[{"scopus_import":1,"file":[{"date_updated":"2020-07-14T12:45:37Z","file_id":"5290","access_level":"open_access","checksum":"b5531bab4c0dec396bf5c8497fe178bf","file_name":"IST-2016-416-v1+1_Pickup_et_al-2013-Ecology_and_Evolution.pdf","date_created":"2018-12-12T10:17:35Z","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":626949}],"date_published":"2013-03-01T00:00:00Z","page":"629 - 639","has_accepted_license":"1","department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"doi":"10.1002/ece3.465","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","type":"journal_article","date_updated":"2021-01-12T06:56:32Z","day":"01","intvolume":"         3","publist_id":"4644","month":"03","date_created":"2018-12-11T11:56:47Z","status":"public","pubrep_id":"416","volume":3,"issue":"3","file_date_updated":"2020-07-14T12:45:37Z","publisher":"Wiley-Blackwell","publication":"Ecology and Evolution","title":"The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant","_id":"2287","oa":1,"ddc":["576"],"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."}],"publication_status":"published","citation":{"mla":"Pickup, Melinda, and Spencer Barrett. “The Influence of Demography and Local Mating Environment on Sex Ratios in a Wind-Pollinated Dioecious Plant.” <i>Ecology and Evolution</i>, vol. 3, no. 3, Wiley-Blackwell, 2013, pp. 629–39, doi:<a href=\"https://doi.org/10.1002/ece3.465\">10.1002/ece3.465</a>.","apa":"Pickup, M., &#38; Barrett, S. (2013). The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant. <i>Ecology and Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/ece3.465\">https://doi.org/10.1002/ece3.465</a>","ieee":"M. Pickup and S. Barrett, “The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant,” <i>Ecology and Evolution</i>, vol. 3, no. 3. Wiley-Blackwell, pp. 629–639, 2013.","ama":"Pickup M, Barrett S. The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant. <i>Ecology and Evolution</i>. 2013;3(3):629-639. doi:<a href=\"https://doi.org/10.1002/ece3.465\">10.1002/ece3.465</a>","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.","short":"M. Pickup, S. Barrett, Ecology and Evolution 3 (2013) 629–639.","chicago":"Pickup, Melinda, and Spencer Barrett. “The Influence of Demography and Local Mating Environment on Sex Ratios in a Wind-Pollinated Dioecious Plant.” <i>Ecology and Evolution</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1002/ece3.465\">https://doi.org/10.1002/ece3.465</a>."},"author":[{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","first_name":"Melinda","last_name":"Pickup"},{"first_name":"Spencer","last_name":"Barrett","full_name":"Barrett, Spencer"}],"quality_controlled":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2013"},{"scopus_import":1,"page":"75 - 89","date_published":"2013-01-03T00:00:00Z","file":[{"file_id":"5376","date_updated":"2020-07-14T12:45:41Z","access_level":"open_access","file_name":"IST-2013-118-v1+1_bartonetalRevision.pdf","checksum":"4274ec1f433b838a7d5b941cc9684ca7","date_created":"2018-12-12T10:18:54Z","relation":"main_file","content_type":"application/pdf","creator":"system","file_size":1706282}],"language":[{"iso":"eng"}],"doi":"10.1016/j.tpb.2012.12.001","has_accepted_license":"1","department":[{"_id":"NiBa"}],"ec_funded":1,"day":"03","type":"journal_article","date_updated":"2021-01-12T06:57:42Z","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_created":"2018-12-11T11:57:52Z","month":"01","publist_id":"4428","intvolume":"        87","publisher":"Elsevier","file_date_updated":"2020-07-14T12:45:41Z","volume":87,"issue":"8","pubrep_id":"118","publication_status":"published","abstract":[{"text":"When a mutation with selective advantage s spreads through a panmictic population, it may cause two lineages at a linked locus to coalesce; the probability of coalescence is exp(−2rT), where T∼log(2Ns)/s is the time to fixation, N is the number of haploid individuals, and r is the recombination rate. Population structure delays fixation, and so weakens the effect of a selective sweep. However, favourable alleles spread through a spatially continuous population behind a narrow wavefront; ancestral lineages are confined at the tip of this front, and so coalesce rapidly. In extremely dense populations, coalescence is dominated by rare fluctuations ahead of the front. However, we show that for moderate densities, a simple quasi-deterministic approximation applies: the rate of coalescence within the front is λ∼2g(η)/(ρℓ), where ρ is the population density and  is the characteristic scale of the wavefront; g(η) depends only on the strength of random drift,  . The net effect of a sweep on coalescence also depends crucially on whether two lineages are ever both within the wavefront at the same time: even in the extreme case when coalescence within the front is instantaneous, the net rate of coalescence may be lower than in a single panmictic population. Sweeps can also have a substantial impact on the rate of gene flow. A single lineage will jump to a new location when it is hit by a sweep, with mean square displacement  ; this can be substantial if the species’ range, L, is large, even if the species-wide rate of sweeps per map length, Λ/R, is small. This effect is half as strong in two dimensions. In contrast, the rate of coalescence between lineages, at random locations in space and on the genetic map, is proportional to (c/L)(Λ/R), where c is the wavespeed: thus, on average, one-dimensional structure is likely to reduce coalescence due to sweeps, relative to panmixis. In two dimensions, genes must move along the front before they can coalesce; this process is rapid, being dominated by rare fluctuations. This leads to a dramatically higher rate of coalescence within the wavefront than if lineages simply diffused along the front. Nevertheless, the net rate of coalescence due to a sweep through a two-dimensional population is likely to be lower than it would be with panmixis.","lang":"eng"}],"project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"oa":1,"ddc":["570"],"_id":"2473","title":"Genetic hitch-hiking in spatially extended populations","publication":"Theoretical Population Biology","year":"2013","quality_controlled":"1","author":[{"first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Etheridge, Alison","last_name":"Etheridge","first_name":"Alison"},{"full_name":"Kelleher, Jerome","first_name":"Jerome","last_name":"Kelleher"},{"full_name":"Véber, Amandine","last_name":"Véber","first_name":"Amandine"}],"citation":{"mla":"Barton, Nicholas H., et al. “Genetic Hitch-Hiking in Spatially Extended Populations.” <i>Theoretical Population Biology</i>, vol. 87, no. 8, Elsevier, 2013, pp. 75–89, doi:<a href=\"https://doi.org/10.1016/j.tpb.2012.12.001\">10.1016/j.tpb.2012.12.001</a>.","apa":"Barton, N. H., Etheridge, A., Kelleher, J., &#38; Véber, A. (2013). Genetic hitch-hiking in spatially extended populations. <i>Theoretical Population Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tpb.2012.12.001\">https://doi.org/10.1016/j.tpb.2012.12.001</a>","short":"N.H. Barton, A. Etheridge, J. Kelleher, A. Véber, Theoretical Population Biology 87 (2013) 75–89.","chicago":"Barton, Nicholas H, Alison Etheridge, Jerome Kelleher, and Amandine Véber. “Genetic Hitch-Hiking in Spatially Extended Populations.” <i>Theoretical Population Biology</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.tpb.2012.12.001\">https://doi.org/10.1016/j.tpb.2012.12.001</a>.","ista":"Barton NH, Etheridge A, Kelleher J, Véber A. 2013. Genetic hitch-hiking in spatially extended populations. Theoretical Population Biology. 87(8), 75–89.","ama":"Barton NH, Etheridge A, Kelleher J, Véber A. Genetic hitch-hiking in spatially extended populations. <i>Theoretical Population Biology</i>. 2013;87(8):75-89. doi:<a href=\"https://doi.org/10.1016/j.tpb.2012.12.001\">10.1016/j.tpb.2012.12.001</a>","ieee":"N. H. Barton, A. Etheridge, J. Kelleher, and A. Véber, “Genetic hitch-hiking in spatially extended populations,” <i>Theoretical Population Biology</i>, vol. 87, no. 8. Elsevier, pp. 75–89, 2013."}},{"department":[{"_id":"NiBa"},{"_id":"CaGu"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"doi":"10.1145/2463372.2463568","ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","oa_version":"Submitted Version","type":"conference","date_updated":"2021-01-12T06:59:15Z","scopus_import":1,"page":"1573 - 1580","file":[{"content_type":"application/pdf","creator":"system","file_size":475844,"relation":"main_file","date_created":"2018-12-12T10:15:38Z","file_name":"IST-2016-564-v1+1_NickGECCO_2013_1_-1.pdf","checksum":"9d9be9090ce5c20766e0eb076ace5b98","access_level":"open_access","date_updated":"2020-07-14T12:45:45Z","file_id":"5159"}],"date_published":"2013-07-01T00:00:00Z","_id":"2718","ddc":["570"],"oa":1,"publication":"Proceedings of the 15th annual conference on Genetic and evolutionary computation","title":"Can quantitative and population genetics help us understand evolutionary computation?","abstract":[{"text":"Even though both population and quantitative genetics, and evolutionary computation, deal with the same questions, they have developed largely independently of each other. I review key results from each field, emphasising those that apply independently of the (usually unknown) relation between genotype and phenotype. The infinitesimal model provides a simple framework for predicting the response of complex traits to selection, which in biology has proved remarkably successful. This allows one to choose the schedule of population sizes and selection intensities that will maximise the response to selection, given that the total number of individuals realised, C = ∑t Nt, is constrained. This argument shows that for an additive trait (i.e., determined by the sum of effects of the genes), the optimum population size and the maximum possible response (i.e., the total change in trait mean) are both proportional to √C.","lang":"eng"}],"publication_status":"published","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"author":[{"last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","first_name":"Tiago"}],"quality_controlled":"1","citation":{"apa":"Barton, N. H., &#38; Paixao, T. (2013). Can quantitative and population genetics help us understand evolutionary computation? In <i>Proceedings of the 15th annual conference on Genetic and evolutionary computation</i> (pp. 1573–1580). Amsterdam, Netherlands: ACM. <a href=\"https://doi.org/10.1145/2463372.2463568\">https://doi.org/10.1145/2463372.2463568</a>","mla":"Barton, Nicholas H., and Tiago Paixao. “Can Quantitative and Population Genetics Help Us Understand Evolutionary Computation?” <i>Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation</i>, ACM, 2013, pp. 1573–80, doi:<a href=\"https://doi.org/10.1145/2463372.2463568\">10.1145/2463372.2463568</a>.","ama":"Barton NH, Paixao T. Can quantitative and population genetics help us understand evolutionary computation? In: <i>Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation</i>. ACM; 2013:1573-1580. doi:<a href=\"https://doi.org/10.1145/2463372.2463568\">10.1145/2463372.2463568</a>","ieee":"N. H. Barton and T. Paixao, “Can quantitative and population genetics help us understand evolutionary computation?,” in <i>Proceedings of the 15th annual conference on Genetic and evolutionary computation</i>, Amsterdam, Netherlands, 2013, pp. 1573–1580.","short":"N.H. Barton, T. Paixao, in:, Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 1573–1580.","chicago":"Barton, Nicholas H, and Tiago Paixao. “Can Quantitative and Population Genetics Help Us Understand Evolutionary Computation?” In <i>Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation</i>, 1573–80. ACM, 2013. <a href=\"https://doi.org/10.1145/2463372.2463568\">https://doi.org/10.1145/2463372.2463568</a>.","ista":"Barton NH, Paixao T. 2013. Can quantitative and population genetics help us understand evolutionary computation? Proceedings of the 15th annual conference on Genetic and evolutionary computation. GECCO: Genetic and evolutionary computation conference, 1573–1580."},"year":"2013","publist_id":"4174","status":"public","conference":{"start_date":"2013-07-06","location":"Amsterdam, Netherlands","name":"GECCO: Genetic and evolutionary computation conference","end_date":"2013-07-10"},"month":"07","date_created":"2018-12-11T11:59:14Z","pubrep_id":"564","publisher":"ACM","file_date_updated":"2020-07-14T12:45:45Z"},{"month":"07","conference":{"name":"GECCO: Genetic and evolutionary computation conference","end_date":"2013-07-10","location":"Amsterdam, Netherlands","start_date":"2013-07-06"},"date_created":"2018-12-11T11:59:15Z","status":"public","scopus_import":1,"publist_id":"4173","publisher":"ACM","date_published":"2013-07-01T00:00:00Z","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"}],"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."}],"publication_status":"published","title":"A variance decomposition approach to the analysis of genetic algorithms","publication":"Proceedings of the 15th annual conference on Genetic and evolutionary computation","ec_funded":1,"_id":"2719","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"doi":"10.1145/2463372.2463470","language":[{"iso":"eng"}],"oa_version":"None","type":"conference","date_updated":"2021-01-12T06:59:15Z","year":"2013","day":"01","citation":{"ieee":"T. Paixao and N. H. Barton, “A variance decomposition approach to the analysis of genetic algorithms,” in <i>Proceedings of the 15th annual conference on Genetic and evolutionary computation</i>, Amsterdam, Netherlands, 2013, pp. 845–852.","ama":"Paixao T, Barton NH. A variance decomposition approach to the analysis of genetic algorithms. In: <i>Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation</i>. ACM; 2013:845-852. doi:<a href=\"https://doi.org/10.1145/2463372.2463470\">10.1145/2463372.2463470</a>","short":"T. Paixao, N.H. Barton, in:, Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 845–852.","chicago":"Paixao, Tiago, and Nicholas H Barton. “A Variance Decomposition Approach to the Analysis of Genetic Algorithms.” In <i>Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation</i>, 845–52. ACM, 2013. <a href=\"https://doi.org/10.1145/2463372.2463470\">https://doi.org/10.1145/2463372.2463470</a>.","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.” <i>Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation</i>, ACM, 2013, pp. 845–52, doi:<a href=\"https://doi.org/10.1145/2463372.2463470\">10.1145/2463372.2463470</a>.","apa":"Paixao, T., &#38; Barton, N. H. (2013). A variance decomposition approach to the analysis of genetic algorithms. In <i>Proceedings of the 15th annual conference on Genetic and evolutionary computation</i> (pp. 845–852). Amsterdam, Netherlands: ACM. <a href=\"https://doi.org/10.1145/2463372.2463470\">https://doi.org/10.1145/2463372.2463470</a>"},"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago","last_name":"Paixao","first_name":"Tiago"},{"first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}]},{"author":[{"full_name":"Long, Hongan","last_name":"Long","first_name":"Hongan"},{"last_name":"Paixao","first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953"},{"last_name":"Azevedo","first_name":"Ricardo","full_name":"Azevedo, Ricardo"},{"first_name":"Rebecca","last_name":"Zufall","full_name":"Zufall, Rebecca"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3781978/"}],"citation":{"apa":"Long, H., Paixao, T., Azevedo, R., &#38; Zufall, R. (2013). Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.113.153536\">https://doi.org/10.1534/genetics.113.153536</a>","mla":"Long, Hongan, et al. “Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.” <i>Genetics</i>, vol. 195, no. 2, Genetics Society of America, 2013, pp. 527–40, doi:<a href=\"https://doi.org/10.1534/genetics.113.153536\">10.1534/genetics.113.153536</a>.","ieee":"H. Long, T. Paixao, R. Azevedo, and R. Zufall, “Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila,” <i>Genetics</i>, vol. 195, no. 2. Genetics Society of America, pp. 527–540, 2013.","ama":"Long H, Paixao T, Azevedo R, Zufall R. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. <i>Genetics</i>. 2013;195(2):527-540. doi:<a href=\"https://doi.org/10.1534/genetics.113.153536\">10.1534/genetics.113.153536</a>","ista":"Long H, Paixao T, Azevedo R, Zufall R. 2013. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics. 195(2), 527–540.","short":"H. Long, T. Paixao, R. Azevedo, R. Zufall, Genetics 195 (2013) 527–540.","chicago":"Long, Hongan, Tiago Paixao, Ricardo Azevedo, and Rebecca Zufall. “Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.” <i>Genetics</i>. Genetics Society of America, 2013. <a href=\"https://doi.org/10.1534/genetics.113.153536\">https://doi.org/10.1534/genetics.113.153536</a>."},"year":"2013","_id":"2720","oa":1,"pmid":1,"publication":"Genetics","title":"Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila","abstract":[{"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 &lt;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.","lang":"eng"}],"publication_status":"published","project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"issue":"2","volume":195,"publisher":"Genetics Society of America","publist_id":"4172","intvolume":"       195","status":"public","month":"10","date_created":"2018-12-11T11:59:15Z","article_processing_charge":"No","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","oa_version":"Submitted Version","date_updated":"2021-01-12T06:59:16Z","type":"journal_article","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"language":[{"iso":"eng"}],"doi":"10.1534/genetics.113.153536","ec_funded":1,"page":"527-540","external_id":{"pmid":["23934880"]},"date_published":"2013-10-01T00:00:00Z","scopus_import":1},{"scopus_import":1,"page":"26 - 34","file":[{"access_level":"open_access","checksum":"3c29059ab03a4b8f97a07646b817ddbb","file_name":"IST-2016-400-v1+1_1-s2.0-S0022519313002609-main.pdf","file_id":"5110","date_updated":"2020-07-14T12:45:49Z","content_type":"application/pdf","creator":"system","file_size":834604,"date_created":"2018-12-12T10:14:54Z","relation":"main_file"}],"date_published":"2013-10-07T00:00:00Z","has_accepted_license":"1","department":[{"_id":"NiBa"},{"_id":"KrCh"}],"doi":"10.1016/j.jtbi.2013.05.029","language":[{"iso":"eng"}],"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"07","oa_version":"Published Version","type":"journal_article","date_updated":"2025-05-28T11:42:43Z","publist_id":"3984","intvolume":"       334","status":"public","month":"10","date_created":"2018-12-11T11:59:45Z","pubrep_id":"400","volume":334,"publisher":"Elsevier","file_date_updated":"2020-07-14T12:45:49Z","_id":"2817","oa":1,"ddc":["000"],"title":"Density games","publication":"Journal of Theoretical Biology","abstract":[{"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.","lang":"eng"}],"publication_status":"published","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory","grant_number":"S11407"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","author":[{"orcid":"0000-0002-2519-824X","full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak","first_name":"Sebastian"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"citation":{"apa":"Novak, S., Chatterjee, K., &#38; Nowak, M. (2013). Density games. <i>Journal of Theoretical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jtbi.2013.05.029\">https://doi.org/10.1016/j.jtbi.2013.05.029</a>","mla":"Novak, Sebastian, et al. “Density Games.” <i>Journal of Theoretical Biology</i>, vol. 334, Elsevier, 2013, pp. 26–34, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2013.05.029\">10.1016/j.jtbi.2013.05.029</a>.","ieee":"S. Novak, K. Chatterjee, and M. Nowak, “Density games,” <i>Journal of Theoretical Biology</i>, vol. 334. Elsevier, pp. 26–34, 2013.","ama":"Novak S, Chatterjee K, Nowak M. Density games. <i>Journal of Theoretical Biology</i>. 2013;334:26-34. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2013.05.029\">10.1016/j.jtbi.2013.05.029</a>","chicago":"Novak, Sebastian, Krishnendu Chatterjee, and Martin Nowak. “Density Games.” <i>Journal of Theoretical Biology</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.jtbi.2013.05.029\">https://doi.org/10.1016/j.jtbi.2013.05.029</a>.","short":"S. Novak, K. Chatterjee, M. Nowak, Journal of Theoretical Biology 334 (2013) 26–34.","ista":"Novak S, Chatterjee K, Nowak M. 2013. Density games. Journal of Theoretical Biology. 334, 26–34."},"year":"2013","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"publist_id":"3978","scopus_import":1,"intvolume":"        38","status":"public","date_created":"2018-12-11T11:59:47Z","month":"05","page":"300 - 312","issue":"3","volume":38,"date_published":"2013-05-01T00:00:00Z","publisher":"Wiley-Blackwell","language":[{"iso":"eng"}],"doi":"10.1111/j.1442-9993.2012.02404.x","department":[{"_id":"NiBa"}],"_id":"2823","publication":"Austral Ecology","title":"Post-fire recovery of revegetated woodland communities in south-eastern Australia","publication_status":"published","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 (&gt;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 &lt;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":[{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","full_name":"Pickup, Melinda","first_name":"Melinda","last_name":"Pickup"},{"first_name":"Susie","last_name":"Wilson","full_name":"Wilson, Susie"},{"last_name":"Freudenberger","first_name":"David","full_name":"Freudenberger, David"},{"full_name":"Nicholls, Nick","last_name":"Nicholls","first_name":"Nick"},{"first_name":"Lori","last_name":"Gould","full_name":"Gould, Lori"},{"first_name":"Sarah","last_name":"Hnatiuk","full_name":"Hnatiuk, Sarah"},{"full_name":"Delandre, Jeni","last_name":"Delandre","first_name":"Jeni"}],"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Pickup, Melinda, et al. “Post-Fire Recovery of Revegetated Woodland Communities in South-Eastern Australia.” <i>Austral Ecology</i>, vol. 38, no. 3, Wiley-Blackwell, 2013, pp. 300–12, doi:<a href=\"https://doi.org/10.1111/j.1442-9993.2012.02404.x\">10.1111/j.1442-9993.2012.02404.x</a>.","apa":"Pickup, M., Wilson, S., Freudenberger, D., Nicholls, N., Gould, L., Hnatiuk, S., &#38; Delandre, J. (2013). Post-fire recovery of revegetated woodland communities in south-eastern Australia. <i>Austral Ecology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1442-9993.2012.02404.x\">https://doi.org/10.1111/j.1442-9993.2012.02404.x</a>","ama":"Pickup M, Wilson S, Freudenberger D, et al. Post-fire recovery of revegetated woodland communities in south-eastern Australia. <i>Austral Ecology</i>. 2013;38(3):300-312. doi:<a href=\"https://doi.org/10.1111/j.1442-9993.2012.02404.x\">10.1111/j.1442-9993.2012.02404.x</a>","ieee":"M. Pickup <i>et al.</i>, “Post-fire recovery of revegetated woodland communities in south-eastern Australia,” <i>Austral Ecology</i>, vol. 38, no. 3. Wiley-Blackwell, pp. 300–312, 2013.","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.” <i>Austral Ecology</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1111/j.1442-9993.2012.02404.x\">https://doi.org/10.1111/j.1442-9993.2012.02404.x</a>.","short":"M. Pickup, S. Wilson, D. Freudenberger, N. Nicholls, L. Gould, S. Hnatiuk, J. Delandre, Austral Ecology 38 (2013) 300–312.","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."},"day":"01","year":"2013","date_updated":"2021-01-12T06:59:58Z","type":"journal_article","oa_version":"None"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","type":"journal_article","date_updated":"2021-01-12T07:00:09Z","oa_version":"Submitted Version","doi":"10.1016/j.tpb.2013.03.001","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"NiBa"}],"ec_funded":1,"page":"105 - 119","date_published":"2013-08-01T00:00:00Z","file":[{"content_type":"application/pdf","creator":"system","file_size":1554712,"date_created":"2018-12-12T10:17:33Z","relation":"main_file","access_level":"open_access","file_name":"IST-2016-558-v1+1_inference_revised3101NB.pdf","checksum":"9bf9d9a6fd03dd9df50906891f393bf8","file_id":"5288","date_updated":"2020-07-14T12:45:50Z"},{"file_size":822964,"content_type":"application/pdf","creator":"system","date_created":"2018-12-12T10:17:34Z","relation":"main_file","access_level":"open_access","file_name":"IST-2016-558-v1+2_inference_revised3101NBApp.pdf","checksum":"2bceddb76edacd0cd5fad73051e2a928","date_updated":"2020-07-14T12:45:50Z","file_id":"5289"}],"scopus_import":1,"author":[{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Etheridge, Alison","last_name":"Etheridge","first_name":"Alison"},{"first_name":"Jerome","last_name":"Kelleher","full_name":"Kelleher, Jerome"},{"full_name":"Véber, Amandine","first_name":"Amandine","last_name":"Véber"}],"quality_controlled":"1","citation":{"ieee":"N. H. Barton, A. Etheridge, J. Kelleher, and A. Véber, “Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks,” <i>Theoretical Population Biology</i>, vol. 87, no. 1. Elsevier, pp. 105–119, 2013.","ama":"Barton NH, Etheridge A, Kelleher J, Véber A. Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks. <i>Theoretical Population Biology</i>. 2013;87(1):105-119. doi:<a href=\"https://doi.org/10.1016/j.tpb.2013.03.001\">10.1016/j.tpb.2013.03.001</a>","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.","chicago":"Barton, Nicholas H, Alison Etheridge, Jerome Kelleher, and Amandine Véber. “Inference in Two Dimensions: Allele Frequencies versus Lengths of Shared Sequence Blocks.” <i>Theoretical Population Biology</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.tpb.2013.03.001\">https://doi.org/10.1016/j.tpb.2013.03.001</a>.","short":"N.H. Barton, A. Etheridge, J. Kelleher, A. Véber, Theoretical Population Biology 87 (2013) 105–119.","apa":"Barton, N. H., Etheridge, A., Kelleher, J., &#38; Véber, A. (2013). Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks. <i>Theoretical Population Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tpb.2013.03.001\">https://doi.org/10.1016/j.tpb.2013.03.001</a>","mla":"Barton, Nicholas H., et al. “Inference in Two Dimensions: Allele Frequencies versus Lengths of Shared Sequence Blocks.” <i>Theoretical Population Biology</i>, vol. 87, no. 1, Elsevier, 2013, pp. 105–19, doi:<a href=\"https://doi.org/10.1016/j.tpb.2013.03.001\">10.1016/j.tpb.2013.03.001</a>."},"year":"2013","oa":1,"ddc":["570"],"_id":"2842","publication":"Theoretical Population Biology","title":"Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks","publication_status":"published","abstract":[{"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 (&gt;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.","lang":"eng"}],"project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"issue":"1","volume":87,"pubrep_id":"558","publisher":"Elsevier","file_date_updated":"2020-07-14T12:45:50Z","publist_id":"3953","intvolume":"        87","status":"public","date_created":"2018-12-11T11:59:53Z","month":"08"},{"publisher":"Princeton University Press","file_date_updated":"2020-07-14T12:45:52Z","page":"328 - 333","pubrep_id":"119","date_published":"2013-11-04T00:00:00Z","file":[{"file_size":79838,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"system","date_created":"2018-12-12T10:16:47Z","relation":"main_file","access_level":"open_access","file_name":"IST-2013-119-v1+1_IV.4_Recombination_and_Sex_Barton_1-13-13-e.docx","checksum":"8332ca9cb40f7e66d1006b175ce36b60","date_updated":"2020-07-14T12:45:52Z","file_id":"5237"},{"date_updated":"2020-07-14T12:45:52Z","file_id":"5238","checksum":"849f418620fb78d6ba23bb4f488ee93f","file_name":"IST-2017-119-v1+2_Barton_Recombination_Sex.pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:16:48Z","file_size":144131,"content_type":"application/pdf","creator":"system"}],"status":"public","date_created":"2018-12-11T12:00:16Z","month":"11","publication_identifier":{"isbn":["9780691149776"]},"publist_id":"3839","day":"04","year":"2013","type":"book_chapter","date_updated":"2021-01-12T07:00:37Z","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"quality_controlled":"1","citation":{"mla":"Barton, Nicholas H. “Recombination and Sex.” <i>The Princeton Guide to Evolution</i>, Princeton University Press, 2013, pp. 328–33.","apa":"Barton, N. H. (2013). Recombination and sex. In <i>The Princeton Guide to Evolution</i> (pp. 328–333). Princeton University Press.","ista":"Barton NH. 2013.Recombination and sex. In: The Princeton Guide to Evolution. , 328–333.","short":"N.H. Barton, in:, The Princeton Guide to Evolution, Princeton University Press, 2013, pp. 328–333.","chicago":"Barton, Nicholas H. “Recombination and Sex.” In <i>The Princeton Guide to Evolution</i>, 328–33. Princeton University Press, 2013.","ieee":"N. H. Barton, “Recombination and sex,” in <i>The Princeton Guide to Evolution</i>, Princeton University Press, 2013, pp. 328–333.","ama":"Barton NH. Recombination and sex. In: <i>The Princeton Guide to Evolution</i>. Princeton University Press; 2013:328-333."},"publication_status":"published","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."}],"oa":1,"ddc":["576"],"language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"_id":"2907","has_accepted_license":"1","title":"Recombination and sex","publication":"The Princeton Guide to Evolution"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"17","oa_version":"Submitted Version","date_updated":"2021-01-12T07:00:37Z","type":"journal_article","department":[{"_id":"NiBa"}],"has_accepted_license":"1","doi":"10.1111/jeb.12015","language":[{"iso":"eng"}],"page":"267 - 269","file":[{"file_size":13339,"content_type":"text/rtf","creator":"system","date_created":"2018-12-12T10:09:38Z","relation":"main_file","access_level":"open_access","checksum":"716e88714c3411cd0bd70928b14ea692","file_name":"IST-2013-111-v1+1_Hybridisation_and_speciation_revised.rtf","date_updated":"2020-07-14T12:45:52Z","file_id":"4762"},{"file_size":103437,"content_type":"application/pdf","creator":"system","relation":"main_file","date_created":"2018-12-12T10:09:39Z","checksum":"957fd07c71c1b1eac2c65ae3311aca78","file_name":"IST-2017-111-v1+2_Hybridisation_and_speciation_revised.pdf","access_level":"open_access","file_id":"4763","date_updated":"2020-07-14T12:45:52Z"}],"date_published":"2013-01-17T00:00:00Z","scopus_import":1,"author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton"}],"quality_controlled":"1","citation":{"ista":"Barton NH. 2013. Does hybridisation influence speciation?  . Journal of Evolutionary Biology. 26(2), 267–269.","chicago":"Barton, Nicholas H. “Does Hybridisation Influence Speciation?  .” <i>Journal of Evolutionary Biology</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1111/jeb.12015\">https://doi.org/10.1111/jeb.12015</a>.","short":"N.H. Barton, Journal of Evolutionary Biology 26 (2013) 267–269.","ama":"Barton NH. Does hybridisation influence speciation?  . <i>Journal of Evolutionary Biology</i>. 2013;26(2):267-269. doi:<a href=\"https://doi.org/10.1111/jeb.12015\">10.1111/jeb.12015</a>","ieee":"N. H. Barton, “Does hybridisation influence speciation?  ,” <i>Journal of Evolutionary Biology</i>, vol. 26, no. 2. Wiley-Blackwell, pp. 267–269, 2013.","mla":"Barton, Nicholas H. “Does Hybridisation Influence Speciation?  .” <i>Journal of Evolutionary Biology</i>, vol. 26, no. 2, Wiley-Blackwell, 2013, pp. 267–69, doi:<a href=\"https://doi.org/10.1111/jeb.12015\">10.1111/jeb.12015</a>.","apa":"Barton, N. H. (2013). Does hybridisation influence speciation?  . <i>Journal of Evolutionary Biology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/jeb.12015\">https://doi.org/10.1111/jeb.12015</a>"},"year":"2013","_id":"2908","ddc":["576"],"oa":1,"publication":"Journal of Evolutionary Biology","title":"Does hybridisation influence speciation?  ","abstract":[{"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.","lang":"eng"}],"publication_status":"published","pubrep_id":"111","volume":26,"issue":"2","publisher":"Wiley-Blackwell","file_date_updated":"2020-07-14T12:45:52Z","publist_id":"3835","intvolume":"        26","status":"public","month":"01","date_created":"2018-12-11T12:00:17Z"},{"oa_version":"Submitted Version","date_updated":"2021-01-12T07:00:37Z","type":"journal_article","day":"16","article_processing_charge":"No","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"department":[{"_id":"NiBa"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"doi":"10.1088/1742-5468/2013/01/P01002","file":[{"creator":"system","content_type":"application/pdf","file_size":702583,"date_created":"2018-12-12T10:16:52Z","relation":"main_file","access_level":"open_access","checksum":"ce8a4424385b3086138a1e054e16e0e3","file_name":"IST-2016-557-v1+1_BEVrevised.pdf","date_updated":"2020-07-14T12:45:52Z","file_id":"5242"}],"date_published":"2013-01-16T00:00:00Z","scopus_import":1,"year":"2013","citation":{"chicago":"Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “Modelling Evolution in a Spatial Continuum.” <i>Journal of Statistical Mechanics Theory and Experiment</i>. IOP Publishing Ltd., 2013. <a href=\"https://doi.org/10.1088/1742-5468/2013/01/P01002\">https://doi.org/10.1088/1742-5468/2013/01/P01002</a>.","short":"N.H. Barton, A. Etheridge, A. Véber, Journal of Statistical Mechanics Theory and Experiment 2013 (2013).","ista":"Barton NH, Etheridge A, Véber A. 2013. Modelling evolution in a spatial continuum. Journal of Statistical Mechanics Theory and Experiment. 2013(1).","ieee":"N. H. Barton, A. Etheridge, and A. Véber, “Modelling evolution in a spatial continuum,” <i>Journal of Statistical Mechanics Theory and Experiment</i>, vol. 2013, no. 1. IOP Publishing Ltd., 2013.","ama":"Barton NH, Etheridge A, Véber A. Modelling evolution in a spatial continuum. <i>Journal of Statistical Mechanics Theory and Experiment</i>. 2013;2013(1). doi:<a href=\"https://doi.org/10.1088/1742-5468/2013/01/P01002\">10.1088/1742-5468/2013/01/P01002</a>","apa":"Barton, N. H., Etheridge, A., &#38; Véber, A. (2013). Modelling evolution in a spatial continuum. <i>Journal of Statistical Mechanics Theory and Experiment</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/1742-5468/2013/01/P01002\">https://doi.org/10.1088/1742-5468/2013/01/P01002</a>","mla":"Barton, Nicholas H., et al. “Modelling Evolution in a Spatial Continuum.” <i>Journal of Statistical Mechanics Theory and Experiment</i>, vol. 2013, no. 1, IOP Publishing Ltd., 2013, doi:<a href=\"https://doi.org/10.1088/1742-5468/2013/01/P01002\">10.1088/1742-5468/2013/01/P01002</a>."},"author":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"last_name":"Etheridge","first_name":"Alison","full_name":"Etheridge, Alison"},{"last_name":"Véber","first_name":"Amandine","full_name":"Véber, Amandine"}],"quality_controlled":"1","project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"abstract":[{"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.","lang":"eng"}],"publication_status":"published","publication":"Journal of Statistical Mechanics Theory and Experiment","title":"Modelling evolution in a spatial continuum","_id":"2909","oa":1,"ddc":["570"],"file_date_updated":"2020-07-14T12:45:52Z","publisher":"IOP Publishing Ltd.","pubrep_id":"557","volume":2013,"issue":"1","month":"01","date_created":"2018-12-11T12:00:17Z","status":"public","intvolume":"      2013","publist_id":"3834"},{"publisher":"Oxford University Press","file_date_updated":"2020-07-14T12:45:52Z","volume":29,"issue":"7","pubrep_id":"556","status":"public","date_created":"2018-12-11T12:00:17Z","month":"02","publist_id":"3833","intvolume":"        29","year":"2013","quality_controlled":"1","author":[{"full_name":"Kelleher, Jerome","first_name":"Jerome","last_name":"Kelleher"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"full_name":"Etheridge, Alison","last_name":"Etheridge","first_name":"Alison"}],"citation":{"mla":"Kelleher, Jerome, et al. “Coalescent Simulation in Continuous Space.” <i>Bioinformatics</i>, vol. 29, no. 7, Oxford University Press, 2013, pp. 955–56, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btt067\">10.1093/bioinformatics/btt067</a>.","apa":"Kelleher, J., Barton, N. H., &#38; Etheridge, A. (2013). Coalescent simulation in continuous space. <i>Bioinformatics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bioinformatics/btt067\">https://doi.org/10.1093/bioinformatics/btt067</a>","ama":"Kelleher J, Barton NH, Etheridge A. Coalescent simulation in continuous space. <i>Bioinformatics</i>. 2013;29(7):955-956. doi:<a href=\"https://doi.org/10.1093/bioinformatics/btt067\">10.1093/bioinformatics/btt067</a>","ieee":"J. Kelleher, N. H. Barton, and A. Etheridge, “Coalescent simulation in continuous space,” <i>Bioinformatics</i>, vol. 29, no. 7. Oxford University Press, pp. 955–956, 2013.","chicago":"Kelleher, Jerome, Nicholas H Barton, and Alison Etheridge. “Coalescent Simulation in Continuous Space.” <i>Bioinformatics</i>. Oxford University Press, 2013. <a href=\"https://doi.org/10.1093/bioinformatics/btt067\">https://doi.org/10.1093/bioinformatics/btt067</a>.","short":"J. Kelleher, N.H. Barton, A. Etheridge, Bioinformatics 29 (2013) 955–956.","ista":"Kelleher J, Barton NH, Etheridge A. 2013. Coalescent simulation in continuous space. Bioinformatics. 29(7), 955–956."},"publication_status":"published","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."}],"project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"ddc":["570"],"oa":1,"_id":"2910","publication":"Bioinformatics","title":"Coalescent simulation in continuous space","page":"955 - 956","date_published":"2013-02-07T00:00:00Z","file":[{"creator":"system","content_type":"application/pdf","file_size":170197,"date_created":"2018-12-12T10:16:04Z","relation":"main_file","access_level":"open_access","checksum":"a3b54d7477fac923815ac082403d9bd0","file_name":"IST-2016-556-v1+1_bioinformatics-2013.pdf","date_updated":"2020-07-14T12:45:52Z","file_id":"5189"}],"scopus_import":1,"day":"07","type":"journal_article","date_updated":"2021-01-12T07:00:38Z","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1093/bioinformatics/btt067","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"has_accepted_license":"1","ec_funded":1},{"status":"public","date_created":"2018-12-11T12:00:28Z","month":"02","publist_id":"3788","intvolume":"        22","publisher":"Wiley-Blackwell","volume":22,"issue":"4","publication_status":"published","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."}],"related_material":{"record":[{"id":"9758","status":"public","relation":"research_data"}]},"_id":"2944","title":"Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. ","publication":"Molecular Ecology","year":"2013","author":[{"first_name":"Simon","last_name":"Aeschbacher","id":"2D35326E-F248-11E8-B48F-1D18A9856A87","full_name":"Aeschbacher, Simon"},{"full_name":"Futschik, Andreas","last_name":"Futschik","first_name":"Andreas"},{"last_name":"Beaumont","first_name":"Mark","full_name":"Beaumont, Mark"}],"quality_controlled":"1","citation":{"apa":"Aeschbacher, S., Futschik, A., &#38; Beaumont, M. (2013). Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . <i>Molecular Ecology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/mec.12165\">https://doi.org/10.1111/mec.12165</a>","mla":"Aeschbacher, Simon, et al. “Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. .” <i>Molecular Ecology</i>, vol. 22, no. 4, Wiley-Blackwell, 2013, pp. 987–1002, doi:<a href=\"https://doi.org/10.1111/mec.12165\">10.1111/mec.12165</a>.","ama":"Aeschbacher S, Futschik A, Beaumont M. Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . <i>Molecular Ecology</i>. 2013;22(4):987-1002. doi:<a href=\"https://doi.org/10.1111/mec.12165\">10.1111/mec.12165</a>","ieee":"S. Aeschbacher, A. Futschik, and M. Beaumont, “Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. ,” <i>Molecular Ecology</i>, 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.","chicago":"Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. .” <i>Molecular Ecology</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1111/mec.12165\">https://doi.org/10.1111/mec.12165</a>.","short":"S. Aeschbacher, A. Futschik, M. Beaumont, Molecular Ecology 22 (2013) 987–1002."},"scopus_import":1,"page":"987 - 1002","date_published":"2013-02-01T00:00:00Z","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).","doi":"10.1111/mec.12165","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"day":"01","date_updated":"2023-02-23T14:07:19Z","type":"journal_article","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"oa_version":"Submitted Version","type":"journal_article","date_updated":"2021-01-12T07:57:25Z","day":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"NiBa"}],"doi":"10.1098/rspb.2012.2058","language":[{"iso":"eng"}],"external_id":{"pmid":["23173202"]},"date_published":"2013-01-07T00:00:00Z","year":"2013","citation":{"ieee":"M. Pickup, D. Field, D. Rowell, and A. Young, “Source population characteristics affect heterosis following genetic rescue of fragmented plant populations,” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 280, no. 1750. Royal Society, The, 2013.","ama":"Pickup M, Field D, Rowell D, Young A. Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. 2013;280(1750). doi:<a href=\"https://doi.org/10.1098/rspb.2012.2058\">10.1098/rspb.2012.2058</a>","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.","chicago":"Pickup, Melinda, David Field, David Rowell, and Andrew Young. “Source Population Characteristics Affect Heterosis Following Genetic Rescue of Fragmented Plant Populations.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society, The, 2013. <a href=\"https://doi.org/10.1098/rspb.2012.2058\">https://doi.org/10.1098/rspb.2012.2058</a>.","short":"M. Pickup, D. Field, D. Rowell, A. Young, Proceedings of the Royal Society of London Series B Biological Sciences 280 (2013).","apa":"Pickup, M., Field, D., Rowell, D., &#38; Young, A. (2013). Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society, The. <a href=\"https://doi.org/10.1098/rspb.2012.2058\">https://doi.org/10.1098/rspb.2012.2058</a>","mla":"Pickup, Melinda, et al. “Source Population Characteristics Affect Heterosis Following Genetic Rescue of Fragmented Plant Populations.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 280, no. 1750, 2058, Royal Society, The, 2013, doi:<a href=\"https://doi.org/10.1098/rspb.2012.2058\">10.1098/rspb.2012.2058</a>."},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574427/","open_access":"1"}],"quality_controlled":"1","author":[{"last_name":"Pickup","first_name":"Melinda","orcid":"0000-0001-6118-0541","full_name":"Pickup, Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David","orcid":"0000-0002-4014-8478","last_name":"Field","first_name":"David"},{"full_name":"Rowell, David","first_name":"David","last_name":"Rowell"},{"last_name":"Young","first_name":"Andrew","full_name":"Young, Andrew"}],"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."}],"publication_status":"published","pmid":1,"title":"Source population characteristics affect heterosis following genetic rescue of fragmented plant populations","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","_id":"450","oa":1,"publisher":"Royal Society, The","volume":280,"issue":"1750","month":"01","date_created":"2018-12-11T11:46:32Z","article_number":"2058","status":"public","intvolume":"       280","publist_id":"7372"},{"status":"public","month":"06","date_created":"2023-05-23T17:01:02Z","publisher":"Dryad","date_published":"2012-06-08T00:00:00Z","abstract":[{"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, C. 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.","lang":"eng"}],"_id":"13075","department":[{"_id":"NiBa"}],"oa":1,"ddc":["570"],"doi":"10.5061/DRYAD.0G0FS","related_material":{"record":[{"id":"2968","status":"public","relation":"used_in_publication"}]},"title":"Data from: A likelihood-based comparison of population histories in a parasitoid guild","year":"2012","day":"08","oa_version":"Published Version","date_updated":"2025-05-28T11:56:58Z","tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"type":"research_data_reference","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Konrad","last_name":"Lohse","full_name":"Lohse, Konrad"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton"},{"last_name":"Stone","first_name":"Graham","full_name":"Stone, Graham"},{"last_name":"Melika","first_name":"George","full_name":"Melika, George"}],"citation":{"ieee":"K. Lohse, N. H. Barton, G. Stone, and G. Melika, “Data from: A likelihood-based comparison of population histories in a parasitoid guild.” Dryad, 2012.","ama":"Lohse K, Barton NH, Stone G, Melika G. Data from: A likelihood-based comparison of population histories in a parasitoid guild. 2012. doi:<a href=\"https://doi.org/10.5061/DRYAD.0G0FS\">10.5061/DRYAD.0G0FS</a>","ista":"Lohse K, Barton NH, Stone G, Melika G. 2012. Data from: A likelihood-based comparison of population histories in a parasitoid guild, Dryad, <a href=\"https://doi.org/10.5061/DRYAD.0G0FS\">10.5061/DRYAD.0G0FS</a>.","chicago":"Lohse, Konrad, Nicholas H Barton, Graham Stone, and George Melika. “Data from: A Likelihood-Based Comparison of Population Histories in a Parasitoid Guild.” Dryad, 2012. <a href=\"https://doi.org/10.5061/DRYAD.0G0FS\">https://doi.org/10.5061/DRYAD.0G0FS</a>.","short":"K. Lohse, N.H. Barton, G. Stone, G. Melika, (2012).","mla":"Lohse, Konrad, et al. <i>Data from: A Likelihood-Based Comparison of Population Histories in a Parasitoid Guild</i>. Dryad, 2012, doi:<a href=\"https://doi.org/10.5061/DRYAD.0G0FS\">10.5061/DRYAD.0G0FS</a>.","apa":"Lohse, K., Barton, N. H., Stone, G., &#38; Melika, G. (2012). Data from: A likelihood-based comparison of population histories in a parasitoid guild. Dryad. <a href=\"https://doi.org/10.5061/DRYAD.0G0FS\">https://doi.org/10.5061/DRYAD.0G0FS</a>"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.0g0fs"}]},{"date_published":"2012-11-14T00:00:00Z","publisher":"Dryad","month":"11","date_created":"2021-07-30T12:36:39Z","status":"public","citation":{"ieee":"S. Aeschbacher, A. Futschik, and M. Beaumont, “Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates.” Dryad, 2012.","ama":"Aeschbacher S, Futschik A, Beaumont M. Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. 2012. doi:<a href=\"https://doi.org/10.5061/dryad.274b1\">10.5061/dryad.274b1</a>","ista":"Aeschbacher S, Futschik A, Beaumont M. 2012. Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates, Dryad, <a href=\"https://doi.org/10.5061/dryad.274b1\">10.5061/dryad.274b1</a>.","chicago":"Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Data from: Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates.” Dryad, 2012. <a href=\"https://doi.org/10.5061/dryad.274b1\">https://doi.org/10.5061/dryad.274b1</a>.","short":"S. Aeschbacher, A. Futschik, M. Beaumont, (2012).","apa":"Aeschbacher, S., Futschik, A., &#38; Beaumont, M. (2012). Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. Dryad. <a href=\"https://doi.org/10.5061/dryad.274b1\">https://doi.org/10.5061/dryad.274b1</a>","mla":"Aeschbacher, Simon, et al. <i>Data from: Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates</i>. Dryad, 2012, doi:<a href=\"https://doi.org/10.5061/dryad.274b1\">10.5061/dryad.274b1</a>."},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.274b1","open_access":"1"}],"author":[{"first_name":"Simon","last_name":"Aeschbacher","full_name":"Aeschbacher, Simon","id":"2D35326E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andreas","last_name":"Futschik","full_name":"Futschik, Andreas"},{"first_name":"Mark","last_name":"Beaumont","full_name":"Beaumont, Mark"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","oa_version":"Published Version","date_updated":"2023-02-23T11:05:19Z","type":"research_data_reference","year":"2012","day":"14","title":"Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates","_id":"9758","department":[{"_id":"NiBa"}],"related_material":{"record":[{"id":"2944","relation":"used_in_publication","status":"public"}]},"oa":1,"doi":"10.5061/dryad.274b1","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."}]},{"scopus_import":1,"publist_id":"3821","intvolume":"        12","status":"public","month":"11","date_created":"2018-12-11T12:00:19Z","volume":12,"issue":"1","page":"53 - 62","date_published":"2012-11-06T00:00:00Z","publisher":"Cambridge University Press","_id":"2917","department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"doi":"10.1017/S1473550412000407","publication":"International Journal of Astrobiology","title":"The game of active search for extra terrestrial intelligence Breaking the Great Silence ","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."}],"publication_status":"published","author":[{"last_name":"Vladar","first_name":"Harold","id":"2A181218-F248-11E8-B48F-1D18A9856A87","full_name":"Vladar, Harold","orcid":"0000-0002-5985-7653"}],"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"H. de Vladar, International Journal of Astrobiology 12 (2012) 53–62.","chicago":"Vladar, Harold de. “The Game of Active Search for Extra Terrestrial Intelligence Breaking the Great Silence .” <i>International Journal of Astrobiology</i>. Cambridge University Press, 2012. <a href=\"https://doi.org/10.1017/S1473550412000407\">https://doi.org/10.1017/S1473550412000407</a>.","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.","ieee":"H. de Vladar, “The game of active search for extra terrestrial intelligence Breaking the Great Silence ,” <i>International Journal of Astrobiology</i>, vol. 12, no. 1. Cambridge University Press, pp. 53–62, 2012.","ama":"de Vladar H. The game of active search for extra terrestrial intelligence Breaking the Great Silence . <i>International Journal of Astrobiology</i>. 2012;12(1):53-62. doi:<a href=\"https://doi.org/10.1017/S1473550412000407\">10.1017/S1473550412000407</a>","mla":"de Vladar, Harold. “The Game of Active Search for Extra Terrestrial Intelligence Breaking the Great Silence .” <i>International Journal of Astrobiology</i>, vol. 12, no. 1, Cambridge University Press, 2012, pp. 53–62, doi:<a href=\"https://doi.org/10.1017/S1473550412000407\">10.1017/S1473550412000407</a>.","apa":"de Vladar, H. (2012). The game of active search for extra terrestrial intelligence Breaking the Great Silence . <i>International Journal of Astrobiology</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/S1473550412000407\">https://doi.org/10.1017/S1473550412000407</a>"},"year":"2012","day":"06","oa_version":"None","date_updated":"2021-01-12T07:00:41Z","type":"journal_article"},{"scopus_import":1,"page":"1027 - 1047","date_published":"2012-11-01T00:00:00Z","external_id":{"pmid":["22960215"]},"doi":"10.1534/genetics.112.143164","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"day":"01","type":"journal_article","date_updated":"2021-01-12T07:40:05Z","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_created":"2018-12-11T12:00:34Z","month":"11","publist_id":"3763","intvolume":"       192","publisher":"Genetics Society of America","issue":"3","volume":192,"publication_status":"published","abstract":[{"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.","lang":"eng"}],"oa":1,"_id":"2962","title":"A novel approach for choosing summary statistics in approximate Bayesian computation","publication":"Genetics","pmid":1,"year":"2012","quality_controlled":"1","author":[{"id":"2D35326E-F248-11E8-B48F-1D18A9856A87","full_name":"Aeschbacher, Simon","last_name":"Aeschbacher","first_name":"Simon"},{"full_name":"Beaumont, Mark","first_name":"Mark","last_name":"Beaumont"},{"last_name":"Futschik","first_name":"Andreas","full_name":"Futschik, Andreas"}],"citation":{"ama":"Aeschbacher S, Beaumont M, Futschik A. A novel approach for choosing summary statistics in approximate Bayesian computation. <i>Genetics</i>. 2012;192(3):1027-1047. doi:<a href=\"https://doi.org/10.1534/genetics.112.143164\">10.1534/genetics.112.143164</a>","ieee":"S. Aeschbacher, M. Beaumont, and A. Futschik, “A novel approach for choosing summary statistics in approximate Bayesian computation,” <i>Genetics</i>, 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.","short":"S. Aeschbacher, M. Beaumont, A. Futschik, Genetics 192 (2012) 1027–1047.","chicago":"Aeschbacher, Simon, Mark Beaumont, and Andreas Futschik. “A Novel Approach for Choosing Summary Statistics in Approximate Bayesian Computation.” <i>Genetics</i>. Genetics Society of America, 2012. <a href=\"https://doi.org/10.1534/genetics.112.143164\">https://doi.org/10.1534/genetics.112.143164</a>.","apa":"Aeschbacher, S., Beaumont, M., &#38; Futschik, A. (2012). A novel approach for choosing summary statistics in approximate Bayesian computation. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.112.143164\">https://doi.org/10.1534/genetics.112.143164</a>","mla":"Aeschbacher, Simon, et al. “A Novel Approach for Choosing Summary Statistics in Approximate Bayesian Computation.” <i>Genetics</i>, vol. 192, no. 3, Genetics Society of America, 2012, pp. 1027–47, doi:<a href=\"https://doi.org/10.1534/genetics.112.143164\">10.1534/genetics.112.143164</a>."},"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3522150/"}]},{"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. ","has_accepted_license":"1","department":[{"_id":"NiBa"}],"doi":"10.1111/j.1365-294X.2012.05700.x","language":[{"iso":"eng"}],"ec_funded":1,"day":"01","oa_version":"Submitted Version","date_updated":"2023-05-30T13:07:47Z","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"page":"4605 - 4617","file":[{"checksum":"c14ee4cb2a8ba9575bfd8a9bb7a883bb","file_name":"IST-2014-296-v1+1_4_wasps_revised3.pdf","access_level":"open_access","file_id":"5304","date_updated":"2020-07-14T12:45:57Z","creator":"system","content_type":"application/pdf","file_size":235820,"relation":"main_file","date_created":"2018-12-12T10:17:47Z"},{"file_id":"5305","date_updated":"2020-07-14T12:45:57Z","checksum":"f00afc5b887c8222014b57375b8caece","file_name":"IST-2014-296-v1+2_4_wasps_Supporting2.pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:17:48Z","file_size":41975,"content_type":"application/pdf","creator":"system"}],"date_published":"2012-09-01T00:00:00Z","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."}],"publication_status":"published","project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"_id":"2968","related_material":{"record":[{"id":"13075","status":"public","relation":"research_data"}]},"ddc":["570","579"],"oa":1,"title":"A likelihood based comparison of population histories in a parasitoid guild","publication":"Molecular Ecology","year":"2012","author":[{"last_name":"Lohse","first_name":"Konrad","full_name":"Lohse, Konrad"},{"first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Melika, George","first_name":"George","last_name":"Melika"},{"full_name":"Stone, Graham","last_name":"Stone","first_name":"Graham"}],"quality_controlled":"1","citation":{"mla":"Lohse, Konrad, et al. “A Likelihood Based Comparison of Population Histories in a Parasitoid Guild.” <i>Molecular Ecology</i>, vol. 21, no. 18, Wiley-Blackwell, 2012, pp. 4605–17, doi:<a href=\"https://doi.org/10.1111/j.1365-294X.2012.05700.x\">10.1111/j.1365-294X.2012.05700.x</a>.","apa":"Lohse, K., Barton, N. H., Melika, G., &#38; Stone, G. (2012). A likelihood based comparison of population histories in a parasitoid guild. <i>Molecular Ecology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1365-294X.2012.05700.x\">https://doi.org/10.1111/j.1365-294X.2012.05700.x</a>","ieee":"K. Lohse, N. H. Barton, G. Melika, and G. Stone, “A likelihood based comparison of population histories in a parasitoid guild,” <i>Molecular Ecology</i>, vol. 21, no. 18. Wiley-Blackwell, pp. 4605–4617, 2012.","ama":"Lohse K, Barton NH, Melika G, Stone G. A likelihood based comparison of population histories in a parasitoid guild. <i>Molecular Ecology</i>. 2012;21(18):4605-4617. doi:<a href=\"https://doi.org/10.1111/j.1365-294X.2012.05700.x\">10.1111/j.1365-294X.2012.05700.x</a>","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.","short":"K. Lohse, N.H. Barton, G. Melika, G. Stone, Molecular Ecology 21 (2012) 4605–4617.","chicago":"Lohse, Konrad, Nicholas H Barton, George Melika, and Graham Stone. “A Likelihood Based Comparison of Population Histories in a Parasitoid Guild.” <i>Molecular Ecology</i>. Wiley-Blackwell, 2012. <a href=\"https://doi.org/10.1111/j.1365-294X.2012.05700.x\">https://doi.org/10.1111/j.1365-294X.2012.05700.x</a>."},"status":"public","month":"09","date_created":"2018-12-11T12:00:36Z","publist_id":"3746","intvolume":"        21","publisher":"Wiley-Blackwell","file_date_updated":"2020-07-14T12:45:57Z","pubrep_id":"296","volume":21,"issue":"18"},{"publist_id":"3577","scopus_import":1,"intvolume":"        21","status":"public","date_created":"2018-12-11T12:01:31Z","month":"08","page":"3640 - 3643","volume":21,"issue":"15","date_published":"2012-08-01T00:00:00Z","publisher":"Wiley-Blackwell","language":[{"iso":"eng"}],"doi":"10.1111/j.1365-294X.2012.05643.x","_id":"3122","department":[{"_id":"NiBa"}],"publication":"Molecular Ecology","title":"Disassortative mating and the maintenance of sexual polymorphism in painted maple","publication_status":"published","abstract":[{"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. ","lang":"eng"}],"author":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","full_name":"Field, David","first_name":"David","last_name":"Field"},{"full_name":"Barrett, Spencer","last_name":"Barrett","first_name":"Spencer"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","citation":{"apa":"Field, D., &#38; Barrett, S. (2012). Disassortative mating and the maintenance of sexual polymorphism in painted maple. <i>Molecular Ecology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1365-294X.2012.05643.x\">https://doi.org/10.1111/j.1365-294X.2012.05643.x</a>","mla":"Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance of Sexual Polymorphism in Painted Maple.” <i>Molecular Ecology</i>, vol. 21, no. 15, Wiley-Blackwell, 2012, pp. 3640–43, doi:<a href=\"https://doi.org/10.1111/j.1365-294X.2012.05643.x\">10.1111/j.1365-294X.2012.05643.x</a>.","ama":"Field D, Barrett S. Disassortative mating and the maintenance of sexual polymorphism in painted maple. <i>Molecular Ecology</i>. 2012;21(15):3640-3643. doi:<a href=\"https://doi.org/10.1111/j.1365-294X.2012.05643.x\">10.1111/j.1365-294X.2012.05643.x</a>","ieee":"D. Field and S. Barrett, “Disassortative mating and the maintenance of sexual polymorphism in painted maple,” <i>Molecular Ecology</i>, 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.","chicago":"Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance of Sexual Polymorphism in Painted Maple.” <i>Molecular Ecology</i>. Wiley-Blackwell, 2012. <a href=\"https://doi.org/10.1111/j.1365-294X.2012.05643.x\">https://doi.org/10.1111/j.1365-294X.2012.05643.x</a>.","short":"D. Field, S. Barrett, Molecular Ecology 21 (2012) 3640–3643."},"day":"01","year":"2012","date_updated":"2021-01-12T07:41:13Z","type":"journal_article","oa_version":"None"}]