[{"abstract":[{"lang":"eng","text":"Cytosine methylation silences transposable elements in plants, vertebrates, and fungi but also regulates gene expression. Plant methylation is catalyzed by three families of enzymes, each with a preferred sequence context: CG, CHG (H = A, C, or T), and CHH, with CHH methylation targeted by the RNAi pathway. Arabidopsis thaliana endosperm, a placenta-like tissue that nourishes the embryo, is globally hypomethylated in the CG context while retaining high non-CG methylation. Global methylation dynamics in seeds of cereal crops that provide the bulk of human nutrition remain unknown. Here, we show that rice endosperm DNA is hypomethylated in all sequence contexts. Non-CG methylation is reduced evenly across the genome, whereas CG hypomethylation is localized. CHH methylation of small transposable elements is increased in embryos, suggesting that endosperm demethylation enhances transposon silencing. Genes preferentially expressed in endosperm, including those coding for major storage proteins and starch synthesizing enzymes, are frequently hypomethylated in endosperm, indicating that DNA methylation is a crucial regulator of rice endosperm biogenesis. Our data show that genome-wide reshaping of seed DNA methylation is conserved among angiosperms and has a profound effect on gene expression in cereal crops."}],"extern":"1","status":"public","day":"26","citation":{"apa":"Zemach, A., Kim, M. Y., Silva, P., Rodrigues, J. A., Dotson, B., Brooks, M. D., & Zilberman, D. (2010). Local DNA hypomethylation activates genes in rice endosperm. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1009695107","chicago":"Zemach, Assaf, M. Yvonne Kim, Pedro Silva, Jessica A. Rodrigues, Bradley Dotson, Matthew D. Brooks, and Daniel Zilberman. “Local DNA Hypomethylation Activates Genes in Rice Endosperm.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2010. https://doi.org/10.1073/pnas.1009695107.","ista":"Zemach A, Kim MY, Silva P, Rodrigues JA, Dotson B, Brooks MD, Zilberman D. 2010. Local DNA hypomethylation activates genes in rice endosperm. Proceedings of the National Academy of Sciences. 107(43), 18729–18734.","ieee":"A. Zemach et al., “Local DNA hypomethylation activates genes in rice endosperm,” Proceedings of the National Academy of Sciences, vol. 107, no. 43. National Academy of Sciences, pp. 18729–18734, 2010.","mla":"Zemach, Assaf, et al. “Local DNA Hypomethylation Activates Genes in Rice Endosperm.” Proceedings of the National Academy of Sciences, vol. 107, no. 43, National Academy of Sciences, 2010, pp. 18729–34, doi:10.1073/pnas.1009695107.","short":"A. Zemach, M.Y. Kim, P. Silva, J.A. Rodrigues, B. Dotson, M.D. Brooks, D. Zilberman, Proceedings of the National Academy of Sciences 107 (2010) 18729–18734.","ama":"Zemach A, Kim MY, Silva P, et al. Local DNA hypomethylation activates genes in rice endosperm. Proceedings of the National Academy of Sciences. 2010;107(43):18729-18734. doi:10.1073/pnas.1009695107"},"intvolume":" 107","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"10","_id":"9485","article_type":"original","title":"Local DNA hypomethylation activates genes in rice endosperm","oa":1,"publication_status":"published","department":[{"_id":"DaZi"}],"date_updated":"2021-12-14T08:40:02Z","quality_controlled":"1","page":"18729-18734","date_created":"2021-06-07T09:31:01Z","year":"2010","volume":107,"article_processing_charge":"No","scopus_import":"1","pmid":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1009695107"}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publisher":"National Academy of Sciences","doi":"10.1073/pnas.1009695107","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2010-10-26T00:00:00Z","external_id":{"pmid":["20937895"]},"oa_version":"Published Version","author":[{"full_name":"Zemach, Assaf","first_name":"Assaf","last_name":"Zemach"},{"last_name":"Kim","full_name":"Kim, M. Yvonne","first_name":"M. Yvonne"},{"last_name":"Silva","full_name":"Silva, Pedro","first_name":"Pedro"},{"full_name":"Rodrigues, Jessica A.","first_name":"Jessica A.","last_name":"Rodrigues"},{"last_name":"Dotson","full_name":"Dotson, Bradley","first_name":"Bradley"},{"last_name":"Brooks","first_name":"Matthew D.","full_name":"Brooks, Matthew D."},{"last_name":"Zilberman","first_name":"Daniel","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"publication":"Proceedings of the National Academy of Sciences","issue":"43"},{"day":"14","intvolume":" 20","citation":{"short":"A. Zemach, D. Zilberman, Current Biology 20 (2010) R780–R785.","ama":"Zemach A, Zilberman D. Evolution of eukaryotic DNA methylation and the pursuit of safer sex. Current Biology. 2010;20(17):R780-R785. doi:10.1016/j.cub.2010.07.007","chicago":"Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation and the Pursuit of Safer Sex.” Current Biology. Elsevier, 2010. https://doi.org/10.1016/j.cub.2010.07.007.","ista":"Zemach A, Zilberman D. 2010. Evolution of eukaryotic DNA methylation and the pursuit of safer sex. Current Biology. 20(17), R780–R785.","apa":"Zemach, A., & Zilberman, D. (2010). Evolution of eukaryotic DNA methylation and the pursuit of safer sex. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2010.07.007","mla":"Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation and the Pursuit of Safer Sex.” Current Biology, vol. 20, no. 17, Elsevier, 2010, pp. R780–85, doi:10.1016/j.cub.2010.07.007.","ieee":"A. Zemach and D. Zilberman, “Evolution of eukaryotic DNA methylation and the pursuit of safer sex,” Current Biology, vol. 20, no. 17. Elsevier, pp. R780–R785, 2010."},"status":"public","abstract":[{"text":"Cytosine methylation is an ancient process with conserved enzymology but diverse biological functions that include defense against transposable elements and regulation of gene expression. Here we will discuss the evolution and biological significance of eukaryotic DNA methylation, the likely drivers of that evolution, and major remaining mysteries.","lang":"eng"}],"extern":"1","department":[{"_id":"DaZi"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"09","_id":"9489","title":"Evolution of eukaryotic DNA methylation and the pursuit of safer sex","oa":1,"publication_status":"published","article_type":"review","article_processing_charge":"No","publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"scopus_import":"1","pmid":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2010.07.007","open_access":"1"}],"page":"R780-R785","quality_controlled":"1","year":"2010","date_created":"2021-06-07T09:45:27Z","date_updated":"2021-12-14T08:52:34Z","volume":20,"oa_version":"Published Version","external_id":{"pmid":["20833323"]},"date_published":"2010-09-14T00:00:00Z","publication":"Current Biology","issue":"17","author":[{"last_name":"Zemach","first_name":"Assaf","full_name":"Zemach, Assaf"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","last_name":"Zilberman","full_name":"Zilberman, Daniel","first_name":"Daniel"}],"doi":"10.1016/j.cub.2010.07.007","publisher":"Elsevier","language":[{"iso":"eng"}],"type":"journal_article"},{"publisher":"Public Library of Science","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"07","_id":"9764","doi":"10.1371/journal.pbio.1000429.s003","type":"research_data_reference","related_material":{"record":[{"id":"3779","relation":"used_in_publication","status":"public"}]},"title":"Heterosis and the drift load","date_published":"2010-07-20T00:00:00Z","department":[{"_id":"NiBa"}],"oa_version":"Published Version","author":[{"full_name":"Rosas, Ulises","first_name":"Ulises","last_name":"Rosas"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H"},{"full_name":"Copsey, Lucy","first_name":"Lucy","last_name":"Copsey"},{"last_name":"Barbier De Reuille","full_name":"Barbier De Reuille, Pierre","first_name":"Pierre"},{"full_name":"Coen, Enrico","first_name":"Enrico","last_name":"Coen"}],"date_updated":"2023-02-23T11:42:17Z","date_created":"2021-08-02T09:45:39Z","year":"2010","status":"public","article_processing_charge":"No","day":"20","citation":{"chicago":"Rosas, Ulises, Nicholas H Barton, Lucy Copsey, Pierre Barbier De Reuille, and Enrico Coen. “Heterosis and the Drift Load.” Public Library of Science, 2010. https://doi.org/10.1371/journal.pbio.1000429.s003.","ista":"Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. 2010. Heterosis and the drift load, Public Library of Science, 10.1371/journal.pbio.1000429.s003.","apa":"Rosas, U., Barton, N. H., Copsey, L., Barbier De Reuille, P., & Coen, E. (2010). Heterosis and the drift load. Public Library of Science. https://doi.org/10.1371/journal.pbio.1000429.s003","ieee":"U. Rosas, N. H. Barton, L. Copsey, P. Barbier De Reuille, and E. Coen, “Heterosis and the drift load.” Public Library of Science, 2010.","mla":"Rosas, Ulises, et al. Heterosis and the Drift Load. Public Library of Science, 2010, doi:10.1371/journal.pbio.1000429.s003.","short":"U. Rosas, N.H. Barton, L. Copsey, P. Barbier De Reuille, E. Coen, (2010).","ama":"Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. Heterosis and the drift load. 2010. doi:10.1371/journal.pbio.1000429.s003"}},{"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"eisbn":["9783642175114"],"isbn":["9783642175107"]},"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://infoscience.epfl.ch/record/186096"}],"article_processing_charge":"No","volume":6355,"page":"103-118","quality_controlled":"1","date_created":"2022-03-21T08:14:35Z","series_title":"LNCS","year":"2010","date_updated":"2022-06-13T07:44:21Z","publication":"Logic for Programming, Artificial Intelligence, and Reasoning","author":[{"first_name":"Régis","full_name":"Blanc, Régis","last_name":"Blanc"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hottelier","first_name":"Thibaud","full_name":"Hottelier, Thibaud"},{"full_name":"Kovács, Laura","first_name":"Laura","last_name":"Kovács"}],"oa_version":"Submitted Version","conference":{"name":"LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning","start_date":"2010-04-25","location":"Dakar, Senegal","end_date":"2010-05-01"},"date_published":"2010-05-01T00:00:00Z","language":[{"iso":"eng"}],"type":"conference","doi":"10.1007/978-3-642-17511-4_7","publisher":"Springer Nature","intvolume":" 6355","citation":{"short":"R. Blanc, T.A. Henzinger, T. Hottelier, L. Kovács, in:, E.M. Clarke, A. Voronkov (Eds.), Logic for Programming, Artificial Intelligence, and Reasoning, Springer Nature, Berlin, Heidelberg, 2010, pp. 103–118.","ama":"Blanc R, Henzinger TA, Hottelier T, Kovács L. ABC: Algebraic Bound Computation for loops. In: Clarke EM, Voronkov A, eds. Logic for Programming, Artificial Intelligence, and Reasoning. Vol 6355. LNCS. Berlin, Heidelberg: Springer Nature; 2010:103-118. doi:10.1007/978-3-642-17511-4_7","apa":"Blanc, R., Henzinger, T. A., Hottelier, T., & Kovács, L. (2010). ABC: Algebraic Bound Computation for loops. In E. M. Clarke & A. Voronkov (Eds.), Logic for Programming, Artificial Intelligence, and Reasoning (Vol. 6355, pp. 103–118). Berlin, Heidelberg: Springer Nature. https://doi.org/10.1007/978-3-642-17511-4_7","ista":"Blanc R, Henzinger TA, Hottelier T, Kovács L. 2010. ABC: Algebraic Bound Computation for loops. Logic for Programming, Artificial Intelligence, and Reasoning. LPAR: Conference on Logic for Programming, Artificial Intelligence and ReasoningLNCS vol. 6355, 103–118.","chicago":"Blanc, Régis, Thomas A Henzinger, Thibaud Hottelier, and Laura Kovács. “ABC: Algebraic Bound Computation for Loops.” In Logic for Programming, Artificial Intelligence, and Reasoning, edited by Edmund M Clarke and Andrei Voronkov, 6355:103–18. LNCS. Berlin, Heidelberg: Springer Nature, 2010. https://doi.org/10.1007/978-3-642-17511-4_7.","ieee":"R. Blanc, T. A. Henzinger, T. Hottelier, and L. Kovács, “ABC: Algebraic Bound Computation for loops,” in Logic for Programming, Artificial Intelligence, and Reasoning, Dakar, Senegal, 2010, vol. 6355, pp. 103–118.","mla":"Blanc, Régis, et al. “ABC: Algebraic Bound Computation for Loops.” Logic for Programming, Artificial Intelligence, and Reasoning, edited by Edmund M Clarke and Andrei Voronkov, vol. 6355, Springer Nature, 2010, pp. 103–18, doi:10.1007/978-3-642-17511-4_7."},"day":"01","status":"public","abstract":[{"lang":"eng","text":"We present ABC, a software tool for automatically computing symbolic upper bounds on the number of iterations of nested program loops. The system combines static analysis of programs with symbolic summation techniques to derive loop invariant relations between program variables. Iteration bounds are obtained from the inferred invariants, by replacing variables with bounds on their greatest values. We have successfully applied ABC to a large number of examples. The derived symbolic bounds express non-trivial polynomial relations over loop variables. We also report on results to automatically infer symbolic expressions over harmonic numbers as upper bounds on loop iteration counts."}],"editor":[{"first_name":"Edmund M","full_name":"Clarke, Edmund M","last_name":"Clarke"},{"last_name":"Voronkov","full_name":"Voronkov, Andrei","first_name":"Andrei"}],"acknowledgement":"This work was supported in part by the Swiss NSF. The fourth author is supported by an FWF Hertha Firnberg Research grant (T425-N23).","department":[{"_id":"ToHe"}],"title":"ABC: Algebraic Bound Computation for loops","oa":1,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","_id":"10908","place":"Berlin, Heidelberg"},{"status":"public","abstract":[{"lang":"eng","text":"We address the problem of localizing homology classes, namely, finding the cycle representing a given class with the most concise geometric measure. We focus on the volume measure, that is, the 1-norm of a cycle. Two main results are presented. First, we prove the problem is NP-hard to approximate within any constant factor. Second, we prove that for homology of dimension two or higher, the problem is NP-hard to approximate even when the Betti number is O(1). A side effect is the inapproximability of the problem of computing the nonbounding cycle with the smallest volume, and computing cycles representing a homology basis with the minimal total volume. We also discuss other geometric measures (diameter and radius) and show their disadvantages in homology localization. Our work is restricted to homology over the ℤ2 field."}],"page":"1594-1604","quality_controlled":"1","year":"2010","date_created":"2022-03-21T08:24:07Z","date_updated":"2023-02-23T11:19:46Z","publication_identifier":{"eisbn":["9781611973075"]},"scopus_import":"1","citation":{"short":"C. Chen, D. Freedman, in:, Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2010, pp. 1594–1604.","ama":"Chen C, Freedman D. Hardness results for homology localization. In: Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2010:1594-1604. doi:10.1137/1.9781611973075.129","ista":"Chen C, Freedman D. 2010. Hardness results for homology localization. Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 1594–1604.","chicago":"Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.” In Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms, 1594–1604. Society for Industrial and Applied Mathematics, 2010. https://doi.org/10.1137/1.9781611973075.129.","apa":"Chen, C., & Freedman, D. (2010). Hardness results for homology localization. In Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 1594–1604). Austin, TX, United States: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611973075.129","ieee":"C. Chen and D. Freedman, “Hardness results for homology localization,” in Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms, Austin, TX, United States, 2010, pp. 1594–1604.","mla":"Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.” Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2010, pp. 1594–604, doi:10.1137/1.9781611973075.129."},"day":"01","article_processing_charge":"No","related_material":{"record":[{"id":"3267","status":"public","relation":"later_version"}]},"title":"Hardness results for homology localization","language":[{"iso":"eng"}],"publication_status":"published","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10909","doi":"10.1137/1.9781611973075.129","month":"02","publisher":"Society for Industrial and Applied Mathematics","publication":"Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms","author":[{"id":"3E92416E-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","first_name":"Chao","full_name":"Chen, Chao"},{"last_name":"Freedman","full_name":"Freedman, Daniel","first_name":"Daniel"}],"oa_version":"None","conference":{"end_date":"2010-01-19","location":"Austin, TX, United States","start_date":"2010-01-17","name":"SODA: Symposium on Discrete Algorithms"},"date_published":"2010-02-01T00:00:00Z","acknowledgement":"Partially supported by the Austrian Science Fund under grantFSP-S9103-N04 and P20134-N13.","department":[{"_id":"HeEd"}]},{"publisher":"BioMed Central","doi":"10.1186/1748-7188-5-37","file_date_updated":"2020-07-14T12:45:40Z","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2010-12-06T00:00:00Z","oa_version":"Published Version","ddc":["576"],"author":[{"last_name":"Kupczok","full_name":"Kupczok, Anne","first_name":"Anne","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schmidt","full_name":"Schmidt, Heiko","first_name":"Heiko"},{"full_name":"Von Haeseler, Arndt","first_name":"Arndt","last_name":"Von Haeseler"}],"publist_id":"4517","publication":"Algorithms for Molecular Biology","issue":"1","date_updated":"2021-01-12T06:57:18Z","quality_controlled":"1","date_created":"2018-12-11T11:57:30Z","year":"2010","volume":5,"file":[{"file_name":"IST-2018-939-v1+1_2010_Kupczok_Accuracy_of.pdf","file_id":"4739","content_type":"application/pdf","date_created":"2018-12-12T10:09:16Z","date_updated":"2020-07-14T12:45:40Z","access_level":"open_access","relation":"main_file","checksum":"e2497285388bc4da629bafb46662eb43","file_size":723929,"creator":"system"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"scopus_import":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2409","month":"12","oa":1,"title":"Accuracy of phylogeny reconstruction methods combining overlapping gene data sets ","publication_status":"published","department":[{"_id":"JoBo"}],"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).","pubrep_id":"939","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."}],"article_number":"37","status":"public","has_accepted_license":"1","day":"06","intvolume":" 5","citation":{"short":"A. Kupczok, H. Schmidt, A. Von Haeseler, Algorithms for Molecular Biology 5 (2010).","ama":"Kupczok A, Schmidt H, Von Haeseler A. Accuracy of phylogeny reconstruction methods combining overlapping gene data sets . Algorithms for Molecular Biology. 2010;5(1). doi:10.1186/1748-7188-5-37","chicago":"Kupczok, Anne, Heiko Schmidt, and Arndt Von Haeseler. “Accuracy of Phylogeny Reconstruction Methods Combining Overlapping Gene Data Sets .” Algorithms for Molecular Biology. BioMed Central, 2010. https://doi.org/10.1186/1748-7188-5-37.","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.","apa":"Kupczok, A., Schmidt, H., & Von Haeseler, A. (2010). Accuracy of phylogeny reconstruction methods combining overlapping gene data sets . Algorithms for Molecular Biology. BioMed Central. https://doi.org/10.1186/1748-7188-5-37","ieee":"A. Kupczok, H. Schmidt, and A. Von Haeseler, “Accuracy of phylogeny reconstruction methods combining overlapping gene data sets ,” Algorithms for Molecular Biology, vol. 5, no. 1. BioMed Central, 2010.","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."}},{"citation":{"ama":"Weissman D, Feldman M, Fisher D. The rate of fitness-valley crossing in sexual populations. Genetics. 2010;186(4):1389-1410. doi:10.1534/genetics.110.123240","short":"D. Weissman, M. Feldman, D. Fisher, Genetics 186 (2010) 1389–1410.","mla":"Weissman, Daniel, et al. “The Rate of Fitness-Valley Crossing in Sexual Populations.” Genetics, vol. 186, no. 4, Genetics Society of America, 2010, pp. 1389–410, doi:10.1534/genetics.110.123240.","ieee":"D. Weissman, M. Feldman, and D. Fisher, “The rate of fitness-valley crossing in sexual populations,” Genetics, vol. 186, no. 4. Genetics Society of America, pp. 1389–1410, 2010.","apa":"Weissman, D., Feldman, M., & Fisher, D. (2010). The rate of fitness-valley crossing in sexual populations. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.110.123240","ista":"Weissman D, Feldman M, Fisher D. 2010. The rate of fitness-valley crossing in sexual populations. Genetics. 186(4), 1389–1410.","chicago":"Weissman, Daniel, Marcus Feldman, and Daniel Fisher. “The Rate of Fitness-Valley Crossing in Sexual Populations.” Genetics. Genetics Society of America, 2010. https://doi.org/10.1534/genetics.110.123240."},"intvolume":" 186","day":"01","abstract":[{"lang":"eng","text":"Biological traits result in part from interactions between different genetic loci. This can lead to sign epistasis, in which a beneficial adaptation involves a combination of individually deleterious or neutral mutations; in this case, a population must cross a “fitness valley” to adapt. Recombination can assist this process by combining mutations from different individuals or retard it by breaking up the adaptive combination. Here, we analyze the simplest fitness valley, in which an adaptation requires one mutation at each of two loci to provide a fitness benefit. We present a theoretical analysis of the effect of recombination on the valley-crossing process across the full spectrum of possible parameter regimes. We find that low recombination rates can speed up valley crossing relative to the asexual case, while higher recombination rates slow down valley crossing, with the transition between the two regimes occurring when the recombination rate between the loci is approximately equal to the selective advantage provided by the adaptation. In large populations, if the recombination rate is high and selection against single mutants is substantial, the time to cross the valley grows exponentially with population size, effectively meaning that the population cannot acquire the adaptation. Recombination at the optimal (low) rate can reduce the valley-crossing time by up to several orders of magnitude relative to that in an asexual population. "}],"status":"public","ec_funded":1,"acknowledgement":"This work was supported in part by a Robert N. Noyce Stanford Graduate Fellowship and European Research Council grant 250152 (to D.B.W.) and by National Institutes of Health grant GM 28016 (to M.W.F.).\r\nWe thank Michael Desai for many ideas and discussions and are grateful to Joanna Masel and an anonymous reviewer for their helpful suggestions. ","department":[{"_id":"NiBa"}],"publication_status":"published","oa":1,"title":"The rate of fitness-valley crossing in sexual populations","month":"12","_id":"3303","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2998319/"}],"scopus_import":1,"volume":186,"project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"date_updated":"2021-01-12T07:42:31Z","date_created":"2018-12-11T12:02:33Z","year":"2010","page":"1389 - 1410","quality_controlled":"1","author":[{"id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","last_name":"Weissman","first_name":"Daniel","full_name":"Weissman, Daniel"},{"last_name":"Feldman","full_name":"Feldman, Marcus","first_name":"Marcus"},{"full_name":"Fisher, Daniel","first_name":"Daniel","last_name":"Fisher"}],"publication":"Genetics","issue":"4","publist_id":"3337","date_published":"2010-12-01T00:00:00Z","oa_version":"Submitted Version","type":"journal_article","language":[{"iso":"eng"}],"publisher":"Genetics Society of America","doi":"10.1534/genetics.110.123240"},{"oa_version":"None","date_published":"2010-03-01T00:00:00Z","department":[{"_id":"NiBa"}],"issue":"5","publication":"Molecular Ecology","publist_id":"2779","author":[{"last_name":"Senn","first_name":"Helen","full_name":"Senn, Helen"},{"last_name":"Goodman","full_name":"Goodman, Simon","first_name":"Simon"},{"last_name":"Swanson","full_name":"Swanson, Graeme","first_name":"Graeme"},{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"full_name":"Pemberton, Josephine","first_name":"Josephine","last_name":"Pemberton"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3604","month":"03","doi":"10.1111/j.1365-294X.2009.04497.x","publisher":"Wiley-Blackwell","title":"Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland","publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","day":"01","scopus_import":1,"intvolume":" 19","citation":{"short":"H. Senn, S. Goodman, G. Swanson, N.H. Barton, J. Pemberton, Molecular Ecology 19 (2010) 910–924.","ama":"Senn H, Goodman S, Swanson G, Barton NH, Pemberton J. Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland. Molecular Ecology. 2010;19(5):910-924. doi:10.1111/j.1365-294X.2009.04497.x","chicago":"Senn, Helen, Simon Goodman, Graeme Swanson, Nicholas H Barton, and Josephine Pemberton. “Investigating Temporal Changes in Hybridisation and Introgression between Invasive Sika (Cervus Nippon) and Native Red Deer (Cervus Elaphus) on the Kintyre Peninsula, Scotland.” Molecular Ecology. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1365-294X.2009.04497.x.","ista":"Senn H, Goodman S, Swanson G, Barton NH, Pemberton J. 2010. Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland. Molecular Ecology. 19(5), 910–924.","apa":"Senn, H., Goodman, S., Swanson, G., Barton, N. H., & Pemberton, J. (2010). Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2009.04497.x","mla":"Senn, Helen, et al. “Investigating Temporal Changes in Hybridisation and Introgression between Invasive Sika (Cervus Nippon) and Native Red Deer (Cervus Elaphus) on the Kintyre Peninsula, Scotland.” Molecular Ecology, vol. 19, no. 5, Wiley-Blackwell, 2010, pp. 910–24, doi:10.1111/j.1365-294X.2009.04497.x.","ieee":"H. Senn, S. Goodman, G. Swanson, N. H. Barton, and J. Pemberton, “Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland,” Molecular Ecology, vol. 19, no. 5. Wiley-Blackwell, pp. 910–924, 2010."},"quality_controlled":"1","page":"910 - 924","date_created":"2018-12-11T12:04:12Z","year":"2010","date_updated":"2021-01-12T07:44:36Z","status":"public","abstract":[{"text":"We investigated temporal changes in hybridization and introgression between native red deer (Cervus elaphus) and invasive Japanese sika (Cervus nippon) on the Kintyre Peninsula, Scotland, over 15 years, through analysis of 1513 samples of deer at 20 microsatellite loci and a mtDNA marker. We found no evidence that either the proportion of recent hybrids, or the levels of introgression had changed over the study period. Nevertheless, in one population where the two species have been in contact since ∼1970, 44% of individuals sampled during the study were hybrids. This suggests that hybridization between these species can proceed fairly rapidly. By analysing the number of alleles that have introgressed from polymorphic red deer into the genetically homogenous sika population, we reconstructed the haplotypes of red deer alleles introduced by backcrossing. Five separate hybridization events could account for all the recently hybridized sika-like individuals found across a large section of the Peninsula. Although we demonstrate that low rates of F1 hybridization can lead to substantial introgression, the progress of hybridization and introgression appears to be unpredictable over the short timescales.","lang":"eng"}],"volume":19},{"day":"01","scopus_import":1,"citation":{"short":"J. Guzmán, H. Schmidt, H. Franke, U. Krügel, J. Eilers, P. Illes, Z. Gerevich, Neuropharmacology 59 (2010) 406–415.","ama":"Guzmán J, Schmidt H, Franke H, et al. P2Y1 receptors inhibit long-term depression in the prefrontal cortex. Neuropharmacology. 2010;59(6):406-415. doi:10.1016/j.neuropharm.2010.05.013","ista":"Guzmán J, Schmidt H, Franke H, Krügel U, Eilers J, Illes P, Gerevich Z. 2010. P2Y1 receptors inhibit long-term depression in the prefrontal cortex. Neuropharmacology. 59(6), 406–415.","chicago":"Guzmán, José, Hartmut Schmidt, Heike Franke, Ute Krügel, Jens Eilers, Peter Illes, and Zoltan Gerevich. “P2Y1 Receptors Inhibit Long-Term Depression in the Prefrontal Cortex.” Neuropharmacology. Elsevier, 2010. https://doi.org/10.1016/j.neuropharm.2010.05.013.","apa":"Guzmán, J., Schmidt, H., Franke, H., Krügel, U., Eilers, J., Illes, P., & Gerevich, Z. (2010). P2Y1 receptors inhibit long-term depression in the prefrontal cortex. Neuropharmacology. Elsevier. https://doi.org/10.1016/j.neuropharm.2010.05.013","mla":"Guzmán, José, et al. “P2Y1 Receptors Inhibit Long-Term Depression in the Prefrontal Cortex.” Neuropharmacology, vol. 59, no. 6, Elsevier, 2010, pp. 406–15, doi:10.1016/j.neuropharm.2010.05.013.","ieee":"J. Guzmán et al., “P2Y1 receptors inhibit long-term depression in the prefrontal cortex.,” Neuropharmacology, vol. 59, no. 6. Elsevier, pp. 406–415, 2010."},"intvolume":" 59","date_updated":"2021-01-12T07:51:42Z","page":"406 - 415","quality_controlled":"1","date_created":"2018-12-11T12:04:47Z","year":"2010","volume":59,"abstract":[{"text":"Long-term depression (LTD) is a form of synaptic plasticity that may contribute to information storage in the central nervous system. Here we report that LTD can be elicited in layer 5 pyramidal neurons of the rat prefrontal cortex by pairing low frequency stimulation with a modest postsynaptic depolarization. The induction of LTD required the activation of both metabotropic glutamate receptors of the mGlu1 subtype and voltage-sensitive Ca(2+) channels (VSCCs) of the T/R, P/Q and N types, leading to the stimulation of intracellular inositol trisphosphate (IP3) receptors by IP3 and Ca(2+). The subsequent release of Ca(2+) from intracellular stores activated the protein phosphatase cascade involving calcineurin and protein phosphatase 1. The activation of purinergic P2Y(1) receptors blocked LTD. This effect was prevented by P2Y(1) receptor antagonists and was absent in mice lacking P2Y(1) but not P2Y(2) receptors. We also found that activation of P2Y(1) receptors inhibits Ca(2+) transients via VSCCs in the apical dendrites and spines of pyramidal neurons. In addition, we show that the release of ATP under hypoxia is able to inhibit LTD by acting on postsynaptic P2Y(1) receptors. In conclusion, these data suggest that the reduction of Ca(2+) influx via VSCCs caused by the activation of P2Y(1) receptors by ATP is the possible mechanism for the inhibition of LTD in prefrontal cortex.","lang":"eng"}],"status":"public","date_published":"2010-11-01T00:00:00Z","acknowledgement":" The financial support of the Deutsche Forschungsgemeinschaft (IL 20/12-1, KI 677/2-4) is gratefully acknowledged.\r\nWe thank B. H. Koller (Department of Genetics and Molecular Biology, University of North Carolina at Chapel Hill, NC, USA) for the generous supply of P2Y1−/− and P2Y2−/− mice. We are grateful to Dr. A. Schulz for reanalysing the genotype of the P2Y1−/− mice. The authors thank P. Jonas and U. Heinemann for many helpful comments and A-K. Krause, L Feige and M. Eberts for their excellent technical support.","department":[{"_id":"PeJo"}],"oa_version":"None","author":[{"id":"30CC5506-F248-11E8-B48F-1D18A9856A87","first_name":"José","full_name":"Guzmán, José","last_name":"Guzmán"},{"first_name":"Hartmut","full_name":"Schmidt, Hartmut","last_name":"Schmidt"},{"first_name":"Heike","full_name":"Franke, Heike","last_name":"Franke"},{"last_name":"Krügel","full_name":"Krügel, Ute","first_name":"Ute"},{"full_name":"Eilers, Jens","first_name":"Jens","last_name":"Eilers"},{"first_name":"Peter","full_name":"Illes, Peter","last_name":"Illes"},{"full_name":"Gerevich, Zoltan","first_name":"Zoltan","last_name":"Gerevich"}],"issue":"6","publication":"Neuropharmacology","publist_id":"2512","publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1016/j.neuropharm.2010.05.013","_id":"3718","month":"11","type":"journal_article","title":"P2Y1 receptors inhibit long-term depression in the prefrontal cortex.","language":[{"iso":"eng"}],"publication_status":"published"},{"has_accepted_license":"1","day":"30","intvolume":" 40","citation":{"ama":"Feret J, Henzinger TA, Koeppl H, Petrov T. Lumpability abstractions of rule-based systems. In: Vol 40. Open Publishing Association; 2010:142-161.","short":"J. Feret, T.A. Henzinger, H. Koeppl, T. Petrov, in:, Open Publishing Association, 2010, pp. 142–161.","mla":"Feret, Jérôme, et al. Lumpability Abstractions of Rule-Based Systems. Vol. 40, Open Publishing Association, 2010, pp. 142–61.","ieee":"J. Feret, T. A. Henzinger, H. Koeppl, and T. Petrov, “Lumpability abstractions of rule-based systems,” presented at the MECBIC: Membrane Computing and Biologically Inspired Process Calculi, Jena, Germany, 2010, vol. 40, pp. 142–161.","ista":"Feret J, Henzinger TA, Koeppl H, Petrov T. 2010. Lumpability abstractions of rule-based systems. MECBIC: Membrane Computing and Biologically Inspired Process Calculi, EPTCS, vol. 40, 142–161.","chicago":"Feret, Jérôme, Thomas A Henzinger, Heinz Koeppl, and Tatjana Petrov. “Lumpability Abstractions of Rule-Based Systems,” 40:142–61. Open Publishing Association, 2010.","apa":"Feret, J., Henzinger, T. A., Koeppl, H., & Petrov, T. (2010). Lumpability abstractions of rule-based systems (Vol. 40, pp. 142–161). Presented at the MECBIC: Membrane Computing and Biologically Inspired Process Calculi, Jena, Germany: Open Publishing Association."},"abstract":[{"lang":"eng","text":"The induction of a signaling pathway is characterized by transient complex formation and mutual posttranslational modification of proteins. To faithfully capture this combinatorial process in a math- ematical model is an important challenge in systems biology. Exploiting the limited context on which most binding and modification events are conditioned, attempts have been made to reduce the com- binatorial complexity by quotienting the reachable set of molecular species, into species aggregates while preserving the deterministic semantics of the thermodynamic limit. Recently we proposed a quotienting that also preserves the stochastic semantics and that is complete in the sense that the semantics of individual species can be recovered from the aggregate semantics. In this paper we prove that this quotienting yields a sufficient condition for weak lumpability and that it gives rise to a backward Markov bisimulation between the original and aggregated transition system. We illustrate the framework on a case study of the EGF/insulin receptor crosstalk."}],"status":"public","department":[{"_id":"ToHe"},{"_id":"CaGu"}],"acknowledgement":"Jérôme Feret’s contribution was partially supported by the ABSTRACTCELL ANR-Chair of Excellence. Heinz Koeppl acknowledges the support from the Swiss National Science Foundation, grant no. 200020-117975/1. Tatjana Petrov acknowledges the support from SystemsX.ch, the Swiss Initiative in Systems Biology.","alternative_title":["EPTCS"],"_id":"3719","month":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","oa":1,"related_material":{"record":[{"status":"public","relation":"later_version","id":"3168"}]},"title":"Lumpability abstractions of rule-based systems","scopus_import":1,"date_updated":"2023-02-23T11:15:19Z","year":"2010","date_created":"2018-12-11T12:04:47Z","page":"142-161","quality_controlled":"1","file":[{"date_created":"2019-01-31T12:09:09Z","content_type":"application/pdf","file_id":"5904","date_updated":"2020-07-14T12:46:14Z","access_level":"open_access","file_name":"Lumpability_abstractions_of_rule-based_systems.pdf","file_size":907155,"creator":"kschuh","relation":"main_file","checksum":"eaaba991a86fff37606b0eb5196878e8"}],"volume":40,"date_published":"2010-10-30T00:00:00Z","external_id":{"arxiv":["1011.0496"]},"conference":{"location":"Jena, Germany","end_date":"2010-08-23","name":"MECBIC: Membrane Computing and Biologically Inspired Process Calculi","start_date":"2010-08-23"},"oa_version":"Submitted Version","author":[{"first_name":"Jérôme","full_name":"Feret, Jérôme","last_name":"Feret"},{"last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"first_name":"Heinz","full_name":"Koeppl, Heinz","last_name":"Koeppl"},{"full_name":"Petrov, Tatjana","first_name":"Tatjana","last_name":"Petrov","orcid":"0000-0002-9041-0905","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570"],"publist_id":"2511","publisher":"Open Publishing Association","type":"conference","file_date_updated":"2020-07-14T12:46:14Z","language":[{"iso":"eng"}],"arxiv":1},{"department":[{"_id":"NiBa"}],"pubrep_id":"524","month":"06","_id":"3772","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","title":"Understanding adaptation in large populations","oa":1,"day":"17","has_accepted_license":"1","citation":{"chicago":"Barton, Nicholas H. “Understanding Adaptation in Large Populations.” PLoS Genetics. Public Library of Science, 2010. https://doi.org/10.1371/journal.pgen.1000987.","apa":"Barton, N. H. (2010). Understanding adaptation in large populations. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1000987","ista":"Barton NH. 2010. Understanding adaptation in large populations. PLoS Genetics. 6(6), e1000987.","ieee":"N. H. Barton, “Understanding adaptation in large populations,” PLoS Genetics, vol. 6, no. 6. Public Library of Science, 2010.","mla":"Barton, Nicholas H. “Understanding Adaptation in Large Populations.” PLoS Genetics, vol. 6, no. 6, e1000987, Public Library of Science, 2010, doi:10.1371/journal.pgen.1000987.","short":"N.H. Barton, PLoS Genetics 6 (2010).","ama":"Barton NH. Understanding adaptation in large populations. PLoS Genetics. 2010;6(6). doi:10.1371/journal.pgen.1000987"},"intvolume":" 6","status":"public","article_number":"e1000987","oa_version":"Published Version","date_published":"2010-06-17T00:00:00Z","issue":"6","publist_id":"2454","publication":"PLoS Genetics","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton"}],"ddc":["570","576"],"doi":"10.1371/journal.pgen.1000987","publisher":"Public Library of Science","language":[{"iso":"eng"}],"type":"journal_article","file_date_updated":"2020-07-14T12:46:15Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"scopus_import":1,"year":"2010","date_created":"2018-12-11T12:05:05Z","quality_controlled":"1","date_updated":"2021-01-12T07:52:05Z","file":[{"file_size":349965,"creator":"system","relation":"main_file","checksum":"5c14de2680ab483cb835096c99ee734d","file_id":"5075","date_created":"2018-12-12T10:14:24Z","content_type":"application/pdf","date_updated":"2020-07-14T12:46:15Z","access_level":"open_access","file_name":"IST-2016-524-v1+1_journal.pgen.1000987.PDF"}],"volume":6},{"oa":1,"title":"What role does natural selection play in speciation?","publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"06","_id":"3773","department":[{"_id":"NiBa"}],"acknowledgement":"The author thanks the Werner-Gren Foundation and the Royal Swedish Academy of Sciences for organizing the symposium on the ‘Origin of Species’. He also thanks Reinhard Bürger, and two anonymous referees, for their helpful comments.\r\n","abstract":[{"text":"If distinct biological species are to coexist in sympatry, they must be reproductively isolated and must exploit different limiting resources. A two-niche Levene model is analysed, in which habitat preference and survival depend on underlying additive traits. The population genetics of preference and viability are equivalent. However, there is a linear trade-off between the chances of settling in either niche, whereas viabilities may be constrained arbitrarily. With a convex trade-off, a sexual population evolves a single generalist genotype, whereas with a concave trade-off, disruptive selection favours maximal variance. A pure habitat preference evolves to global linkage equilibrium if mating occurs in a single pool, but remarkably, evolves to pairwise linkage equilibrium within niches if mating is within those niches--independent of the genetics. With a concave trade-off, the population shifts sharply between a unimodal distribution with high gene flow and a bimodal distribution with strong isolation, as the underlying genetic variance increases. However, these alternative states are only simultaneously stable for a narrow parameter range. A sharp threshold is only seen if survival in the 'wrong' niche is low; otherwise, strong isolation is impossible. Gene flow from divergent demes makes speciation much easier in parapatry than in sympatry.","lang":"eng"}],"status":"public","intvolume":" 365","citation":{"ama":"Barton NH. What role does natural selection play in speciation? Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2010;365(1547):1825-1840. doi:10.1098/rstb.2010.0001","short":"N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 1825–1840.","mla":"Barton, Nicholas H. “What Role Does Natural Selection Play in Speciation?” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1547, Royal Society, 2010, pp. 1825–40, doi:10.1098/rstb.2010.0001.","ieee":"N. H. Barton, “What role does natural selection play in speciation?,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1547. Royal Society, pp. 1825–1840, 2010.","chicago":"Barton, Nicholas H. “What Role Does Natural Selection Play in Speciation?” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, 2010. https://doi.org/10.1098/rstb.2010.0001.","ista":"Barton NH. 2010. What role does natural selection play in speciation? Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1547), 1825–1840.","apa":"Barton, N. H. (2010). What role does natural selection play in speciation? Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society. https://doi.org/10.1098/rstb.2010.0001"},"day":"12","type":"journal_article","language":[{"iso":"eng"}],"publisher":"Royal Society","doi":"10.1098/rstb.2010.0001","author":[{"last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","issue":"1547","publist_id":"2455","date_published":"2010-06-12T00:00:00Z","oa_version":"Submitted Version","external_id":{"pmid":["20439284"]},"volume":365,"date_updated":"2021-01-12T07:52:06Z","quality_controlled":"1","page":"1825 - 1840","year":"2010","date_created":"2018-12-11T12:05:05Z","scopus_import":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pubmed/20439284","open_access":"1"}],"pmid":1},{"scopus_import":1,"pmid":1,"date_updated":"2021-01-12T07:52:06Z","quality_controlled":"1","page":"414 - 425","year":"2010","date_created":"2018-12-11T12:05:06Z","volume":79,"date_published":"2010-03-01T00:00:00Z","oa_version":"None","external_id":{"pmid":["20002231"]},"author":[{"full_name":"Senn, Helen","first_name":"Helen","last_name":"Senn"},{"last_name":"Swanson","full_name":"Swanson, Graeme","first_name":"Graeme"},{"last_name":"Goodman","first_name":"Simon","full_name":"Goodman, Simon"},{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Josephine","full_name":"Pemberton, Josephine","last_name":"Pemberton"}],"publist_id":"2453","publication":"Journal of Animal Ecology","issue":"2","publisher":"Wiley-Blackwell","doi":"10.1111/j.1365-2656.2009.01633.x","type":"journal_article","language":[{"iso":"eng"}],"day":"01","intvolume":" 79","citation":{"ama":"Senn H, Swanson G, Goodman S, Barton NH, Pemberton J. Phenotypic correlates of hybridisation between red and sika deer (genus Cervus). Journal of Animal Ecology. 2010;79(2):414-425. doi:10.1111/j.1365-2656.2009.01633.x","short":"H. Senn, G. Swanson, S. Goodman, N.H. Barton, J. Pemberton, Journal of Animal Ecology 79 (2010) 414–425.","mla":"Senn, Helen, et al. “Phenotypic Correlates of Hybridisation between Red and Sika Deer (Genus Cervus).” Journal of Animal Ecology, vol. 79, no. 2, Wiley-Blackwell, 2010, pp. 414–25, doi:10.1111/j.1365-2656.2009.01633.x.","ieee":"H. Senn, G. Swanson, S. Goodman, N. H. Barton, and J. Pemberton, “Phenotypic correlates of hybridisation between red and sika deer (genus Cervus),” Journal of Animal Ecology, vol. 79, no. 2. Wiley-Blackwell, pp. 414–425, 2010.","ista":"Senn H, Swanson G, Goodman S, Barton NH, Pemberton J. 2010. Phenotypic correlates of hybridisation between red and sika deer (genus Cervus). Journal of Animal Ecology. 79(2), 414–425.","apa":"Senn, H., Swanson, G., Goodman, S., Barton, N. H., & Pemberton, J. (2010). Phenotypic correlates of hybridisation between red and sika deer (genus Cervus). Journal of Animal Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-2656.2009.01633.x","chicago":"Senn, Helen, Graeme Swanson, Simon Goodman, Nicholas H Barton, and Josephine Pemberton. “Phenotypic Correlates of Hybridisation between Red and Sika Deer (Genus Cervus).” Journal of Animal Ecology. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1365-2656.2009.01633.x."},"abstract":[{"text":"1. Hybridisation with an invasive species has the potential to alter the phenotype and hence the ecology of a native counterpart. 2. Here data from populations of native red deer Cervus elaphus and invasive sika deer Cervus nippon in Scotland is used to assess the extent to which hybridisation between them is causing phenotypic change. This is done by regression of phenotypic traits against genetic hybrid scores. 3. Hybridisation is causing increases in the body weight of sika-like deer and decreases in the body weight of red-like females. Hybridisation is causing increases in jaw length and increases in incisor arcade breadth in sika-like females. Hybridisation is also causing decreases in incisor arcade breadth in red-like females. 4. There is currently no evidence that hybridisation is causing changes in the kidney fat weight or pregnancy rates of either population. 5. Increased phenotypic similarity between the two species is likely to lead to further hybridisation. The ecological consequences of this are difficult to predict.","lang":"eng"}],"status":"public","acknowledgement":"This project was funded through a NERC studentship to HVS which was CASE partnered by the Macaulay Institute.\r\nWe thank the Forestry Commission Scotland rangers for all their help with providing the larder data for and samples from red and sika deer, Stephen Senn and Jarrod Hadfield for statistical advice and Steve Albon for helpful comments on the manuscript.","department":[{"_id":"NiBa"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3774","month":"03","title":"Phenotypic correlates of hybridisation between red and sika deer (genus Cervus)","publication_status":"published"},{"publisher":"Royal Society","doi":"10.1098/rstb.2010.0106","type":"journal_article","file_date_updated":"2020-07-14T12:46:15Z","language":[{"iso":"eng"}],"date_published":"2010-08-27T00:00:00Z","oa_version":"Submitted Version","author":[{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"ddc":["570"],"publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","issue":"1552","publist_id":"2450","date_updated":"2021-01-12T07:52:07Z","year":"2010","date_created":"2018-12-11T12:05:06Z","quality_controlled":"1","page":"2559 - 2569","file":[{"relation":"main_file","checksum":"4d8aade10db030124ab158b622e337e0","file_size":250255,"creator":"system","file_name":"IST-2016-555-v1+1_RS2009_revised.pdf","date_created":"2018-12-12T10:14:40Z","file_id":"5093","content_type":"application/pdf","date_updated":"2020-07-14T12:46:15Z","access_level":"open_access"}],"volume":365,"scopus_import":1,"_id":"3776","month":"08","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","title":"Genetic linkage and natural selection","oa":1,"department":[{"_id":"NiBa"}],"acknowledgement":"Royal Society and Wolfson Foundation for their support\r\nWe would like to thank Brian Charlesworth and Sally Otto for their helpful comments.","pubrep_id":"555","abstract":[{"lang":"eng","text":"The prevalence of recombination in eukaryotes poses one of the most puzzling questions in biology. The most compelling general explanation is that recombination facilitates selection by breaking down the negative associations generated by random drift (i.e. Hill-Robertson interference, HRI). I classify the effects of HRI owing to: deleterious mutation, balancing selection and selective sweeps on: neutral diversity, rates of adaptation and the mutation load. These effects are mediated primarily by the density of deleterious mutations and of selective sweeps. Sequence polymorphism and divergence suggest that these rates may be high enough to cause significant interference even in genomic regions of high recombination. However, neither seems able to generate enough variance in fitness to select strongly for high rates of recombination. It is plausible that spatial and temporal fluctuations in selection generate much more fitness variance, and hence selection for recombination, than can be explained by uniformly deleterious mutations or species-wide selective sweeps."}],"status":"public","has_accepted_license":"1","day":"27","intvolume":" 365","citation":{"mla":"Barton, Nicholas H. “Genetic Linkage and Natural Selection.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1552, Royal Society, 2010, pp. 2559–69, doi:10.1098/rstb.2010.0106.","ieee":"N. H. Barton, “Genetic linkage and natural selection,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1552. Royal Society, pp. 2559–2569, 2010.","ista":"Barton NH. 2010. Genetic linkage and natural selection. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1552), 2559–2569.","apa":"Barton, N. H. (2010). Genetic linkage and natural selection. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society. https://doi.org/10.1098/rstb.2010.0106","chicago":"Barton, Nicholas H. “Genetic Linkage and Natural Selection.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, 2010. https://doi.org/10.1098/rstb.2010.0106.","ama":"Barton NH. Genetic linkage and natural selection. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2010;365(1552):2559-2569. doi:10.1098/rstb.2010.0106","short":"N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 2559–2569."}},{"author":[{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","issue":"1544","publist_id":"2451","date_published":"2010-04-27T00:00:00Z","external_id":{"pmid":["20308104"]},"oa_version":"Submitted Version","type":"journal_article","language":[{"iso":"eng"}],"publisher":"Royal Society","doi":"10.1098/rstb.2009.0320","pmid":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pubmed/20308104"}],"scopus_import":1,"volume":365,"date_updated":"2021-01-12T07:52:07Z","year":"2010","date_created":"2018-12-11T12:05:07Z","quality_controlled":"1","page":"1281 - 1294","acknowledgement":"I would like to thank W. G. Hill and L. Loewe for organizing this special issue, and the Royal Society and Wolfson Foundation for their support. Also, A. Kondrashov and L. Loewe gave very helpful comments that helped improve the manuscript.","department":[{"_id":"NiBa"}],"publication_status":"published","oa":1,"title":"Mutation and the evolution of recombination","_id":"3777","month":"04","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Barton, Nicholas H. “Mutation and the Evolution of Recombination.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1544, Royal Society, 2010, pp. 1281–94, doi:10.1098/rstb.2009.0320.","ieee":"N. H. Barton, “Mutation and the evolution of recombination,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1544. Royal Society, pp. 1281–1294, 2010.","ista":"Barton NH. 2010. Mutation and the evolution of recombination. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1544), 1281–1294.","chicago":"Barton, Nicholas H. “Mutation and the Evolution of Recombination.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, 2010. https://doi.org/10.1098/rstb.2009.0320.","apa":"Barton, N. H. (2010). Mutation and the evolution of recombination. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society. https://doi.org/10.1098/rstb.2009.0320","ama":"Barton NH. Mutation and the evolution of recombination. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2010;365(1544):1281-1294. doi:10.1098/rstb.2009.0320","short":"N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 1281–1294."},"intvolume":" 365","day":"27","abstract":[{"text":"Under the classical view, selection depends more or less directly on mutation: standing genetic variance is maintained by a balance between selection and mutation, and adaptation is fuelled by new favourable mutations. Recombination is favoured if it breaks negative associations among selected alleles, which interfere with adaptation. Such associations may be generated by negative epistasis, or by random drift (leading to the Hill-Robertson effect). Both deterministic and stochastic explanations depend primarily on the genomic mutation rate, U. This may be large enough to explain high recombination rates in some organisms, but seems unlikely to be so in general. Random drift is a more general source of negative linkage disequilibria, and can cause selection for recombination even in large populations, through the chance loss of new favourable mutations. The rate of species-wide substitutions is much too low to drive this mechanism, but local fluctuations in selection, combined with gene flow, may suffice. These arguments are illustrated by comparing the interaction between good and bad mutations at unlinked loci under the infinitesimal model.","lang":"eng"}],"status":"public"},{"pubrep_id":"366","acknowledgement":"This was supported by a Marie Curie grant for early stage training and the BBSRC-John Innes Centre PhD Rotation Program.\r\nWe would like to thank X. Feng and A. Hudson for assistance with introgressions and genotyping; A. Green, A. Bangham and J. Pateman for advice and assistance on shape model procedures; F. Alderson and S.Mitchell from JIC horticultural services; P.J. Wittkopp for protocols and advice on pyrosequencing; and R. Sablowski for discussions and comments.\r\n","department":[{"_id":"NiBa"}],"related_material":{"record":[{"id":"9764","relation":"research_data","status":"public"}]},"oa":1,"title":"Cryptic variation between species and the basis of hybrid performance","publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3779","month":"07","intvolume":" 8","citation":{"ista":"Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. 2010. Cryptic variation between species and the basis of hybrid performance. PLoS Biology. 8(7), e1000429.","apa":"Rosas, U., Barton, N. H., Copsey, L., Barbier De Reuille, P., & Coen, E. (2010). Cryptic variation between species and the basis of hybrid performance. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1000429","chicago":"Rosas, Ulises, Nicholas H Barton, Lucy Copsey, Pierre Barbier De Reuille, and Enrico Coen. “Cryptic Variation between Species and the Basis of Hybrid Performance.” PLoS Biology. Public Library of Science, 2010. https://doi.org/10.1371/journal.pbio.1000429.","ieee":"U. Rosas, N. H. Barton, L. Copsey, P. Barbier De Reuille, and E. Coen, “Cryptic variation between species and the basis of hybrid performance,” PLoS Biology, vol. 8, no. 7. Public Library of Science, 2010.","mla":"Rosas, Ulises, et al. “Cryptic Variation between Species and the Basis of Hybrid Performance.” PLoS Biology, vol. 8, no. 7, e1000429, Public Library of Science, 2010, doi:10.1371/journal.pbio.1000429.","short":"U. Rosas, N.H. Barton, L. Copsey, P. Barbier De Reuille, E. Coen, PLoS Biology 8 (2010).","ama":"Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. Cryptic variation between species and the basis of hybrid performance. PLoS Biology. 2010;8(7). doi:10.1371/journal.pbio.1000429"},"has_accepted_license":"1","day":"20","abstract":[{"lang":"eng","text":"Crosses between closely related species give two contrasting results. One result is that species hybrids may be inferior to their parents, for example, being less fertile [1]. The other is that F1 hybrids may display superior performance (heterosis), for example with increased vigour [2]. Although various hypotheses have been proposed to account for these two aspects of hybridisation, their biological basis is still poorly understood [3]. To gain further insights into this issue, we analysed the role that variation in gene expression may play. We took a conserved trait, flower asymmetry in Antirrhinum, and determined the extent to which the underlying regulatory genes varied in expression among closely related species. We show that expression of both genes analysed, CYC and RAD, varies significantly between species because of cis-acting differences. By making a quantitative genotype-phenotype map, using a range of mutant alleles, we demonstrate that the species lie on a plateau in gene expression-morphology space, so that the variation has no detectable phenotypic effect. However, phenotypic differences can be revealed by shifting genotypes off the plateau through genetic crosses. Our results can be readily explained if genomes are free to evolve within an effectively neutral zone in gene expression space. The consequences of this drift will be negligible for individual loci, but when multiple loci across the genome are considered, we show that the variation may have significant effects on phenotype and fitness, causing a significant drift load. By considering these consequences for various gene-expression-fitness landscapes, we conclude that F1 hybrids might be expected to show increased performance with regard to conserved traits, such as basic physiology, but reduced performance with regard to others. Thus, our study provides a new way of explaining how various aspects of hybrid performance may arise through natural variation in gene activity."}],"article_number":"e1000429","status":"public","ddc":["576"],"author":[{"first_name":"Ulises","full_name":"Rosas, Ulises","last_name":"Rosas"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"first_name":"Lucy","full_name":"Copsey, Lucy","last_name":"Copsey"},{"last_name":"Barbier De Reuille","full_name":"Barbier De Reuille, Pierre","first_name":"Pierre"},{"last_name":"Coen","full_name":"Coen, Enrico","first_name":"Enrico"}],"publist_id":"2448","publication":"PLoS Biology","issue":"7","date_published":"2010-07-20T00:00:00Z","oa_version":"Published Version","file_date_updated":"2020-07-14T12:46:15Z","type":"journal_article","language":[{"iso":"eng"}],"publisher":"Public Library of Science","doi":"10.1371/journal.pbio.1000429","scopus_import":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":8,"file":[{"relation":"main_file","checksum":"ee1ce2fb283a6b4127544ae532d0b4a1","file_size":1089530,"creator":"system","file_name":"IST-2015-366-v1+1_journal.pbio.1000429.pdf","file_id":"5060","content_type":"application/pdf","date_created":"2018-12-12T10:14:11Z","access_level":"open_access","date_updated":"2020-07-14T12:46:15Z"}],"date_updated":"2023-02-23T14:07:34Z","quality_controlled":"1","date_created":"2018-12-11T12:05:07Z","year":"2010"},{"day":"31","scopus_import":1,"intvolume":" 6533","citation":{"ama":"Chen C, Freedman D. Topology noise removal for curve and surface evolution. In: Conference Proceedings MCV 2010. Vol 6533. Springer; 2010:31-42. doi:10.1007/978-3-642-18421-5_4","short":"C. Chen, D. Freedman, in:, Conference Proceedings MCV 2010, Springer, 2010, pp. 31–42.","ieee":"C. Chen and D. Freedman, “Topology noise removal for curve and surface evolution,” in Conference proceedings MCV 2010, Beijing, China, 2010, vol. 6533, pp. 31–42.","mla":"Chen, Chao, and Daniel Freedman. “Topology Noise Removal for Curve and Surface Evolution.” Conference Proceedings MCV 2010, vol. 6533, Springer, 2010, pp. 31–42, doi:10.1007/978-3-642-18421-5_4.","ista":"Chen C, Freedman D. 2010. Topology noise removal for curve and surface evolution. Conference proceedings MCV 2010. MCV: Medical Computer Vision, LNCS, vol. 6533, 31–42.","apa":"Chen, C., & Freedman, D. (2010). Topology noise removal for curve and surface evolution. In Conference proceedings MCV 2010 (Vol. 6533, pp. 31–42). Beijing, China: Springer. https://doi.org/10.1007/978-3-642-18421-5_4","chicago":"Chen, Chao, and Daniel Freedman. “Topology Noise Removal for Curve and Surface Evolution.” In Conference Proceedings MCV 2010, 6533:31–42. Springer, 2010. https://doi.org/10.1007/978-3-642-18421-5_4."},"page":"31 - 42","quality_controlled":"1","year":"2010","date_created":"2018-12-11T12:05:08Z","date_updated":"2021-01-12T07:52:10Z","status":"public","volume":6533,"abstract":[{"lang":"eng","text":"In cortex surface segmentation, the extracted surface is required to have a particular topology, namely, a two-sphere. We present a new method for removing topology noise of a curve or surface within the level set framework, and thus produce a cortical surface with correct topology. We define a new energy term which quantifies topology noise. We then show how to minimize this term by computing its functional derivative with respect to the level set function. This method differs from existing methods in that it is inherently continuous and not digital; and in the way that our energy directly relates to the topology of the underlying curve or surface, versus existing knot-based measures which are related in a more indirect fashion. The proposed flow is validated empirically."}],"conference":{"end_date":"2010-09-20","location":"Beijing, China","start_date":"2010-09-20","name":"MCV: Medical Computer Vision"},"oa_version":"None","date_published":"2010-12-31T00:00:00Z","acknowledgement":"Partially supported by the Austri an Science Fund unde r grant P20134-N13.\r\nWe thank Helena Molina-Abril for very helpful discussion. We thank anonymous reviewers for helpful comments.","department":[{"_id":"HeEd"}],"publication":" Conference proceedings MCV 2010","publist_id":"2445","alternative_title":["LNCS"],"author":[{"id":"3E92416E-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","first_name":"Chao","full_name":"Chen, Chao"},{"first_name":"Daniel","full_name":"Freedman, Daniel","last_name":"Freedman"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-3-642-18421-5_4","_id":"3782","month":"12","publisher":"Springer","title":"Topology noise removal for curve and surface evolution","publication_status":"published","language":[{"iso":"eng"}],"type":"conference"},{"date_updated":"2021-01-12T07:52:10Z","year":"2010","date_created":"2018-12-11T12:05:09Z","quality_controlled":"1","page":"247 - 249","volume":102,"abstract":[{"lang":"eng","text":"MICROSATELIGHT is a Perl/Tk pipeline with a graphical user interface that facilitates several tasks when scoring microsatellites. It implements new subroutines in R and PERL and takes advantage of features provided by previously developed freeware. MICROSATELIGHT takes raw genotype data and automates the peak identification through PeakScanner. The PeakSelect subroutine assigns peaks to different microsatellite markers according to their multiplex group, fluorochrome type, and size range. After peak selection, binning of alleles can be carried out 1) automatically through AlleloBin or 2) by manual bin definition through Binator. In both cases, several features for quality checking and further binning improvement are provided. The genotype table can then be converted into input files for several population genetics programs through CREATE. Finally, Hardy–Weinberg equilibrium tests and confidence intervals for null allele frequency can be obtained through GENEPOP. MICROSATELIGHT is the only freely available public-domain software that facilitates full multiplex microsatellite scoring, from electropherogram files to user-defined text files to be used with population genetics software. MICROSATELIGHT has been created for the Windows XP operating system and has been successfully tested under Windows 7. It is available at http://sourceforge.net/projects/microsatelight/."}],"status":"public","day":"02","citation":{"ama":"Palero F, González Candelas F, Pascual M. Microsatelight – Pipeline to expedite microsatellite analysis. Journal of Heredity. 2010;102(2):247-249. doi:10.1093/jhered/esq111","short":"F. Palero, F. González Candelas, M. Pascual, Journal of Heredity 102 (2010) 247–249.","ieee":"F. Palero, F. González Candelas, and M. Pascual, “Microsatelight – Pipeline to expedite microsatellite analysis,” Journal of Heredity, vol. 102, no. 2. Oxford University Press, pp. 247–249, 2010.","mla":"Palero, Ferran, et al. “Microsatelight – Pipeline to Expedite Microsatellite Analysis.” Journal of Heredity, vol. 102, no. 2, Oxford University Press, 2010, pp. 247–49, doi:10.1093/jhered/esq111.","chicago":"Palero, Ferran, Fernando González Candelas, and Marta Pascual. “Microsatelight – Pipeline to Expedite Microsatellite Analysis.” Journal of Heredity. Oxford University Press, 2010. https://doi.org/10.1093/jhered/esq111.","apa":"Palero, F., González Candelas, F., & Pascual, M. (2010). Microsatelight – Pipeline to expedite microsatellite analysis. Journal of Heredity. Oxford University Press. https://doi.org/10.1093/jhered/esq111","ista":"Palero F, González Candelas F, Pascual M. 2010. Microsatelight – Pipeline to expedite microsatellite analysis. Journal of Heredity. 102(2), 247–249."},"intvolume":" 102","scopus_import":1,"publisher":"Oxford University Press","_id":"3783","month":"12","doi":"10.1093/jhered/esq111","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","title":"Microsatelight – Pipeline to expedite microsatellite analysis","department":[{"_id":"NiBa"}],"acknowledgement":"Ministerio de Educación y Ciencia (CGL2006-13423, CTM2007-66635). M.P. and FP are part of the research group 2009SGR-636 of the Generalitat de Catalunya. F.P. acknowledges an EU-Synthesys grant (GB-TAF-4474).\r\n\r\nThanks to José Gabriel Segarra-Moragues (Centro de Investigaciones sobre Desertificación) for sending us pictures with several types of stuttering and Pedro Simões and Gemma Calàbria (Universitat de Barcelona) for testing this software. Finally, thanks are due to 2 anonymous referees for their valuable comments. These comments certainly helped to improve the manuscript.","date_published":"2010-12-02T00:00:00Z","oa_version":"None","author":[{"full_name":"Palero, Ferran","first_name":"Ferran","last_name":"Palero","orcid":"0000-0002-0343-8329","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87"},{"full_name":"González Candelas, Fernando","first_name":"Fernando","last_name":"González Candelas"},{"full_name":"Pascual, Marta","first_name":"Marta","last_name":"Pascual"}],"issue":"2","publication":"Journal of Heredity","publist_id":"2444"},{"publist_id":"2442","issue":"4","publication":"Journal of Crustacean Biology","author":[{"id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0343-8329","full_name":"Palero, Ferran","first_name":"Ferran","last_name":"Palero"},{"full_name":"Abello, Pere","first_name":"Pere","last_name":"Abello"},{"last_name":"Macpherson","first_name":"E.","full_name":"Macpherson, E."},{"first_name":"C.","full_name":"Matthee, C.","last_name":"Matthee"},{"last_name":"Pascual","full_name":"Pascual, Marta","first_name":"Marta"}],"oa_version":"None","department":[{"_id":"NiBa"}],"date_published":"2010-10-01T00:00:00Z","publication_status":"published","language":[{"iso":"eng"}],"title":"Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata)","type":"journal_article","_id":"3785","month":"10","doi":"10.1651/09-3192.1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Oxford University Press","publication_identifier":{"eissn":["1937-240X"],"issn":["0278-0372"]},"intvolume":" 30","citation":{"chicago":"Palero, Ferran, Pere Abello, E. Macpherson, C. Matthee, and Marta Pascual. “Genetic Diversity Levels in Fishery-Exploited Spiny Lobsters of the Genus Palinurus (Decapoda: Achelata).” Journal of Crustacean Biology. Oxford University Press, 2010. https://doi.org/10.1651/09-3192.1.","ista":"Palero F, Abello P, Macpherson E, Matthee C, Pascual M. 2010. Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata). Journal of Crustacean Biology. 30(4), 658–663.","apa":"Palero, F., Abello, P., Macpherson, E., Matthee, C., & Pascual, M. (2010). Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata). Journal of Crustacean Biology. Oxford University Press. https://doi.org/10.1651/09-3192.1","ieee":"F. Palero, P. Abello, E. Macpherson, C. Matthee, and M. Pascual, “Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata),” Journal of Crustacean Biology, vol. 30, no. 4. Oxford University Press, pp. 658–663, 2010.","mla":"Palero, Ferran, et al. “Genetic Diversity Levels in Fishery-Exploited Spiny Lobsters of the Genus Palinurus (Decapoda: Achelata).” Journal of Crustacean Biology, vol. 30, no. 4, Oxford University Press, 2010, pp. 658–63, doi:10.1651/09-3192.1.","short":"F. Palero, P. Abello, E. Macpherson, C. Matthee, M. Pascual, Journal of Crustacean Biology 30 (2010) 658–663.","ama":"Palero F, Abello P, Macpherson E, Matthee C, Pascual M. Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata). Journal of Crustacean Biology. 2010;30(4):658-663. doi:10.1651/09-3192.1"},"scopus_import":"1","day":"01","article_processing_charge":"No","status":"public","volume":30,"abstract":[{"lang":"eng","text":"Most fisheries involving spiny lobsters of the genus Palinurus have been over exploited during the last decades, so there is a raising concern about management decisions for these valuable resources. A total of 13 microsatellite DNA loci recently developed in Palinurus elephas were assayed in order to assess genetic diversity levels in every known species of the genus. Microsatellite markers gave amplifications and showed polymorphism in all species, with gene diversity values varying from 0.65060.077 SD (Palinurus barbarae) to 0.79260.051 SD (Palinurus elephas). Most importantly, when depth distribution was taken into account, shallower waters pecies consistently showed larger historical effective population sizes than their deeper-water counterparts. This could explain why deeper-water species are more sensitive to overfishing, and would indicate that overexploitation may have a larger impact on their long-term genetic diversity."}],"year":"2010","date_created":"2018-12-11T12:05:09Z","quality_controlled":"1","page":"658 - 663","date_updated":"2023-10-16T09:51:05Z"},{"publisher":"Magnolia Press","month":"03","_id":"3786","doi":"10.11646/zootaxa.2403.1.4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","article_type":"original","publication_status":"published","language":[{"iso":"eng"}],"title":"Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description","department":[{"_id":"NiBa"}],"date_published":"2010-03-19T00:00:00Z","oa_version":"None","author":[{"orcid":"0000-0002-0343-8329","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","last_name":"Palero","full_name":"Palero, Ferran","first_name":"Ferran"},{"full_name":"Guerao, Guillermo","first_name":"Guillermo","last_name":"Guerao"},{"first_name":"Paul","full_name":"Clark, Paul","last_name":"Clark"},{"full_name":"Abello, Pere","first_name":"Pere","last_name":"Abello"}],"publist_id":"2441","publication":"Zootaxa","issue":"1","date_updated":"2022-03-21T08:22:58Z","year":"2010","date_created":"2018-12-11T12:05:10Z","quality_controlled":"1","page":"42 - 58","volume":2403,"abstract":[{"text":"Four rare palinurid phyllosoma larvae, one mid-stage and three final stage, were found among the unclassified collections in the Crustacea Section, Natural History Museum, London. Detailed morphological analysis of the larvae indicated that they belong to several Palinustus species given the presence of incipient blunt-horns, length of antennula, length ratio of segments of antennular peduncle, distribution of pereiopod spines, and shape of uropods and telson. Moreover, the size of the final-stage larvae agrees with that expected given the size of the recently described puerulus stage of Palinustus mossambicus. This constitutes the first description of a complete phyllosoma assigned to Palinustus species. The phyllosoma described in the present study include the largest Palinuridae larva ever found.","lang":"eng"}],"status":"public","article_processing_charge":"No","day":"19","intvolume":" 2403","citation":{"short":"F. Palero, G. Guerao, P. Clark, P. Abello, Zootaxa 2403 (2010) 42–58.","ama":"Palero F, Guerao G, Clark P, Abello P. Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description. Zootaxa. 2010;2403(1):42-58. doi:10.11646/zootaxa.2403.1.4","chicago":"Palero, Ferran, Guillermo Guerao, Paul Clark, and Pere Abello. “Final-Stage Phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The First Complete Description.” Zootaxa. Magnolia Press, 2010. https://doi.org/10.11646/zootaxa.2403.1.4.","ista":"Palero F, Guerao G, Clark P, Abello P. 2010. Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description. Zootaxa. 2403(1), 42–58.","apa":"Palero, F., Guerao, G., Clark, P., & Abello, P. (2010). Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description. Zootaxa. Magnolia Press. https://doi.org/10.11646/zootaxa.2403.1.4","mla":"Palero, Ferran, et al. “Final-Stage Phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The First Complete Description.” Zootaxa, vol. 2403, no. 1, Magnolia Press, 2010, pp. 42–58, doi:10.11646/zootaxa.2403.1.4.","ieee":"F. Palero, G. Guerao, P. Clark, and P. Abello, “Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description,” Zootaxa, vol. 2403, no. 1. Magnolia Press, pp. 42–58, 2010."},"scopus_import":"1"}]