--- _id: '2719' abstract: - lang: eng text: Prediction of the evolutionary process is a long standing problem both in the theory of evolutionary biology and evolutionary computation (EC). It has long been realized that heritable variation is crucial to both the response to selection and the success of genetic algorithms. However, not all variation contributes in the same way to the response. Quantitative genetics has developed a large body of work trying to estimate and understand how different components of the variance in fitness in the population contribute to the response to selection. We illustrate how to apply some concepts of quantitative genetics to the analysis of genetic algorithms. In particular, we derive estimates for the short term prediction of the response to selection and we use variance decomposition to gain insight on local aspects of the landscape. Finally, we propose a new population based genetic algorithm that uses these methods to improve its operation. author: - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Paixao T, Barton NH. A variance decomposition approach to the analysis of genetic algorithms. In: Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation. ACM; 2013:845-852. doi:10.1145/2463372.2463470' apa: 'Paixao, T., & Barton, N. H. (2013). A variance decomposition approach to the analysis of genetic algorithms. In Proceedings of the 15th annual conference on Genetic and evolutionary computation (pp. 845–852). Amsterdam, Netherlands: ACM. https://doi.org/10.1145/2463372.2463470' chicago: Paixao, Tiago, and Nicholas H Barton. “A Variance Decomposition Approach to the Analysis of Genetic Algorithms.” In Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, 845–52. ACM, 2013. https://doi.org/10.1145/2463372.2463470. ieee: T. Paixao and N. H. Barton, “A variance decomposition approach to the analysis of genetic algorithms,” in Proceedings of the 15th annual conference on Genetic and evolutionary computation, Amsterdam, Netherlands, 2013, pp. 845–852. ista: 'Paixao T, Barton NH. 2013. A variance decomposition approach to the analysis of genetic algorithms. Proceedings of the 15th annual conference on Genetic and evolutionary computation. GECCO: Genetic and evolutionary computation conference, 845–852.' mla: Paixao, Tiago, and Nicholas H. Barton. “A Variance Decomposition Approach to the Analysis of Genetic Algorithms.” Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 845–52, doi:10.1145/2463372.2463470. short: T. Paixao, N.H. Barton, in:, Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 845–852. conference: end_date: 2013-07-10 location: Amsterdam, Netherlands name: 'GECCO: Genetic and evolutionary computation conference' start_date: 2013-07-06 date_created: 2018-12-11T11:59:15Z date_published: 2013-07-01T00:00:00Z date_updated: 2021-01-12T06:59:15Z day: '01' department: - _id: NiBa - _id: CaGu doi: 10.1145/2463372.2463470 ec_funded: 1 language: - iso: eng month: '07' oa_version: None page: 845 - 852 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Proceedings of the 15th annual conference on Genetic and evolutionary computation publication_status: published publisher: ACM publist_id: '4173' quality_controlled: '1' scopus_import: 1 status: public title: A variance decomposition approach to the analysis of genetic algorithms type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2720' abstract: - lang: eng text: 'Knowledge of the rate and fitness effects of mutations is essential for understanding the process of evolution. Mutations are inherently difficult to study because they are rare and are frequently eliminated by natural selection. In the ciliate Tetrahymena thermophila, mutations can accumulate in the germline genome without being exposed to selection. We have conducted a mutation accumulation (MA) experiment in this species. Assuming that all mutations are deleterious and have the same effect, we estimate that the deleterious mutation rate per haploid germline genome per generation is U = 0.0047 (95% credible interval: 0.0015, 0.0125), and that germline mutations decrease fitness by s = 11% when expressed in a homozygous state (95% CI: 4.4%, 27%). We also estimate that deleterious mutations are partially recessive on average (h = 0.26; 95% CI: –0.022, 0.62) and that the rate of lethal mutations is <10% of the deleterious mutation rate. Comparisons between the observed evolutionary responses in the germline and somatic genomes and the results from individual-based simulations of MA suggest that the two genomes have similar mutational parameters. These are the first estimates of the deleterious mutation rate and fitness effects from the eukaryotic supergroup Chromalveolata and are within the range of those of other eukaryotes.' article_processing_charge: No author: - first_name: Hongan full_name: Long, Hongan last_name: Long - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Ricardo full_name: Azevedo, Ricardo last_name: Azevedo - first_name: Rebecca full_name: Zufall, Rebecca last_name: Zufall citation: ama: Long H, Paixao T, Azevedo R, Zufall R. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics. 2013;195(2):527-540. doi:10.1534/genetics.113.153536 apa: Long, H., Paixao, T., Azevedo, R., & Zufall, R. (2013). Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.113.153536 chicago: Long, Hongan, Tiago Paixao, Ricardo Azevedo, and Rebecca Zufall. “Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.” Genetics. Genetics Society of America, 2013. https://doi.org/10.1534/genetics.113.153536. ieee: H. Long, T. Paixao, R. Azevedo, and R. Zufall, “Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila,” Genetics, vol. 195, no. 2. Genetics Society of America, pp. 527–540, 2013. ista: Long H, Paixao T, Azevedo R, Zufall R. 2013. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics. 195(2), 527–540. mla: Long, Hongan, et al. “Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.” Genetics, vol. 195, no. 2, Genetics Society of America, 2013, pp. 527–40, doi:10.1534/genetics.113.153536. short: H. Long, T. Paixao, R. Azevedo, R. Zufall, Genetics 195 (2013) 527–540. date_created: 2018-12-11T11:59:15Z date_published: 2013-10-01T00:00:00Z date_updated: 2021-01-12T06:59:16Z day: '01' department: - _id: NiBa - _id: CaGu doi: 10.1534/genetics.113.153536 ec_funded: 1 external_id: pmid: - '23934880' intvolume: ' 195' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3781978/ month: '10' oa: 1 oa_version: Submitted Version page: 527-540 pmid: 1 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '4172' quality_controlled: '1' scopus_import: 1 status: public title: Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 195 year: '2013' ... --- _id: '2817' abstract: - lang: eng text: The basic idea of evolutionary game theory is that payoff determines reproductive rate. Successful individuals have a higher payoff and produce more offspring. But in evolutionary and ecological situations there is not only reproductive rate but also carrying capacity. Individuals may differ in their exposure to density limiting effects. Here we explore an alternative approach to evolutionary game theory by assuming that the payoff from the game determines the carrying capacity of individual phenotypes. Successful strategies are less affected by density limitation (crowding) and reach higher equilibrium abundance. We demonstrate similarities and differences between our framework and the standard replicator equation. Our equation is defined on the positive orthant, instead of the simplex, but has the same equilibrium points as the replicator equation. Linear stability analysis produces the classical conditions for asymptotic stability of pure strategies, but the stability properties of internal equilibria can differ in the two frameworks. For example, in a two-strategy game with an internal equilibrium that is always stable under the replicator equation, the corresponding equilibrium can be unstable in the new framework resulting in a limit cycle. author: - first_name: Sebastian full_name: Novak, Sebastian id: 461468AE-F248-11E8-B48F-1D18A9856A87 last_name: Novak orcid: 0000-0002-2519-824X - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Novak S, Chatterjee K, Nowak M. Density games. Journal of Theoretical Biology. 2013;334:26-34. doi:10.1016/j.jtbi.2013.05.029 apa: Novak, S., Chatterjee, K., & Nowak, M. (2013). Density games. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2013.05.029 chicago: Novak, Sebastian, Krishnendu Chatterjee, and Martin Nowak. “Density Games.” Journal of Theoretical Biology. Elsevier, 2013. https://doi.org/10.1016/j.jtbi.2013.05.029. ieee: S. Novak, K. Chatterjee, and M. Nowak, “Density games,” Journal of Theoretical Biology, vol. 334. Elsevier, pp. 26–34, 2013. ista: Novak S, Chatterjee K, Nowak M. 2013. Density games. Journal of Theoretical Biology. 334, 26–34. mla: Novak, Sebastian, et al. “Density Games.” Journal of Theoretical Biology, vol. 334, Elsevier, 2013, pp. 26–34, doi:10.1016/j.jtbi.2013.05.029. short: S. Novak, K. Chatterjee, M. Nowak, Journal of Theoretical Biology 334 (2013) 26–34. date_created: 2018-12-11T11:59:45Z date_published: 2013-10-07T00:00:00Z date_updated: 2025-05-28T11:42:43Z day: '07' ddc: - '000' department: - _id: NiBa - _id: KrCh doi: 10.1016/j.jtbi.2013.05.029 ec_funded: 1 file: - access_level: open_access checksum: 3c29059ab03a4b8f97a07646b817ddbb content_type: application/pdf creator: system date_created: 2018-12-12T10:14:54Z date_updated: 2020-07-14T12:45:49Z file_id: '5110' file_name: IST-2016-400-v1+1_1-s2.0-S0022519313002609-main.pdf file_size: 834604 relation: main_file file_date_updated: 2020-07-14T12:45:49Z has_accepted_license: '1' intvolume: ' 334' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 26 - 34 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Journal of Theoretical Biology publication_status: published publisher: Elsevier publist_id: '3984' pubrep_id: '400' quality_controlled: '1' scopus_import: 1 status: public title: Density games tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 334 year: '2013' ... --- _id: '2823' abstract: - lang: eng text: The primary goal of restoration is to create self-sustaining ecological communities that are resilient to periodic disturbance. Currently, little is known about how restored communities respond to disturbance events such as fire and how this response compares to remnant vegetation. Following the 2003 fires in south-eastern Australia we examined the post-fire response of revegetation plantings and compared this to remnant vegetation. Ten burnt and 10 unburnt (control) sites were assessed for each of three types of vegetation (direct seeding revegetation, revegetation using nursery seedlings (tubestock) and remnant woodland). Sixty sampling sites were surveyed 6months after fire to quantify the initial survival of mid- and overstorey plant species in each type of vegetation. Three and 5years after fire all sites were resurveyed to assess vegetation structure, species diversity and vigour, as well as indicators of soil function. Overall, revegetation showed high (>60%) post-fire survival, but this varied among species depending on regeneration strategy (obligate seeder or resprouter). The native ground cover, mid- and overstorey in both types of plantings showed rapid recovery of vegetation structure and cover within 3years of fire. This recovery was similar to the burnt remnant woodlands. Non-native (exotic) ground cover initially increased after fire, but was no different in burnt and unburnt sites 5years after fire. Fire had no effect on species richness, but burnt direct seeding sites had reduced species diversity (Simpson's Diversity Index) while diversity was higher in burnt remnant woodlands. Indices of soil function in all types of vegetation had recovered to levels found in unburnt sites 5years after fire. These results indicate that even young revegetation (stands <10years old) showed substantial recovery from disturbance by fire. This suggests that revegetation can provide an important basis for restoring woodland communities in the fire-prone Australian environment. author: - first_name: Melinda full_name: Pickup, Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - first_name: Susie full_name: Wilson, Susie last_name: Wilson - first_name: David full_name: Freudenberger, David last_name: Freudenberger - first_name: Nick full_name: Nicholls, Nick last_name: Nicholls - first_name: Lori full_name: Gould, Lori last_name: Gould - first_name: Sarah full_name: Hnatiuk, Sarah last_name: Hnatiuk - first_name: Jeni full_name: Delandre, Jeni last_name: Delandre citation: ama: Pickup M, Wilson S, Freudenberger D, et al. Post-fire recovery of revegetated woodland communities in south-eastern Australia. Austral Ecology. 2013;38(3):300-312. doi:10.1111/j.1442-9993.2012.02404.x apa: Pickup, M., Wilson, S., Freudenberger, D., Nicholls, N., Gould, L., Hnatiuk, S., & Delandre, J. (2013). Post-fire recovery of revegetated woodland communities in south-eastern Australia. Austral Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1442-9993.2012.02404.x chicago: Pickup, Melinda, Susie Wilson, David Freudenberger, Nick Nicholls, Lori Gould, Sarah Hnatiuk, and Jeni Delandre. “Post-Fire Recovery of Revegetated Woodland Communities in South-Eastern Australia.” Austral Ecology. Wiley-Blackwell, 2013. https://doi.org/10.1111/j.1442-9993.2012.02404.x. ieee: M. Pickup et al., “Post-fire recovery of revegetated woodland communities in south-eastern Australia,” Austral Ecology, vol. 38, no. 3. Wiley-Blackwell, pp. 300–312, 2013. ista: Pickup M, Wilson S, Freudenberger D, Nicholls N, Gould L, Hnatiuk S, Delandre J. 2013. Post-fire recovery of revegetated woodland communities in south-eastern Australia. Austral Ecology. 38(3), 300–312. mla: Pickup, Melinda, et al. “Post-Fire Recovery of Revegetated Woodland Communities in South-Eastern Australia.” Austral Ecology, vol. 38, no. 3, Wiley-Blackwell, 2013, pp. 300–12, doi:10.1111/j.1442-9993.2012.02404.x. short: M. Pickup, S. Wilson, D. Freudenberger, N. Nicholls, L. Gould, S. Hnatiuk, J. Delandre, Austral Ecology 38 (2013) 300–312. date_created: 2018-12-11T11:59:47Z date_published: 2013-05-01T00:00:00Z date_updated: 2021-01-12T06:59:58Z day: '01' department: - _id: NiBa doi: 10.1111/j.1442-9993.2012.02404.x intvolume: ' 38' issue: '3' language: - iso: eng month: '05' oa_version: None page: 300 - 312 publication: Austral Ecology publication_status: published publisher: Wiley-Blackwell publist_id: '3978' quality_controlled: '1' scopus_import: 1 status: public title: Post-fire recovery of revegetated woodland communities in south-eastern Australia type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 38 year: '2013' ... --- _id: '2842' abstract: - lang: eng text: 'We outline two approaches to inference of neighbourhood size, N, and dispersal rate, σ2, based on either allele frequencies or on the lengths of sequence blocks that are shared between genomes. Over intermediate timescales (10-100 generations, say), populations that live in two dimensions approach a quasi-equilibrium that is independent of both their local structure and their deeper history. Over such scales, the standardised covariance of allele frequencies (i.e. pairwise FS T) falls with the logarithm of distance, and depends only on neighbourhood size, N, and a ''local scale'', κ; the rate of gene flow, σ2, cannot be inferred. We show how spatial correlations can be accounted for, assuming a Gaussian distribution of allele frequencies, giving maximum likelihood estimates of N and κ. Alternatively, inferences can be based on the distribution of the lengths of sequence that are identical between blocks of genomes: long blocks (>0.1 cM, say) tell us about intermediate timescales, over which we assume a quasi-equilibrium. For large neighbourhood size, the distribution of long blocks is given directly by the classical Wright-Malécot formula; this relationship can be used to infer both N and σ2. With small neighbourhood size, there is an appreciable chance that recombinant lineages will coalesce back before escaping into the distant past. For this case, we show that if genomes are sampled from some distance apart, then the distribution of lengths of blocks that are identical in state is geometric, with a mean that depends on N and σ2.' author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Alison full_name: Etheridge, Alison last_name: Etheridge - first_name: Jerome full_name: Kelleher, Jerome last_name: Kelleher - first_name: Amandine full_name: Véber, Amandine last_name: Véber citation: ama: 'Barton NH, Etheridge A, Kelleher J, Véber A. Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks. Theoretical Population Biology. 2013;87(1):105-119. doi:10.1016/j.tpb.2013.03.001' apa: 'Barton, N. H., Etheridge, A., Kelleher, J., & Véber, A. (2013). Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks. Theoretical Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2013.03.001' chicago: 'Barton, Nicholas H, Alison Etheridge, Jerome Kelleher, and Amandine Véber. “Inference in Two Dimensions: Allele Frequencies versus Lengths of Shared Sequence Blocks.” Theoretical Population Biology. Elsevier, 2013. https://doi.org/10.1016/j.tpb.2013.03.001.' ieee: 'N. H. Barton, A. Etheridge, J. Kelleher, and A. Véber, “Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks,” Theoretical Population Biology, vol. 87, no. 1. Elsevier, pp. 105–119, 2013.' ista: 'Barton NH, Etheridge A, Kelleher J, Véber A. 2013. Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks. Theoretical Population Biology. 87(1), 105–119.' mla: 'Barton, Nicholas H., et al. “Inference in Two Dimensions: Allele Frequencies versus Lengths of Shared Sequence Blocks.” Theoretical Population Biology, vol. 87, no. 1, Elsevier, 2013, pp. 105–19, doi:10.1016/j.tpb.2013.03.001.' short: N.H. Barton, A. Etheridge, J. Kelleher, A. Véber, Theoretical Population Biology 87 (2013) 105–119. date_created: 2018-12-11T11:59:53Z date_published: 2013-08-01T00:00:00Z date_updated: 2021-01-12T07:00:09Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1016/j.tpb.2013.03.001 ec_funded: 1 file: - access_level: open_access checksum: 9bf9d9a6fd03dd9df50906891f393bf8 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:33Z date_updated: 2020-07-14T12:45:50Z file_id: '5288' file_name: IST-2016-558-v1+1_inference_revised3101NB.pdf file_size: 1554712 relation: main_file - access_level: open_access checksum: 2bceddb76edacd0cd5fad73051e2a928 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:34Z date_updated: 2020-07-14T12:45:50Z file_id: '5289' file_name: IST-2016-558-v1+2_inference_revised3101NBApp.pdf file_size: 822964 relation: main_file file_date_updated: 2020-07-14T12:45:50Z has_accepted_license: '1' intvolume: ' 87' issue: '1' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 105 - 119 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Theoretical Population Biology publication_status: published publisher: Elsevier publist_id: '3953' pubrep_id: '558' quality_controlled: '1' scopus_import: 1 status: public title: 'Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 87 year: '2013' ... --- _id: '2907' abstract: - lang: eng text: 'Sex and recombination are among the most striking features of the living world, and they play a crucial role in allowing the evolution of complex adaptation. The sharing of genomes through the sexual union of different individuals requires elaborate behavioral and physiological adaptations. At the molecular level, the alignment of two DNA double helices, followed by their precise cutting and rejoining, is an extraordinary feat. Sex and recombination have diverse—and often surprising—evolutionary consequences: distinct sexes, elaborate mating displays, selfish genetic elements, and so on.' author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Barton NH. Recombination and sex. In: The Princeton Guide to Evolution. Princeton University Press; 2013:328-333.' apa: Barton, N. H. (2013). Recombination and sex. In The Princeton Guide to Evolution (pp. 328–333). Princeton University Press. chicago: Barton, Nicholas H. “Recombination and Sex.” In The Princeton Guide to Evolution, 328–33. Princeton University Press, 2013. ieee: N. H. Barton, “Recombination and sex,” in The Princeton Guide to Evolution, Princeton University Press, 2013, pp. 328–333. ista: 'Barton NH. 2013.Recombination and sex. In: The Princeton Guide to Evolution. , 328–333.' mla: Barton, Nicholas H. “Recombination and Sex.” The Princeton Guide to Evolution, Princeton University Press, 2013, pp. 328–33. short: N.H. Barton, in:, The Princeton Guide to Evolution, Princeton University Press, 2013, pp. 328–333. date_created: 2018-12-11T12:00:16Z date_published: 2013-11-04T00:00:00Z date_updated: 2021-01-12T07:00:37Z day: '04' ddc: - '576' department: - _id: NiBa file: - access_level: open_access checksum: 8332ca9cb40f7e66d1006b175ce36b60 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: system date_created: 2018-12-12T10:16:47Z date_updated: 2020-07-14T12:45:52Z file_id: '5237' file_name: IST-2013-119-v1+1_IV.4_Recombination_and_Sex_Barton_1-13-13-e.docx file_size: 79838 relation: main_file - access_level: open_access checksum: 849f418620fb78d6ba23bb4f488ee93f content_type: application/pdf creator: system date_created: 2018-12-12T10:16:48Z date_updated: 2020-07-14T12:45:52Z file_id: '5238' file_name: IST-2017-119-v1+2_Barton_Recombination_Sex.pdf file_size: 144131 relation: main_file file_date_updated: 2020-07-14T12:45:52Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Submitted Version page: 328 - 333 publication: The Princeton Guide to Evolution publication_identifier: isbn: - '9780691149776' publication_status: published publisher: Princeton University Press publist_id: '3839' pubrep_id: '119' quality_controlled: '1' status: public title: Recombination and sex type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2908' abstract: - lang: eng text: 'Hybridization is an almost inevitable component of speciation, and its study can tell us much about that process. However, hybridization itself may have a negligible influence on the origin of species: on the one hand, universally favoured alleles spread readily across hybrid zones, whilst on the other, spatially heterogeneous selection causes divergence despite gene flow. Thus, narrow hybrid zones or occasional hybridisation may hardly affect the process of divergence.' author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Barton NH. Does hybridisation influence speciation?  . Journal of Evolutionary Biology. 2013;26(2):267-269. doi:10.1111/jeb.12015 apa: Barton, N. H. (2013). Does hybridisation influence speciation?  . Journal of Evolutionary Biology. Wiley-Blackwell. https://doi.org/10.1111/jeb.12015 chicago: Barton, Nicholas H. “Does Hybridisation Influence Speciation?  .” Journal of Evolutionary Biology. Wiley-Blackwell, 2013. https://doi.org/10.1111/jeb.12015. ieee: N. H. Barton, “Does hybridisation influence speciation?  ,” Journal of Evolutionary Biology, vol. 26, no. 2. Wiley-Blackwell, pp. 267–269, 2013. ista: Barton NH. 2013. Does hybridisation influence speciation?  . Journal of Evolutionary Biology. 26(2), 267–269. mla: Barton, Nicholas H. “Does Hybridisation Influence Speciation?  .” Journal of Evolutionary Biology, vol. 26, no. 2, Wiley-Blackwell, 2013, pp. 267–69, doi:10.1111/jeb.12015. short: N.H. Barton, Journal of Evolutionary Biology 26 (2013) 267–269. date_created: 2018-12-11T12:00:17Z date_published: 2013-01-17T00:00:00Z date_updated: 2021-01-12T07:00:37Z day: '17' ddc: - '576' department: - _id: NiBa doi: 10.1111/jeb.12015 file: - access_level: open_access checksum: 716e88714c3411cd0bd70928b14ea692 content_type: text/rtf creator: system date_created: 2018-12-12T10:09:38Z date_updated: 2020-07-14T12:45:52Z file_id: '4762' file_name: IST-2013-111-v1+1_Hybridisation_and_speciation_revised.rtf file_size: 13339 relation: main_file - access_level: open_access checksum: 957fd07c71c1b1eac2c65ae3311aca78 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:39Z date_updated: 2020-07-14T12:45:52Z file_id: '4763' file_name: IST-2017-111-v1+2_Hybridisation_and_speciation_revised.pdf file_size: 103437 relation: main_file file_date_updated: 2020-07-14T12:45:52Z has_accepted_license: '1' intvolume: ' 26' issue: '2' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 267 - 269 publication: Journal of Evolutionary Biology publication_status: published publisher: Wiley-Blackwell publist_id: '3835' pubrep_id: '111' quality_controlled: '1' scopus_import: 1 status: public title: 'Does hybridisation influence speciation? ' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 26 year: '2013' ... --- _id: '2909' abstract: - lang: eng text: "We survey a class of models for spatially structured populations\r\nwhich we have called spatial Λ-Fleming–Viot processes. They arise from a flexible\r\nframework for modelling in which the key innovation is that random genetic drift\r\nis driven by a Poisson point process of spatial ‘events’. We demonstrate how this\r\novercomes some of the obstructions to modelling populations which evolve in two-\r\n(and higher-) dimensional spatial continua, how its predictions match phenomena\r\nobserved in data and how it fits with classical models. Finally we outline some\r\ndirections for future research." article_processing_charge: No author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Alison full_name: Etheridge, Alison last_name: Etheridge - first_name: Amandine full_name: Véber, Amandine last_name: Véber citation: ama: Barton NH, Etheridge A, Véber A. Modelling evolution in a spatial continuum. Journal of Statistical Mechanics Theory and Experiment. 2013;2013(1). doi:10.1088/1742-5468/2013/01/P01002 apa: Barton, N. H., Etheridge, A., & Véber, A. (2013). Modelling evolution in a spatial continuum. Journal of Statistical Mechanics Theory and Experiment. IOP Publishing Ltd. https://doi.org/10.1088/1742-5468/2013/01/P01002 chicago: Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “Modelling Evolution in a Spatial Continuum.” Journal of Statistical Mechanics Theory and Experiment. IOP Publishing Ltd., 2013. https://doi.org/10.1088/1742-5468/2013/01/P01002. ieee: N. H. Barton, A. Etheridge, and A. Véber, “Modelling evolution in a spatial continuum,” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 1. IOP Publishing Ltd., 2013. ista: Barton NH, Etheridge A, Véber A. 2013. Modelling evolution in a spatial continuum. Journal of Statistical Mechanics Theory and Experiment. 2013(1). mla: Barton, Nicholas H., et al. “Modelling Evolution in a Spatial Continuum.” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 1, IOP Publishing Ltd., 2013, doi:10.1088/1742-5468/2013/01/P01002. short: N.H. Barton, A. Etheridge, A. Véber, Journal of Statistical Mechanics Theory and Experiment 2013 (2013). date_created: 2018-12-11T12:00:17Z date_published: 2013-01-16T00:00:00Z date_updated: 2021-01-12T07:00:37Z day: '16' ddc: - '570' department: - _id: NiBa doi: 10.1088/1742-5468/2013/01/P01002 ec_funded: 1 file: - access_level: open_access checksum: ce8a4424385b3086138a1e054e16e0e3 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:52Z date_updated: 2020-07-14T12:45:52Z file_id: '5242' file_name: IST-2016-557-v1+1_BEVrevised.pdf file_size: 702583 relation: main_file file_date_updated: 2020-07-14T12:45:52Z has_accepted_license: '1' intvolume: ' 2013' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Journal of Statistical Mechanics Theory and Experiment publication_status: published publisher: IOP Publishing Ltd. publist_id: '3834' pubrep_id: '557' quality_controlled: '1' scopus_import: 1 status: public title: Modelling evolution in a spatial continuum type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 2013 year: '2013' ... --- _id: '2910' abstract: - lang: eng text: "Coalescent simulation has become an indispensable tool in population genetics and many complex evolutionary scenarios have been incorporated into the basic algorithm. Despite many years of intense interest in spatial structure, however, there are no available methods to simulate the ancestry of a sample of genes that occupy a spatial continuum. This is mainly due to the severe technical problems encountered by the classical model of isolation\r\nby distance. A recently introduced model solves these technical problems and provides a solid theoretical basis for the study of populations evolving in continuous space. We present a detailed algorithm to simulate the coalescent process in this model, and provide an efficient implementation of a generalised version of this algorithm as a freely available Python module." author: - first_name: Jerome full_name: Kelleher, Jerome last_name: Kelleher - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Alison full_name: Etheridge, Alison last_name: Etheridge citation: ama: Kelleher J, Barton NH, Etheridge A. Coalescent simulation in continuous space. Bioinformatics. 2013;29(7):955-956. doi:10.1093/bioinformatics/btt067 apa: Kelleher, J., Barton, N. H., & Etheridge, A. (2013). Coalescent simulation in continuous space. Bioinformatics. Oxford University Press. https://doi.org/10.1093/bioinformatics/btt067 chicago: Kelleher, Jerome, Nicholas H Barton, and Alison Etheridge. “Coalescent Simulation in Continuous Space.” Bioinformatics. Oxford University Press, 2013. https://doi.org/10.1093/bioinformatics/btt067. ieee: J. Kelleher, N. H. Barton, and A. Etheridge, “Coalescent simulation in continuous space,” Bioinformatics, vol. 29, no. 7. Oxford University Press, pp. 955–956, 2013. ista: Kelleher J, Barton NH, Etheridge A. 2013. Coalescent simulation in continuous space. Bioinformatics. 29(7), 955–956. mla: Kelleher, Jerome, et al. “Coalescent Simulation in Continuous Space.” Bioinformatics, vol. 29, no. 7, Oxford University Press, 2013, pp. 955–56, doi:10.1093/bioinformatics/btt067. short: J. Kelleher, N.H. Barton, A. Etheridge, Bioinformatics 29 (2013) 955–956. date_created: 2018-12-11T12:00:17Z date_published: 2013-02-07T00:00:00Z date_updated: 2021-01-12T07:00:38Z day: '07' ddc: - '570' department: - _id: NiBa doi: 10.1093/bioinformatics/btt067 ec_funded: 1 file: - access_level: open_access checksum: a3b54d7477fac923815ac082403d9bd0 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:04Z date_updated: 2020-07-14T12:45:52Z file_id: '5189' file_name: IST-2016-556-v1+1_bioinformatics-2013.pdf file_size: 170197 relation: main_file file_date_updated: 2020-07-14T12:45:52Z has_accepted_license: '1' intvolume: ' 29' issue: '7' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 955 - 956 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Bioinformatics publication_status: published publisher: Oxford University Press publist_id: '3833' pubrep_id: '556' quality_controlled: '1' scopus_import: 1 status: public title: Coalescent simulation in continuous space type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2013' ... --- _id: '2944' abstract: - lang: eng text: 'We propose a two-step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters ancestral mutation rate and male mating skew have been estimated for the whole population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step, we estimate in this study the migration rates independently for clusters of demes putatively connected by migration. For large clusters (many migration rates), ABC faces the problem of too many summary statistics. We therefore assess by simulation if estimation per pair of demes is a valid alternative. We find that the trade-off between reduced dimensionality for the pairwise estimation on the one hand and lower accuracy due to the assumption of pairwise independence on the other depends on the number of migration rates to be inferred: the accuracy of the pairwise approach increases with the number of parameters, relative to the joint estimation approach. To distinguish between low and zero migration, we perform ABC-type model comparison between a model with migration and one without. Applying the approach to microsatellite data from Alpine ibex, we find no evidence for substantial gene flow via migration, except for one pair of demes in one direction.' acknowledged_ssus: - _id: ScienComp acknowledgement: This study has made use of the computational resources provided by IST Austria and the Edinburgh Compute and Data Facility (ECDF; http://www.ecdf.ed.ac.uk). The ECDF is partially supported by the eDIKT initiative (http://www.edikt.org.uk). S.A. acknowledges financial support by IST Austria, the Janggen-Pöhn Foundation, St. Gallen, the Roche Research Foundation, Basel, the University of Edinburgh in the form of a Torrance Studentship, and the Austrian Science Fund (FWF P21305-N13). author: - first_name: Simon full_name: Aeschbacher, Simon id: 2D35326E-F248-11E8-B48F-1D18A9856A87 last_name: Aeschbacher - first_name: Andreas full_name: Futschik, Andreas last_name: Futschik - first_name: Mark full_name: Beaumont, Mark last_name: Beaumont citation: ama: 'Aeschbacher S, Futschik A, Beaumont M. Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . Molecular Ecology. 2013;22(4):987-1002. doi:10.1111/mec.12165' apa: 'Aeschbacher, S., Futschik, A., & Beaumont, M. (2013). Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/mec.12165' chicago: 'Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. .” Molecular Ecology. Wiley-Blackwell, 2013. https://doi.org/10.1111/mec.12165.' ieee: 'S. Aeschbacher, A. Futschik, and M. Beaumont, “Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. ,” Molecular Ecology, vol. 22, no. 4. Wiley-Blackwell, pp. 987–1002, 2013.' ista: 'Aeschbacher S, Futschik A, Beaumont M. 2013. Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . Molecular Ecology. 22(4), 987–1002.' mla: 'Aeschbacher, Simon, et al. “Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. .” Molecular Ecology, vol. 22, no. 4, Wiley-Blackwell, 2013, pp. 987–1002, doi:10.1111/mec.12165.' short: S. Aeschbacher, A. Futschik, M. Beaumont, Molecular Ecology 22 (2013) 987–1002. date_created: 2018-12-11T12:00:28Z date_published: 2013-02-01T00:00:00Z date_updated: 2023-02-23T14:07:19Z day: '01' department: - _id: NiBa doi: 10.1111/mec.12165 intvolume: ' 22' issue: '4' language: - iso: eng month: '02' oa_version: None page: 987 - 1002 publication: Molecular Ecology publication_status: published publisher: Wiley-Blackwell publist_id: '3788' quality_controlled: '1' related_material: record: - id: '9758' relation: research_data status: public scopus_import: 1 status: public title: 'Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. ' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2013' ... --- _id: '10899' article_processing_charge: No author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Barton NH. Differentiation. In: Encyclopedia of Biodiversity. 2nd ed. Elsevier; 2013:508-515. doi:10.1016/b978-0-12-384719-5.00031-9' apa: Barton, N. H. (2013). Differentiation. In Encyclopedia of Biodiversity (2nd ed., pp. 508–515). Elsevier. https://doi.org/10.1016/b978-0-12-384719-5.00031-9 chicago: Barton, Nicholas H. “Differentiation.” In Encyclopedia of Biodiversity, 2nd ed., 508–15. Elsevier, 2013. https://doi.org/10.1016/b978-0-12-384719-5.00031-9. ieee: N. H. Barton, “Differentiation,” in Encyclopedia of Biodiversity, 2nd ed., Elsevier, 2013, pp. 508–515. ista: 'Barton NH. 2013.Differentiation. In: Encyclopedia of Biodiversity. , 508–515.' mla: Barton, Nicholas H. “Differentiation.” Encyclopedia of Biodiversity, 2nd ed., Elsevier, 2013, pp. 508–15, doi:10.1016/b978-0-12-384719-5.00031-9. short: N.H. Barton, in:, Encyclopedia of Biodiversity, 2nd ed., Elsevier, 2013, pp. 508–515. date_created: 2022-03-21T07:46:22Z date_published: 2013-01-01T00:00:00Z date_updated: 2022-06-20T09:18:06Z day: '01' department: - _id: NiBa doi: 10.1016/b978-0-12-384719-5.00031-9 edition: '2' keyword: - Adaptive landscape - Cline - Coalescent process - Gene flow - Hybrid zone - Local adaptation - Natural selection - Neutral theory - Population structure - Speciation language: - iso: eng month: '01' oa_version: None page: 508-515 publication: Encyclopedia of Biodiversity publication_identifier: isbn: - 978-0-12-384720-1 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Differentiation type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2287' abstract: - lang: eng text: Negative frequency-dependent selection should result in equal sex ratios in large populations of dioecious flowering plants, but deviations from equality are commonly reported. A variety of ecological and genetic factors can explain biased sex ratios, although the mechanisms involved are not well understood. Most dioecious species are long-lived and/or clonal complicating efforts to identify stages during the life cycle when biases develop. We investigated the demographic correlates of sex-ratio variation in two chromosome races of Rumex hastatulus, an annual, wind-pollinated colonizer of open habitats from the southern USA. We examined sex ratios in 46 populations and evaluated the hypothesis that the proximity of males in the local mating environment, through its influence on gametophytic selection, is the primary cause of female-biased sex ratios. Female-biased sex ratios characterized most populations of R. hastatulus (mean sex ratio = 0.62), with significant female bias in 89% of populations. Large, high-density populations had the highest proportion of females, whereas smaller, low-density populations had sex ratios closer to equality. Progeny sex ratios were more female biased when males were in closer proximity to females, a result consistent with the gametophytic selection hypothesis. Our results suggest that interactions between demographic and genetic factors are probably the main cause of female-biased sex ratios in R. hastatulus. The annual life cycle of this species may limit the scope for selection against males and may account for the weaker degree of bias in comparison with perennial Rumex species. author: - first_name: Melinda full_name: Pickup, Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - first_name: Spencer full_name: Barrett, Spencer last_name: Barrett citation: ama: Pickup M, Barrett S. The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant. Ecology and Evolution. 2013;3(3):629-639. doi:10.1002/ece3.465 apa: Pickup, M., & Barrett, S. (2013). The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant. Ecology and Evolution. Wiley-Blackwell. https://doi.org/10.1002/ece3.465 chicago: Pickup, Melinda, and Spencer Barrett. “The Influence of Demography and Local Mating Environment on Sex Ratios in a Wind-Pollinated Dioecious Plant.” Ecology and Evolution. Wiley-Blackwell, 2013. https://doi.org/10.1002/ece3.465. ieee: M. Pickup and S. Barrett, “The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant,” Ecology and Evolution, vol. 3, no. 3. Wiley-Blackwell, pp. 629–639, 2013. ista: Pickup M, Barrett S. 2013. The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant. Ecology and Evolution. 3(3), 629–639. mla: Pickup, Melinda, and Spencer Barrett. “The Influence of Demography and Local Mating Environment on Sex Ratios in a Wind-Pollinated Dioecious Plant.” Ecology and Evolution, vol. 3, no. 3, Wiley-Blackwell, 2013, pp. 629–39, doi:10.1002/ece3.465. short: M. Pickup, S. Barrett, Ecology and Evolution 3 (2013) 629–639. date_created: 2018-12-11T11:56:47Z date_published: 2013-03-01T00:00:00Z date_updated: 2021-01-12T06:56:32Z day: '01' ddc: - '576' department: - _id: NiBa doi: 10.1002/ece3.465 file: - access_level: open_access checksum: b5531bab4c0dec396bf5c8497fe178bf content_type: application/pdf creator: system date_created: 2018-12-12T10:17:35Z date_updated: 2020-07-14T12:45:37Z file_id: '5290' file_name: IST-2016-416-v1+1_Pickup_et_al-2013-Ecology_and_Evolution.pdf file_size: 626949 relation: main_file file_date_updated: 2020-07-14T12:45:37Z has_accepted_license: '1' intvolume: ' 3' issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 629 - 639 publication: Ecology and Evolution publication_status: published publisher: Wiley-Blackwell publist_id: '4644' pubrep_id: '416' quality_controlled: '1' scopus_import: 1 status: public title: The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2013' ... --- _id: '9754' 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 among recent, non-equilibrium 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 theWestern 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. article_processing_charge: No author: - first_name: Jack full_name: Hearn, Jack last_name: Hearn - first_name: Graham full_name: Stone, Graham last_name: Stone - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Konrad full_name: Lohse, Konrad last_name: Lohse - first_name: Lynsey full_name: Bunnefeld, Lynsey last_name: Bunnefeld citation: ama: 'Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies. 2013. doi:10.5061/dryad.r3r60' apa: 'Hearn, J., Stone, G., Barton, N. H., Lohse, K., & Bunnefeld, L. (2013). Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies. Dryad. https://doi.org/10.5061/dryad.r3r60' chicago: 'Hearn, Jack, Graham Stone, Nicholas H Barton, Konrad Lohse, and Lynsey Bunnefeld. “Data from: Likelihood-Based Inference of Population History from Low Coverage de Novo Genome Assemblies.” Dryad, 2013. https://doi.org/10.5061/dryad.r3r60.' ieee: 'J. Hearn, G. Stone, N. H. Barton, K. Lohse, and L. Bunnefeld, “Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies.” Dryad, 2013.' ista: 'Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. 2013. Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies, Dryad, 10.5061/dryad.r3r60.' mla: 'Hearn, Jack, et al. Data from: Likelihood-Based Inference of Population History from Low Coverage de Novo Genome Assemblies. Dryad, 2013, doi:10.5061/dryad.r3r60.' short: J. Hearn, G. Stone, N.H. Barton, K. Lohse, L. Bunnefeld, (2013). date_created: 2021-07-30T08:31:22Z date_published: 2013-10-01T00:00:00Z date_updated: 2023-02-23T10:31:17Z day: '01' department: - _id: NiBa doi: 10.5061/dryad.r3r60 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.r3r60 month: '10' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '2170' relation: used_in_publication status: public status: public title: 'Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2013' ... --- _id: '450' abstract: - lang: eng text: Understanding the relative importance of heterosis and outbreeding depression over multiple generations is a key question in evolutionary biology and is essential for identifying appropriate genetic sources for population and ecosystem restoration. Here we use 2455 experimental crosses between 12 population pairs of the rare perennial plant Rutidosis leptorrhynchoides (Asteraceae) to investigate the multi-generational (F1, F2, F3) fitness outcomes of inter-population hybridization. We detected no evidence of outbreeding depression, with inter-population hybrids and backcrosses showing either similar fitness or significant heterosis for fitness components across the three generations. Variation in heterosis among population pairs was best explained by characteristics of the foreign source or home population, and was greatest when the source population was large, with high genetic diversity and low inbreeding, and the home population was small and inbred. Our results indicate that the primary consideration for maximizing progeny fitness following population augmentation or restoration is the use of seed from large, genetically diverse populations. article_number: '2058' author: - first_name: Melinda full_name: Pickup, Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - first_name: David full_name: Rowell, David last_name: Rowell - first_name: Andrew full_name: Young, Andrew last_name: Young citation: ama: Pickup M, Field D, Rowell D, Young A. Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. Proceedings of the Royal Society of London Series B Biological Sciences. 2013;280(1750). doi:10.1098/rspb.2012.2058 apa: Pickup, M., Field, D., Rowell, D., & Young, A. (2013). Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2012.2058 chicago: Pickup, Melinda, David Field, David Rowell, and Andrew Young. “Source Population Characteristics Affect Heterosis Following Genetic Rescue of Fragmented Plant Populations.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The, 2013. https://doi.org/10.1098/rspb.2012.2058. ieee: M. Pickup, D. Field, D. Rowell, and A. Young, “Source population characteristics affect heterosis following genetic rescue of fragmented plant populations,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 280, no. 1750. Royal Society, The, 2013. ista: Pickup M, Field D, Rowell D, Young A. 2013. Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. Proceedings of the Royal Society of London Series B Biological Sciences. 280(1750), 2058. mla: Pickup, Melinda, et al. “Source Population Characteristics Affect Heterosis Following Genetic Rescue of Fragmented Plant Populations.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 280, no. 1750, 2058, Royal Society, The, 2013, doi:10.1098/rspb.2012.2058. short: M. Pickup, D. Field, D. Rowell, A. Young, Proceedings of the Royal Society of London Series B Biological Sciences 280 (2013). date_created: 2018-12-11T11:46:32Z date_published: 2013-01-07T00:00:00Z date_updated: 2021-01-12T07:57:25Z day: '07' department: - _id: NiBa doi: 10.1098/rspb.2012.2058 external_id: pmid: - '23173202' intvolume: ' 280' issue: '1750' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574427/ month: '01' oa: 1 oa_version: Submitted Version pmid: 1 publication: Proceedings of the Royal Society of London Series B Biological Sciences publication_status: published publisher: Royal Society, The publist_id: '7372' quality_controlled: '1' status: public title: Source population characteristics affect heterosis following genetic rescue of fragmented plant populations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 280 year: '2013' ... --- _id: '2917' abstract: - lang: eng text: 'The search for extra-terrestrial intelligence (SETI) has been performed principally as a one-way survey, listening of radio frequencies across the Milky Way and other galaxies. However, scientists have engaged in an active messaging only rarely. This suggests the simple rationale that if other civilizations exist and take a similar approach to ours, namely listening but not broadcasting, the result is a silent universe. A simple game theoretical model, the prisoner''s dilemma, explains this situation: each player (civilization) can passively search (defect), or actively search and broadcast (cooperate). In order to maximize the payoff (or, equivalently, minimize the risks) the best strategy is not to broadcast. In fact, the active search has been opposed on the basis that it might be dangerous to expose ourselves. However, most of these ideas have not been based on objective arguments, and ignore accounting of the possible gains and losses. Thus, the question stands: should we perform an active search? I develop a game-theoretical framework where civilizations can be of different types, and explicitly apply it to a situation where societies are either interested in establishing a two-way communication or belligerent and in urge to exploit ours. The framework gives a quantitative solution (a mixed-strategy), which is how frequent we should perform the active SETI. This frequency is roughly proportional to the inverse of the risk, and can be extremely small. However, given the immense amount of stars being scanned, it supports active SETI. The model is compared with simulations, and the possible actions are evaluated through the San Marino scale, measuring the risks of messaging.' author: - first_name: Harold full_name: Vladar, Harold id: 2A181218-F248-11E8-B48F-1D18A9856A87 last_name: Vladar orcid: 0000-0002-5985-7653 citation: ama: de Vladar H. The game of active search for extra terrestrial intelligence Breaking the Great Silence . International Journal of Astrobiology. 2012;12(1):53-62. doi:10.1017/S1473550412000407 apa: de Vladar, H. (2012). The game of active search for extra terrestrial intelligence Breaking the Great Silence . International Journal of Astrobiology. Cambridge University Press. https://doi.org/10.1017/S1473550412000407 chicago: Vladar, Harold de. “The Game of Active Search for Extra Terrestrial Intelligence Breaking the Great Silence .” International Journal of Astrobiology. Cambridge University Press, 2012. https://doi.org/10.1017/S1473550412000407. ieee: H. de Vladar, “The game of active search for extra terrestrial intelligence Breaking the Great Silence ,” International Journal of Astrobiology, vol. 12, no. 1. Cambridge University Press, pp. 53–62, 2012. ista: de Vladar H. 2012. The game of active search for extra terrestrial intelligence Breaking the Great Silence . International Journal of Astrobiology. 12(1), 53–62. mla: de Vladar, Harold. “The Game of Active Search for Extra Terrestrial Intelligence Breaking the Great Silence .” International Journal of Astrobiology, vol. 12, no. 1, Cambridge University Press, 2012, pp. 53–62, doi:10.1017/S1473550412000407. short: H. de Vladar, International Journal of Astrobiology 12 (2012) 53–62. date_created: 2018-12-11T12:00:19Z date_published: 2012-11-06T00:00:00Z date_updated: 2021-01-12T07:00:41Z day: '06' department: - _id: NiBa doi: 10.1017/S1473550412000407 intvolume: ' 12' issue: '1' language: - iso: eng month: '11' oa_version: None page: 53 - 62 publication: International Journal of Astrobiology publication_status: published publisher: Cambridge University Press publist_id: '3821' quality_controlled: '1' scopus_import: 1 status: public title: 'The game of active search for extra terrestrial intelligence Breaking the Great Silence ' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2012' ... --- _id: '2962' abstract: - lang: eng text: The choice of summary statistics is a crucial step in approximate Bayesian computation (ABC). Since statistics are often not sufficient, this choice involves a trade-off between loss of information and reduction of dimensionality. The latter may increase the efficiency of ABC. Here, we propose an approach for choosing summary statistics based on boosting, a technique from the machine learning literature. We consider different types of boosting and compare them to partial least squares regression as an alternative. To mitigate the lack of sufficiency, we also propose an approach for choosing summary statistics locally, in the putative neighborhood of the true parameter value. We study a demographic model motivated by the re-introduction of Alpine ibex (Capra ibex) into the Swiss Alps. The parameters of interest are the mean and standard deviation across microsatellites of the scaled ancestral mutation rate (θanc = 4 Ne u), and the proportion of males obtaining access to matings per breeding season (ω). By simulation, we assess the properties of the posterior distribution obtained with the various methods. According to our criteria, ABC with summary statistics chosen locally via boosting with the L2-loss performs best. Applying that method to the ibex data, we estimate θanc ≈ 1.288, and find that most of the variation across loci of the ancestral mutation rate u is between 7.7×10−4 and 3.5×10−3 per locus per generation. The proportion of males with access to matings is estimated to ω ≈ 0.21, which is in good agreement with recent independent estimates. acknowledged_ssus: - _id: ScienComp author: - first_name: Simon full_name: Aeschbacher, Simon id: 2D35326E-F248-11E8-B48F-1D18A9856A87 last_name: Aeschbacher - first_name: Mark full_name: Beaumont, Mark last_name: Beaumont - first_name: Andreas full_name: Futschik, Andreas last_name: Futschik citation: ama: Aeschbacher S, Beaumont M, Futschik A. A novel approach for choosing summary statistics in approximate Bayesian computation. Genetics. 2012;192(3):1027-1047. doi:10.1534/genetics.112.143164 apa: Aeschbacher, S., Beaumont, M., & Futschik, A. (2012). A novel approach for choosing summary statistics in approximate Bayesian computation. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.112.143164 chicago: Aeschbacher, Simon, Mark Beaumont, and Andreas Futschik. “A Novel Approach for Choosing Summary Statistics in Approximate Bayesian Computation.” Genetics. Genetics Society of America, 2012. https://doi.org/10.1534/genetics.112.143164. ieee: S. Aeschbacher, M. Beaumont, and A. Futschik, “A novel approach for choosing summary statistics in approximate Bayesian computation,” Genetics, vol. 192, no. 3. Genetics Society of America, pp. 1027–1047, 2012. ista: Aeschbacher S, Beaumont M, Futschik A. 2012. A novel approach for choosing summary statistics in approximate Bayesian computation. Genetics. 192(3), 1027–1047. mla: Aeschbacher, Simon, et al. “A Novel Approach for Choosing Summary Statistics in Approximate Bayesian Computation.” Genetics, vol. 192, no. 3, Genetics Society of America, 2012, pp. 1027–47, doi:10.1534/genetics.112.143164. short: S. Aeschbacher, M. Beaumont, A. Futschik, Genetics 192 (2012) 1027–1047. date_created: 2018-12-11T12:00:34Z date_published: 2012-11-01T00:00:00Z date_updated: 2021-01-12T07:40:05Z day: '01' department: - _id: NiBa doi: 10.1534/genetics.112.143164 external_id: pmid: - '22960215' intvolume: ' 192' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3522150/ month: '11' oa: 1 oa_version: Submitted Version page: 1027 - 1047 pmid: 1 publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '3763' quality_controlled: '1' scopus_import: 1 status: public title: A novel approach for choosing summary statistics in approximate Bayesian computation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 192 year: '2012' ... --- _id: '2968' abstract: - lang: eng text: Little is known about the stability of trophic relationships in complex natural communities over evolutionary timescales. Here, we use sequence data from 18 nuclear loci to reconstruct and compare the intraspecific histories of major Pleistocene refugial populations in the Middle East, the Balkans and Iberia in a guild of four Chalcid parasitoids (Cecidostiba fungosa, Cecidostiba semifascia, Hobbya stenonota and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood method to numerically estimate models of divergence between three populations from multilocus data. We investigate the power of this framework on simulated data, and-using triplet alignments of intronic loci-quantify the support for all possible divergence relationships between refugial populations in the four parasitoids. Although an East to West order of population divergence has highest support in all but one species, we cannot rule out alternative population tree topologies. Comparing the estimated times of population splits between species, we find that one species, M. amaenus, has a significantly older history than the rest of the guild and must have arrived in central Europe at least one glacial cycle prior to other guild members. This suggests that although all four species may share a common origin in the East, they expanded westwards into Europe at different times. © 2012 Blackwell Publishing Ltd. acknowledgement: "This work was supported by funding from the UK Natural Environment Research Council to KL (NE/I020288/1) and GS (NE/H000038/1, NE/E014453/1, NER/B/504406/1, NER/B/S2003/00856) and a grant from the European Research Council (250152) to NB.\r\nWe thank Majide Tavakoli, Juli Pujade-Villar and Pablo-Fuentes Utrilla for contributing specimens. Mike Hickerson and three anonymous reviewers gave helpful comments on earlier versions of the manuscript. " author: - first_name: Konrad full_name: Lohse, Konrad last_name: Lohse - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: George full_name: Melika, George last_name: Melika - first_name: Graham full_name: Stone, Graham last_name: Stone citation: ama: Lohse K, Barton NH, Melika G, Stone G. A likelihood based comparison of population histories in a parasitoid guild. Molecular Ecology. 2012;21(18):4605-4617. doi:10.1111/j.1365-294X.2012.05700.x apa: Lohse, K., Barton, N. H., Melika, G., & Stone, G. (2012). A likelihood based comparison of population histories in a parasitoid guild. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2012.05700.x chicago: Lohse, Konrad, Nicholas H Barton, George Melika, and Graham Stone. “A Likelihood Based Comparison of Population Histories in a Parasitoid Guild.” Molecular Ecology. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1365-294X.2012.05700.x. ieee: K. Lohse, N. H. Barton, G. Melika, and G. Stone, “A likelihood based comparison of population histories in a parasitoid guild,” Molecular Ecology, vol. 21, no. 18. Wiley-Blackwell, pp. 4605–4617, 2012. ista: Lohse K, Barton NH, Melika G, Stone G. 2012. A likelihood based comparison of population histories in a parasitoid guild. Molecular Ecology. 21(18), 4605–4617. mla: Lohse, Konrad, et al. “A Likelihood Based Comparison of Population Histories in a Parasitoid Guild.” Molecular Ecology, vol. 21, no. 18, Wiley-Blackwell, 2012, pp. 4605–17, doi:10.1111/j.1365-294X.2012.05700.x. short: K. Lohse, N.H. Barton, G. Melika, G. Stone, Molecular Ecology 21 (2012) 4605–4617. date_created: 2018-12-11T12:00:36Z date_published: 2012-09-01T00:00:00Z date_updated: 2023-05-30T13:07:47Z day: '01' ddc: - '570' - '579' department: - _id: NiBa doi: 10.1111/j.1365-294X.2012.05700.x ec_funded: 1 file: - access_level: open_access checksum: c14ee4cb2a8ba9575bfd8a9bb7a883bb content_type: application/pdf creator: system date_created: 2018-12-12T10:17:47Z date_updated: 2020-07-14T12:45:57Z file_id: '5304' file_name: IST-2014-296-v1+1_4_wasps_revised3.pdf file_size: 235820 relation: main_file - access_level: open_access checksum: f00afc5b887c8222014b57375b8caece content_type: application/pdf creator: system date_created: 2018-12-12T10:17:48Z date_updated: 2020-07-14T12:45:57Z file_id: '5305' file_name: IST-2014-296-v1+2_4_wasps_Supporting2.pdf file_size: 41975 relation: main_file file_date_updated: 2020-07-14T12:45:57Z has_accepted_license: '1' intvolume: ' 21' issue: '18' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 4605 - 4617 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Molecular Ecology publication_status: published publisher: Wiley-Blackwell publist_id: '3746' pubrep_id: '296' quality_controlled: '1' related_material: record: - id: '13075' relation: research_data status: public scopus_import: 1 status: public title: A likelihood based comparison of population histories in a parasitoid guild type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2012' ... --- _id: '3122' abstract: - lang: eng text: 'Since Darwin''s pioneering research on plant reproductive biology (e.g. Darwin 1877), understanding the mechanisms maintaining the diverse sexual strategies of plants has remained an important challenge for evolutionary biologists. In some species, populations are sexually polymorphic and contain two or more mating morphs (sex phenotypes). Differences in morphology or phenology among the morphs influence patterns of non-random mating. In these populations, negative frequency-dependent selection arising from disassortative (intermorph) mating is usually required for the evolutionary maintenance of sexual polymorphism, but few studies have demonstrated the required patterns of non-random mating. In the current issue of Molecular Ecology, Shang (2012) make an important contribution to our understanding of how disassortative mating influences sex phenotype ratios in Acer pictum subsp. mono (painted maple), a heterodichogamous, deciduous tree of eastern China. They monitored sex expression in 97 adults and used paternity analysis of open-pollinated seed to examine disassortative mating among three sex phenotypes. Using a deterministic ''pollen transfer'' model, Shang et al. present convincing evidence that differences in the degree of disassortative mating in progeny arrays of the sex phenotypes can explain their uneven frequencies in the adult population. This study provides a useful example of how the deployment of genetic markers, demographic monitoring and modelling can be integrated to investigate the maintenance of sexual diversity in plants. ' author: - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - first_name: Spencer full_name: Barrett, Spencer last_name: Barrett citation: ama: Field D, Barrett S. Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. 2012;21(15):3640-3643. doi:10.1111/j.1365-294X.2012.05643.x apa: Field, D., & Barrett, S. (2012). Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2012.05643.x chicago: Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance of Sexual Polymorphism in Painted Maple.” Molecular Ecology. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1365-294X.2012.05643.x. ieee: D. Field and S. Barrett, “Disassortative mating and the maintenance of sexual polymorphism in painted maple,” Molecular Ecology, vol. 21, no. 15. Wiley-Blackwell, pp. 3640–3643, 2012. ista: Field D, Barrett S. 2012. Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. 21(15), 3640–3643. mla: Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance of Sexual Polymorphism in Painted Maple.” Molecular Ecology, vol. 21, no. 15, Wiley-Blackwell, 2012, pp. 3640–43, doi:10.1111/j.1365-294X.2012.05643.x. short: D. Field, S. Barrett, Molecular Ecology 21 (2012) 3640–3643. date_created: 2018-12-11T12:01:31Z date_published: 2012-08-01T00:00:00Z date_updated: 2021-01-12T07:41:13Z day: '01' department: - _id: NiBa doi: 10.1111/j.1365-294X.2012.05643.x intvolume: ' 21' issue: '15' language: - iso: eng month: '08' oa_version: None page: 3640 - 3643 publication: Molecular Ecology publication_status: published publisher: Wiley-Blackwell publist_id: '3577' quality_controlled: '1' scopus_import: 1 status: public title: Disassortative mating and the maintenance of sexual polymorphism in painted maple type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2012' ... --- _id: '3131' abstract: - lang: eng text: 'In large populations, many beneficial mutations may be simultaneously available and may compete with one another, slowing adaptation. By finding the probability of fixation of a favorable allele in a simple model of a haploid sexual population, we find limits to the rate of adaptive substitution, Λ, that depend on simple parameter combinations. When variance in fitness is low and linkage is loose, the baseline rate of substitution is Λ 0=2NU〈s〉 is the population size, U is the rate of beneficial mutations per genome, and 〈s〉 is their mean selective advantage. Heritable variance ν in log fitness due to unlinked loci reduces Λ by e -4ν under polygamy and e -8ν under monogamy. With a linear genetic map of length R Morgans, interference is yet stronger. We use a scaling argument to show that the density of adaptive substitutions depends on s, N, U, and R only through the baseline density: Λ/R=F(Λ 0/R). Under the approximation that the interference due to different sweeps adds up, we show that Λ/R~(Λ 0/R)/(1+2Λ 0/R), implying that interference prevents the rate of adaptive substitution from exceeding one per centimorgan per 200 generations. Simulations and numerical calculations confirm the scaling argument and confirm the additive approximation for Λ 0/R 1; for higher Λ 0/R, the rate of adaptation grows above R/2, but only very slowly. We also consider the effect of sweeps on neutral diversity and show that, while even occasional sweeps can greatly reduce neutral diversity, this effect saturates as sweeps become more common-diversity can be maintained even in populations experiencing very strong interference. Our results indicate that for some organisms the rate of adaptive substitution may be primarily recombination-limited, depending only weakly on the mutation supply and the strength of selection.' acknowledgement: "The work was funded by ERC grant 250152.\r\nWe thank B. Charlesworth, O. Hallatschek, W. G. Hill, R. A. Neher, S. P. Otto, and the anonymous reviewers for their helpful suggestions." article_number: e1002740 author: - first_name: Daniel full_name: Weissman, Daniel id: 2D0CE020-F248-11E8-B48F-1D18A9856A87 last_name: Weissman - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Weissman D, Barton NH. Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. 2012;8(6). doi:10.1371/journal.pgen.1002740 apa: Weissman, D., & Barton, N. H. (2012). Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002740 chicago: Weissman, Daniel, and Nicholas H Barton. “Limits to the Rate of Adaptive Substitution in Sexual Populations.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002740. ieee: D. Weissman and N. H. Barton, “Limits to the rate of adaptive substitution in sexual populations,” PLoS Genetics, vol. 8, no. 6. Public Library of Science, 2012. ista: Weissman D, Barton NH. 2012. Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. 8(6), e1002740. mla: Weissman, Daniel, and Nicholas H. Barton. “Limits to the Rate of Adaptive Substitution in Sexual Populations.” PLoS Genetics, vol. 8, no. 6, e1002740, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002740. short: D. Weissman, N.H. Barton, PLoS Genetics 8 (2012). date_created: 2018-12-11T12:01:34Z date_published: 2012-06-07T00:00:00Z date_updated: 2021-01-12T07:41:17Z day: '07' ddc: - '570' - '576' department: - _id: NiBa doi: 10.1371/journal.pgen.1002740 ec_funded: 1 file: - access_level: open_access checksum: 729a4becda7d786c4c3db8f9a1f77953 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:00Z date_updated: 2020-07-14T12:46:01Z file_id: '4659' file_name: IST-2013-114-v1+1_WeissmanBarton2012.pdf file_size: 1284801 relation: main_file file_date_updated: 2020-07-14T12:46:01Z has_accepted_license: '1' intvolume: ' 8' issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: PLoS Genetics publication_status: published publisher: Public Library of Science publist_id: '3566' pubrep_id: '114' quality_controlled: '1' scopus_import: 1 status: public title: Limits to the rate of adaptive substitution in sexual populations tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2012' ... --- _id: '3166' abstract: - lang: eng text: 'There is evidence that the genetic code was established prior to the existence of proteins, when metabolism was powered by ribozymes. Also, early proto-organisms had to rely on simple anaerobic bioenergetic processes. In this work I propose that amino acid fermentation powered metabolism in the RNA world, and that this was facilitated by proto-adapters, the precursors of the tRNAs. Amino acids were used as carbon sources rather than as catalytic or structural elements. In modern bacteria, amino acid fermentation is known as the Stickland reaction. This pathway involves two amino acids: the first undergoes oxidative deamination, and the second acts as an electron acceptor through reductive deamination. This redox reaction results in two keto acids that are employed to synthesise ATP via substrate-level phosphorylation. The Stickland reaction is the basic bioenergetic pathway of some bacteria of the genus Clostridium. Two other facts support Stickland fermentation in the RNA world. First, several Stickland amino acid pairs are synthesised in abiotic amino acid synthesis. This suggests that amino acids that could be used as an energy substrate were freely available. Second, anticodons that have complementary sequences often correspond to amino acids that form Stickland pairs. The main hypothesis of this paper is that pairs of complementary proto-adapters were assigned to Stickland amino acids pairs. There are signatures of this hypothesis in the genetic code. Furthermore, it is argued that the proto-adapters formed double strands that brought amino acid pairs into proximity to facilitate their mutual redox reaction, structurally constraining the anticodon pairs that are assigned to these amino acid pairs. Significance tests which randomise the code are performed to study the extent of the variability of the energetic (ATP) yield. Random assignments can lead to a substantial yield of ATP and maintain enough variability, thus selection can act and refine the assignments into a proto-code that optimises the energetic yield. Monte Carlo simulations are performed to evaluate the establishment of these simple proto-codes, based on amino acid substitutions and codon swapping. In all cases, donor amino acids are assigned to anticodons composed of U+G, and have low redundancy (1-2 codons), whereas acceptor amino acids are assigned to the the remaining codons. These bioenergetic and structural constraints allow for a metabolic role for amino acids before their co-option as catalyst cofactors. Reviewers: this article was reviewed by Prof. William Martin, Prof. Eors Szathmary (nominated by Dr. Gaspar Jekely) and Dr. Adam Kun (nominated by Dr. Sandor Pongor)' acknowledgement: 'The author was supported by the ERC-2009-AdG Grant for project 250152 SELECTIONINFORMATION. ' article_number: '6' author: - first_name: Harold full_name: Vladar, Harold id: 2A181218-F248-11E8-B48F-1D18A9856A87 last_name: Vladar orcid: 0000-0002-5985-7653 citation: ama: de Vladar H. Amino acid fermentation at the origin of the genetic code. Biology Direct. 2012;7. doi:10.1186/1745-6150-7-6 apa: de Vladar, H. (2012). Amino acid fermentation at the origin of the genetic code. Biology Direct. BioMed Central. https://doi.org/10.1186/1745-6150-7-6 chicago: Vladar, Harold de. “Amino Acid Fermentation at the Origin of the Genetic Code.” Biology Direct. BioMed Central, 2012. https://doi.org/10.1186/1745-6150-7-6. ieee: H. de Vladar, “Amino acid fermentation at the origin of the genetic code,” Biology Direct, vol. 7. BioMed Central, 2012. ista: de Vladar H. 2012. Amino acid fermentation at the origin of the genetic code. Biology Direct. 7, 6. mla: de Vladar, Harold. “Amino Acid Fermentation at the Origin of the Genetic Code.” Biology Direct, vol. 7, 6, BioMed Central, 2012, doi:10.1186/1745-6150-7-6. short: H. de Vladar, Biology Direct 7 (2012). date_created: 2018-12-11T12:01:46Z date_published: 2012-02-10T00:00:00Z date_updated: 2021-01-12T07:41:31Z day: '10' ddc: - '570' - '576' department: - _id: NiBa doi: 10.1186/1745-6150-7-6 ec_funded: 1 file: - access_level: open_access checksum: e511e401e239ef608a7fd79b21a06d78 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:44Z date_updated: 2020-07-14T12:46:02Z file_id: '5166' file_name: IST-2012-99-v1+1_1745-6150-7-6.pdf file_size: 4099536 relation: main_file file_date_updated: 2020-07-14T12:46:02Z has_accepted_license: '1' intvolume: ' 7' language: - iso: eng month: '02' oa: 1 oa_version: Published Version project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Biology Direct publication_status: published publisher: BioMed Central publist_id: '3518' pubrep_id: '99' quality_controlled: '1' status: public title: Amino acid fermentation at the origin of the genetic code tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2012' ...