Arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. Arlequin 3 introduces a completely new graphical interface written in C++, a more robust semantic analysis of input files, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism. Arlequin can handle several data types like DNA sequences, microsatellite data, or standard multi-locus genotypes. A Windows version of the software is freely available on http://cmpg.unibe.ch/software/arlequin3.

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Arlequin (version 3.0): An integrated software package for population genetics data analysis

1 GAs: What Are They?.- 2 GAs: How Do They Work?.- 3 GAs: Why Do They Work?.- 4 GAs: Selected Topics.- 5 Binary or Float?.- 6 Fine Local Tuning.- 7 Handling Constraints.- 8 Evolution Strategies and Other Methods.- 9 The Transportation Problem.- 10 The Traveling Salesman Problem.- 11 Evolution Programs for Various Discrete Problems.- 12 Machine Learning.- 13 Evolutionary Programming and Genetic Programming.- 14 A Hierarchy of Evolution Programs.- 15 Evolution Programs and Heuristics.- 16 Conclusions.- Appendix A.- Appendix B.- Appendix C.- Appendix D.- References.

Genetic Algorithms + Data Structures = Evolution Programs

Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

Stakeholder theory has been a popular heuristic for describing the management environment for years, but it has not attained full theoretical status. Our aim in this article is to contribute to a theory of stakeholder identification and salience based on stakeholders possessing one or more of three relationship attributes: power, legitimacy, and urgency. By combining these attributes, we generate a typology of stakeholders, propositions concerning their salience to managers of the firm, and research and management implications.

https://www.jstor.org/stable/pdfplus/259247.pdf

Toward a Theory of Stakeholder Identification and Salience: Defining the Principle of who and What Really Counts

Ecological changes in the phenology and distribution of plants and animals are occurring in all well-studied marine, freshwater, and terrestrial groups These observed changes are heavily biased in the directions predicted from global warming and have been linked to local or regional climate change through correlations between climate and biological variation, field and laboratory experiments, and physiological research Range-restricted species, particularly polar and mountaintop species, show severe range contractions and have been the first groups in which entire species have gone extinct due to recent climate change Tropical coral reefs and amphibians have been most negatively affected Predator-prey and plant-insect interactions have been disrupted when interacting species have responded differently to warming Evolutionary adaptations to warmer conditions have occurred in the interiors of species’ ranges, and resource use and dispersal have evolved rapidly at expanding range margins Observed genetic shifts modulate local effects of climate change, but there is little evidence that they will mitigate negative effects at the species level

https://www.fws.gov/southwest/es/documents/R2ES/LitCited/LPC_2012/Parmesan_2006.pdf

Ecological and Evolutionary Responses to Recent Climate Change

The Selfish Gene

An adaptationist programme has dominated evolutionary thought in England and the United States during the past 40 years. It is based on faith in the power of natural selection as an optimizing agent. It proceeds by breaking an organism into unitary ‘traits’ and proposing an adaptive story for each considered separately. Trade-offs among competing selective demands exert the only brake upon perfection; non-optimality is thereby rendered as a result of adaptation as well. We criticize this approach and attempt to reassert a competing notion (long popular in continental Europe) that organisms must be analysed as integrated wholes, with Baupläne so constrained by phyletic heritage, pathways of development and general architecture that the constraints themselves become more interesting and more important in delimiting pathways of change than the selective force that may mediate change when it occurs. We fault the adaptationist programme for its failure to distinguish current utility from reasons for origin (male tyrannosaurs may have used their diminutive front legs to titillate female partners, but this will not explain why they got so small); for its unwillingness to consider alternatives to adaptive stories; for its reliance upon plausibility alone as a criterion for accepting speculative tales; and for its failure to consider adequately such competing themes as random fixation of alleles, production of non-adaptive structures by developmental correlation with selected features (allometry, pleiotropy, material compensation, mechanically forced correlation), the separability of adaptation and selection, multiple adaptive peaks, and current utility as an epiphenomenon of non-adaptive structures. We support Darwin’s own pluralistic approach to identifying the agents of evolutionary change.

The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme

An adaptationist programme has dominated evolutionary thought in England and the United States during the past 40 years. It is based on faith in the power of natural selection as an optimizing agent. It proceeds by breaking an organism into unitary 'traits' and proposing an adaptive story for each considered separately. Trade-offs among competing selective demands exert the onlv brake upon perfection; non-optimality is thereby rendered as a result of adaptation as well. We criticize this approach and attempt to reassert a competing notion (long popular in continental Europe) that organisms must be analysed as integrated wholes, with Bauplane so constrained by phyletic heritage, pathways of development and general architecture that the constraints themselves become more interesting and more important in delimiting pathways of change than the selective force that may mediate change when it occurs. We fault the adaptationist programme for its failure to distinguish current utility from reasons for origin (male tyrannosaurs may have used their diminutive front legs to titillate female partners, but this will not explain why they got so small); for its unwillingness to consider alternatives to adaptive stories; for its reliance upon plausibility alone as a criterion for accepting speculative tales; and for its failure to consider adequately such competing themes as random fixation of alleles, production of nonadaptive structures by developmental correlation with selected features (allometry, pleiotropy, material compensation, mechanically forced correlation), the separability of adaptation and selection, multiple adaptive peaks, and current utility as an epiphenomenon of non-adaptive structures. We support Darwin's own pluralistic approach to identifying the agents of evolutionary change.

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It has always been obvious that organisms vary, even to those pre-Darwinian idealists who saw most individual variation as distorted shadows of an ideal. It has been equally apparent, even to those post-Darwinians for whom variation between individuals is the central fact of evolutionary dynamics, that variation is nodal, that individuals fall in clusters in the space of phenotypic description, and that those clusters, which we call demes, or races, or species, are the outcome of an evolutionary process acting on the individual variation. What has changed during the evolution of scientific thought, and is still changing, is our perception of the relative importance and extent of intragroup as opposed to intergroup variation. These changes have been in part a reflection of the uncovering of new biological facts, but only in part. They have also reflected general sociopolitical biases derived from human social experience and carried over into “scientific” realms. I have discussed elsewhere (Lewontin, 1968) long-term trends in evolutionary doctrine as a reflection of long-term changes in socioeconomic relations, but even in the present era of Darwinism there is considerable diversity of opinion about the amount or importance of intragroup variation as opposed to the variation between races and species. Muller, for example (1950), maintained that for sexually reproducing species, man in particular, there was very little genetic variation within populations and that most men were homozygous for wild-type genes at virtually all their loci.

The Apportionment of Human Diversity

HILE the theory of the genetic changes in a population due to selection is quite well understood for single loci, our theory for multiple-gene characters is in a rudimentary stage. Most of the formulations for multiple-gene characters are simply extensions of single-locus models, extensions which ignore the problem of linkage. There are, however, a few papers in which the role of linkage has been investigated for more or less special cases of selection (KIMURA 1956; LEWONTIN and KOJIMA 1960; BODMER and PARSONS 1962). The results of these investigations were sufficient to show that even for relatively simple cases (two loci, simple symmetrical selective values) linkage might have profound effects on the course of natural selection and, pari passu, natural selection may have major effects on the distribution of coupling and repulsion linkage in a population. The results of the investigations of LEWONTIN and KOJIMA (1960) of the twolocus model can be summarized as follows: (1) If the fitnesses are additive between loci (no epistasis), linkage does not effect the final equilibrium state of the population. (2) If linkage is tighter than the value demanded by the magnitude of the epistasis (the greater the epistasis the greater the value) there may be permanent linkage disequilibrium and alteration of equilibrium gene frequencies. (3) The rate of genetic change with time is affected by the tightness of the linkage. (4) In some cases stable gene frequency equilibria are possible only if linkage is tight enough. Although these conclusions were based only on two-locus model and for selective values of a fairly restricted sort, they point clearly to the importance of taking linkage into account in understanding the changes of gene frequencies in populations. In fact, some experimental results (an example of which will be given below) can be understood only if the interaction of selection and linkage is taken into account, The equations describing the interaction between selection and linkage (see below) do not usually have general literal solutions. It is for this reason that the authors cited above have restricted themselves to relatively simple cases. In view of the interesting findings of those previous papers, however, it is worthwhile to explore the subject more intensively. To do so requires the numerical rather than general literal solutions to the equations, but such numerical solutions apply, obviously, only to the particular parameter values chosen. To make such a nu-

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Richard C Lewontin

Papers

The Selfish Gene

The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme

The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme

The Apportionment of Human Diversity

The Interaction of Selection and Linkage. I. General Considerations; Heterotic Models.