[{"type":"journal_article","date_updated":"2025-05-28T11:42:51Z","_id":"1077","publisher":"Royal Society of London","doi":"10.1098/rsif.2016.0139","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","ddc":["570"],"publist_id":"6303","external_id":{"isi":["000393380400001"]},"related_material":{"record":[{"relation":"research_data","status":"public","id":"9864"}]},"isi":1,"year":"2017","date_published":"2017-01-04T00:00:00Z","ec_funded":1,"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"},{"name":"Selective Barriers to Horizontal Gene Transfer","grant_number":"648440","call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425"}],"status":"public","publication":"Journal of the Royal Society Interface","date_created":"2018-12-11T11:50:01Z","volume":14,"oa_version":"Published Version","title":"Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","author":[{"full_name":"Fernandes Redondo, Rodrigo A","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","last_name":"Fernandes Redondo","orcid":"0000-0002-5837-2793","first_name":"Rodrigo A"},{"last_name":"Vladar","id":"2A181218-F248-11E8-B48F-1D18A9856A87","full_name":"Vladar, Harold","first_name":"Harold","orcid":"0000-0002-5985-7653"},{"first_name":"Tomasz","full_name":"Włodarski, Tomasz","last_name":"Włodarski"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P","last_name":"Bollback","first_name":"Jonathan P","orcid":"0000-0002-4624-4612"}],"day":"04","scopus_import":"1","publication_status":"published","publication_identifier":{"issn":["17425689"]},"file_date_updated":"2019-01-18T09:14:02Z","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."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        14","has_accepted_license":"1","article_number":"20160139","file":[{"relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2017_JRSI_Redondo.pdf","success":1,"file_id":"5843","creator":"dernst","date_updated":"2019-01-18T09:14:02Z","file_size":1092015,"date_created":"2019-01-18T09:14:02Z"}],"department":[{"_id":"NiBa"},{"_id":"JoBo"}],"month":"01","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"126","citation":{"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.","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.” <i>Journal of the Royal Society Interface</i>. Royal Society of London, 2017. <a href=\"https://doi.org/10.1098/rsif.2016.0139\">https://doi.org/10.1098/rsif.2016.0139</a>.","mla":"Fernandes Redondo, Rodrigo A., et al. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” <i>Journal of the Royal Society Interface</i>, vol. 14, no. 126, 20160139, Royal Society of London, 2017, doi:<a href=\"https://doi.org/10.1098/rsif.2016.0139\">10.1098/rsif.2016.0139</a>.","apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., &#38; Bollback, J. P. (2017). Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. <i>Journal of the Royal Society Interface</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rsif.2016.0139\">https://doi.org/10.1098/rsif.2016.0139</a>","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. <i>Journal of the Royal Society Interface</i>. 2017;14(126). doi:<a href=\"https://doi.org/10.1098/rsif.2016.0139\">10.1098/rsif.2016.0139</a>","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, Journal of the Royal Society Interface 14 (2017).","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,” <i>Journal of the Royal Society Interface</i>, vol. 14, no. 126. Royal Society of London, 2017."},"language":[{"iso":"eng"}],"oa":1},{"abstract":[{"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.","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.4315652.v1","open_access":"1"}],"oa_version":"Published Version","title":"Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","publisher":"The Royal Society","article_processing_charge":"No","day":"14","author":[{"orcid":"0000-0002-5837-2793","first_name":"Rodrigo A","full_name":"Fernandes Redondo, Rodrigo A","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","last_name":"Fernandes Redondo"},{"first_name":"Harold","orcid":"0000-0002-5985-7653","id":"2A181218-F248-11E8-B48F-1D18A9856A87","full_name":"de Vladar, Harold","last_name":"de Vladar"},{"full_name":"Włodarski, Tomasz","last_name":"Włodarski","first_name":"Tomasz"},{"last_name":"Bollback","full_name":"Bollback, Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","orcid":"0000-0002-4624-4612"}],"doi":"10.6084/m9.figshare.4315652.v1","date_created":"2021-08-10T08:29:47Z","type":"research_data_reference","_id":"9864","date_updated":"2025-05-28T11:57:06Z","status":"public","oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_published":"2016-12-14T00:00:00Z","citation":{"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. <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">https://doi.org/10.6084/m9.figshare.4315652.v1</a>.","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, <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>.","apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., &#38; 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. <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">https://doi.org/10.6084/m9.figshare.4315652.v1</a>","mla":"Fernandes Redondo, Rodrigo A., et al. <i>Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family</i>. The Royal Society, 2016, doi:<a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>.","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:<a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>","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.","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, (2016)."},"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1077"}]},"month":"12","year":"2016","department":[{"_id":"NiBa"},{"_id":"JoBo"}]},{"oa":1,"pubrep_id":"398","language":[{"iso":"eng"}],"issue":"3","citation":{"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).","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.” <i>Genome Announcements</i>. American Society for Microbiology, 2013. <a href=\"https://doi.org/10.1128/genomeA.00216-13\">https://doi.org/10.1128/genomeA.00216-13</a>.","apa":"Fernandes Redondo, R. A., Kupczok, A., Stift, G., &#38; Bollback, J. P. (2013). Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. <i>Genome Announcements</i>. American Society for Microbiology. <a href=\"https://doi.org/10.1128/genomeA.00216-13\">https://doi.org/10.1128/genomeA.00216-13</a>","mla":"Fernandes Redondo, Rodrigo A., et al. “Complete Genome Sequence of the Novel Phage MG-B1 Infecting Bacillus Weihenstephanensis.” <i>Genome Announcements</i>, vol. 1, no. 3, American Society for Microbiology, 2013, doi:<a href=\"https://doi.org/10.1128/genomeA.00216-13\">10.1128/genomeA.00216-13</a>.","ama":"Fernandes Redondo RA, Kupczok A, Stift G, Bollback JP. Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. <i>Genome Announcements</i>. 2013;1(3). doi:<a href=\"https://doi.org/10.1128/genomeA.00216-13\">10.1128/genomeA.00216-13</a>","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,” <i>Genome Announcements</i>, vol. 1, no. 3. American Society for Microbiology, 2013.","short":"R.A. Fernandes Redondo, A. Kupczok, G. Stift, J.P. Bollback, Genome Announcements 1 (2013)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"06","department":[{"_id":"JoBo"},{"_id":"LifeSc"}],"file":[{"file_id":"5291","creator":"system","date_updated":"2020-07-14T12:45:40Z","date_created":"2018-12-12T10:17:36Z","file_size":130026,"checksum":"0751ec74b695567e0cdf02aaf9c26829","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2015-398-v1+1_Genome_Announc.-2013-Redondo-.pdf"}],"has_accepted_license":"1","abstract":[{"text":"Here, we describe a novel virulent bacteriophage that infects Bacillus weihenstephanensis, isolated from soil in Austria. It is the first phage to be discovered that infects this species. Here, we present the complete genome sequence of this podovirus. ","lang":"eng"}],"intvolume":"         1","publication_status":"published","file_date_updated":"2020-07-14T12:45:40Z","author":[{"orcid":"0000-0002-5837-2793","first_name":"Rodrigo A","last_name":"Fernandes Redondo","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","full_name":"Fernandes Redondo, Rodrigo A"},{"full_name":"Kupczok, Anne","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Kupczok","first_name":"Anne"},{"last_name":"Stift","full_name":"Stift, Gertraud","id":"2DB195CA-F248-11E8-B48F-1D18A9856A87","first_name":"Gertraud"},{"first_name":"Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P","last_name":"Bollback"}],"scopus_import":1,"day":"13","title":"Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis","oa_version":"Published Version","volume":1,"date_created":"2018-12-11T11:57:30Z","publication":"Genome Announcements","status":"public","date_published":"2013-06-13T00:00:00Z","year":"2013","publist_id":"4516","ddc":["576"],"quality_controlled":"1","doi":"10.1128/genomeA.00216-13","publisher":"American Society for Microbiology","date_updated":"2021-01-12T06:57:19Z","_id":"2410","type":"journal_article"},{"oa_version":"Published Version","title":"A new species of tapir from the Amazon","scopus_import":1,"day":"01","author":[{"first_name":"Mario","full_name":"Cozzuol, Mario","last_name":"Cozzuol"},{"full_name":"Clozato, Camila","last_name":"Clozato","first_name":"Camila"},{"first_name":"Elizete","last_name":"Holanda","full_name":"Holanda, Elizete"},{"first_name":"Flávio","last_name":"Rodrigues","full_name":"Rodrigues, Flávio"},{"first_name":"Samuel","last_name":"Nienow","full_name":"Nienow, Samuel"},{"first_name":"Benoit","last_name":"De Thoisy","full_name":"De Thoisy, Benoit"},{"first_name":"Rodrigo A","orcid":"0000-0002-5837-2793","last_name":"Fernandes Redondo","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","full_name":"Fernandes Redondo, Rodrigo A"},{"first_name":"Fabrício","full_name":"Santos, Fabrício","last_name":"Santos"}],"date_created":"2018-12-11T11:46:49Z","volume":94,"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"abstract":[{"text":"All known species of extant tapirs are allopatric: 1 in southeastern Asia and 3 in Central and South America. The fossil record for tapirs, however, is much wider in geographical range, including Europe, Asia, and North and South America, going back to the late Oligocene, making the present distribution a relict of the original one. We here describe a new species of living Tapirus from the Amazon rain forest, the 1st since T. bairdii Gill, 1865, and the 1st new Perissodactyla in more than 100 years, from both morphological and molecular characters. It is shorter in stature than T. terrestris (Linnaeus, 1758) and has distinctive skull morphology, and it is basal to the clade formed by T. terrestris and T. pinchaque (Roulin, 1829). This highlights the unrecognized biodiversity in western Amazonia, where the biota faces increasing threats. Local peoples have long recognized our new species, suggesting a key role for traditional knowledge in understanding the biodiversity of the region.","lang":"eng"}],"intvolume":"        94","has_accepted_license":"1","file_date_updated":"2020-07-14T12:46:36Z","publication_status":"published","month":"12","file":[{"file_name":"IST-2018-940-v1+1_2013_Redondo_A_new.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"8007815078dccac21ecd1cf73a269dc6","date_created":"2018-12-12T10:12:59Z","file_size":1040765,"date_updated":"2020-07-14T12:46:36Z","creator":"system","file_id":"4980"}],"department":[{"_id":"JoBo"}],"language":[{"iso":"eng"}],"pubrep_id":"940","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"M. Cozzuol <i>et al.</i>, “A new species of tapir from the Amazon,” <i>Journal of Mammalogy</i>, vol. 94, no. 6. Oxford University Press, pp. 1331–1345, 2013.","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.","ama":"Cozzuol M, Clozato C, Holanda E, et al. A new species of tapir from the Amazon. <i>Journal of Mammalogy</i>. 2013;94(6):1331-1345. doi:<a href=\"https://doi.org/10.1644/12-MAMM-A-169.1\">10.1644/12-MAMM-A-169.1</a>","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. <i>Journal of Mammalogy</i>. Oxford University Press. <a href=\"https://doi.org/10.1644/12-MAMM-A-169.1\">https://doi.org/10.1644/12-MAMM-A-169.1</a>","mla":"Cozzuol, Mario, et al. “A New Species of Tapir from the Amazon.” <i>Journal of Mammalogy</i>, vol. 94, no. 6, Oxford University Press, 2013, pp. 1331–45, doi:<a href=\"https://doi.org/10.1644/12-MAMM-A-169.1\">10.1644/12-MAMM-A-169.1</a>.","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.","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.” <i>Journal of Mammalogy</i>. Oxford University Press, 2013. <a href=\"https://doi.org/10.1644/12-MAMM-A-169.1\">https://doi.org/10.1644/12-MAMM-A-169.1</a>."},"issue":"6","publisher":"Oxford University Press","doi":"10.1644/12-MAMM-A-169.1","type":"journal_article","_id":"501","date_updated":"2021-01-12T08:01:09Z","ddc":["570"],"page":"1331 - 1345","quality_controlled":"1","year":"2013","publist_id":"7319","publication":"Journal of Mammalogy","status":"public","date_published":"2013-12-01T00:00:00Z"},{"date_created":"2018-12-11T11:46:52Z","volume":30,"oa_version":"Submitted Version","title":"Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications","author":[{"first_name":"Eduardo","last_name":"Tarazona Santos","full_name":"Tarazona Santos, Eduardo"},{"last_name":"Machado","full_name":"Machado, Moara","first_name":"Moara"},{"first_name":"Wagner","last_name":"Magalhães","full_name":"Magalhães, Wagner"},{"full_name":"Chen, Renee","last_name":"Chen","first_name":"Renee"},{"full_name":"Lyon, Fernanda","last_name":"Lyon","first_name":"Fernanda"},{"first_name":"Laurie","full_name":"Burdett, Laurie","last_name":"Burdett"},{"first_name":"Andrew","last_name":"Crenshaw","full_name":"Crenshaw, Andrew"},{"first_name":"Cristina","full_name":"Fabbri, Cristina","last_name":"Fabbri"},{"last_name":"Pereira","full_name":"Pereira, Latife","first_name":"Latife"},{"first_name":"Laelia","last_name":"Pinto","full_name":"Pinto, Laelia"},{"last_name":"Fernandes Redondo","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","full_name":"Fernandes Redondo, Rodrigo A","orcid":"0000-0002-5837-2793","first_name":"Rodrigo A"},{"last_name":"Sestanovich","full_name":"Sestanovich, Ben","first_name":"Ben"},{"first_name":"Meredith","last_name":"Yeager","full_name":"Yeager, Meredith"},{"first_name":"Stephen","full_name":"Chanock, Stephen","last_name":"Chanock"}],"scopus_import":1,"day":"01","publication_status":"published","intvolume":"        30","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."}],"department":[{"_id":"JoBo"}],"month":"09","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"9","citation":{"ista":"Tarazona Santos E, Machado M, Magalhães W, Chen R, Lyon F, Burdett L, Crenshaw A, Fabbri C, Pereira L, Pinto L, Fernandes Redondo RA, Sestanovich B, Yeager M, Chanock S. 2013. Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications. Molecular Biology and Evolution. 30(9), 2157–2167.","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.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2013. <a href=\"https://doi.org/10.1093/molbev/mst119\">https://doi.org/10.1093/molbev/mst119</a>.","mla":"Tarazona Santos, Eduardo, et al. “Evolutionary Dynamics of the Human NADPH Oxidase Genes CYBB, CYBA, NCF2, and NCF4: Functional Implications.” <i>Molecular Biology and Evolution</i>, vol. 30, no. 9, Oxford University Press, 2013, pp. 2157–67, doi:<a href=\"https://doi.org/10.1093/molbev/mst119\">10.1093/molbev/mst119</a>.","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. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/mst119\">https://doi.org/10.1093/molbev/mst119</a>","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. <i>Molecular Biology and Evolution</i>. 2013;30(9):2157-2167. doi:<a href=\"https://doi.org/10.1093/molbev/mst119\">10.1093/molbev/mst119</a>","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.","ieee":"E. Tarazona Santos <i>et al.</i>, “Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications,” <i>Molecular Biology and Evolution</i>, vol. 30, no. 9. Oxford University Press, pp. 2157–2167, 2013."},"language":[{"iso":"eng"}],"oa":1,"type":"journal_article","date_updated":"2021-01-12T08:01:12Z","_id":"508","publisher":"Oxford University Press","doi":"10.1093/molbev/mst119","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3748357/"}],"page":"2157 - 2167","publist_id":"7310","external_id":{"pmid":["23821607"]},"year":"2013","date_published":"2013-09-01T00:00:00Z","pmid":1,"publication":"Molecular Biology and Evolution","status":"public"},{"issue":"1","citation":{"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.","chicago":"Vilaça, Sibelle, Rodrigo A Fernandes Redondo, Lívia Lins, and Fabrício Santos. “Remaining Genetic Diversity in Brazilian Merganser (Mergus Octosetaceus).” <i>Conservation Genetics</i>. Springer, 2012. <a href=\"https://doi.org/10.1007/s10592-011-0262-5\">https://doi.org/10.1007/s10592-011-0262-5</a>.","apa":"Vilaça, S., Fernandes Redondo, R. A., Lins, L., &#38; Santos, F. (2012). Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus). <i>Conservation Genetics</i>. Springer. <a href=\"https://doi.org/10.1007/s10592-011-0262-5\">https://doi.org/10.1007/s10592-011-0262-5</a>","mla":"Vilaça, Sibelle, et al. “Remaining Genetic Diversity in Brazilian Merganser (Mergus Octosetaceus).” <i>Conservation Genetics</i>, vol. 13, no. 1, Springer, 2012, pp. 293–98, doi:<a href=\"https://doi.org/10.1007/s10592-011-0262-5\">10.1007/s10592-011-0262-5</a>.","ama":"Vilaça S, Fernandes Redondo RA, Lins L, Santos F. Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus). <i>Conservation Genetics</i>. 2012;13(1):293-298. doi:<a href=\"https://doi.org/10.1007/s10592-011-0262-5\">10.1007/s10592-011-0262-5</a>","ieee":"S. Vilaça, R. A. Fernandes Redondo, L. Lins, and F. Santos, “Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus),” <i>Conservation Genetics</i>, vol. 13, no. 1. Springer, pp. 293–298, 2012.","short":"S. Vilaça, R.A. Fernandes Redondo, L. Lins, F. Santos, Conservation Genetics 13 (2012) 293–298."},"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.","date_published":"2012-02-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"publication":"Conservation Genetics","status":"public","department":[{"_id":"JoBo"}],"publist_id":"3420","year":"2012","month":"02","quality_controlled":"1","publication_status":"published","page":"293 - 298","intvolume":"        13","abstract":[{"text":"The Brazilian Merganser is a very rare and threatened species that nowadays inhabits only a few protected areas and their surroundings in the Brazilian territory. In order to estimate the remaining genetic diversity and population structure in this species, two mitochondrial genes were sequenced in 39 individuals belonging to two populations and in one individual collected in Argentina in 1950. We found a highly significant divergence between two major remaining populations of Mergus octosetaceus, which suggests a historical population structure in this species. Furthermore, two deeply divergent lineages were found in a single location, which could due to current or historical secondary contact. Based on the available genetic data, we point out future directions which would contribute to design strategies for conservation and management of this threatened species.","lang":"eng"}],"date_updated":"2021-01-12T07:42:05Z","_id":"3247","volume":13,"type":"journal_article","date_created":"2018-12-11T12:02:15Z","author":[{"first_name":"Sibelle","last_name":"Vilaça","full_name":"Vilaça, Sibelle"},{"full_name":"Fernandes Redondo, Rodrigo A","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","last_name":"Fernandes Redondo","first_name":"Rodrigo A","orcid":"0000-0002-5837-2793"},{"full_name":"Lins, Lívia","last_name":"Lins","first_name":"Lívia"},{"first_name":"Fabrício","full_name":"Santos, Fabrício","last_name":"Santos"}],"doi":"10.1007/s10592-011-0262-5","scopus_import":1,"day":"01","publisher":"Springer","oa_version":"None","title":"Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus)"},{"date_created":"2018-12-11T12:05:04Z","type":"journal_article","volume":102,"_id":"3770","date_updated":"2021-01-12T07:52:05Z","oa_version":"None","title":"The Amazon River system as an ecological barrier driving genetic differentiation of the pink dolphin (Inia geoffrensis)","publisher":"Wiley","article_processing_charge":"No","day":"01","doi":"10.1111/j.1095-8312.2011.01616.x","author":[{"first_name":"Claudia","last_name":"Hollatz","full_name":"Hollatz, Claudia"},{"first_name":"Sibelle","last_name":"Vilaça","full_name":"Vilaça, Sibelle"},{"orcid":"0000-0002-5837-2793","first_name":"Rodrigo A","last_name":"Fernandes Redondo","full_name":"Fernandes Redondo, Rodrigo A","id":"409D5C96-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Míriam","last_name":"Marmontel","full_name":"Marmontel, Míriam"},{"full_name":"Baker, Cyndi","last_name":"Baker","first_name":"Cyndi"},{"full_name":"Santos, Fabrício","last_name":"Santos","first_name":"Fabrício"}],"publication_status":"published","abstract":[{"text":"The pink dolphin (Inia geoffrensis) is widely distributed along the Amazon and Orinoco basins, covering an area of approximately 7 million km2. Previous morphological and genetic studies have proposed the existence of at least two evolutionary significant units: one distributed across the Orinoco and Amazon basins and another confined to the Bolivian Amazon. The presence of barriers in the riverine environment has been suggested to play a significant role in shaping present-day patterns of ecological and genetic structure for this species. In the present study, we examined the phylogeographic structure, lineage divergence time and historical demography using mitochondrial (mt)DNA sequences in different pink dolphin populations distributed in large and small spatial scales, including two neighbouring Brazilian Amazon populations. mtDNA control region (CR) analysis revealed that the Brazilian haplotypes occupy an intermediate position compared to three previously studied geographic locations: the Colombian Amazon, the Colombian Orinoco, and the Bolivian Amazon. On a local scale, we have identified a pattern of maternal isolation between two neighbouring populations from Brazil. Six mtDNA CR haplotypes were identified in Brazil with no sharing between the two populations, as well as specific cytochrome b (cyt b) haplotypes identified in each locality. In addition, we analyzed autosomal microsatellites to investigate male-mediated gene flow and demographic changes within the study area in Brazil. Data analysis of 14 microsatellite loci failed to detect significant population subdivision, suggesting that male-mediated gene flow may maintain homogeneity between these two locations. Moreover, both mtDNA and microsatellite data indicate a major demographic collapse within Brazil in the late Pleistocene. Bayesian skyline plots (BSP) of mtDNA data revealed a stable population for Colombian and Brazilian Amazon lineages through time, whereas a population decline was demonstrated in the Colombian Orinoco lineage. Moreover, BSP and Tajima's D and Fu's Fs tests revealed a recent population expansion exclusively in the Bolivian sample. Finally, we estimated that the diversification of the Inia sp. lineage began in the Late Pliocene (approximately 3.1 Mya) and continued throughout the Pleistocene.","lang":"eng"}],"intvolume":"       102","page":"812 - 827","publist_id":"2457","month":"04","year":"2011","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2011-04-01T00:00:00Z","citation":{"ieee":"C. Hollatz, S. Vilaça, R. A. Fernandes Redondo, M. Marmontel, C. Baker, and F. Santos, “The Amazon River system as an ecological barrier driving genetic differentiation of the pink dolphin (Inia geoffrensis),” <i>Biological Journal of the Linnean Society</i>, vol. 102, no. 4. Wiley, pp. 812–827, 2011.","short":"C. Hollatz, S. Vilaça, R.A. Fernandes Redondo, M. Marmontel, C. Baker, F. Santos, Biological Journal of the Linnean Society 102 (2011) 812–827.","ama":"Hollatz C, Vilaça S, Fernandes Redondo RA, Marmontel M, Baker C, Santos F. The Amazon River system as an ecological barrier driving genetic differentiation of the pink dolphin (Inia geoffrensis). <i>Biological Journal of the Linnean Society</i>. 2011;102(4):812-827. doi:<a href=\"https://doi.org/10.1111/j.1095-8312.2011.01616.x\">10.1111/j.1095-8312.2011.01616.x</a>","apa":"Hollatz, C., Vilaça, S., Fernandes Redondo, R. A., Marmontel, M., Baker, C., &#38; Santos, F. (2011). The Amazon River system as an ecological barrier driving genetic differentiation of the pink dolphin (Inia geoffrensis). <i>Biological Journal of the Linnean Society</i>. Wiley. <a href=\"https://doi.org/10.1111/j.1095-8312.2011.01616.x\">https://doi.org/10.1111/j.1095-8312.2011.01616.x</a>","mla":"Hollatz, Claudia, et al. “The Amazon River System as an Ecological Barrier Driving Genetic Differentiation of the Pink Dolphin (Inia Geoffrensis).” <i>Biological Journal of the Linnean Society</i>, vol. 102, no. 4, Wiley, 2011, pp. 812–27, doi:<a href=\"https://doi.org/10.1111/j.1095-8312.2011.01616.x\">10.1111/j.1095-8312.2011.01616.x</a>.","ista":"Hollatz C, Vilaça S, Fernandes Redondo RA, Marmontel M, Baker C, Santos F. 2011. The Amazon River system as an ecological barrier driving genetic differentiation of the pink dolphin (Inia geoffrensis). Biological Journal of the Linnean Society. 102(4), 812–827.","chicago":"Hollatz, Claudia, Sibelle Vilaça, Rodrigo A Fernandes Redondo, Míriam Marmontel, Cyndi Baker, and Fabrício Santos. “The Amazon River System as an Ecological Barrier Driving Genetic Differentiation of the Pink Dolphin (Inia Geoffrensis).” <i>Biological Journal of the Linnean Society</i>. Wiley, 2011. <a href=\"https://doi.org/10.1111/j.1095-8312.2011.01616.x\">https://doi.org/10.1111/j.1095-8312.2011.01616.x</a>."},"issue":"4","status":"public","publication":"Biological Journal of the Linnean Society","language":[{"iso":"eng"}],"extern":"1"},{"publication_status":"published","quality_controlled":"1","intvolume":"       102","abstract":[{"lang":"eng","text":"The small-sized frugivorous bat Carollia perspicillata is an understory specialist and occurs in a wide range of lowland habitats, tending to be more common in tropical dry or moist forests of South and Central America. Its sister species, Carollia brevicauda, occurs almost exclusively in the Amazon rainforest. A recent phylogeographic study proposed a hypothesis of origin and subsequent diversification for C. perspicillata along the Atlantic coastal forest of Brazil. Additionally, it also found two allopatric clades for C. brevicauda separated by the Amazon Basin. We used cytochrome b gene sequences and a more extensive sampling to test hypotheses related to the origin and diversification of C. perspicillata plus C. brevicauda clade in South America. The results obtained indicate that there are two sympatric evolutionary lineages within each species. In C. perspicillata, one lineage is limited to the Southern Atlantic Forest, whereas the other is widely distributed. Coalescent analysis points to a simultaneous origin for C. perspicillata and C. brevicauda, although no place for the diversification of each species can be firmly suggested. The phylogeographic pattern shown by C. perspicillata is also congruent with the Pleistocene refugia hypothesis as a likely vicariant phenomenon shaping the present distribution of its intraspecific lineages."}],"page":"527 - 539","type":"journal_article","date_created":"2018-12-11T12:05:05Z","date_updated":"2021-01-12T07:52:05Z","volume":102,"_id":"3771","title":"Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests.","publisher":"Wiley-Blackwell","oa_version":"None","author":[{"last_name":"Pavan","full_name":"Pavan, Ana","first_name":"Ana"},{"first_name":"Felipe","full_name":"Martins, Felipe","last_name":"Martins"},{"last_name":"Santos","full_name":"Santos, Fabrício","first_name":"Fabrício"},{"first_name":"Albert","last_name":"Ditchfield","full_name":"Ditchfield, Albert"},{"last_name":"Fernandes Redondo","full_name":"Fernandes Redondo, Rodrigo A","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5837-2793","first_name":"Rodrigo A"}],"doi":"10.1111/j.1095-8312.2010.01601.x","scopus_import":1,"day":"10","date_published":"2011-02-10T00:00:00Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","issue":"3","citation":{"ieee":"A. Pavan, F. Martins, F. Santos, A. Ditchfield, and R. A. Fernandes Redondo, “Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests.,” <i>Biological Journal of the Linnean Society</i>, vol. 102, no. 3. Wiley-Blackwell, pp. 527–539, 2011.","short":"A. Pavan, F. Martins, F. Santos, A. Ditchfield, R.A. Fernandes Redondo, Biological Journal of the Linnean Society 102 (2011) 527–539.","ama":"Pavan A, Martins F, Santos F, Ditchfield A, Fernandes Redondo RA. Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests. <i>Biological Journal of the Linnean Society</i>. 2011;102(3):527-539. doi:<a href=\"https://doi.org/10.1111/j.1095-8312.2010.01601.x\">10.1111/j.1095-8312.2010.01601.x</a>","apa":"Pavan, A., Martins, F., Santos, F., Ditchfield, A., &#38; Fernandes Redondo, R. A. (2011). Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests. <i>Biological Journal of the Linnean Society</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1095-8312.2010.01601.x\">https://doi.org/10.1111/j.1095-8312.2010.01601.x</a>","mla":"Pavan, Ana, et al. “Patterns of Diversification in Two Species of Short-Tailed Bats (Carollia Gray, 1838): The Effects of Historical Fragmentation of Brazilian Rainforests.” <i>Biological Journal of the Linnean Society</i>, vol. 102, no. 3, Wiley-Blackwell, 2011, pp. 527–39, doi:<a href=\"https://doi.org/10.1111/j.1095-8312.2010.01601.x\">10.1111/j.1095-8312.2010.01601.x</a>.","ista":"Pavan A, Martins F, Santos F, Ditchfield A, Fernandes Redondo RA. 2011. Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests. Biological Journal of the Linnean Society. 102(3), 527–539.","chicago":"Pavan, Ana, Felipe Martins, Fabrício Santos, Albert Ditchfield, and Rodrigo A Fernandes Redondo. “Patterns of Diversification in Two Species of Short-Tailed Bats (Carollia Gray, 1838): The Effects of Historical Fragmentation of Brazilian Rainforests.” <i>Biological Journal of the Linnean Society</i>. Wiley-Blackwell, 2011. <a href=\"https://doi.org/10.1111/j.1095-8312.2010.01601.x\">https://doi.org/10.1111/j.1095-8312.2010.01601.x</a>."},"language":[{"iso":"eng"}],"status":"public","publication":"Biological Journal of the Linnean Society","publist_id":"2456","department":[{"_id":"FyKo"}],"month":"02","year":"2011"}]