[{"volume":70,"publist_id":"5442","title":"Adaptive gene introgression after secondary contact","isi":1,"acknowledgement":"This work was made possible with financial support by the Vienna Science and Technology Fund (WWTF), by the Deutsche Forschungsgemeinschaft (DFG), Research Unit 1078 Natural selection in structured populations, by the Austrian Science Fund (FWF) via funding for the Vienna Graduate School for Population Genetics, and by a “For Women in Science” fellowship (L’Oréal Österreich in cooperation with the Austrian Commission for UNESCO and the Austrian Academy of Sciences with financial support from the Federal Ministry for Science and Research Austria).","date_published":"2015-06-01T00:00:00Z","article_processing_charge":"No","external_id":{"isi":["000354196800003"]},"quality_controlled":"1","date_updated":"2025-09-23T07:31:45Z","month":"06","oa_version":"Published Version","scopus_import":"1","citation":{"ama":"Uecker H, Setter D, Hermisson J. Adaptive gene introgression after secondary contact. <i>Journal of Mathematical Biology</i>. 2015;70(7):1523-1580. doi:<a href=\"https://doi.org/10.1007/s00285-014-0802-y\">10.1007/s00285-014-0802-y</a>","ieee":"H. Uecker, D. Setter, and J. Hermisson, “Adaptive gene introgression after secondary contact,” <i>Journal of Mathematical Biology</i>, vol. 70, no. 7. Springer, pp. 1523–1580, 2015.","mla":"Uecker, Hildegard, et al. “Adaptive Gene Introgression after Secondary Contact.” <i>Journal of Mathematical Biology</i>, vol. 70, no. 7, Springer, 2015, pp. 1523–80, doi:<a href=\"https://doi.org/10.1007/s00285-014-0802-y\">10.1007/s00285-014-0802-y</a>.","ista":"Uecker H, Setter D, Hermisson J. 2015. Adaptive gene introgression after secondary contact. Journal of Mathematical Biology. 70(7), 1523–1580.","short":"H. Uecker, D. Setter, J. Hermisson, Journal of Mathematical Biology 70 (2015) 1523–1580.","apa":"Uecker, H., Setter, D., &#38; Hermisson, J. (2015). Adaptive gene introgression after secondary contact. <i>Journal of Mathematical Biology</i>. Springer. <a href=\"https://doi.org/10.1007/s00285-014-0802-y\">https://doi.org/10.1007/s00285-014-0802-y</a>","chicago":"Uecker, Hildegard, Derek Setter, and Joachim Hermisson. “Adaptive Gene Introgression after Secondary Contact.” <i>Journal of Mathematical Biology</i>. Springer, 2015. <a href=\"https://doi.org/10.1007/s00285-014-0802-y\">https://doi.org/10.1007/s00285-014-0802-y</a>."},"abstract":[{"text":"By hybridization and backcrossing, alleles can surmount species boundaries and be incorporated into the genome of a related species. This introgression of genes is of particular evolutionary relevance if it involves the transfer of adaptations between populations. However, any beneficial allele will typically be associated with other alien alleles that are often deleterious and hamper the introgression process. In order to describe the introgression of an adaptive allele, we set up a stochastic model with an explicit genetic makeup of linked and unlinked deleterious alleles. Based on the theory of reducible multitype branching processes, we derive a recursive expression for the establishment probability of the beneficial allele after a single hybridization event. We furthermore study the probability that slightly deleterious alleles hitchhike to fixation. The key to the analysis is a split of the process into a stochastic phase in which the advantageous alleles establishes and a deterministic phase in which it sweeps to fixation. We thereafter apply the theory to a set of biologically relevant scenarios such as introgression in the presence of many unlinked or few closely linked deleterious alleles. A comparison to computer simulations shows that the approximations work well over a large parameter range.","lang":"eng"}],"publisher":"Springer","type":"journal_article","status":"public","year":"2015","date_created":"2018-12-11T11:53:32Z","pubrep_id":"458","file_date_updated":"2020-07-14T12:45:12Z","author":[{"full_name":"Uecker, Hildegard","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9435-2813","first_name":"Hildegard","last_name":"Uecker"},{"first_name":"Derek","last_name":"Setter","full_name":"Setter, Derek"},{"last_name":"Hermisson","first_name":"Joachim","full_name":"Hermisson, Joachim"}],"language":[{"iso":"eng"}],"ddc":["576"],"file":[{"access_level":"open_access","file_name":"IST-2016-458-v1+1_s00285-014-0802-y.pdf","creator":"system","checksum":"00e3a67bda05d4cc165b3a48b41ef9ad","file_id":"5079","date_created":"2018-12-12T10:14:27Z","date_updated":"2020-07-14T12:45:12Z","content_type":"application/pdf","relation":"main_file","file_size":1321527}],"project":[{"_id":"25B67606-B435-11E9-9278-68D0E5697425","name":"Evolutionary rescue"}],"doi":"10.1007/s00285-014-0802-y","oa":1,"publication_status":"published","intvolume":"        70","issue":"7","department":[{"_id":"NiBa"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"1699","page":"1523 - 1580","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","corr_author":"1","publication":"Journal of Mathematical Biology"},{"external_id":{"isi":["000363276500009"]},"quality_controlled":"1","date_updated":"2025-09-23T07:51:07Z","month":"05","volume":63,"publist_id":"5434","title":"An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas","isi":1,"article_processing_charge":"No","date_published":"2015-05-26T00:00:00Z","type":"journal_article","status":"public","oa_version":"None","abstract":[{"lang":"eng","text":"Vegetation clearing and land-use change have depleted many natural plant communities to the point where restoration is required. A major impediment to the success of rebuilding complex vegetation communities is having regular access to sufficient quantities of high-quality seed. Seed-production areas (SPAs) can help generate this seed, but these must be underpinned by a broad genetic base to maximise the evolutionary potential of restored populations. However, genetic bottlenecks can occur at the collection, establishment and production stages in SPAs, requiring genetic evaluation. This is especially relevant for species that may take many years before a return on SPA investment is realised. Two recently established yellow box (Eucalyptus melliodora A.Cunn. ex Schauer, Myrtaceae) SPAs were evaluated to determine whether genetic bottlenecks had occurred between seed collection and SPA establishment. No evidence was found to suggest that a significant loss of genetic diversity had occurred at this stage, although there was a significant difference in diversity between the two SPAs. Complex population genetic structure was also observed in the seed used to source the SPAs, with up to eight groups identified. Plant survival in the SPAs was influenced by seed collection location but not by SPA location and was not associated with genetic diversity. There were also no associations between genetic diversity and plant growth. These data highlighted the importance of chance events when establishing SPAs and indicated that the two yellow box SPAs are likely to provide genetically diverse seed sources for future restoration projects, especially by pooling seed from both SPAs."}],"citation":{"ama":"Broadhurst L, Fifield G, Vanzella B, Pickup M. An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas. <i>Australian Journal of Botany</i>. 2015;63(5):455-466. doi:<a href=\"https://doi.org/10.1071/BT15023\">10.1071/BT15023</a>","ieee":"L. Broadhurst, G. Fifield, B. Vanzella, and M. Pickup, “An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas,” <i>Australian Journal of Botany</i>, vol. 63, no. 5. CSIRO, pp. 455–466, 2015.","ista":"Broadhurst L, Fifield G, Vanzella B, Pickup M. 2015. An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas. Australian Journal of Botany. 63(5), 455–466.","short":"L. Broadhurst, G. Fifield, B. Vanzella, M. Pickup, Australian Journal of Botany 63 (2015) 455–466.","mla":"Broadhurst, Linda, et al. “An Evaluation of the Genetic Structure of Seed Sources and the Maintenance of Genetic Diversity during Establishment of Two Yellow Box (Eucalyptus Melliodora) Seed-Production Areas.” <i>Australian Journal of Botany</i>, vol. 63, no. 5, CSIRO, 2015, pp. 455–66, doi:<a href=\"https://doi.org/10.1071/BT15023\">10.1071/BT15023</a>.","chicago":"Broadhurst, Linda, Graham Fifield, Bindi Vanzella, and Melinda Pickup. “An Evaluation of the Genetic Structure of Seed Sources and the Maintenance of Genetic Diversity during Establishment of Two Yellow Box (Eucalyptus Melliodora) Seed-Production Areas.” <i>Australian Journal of Botany</i>. CSIRO, 2015. <a href=\"https://doi.org/10.1071/BT15023\">https://doi.org/10.1071/BT15023</a>.","apa":"Broadhurst, L., Fifield, G., Vanzella, B., &#38; Pickup, M. (2015). An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas. <i>Australian Journal of Botany</i>. CSIRO. <a href=\"https://doi.org/10.1071/BT15023\">https://doi.org/10.1071/BT15023</a>"},"scopus_import":"1","publisher":"CSIRO","author":[{"first_name":"Linda","last_name":"Broadhurst","full_name":"Broadhurst, Linda"},{"last_name":"Fifield","first_name":"Graham","full_name":"Fifield, Graham"},{"last_name":"Vanzella","first_name":"Bindi","full_name":"Vanzella, Bindi"},{"last_name":"Pickup","first_name":"Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","full_name":"Pickup, Melinda"}],"language":[{"iso":"eng"}],"doi":"10.1071/BT15023","publication_status":"published","intvolume":"        63","year":"2015","date_created":"2018-12-11T11:53:34Z","day":"26","publication":"Australian Journal of Botany","issue":"5","department":[{"_id":"NiBa"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"1703","page":"455 - 466"},{"type":"journal_article","status":"public","publisher":"Elsevier","citation":{"ieee":"S. Novak and S. Cremer, “Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates,” <i>Journal of Theoretical Biology</i>, vol. 372, no. 5. Elsevier, pp. 54–64, 2015.","ama":"Novak S, Cremer S. Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates. <i>Journal of Theoretical Biology</i>. 2015;372(5):54-64. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2015.02.018\">10.1016/j.jtbi.2015.02.018</a>","chicago":"Novak, Sebastian, and Sylvia Cremer. “Fungal Disease Dynamics in Insect Societies: Optimal Killing Rates and the Ambivalent Effect of High Social Interaction Rates.” <i>Journal of Theoretical Biology</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.jtbi.2015.02.018\">https://doi.org/10.1016/j.jtbi.2015.02.018</a>.","apa":"Novak, S., &#38; Cremer, S. (2015). Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates. <i>Journal of Theoretical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jtbi.2015.02.018\">https://doi.org/10.1016/j.jtbi.2015.02.018</a>","short":"S. Novak, S. Cremer, Journal of Theoretical Biology 372 (2015) 54–64.","ista":"Novak S, Cremer S. 2015. Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates. Journal of Theoretical Biology. 372(5), 54–64.","mla":"Novak, Sebastian, and Sylvia Cremer. “Fungal Disease Dynamics in Insect Societies: Optimal Killing Rates and the Ambivalent Effect of High Social Interaction Rates.” <i>Journal of Theoretical Biology</i>, vol. 372, no. 5, Elsevier, 2015, pp. 54–64, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2015.02.018\">10.1016/j.jtbi.2015.02.018</a>."},"abstract":[{"text":"Entomopathogenic fungi are potent biocontrol agents that are widely used against insect pests, many of which are social insects. Nevertheless, theoretical investigations of their particular life history are scarce. We develop a model that takes into account the main distinguishing features between traditionally studied diseases and obligate killing pathogens, like the (biocontrol-relevant) insect-pathogenic fungi Metarhizium and Beauveria. First, obligate killing entomopathogenic fungi produce new infectious particles (conidiospores) only after host death and not yet on the living host. Second, the killing rates of entomopathogenic fungi depend strongly on the initial exposure dosage, thus we explicitly consider the pathogen load of individual hosts. Further, we make the model applicable not only to solitary host species, but also to group living species by incorporating social interactions between hosts, like the collective disease defences of insect societies. Our results identify the optimal killing rate for the pathogen that minimises its invasion threshold. Furthermore, we find that the rate of contact between hosts has an ambivalent effect: dense interaction networks between individuals are considered to facilitate disease outbreaks because of increased pathogen transmission. In social insects, this is compensated by their collective disease defences, i.e., social immunity. For the type of pathogens considered here, we show that even without social immunity, high contact rates between live individuals dilute the pathogen in the host colony and hence can reduce individual pathogen loads below disease-causing levels.","lang":"eng"}],"scopus_import":"1","oa_version":"Submitted Version","month":"05","external_id":{"isi":["000353311700006"]},"date_updated":"2025-09-23T08:54:35Z","quality_controlled":"1","title":"Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates","article_processing_charge":"No","date_published":"2015-05-07T00:00:00Z","isi":1,"volume":372,"publist_id":"5251","corr_author":"1","publication":"Journal of Theoretical Biology","day":"07","page":"54 - 64","has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"1850","issue":"5","department":[{"_id":"NiBa"},{"_id":"SyCr"}],"ec_funded":1,"oa":1,"publication_status":"published","file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:45:19Z","relation":"main_file","file_size":1546914,"file_name":"IST-2015-329-v1+1_manuscript.pdf","access_level":"open_access","checksum":"3c0dcacc900bc45cc65a453dfda4ca43","creator":"system","file_id":"5326","date_created":"2018-12-12T10:18:07Z"}],"doi":"10.1016/j.jtbi.2015.02.018","project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"grant_number":"243071","_id":"25DC711C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects"}],"intvolume":"       372","file_date_updated":"2020-07-14T12:45:19Z","pubrep_id":"329","ddc":["576"],"language":[{"iso":"eng"}],"author":[{"full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-824X","last_name":"Novak","first_name":"Sebastian"},{"full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","last_name":"Cremer","first_name":"Sylvia"}],"date_created":"2018-12-11T11:54:21Z","year":"2015"},{"has_accepted_license":"1","page":"1015 - 1026","pmid":1,"department":[{"_id":"NiBa"},{"_id":"KrCh"}],"issue":"4","ec_funded":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"1851","publication":"Evolution","corr_author":"1","day":"09","article_type":"original","date_created":"2018-12-11T11:54:21Z","year":"2015","intvolume":"        69","file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:45:19Z","relation":"main_file","file_size":967214,"file_id":"7855","date_created":"2020-05-15T09:05:34Z","file_name":"2015_Evolution_Priklopil.pdf","access_level":"open_access","creator":"dernst","checksum":"1e8be0b1d7598a78cd2623d8ee8e7798"}],"doi":"10.1111/evo.12618","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"oa":1,"publication_status":"published","author":[{"last_name":"Priklopil","first_name":"Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","full_name":"Priklopil, Tadeas"},{"first_name":"Eva","last_name":"Kisdi","full_name":"Kisdi, Eva"},{"last_name":"Gyllenberg","first_name":"Mats","full_name":"Gyllenberg, Mats"}],"ddc":["570"],"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:19Z","publisher":"Wiley","oa_version":"Submitted Version","citation":{"ieee":"T. Priklopil, E. Kisdi, and M. Gyllenberg, “Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating,” <i>Evolution</i>, vol. 69, no. 4. Wiley, pp. 1015–1026, 2015.","ama":"Priklopil T, Kisdi E, Gyllenberg M. Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating. <i>Evolution</i>. 2015;69(4):1015-1026. doi:<a href=\"https://doi.org/10.1111/evo.12618\">10.1111/evo.12618</a>","apa":"Priklopil, T., Kisdi, E., &#38; Gyllenberg, M. (2015). Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.12618\">https://doi.org/10.1111/evo.12618</a>","chicago":"Priklopil, Tadeas, Eva Kisdi, and Mats Gyllenberg. “Evolutionarily Stable Mating Decisions for Sequentially Searching Females and the Stability of Reproductive Isolation by Assortative Mating.” <i>Evolution</i>. Wiley, 2015. <a href=\"https://doi.org/10.1111/evo.12618\">https://doi.org/10.1111/evo.12618</a>.","mla":"Priklopil, Tadeas, et al. “Evolutionarily Stable Mating Decisions for Sequentially Searching Females and the Stability of Reproductive Isolation by Assortative Mating.” <i>Evolution</i>, vol. 69, no. 4, Wiley, 2015, pp. 1015–26, doi:<a href=\"https://doi.org/10.1111/evo.12618\">10.1111/evo.12618</a>.","short":"T. Priklopil, E. Kisdi, M. Gyllenberg, Evolution 69 (2015) 1015–1026.","ista":"Priklopil T, Kisdi E, Gyllenberg M. 2015. Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating. Evolution. 69(4), 1015–1026."},"abstract":[{"lang":"eng","text":"We consider mating strategies for females who search for males sequentially during a season of limited length. We show that the best strategy rejects a given male type if encountered before a time-threshold but accepts him after. For frequency-independent benefits, we obtain the optimal time-thresholds explicitly for both discrete and continuous distributions of males, and allow for mistakes being made in assessing the correct male type. When the benefits are indirect (genes for the offspring) and the population is under frequency-dependent ecological selection, the benefits depend on the mating strategy of other females as well. This case is particularly relevant to speciation models that seek to explore the stability of reproductive isolation by assortative mating under frequency-dependent ecological selection. We show that the indirect benefits are to be quantified by the reproductive values of couples, and describe how the evolutionarily stable time-thresholds can be found. We conclude with an example based on the Levene model, in which we analyze the evolutionarily stable assortative mating strategies and the strength of reproductive isolation provided by them."}],"scopus_import":"1","status":"public","publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"type":"journal_article","isi":1,"article_processing_charge":"No","date_published":"2015-02-09T00:00:00Z","title":"Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating","publist_id":"5249","volume":69,"month":"02","date_updated":"2025-09-22T14:27:30Z","quality_controlled":"1","external_id":{"isi":["000353236000014"],"pmid":["25662095"]}},{"date_created":"2018-12-11T11:54:31Z","article_type":"original","year":"2015","doi":"10.1103/PhysRevE.91.022803","oa":1,"publication_status":"published","intvolume":"        91","author":[{"full_name":"Keller-Schmidt, Stephanie","last_name":"Keller-Schmidt","first_name":"Stephanie"},{"id":"37C323C6-F248-11E8-B48F-1D18A9856A87","full_name":"Tugrul, Murat","last_name":"Tugrul","first_name":"Murat","orcid":"0000-0002-8523-0758"},{"last_name":"Eguíluz","first_name":"Víctor","full_name":"Eguíluz, Víctor"},{"first_name":"Emilio","last_name":"Hernandez Garcia","full_name":"Hernandez Garcia, Emilio"},{"full_name":"Klemm, Konstantin","first_name":"Konstantin","last_name":"Klemm"}],"language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"issue":"2","_id":"1883","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","day":"02","title":"Anomalous scaling in an age-dependent branching model","isi":1,"arxiv":1,"date_published":"2015-02-02T00:00:00Z","article_processing_charge":"No","volume":91,"publist_id":"5213","month":"02","external_id":{"isi":["000349860900006"],"arxiv":["1012.3298"]},"quality_controlled":"1","date_updated":"2025-09-23T07:53:52Z","publisher":"American Institute of Physics","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1012.3298"}],"oa_version":"Preprint","abstract":[{"text":"We introduce a one-parametric family of tree growth models, in which branching probabilities decrease with branch age τ as τ-α. Depending on the exponent α, the scaling of tree depth with tree size n displays a transition between the logarithmic scaling of random trees and an algebraic growth. At the transition (α=1) tree depth grows as (logn)2. This anomalous scaling is in good agreement with the trend observed in evolution of biological species, thus providing a theoretical support for age-dependent speciation and associating it to the occurrence of a critical point.\r\n","lang":"eng"}],"article_number":"022803","citation":{"ista":"Keller-Schmidt S, Tugrul M, Eguíluz V, Hernandez Garcia E, Klemm K. 2015. Anomalous scaling in an age-dependent branching model. Physical Review E Statistical Nonlinear and Soft Matter Physics. 91(2), 022803.","short":"S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, K. Klemm, Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).","mla":"Keller-Schmidt, Stephanie, et al. “Anomalous Scaling in an Age-Dependent Branching Model.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 91, no. 2, 022803, American Institute of Physics, 2015, doi:<a href=\"https://doi.org/10.1103/PhysRevE.91.022803\">10.1103/PhysRevE.91.022803</a>.","chicago":"Keller-Schmidt, Stephanie, Murat Tugrul, Víctor Eguíluz, Emilio Hernandez Garcia, and Konstantin Klemm. “Anomalous Scaling in an Age-Dependent Branching Model.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics, 2015. <a href=\"https://doi.org/10.1103/PhysRevE.91.022803\">https://doi.org/10.1103/PhysRevE.91.022803</a>.","apa":"Keller-Schmidt, S., Tugrul, M., Eguíluz, V., Hernandez Garcia, E., &#38; Klemm, K. (2015). Anomalous scaling in an age-dependent branching model. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.91.022803\">https://doi.org/10.1103/PhysRevE.91.022803</a>","ama":"Keller-Schmidt S, Tugrul M, Eguíluz V, Hernandez Garcia E, Klemm K. Anomalous scaling in an age-dependent branching model. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. 2015;91(2). doi:<a href=\"https://doi.org/10.1103/PhysRevE.91.022803\">10.1103/PhysRevE.91.022803</a>","ieee":"S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, and K. Klemm, “Anomalous scaling in an age-dependent branching model,” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 91, no. 2. American Institute of Physics, 2015."},"scopus_import":"1","type":"journal_article","status":"public"},{"date_updated":"2025-09-23T08:31:14Z","author":[{"last_name":"Tugrul","first_name":"Murat","orcid":"0000-0002-8523-0758","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","full_name":"Tugrul, Murat"},{"orcid":"0000-0003-2361-3953","last_name":"Paixao","first_name":"Tiago","full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"},{"orcid":"0000-0002-6699-1455","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"month":"11","doi":"10.1371/journal.pgen.1005639.s001","year":"2015","title":"Other fitness models for comparison & for interacting TFBSs","date_created":"2021-07-23T12:00:37Z","article_processing_charge":"No","date_published":"2015-11-06T00:00:00Z","related_material":{"record":[{"id":"1666","relation":"used_in_publication","status":"public"}]},"day":"06","type":"research_data_reference","status":"public","_id":"9712","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"NiBa"},{"_id":"CaGu"},{"_id":"GaTk"}],"citation":{"ieee":"M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Other fitness models for comparison &#38; for interacting TFBSs.” Public Library of Science, 2015.","ama":"Tugrul M, Paixao T, Barton NH, Tkačik G. Other fitness models for comparison &#38; for interacting TFBSs. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005639.s001\">10.1371/journal.pgen.1005639.s001</a>","apa":"Tugrul, M., Paixao, T., Barton, N. H., &#38; Tkačik, G. (2015). Other fitness models for comparison &#38; for interacting TFBSs. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1005639.s001\">https://doi.org/10.1371/journal.pgen.1005639.s001</a>","chicago":"Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Other Fitness Models for Comparison &#38; for Interacting TFBSs.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pgen.1005639.s001\">https://doi.org/10.1371/journal.pgen.1005639.s001</a>.","mla":"Tugrul, Murat, et al. <i>Other Fitness Models for Comparison &#38; for Interacting TFBSs</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005639.s001\">10.1371/journal.pgen.1005639.s001</a>.","short":"M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, (2015).","ista":"Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Other fitness models for comparison &#38; for interacting TFBSs, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pgen.1005639.s001\">10.1371/journal.pgen.1005639.s001</a>."},"oa_version":"Published Version","publisher":"Public Library of Science"},{"day":"18","related_material":{"record":[{"status":"public","id":"1809","relation":"used_in_publication"}]},"status":"public","type":"research_data_reference","oa_version":"Published Version","citation":{"ama":"Trubenova B, Novak S, Hager R. Mathematical inference of the results. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907.s001\">10.1371/journal.pone.0126907.s001</a>","ieee":"B. Trubenova, S. Novak, and R. Hager, “Mathematical inference of the results.” Public Library of Science, 2015.","ista":"Trubenova B, Novak S, Hager R. 2015. Mathematical inference of the results, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0126907.s001\">10.1371/journal.pone.0126907.s001</a>.","short":"B. Trubenova, S. Novak, R. Hager, (2015).","mla":"Trubenova, Barbora, et al. <i>Mathematical Inference of the Results</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907.s001\">10.1371/journal.pone.0126907.s001</a>.","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Mathematical Inference of the Results.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0126907.s001\">https://doi.org/10.1371/journal.pone.0126907.s001</a>.","apa":"Trubenova, B., Novak, S., &#38; Hager, R. (2015). Mathematical inference of the results. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0126907.s001\">https://doi.org/10.1371/journal.pone.0126907.s001</a>"},"department":[{"_id":"NiBa"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9715","publisher":"Public Library of Science","author":[{"first_name":"Barbora","last_name":"Trubenova","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87","full_name":"Trubenova, Barbora"},{"full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-824X","last_name":"Novak","first_name":"Sebastian"},{"full_name":"Hager, Reinmar","last_name":"Hager","first_name":"Reinmar"}],"date_updated":"2025-09-23T09:21:54Z","month":"05","doi":"10.1371/journal.pone.0126907.s001","year":"2015","article_processing_charge":"No","date_published":"2015-05-18T00:00:00Z","date_created":"2021-07-23T12:11:30Z","title":"Mathematical inference of the results"},{"type":"research_data_reference","status":"public","related_material":{"record":[{"id":"1809","relation":"used_in_publication","status":"public"}]},"day":"18","publisher":"Public Library of Science","_id":"9772","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"NiBa"}],"citation":{"chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Description of the Agent Based Simulations.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">https://doi.org/10.1371/journal.pone.0126907.s003</a>.","apa":"Trubenova, B., Novak, S., &#38; Hager, R. (2015). Description of the agent based simulations. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">https://doi.org/10.1371/journal.pone.0126907.s003</a>","ista":"Trubenova B, Novak S, Hager R. 2015. Description of the agent based simulations, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">10.1371/journal.pone.0126907.s003</a>.","short":"B. Trubenova, S. Novak, R. Hager, (2015).","mla":"Trubenova, Barbora, et al. <i>Description of the Agent Based Simulations</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">10.1371/journal.pone.0126907.s003</a>.","ieee":"B. Trubenova, S. Novak, and R. Hager, “Description of the agent based simulations.” Public Library of Science, 2015.","ama":"Trubenova B, Novak S, Hager R. Description of the agent based simulations. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">10.1371/journal.pone.0126907.s003</a>"},"oa_version":"Published Version","month":"05","doi":"10.1371/journal.pone.0126907.s003","date_updated":"2025-09-23T09:21:54Z","author":[{"last_name":"Trubenova","first_name":"Barbora","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87","full_name":"Trubenova, Barbora"},{"first_name":"Sebastian","last_name":"Novak","orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian"},{"last_name":"Hager","first_name":"Reinmar","full_name":"Hager, Reinmar"}],"title":"Description of the agent based simulations","date_created":"2021-08-05T12:55:20Z","date_published":"2015-05-18T00:00:00Z","article_processing_charge":"No","year":"2015"},{"year":"2015","date_created":"2018-12-11T11:54:07Z","ddc":["570","576"],"language":[{"iso":"eng"}],"author":[{"last_name":"Trubenova","first_name":"Barbora","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87","full_name":"Trubenova, Barbora"},{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian","first_name":"Sebastian","last_name":"Novak","orcid":"0000-0002-2519-824X"},{"first_name":"Reinmar","last_name":"Hager","full_name":"Hager, Reinmar"}],"file_date_updated":"2020-07-14T12:45:17Z","pubrep_id":"453","intvolume":"        10","oa":1,"publication_status":"published","doi":"10.1371/journal.pone.0126907","file":[{"date_created":"2018-12-12T10:09:07Z","file_id":"4730","creator":"system","checksum":"d3a4a58ef4bd3b3e2f32b7fd7af4a743","access_level":"open_access","file_name":"IST-2016-453-v1+1_journal.pone.0126907.pdf","file_size":2748982,"content_type":"application/pdf","relation":"main_file","date_updated":"2020-07-14T12:45:17Z"}],"_id":"1809","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"5","department":[{"_id":"NiBa"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","day":"18","publication":"PLoS One","corr_author":"1","publist_id":"5299","volume":10,"article_processing_charge":"No","date_published":"2015-05-18T00:00:00Z","isi":1,"title":"Indirect genetic effects and the dynamics of social interactions","quality_controlled":"1","date_updated":"2025-09-23T09:21:54Z","external_id":{"isi":["000354917300064"]},"month":"05","citation":{"ama":"Trubenova B, Novak S, Hager R. Indirect genetic effects and the dynamics of social interactions. <i>PLoS One</i>. 2015;10(5). doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907\">10.1371/journal.pone.0126907</a>","ieee":"B. Trubenova, S. Novak, and R. Hager, “Indirect genetic effects and the dynamics of social interactions,” <i>PLoS One</i>, vol. 10, no. 5. Public Library of Science, 2015.","mla":"Trubenova, Barbora, et al. “Indirect Genetic Effects and the Dynamics of Social Interactions.” <i>PLoS One</i>, vol. 10, no. 5, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907\">10.1371/journal.pone.0126907</a>.","ista":"Trubenova B, Novak S, Hager R. 2015. Indirect genetic effects and the dynamics of social interactions. PLoS One. 10(5).","short":"B. Trubenova, S. Novak, R. Hager, PLoS One 10 (2015).","apa":"Trubenova, B., Novak, S., &#38; Hager, R. (2015). Indirect genetic effects and the dynamics of social interactions. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0126907\">https://doi.org/10.1371/journal.pone.0126907</a>","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Indirect Genetic Effects and the Dynamics of Social Interactions.” <i>PLoS One</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0126907\">https://doi.org/10.1371/journal.pone.0126907</a>."},"scopus_import":"1","abstract":[{"lang":"eng","text":"Background: Indirect genetic effects (IGEs) occur when genes expressed in one individual alter the expression of traits in social partners. Previous studies focused on the evolutionary consequences and evolutionary dynamics of IGEs, using equilibrium solutions to predict phenotypes in subsequent generations. However, whether or not such steady states may be reached may depend on the dynamics of interactions themselves. Results: In our study, we focus on the dynamics of social interactions and indirect genetic effects and investigate how they modify phenotypes over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics; rather we consider within-individual phenotypic changes, also referred to as phenotypic plasticity. We analyse iterative interactions, when individuals interact in a series of discontinuous events, and investigate the stability of steady state solutions and the dependence on model parameters, such as population size, strength, and the nature of interactions. We show that for interactions where a feedback loop occurs, the possible parameter space of interaction strength is fairly limited, affecting the evolutionary consequences of IGEs. We discuss the implications of our results for current IGE model predictions and their limitations."}],"oa_version":"Published Version","publisher":"Public Library of Science","related_material":{"record":[{"relation":"research_data","id":"9715","status":"public"},{"status":"public","relation":"research_data","id":"9772"}]},"status":"public","type":"journal_article"},{"volume":112,"publist_id":"5288","title":"Limits to adaptation along environmental gradients","article_processing_charge":"No","date_published":"2015-05-19T00:00:00Z","isi":1,"external_id":{"isi":["000354729500058"],"pmid":["25941385"]},"quality_controlled":"1","date_updated":"2025-09-23T09:27:16Z","month":"05","scopus_import":"1","abstract":[{"lang":"eng","text":"Why do species not adapt to ever-wider ranges of conditions, gradually expanding their ecological niche and geographic range? Gene flow across environments has two conflicting effects: although it increases genetic variation, which is a prerequisite for adaptation, gene flow may swamp adaptation to local conditions. In 1956, Haldane proposed that, when the environment varies across space, &quot;swamping&quot; by gene flow creates a positive feedback between low population size and maladaptation, leading to a sharp range margin. However, current deterministic theory shows that, when variance can evolve, there is no such limit. Using simple analytical tools and simulations, we show that genetic drift can generate a sharp margin to a species' range, by reducing genetic variance below the level needed for adaptation to spatially variable conditions. Aided by separation of ecological and evolutionary timescales, the identified effective dimensionless parameters reveal a simple threshold that predicts when adaptation at the range margin fails. Two observable parameters determine the threshold: (i) the effective environmental gradient, which can be measured by the loss of fitness due to dispersal to a different environment; and (ii) the efficacy of selection relative to genetic drift. The theory predicts sharp range margins even in the absence of abrupt changes in the environment. Furthermore, it implies that gradual worsening of conditions across a species' habitat may lead to a sudden range fragmentation, when adaptation to a wide span of conditions within a single species becomes impossible."}],"citation":{"apa":"Polechova, J., &#38; Barton, N. H. (2015). Limits to adaptation along environmental gradients. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1421515112\">https://doi.org/10.1073/pnas.1421515112</a>","chicago":"Polechova, Jitka, and Nicholas H Barton. “Limits to Adaptation along Environmental Gradients.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1421515112\">https://doi.org/10.1073/pnas.1421515112</a>.","mla":"Polechova, Jitka, and Nicholas H. Barton. “Limits to Adaptation along Environmental Gradients.” <i>PNAS</i>, vol. 112, no. 20, National Academy of Sciences, 2015, pp. 6401–06, doi:<a href=\"https://doi.org/10.1073/pnas.1421515112\">10.1073/pnas.1421515112</a>.","short":"J. Polechova, N.H. Barton, PNAS 112 (2015) 6401–6406.","ista":"Polechova J, Barton NH. 2015. Limits to adaptation along environmental gradients. PNAS. 112(20), 6401–6406.","ieee":"J. Polechova and N. H. Barton, “Limits to adaptation along environmental gradients,” <i>PNAS</i>, vol. 112, no. 20. National Academy of Sciences, pp. 6401–6406, 2015.","ama":"Polechova J, Barton NH. Limits to adaptation along environmental gradients. <i>PNAS</i>. 2015;112(20):6401-6406. doi:<a href=\"https://doi.org/10.1073/pnas.1421515112\">10.1073/pnas.1421515112</a>"},"oa_version":"Submitted Version","publisher":"National Academy of Sciences","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443383/"}],"type":"journal_article","status":"public","year":"2015","date_created":"2018-12-11T11:54:11Z","language":[{"iso":"eng"}],"author":[{"full_name":"Polechova, Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0951-3112","first_name":"Jitka","last_name":"Polechova"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"oa":1,"publication_status":"published","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"doi":"10.1073/pnas.1421515112","intvolume":"       112","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"1818","issue":"20","department":[{"_id":"NiBa"}],"ec_funded":1,"pmid":1,"page":"6401 - 6406","day":"19","corr_author":"1","publication":"PNAS"},{"department":[{"_id":"ToHe"},{"_id":"CaGu"},{"_id":"NiBa"}],"ec_funded":1,"conference":{"location":"London, United Kingdom","end_date":"2015-04-18","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","start_date":"2015-04-11"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1835","page":"469 - 483","day":"01","year":"2015","alternative_title":["LNCS"],"date_created":"2018-12-11T11:54:16Z","author":[{"last_name":"Giacobbe","first_name":"Mirco","orcid":"0000-0001-8180-0904","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","full_name":"Giacobbe, Mirco"},{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet"},{"id":"335E5684-F248-11E8-B48F-1D18A9856A87","full_name":"Gupta, Ashutosh","last_name":"Gupta","first_name":"Ashutosh"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A"},{"orcid":"0000-0003-2361-3953","last_name":"Paixao","first_name":"Tiago","full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Petrov","first_name":"Tatjana","orcid":"0000-0002-9041-0905","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","full_name":"Petrov, Tatjana"}],"language":[{"iso":"eng"}],"intvolume":"      9035","project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"doi":"10.1007/978-3-662-46681-0_47","series_title":"Lecture Notes in Computer Science","oa":1,"publication_status":"published","oa_version":"Preprint","abstract":[{"text":"The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives higher assurance and scalability. We focus on Wagner’s weighted GRN model with varying weights, which is used in evolutionary biology. In the model, weight parameters represent the gene interaction strength that may change due to genetic mutations. For a property of interest, we synthesise the constraints over the parameter space that represent the set of GRNs satisfying the property. We experimentally show that our parameter synthesis procedure computes the mutational robustness of GRNs –an important problem of interest in evolutionary biology– more efficiently than the classical simulation method. We specify the property in linear temporal logics. We employ symbolic bounded model checking and SMT solving to compute the space of GRNs that satisfy the property, which amounts to synthesizing a set of linear constraints on the weights.","lang":"eng"}],"citation":{"chicago":"Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking Gene Regulatory Networks.” Lecture Notes in Computer Science. Springer, 2015. <a href=\"https://doi.org/10.1007/978-3-662-46681-0_47\">https://doi.org/10.1007/978-3-662-46681-0_47</a>.","apa":"Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., &#38; Petrov, T. (2015). Model checking gene regulatory networks. Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom: Springer. <a href=\"https://doi.org/10.1007/978-3-662-46681-0_47\">https://doi.org/10.1007/978-3-662-46681-0_47</a>","ista":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2015. Model checking gene regulatory networks. 9035, 469–483.","short":"M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, 9035 (2015) 469–483.","mla":"Giacobbe, Mirco, et al. <i>Model Checking Gene Regulatory Networks</i>. Vol. 9035, Springer, 2015, pp. 469–83, doi:<a href=\"https://doi.org/10.1007/978-3-662-46681-0_47\">10.1007/978-3-662-46681-0_47</a>.","ieee":"M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov, “Model checking gene regulatory networks,” vol. 9035. Springer, pp. 469–483, 2015.","ama":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking gene regulatory networks. 2015;9035:469-483. doi:<a href=\"https://doi.org/10.1007/978-3-662-46681-0_47\">10.1007/978-3-662-46681-0_47</a>"},"scopus_import":"1","main_file_link":[{"url":"http://arxiv.org/abs/1410.7704","open_access":"1"}],"publisher":"Springer","related_material":{"record":[{"id":"1351","relation":"later_version","status":"public"}]},"status":"public","type":"conference","publist_id":"5267","volume":9035,"acknowledgement":"SNSF Early Postdoc.Mobility Fellowship, the grant number P2EZP2 148797.\r\n","arxiv":1,"article_processing_charge":"No","date_published":"2015-04-01T00:00:00Z","title":"Model checking gene regulatory networks","quality_controlled":"1","date_updated":"2025-07-10T11:50:42Z","external_id":{"arxiv":["1410.7704"]},"month":"04"},{"abstract":[{"text":"The theory of population genetics and evolutionary computation have been evolving separately for nearly 30 years. Many results have been independently obtained in both fields and many others are unique to its respective field. We aim to bridge this gap by developing a unifying framework for evolutionary processes that allows both evolutionary algorithms and population genetics models to be cast in the same formal framework. The framework we present here decomposes the evolutionary process into its several components in order to facilitate the identification of similarities between different models. In particular, we propose a classification of evolutionary operators based on the defining properties of the different components. We cast several commonly used operators from both fields into this common framework. Using this, we map different evolutionary and genetic algorithms to different evolutionary regimes and identify candidates with the most potential for the translation of results between the fields. This provides a unified description of evolutionary processes and represents a stepping stone towards new tools and results to both fields. ","lang":"eng"}],"citation":{"ista":"Paixao T, Badkobeh G, Barton NH, Çörüş D, Dang D, Friedrich T, Lehre P, Sudholt D, Sutton A, Trubenova B. 2015. Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. 383, 28–43.","short":"T. Paixao, G. Badkobeh, N.H. Barton, D. Çörüş, D. Dang, T. Friedrich, P. Lehre, D. Sudholt, A. Sutton, B. Trubenova, Journal of Theoretical Biology 383 (2015) 28–43.","mla":"Paixao, Tiago, et al. “Toward a Unifying Framework for Evolutionary Processes.” <i>Journal of Theoretical Biology</i>, vol. 383, Elsevier, 2015, pp. 28–43, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">10.1016/j.jtbi.2015.07.011</a>.","chicago":"Paixao, Tiago, Golnaz Badkobeh, Nicholas H Barton, Doğan Çörüş, Duccuong Dang, Tobias Friedrich, Per Lehre, Dirk Sudholt, Andrew Sutton, and Barbora Trubenova. “Toward a Unifying Framework for Evolutionary Processes.” <i>Journal of Theoretical Biology</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">https://doi.org/10.1016/j.jtbi.2015.07.011</a>.","apa":"Paixao, T., Badkobeh, G., Barton, N. H., Çörüş, D., Dang, D., Friedrich, T., … Trubenova, B. (2015). Toward a unifying framework for evolutionary processes. <i>Journal of Theoretical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">https://doi.org/10.1016/j.jtbi.2015.07.011</a>","ama":"Paixao T, Badkobeh G, Barton NH, et al. Toward a unifying framework for evolutionary processes. <i>Journal of Theoretical Biology</i>. 2015;383:28-43. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">10.1016/j.jtbi.2015.07.011</a>","ieee":"T. Paixao <i>et al.</i>, “Toward a unifying framework for evolutionary processes,” <i>Journal of Theoretical Biology</i>, vol. 383. Elsevier, pp. 28–43, 2015."},"scopus_import":"1","oa_version":"Published Version","das_tickbox":"1","publisher":"Elsevier","status":"public","type":"journal_article","publist_id":"5629","volume":383,"article_processing_charge":"No","date_published":"2015-10-21T00:00:00Z","isi":1,"title":"Toward a unifying framework for evolutionary processes","date_updated":"2026-07-07T13:12:13Z","quality_controlled":"1","external_id":{"isi":["000362056300005"]},"month":"10","_id":"1542","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"ec_funded":1,"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"has_accepted_license":"1","page":"28 - 43","day":"21","publication":"Journal of Theoretical Biology","corr_author":"1","year":"2015","date_created":"2018-12-11T11:52:37Z","language":[{"iso":"eng"}],"ddc":["570"],"author":[{"last_name":"Paixao","first_name":"Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago"},{"full_name":"Badkobeh, Golnaz","last_name":"Badkobeh","first_name":"Golnaz"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"},{"first_name":"Doğan","last_name":"Çörüş","full_name":"Çörüş, Doğan"},{"full_name":"Dang, Duccuong","last_name":"Dang","first_name":"Duccuong"},{"full_name":"Friedrich, Tobias","first_name":"Tobias","last_name":"Friedrich"},{"first_name":"Per","last_name":"Lehre","full_name":"Lehre, Per"},{"full_name":"Sudholt, Dirk","first_name":"Dirk","last_name":"Sudholt"},{"last_name":"Sutton","first_name":"Andrew","full_name":"Sutton, Andrew"},{"last_name":"Trubenova","first_name":"Barbora","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87","full_name":"Trubenova, Barbora"}],"file_date_updated":"2020-07-14T12:45:01Z","pubrep_id":"483","intvolume":"       383","oa":1,"publication_status":"published","file":[{"file_size":595307,"content_type":"application/pdf","date_updated":"2020-07-14T12:45:01Z","relation":"main_file","date_created":"2018-12-12T10:16:53Z","file_id":"5244","checksum":"33b60ecfea60764756a9ee9df5eb65ca","creator":"system","file_name":"IST-2016-483-v1+1_1-s2.0-S0022519315003409-main.pdf","access_level":"open_access"}],"doi":"10.1016/j.jtbi.2015.07.011","project":[{"grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"},{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}]},{"citation":{"ama":"Tugrul M, Paixao T, Barton NH, Tkačik G. Dynamics of transcription factor binding site evolution. <i>PLoS Genetics</i>. 2015;11(11). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005639\">10.1371/journal.pgen.1005639</a>","ieee":"M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Dynamics of transcription factor binding site evolution,” <i>PLoS Genetics</i>, vol. 11, no. 11. Public Library of Science, 2015.","mla":"Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.” <i>PLoS Genetics</i>, vol. 11, no. 11, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005639\">10.1371/journal.pgen.1005639</a>.","short":"M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, PLoS Genetics 11 (2015).","ista":"Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Dynamics of transcription factor binding site evolution. PLoS Genetics. 11(11).","apa":"Tugrul, M., Paixao, T., Barton, N. H., &#38; Tkačik, G. (2015). Dynamics of transcription factor binding site evolution. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1005639\">https://doi.org/10.1371/journal.pgen.1005639</a>","chicago":"Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Dynamics of Transcription Factor Binding Site Evolution.” <i>PLoS Genetics</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pgen.1005639\">https://doi.org/10.1371/journal.pgen.1005639</a>."},"scopus_import":"1","abstract":[{"text":"Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key regulatory mechanism that determines gene expression and hence heritable phenotypic variation. We use a biophysical model for directional selection on gene expression to estimate the rates of gain and loss of transcription factor binding sites (TFBS) in finite populations under both point and insertion/deletion mutations. Our results show that these rates are typically slow for a single TFBS in an isolated DNA region, unless the selection is extremely strong. These rates decrease drastically with increasing TFBS length or increasingly specific protein-DNA interactions, making the evolution of sites longer than ∼ 10 bp unlikely on typical eukaryotic speciation timescales. Similarly, evolution converges to the stationary distribution of binding sequences very slowly, making the equilibrium assumption questionable. The availability of longer regulatory sequences in which multiple binding sites can evolve simultaneously, the presence of “pre-sites” or partially decayed old sites in the initial sequence, and biophysical cooperativity between transcription factors, can all facilitate gain of TFBS and reconcile theoretical calculations with timescales inferred from comparative genomics.","lang":"eng"}],"oa_version":"Published Version","publisher":"Public Library of Science","related_material":{"record":[{"status":"public","relation":"research_data","id":"9712"},{"status":"public","relation":"dissertation_contains","id":"1131"}]},"type":"journal_article","status":"public","volume":11,"publist_id":"5483","title":"Dynamics of transcription factor binding site evolution","date_published":"2015-11-06T00:00:00Z","article_processing_charge":"No","isi":1,"external_id":{"isi":["000366179000022"]},"quality_controlled":"1","date_updated":"2026-07-29T11:31:13Z","month":"11","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"1666","issue":"11","department":[{"_id":"NiBa"},{"_id":"CaGu"},{"_id":"GaTk"}],"ec_funded":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","day":"06","publication":"PLoS Genetics","year":"2015","date_created":"2018-12-11T11:53:21Z","file_date_updated":"2020-07-14T12:45:10Z","pubrep_id":"463","language":[{"iso":"eng"}],"ddc":["576"],"author":[{"full_name":"Tugrul, Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8523-0758","first_name":"Murat","last_name":"Tugrul"},{"last_name":"Paixao","first_name":"Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"},{"orcid":"0000-0002-6699-1455","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","oa":1,"doi":"10.1371/journal.pgen.1005639","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"file":[{"content_type":"application/pdf","relation":"main_file","date_updated":"2020-07-14T12:45:10Z","file_size":2580778,"access_level":"open_access","file_name":"IST-2016-463-v1+1_journal.pgen.1005639.pdf","creator":"system","checksum":"a4e72fca5ccf40ddacf4d08c8e46b554","file_id":"4657","date_created":"2018-12-12T10:07:58Z"}],"intvolume":"        11"},{"language":[{"iso":"eng"}],"author":[{"full_name":"Phadke, Sujal","last_name":"Phadke","first_name":"Sujal"},{"last_name":"Paixao","first_name":"Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago"},{"full_name":"Pham, Tuan","first_name":"Tuan","last_name":"Pham"},{"full_name":"Pham, Stephanie","first_name":"Stephanie","last_name":"Pham"},{"last_name":"Zufall","first_name":"Rebecca","full_name":"Zufall, Rebecca"}],"intvolume":"       105","publication_status":"published","doi":"10.1093/jhered/est063","year":"2014","date_created":"2018-12-11T11:56:35Z","day":"01","publication":"Journal of Heredity","corr_author":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"2252","issue":"1","department":[{"_id":"NiBa"}],"page":"130 - 135","date_updated":"2025-09-29T11:16:03Z","quality_controlled":"1","external_id":{"isi":["000328427800013"]},"month":"01","publist_id":"4695","volume":105,"date_published":"2014-01-01T00:00:00Z","article_processing_charge":"No","isi":1,"title":"Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila","status":"public","type":"journal_article","publication_identifier":{"issn":["0022-1503"]},"citation":{"ieee":"S. Phadke, T. Paixao, T. Pham, S. Pham, and R. Zufall, “Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila,” <i>Journal of Heredity</i>, vol. 105, no. 1. Oxford University Press, pp. 130–135, 2014.","ama":"Phadke S, Paixao T, Pham T, Pham S, Zufall R. Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila. <i>Journal of Heredity</i>. 2014;105(1):130-135. doi:<a href=\"https://doi.org/10.1093/jhered/est063\">10.1093/jhered/est063</a>","chicago":"Phadke, Sujal, Tiago Paixao, Tuan Pham, Stephanie Pham, and Rebecca Zufall. “Genetic Background Alters Dominance Relationships between Mat Alleles in the Ciliate Tetrahymena Thermophila.” <i>Journal of Heredity</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/jhered/est063\">https://doi.org/10.1093/jhered/est063</a>.","apa":"Phadke, S., Paixao, T., Pham, T., Pham, S., &#38; Zufall, R. (2014). Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila. <i>Journal of Heredity</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jhered/est063\">https://doi.org/10.1093/jhered/est063</a>","short":"S. Phadke, T. Paixao, T. Pham, S. Pham, R. Zufall, Journal of Heredity 105 (2014) 130–135.","ista":"Phadke S, Paixao T, Pham T, Pham S, Zufall R. 2014. Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila. Journal of Heredity. 105(1), 130–135.","mla":"Phadke, Sujal, et al. “Genetic Background Alters Dominance Relationships between Mat Alleles in the Ciliate Tetrahymena Thermophila.” <i>Journal of Heredity</i>, vol. 105, no. 1, Oxford University Press, 2014, pp. 130–35, doi:<a href=\"https://doi.org/10.1093/jhered/est063\">10.1093/jhered/est063</a>."},"scopus_import":"1","abstract":[{"text":"The pattern of inheritance and mechanism of sex determination can have important evolutionary consequences. We studied probabilistic sex determination in the ciliate Tetrahymena thermophila, which was previously shown to cause evolution of skewed sex ratios. We find that the genetic background alters the sex determination patterns of mat alleles in heterozygotes and that allelic interaction can differentially influence the expression probability of the 7 sexes. We quantify the dominance relationships between several mat alleles and find that A-type alleles, which specify sex I, are indeed recessive to B-type alleles, which are unable to specify that sex. Our results provide additional support for the presence of modifier loci and raise implications for the dynamics of sex ratios in populations of T. thermophila.","lang":"eng"}],"oa_version":"None","publisher":"Oxford University Press"},{"date_created":"2018-12-11T11:56:06Z","year":"2014","oa":1,"publication_status":"published","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"file":[{"date_created":"2018-12-12T10:10:49Z","file_id":"4839","checksum":"979d7a8034e9df198f068f0d251f31bd","creator":"system","access_level":"open_access","file_name":"IST-2015-391-v1+1_1-s2.0-S0040580914000355-main.pdf","file_size":569005,"content_type":"application/pdf","relation":"main_file","date_updated":"2020-07-14T12:45:31Z"}],"doi":"10.1016/j.tpb.2014.05.001","intvolume":"        95","file_date_updated":"2020-07-14T12:45:31Z","pubrep_id":"391","ddc":["570"],"language":[{"iso":"eng"}],"author":[{"last_name":"Kelleher","first_name":"Jerome","full_name":"Kelleher, Jerome"},{"first_name":"Alison","last_name":"Etheridge","full_name":"Etheridge, Alison"},{"first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"page":"13 - 23","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"2168","ec_funded":1,"department":[{"_id":"NiBa"}],"publication":"Theoretical Population Biology","day":"01","title":"Coalescent simulation in continuous space: Algorithms for large neighbourhood size","article_processing_charge":"No","date_published":"2014-08-01T00:00:00Z","isi":1,"volume":95,"publist_id":"4816","month":"08","external_id":{"isi":["000339460300002"]},"date_updated":"2025-09-29T11:39:51Z","quality_controlled":"1","publisher":"Academic Press","abstract":[{"text":"Many species have an essentially continuous distribution in space, in which there are no natural divisions between randomly mating subpopulations. Yet, the standard approach to modelling these populations is to impose an arbitrary grid of demes, adjusting deme sizes and migration rates in an attempt to capture the important features of the population. Such indirect methods are required because of the failure of the classical models of isolation by distance, which have been shown to have major technical flaws. A recently introduced model of extinction and recolonisation in two dimensions solves these technical problems, and provides a rigorous technical foundation for the study of populations evolving in a spatial continuum. The coalescent process for this model is simply stated, but direct simulation is very inefficient for large neighbourhood sizes. We present efficient and exact algorithms to simulate this coalescent process for arbitrary sample sizes and numbers of loci, and analyse these algorithms in detail.","lang":"eng"}],"citation":{"ista":"Kelleher J, Etheridge A, Barton NH. 2014. Coalescent simulation in continuous space: Algorithms for large neighbourhood size. Theoretical Population Biology. 95, 13–23.","short":"J. Kelleher, A. Etheridge, N.H. Barton, Theoretical Population Biology 95 (2014) 13–23.","mla":"Kelleher, Jerome, et al. “Coalescent Simulation in Continuous Space: Algorithms for Large Neighbourhood Size.” <i>Theoretical Population Biology</i>, vol. 95, Academic Press, 2014, pp. 13–23, doi:<a href=\"https://doi.org/10.1016/j.tpb.2014.05.001\">10.1016/j.tpb.2014.05.001</a>.","chicago":"Kelleher, Jerome, Alison Etheridge, and Nicholas H Barton. “Coalescent Simulation in Continuous Space: Algorithms for Large Neighbourhood Size.” <i>Theoretical Population Biology</i>. Academic Press, 2014. <a href=\"https://doi.org/10.1016/j.tpb.2014.05.001\">https://doi.org/10.1016/j.tpb.2014.05.001</a>.","apa":"Kelleher, J., Etheridge, A., &#38; Barton, N. H. (2014). Coalescent simulation in continuous space: Algorithms for large neighbourhood size. <i>Theoretical Population Biology</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.tpb.2014.05.001\">https://doi.org/10.1016/j.tpb.2014.05.001</a>","ama":"Kelleher J, Etheridge A, Barton NH. Coalescent simulation in continuous space: Algorithms for large neighbourhood size. <i>Theoretical Population Biology</i>. 2014;95:13-23. doi:<a href=\"https://doi.org/10.1016/j.tpb.2014.05.001\">10.1016/j.tpb.2014.05.001</a>","ieee":"J. Kelleher, A. Etheridge, and N. H. Barton, “Coalescent simulation in continuous space: Algorithms for large neighbourhood size,” <i>Theoretical Population Biology</i>, vol. 95. Academic Press, pp. 13–23, 2014."},"scopus_import":"1","oa_version":"Published Version","type":"journal_article","status":"public"},{"month":"07","external_id":{"isi":["000339310700017"]},"date_updated":"2025-09-29T11:39:19Z","quality_controlled":"1","title":"Diverse forms of selection in evolution and computer science","article_processing_charge":"No","date_published":"2014-07-22T00:00:00Z","isi":1,"volume":111,"publist_id":"4815","type":"journal_article","status":"public","publisher":"National Academy of Sciences","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4115508/"}],"citation":{"ama":"Barton NH, Novak S, Paixao T. Diverse forms of selection in evolution and computer science. <i>PNAS</i>. 2014;111(29):10398-10399. doi:<a href=\"https://doi.org/10.1073/pnas.1410107111\">10.1073/pnas.1410107111</a>","ieee":"N. H. Barton, S. Novak, and T. Paixao, “Diverse forms of selection in evolution and computer science,” <i>PNAS</i>, vol. 111, no. 29. National Academy of Sciences, pp. 10398–10399, 2014.","mla":"Barton, Nicholas H., et al. “Diverse Forms of Selection in Evolution and Computer Science.” <i>PNAS</i>, vol. 111, no. 29, National Academy of Sciences, 2014, pp. 10398–99, doi:<a href=\"https://doi.org/10.1073/pnas.1410107111\">10.1073/pnas.1410107111</a>.","ista":"Barton NH, Novak S, Paixao T. 2014. Diverse forms of selection in evolution and computer science. PNAS. 111(29), 10398–10399.","short":"N.H. Barton, S. Novak, T. Paixao, PNAS 111 (2014) 10398–10399.","apa":"Barton, N. H., Novak, S., &#38; Paixao, T. (2014). Diverse forms of selection in evolution and computer science. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1410107111\">https://doi.org/10.1073/pnas.1410107111</a>","chicago":"Barton, Nicholas H, Sebastian Novak, and Tiago Paixao. “Diverse Forms of Selection in Evolution and Computer Science.” <i>PNAS</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1410107111\">https://doi.org/10.1073/pnas.1410107111</a>."},"scopus_import":"1","oa_version":"Submitted Version","publication_status":"published","oa":1,"doi":"10.1073/pnas.1410107111","intvolume":"       111","language":[{"iso":"eng"}],"author":[{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"orcid":"0000-0002-2519-824X","first_name":"Sebastian","last_name":"Novak","full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2361-3953","first_name":"Tiago","last_name":"Paixao","full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:56:07Z","year":"2014","corr_author":"1","publication":"PNAS","day":"22","page":"10398 - 10399","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"2169","issue":"29","department":[{"_id":"NiBa"}]},{"date_created":"2018-12-11T11:56:07Z","year":"2014","publication_status":"published","oa":1,"doi":"10.1111/mec.12578","file":[{"creator":"system","checksum":"4de1ab255976a8ae77eb0e55ad62ecc9","access_level":"open_access","file_name":"IST-2016-559-v1+1_Hearn_et_al.pdf","date_created":"2018-12-12T10:07:52Z","file_id":"4651","file_size":807444,"content_type":"application/pdf","relation":"main_file","date_updated":"2020-07-14T12:45:31Z"},{"checksum":"01a8073e071c088500425f910b0f1f71","creator":"system","file_name":"IST-2016-559-v1+2_Hearn_et_al_Suppl.pdf","access_level":"open_access","date_created":"2018-12-12T10:07:53Z","file_id":"4652","file_size":1518088,"date_updated":"2020-07-14T12:45:31Z","content_type":"application/pdf","relation":"main_file"}],"intvolume":"        23","file_date_updated":"2020-07-14T12:45:31Z","pubrep_id":"559","language":[{"iso":"eng"}],"ddc":["570"],"author":[{"full_name":"Hearn, Jack","last_name":"Hearn","first_name":"Jack"},{"full_name":"Stone, Graham","last_name":"Stone","first_name":"Graham"},{"full_name":"Bunnefeld, Lynsey","first_name":"Lynsey","last_name":"Bunnefeld"},{"first_name":"James","last_name":"Nicholls","full_name":"Nicholls, James"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"},{"full_name":"Lohse, Konrad","last_name":"Lohse","first_name":"Konrad"}],"page":"198 - 211","has_accepted_license":"1","_id":"2170","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"1","department":[{"_id":"NiBa"}],"publication":"Molecular Ecology","day":"01","title":"Likelihood-based inference of population history from low-coverage de novo genome assemblies","date_published":"2014-01-01T00:00:00Z","article_processing_charge":"No","isi":1,"acknowledgement":"This work was funded by NERC grants to G Stone, J Nicholls, K Lohse and N Barton (NE/J010499, NBAF375, NE/E014453/1 and NER/B/S2003/00856).","volume":23,"publist_id":"4814","month":"01","external_id":{"isi":["000330950900017"]},"date_updated":"2025-09-29T11:38:51Z","quality_controlled":"1","publisher":"Wiley-Blackwell","abstract":[{"lang":"eng","text":" Short-read sequencing technologies have in principle made it feasible to draw detailed inferences about the recent history of any organism. In practice, however, this remains challenging due to the difficulty of genome assembly in most organisms and the lack of statistical methods powerful enough to discriminate between recent, nonequilibrium histories. We address both the assembly and inference challenges. We develop a bioinformatic pipeline for generating outgroup-rooted alignments of orthologous sequence blocks from de novo low-coverage short-read data for a small number of genomes, and show how such sequence blocks can be used to fit explicit models of population divergence and admixture in a likelihood framework. To illustrate our approach, we reconstruct the Pleistocene history of an oak-feeding insect (the oak gallwasp Biorhiza pallida), which, in common with many other taxa, was restricted during Pleistocene ice ages to a longitudinal series of southern refugia spanning the Western Palaearctic. Our analysis of sequence blocks sampled from a single genome from each of three major glacial refugia reveals support for an unexpected history dominated by recent admixture. Despite the fact that 80% of the genome is affected by admixture during the last glacial cycle, we are able to infer the deeper divergence history of these populations. These inferences are robust to variation in block length, mutation model and the sampling location of individual genomes within refugia. This combination of de novo assembly and numerical likelihood calculation provides a powerful framework for estimating recent population history that can be applied to any organism without the need for prior genetic resources."}],"citation":{"mla":"Hearn, Jack, et al. “Likelihood-Based Inference of Population History from Low-Coverage de Novo Genome Assemblies.” <i>Molecular Ecology</i>, vol. 23, no. 1, Wiley-Blackwell, 2014, pp. 198–211, doi:<a href=\"https://doi.org/10.1111/mec.12578\">10.1111/mec.12578</a>.","ista":"Hearn J, Stone G, Bunnefeld L, Nicholls J, Barton NH, Lohse K. 2014. Likelihood-based inference of population history from low-coverage de novo genome assemblies. Molecular Ecology. 23(1), 198–211.","short":"J. Hearn, G. Stone, L. Bunnefeld, J. Nicholls, N.H. Barton, K. Lohse, Molecular Ecology 23 (2014) 198–211.","apa":"Hearn, J., Stone, G., Bunnefeld, L., Nicholls, J., Barton, N. H., &#38; Lohse, K. (2014). Likelihood-based inference of population history from low-coverage de novo genome assemblies. <i>Molecular Ecology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/mec.12578\">https://doi.org/10.1111/mec.12578</a>","chicago":"Hearn, Jack, Graham Stone, Lynsey Bunnefeld, James Nicholls, Nicholas H Barton, and Konrad Lohse. “Likelihood-Based Inference of Population History from Low-Coverage de Novo Genome Assemblies.” <i>Molecular Ecology</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1111/mec.12578\">https://doi.org/10.1111/mec.12578</a>.","ama":"Hearn J, Stone G, Bunnefeld L, Nicholls J, Barton NH, Lohse K. Likelihood-based inference of population history from low-coverage de novo genome assemblies. <i>Molecular Ecology</i>. 2014;23(1):198-211. doi:<a href=\"https://doi.org/10.1111/mec.12578\">10.1111/mec.12578</a>","ieee":"J. Hearn, G. Stone, L. Bunnefeld, J. Nicholls, N. H. Barton, and K. Lohse, “Likelihood-based inference of population history from low-coverage de novo genome assemblies,” <i>Molecular Ecology</i>, vol. 23, no. 1. Wiley-Blackwell, pp. 198–211, 2014."},"scopus_import":"1","oa_version":"Submitted Version","type":"journal_article","status":"public","related_material":{"record":[{"id":"9754","relation":"research_data","status":"public"}]}},{"day":"01","corr_author":"1","publication":"Genetics","ec_funded":1,"department":[{"_id":"NiBa"}],"issue":"2","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"2174","page":"749 - 767","author":[{"full_name":"De Vladar, Harold","first_name":"Harold","last_name":"De Vladar"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"doi":"10.1534/genetics.113.159111","publication_status":"published","oa":1,"intvolume":"       197","year":"2014","date_created":"2018-12-11T11:56:08Z","type":"journal_article","status":"public","oa_version":"Submitted Version","citation":{"apa":"De Vladar, H., &#38; Barton, N. H. (2014). Stability and response of polygenic traits to stabilizing selection and mutation. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.113.159111\">https://doi.org/10.1534/genetics.113.159111</a>","chicago":"De Vladar, Harold, and Nicholas H Barton. “Stability and Response of Polygenic Traits to Stabilizing Selection and Mutation.” <i>Genetics</i>. Genetics Society of America, 2014. <a href=\"https://doi.org/10.1534/genetics.113.159111\">https://doi.org/10.1534/genetics.113.159111</a>.","mla":"De Vladar, Harold, and Nicholas H. Barton. “Stability and Response of Polygenic Traits to Stabilizing Selection and Mutation.” <i>Genetics</i>, vol. 197, no. 2, Genetics Society of America, 2014, pp. 749–67, doi:<a href=\"https://doi.org/10.1534/genetics.113.159111\">10.1534/genetics.113.159111</a>.","ista":"De Vladar H, Barton NH. 2014. Stability and response of polygenic traits to stabilizing selection and mutation. Genetics. 197(2), 749–767.","short":"H. De Vladar, N.H. Barton, Genetics 197 (2014) 749–767.","ieee":"H. De Vladar and N. H. Barton, “Stability and response of polygenic traits to stabilizing selection and mutation,” <i>Genetics</i>, vol. 197, no. 2. Genetics Society of America, pp. 749–767, 2014.","ama":"De Vladar H, Barton NH. Stability and response of polygenic traits to stabilizing selection and mutation. <i>Genetics</i>. 2014;197(2):749-767. doi:<a href=\"https://doi.org/10.1534/genetics.113.159111\">10.1534/genetics.113.159111</a>"},"scopus_import":"1","abstract":[{"lang":"eng","text":"When polygenic traits are under stabilizing selection, many different combinations of alleles allow close adaptation to the optimum. If alleles have equal effects, all combinations that result in the same deviation from the optimum are equivalent. Furthermore, the genetic variance that is maintained by mutation-selection balance is 2μ/S per locus, where μ is the mutation rate and S the strength of stabilizing selection. In reality, alleles vary in their effects, making the fitness landscape asymmetric and complicating analysis of the equilibria. We show that that the resulting genetic variance depends on the fraction of alleles near fixation, which contribute by 2μ/S, and on the total mutational effects of alleles that are at intermediate frequency. The inpplayfi between stabilizing selection and mutation leads to a sharp transition: alleles with effects smaller than a threshold value of 2 remain polymorphic, whereas those with larger effects are fixed. The genetic load in equilibrium is less than for traits of equal effects, and the fitness equilibria are more similar. We find p the optimum is displaced, alleles with effects close to the threshold value sweep first, and their rate of increase is bounded by Long-term response leads in general to well-adapted traits, unlike the case of equal effects that often end up at a suboptimal fitness peak. However, the particular peaks to which the populations converge are extremely sensitive to the initial states and to the speed of the shift of the optimum trait value."}],"publisher":"Genetics Society of America","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1404.1017"}],"external_id":{"arxiv":["1404.1017"],"isi":["000338697000027"]},"quality_controlled":"1","date_updated":"2025-09-29T11:37:14Z","month":"06","volume":197,"publist_id":"4809","title":"Stability and response of polygenic traits to stabilizing selection and mutation","isi":1,"arxiv":1,"date_published":"2014-06-01T00:00:00Z","article_processing_charge":"No"},{"doi":"10.1103/PhysRevE.89.032701","publication_status":"published","oa":1,"intvolume":"        89","author":[{"last_name":"Kollár","first_name":"Richard","full_name":"Kollár, Richard"},{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","full_name":"Bod'ová, Katarína","last_name":"Bod'ová","first_name":"Katarína","orcid":"0000-0002-7214-0171"},{"last_name":"Nosek","first_name":"Jozef","full_name":"Nosek, Jozef"},{"last_name":"Tomáška","first_name":"Ľubomír","full_name":"Tomáška, Ľubomír"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:54:35Z","year":"2014","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","day":"04","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"issue":"3","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"1896","month":"03","external_id":{"arxiv":["1402.0430"],"isi":["000332274100002"]},"date_updated":"2025-09-29T13:03:34Z","title":"Mathematical model of alternative mechanism of telomere length maintenance","isi":1,"acknowledgement":"The work was supported by the VEGA Grant No. 1/0459/13 (R.K. and K.B.).","arxiv":1,"date_published":"2014-03-04T00:00:00Z","article_processing_charge":"No","volume":89,"publist_id":"5198","type":"journal_article","status":"public","publisher":"American Institute of Physics","main_file_link":[{"url":"http://arxiv.org/abs/1402.0430","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"text":"Biopolymer length regulation is a complex process that involves a large number of biological, chemical, and physical subprocesses acting simultaneously across multiple spatial and temporal scales. An illustrative example important for genomic stability is the length regulation of telomeres - nucleoprotein structures at the ends of linear chromosomes consisting of tandemly repeated DNA sequences and a specialized set of proteins. Maintenance of telomeres is often facilitated by the enzyme telomerase but, particularly in telomerase-free systems, the maintenance of chromosomal termini depends on alternative lengthening of telomeres (ALT) mechanisms mediated by recombination. Various linear and circular DNA structures were identified to participate in ALT, however, dynamics of the whole process is still poorly understood. We propose a chemical kinetics model of ALT with kinetic rates systematically derived from the biophysics of DNA diffusion and looping. The reaction system is reduced to a coagulation-fragmentation system by quasi-steady-state approximation. The detailed treatment of kinetic rates yields explicit formulas for expected size distributions of telomeres that demonstrate the key role played by the J factor, a quantitative measure of bending of polymers. The results are in agreement with experimental data and point out interesting phenomena: an appearance of very long telomeric circles if the total telomere density exceeds a critical value (excess mass) and a nonlinear response of the telomere size distributions to the amount of telomeric DNA in the system. The results can be of general importance for understanding dynamics of telomeres in telomerase-independent systems as this mode of telomere maintenance is similar to the situation in tumor cells lacking telomerase activity. Furthermore, due to its universality, the model may also serve as a prototype of an interaction between linear and circular DNA structures in various settings.","lang":"eng"}],"citation":{"ama":"Kollár R, Bodova K, Nosek J, Tomáška Ľ. Mathematical model of alternative mechanism of telomere length maintenance. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. 2014;89(3). doi:<a href=\"https://doi.org/10.1103/PhysRevE.89.032701\">10.1103/PhysRevE.89.032701</a>","ieee":"R. Kollár, K. Bodova, J. Nosek, and Ľ. Tomáška, “Mathematical model of alternative mechanism of telomere length maintenance,” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 89, no. 3. American Institute of Physics, 2014.","short":"R. Kollár, K. Bodova, J. Nosek, Ľ. Tomáška, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014).","ista":"Kollár R, Bodova K, Nosek J, Tomáška Ľ. 2014. Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. 89(3), 032701.","mla":"Kollár, Richard, et al. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 89, no. 3, 032701, American Institute of Physics, 2014, doi:<a href=\"https://doi.org/10.1103/PhysRevE.89.032701\">10.1103/PhysRevE.89.032701</a>.","chicago":"Kollár, Richard, Katarina Bodova, Jozef Nosek, and Ľubomír Tomáška. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics, 2014. <a href=\"https://doi.org/10.1103/PhysRevE.89.032701\">https://doi.org/10.1103/PhysRevE.89.032701</a>.","apa":"Kollár, R., Bodova, K., Nosek, J., &#38; Tomáška, Ľ. (2014). Mathematical model of alternative mechanism of telomere length maintenance. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.89.032701\">https://doi.org/10.1103/PhysRevE.89.032701</a>"},"article_number":"032701","scopus_import":"1"},{"language":[{"iso":"eng"}],"author":[{"id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","full_name":"Weissman, Daniel","last_name":"Weissman","first_name":"Daniel"},{"full_name":"Hallatschek, Oskar","last_name":"Hallatschek","first_name":"Oskar"}],"publication_status":"published","oa":1,"project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"doi":"10.1534/genetics.113.160705","intvolume":"       196","year":"2014","date_created":"2018-12-11T11:54:39Z","day":"01","corr_author":"1","publication":"Genetics","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"1908","issue":"4","department":[{"_id":"NiBa"}],"ec_funded":1,"page":"1167 - 1183","external_id":{"arxiv":["1307.0737"],"isi":["000334179300022"]},"quality_controlled":"1","date_updated":"2025-09-29T12:27:03Z","month":"04","volume":196,"publist_id":"5187","title":"The rate of adaptation in large sexual populations with linear chromosomes","article_processing_charge":"No","arxiv":1,"date_published":"2014-04-01T00:00:00Z","isi":1,"type":"journal_article","status":"public","abstract":[{"text":"In large populations, multiple beneficial mutations may be simultaneously spreading. In asexual populations, these mutations must either arise on the same background or compete against each other. In sexual populations, recombination can bring together beneficial alleles from different backgrounds, but tightly linked alleles may still greatly interfere with each other. We show for well-mixed populations that when this interference is strong, the genome can be seen as consisting of many effectively asexual stretches linked together. The rate at which beneficial alleles fix is thus roughly proportional to the rate of recombination and depends only logarithmically on the mutation supply and the strength of selection. Our scaling arguments also allow us to predict, with reasonable accuracy, the fitness distribution of fixed mutations when the mutational effect sizes are broad. We focus on the regime in which crossovers occur more frequently than beneficial mutations, as is likely to be the case for many natural populations.","lang":"eng"}],"citation":{"apa":"Weissman, D., &#38; Hallatschek, O. (2014). The rate of adaptation in large sexual populations with linear chromosomes. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.113.160705\">https://doi.org/10.1534/genetics.113.160705</a>","chicago":"Weissman, Daniel, and Oskar Hallatschek. “The Rate of Adaptation in Large Sexual Populations with Linear Chromosomes.” <i>Genetics</i>. Genetics Society of America, 2014. <a href=\"https://doi.org/10.1534/genetics.113.160705\">https://doi.org/10.1534/genetics.113.160705</a>.","mla":"Weissman, Daniel, and Oskar Hallatschek. “The Rate of Adaptation in Large Sexual Populations with Linear Chromosomes.” <i>Genetics</i>, vol. 196, no. 4, Genetics Society of America, 2014, pp. 1167–83, doi:<a href=\"https://doi.org/10.1534/genetics.113.160705\">10.1534/genetics.113.160705</a>.","ista":"Weissman D, Hallatschek O. 2014. The rate of adaptation in large sexual populations with linear chromosomes. Genetics. 196(4), 1167–1183.","short":"D. Weissman, O. Hallatschek, Genetics 196 (2014) 1167–1183.","ieee":"D. Weissman and O. Hallatschek, “The rate of adaptation in large sexual populations with linear chromosomes,” <i>Genetics</i>, vol. 196, no. 4. Genetics Society of America, pp. 1167–1183, 2014.","ama":"Weissman D, Hallatschek O. The rate of adaptation in large sexual populations with linear chromosomes. <i>Genetics</i>. 2014;196(4):1167-1183. doi:<a href=\"https://doi.org/10.1534/genetics.113.160705\">10.1534/genetics.113.160705</a>"},"scopus_import":"1","oa_version":"Submitted Version","publisher":"Genetics Society of America","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1307.0737"}]}]