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@article{Woods2006,
abstract = {The repeatability of evolutionary change is difficult to quantify because only a single outcome can usually be observed for any precise set of circumstances. In this study, however, we have quantified the frequency of parallel and divergent genetic changes in 12 initially identical populations of Escherichia coli that evolved in identical environments for 20,000 cell generations. Unlike previous analyses in which candidate genes were identified based on parallel phenotypic changes, here we sequenced four loci (pykF, nadR, pbpA-rodA, and hokB/sokB) in which mutations of unknown effect had been discovered in one population, and then we compared the substitution pattern in these "blind" candidate genes with the pattern found in 36 randomly chosen genes. Two candidate genes, pykF and nadR, had substitutions in all 11 other populations, and the other 2 in several populations. There were very few cases, however, in which the exact same mutations were substituted, in contrast to the findings from conceptually related work performed with evolving virus populations. No random genes had any substitutions except in four populations that evolved defects in DNA repair. Tests of four different statistical aspects of the pattern of molecular evolution all indicate that adaptation by natural selection drove the parallel changes in these candidate genes.},
author = {Woods, Robert and Schneider, Dominique and Winkworth, Cynthia L and Riley, Margaret a and Lenski, Richard E},
doi = {10.1073/pnas.0602917103},
file = {:home/cboettig/Documents/Mendeley Desktop/Proceedings of the National Academy of Sciences of the United States of America/Tests of parallel molecular evolution in a long-term experiment with Escherichia coli..pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Animals,Escherichia coli,Escherichia coli: genetics,Evolution, Molecular,Models, Theoretical,Molecular Sequence Data,Mutation,Random Allocation,Time Factors},
month = {June},
number = {24},
pages = {9107--12},
pmid = {16751270},
title = {{Tests of parallel molecular evolution in a long-term experiment with Escherichia coli.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16751270},
volume = {103},
year = {2006}
}
@article{Kirkpatrick2005,
author = {Kirkpatrick, M and Rousset, F},
doi = {10.1111/j.1420-9101.2004.00847.x},
file = {:home/cboettig/Documents/Mendeley Desktop/Journal of evolutionary biology/Wright meets AD not all landscapes are adaptive..pdf:pdf},
issn = {1010-061X},
journal = {Journal of evolutionary biology},
keywords = {Adaptation, Biological,Adaptation, Biological: genetics,Evolution,Game Theory,Genetics, Population,Models, Theoretical,Phenotype,Population Dynamics,Selection, Genetic},
number = {5},
pages = {1166--9},
pmid = {16135106},
title = {{Wright meets AD: not all landscapes are adaptive.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16135106},
volume = {18},
year = {2005}
}
@article{Butlin2005,
author = {Butlin, R K and Tregenza, T},
doi = {10.1111/j.1420-9101.2004.00845.x},
file = {:home/cboettig/Documents/Mendeley Desktop/Journal of evolutionary biology/The way the world might be..pdf:pdf},
issn = {1010-061X},
journal = {Journal of evolutionary biology},
keywords = {Adaptation, Biological,Adaptation, Biological: genetics,Empirical Research,Evolution,Genetics, Population,Models, Theoretical,Population Dynamics,Species Specificity},
number = {5},
pages = {1205--8},
pmid = {16135115},
title = {{The way the world might be.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16135115},
volume = {18},
year = {2005}
}
@article{Kokko2005,
author = {Kokko, H},
doi = {10.1111/j.1420-9101.2004.00853.x},
file = {:home/cboettig/Documents/Mendeley Desktop/Journal of evolutionary biology/Useful ways of being wrong.pdf:pdf},
issn = {1010-061X},
journal = {Journal of evolutionary biology},
keywords = {Adaptation,Biological,Evolution,Genetic,Genetics,Models,Population,Population Dynamics,Selection,Theoretical},
number = {5},
pages = {1155--7},
pmid = {16135103},
title = {{Useful ways of being wrong}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16135103},
volume = {18},
year = {2005}
}
@article{Dieckmann2005,
author = {Dieckmann, Ulf and Doebeli, M.},
doi = {10.1111/j.1420-9101.2005.00960.x},
file = {:home/cboettig/Documents/Mendeley Desktop/Journal of evolutionary biology/Pluralism in evolutionary theory..pdf:pdf},
issn = {1010-061X},
journal = {Journal of evolutionary biology},
keywords = {Adaptation,Biological,Biological: genetics,Evolution,Game Theory,Genetic Variation,Genetics,Models,Population,Population Dynamics,Theoretical},
number = {5},
pages = {1209--13},
pmid = {16135116},
title = {{Pluralism in evolutionary theory.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16135116},
volume = {18},
year = {2005}
}
@article{Perthame2009,
abstract = {Deterministic population models for adaptive dynamics are derived mathematically from individual-centred stochastic models in the limit of large populations. However, it is common that numerical simulations of both models fit poorly and give rather different behaviours in terms of evolution speeds and branching patterns. Stochastic simulations involve extinction phenomenon operating through demographic stochasticity, when the number of individual 'units' is small. Focusing on the class of integro-differential adaptive models, we include a similar notion in the deterministic formulations, a survival threshold, which allows phenotypical traits in the population to vanish when represented by few 'individuals'. Based on numerical simulations, we show that the survival threshold changes drastically the solution; (i) the evolution speed is much slower, (ii) the branching patterns are reduced continuously and (iii) these patterns are comparable to those obtained with stochastic simulations. The rescaled models can also be analysed theoretically. One can recover the concentration phenomena on well-separated Dirac masses through the constrained Hamilton-Jacobi equation in the limit of small mutations and large observation times.},
author = {Perthame, Beno\^{\i}t and Gauduchon, Mathias},
doi = {10.1093/imammb/dqp018},
file = {:home/cboettig/Documents/Mendeley Desktop/Mathematical medicine and biology a journal of the IMA/Survival thresholds and mortality rates in adaptive dynamics conciliating deterministic and stochastic simulations..pdf:pdf},
issn = {1477-8602},
journal = {Mathematical medicine and biology : a journal of the IMA},
keywords = {adaptative dynamics,asymptotic analysis,demographic stochasticity,evolution,evolutionary branching,hamilton-jacobi equation,individual based model},
month = {September},
pmid = {19734200},
title = {{Survival thresholds and mortality rates in adaptive dynamics: conciliating deterministic and stochastic simulations.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19734200},
year = {2009}
}
@article{Claessen2007a,
author = {Claessen, David and Andersson, Jens and Persson, Lennart and de Roos, Andr\'{e} M},
file = {:home/cboettig/Documents/Mendeley Desktop/Evolutionary Ecology Research/Delayed evolutionary branching in small populations.pdf:pdf},
journal = {Evolutionary Ecology Research},
number = {1},
pages = {51–69},
title = {{Delayed evolutionary branching in small populations}},
url = {http://www.environnement.ens.fr/perso/claessen/evad/papers/Claessen\_etal2007.pdf},
volume = {9},
year = {2007}
}
@article{Pelosi2006,
author = {Pelosi, L.},
doi = {10.1534/genetics.105.049619},
file = {:home/cboettig/Documents/Mendeley Desktop/Genetics/Parallel Changes in Global Protein Profiles During Long-Term Experimental Evolution in Escherichia coli.pdf:pdf},
issn = {0016-6731},
journal = {Genetics},
number = {4},
pages = {1851--1869},
title = {{Parallel Changes in Global Protein Profiles During Long-Term Experimental Evolution in Escherichia coli}},
url = {http://www.genetics.org/cgi/doi/10.1534/genetics.105.049619},
volume = {173},
year = {2006}
}
@article{Musset2007,
abstract = {Here we provide direct evidence that two adaptive nucleotide changes in the same codon (268) of the cytochrome b gene (pfcytb) each occurred repeatedly in independent Plasmodium falciparum lineages exposed to the antimalarial drug atovaquone-proguanil (AP). We analyzed the history of 7 AP resistance alleles from clinical isolates by sequencing the mitochondrial (mt) genome that encodes the pfcytb gene and found that a distinct mt haplotype was associated with each AP resistance allele. By comparing mt sequences and microsatellite genotypes of the isolates both before treatment initiation and at the day of failure for each uncured patient, we observed that the AP resistance alleles occurred and spread within the patients. These data demonstrate that identical AP resistance alleles have multiple independent origins and provide an example of parallel evolution driven by drug treatment selection in P. falciparum.},
author = {Musset, Lise and {Le Bras}, Jacques and Clain, J\'{e}r\^{o}me},
doi = {10.1093/molbev/msm087},
file = {:home/cboettig/Documents/Mendeley Desktop/Molecular biology and evolution/Parallel evolution of adaptive mutations in Plasmodium falciparum mitochondrial DNA during atovaquone-proguanil treatment..pdf:pdf},
issn = {0737-4038},
journal = {Molecular biology and evolution},
keywords = {Animals,Antimalarials,Antimalarials: therapeutic use,Atovaquone,Atovaquone: therapeutic use,Base Sequence,Chloroguanide,Chloroguanide: therapeutic use,Cytochromes b,Cytochromes b: genetics,DNA Mutational Analysis,DNA, Mitochondrial,DNA, Mitochondrial: genetics,Drug Resistance,Drug Resistance: genetics,Evolution,Humans,Malaria, Falciparum,Malaria, Falciparum: drug therapy,Malaria, Falciparum: parasitology,Molecular Sequence Data,Mutation,Mutation: genetics,Parasitic Sensitivity Tests,Plasmodium falciparum,Plasmodium falciparum: drug effects,Plasmodium falciparum: genetics,Sequence Homology, Nucleic Acid},
number = {8},
pages = {1582--5},
pmid = {17488741},
title = {{Parallel evolution of adaptive mutations in Plasmodium falciparum mitochondrial DNA during atovaquone-proguanil treatment.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17488741},
volume = {24},
year = {2007}
}
@article{Rueffler2004,
abstract = {The assumption that trade-offs exist is fundamental in evolutionary theory. Levins (Am. Nat. 96 (1962) 361-372) introduced a widely adopted graphical method for analyzing evolution towards an optimal combination of two quantitative traits, which are traded off. His approach explicitly excluded the possibility of density- and frequency-dependent selection. Here we extend Levins method towards models, which include these selection regimes and where therefore fitness landscapes change with population state. We employ the same kind of curves Levins used: trade-off curves and fitness contours. However, fitness contours are not fixed but a function of the resident traits and we only consider those that divide the trait space into potentially successful mutants and mutants which are not able to invade ('invasion boundaries'). The developed approach allows to make a priori predictions about evolutionary endpoints and about their bifurcations. This is illustrated by applying the approach to several examples from the recent literature.},
author = {Rueffler, C. and {Van Dooren}, TJM and Metz, J. A. J.},
doi = {10.1016/j.tpb.2003.10.001},
file = {::},
issn = {0040-5809},
journal = {Theoretical Population Biology},
keywords = {Adaptation,Animals,Biological,Ecology,Evolution,Genetic,Models,Physiological,Population Dynamics,Selection},
number = {2},
pages = {165–178},
pmid = {14766190},
publisher = {Elsevier},
title = {{Adaptive walks on changing landscapes: Levins’ approach extended}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0040580903001333},
volume = {65},
year = {2004}
}
@article{Meszena2005,
author = {Mesz\'{e}na, G\'{e}za},
doi = {10.1111/j.1420-9101.2004.00851.x},
file = {:home/cboettig/Documents/Mendeley Desktop/Journal of evolutionary biology/Adaptive dynamics the continuity argument..pdf:pdf},
issn = {1010-061X},
journal = {Journal of evolutionary biology},
keywords = {Adaptation,Biological,Biological: genetics,Evolution,Genetic,Genetics,Models,Mutation,Mutation: genetics,Phenotype,Population,Population Dynamics,Selection,Species Specificity,Theoretical},
number = {5},
pages = {1182--5},
pmid = {16135110},
title = {{Adaptive dynamics: the continuity argument.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16135110},
volume = {18},
year = {2005}
}
@article{Levins1964,
author = {Levins, Richard},
file = {:home/cboettig/Documents/Mendeley Desktop/Journal of theoretical biology/THEORY OF FITNESS IN A HETEROGENEOUS ENVIRONMENT. 3..pdf:pdf},
journal = {Journal of theoretical biology},
pages = {224--240},
title = {{THEORY OF FITNESS IN A HETEROGENEOUS ENVIRONMENT. 3.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/14212273},
year = {1964}
}
@article{Levins1962,
author = {Levins, Richard},
doi = {10.1086/282223},
file = {:home/cboettig/Documents/Mendeley Desktop/The American Naturalist/Theory of Fitness in a heterogeneous environment. I. The Fitness set and adaptive function.pdf:pdf},
issn = {0003-0147},
journal = {The American Naturalist},
month = {January},
number = {891},
pages = {361--373},
title = {{Theory of Fitness in a heterogeneous environment. I. The Fitness set and adaptive function}},
url = {http://www.journals.uchicago.edu/doi/abs/10.1086/282223},
volume = {96},
year = {1962}
}
@article{Lande1982,
author = {Lande, R.},
file = {:home/cboettig/Documents/Mendeley Desktop/Ecology/A quantitative genetic theory of life history evolution.pdf:pdf},
journal = {Ecology},
number = {3},
pages = {607–615},
publisher = {Ecological Society of America},
title = {{A quantitative genetic theory of life history evolution}},
url = {http://www.jstor.org/stable/1936778},
volume = {63},
year = {1982}
}
@unpublished{Kisdi2004,
author = {Kisdi, E. and Gyllenberg, M.},
booktitle = {Statistics},
file = {:home/cboettig/Documents/Mendeley Desktop/Statistics/On Some Misconceptions About Adaptive Dynamics.pdf:pdf},
institution = {U. of Turku},
number = {624},
series = {TUCS},
title = {{On Some Misconceptions About Adaptive Dynamics}},
year = {2004}
}
@article{Johansson2006,
abstract = {Sympatric speciation requires coexistence of the newly formed species. If divergence proceeds by small mutational steps, the new species utilize almost the same resources initially, and full speciation may be impeded by competitive exclusion in stochastic environments. We investigate this primarily ecological problem of sympatric speciation by studying the population dynamics of a diverging asexual population in a fluctuating environment. Correlation between species responses to environmental fluctuation is assumed to decrease with distance in trait space. Rapidly declining correlation in combination with high environmental variability may delay full speciation or even render it impossible. Stochastic extinctions impeding speciation are most likely when correlation decays faster than competition, for example, when demographic stochasticity is strong or when divergence is not accompanied by niche separation, such as in speciation driven entirely by sexual selection. Our general theoretical results show an interesting connection between short-term ecological dynamics and long-term, large-scale evolution.},
author = {Johansson, Jacob and Ripa, J\"{o}rgen},
doi = {10.1086/507996},
file = {:home/cboettig/Documents/Mendeley Desktop/The American naturalist/Will sympatric speciation fail due to stochastic competitive exclusion.pdf:pdf},
issn = {1537-5323},
journal = {The American naturalist},
keywords = {Computer Simulation,Environment,Extinction, Biological,Genetic Speciation,Genetics, Population,Models, Genetic,Population Dynamics},
month = {October},
number = {4},
pages = {572--8},
pmid = {17004229},
title = {{Will sympatric speciation fail due to stochastic competitive exclusion?}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17004229},
volume = {168},
year = {2006}
}
@article{Doebeli2005,
author = {Doebeli, M. and Dieckmann, Ulf},
file = {:home/cboettig/Documents/Mendeley Desktop/Journal of evolutionary biology/Adaptive dynamics as a mathematical tool for studying the ecology of speciation processes.pdf:pdf},
journal = {Journal of evolutionary biology},
number = {5},
pages = {1194–1200},
publisher = {Basel, Switzerland: Birkhauser, 1987-},
title = {{Adaptive dynamics as a mathematical tool for studying the ecology of speciation processes}},
url = {http://www.lifesci.sussex.ac.uk/home/David\_Waxman/Papers/AD/Commentary11.pdf},
volume = {18},
year = {2005}
}
@article{Gourbiere2005,
author = {Gourbiere, S and Mallet, J},
doi = {10.1111/j.1420-9101.2004.00865.x},
file = {:home/cboettig/Documents/Mendeley Desktop/Journal of evolutionary biology/Has adaptive dynamics contributed to the understanding of adaptive and sympatric speciation.pdf:pdf},
issn = {1010-061X},
journal = {Journal of evolutionary biology},
keywords = {Adaptation, Biological,Adaptation, Biological: genetics,Evolution,Genetics, Population,Models, Theoretical,Mutation,Mutation: genetics,Phenotype,Population Dynamics,Selection, Genetic,Species Specificity},
number = {5},
pages = {1201--4},
pmid = {16135114},
title = {{Has adaptive dynamics contributed to the understanding of adaptive and sympatric speciation?}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16135114},
volume = {18},
year = {2005}
}
@article{Geritz1997,
author = {Geritz, SAH and Kisdi, E. and Mesz\'{e}na, G\'{e}za and Metz, J. A. J.},
file = {:home/cboettig/Documents/Mendeley Desktop/Evolutionary Ecology/Evolutionarily singular strategies and the adaptive growth and branching of the evolutionary tree.pdf:pdf},
journal = {Evolutionary Ecology},
keywords = {adaptive dynamics,evolutionarily singular strategy,evolutionary,evolutionary branching},
number = {1},
pages = {35–57},
publisher = {Springer},
title = {{Evolutionarily singular strategies and the adaptive growth and branching of the evolutionary tree}},
url = {http://www.springerlink.com/index/J7073UU8U1701MG2.pdf},
volume = {12},
year = {1997}
}
@article{Gillespie1975,
author = {Gillespie, John H},
file = {:home/cboettig/Documents/Mendeley Desktop/Genetics/Natural selection for within-generation variance in offspring number II. Discrete Haploid Models.pdf:pdf},
journal = {Genetics},
pages = {403--413},
title = {{Natural selection for within-generation variance in offspring number II. Discrete Haploid Models}},
volume = {81},
year = {1975}
}
@article{Geritz2005,
author = {Geritz, SAH and Gyllenberg, M.},
doi = {10.1111/j.1420-9101.2004.00841.x},
file = {:home/cboettig/Documents/Mendeley Desktop/Journal of evolutionary biology/Seven answers from adaptive dynamics..pdf:pdf},
issn = {1010-061X},
journal = {Journal of evolutionary biology},
keywords = {Adaptation,Biological,Biological: genetics,Evolution,Genetics,Models,Mutation,Mutation: genetics,Phenotype,Population,Population Dynamics,Theoretical},
number = {5},
pages = {1174--7},
pmid = {16135108},
title = {{Seven answers from adaptive dynamics.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16135108},
volume = {18},
year = {2005}
}
@article{Geritz2002,
author = {Geritz, SAH and Gyllenberg, M. and Jacobs, FJA and Parvinen, K.},
file = {:home/cboettig/Documents/Mendeley Desktop/Journal of Mathematical Biology/Invasion dynamics and attractor inheritance.pdf:pdf},
journal = {Journal of Mathematical Biology},
number = {6},
pages = {548–560},
publisher = {Springer},
title = {{Invasion dynamics and attractor inheritance}},
url = {http://www.springerlink.com/index/RW0UV7MJEC91NM0X.pdf},
volume = {44},
year = {2002}
}
@article{Metz2005,
author = {Metz, J. A. J.},
doi = {10.1111/j.1420-9101.2004.00840.x},
file = {:home/cboettig/Documents/Mendeley Desktop/Journal of evolutionary biology/Eight personal rules for doing science..pdf:pdf},
issn = {1010-061X},
journal = {Journal of evolutionary biology},
keywords = {Evolution,Genetics,Mathematics,Models,Population,Science,Science: methods,Terminology as Topic,Theoretical},
number = {5},
pages = {1178--81},
pmid = {16135109},
title = {{Eight personal rules for doing science.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16135109},
volume = {18},
year = {2005}
}
@article{Durinx2008,
abstract = {We develop a systematic toolbox for analyzing the adaptive dynamics of multidimensional traits in physiologically structured population models with point equilibria (sensu Dieckmann et al. in Theor. Popul. Biol. 63:309-338, 2003). Firstly, we show how the canonical equation of adaptive dynamics (Dieckmann and Law in J. Math. Biol. 34:579-612, 1996), an approximation for the rate of evolutionary change in characters under directional selection, can be extended so as to apply to general physiologically structured population models with multiple birth states. Secondly, we show that the invasion fitness function (up to and including second order terms, in the distances of the trait vectors to the singularity) for a community of N coexisting types near an evolutionarily singular point has a rational form, which is model-independent in the following sense: the form depends on the strategies of the residents and the invader, and on the second order partial derivatives of the one-resident fitness function at the singular point. This normal form holds for Lotka-Volterra models as well as for physiologically structured population models with multiple birth states, in discrete as well as continuous time and can thus be considered universal for the evolutionary dynamics in the neighbourhood of singular points. Only in the case of one-dimensional trait spaces or when N = 1 can the normal form be reduced to a Taylor polynomial. Lastly we show, in the form of a stylized recipe, how these results can be combined into a systematic approach for the analysis of the (large) class of evolutionary models that satisfy the above restrictions.},
author = {Durinx, Michel and Metz, J. A. J. and Mesz\'{e}na, G\'{e}za},
doi = {10.1007/s00285-007-0134-2},
file = {:home/cboettig/Documents/Mendeley Desktop/Journal of mathematical biology/Adaptive dynamics for physiologically structured population models..pdf:pdf},
issn = {0303-6812},
journal = {Journal of mathematical biology},
keywords = {Adaptation,Ecosystem,Evolution,Genetic,Models,Mutation,Physiological,Population Dynamics},
number = {5},
pages = {673--742},
pmid = {17943289},
title = {{Adaptive dynamics for physiologically structured population models.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17943289},
volume = {56},
year = {2008}
}
@article{Doebeli2003,
author = {Doebeli, M. and Dieckmann, Ulf},
doi = {10.1038/nature01312.Published},
file = {:home/cboettig/Documents/Mendeley Desktop/Nature/Speciation along environmental gradients.pdf:pdf},
journal = {Nature},
number = {6920},
pages = {259–264},
title = {{Speciation along environmental gradients}},
url = {http://www.iiasa.ac.at/docs/HOTP/Jan03/speciation.pdf},
volume = {421},
year = {2003}
}
@article{Whitlock2003,
abstract = {New alleles arising in a population by mutation ultimately are either fixed or lost. Either is possible, for both beneficial and deleterious alleles, because of stochastic changes in allele frequency due to genetic drift. Spatially structured populations differ from unstructured populations in the probability of fixation and the time that this fixation takes. Previous results have generally made many assumptions: that all demes contribute to the next generation in exact proportion to their current sizes, that new mutations are beneficial, and that new alleles have additive effects. In this article these assumptions are relaxed, allowing for an arbitrary distribution among demes of reproductive success, both beneficial and deleterious effects, and arbitrary dominance. The effects of population structure can be expressed with two summary statistics: the effective population size and a variant of Wright's F(ST). In general, the probability of fixation is strongly affected by population structure, as is the expected time to fixation or loss. Population structure changes the effective size of the species, often strongly downward; smaller effective size increases the probability of fixing deleterious alleles and decreases the probability of fixing beneficial alleles. On the other hand, population structure causes an increase in the homozygosity of alleles, which increases the probability of fixing beneficial alleles but somewhat decreases the probability of fixing deleterious alleles. The probability of fixing new beneficial alleles can be simply described by 2hs(1 - F(ST))N(e)/N(tot), where hs is the change in fitness of heterozygotes relative to the ancestral homozygote, F(ST) is a weighted version of Wright's measure of population subdivision, and N(e) and N(tot) are the effective and census sizes, respectively. These results are verified by simulation for a broad range of population structures, including the island model, the stepping-stone model, and a model with extinction and recolonization.},
author = {Whitlock, Michael C},
file = {:home/cboettig/Documents/Mendeley Desktop/Genetics/Fixation probability and time in subdivided populations..pdf:pdf},
issn = {0016-6731},
journal = {Genetics},
keywords = {Alleles,Diploidy,Extinction, Psychological,Gene Frequency,Genetic Drift,Genetic Variation,Genetics, Population,Heterozygote,Homozygote,Models, Genetic,Models, Statistical,Mutation,Time,Time Factors},
month = {June},
number = {2},
pages = {767--79},
pmid = {12807795},
title = {{Fixation probability and time in subdivided populations.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12807795},
volume = {164},
year = {2003}
}
@article{Watterson1996,
author = {Watterson, G},
doi = {10.1006/tpbi.1996.0010},
file = {:home/cboettig/Documents/Mendeley Desktop/Theoretical Population Biology/Motoo Kimura's Use of Diffusion Theory in Population Genetics.pdf:pdf},
issn = {00405809},
journal = {Theoretical Population Biology},
month = {April},
number = {2},
pages = {154--188},
title = {{Motoo Kimura's Use of Diffusion Theory in Population Genetics}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0040580996900106},
volume = {49},
year = {1996}
}
@article{Champagnat2007a,
arxivId = {arXiv:math/0601643v4},
author = {Champagnat, Nicolas and Lambert, Amaury},
doi = {10.1214/105051606000000628},
file = {:home/cboettig/Documents/Mendeley Desktop/The Annals of Applied Probability/Evolution of discrete populations and the canonical diffusion of adaptive dynamics.pdf:pdf},
issn = {1050-5164},
journal = {The Annals of Applied Probability},
number = {1},
pages = {102--155},
title = {{Evolution of discrete populations and the canonical diffusion of adaptive dynamics}},
url = {http://projecteuclid.org/getRecord?id=euclid.aoap/1171377179},
volume = {17},
year = {2007}
}
@article{Kisdi2005,
author = {Kisdi, E. and Gyllenberg, M.},
file = {:home/cboettig/Documents/Mendeley Desktop/Journal of Evolutionary Biology/Adaptive dynamics and the paradigm of diversity.pdf:pdf},
journal = {Journal of Evolutionary Biology},
number = {5},
pages = {1170–1173},
publisher = {Basel, Switzerland: Birkhauser, 1987-},
title = {{Adaptive dynamics and the paradigm of diversity}},
url = {http://www.lifesci.sussex.ac.uk/home/David\_Waxman/Papers/AD/Commentary5.pdf},
volume = {18},
year = {2005}
}
@article{Diekmann2003,
address = {Warsaw},
author = {Diekmann, Odo},
doi = {10.4064/bc63-0-2},
file = {:home/cboettig/Documents/Mendeley Desktop/Mathematical Modelling of Population Dynamics/A beginner's guide to adaptive dynamics.pdf:pdf},
journal = {Mathematical Modelling of Population Dynamics},
pages = {47--86},
publisher = {Institute of Mathematics Polish Academy of Sciences},
title = {{A beginner's guide to adaptive dynamics}},
url = {http://journals.impan.pl/cgi-bin/doi?bc63-0-2},
volume = {63},
year = {2003}
}
@article{Doebeli2000,
author = {Doebeli, M. and Dieckmann, Ulf},
file = {:home/cboettig/Documents/Mendeley Desktop/the american naturalist/Evolutionary branching and sympatric speciation caused by different types of ecological interactions.pdf:pdf},
journal = {the american naturalist},
number = {S4},
pages = {77–101},
publisher = {UChicago Press},
title = {{Evolutionary branching and sympatric speciation caused by different types of ecological interactions}},
url = {http://www.journals.uchicago.edu/doi/abs/10.1086/303417},
volume = {156},
year = {2000}
}
@article{Mylius2001,
author = {Mylius, S.D. and Diekmann, Odo},
file = {:home/cboettig/Documents/Mendeley Desktop/Journal of Theoretical Biology/The resident strikes back invader-induced switching of resident attractor.pdf:pdf},
journal = {Journal of Theoretical Biology},
number = {4},
pages = {297–311},
publisher = {Elsevier},
title = {{The resident strikes back: invader-induced switching of resident attractor}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0022519301923495},
volume = {211},
year = {2001}
}
@article{Claessen2008,
abstract = {Recent theory suggests that absolute population size may qualitatively influence the outcome of evolution under disruptive selection in asexual populations. Large populations are predicted to undergo rapid evolutionary branching; however, in small populations, the waiting time to branching increases steeply with decreasing abundance, and below a critical size, the population remains monomorphic indefinitely. Here, we (1) extend the theory to sexual populations and (2) confront its predictions with empirical data, testing statistically whether lake size affects the level of resource polymorphism in arctic char (Salvelinus alpinus) in 22 lakes of different sizes. For a given level of recombination, our model predicts qualitatively similar relations between population size and time to evolutionary branching (either speciation or evolution of genetic polymorphism) as the asexual model, while recombination further increases the delay to branching. The loss of polymorphism at certain loci, an inherent aspect of multilocus-trait evolution, may increase the delay to speciation, resulting in stable genetic polymorphism without speciation. The empirical analysis demonstrates that the occurrence of resource polymorphism depends on both lake size and the number of coexisting fish species. For a given number of coexisting species, the level of polymorphism increases significantly with lake size, thus confirming our model prediction.},
author = {Claessen, David and Andersson, Jens and Persson, Lennart and de Roos, Andr\'{e} M},
doi = {10.1086/588062},
file = {:home/cboettig/Documents/Mendeley Desktop/The American naturalist/The effect of population size and recombination on delayed evolution of polymorphism and speciation in sexual populations..pdf:pdf},
issn = {1537-5323},
journal = {The American naturalist},
keywords = {Animals,Ecosystem,Evolution,Fresh Water,Genetic Speciation,Genotype,Models, Biological,Mutation,Polymorphism, Genetic,Population Density,Reproduction,Reproduction: genetics,Reproduction: physiology,Time Factors,Trout,Trout: genetics,Trout: physiology},
number = {1},
pages = {E18--34},
pmid = {18481920},
title = {{The effect of population size and recombination on delayed evolution of polymorphism and speciation in sexual populations.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18481920},
volume = {172},
year = {2008}
}
@article{Claessen2007,
author = {Claessen, David and Andersson, Jens and Persson, Lennart and de Roos, Andr\'{e} M},
file = {:home/cboettig/Documents/Mendeley Desktop/Evolutionary Ecology Research/Delayed evolutionary branching in small populations.pdf:pdf},
journal = {Evolutionary Ecology Research},
keywords = {adaptive dynamics,demographic stochasticity,evolutionary branching,extinction,finite population size,incipient species,random genetic drift},
number = {1},
pages = {51–69},
title = {{Delayed evolutionary branching in small populations}},
url = {http://www.environnement.ens.fr/perso/claessen/evad/papers/Claessen\_etal2007.pdf},
volume = {9},
year = {2007}
}
@article{Dieckmann1996b,
author = {Dieckmann, Ulf and Law, Richard},
file = {:home/cboettig/Documents/Mendeley Desktop/J. Math. Biol/The dynamical theory of coevolution a derivation from stochastic ecological processes.pdf:pdf},
journal = {Journal of Mathematical Biology},
number = {5},
pages = {579–612},
publisher = {Springer},
title = {{The dynamical theory of coevolution: a derivation from stochastic ecological processes}},
url = {http://www.springerlink.com/index/K222445823186421.pdf},
volume = {34},
year = {1996}
}
@article{Champagnat2006,
author = {Champagnat, Nicolas},
doi = {10.1016/j.spa.2006.01.004},
file = {:home/cboettig/Documents/Mendeley Desktop/Stochastic Processes and their Applications/A microscopic interpretation for adaptive dynamics trait substitution sequence models.pdf:pdf},
issn = {03044149},
journal = {Stochastic Processes and their Applications},
keywords = {adaptive dynamics,branching processes,darwinian evolution,finite dimensional distributions convergence,interacting particle system,large deviations,measure-valued process,mutation-selection processes,stochastic domination,timescale separation,trait substitution sequence},
number = {8},
pages = {1127--1160},
title = {{A microscopic interpretation for adaptive dynamics trait substitution sequence models}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0304414906000056},
volume = {116},
year = {2006}
}
@article{Barton2005,
author = {Barton, N.H. and Polechov\'{a}, J.},
file = {:home/cboettig/Documents/Mendeley Desktop/Journal of evolutionary biology/The limitations of adaptive dynamics as a model of evolution.pdf:pdf},
journal = {Journal of evolutionary biology},
pages = {90},
title = {{The limitations of adaptive dynamics as a model of evolution}},
url = {http://bartongroup.icapb.ed.ac.uk/resources/papers/JitkaPhD.pdf\#page=91},
volume = {1186-1190},
year = {2005}
}
@article{Abrams2005,
author = {Abrams, Peter a.},
doi = {10.1111/j.1420-9101.2004.00843.x},
file = {:home/cboettig/Documents/Mendeley Desktop/Journal of evolutionary biology/'Adaptive Dynamics' vs. 'adaptive dynamics'..pdf:pdf},
issn = {1010-061X},
journal = {Journal of evolutionary biology},
keywords = {Adaptation,Biological,Biological: genetics,Evolution,Genetic,Genetics,Models,Mutation,Mutation: genetics,Phenotype,Population,Population Dynamics,Selection,Theoretical},
number = {5},
pages = {1162--5},
pmid = {16135105},
title = {{'Adaptive Dynamics' vs. 'adaptive dynamics'.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16135105},
volume = {18},
year = {2005}
}
@article{Spencer2005,
author = {Spencer, H G and Feldman, M W},
doi = {10.1111/j.1420-9101.2004.00842.x},
file = {:home/cboettig/Documents/Mendeley Desktop/Journal of evolutionary biology/Adaptive dynamics, game theory and evolutionary population genetics..pdf:pdf},
issn = {1010-061X},
journal = {Journal of evolutionary biology},
keywords = {Adaptation, Biological,Adaptation, Biological: genetics,Evolution,Game Theory,Genetics, Population,Models, Theoretical,Phenotype,Population Dynamics,Selection, Genetic},
number = {5},
pages = {1191--3},
pmid = {16135112},
title = {{Adaptive dynamics, game theory and evolutionary population genetics.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16135112},
volume = {18},
year = {2005}
}
@article{Abrams1993,
author = {Abrams, Peter a. and Matsuda, Hiroyuki and Harada, Yasushi},
doi = {10.1007/BF01237642},
file = {:home/cboettig/Documents/Mendeley Desktop/Evolutionary Ecology/Evolutionarily unstable fitness maxima and stable fitness minima of continuous traits.pdf:pdf},
issn = {0269-7653},
journal = {Evolutionary Ecology},
keywords = {continuous traits,evolutionary stable strategy,fitness,frequency dependence},
month = {September},
number = {5},
pages = {465--487},
title = {{Evolutionarily unstable fitness maxima and stable fitness minima of continuous traits}},
url = {http://www.springerlink.com/index/10.1007/BF01237642},
volume = {7},
year = {1993}
}
@article{Boettiger2010,
abstract = {We derive an expression for the variation between parallel trajectories in phenotypic evolution, extending the well known result that predicts the mean evolutionary path in adaptive dynamics or quantitative genetics. We show how this expression gives rise to the notion of fluctuation domains-parts of the fitness landscape where the rate of evolution is very predictable (due to fluctuation dissipation) and parts where it is highly variable (due to fluctuation enhancement). These fluctuation domains are determined by the curvature of the fitness landscape. Regions of the fitness landscape with positive curvature, such as adaptive valleys or branching points, experience enhancement. Regions with negative curvature, such as adaptive peaks, experience dissipation. We explore these dynamics in the ecological scenarios of implicit and explicit competition for a limiting resource.},
author = {Boettiger, Carl and Dushoff, Jonathan and Weitz, Joshua S},
doi = {10.1016/j.tpb.2009.10.003},
file = {:home/cboettig/Documents/Mendeley Desktop/Theoretical population biology/Fluctuation domains in adaptive evolution..pdf:pdf},
issn = {1096-0325},
journal = {Theoretical population biology},
number = {1},
pages = {6--13},
pmid = {19843477},
title = {{Fluctuation domains in adaptive evolution.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19843477},
volume = {77},
year = {2010}
}
@article{Dieckmann1999a,
author = {Dieckmann, Ulf and Doebeli, M.},
file = {:home/cboettig/Documents/Mendeley Desktop/Nature/On the origin of species by sympatric speciation.pdf:pdf},
journal = {Nature},
number = {6742},
pages = {354–357},
publisher = {Nature Publishing Group},
title = {{On the origin of species by sympatric speciation}},
url = {http://www.nature.com/nature/journal/v400/n6742/abs/400354a0.html},
volume = {400},
year = {1999}
}
@article{Lambert2006,
abstract = {We link two-allele population models by Haldane and Fisher with Kimura's diffusion approximations of the Wright-Fisher model, by considering continuous-state branching (CB) processes which are either independent (model I) or conditioned to have constant sum (model II). Recent works by the author allow us to further include logistic density-dependence (model III), which is ubiquitous in ecology. In all models, each allele (mutant or resident) is then characterized by a triple demographic trait: intrinsic growth rate r, reproduction variance sigma and competition sensitivity c. Generally, the fixation probability u of the mutant depends on its initial proportion p, the total initial population size z, and the six demographic traits. Under weak selection, we can linearize u in all models thanks to the same master formula u = p + p(1 - p)[g(r)s(r) + g(sigma)s(sigma) + g(c)s(c)] + o(s(r),s(sigma),s(c), where s(r) = r' - r, s(sigma) = sigma-sigma' and s(c) = c - c' are selection coefficients, and g(r), g(sigma), g(c) are invasibility coefficients (' refers to the mutant traits), which are positive and do not depend on p. In particular, increased reproduction variance is always deleterious. We prove that in all three models g(sigma) = 1/sigma and g(r) = z/sigma for small initial population sizes z. In model II, g(r) = z/sigma for all z, and we display invasion isoclines of the 'mean vs variance' type. A slight departure from the isocline is shown to be more beneficial to alleles with low sigma than with high r. In model III, g(c) increases with z like ln(z)/c, and g(r)(z) converges to a finite limit L > K/sigma, where K = r/c is the carrying capacity. For r > 0 the growth invasibility is above z/sigma when z < K, and below z/sigma when z > K, showing that classical models I and II underestimate the fixation probabilities in growing populations, and overestimate them in declining populations.},
author = {Lambert, Amaury},
doi = {10.1016/j.tpb.2006.01.002},
file = {:home/cboettig/Documents/Mendeley Desktop/Theoretical population biology/Probability of fixation under weak selection a branching process unifying approach..pdf:pdf},
issn = {0040-5809},
journal = {Theoretical population biology},
keywords = {Alleles,Animals,Evolution, Molecular,Genetic Speciation,Genetics, Population,Genetics, Population: statistics \& numerical data,Linkage (Genetics),Logistic Models,Models, Genetic,Mutation,Population Density,Population Dynamics,Probability,Selection (Genetics),Stochastic Processes},
number = {4},
pages = {419--41},
pmid = {16504230},
title = {{Probability of fixation under weak selection: a branching process unifying approach.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16504230},
volume = {69},
year = {2006}
}
@article{Boettiger2007a,
author = {Boettiger, Carl},
file = {:home/cboettig/Documents/Mendeley Desktop/Unknown/Adaptive Dynamics Branching Phenomena and the Canonical Equation.pdf:pdf},
title = {{Adaptive Dynamics: Branching Phenomena and the Canonical Equation}},
year = {2007}
}
@article{Dieckmann1999,
abstract = {Understanding speciation is a fundamental biological problem. It is believed that many species originated through allopatric divergence, where new species arise from geographically isolated populations of the same ancestral species. In contrast, the possibility of sympatric speciation (in which new species arise without geographical isolation) has often been dismissed, partly because of theoretical difficulties. Most previous models analysing sympatric speciation concentrated on particular aspects of the problem while neglecting others. Here we present a model that integrates a novel combination of different features and show that sympatric speciation is a likely outcome of competition for resources. We use multilocus genetics to describe sexual reproduction in an individual-based model, and we consider the evolution of assortative mating (where individuals mate preferentially with like individuals) depending either on an ecological character affecting resource use or on a selectively neutral marker trait. In both cases, evolution of assortative mating often leads to reproductive isolation between ecologically diverging subpopulations. When assortative mating depends on a marker trait, and is therefore not directly linked to resource competition, speciation occurs when genetic drift breaks the linkage equilibrium between the marker and the ecological trait. Our theory conforms well with mounting empirical evidence for the sympatric origin of many species.},
author = {Dieckmann, Ulf and Doebeli, M.},
doi = {10.1038/22521},
file = {:home/cboettig/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Dieckmann, Doebeli - 1999 - On the origin of species by sympatric speciation..pdf:pdf},
issn = {0028-0836},
journal = {Nature},
keywords = {Animal,Animals,Biological,Competitive Behavior,Ecology,Evolution,Genetic,Models,Reproduction,Sexual Behavior,Species Specificity,Stochastic Processes},
month = {July},
number = {6742},
pages = {354--7},
pmid = {10432112},
title = {{On the origin of species by sympatric speciation.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10432112},
volume = {400},
year = {1999}
}
@article{Dieckmann1996,
abstract = {In this paper we develop a dynamical theory of coevolution in ecological communities. The derivation explicitly accounts for the stochastic components of evolutionary change and is based on ecological processes at the level of the individual. We show that the coevolutionary dynamic can be envisaged as a directed random walk in the community's trait space. A quantitative description of this stochastic process in terms of a master equation is derived. By determining the first jump moment of this process we abstract the dynamic of the mean evolutionary path. To first order the resulting equation coincides with a dynamic that has frequently been assumed in evolutionary game theory. Apart from recovering this canonical equation we systematically establish the underlying assumptions. We provide higher order corrections and show that these can give rise to new, unexpected evolutionary effects including shifting evolutionary isoclines and evolutionary slowing down of mean paths as they approach evolutionary equilibria. Extensions of the derivation to more general ecological settings are discussed. In particular we allow for multi-trait coevolution and analyze coevolution under nonequilibrium population dynamics.},
author = {Law, Richard},
file = {:home/cboettig/Documents/Mendeley Desktop/Journal of mathematical biology/The dynamical theory of coevolution a derivation from stochastic ecological processes..pdf:pdf},
issn = {0303-6812},
journal = {Journal of mathematical biology},
keywords = {Animals,Biological,Ecology,Ecosystem,Evolution,Game Theory,Genetic,Mathematics,Models,Mutation,Polymorphism,Predatory Behavior,Selection (Genetics),Stochastic Processes},
month = {January},
number = {5-6},
pages = {579--612},
pmid = {8691086},
title = {{The dynamical theory of coevolution: a derivation from stochastic ecological processes.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/8691086},
volume = {34},
year = {1996}
}

repository: cboettig/AdaptiveDynamics

license_type: permissive

repo_name: cboettig/AdaptiveDynamics

branch_name: refs/heads/master

extension: bib


text:
DESCRIPTION = "Video 4 Linux 2 Tools for Bug 2.0"
LICENSE = "BSD"
DEPENDS = "virtual/kernel python"

inherit distutils-base

PV = "0.01"
PR = "r2"

PACKAGE_ARCH = "${MACHINE_ARCH}"
COMPATIBLE_MACHINE = "bug20"

SRCREV = "8321b5766b464a4cf80ff5f1c03276ee7f136d81"
SRC_URI = "git://gitorious.org/bl-camera2-test-app/bl-camera2-test-app.git;protocol=git"

S = "${WORKDIR}/git"

EXTRA_OEMAKE += " KDIR=${STAGING_KERNEL_DIR} OE_PATH=${STAGING_INCDIR} "

do_install () {
    install -d ${D}${bindir}/
    install -m 0755 ${S}/bug2v4l2 ${D}${bindir}/

    install -d ${D}${libdir}/${PYTHON_DIR}/site-packages/bug2v4l2
    install -m 0755 ${S}/python/build/bug2v4l2/* ${D}${libdir}/${PYTHON_DIR}/site-packages/bug2v4l2

    install -d ${D}${datadir}/bug2v4l2/examples
    install -m 0755 ${S}/python/examples/* ${D}${datadir}/bug2v4l2/examples
    install -m 0755 ${S}/examples/* ${D}${datadir}/bug2v4l2/examples
}

FILES_${PN} += "${bindir}/bug2v4l2"
FILES_${PN} += "${libdir}/${PYTHON_DIR}/site-packages/bug2v4l2"
FILES_${PN}-debug += "${bindir}/.debug/bug2v4l2"

PACKAGES =+ "${PN}-examples"
FILES_${PN}-examples = "${datadir}/bug2v4l2/examples"

license: MIT

repository: overo/overo-oe-natty

repo_name: overo/overo-oe-natty

branch_name: HEAD

extension: bb


text:
# Copyright (c) 2013 LG Electronics, Inc.

SUMMARY = "BMP Library"
DESCRIPTION = "Libnsbmp is a decoding library for BMP and ICO image file formats, written in C"
HOMEPAGE = "http://www.netsurf-browser.org/projects/libnsbmp/"
SECTION = "libs"
LICENSE = "MIT"
LIC_FILES_CHKSUM = "file://COPYING;beginline=7;md5=f2b61f6f29dddc6cffb3a86382ff97b1"

inherit autotools pkgconfig cmake

SRC_URI = "http://download.netsurf-browser.org/libs/releases/${BP}-src.tar.gz \
           file://replace-makefile-with-cmake.patch"
SRC_URI[md5sum] = "5b33ff44dfb48e628bcadbe7e51edf90"
SRC_URI[sha256sum] = "fb576af6bd4d02d3626d5c2092bc06c80b2a80089a14decf40c813d9ec80ddc0"

repository: skrishnakar/meta-webos-ports

repo_name: skrishnakar/meta-webos-ports


text:
// Copyright 2021 The Chromium Authors. All rights reserved.
// Use of this source code is governed by a BSD-style license that can be
// found in the LICENSE file.

#ifndef CC_TEST_LOTTIE_TEST_DATA_H_
#define CC_TEST_LOTTIE_TEST_DATA_H_

#include "base/strings/string_piece.h"

namespace cc {

// A skottie animation with solid green color for the first 2.5 seconds and then
// a solid blue color for the next 2.5 seconds.
constexpr base::StringPiece kLottieDataWithoutAssets1 =
    R"({
      "v" : "4.12.0",
      "fr": 30,
      "w" : 400,
      "h" : 200,
      "ip": 0,
      "op": 150,
      "assets": [],
      "layers": [
        {
          "ty": 1,
          "sw": 400,
          "sh": 200,
          "sc": "#00ff00",
          "ip": 0,
          "op": 75
        },
        {
          "ty": 1,
          "sw": 400,
          "sh": 200,
          "sc": "#0000ff",
          "ip": 76,
          "op": 150
        }
      ]
    })";

// A skottie animation with solid green color for the first second and then
// a solid blue color for the next second.
constexpr base::StringPiece kLottieDataWithoutAssets2 =
    R"({
      "v" : "4.12.0",
      "fr": 30,
      "w" : 400,
      "h" : 200,
      "ip": 0,
      "op": 60,
      "assets": [],
      "layers": [
        {
          "ty": 1,
          "sw": 400,
          "sh": 200,
          "sc": "#00ff00",
          "ip": 0,
          "op": 30
        },
        {
          "ty": 1,
          "sw": 400,
          "sh": 200,
          "sc": "#0000ff",
          "ip": 31,
          "op": 60
        }
      ]
    })";

}  // namespace cc

#endif  // CC_TEST_LOTTIE_TEST_DATA_H_

repository: ddbxzz/chromium

repo_name: ddbxzz/chromium

extension: h