vladar orcid: 0000-0002-5985-7653 - first_name: Tomasz full_name: Włodarski, Tomasz last_name: Włodarski - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: ama: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. 2016. doi:10.6084/m9.figshare.4315652.v1 apa: Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., & Bollback, J. P. (2016). Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. The Royal Society. https://doi.org/10.6084/m9.figshare.4315652.v1 chicago: Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” The Royal Society, 2016. https://doi.org/10.6084/m9.figshare.4315652.v1. ieee: R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family.” The Royal Society, 2016. ista: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2016. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family, The Royal Society, 10.6084/m9.figshare.4315652.v1. mla: Fernandes Redondo, Rodrigo A., et al. Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family. The Royal Society, 2016, doi:10.6084/m9.figshare.4315652.v1. short: R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, (2016). date_created: 2021-08-10T08:29:47Z date_published: 2016-12-14T00:00:00Z date_updated: 2023-09-20T11:56:33Z day: '14' department: - _id: NiBa - _id: JoBo doi: 10.6084/m9.figshare.4315652.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.4315652.v1 month: '12' oa: 1 oa_version: Published Version publisher: The Royal Society related_material: record: - id: '1077' relation: used_in_publication status: public status: public title: Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2016' ... --- _id: '5554' abstract: - lang: eng text: "The data stored here is used in Murat Tugrul's PhD thesis (Chapter 3), which is related to the evolution of bacterial RNA polymerase binding.\r\nMagdalena Steinrueck (PhD Student in Calin Guet's group at IST Austria) performed the experiments and created the data on de novo promoter evolution. Fabienne Jesse (PhD Student in Jon Bollback's group at IST Austria) performed the experiments and created the data on lac promoter evolution." article_processing_charge: No author: - first_name: Murat full_name: Tugrul, Murat id: 37C323C6-F248-11E8-B48F-1D18A9856A87 last_name: Tugrul orcid: 0000-0002-8523-0758 citation: ama: Tugrul M. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. 2016. doi:10.15479/AT:ISTA:43 apa: Tugrul, M. (2016). Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:43 chicago: Tugrul, Murat. “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:43. ieee: M. Tugrul, “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016. ista: Tugrul M. 2016. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase, Institute of Science and Technology Austria, 10.15479/AT:ISTA:43. mla: Tugrul, Murat. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:43. short: M. Tugrul, (2016). contributor: - contributor_type: researcher first_name: Magdalena id: 2C023F40-F248-11E8-B48F-1D18A9856A87 last_name: Steinrück - contributor_type: researcher first_name: Fabienne id: 4C8C26A4-F248-11E8-B48F-1D18A9856A87 last_name: Jesse datarep_id: '43' date_created: 2018-12-12T12:31:30Z date_published: 2016-05-12T00:00:00Z date_updated: 2024-02-21T13:50:34Z day: '12' department: - _id: NiBa - _id: JoBo doi: 10.15479/AT:ISTA:43 file: - access_level: open_access checksum: 1fc0a10bb7ce110fcb5e1fbe3cf0c4e2 content_type: application/zip creator: system date_created: 2018-12-12T13:03:08Z date_updated: 2020-07-14T12:47:01Z file_id: '5626' file_name: IST-2016-43-v1+1_DATA_MTugrul_PhDThesis_Chapter3.zip file_size: 1123495 relation: main_file file_date_updated: 2020-07-14T12:47:01Z has_accepted_license: '1' keyword: - RNAP binding - de novo promoter evolution - lac promoter license: https://creativecommons.org/publicdomain/zero/1.0/ month: '05' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '1131' relation: used_in_publication status: public status: public title: Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2016' ... --- _id: '1902' abstract: - lang: eng text: In the 1960s-1980s, determination of bacterial growth rates was an important tool in microbial genetics, biochemistry, molecular biology, and microbial physiology. The exciting technical developments of the 1990s and the 2000s eclipsed that tool; as a result, many investigators today lack experience with growth rate measurements. Recently, investigators in a number of areas have started to use measurements of bacterial growth rates for a variety of purposes. Those measurements have been greatly facilitated by the availability of microwell plate readers that permit the simultaneous measurements on up to 384 different cultures. Only the exponential (logarithmic) portions of the resulting growth curves are useful for determining growth rates, and manual determination of that portion and calculation of growth rates can be tedious for high-throughput purposes. Here, we introduce the program GrowthRates that uses plate reader output files to automatically determine the exponential portion of the curve and to automatically calculate the growth rate, the maximum culture density, and the duration of the growth lag phase. GrowthRates is freely available for Macintosh, Windows, and Linux.We discuss the effects of culture volume, the classical bacterial growth curve, and the differences between determinations in rich media and minimal (mineral salts) media. This protocol covers calibration of the plate reader, growth of culture inocula for both rich and minimal media, and experimental setup. As a guide to reliability, we report typical day-to-day variation in growth rates and variation within experiments with respect to position of wells within the plates. article_processing_charge: No article_type: original author: - first_name: Barry full_name: Hall, Barry last_name: Hall - first_name: Hande full_name: Acar, Hande id: 2DDF136A-F248-11E8-B48F-1D18A9856A87 last_name: Acar orcid: 0000-0003-1986-9753 - first_name: Anna full_name: Nandipati, Anna last_name: Nandipati - first_name: Miriam full_name: Barlow, Miriam last_name: Barlow citation: ama: Hall B, Acar H, Nandipati A, Barlow M. Growth rates made easy. Molecular Biology and Evolution. 2014;31(1):232-238. doi:10.1093/molbev/mst187 apa: Hall, B., Acar, H., Nandipati, A., & Barlow, M. (2014). Growth rates made easy. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/mst187 chicago: Hall, Barry, Hande Acar, Anna Nandipati, and Miriam Barlow. “Growth Rates Made Easy.” Molecular Biology and Evolution. Oxford University Press, 2014. https://doi.org/10.1093/molbev/mst187. ieee: B. Hall, H. Acar, A. Nandipati, and M. Barlow, “Growth rates made easy,” Molecular Biology and Evolution, vol. 31, no. 1. Oxford University Press, pp. 232–238, 2014. ista: Hall B, Acar H, Nandipati A, Barlow M. 2014. Growth rates made easy. Molecular Biology and Evolution. 31(1), 232–238. mla: Hall, Barry, et al. “Growth Rates Made Easy.” Molecular Biology and Evolution, vol. 31, no. 1, Oxford University Press, 2014, pp. 232–38, doi:10.1093/molbev/mst187. short: B. Hall, H. Acar, A. Nandipati, M. Barlow, Molecular Biology and Evolution 31 (2014) 232–238. date_created: 2018-12-11T11:54:37Z date_published: 2014-01-01T00:00:00Z date_updated: 2022-06-07T11:08:13Z day: '01' department: - _id: JoBo doi: 10.1093/molbev/mst187 external_id: pmid: - '24170494' intvolume: ' 31' issue: '1' language: - iso: eng month: '01' oa_version: None page: 232 - 238 pmid: 1 publication: Molecular Biology and Evolution publication_identifier: eissn: - 1537-1719 issn: - 0737-4038 publication_status: published publisher: Oxford University Press publist_id: '5193' quality_controlled: '1' scopus_import: '1' status: public title: Growth rates made easy type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 31 year: '2014' ... --- _id: '2042' abstract: - lang: eng text: 'Background: CRISPR is a microbial immune system likely to be involved in host-parasite coevolution. It functions using target sequences encoded by the bacterial genome, which interfere with invading nucleic acids using a homology-dependent system. The system also requires protospacer associated motifs (PAMs), short motifs close to the target sequence that are required for interference in CRISPR types I and II. Here, we investigate whether PAMs are depleted in phage genomes due to selection pressure to escape recognition.Results: To this end, we analyzed two data sets. Phages infecting all bacterial hosts were analyzed first, followed by a detailed analysis of phages infecting the genus Streptococcus, where PAMs are best understood. We use two different measures of motif underrepresentation that control for codon bias and the frequency of submotifs. We compare phages infecting species with a particular CRISPR type to those infecting species without that type. Since only known PAMs were investigated, the analysis is restricted to CRISPR types I-C and I-E and in Streptococcus to types I-C and II. We found evidence for PAM depletion in Streptococcus phages infecting hosts with CRISPR type I-C, in Vibrio phages infecting hosts with CRISPR type I-E and in Streptococcus thermopilus phages infecting hosts with type II-A, known as CRISPR3.Conclusions: The observed motif depletion in phages with hosts having CRISPR can be attributed to selection rather than to mutational bias, as mutational bias should affect the phages of all hosts. This observation implies that the CRISPR system has been efficient in the groups discussed here.' article_number: '663' author: - first_name: Anne full_name: Kupczok, Anne id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87 last_name: Kupczok - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: ama: Kupczok A, Bollback JP. Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics. 2014;15(1). doi:10.1186/1471-2164-15-663 apa: Kupczok, A., & Bollback, J. P. (2014). Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics. BioMed Central. https://doi.org/10.1186/1471-2164-15-663 chicago: Kupczok, Anne, and Jonathan P Bollback. “Motif Depletion in Bacteriophages Infecting Hosts with CRISPR Systems.” BMC Genomics. BioMed Central, 2014. https://doi.org/10.1186/1471-2164-15-663. ieee: A. Kupczok and J. P. Bollback, “Motif depletion in bacteriophages infecting hosts with CRISPR systems,” BMC Genomics, vol. 15, no. 1. BioMed Central, 2014. ista: Kupczok A, Bollback JP. 2014. Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics. 15(1), 663. mla: Kupczok, Anne, and Jonathan P. Bollback. “Motif Depletion in Bacteriophages Infecting Hosts with CRISPR Systems.” BMC Genomics, vol. 15, no. 1, 663, BioMed Central, 2014, doi:10.1186/1471-2164-15-663. short: A. Kupczok, J.P. Bollback, BMC Genomics 15 (2014). date_created: 2018-12-11T11:55:23Z date_published: 2014-08-08T00:00:00Z date_updated: 2021-01-12T06:54:56Z day: '08' ddc: - '570' department: - _id: JoBo doi: 10.1186/1471-2164-15-663 file: - access_level: open_access checksum: 3f6d2776b90a842a28359cc957d3d04b content_type: application/pdf creator: system date_created: 2018-12-12T10:11:24Z date_updated: 2020-07-14T12:45:26Z file_id: '4878' file_name: IST-2015-396-v1+1_1471-2164-15-663.pdf file_size: 1489769 relation: main_file file_date_updated: 2020-07-14T12:45:26Z has_accepted_license: '1' intvolume: ' 15' issue: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version publication: BMC Genomics publication_status: published publisher: BioMed Central publist_id: '5009' pubrep_id: '396' quality_controlled: '1' scopus_import: 1 status: public title: Motif depletion in bacteriophages infecting hosts with CRISPR systems tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2014' ... --- _id: '2412' abstract: - lang: eng text: 'Background: The CRISPR/Cas system is known to act as an adaptive and heritable immune system in Eubacteria and Archaea. Immunity is encoded in an array of spacer sequences. Each spacer can provide specific immunity to invasive elements that carry the same or a similar sequence. Even in closely related strains, spacer content is very dynamic and evolves quickly. Standard models of nucleotide evolutioncannot be applied to quantify its rate of change since processes other than single nucleotide changes determine its evolution.Methods We present probabilistic models that are specific for spacer content evolution. They account for the different processes of insertion and deletion. Insertions can be constrained to occur on one end only or are allowed to occur throughout the array. One deletion event can affect one spacer or a whole fragment of adjacent spacers. Parameters of the underlying models are estimated for a pair of arrays by maximum likelihood using explicit ancestor enumeration.Results Simulations show that parameters are well estimated on average under the models presented here. There is a bias in the rate estimation when including fragment deletions. The models also estimate times between pairs of strains. But with increasing time, spacer overlap goes to zero, and thus there is an upper bound on the distance that can be estimated. Spacer content similarities are displayed in a distance based phylogeny using the estimated times.We use the presented models to analyze different Yersinia pestis data sets and find that the results among them are largely congruent. The models also capture the variation in diversity of spacers among the data sets. A comparison of spacer-based phylogenies and Cas gene phylogenies shows that they resolve very different time scales for this data set.Conclusions The simulations and data analyses show that the presented models are useful for quantifying spacer content evolution and for displaying spacer content similarities of closely related strains in a phylogeny. This allows for comparisons of different CRISPR arrays or for comparisons between CRISPR arrays and nucleotide substitution rates.' author: - first_name: Anne full_name: Kupczok, Anne id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87 last_name: Kupczok - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: ama: Kupczok A, Bollback JP. Probabilistic models for CRISPR spacer content evolution . BMC Evolutionary Biology. 2013;13(1):54-54. doi:10.1186/1471-2148-13-54 apa: Kupczok, A., & Bollback, J. P. (2013). Probabilistic models for CRISPR spacer content evolution . BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-13-54 chicago: Kupczok, Anne, and Jonathan P Bollback. “Probabilistic Models for CRISPR Spacer Content Evolution .” BMC Evolutionary Biology. BioMed Central, 2013. https://doi.org/10.1186/1471-2148-13-54. ieee: A. Kupczok and J. P. Bollback, “Probabilistic models for CRISPR spacer content evolution ,” BMC Evolutionary Biology, vol. 13, no. 1. BioMed Central, pp. 54–54, 2013. ista: Kupczok A, Bollback JP. 2013. Probabilistic models for CRISPR spacer content evolution . BMC Evolutionary Biology. 13(1), 54–54. mla: Kupczok, Anne, and Jonathan P. Bollback. “Probabilistic Models for CRISPR Spacer Content Evolution .” BMC Evolutionary Biology, vol. 13, no. 1, BioMed Central, 2013, pp. 54–54, doi:10.1186/1471-2148-13-54. short: A. Kupczok, J.P. Bollback, BMC Evolutionary Biology 13 (2013) 54–54. date_created: 2018-12-11T11:57:31Z date_published: 2013-02-26T00:00:00Z date_updated: 2021-01-12T06:57:20Z day: '26' ddc: - '576' department: - _id: JoBo doi: 10.1186/1471-2148-13-54 file: - access_level: open_access checksum: 029c7e0b198c19312b66ecce3cabb22f content_type: application/pdf creator: system date_created: 2018-12-12T10:17:15Z date_updated: 2020-07-14T12:45:40Z file_id: '5268' file_name: IST-2015-397-v1+1_1471-2148-13-54.pdf file_size: 518729 relation: main_file file_date_updated: 2020-07-14T12:45:40Z has_accepted_license: '1' intvolume: ' 13' issue: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 54 - 54 publication: BMC Evolutionary Biology publication_status: published publisher: BioMed Central publist_id: '4514' pubrep_id: '397' quality_controlled: '1' scopus_import: 1 status: public title: 'Probabilistic models for CRISPR spacer content evolution ' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2013' ... --- _id: '2410' abstract: - lang: eng 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. ' author: - first_name: Rodrigo A full_name: Fernandes Redondo, Rodrigo A id: 409D5C96-F248-11E8-B48F-1D18A9856A87 last_name: Fernandes Redondo orcid: 0000-0002-5837-2793 - first_name: Anne full_name: Kupczok, Anne id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87 last_name: Kupczok - first_name: Gertraud full_name: Stift, Gertraud id: 2DB195CA-F248-11E8-B48F-1D18A9856A87 last_name: Stift - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: 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 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 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. 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. 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). 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. short: R.A. Fernandes Redondo, A. Kupczok, G. Stift, J.P. Bollback, Genome Announcements 1 (2013). date_created: 2018-12-11T11:57:30Z date_published: 2013-06-13T00:00:00Z date_updated: 2021-01-12T06:57:19Z day: '13' ddc: - '576' department: - _id: JoBo - _id: LifeSc doi: 10.1128/genomeA.00216-13 file: - access_level: open_access checksum: 0751ec74b695567e0cdf02aaf9c26829 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:36Z date_updated: 2020-07-14T12:45:40Z file_id: '5291' file_name: IST-2015-398-v1+1_Genome_Announc.-2013-Redondo-.pdf file_size: 130026 relation: main_file file_date_updated: 2020-07-14T12:45:40Z has_accepted_license: '1' intvolume: ' 1' issue: '3' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: Genome Announcements publication_status: published publisher: American Society for Microbiology publist_id: '4516' pubrep_id: '398' quality_controlled: '1' scopus_import: 1 status: public title: Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2013' ... --- _id: '500' abstract: - lang: eng 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.' 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" article_number: '222' author: - first_name: Melissa full_name: Ward, Melissa last_name: Ward - first_name: Samantha full_name: Lycett, Samantha last_name: Lycett - first_name: Dorita full_name: Avila, Dorita last_name: Avila - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 - first_name: Andrew full_name: Leigh Brown, Andrew last_name: Leigh Brown 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 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 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. 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. 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. 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. short: M. Ward, S. Lycett, D. Avila, J.P. Bollback, A. Leigh Brown, BMC Evolutionary Biology 13 (2013). date_created: 2018-12-11T11:46:49Z date_published: 2013-10-09T00:00:00Z date_updated: 2021-01-12T08:01:08Z day: '09' ddc: - '576' department: - _id: JoBo doi: 10.1186/1471-2148-13-222 file: - access_level: open_access checksum: 52cf48a7c1794676ae8b0029573a84a9 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:59Z date_updated: 2020-07-14T12:46:36Z file_id: '4722' file_name: IST-2018-941-v1+1_2013_Bollback_Evolutionary_interactionspdf.pdf file_size: 1150052 relation: main_file file_date_updated: 2020-07-14T12:46:36Z has_accepted_license: '1' intvolume: ' 13' issue: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: BMC Evolutionary Biology publication_status: published publisher: BioMed Central publist_id: '7320' pubrep_id: '941' quality_controlled: '1' scopus_import: 1 status: public title: Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2013' ... --- _id: '501' abstract: - lang: eng 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.' author: - first_name: Mario full_name: Cozzuol, Mario last_name: Cozzuol - first_name: Camila full_name: Clozato, Camila last_name: Clozato - first_name: Elizete full_name: Holanda, Elizete last_name: Holanda - first_name: Flávio full_name: Rodrigues, Flávio last_name: Rodrigues - first_name: Samuel full_name: Nienow, Samuel last_name: Nienow - first_name: Benoit full_name: De Thoisy, Benoit last_name: De Thoisy - first_name: Rodrigo A full_name: Fernandes Redondo, Rodrigo A id: 409D5C96-F248-11E8-B48F-1D18A9856A87 last_name: Fernandes Redondo orcid: 0000-0002-5837-2793 - first_name: Fabrício full_name: Santos, Fabrício last_name: Santos citation: 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:46:49Z date_published: 2013-12-01T00:00:00Z date_updated: 2021-01-12T08:01:09Z day: '01' ddc: - '570' department: - _id: JoBo doi: 10.1644/12-MAMM-A-169.1 file: - access_level: open_access checksum: 8007815078dccac21ecd1cf73a269dc6 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:59Z date_updated: 2020-07-14T12:46:36Z file_id: '4980' file_name: IST-2018-940-v1+1_2013_Redondo_A_new.pdf file_size: 1040765 relation: main_file file_date_updated: 2020-07-14T12:46:36Z has_accepted_license: '1' intvolume: ' 94' issue: '6' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 1331 - 1345 publication: Journal of Mammalogy publication_status: published publisher: Oxford University Press publist_id: '7319' pubrep_id: '940' quality_controlled: '1' scopus_import: 1 status: public title: A new species of tapir from the Amazon tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 94 year: '2013' ... --- _id: '508' abstract: - lang: eng 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. author: - first_name: Eduardo full_name: Tarazona Santos, Eduardo last_name: Tarazona Santos - first_name: Moara full_name: Machado, Moara last_name: Machado - first_name: Wagner full_name: Magalhães, Wagner last_name: Magalhães - first_name: Renee full_name: Chen, Renee last_name: Chen - first_name: Fernanda full_name: Lyon, Fernanda last_name: Lyon - first_name: Laurie full_name: Burdett, Laurie last_name: Burdett - first_name: Andrew full_name: Crenshaw, Andrew last_name: Crenshaw - first_name: Cristina full_name: Fabbri, Cristina last_name: Fabbri - first_name: Latife full_name: Pereira, Latife last_name: Pereira - first_name: Laelia full_name: Pinto, Laelia last_name: Pinto - first_name: Rodrigo A full_name: Fernandes Redondo, Rodrigo A id: 409D5C96-F248-11E8-B48F-1D18A9856A87 last_name: Fernandes Redondo orcid: 0000-0002-5837-2793 - first_name: Ben full_name: Sestanovich, Ben last_name: Sestanovich - first_name: Meredith full_name: Yeager, Meredith last_name: Yeager - first_name: Stephen full_name: Chanock, Stephen last_name: Chanock citation: 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' 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' 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.' 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.' 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.' 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. date_created: 2018-12-11T11:46:52Z date_published: 2013-09-01T00:00:00Z date_updated: 2021-01-12T08:01:12Z day: '01' department: - _id: JoBo doi: 10.1093/molbev/mst119 external_id: pmid: - '23821607' intvolume: ' 30' issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3748357/ month: '09' oa: 1 oa_version: Submitted Version page: 2157 - 2167 pmid: 1 publication: Molecular Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '7310' quality_controlled: '1' scopus_import: 1 status: public title: 'Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 30 year: '2013' ... --- _id: '2411' 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. author: - first_name: Ingo full_name: Ebersberger, Ingo last_name: Ebersberger - first_name: Ricardo full_name: De Matos Simoes, Ricardo last_name: De Matos Simoes - first_name: Anne full_name: Kupczok, Anne id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87 last_name: Kupczok - first_name: Matthias full_name: Gube, Matthias last_name: Gube - first_name: Erika full_name: Kothe, Erika last_name: Kothe - first_name: Kerstin full_name: Voigt, Kerstin last_name: Voigt - first_name: Arndt full_name: Von Haeseler, Arndt last_name: Von Haeseler 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 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. 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. 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. 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. date_created: 2018-12-11T11:57:30Z date_published: 2012-05-01T00:00:00Z date_updated: 2021-01-12T06:57:19Z day: '01' ddc: - '570' - '576' department: - _id: JoBo doi: 10.1093/molbev/msr285 file: - access_level: open_access checksum: d565dcac27d1736c0c378ea6fcf22d69 content_type: application/pdf creator: system date_created: 2018-12-12T10:13:30Z date_updated: 2020-07-14T12:45:40Z file_id: '5013' file_name: IST-2015-384-v1+1_Mol_Biol_Evol-2012-Ebersberger-1319-34.pdf file_size: 754922 relation: main_file file_date_updated: 2020-07-14T12:45:40Z has_accepted_license: '1' intvolume: ' 29' issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 1319 - 1334 publication: Molecular Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '4515' pubrep_id: '384' quality_controlled: '1' scopus_import: 1 status: public title: A consistent phylogenetic backbone for the fungi tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2012' ... --- _id: '2963' abstract: - lang: eng 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. ' author: - first_name: Fabienne full_name: Jesse, Fabienne id: 4C8C26A4-F248-11E8-B48F-1D18A9856A87 last_name: Jesse - first_name: Katharina full_name: Riebel, Katharina last_name: Riebel citation: 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 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 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. 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. 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. 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. date_created: 2018-12-11T12:00:35Z date_published: 2012-11-01T00:00:00Z date_updated: 2021-01-12T07:40:06Z day: '01' department: - _id: JoBo doi: 10.1016/j.beproc.2012.09.006 intvolume: ' 91' issue: '3' language: - iso: eng month: '11' oa_version: None page: 262 - 266 publication: Behavioural Processes publication_status: published publisher: Elsevier publist_id: '3756' quality_controlled: '1' status: public title: Social facilitation of male song by male and female conspecifics in the zebra finch, Taeniopygia guttata type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 91 year: '2012' ... --- _id: '3247' abstract: - lang: eng 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. 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." author: - first_name: Sibelle full_name: Vilaça, Sibelle last_name: Vilaça - first_name: Rodrigo A full_name: Fernandes Redondo, Rodrigo A id: 409D5C96-F248-11E8-B48F-1D18A9856A87 last_name: Fernandes Redondo orcid: 0000-0002-5837-2793 - first_name: Lívia full_name: Lins, Lívia last_name: Lins - first_name: Fabrício full_name: Santos, Fabrício last_name: Santos 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 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 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. 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. 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. 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. date_created: 2018-12-11T12:02:15Z date_published: 2012-02-01T00:00:00Z date_updated: 2021-01-12T07:42:05Z day: '01' department: - _id: JoBo doi: 10.1007/s10592-011-0262-5 intvolume: ' 13' issue: '1' language: - iso: eng month: '02' oa_version: None page: 293 - 298 publication: Conservation Genetics publication_status: published publisher: Springer publist_id: '3420' quality_controlled: '1' scopus_import: 1 status: public title: Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2012' ... --- _id: '3289' 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" 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." author: - first_name: Anna full_name: Pereira, Anna last_name: Pereira - first_name: Flávia full_name: Leite, Flávia id: 36705F98-F248-11E8-B48F-1D18A9856A87 last_name: Leite - first_name: Bruno full_name: Brasil, Bruno last_name: Brasil - first_name: Jamaria full_name: Soares Martins, Jamaria last_name: Soares Martins - first_name: Alice full_name: Torres, Alice last_name: Torres - first_name: Paulo full_name: Pimenta, Paulo last_name: Pimenta - first_name: Thais full_name: Souto Padrón, Thais last_name: Souto Padrón - first_name: Paula full_name: Tranktman, Paula last_name: Tranktman - first_name: Paulo full_name: Ferreira, Paulo last_name: Ferreira - first_name: Erna full_name: Kroon, Erna last_name: Kroon - first_name: Cláudio full_name: Bonjardim, Cláudio last_name: Bonjardim citation: 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 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 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. 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. 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. 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. 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. date_created: 2018-12-11T12:02:29Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T07:42:25Z day: '01' department: - _id: JoBo doi: 10.1128/JVI.05638-11 external_id: pmid: - '22031940' intvolume: ' 86' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3255887/ month: '01' oa: 1 oa_version: Submitted Version page: 172 - 184 pmid: 1 publication: Journal of Virology publication_status: published publisher: ASM publist_id: '3356' quality_controlled: '1' scopus_import: 1 status: public title: A vaccinia virus-driven interplay between the MKK4/7-JNK1/2 pathway and cytoskeleton reorganization type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 86 year: '2012' ... --- _id: '3370' 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. author: - first_name: Anne full_name: Kupczok, Anne id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87 last_name: Kupczok citation: 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 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 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. 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. 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. short: A. Kupczok, Systematic Biology 60 (2011) 218–225. date_created: 2018-12-11T12:02:57Z date_published: 2011-03-01T00:00:00Z date_updated: 2021-01-12T07:43:01Z day: '01' department: - _id: JoBo doi: 10.1093/sysbio/syq086 intvolume: ' 60' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://eprints.cs.univie.ac.at/3226/ month: '03' oa: 1 oa_version: Submitted Version page: 218 - 225 publication: Systematic Biology publication_status: published publisher: Oxford University Press publist_id: '3241' quality_controlled: '1' status: public title: Consequences of different null models on the tree shape bias of supertree methods type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 60 year: '2011' ... --- _id: '3387' 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.' article_number: '205' author: - first_name: Anne full_name: Kupczok, Anne id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87 last_name: Kupczok citation: ama: Kupczok A. Split based computation of majority rule supertrees. BMC Evolutionary Biology. 2011;11(205). doi:10.1186/1471-2148-11-205 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 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. ieee: A. Kupczok, “Split based computation of majority rule supertrees,” BMC Evolutionary Biology, vol. 11, no. 205. BioMed Central, 2011. 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.” BMC Evolutionary Biology, vol. 11, no. 205, 205, BioMed Central, 2011, doi:10.1186/1471-2148-11-205. short: A. Kupczok, BMC Evolutionary Biology 11 (2011). date_created: 2018-12-11T12:03:03Z date_published: 2011-07-13T00:00:00Z date_updated: 2021-01-12T07:43:08Z day: '13' ddc: - '576' department: - _id: JoBo doi: 10.1186/1471-2148-11-205 file: - access_level: open_access checksum: 68da8d04af1b97b4cbe8606e2f92ddd8 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:09Z date_updated: 2020-07-14T12:46:11Z file_id: '5058' file_name: IST-2015-372-v1+1_1471-2148-11-205.pdf file_size: 465042 relation: main_file file_date_updated: 2020-07-14T12:46:11Z has_accepted_license: '1' intvolume: ' 11' issue: '205' language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: BMC Evolutionary Biology publication_status: published publisher: BioMed Central publist_id: '3219' pubrep_id: '372' quality_controlled: '1' scopus_import: 1 status: public title: Split based computation of majority rule supertrees tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2011' ... --- _id: '2409' 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." 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). article_number: '37' author: - first_name: Anne full_name: Kupczok, Anne id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87 last_name: Kupczok - first_name: Heiko full_name: Schmidt, Heiko last_name: Schmidt - first_name: Arndt full_name: Von Haeseler, Arndt last_name: Von Haeseler citation: 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 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 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. 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. 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. short: A. Kupczok, H. Schmidt, A. Von Haeseler, Algorithms for Molecular Biology 5 (2010). date_created: 2018-12-11T11:57:30Z date_published: 2010-12-06T00:00:00Z date_updated: 2021-01-12T06:57:18Z day: '06' ddc: - '576' department: - _id: JoBo doi: 10.1186/1748-7188-5-37 file: - access_level: open_access checksum: e2497285388bc4da629bafb46662eb43 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:16Z date_updated: 2020-07-14T12:45:40Z file_id: '4739' file_name: IST-2018-939-v1+1_2010_Kupczok_Accuracy_of.pdf file_size: 723929 relation: main_file file_date_updated: 2020-07-14T12:45:40Z has_accepted_license: '1' intvolume: ' 5' issue: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: Algorithms for Molecular Biology publication_status: published publisher: BioMed Central publist_id: '4517' pubrep_id: '939' quality_controlled: '1' scopus_import: 1 status: public title: 'Accuracy of phylogeny reconstruction methods combining overlapping gene data sets ' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2010' ...